computational studies of structure, stability and

Computational Studies of Structure Stability and Properties

of Nanoporous Framework Materials

by

Binit Lukose

A thesis submitted in partial fulfillment

of the requirement for the degree of

Doctor of Philosophy in Physics

Approved by Thesis Committee

_____________________________________ (Chair Prof Dr Thomas Heine JUB)

_____________________________________ (Prof Dr Ulrich Kleinekathoumlfer JUB)

_____________________________________ (Prof Dr Christof Woumlll KIT)

_____________________________________ (Prof Dr Petko Petkov Univ Sofia)

Date of Defense July 19 2012

School of Engineering and Science

Statutory Declaration

I Binit Lukose hereby declare that I have written this PhD thesis independently

unless where clearly stated otherwise I have used only the sources the data

and the support that I have clearly mentioned This PhD thesis has not been

submitted for conferral of degree elsewhere

Bremen 2012

Signature _________________________

i

List of Articles

1 Binit Lukose Agnieszka Kuc Johannes Frenzel Thomas Heine On the reticular construction

concept of covalent organic frameworks Beilstein J Nanotechnol 2010 1 60ndash70

DOI103762bjnano18

2 Binit Lukose Agnieszka Kuc Thomas Heine The Structure of Layered Covalent-Organic

Frameworks Chem Eur J 2011 17 2388 ndash 2392 DOI 101002chem201001290

3 Binit Lukose Barbara Supronowicz Petko St Petkov Johannes Frenzel Agnieszka B Kuc

Gotthard Seifert Georgi N Vayssilov and Thomas Heine Structural properties of metal-

organic frameworks within the density-functional based tight-binding method Phys Status

Solidi B 2012 249 335ndash342 DOI 101002pssb201100634

4 Binit Lukose Agnieszka Kuc Thomas Heine Stability and electronic properties of 3D covalent

organic frameworks Prepared for publication

5 Binit Lukose Mohammad Wahiduzzaman Agnieszka Kuc Thomas Heine Structure

electronic structure and hydrogen adsorption capacity of porous aromatic frameworks

Prepared for publication

6 Jinxuan Liu Binit Lukose Osama Shekhah Hasan Kemal Arslan Peter Weidler Hartmut

Gliemann Stefan Braumlse Sylvain Grosjean Adelheid Godt Xinliang Feng Klaus Muumlllen Ioan-

Bogdan Magdau Thomas Heine Christof Woumlll A novel series of isoreticular metal organic

frameworks realizing metastable structures by liquid phase epitaxy Prepared for publication

7 Binit Lukose Gabriel Merino Christof Woumlll Thomas Heine Linker guided metastability in

templated Metal-Organic Framework-2 derivatives (SURMOFs-2) Prepared for publication

8 Binit Lukose Thomas Heine Review Covalently-bound organic frameworks Prepared for

publication

ii

Acknowledgment

Foremost I would like to thank my supervisor Prof Dr Thomas Heine for the wonderful opportunity to join his group as his PhD student I am greatly thankful to him for giving me the topic and sharing with me his expertise and research insight His thoughtful advices have served to give me senses of motion and direction His ambitious approach to science has given me motivation as well as chances and exposures to develop in science His constant attention and guidance have led my scientific outputs to the best levels possible I am also thankful for the financial support and the comfortable stay in his group during my PhD time Additionally he is acknowledged for correcting and reviewing my thesis

Prof Dr Ulrich Kleinekathoumlfer deserves special thanks as my Thesis Committee member I am very glad to have him in the Committee and greatly thankful for reviewing and evaluating the thesis I also thank him and Prof Ulrich Kortz for the evaluation of my PhD proposal I am thankful also for their friendly manners and considerations throughout my PhD time

Prof Dr Christof Woumlll Director of Functional Interfaces Karlsruhe Institute of Technology is greatly acknowledged for being the external Thesis Committee member I am greatly thankful for the evaluation and reviewing of the thesis I am very much moved by his research outcomes and thankful for sharing them with us Our collaborations with his group have particularly enriched my thesis

Prof Dr Petko Petkov is also acknowledged for reviewing my thesis I particlulary thank him for the friendship and discussions thoughout my PhD time

I am indebted to Dr Agnieszka Kuc for introducing me to the topic of nanoporous materials Her experience and expertise have helped me to begin a career in this field I extend my gratitude for sharing with me her scientific skills and correcting our joint-articles

Dr Lyuben Zhechkov and Dr Achim Gelessus have been great in providing computational assistance I have benefitted from their knowledge and sincerity through fast and timely helps

I owe my heartfelt thanks to Dr Lyuben Zhechkov Dr Nina Vankova Dr Augusto Oliveira Dr Andreas Mavrantonakis Dr Stefano Borini and Dr Christian Walther for all discussions suggestions support help and particularly their lectures Dr Lyuben Zhechkov and Dr Nina Vankova are specially mentioned for their long-term attentions and helps Dr Akhilesh Tanwar is acknowledged for his helps in the beginning of my PhD

In my daily work I have been blessed with a friendly and cheerful group of fellow students Barbara Jianping Wahid Nourdine Mahdi Lei Rosalba Ievgenia Wenqing Guilherme Farjana Maicon Aleksandar Ionut Yulia and Gabriel Discussions aside I had great fun times with them Our interactions have also helped me to develop in a personal level I thank them from my full heart although just a few words are not enough I specially thank Barbara Wahid and Ionut for the joint works and publications

Mrs Britta Berninghausen our project assistant deserves special thanks for the friendly assistance on all matters with the university administration

I thank all the members of the group for a lot of good things From the supervisor to the newly joined member everyone has contributed for the general good fun and easiness All those ldquobio-fuelrdquo workshops barbecues parties retreats and gatherings are unforgettable The group also kept good phase with other groups and visitors I thank all the members once again for the good times I would not have been happier anywhere else

iii

I extend my thanks to the research groups that I visited during the PhD time Dr Sourav Pal Director of National Chemical Laboratory Pune and Dr V Subrahmanian Central Leather Research Institute Chennai deserve my gratitude for giving me the opportunity to visit and work with their group members Also I am very thankful to Prof D Sc Georgi N Vayssilov Faculty of Chemistry University of Sofia for the interesting collaboration and visit to his group The financial assistance during each stay is greatly acknowledged I also thank the members of the respective groups namely Dr Petko Petkov and his family who made the visit to Bulgaria very much entertaining

Prof Dr Lars Pettersson of University of Stockholm Dr Tzonka Mineva of CNRS Montpellier and all other members of the HYPOMAP research project are acknowledged for the scientific discussions exposures and promotions

I acknowledge several projects of Prof Dr Thomas Heine for the financial support of my work and travel the funding sources include the European Commission Deutsche Forschungsgemeinschaft (DFG) and the joint Bulgarian-German exchange program (DAAD)

I thank all the co-authors of my publications who have contributed their knowledge ideas and work to accomplish our scientific goals Without their efforts all those works would not have been complete

Members of Research III of SES at Jacobs University namely Robert Carsten Joumlrg Bogdan Meisam Niraj Mahesh Vinu Pinky Patrice Mehdi Sidhant and all professors postdocs and students in Nanofun center are thankfully mentioned here

A lot of my friends in the campus deserve my thanks Mahesh Mahendran Vinu Deepa Srikanth Rajesh Arumugam Prasad Dhananjay Sunil Tripti Raghu Suneetha Rami Susruta Niraj Abhishek Ashok Rakesh Sagar Rohan Naveen Yauhen Yannic Mila and Samira are thanked for the gatherings travels making funs and those cricket and volleyball evenings Some of them are specially thanked for the occasional ldquogahn bayrdquo parties I owe many thanks to Yauhen Srikanth and Prasad for being good flat-mates and having talks on any matters Srikanth and Prasad are thanked again for generously extending their cooking skills to me

I wish to thank everybody with whom I have shared experiences in life I am obliged to my MSc lecturer Dr Rajan K John whose dreams have inspired and driven me to research In particular his accomplishments in the George Sudarshan Center CMS College Kottayam have molded me to take up this career My previous research supervisors Prof S Lakshmibala and Prof V Balakrishnan of IIT Madras and Dr Anita Mehta of SNBNCBS Kolkata are also acknowledged for their important influences in my academic life Additionally all my teachers friends and well-wishers from neighborhood school college GS Center IIT-M and SN Bose center are thanked and acknowledged Members of St Antonyrsquos Parish Olassa are also thanked for the regards and encouragement

Jacobs University Bremen and its people have been amazing in all sorts of things I am glad that I have been a member of the University With my full heart I thank the university authority for all its facilities that were open for me I also thank Dr Svenja Frischholz Mr Peter Tsvetkov and Ms Kaija Gruumlenefeld in the administration departments for the timely helps

Lastly and most importantly I wish to thank my dearest ones for all the sacrifices and love My parents K P Lukose and Molly and my brother Anit deserve to be thanked They have always supported and encouraged me to do my best in all matters of life I also wish to thank my entire extended family for providing me a loving environment

iv

Abstract

Framework materials are extended structures that are built into destined nanoscale architectures

using molecular building units Reticular synthesis methods allow stitching of a large variety of

molecules into predicted networks Porosity is an obvious outcome of the stitching process These

materials are classified and named according to the chemical composition of the building blocks For

instance Metal-Organic Frameworks (MOFs) consists of metal-oxide centers that are linked together

by organic entities The stitching process is straight-forward so that there are already thousands of

them synthesized Controlled growth of MOFs on substrates leads to what is known as surface-MOFs

(SURMOFs) A low-weight metal-free version of MOFs is known as Covalent Organic Frameworks

(COFs) They consist of light elements such as boron oxygen silicon nitrogen carbon and hydrogen

atoms Diamond-like structures with a variety of linear organic linkers between tetrahedral nodes is

called Porous Aromatic Frameworks (PAFs)

The thesis is composed of computational studies of the above mentioned classes of materials The

significance of such studies lies in the insights that it gives about the structure-property relationships

Density Functional Theory (DFT) and its Tight-Binding approximate method (DFTB) were used in

order to perform extensive calculations on finite and periodic structures of several frameworks DFTB

provides an ab-initio base on periodic structure calculations of very large crystals which are typically

studied only using force-field methods The accuracy of this approximate method is validated prior to

reasoning

As the materials are energized from building units and coordination (or binding) stability vs

structure is discussed Energy of formation and mechanical strength are particularly calculated Using

dispersion corrected (DC)-Self Consistent Charge (SCC) DFTB we asserted that 2D COFs should have a

layer arrangement different from experimental suggestions Our arguments supported by simulated

PXRDs were later verified using higher level theories in the literature Another benchmark is giving an

insightful view on the recently reported difference in symmetries of two-dimensional MOFs and

SURMOFs The result of it shows an extra-ordinary role of linkers in SURMOFs providing

metastability

Electronic properties of all the materials and hydrogen adsorption capacities of PAFs are discussed

COFs PAFs and many of the MOFs are semiconductors HOMO-LUMO gaps of molecular units have

crucial influence in the band gaps of the solids Density of states (DOS) of solids corresponds to that

of cluster models Designed PAFs give a large choice of adsorption capacities one of them exceeds

the DOE (US) 2005 target Generally the studies covered under the scheme of the thesis illustrate

the structure stability and properties of framework materials

- Dedicated to my Family and Rajan sir

Table of Contents 1 Outline 1

2 Introduction 2

21 Nanoporous Materials 2

22 Reticular Chemistry 3

23 Metal-Organic Frameworks 5

24 Covalently-bound Organic Frameworks 8

3 Methodology and Validation 10

31 Methods and Codes 10

32 DFTB Validation 11

4 2D Covalent Organic Frameworks 13

41 Stacking 13

42 Concept of Reticular Chemistry 15

5 3D Frameworks 17


52 Porous Aromatic Frameworks 18

6 New Building Concepts 20

61 Isoreticular Series of SURMOFs 20

62 Metastability of SURMOFs 21

7 Summary 23

71 Validation of Methods 23

72 Weak Interactions in 2D Materials 25

73 Structure-Property Relationships 27

List of Abbreviations 31

List of Figures 32

References 33

Appendix A Review of covalently-bound organic frameworks 37

Appendix B Properties of MOFs within DFTB 81

Appendix C Stacking of 2D COFs 96

Appendix D Reticular concepts applied to 2D COFs 105

Appendix E Properties of 3D COFs 122

Appendix F Properties of PAFs 131

Appendix G Isoreticular SURMOFs of varying pore sizes 145

Appendix H Metastability in 2D SURMOFs 160

1

1 Outline

I prepared this cumulative thesis as it is permitted by Jacobs University Bremen as all work has been

published in international peer-reviewed journals is submitted for publication or in a late

manuscript state in order to be submitted soon The list of articles contains three published papers

three submitted manuscripts and two manuscripts that are to be submitted The articles are given in

Appendices A-H in the order of their discussions Each appendix has one paper and its supporting

information

The chapters from ldquoIntroductionrdquo to ldquoNew Building Conceptsrdquo contain general discussions about the

articles and provide a red thread leading through the articles The discussions mainly circle around

the context and the content of the articles

The chapter ldquoIntroductionrdquo provides a general introduction to the topic and a review of the materials

discussed in this thesis As no comprehensive review on ldquoCovalently-bound Organic Frameworksrdquo is

available in the literature we prepared a manuscript (Appendix A) covering that subject The chapter

ldquoMethodology and Validationrdquo discusses one article on validation of DFTB method in Metal-Organic

Frameworks (Appendix B) Each consecutive chapter discusses two articles The chapter ldquo2D

Covalent Organic Frameworksrdquo covers the studies on layer arrangements (Appendix C) followed by

analysis on how reticular chemistry concepts can be used to design new materials (Appendix D) The

chapter ldquo3D Frameworksrdquo discusses the stability and properties of 3D COFs (Appendix E) and PAFs

(Appendix F) It also discusses hydrogen storage capacities of PAFs The chapter ldquoNew Building

Conceptsrdquo has coverage on 2D MOFs that are built on organic surfaces The first article in this chapter

describes the achievement of our collaborators in synthesizing a series of SURMOFs of varying pore

sizes supported by our calculations indicating their matastability Extensive calculations revealing the

role of linkers in creating the unprecedented difference of SURMOFs in comparison with the bulk

MOFs is described in another article

Details of the articles and references to the appendices are given in the respective places in each

chapter The chapter ldquoSummaryrdquo gives an overview of all the results and discussions It also discusses

some impacts of the publications and concludes the thesis Overall the studies bring into picture

different classes of materials and analyze their structural stabilities and properties

2

2 Introduction

21 Nanoporous Materials

The field of nanomaterials covers materials that have properties stemming from their nanoscale

dimensions (1-100 nm) In contrast to nanomaterials which define size scaling of bulk materials the

major determinant of nanoporous materials is their pores Nanoporous materials are defined as

porous materials with pore diameters less than 100 nm and are classified as micropores of less than

2 nm in diameter mesopores between 2 and 50 nm and macropores of greater than 50 nm They

have perfectly ordered voids to accommodate interact with and discriminate molecules leading to

prominent applications such as gas storage separation and sieving catalysis filtration and

sensoring1-4 They differ from the generally defined nanomaterials in the sense that their properties

are mostly determined by pore specifications rather than by bulk and surface scales Hence the

focus is onto the porous properties of the materials

Utilization of the pores for certain applications relies on certain parameters such as pore size pore

volume internal surface area and wall composition For example physical adsorption of gases is high

in a material with large surface area which implies significantly high storage in comparison to a tank

Porosity can be measured using some inert or simple gas adsorption measurements Distribution of

pore size can be sketched from the adsorptiondesorption isotherm

Nanoporous materials abound in nature Zeolites for instance many of them are available as mineals

have been used in petroleum industry as catalysts for decades The walls of human cells are

nanoporous membranes Other examples are clays aluminosilicate minerals and microporous

charcoals Zeolites are microporous materials from the aluminosilicate family and are often known as

molecular sieves due to their ability to selectively sort molecules primarily based on a size exclusion

principle A material with high carbon content (coal wood coconut shells etc) can be converted to

activated carbon (AC) by controlled thermal decomposition in a furnace The resultant product has

large surface area (~ 500 m2 g-1) Porous glass is a material produced from borosilicate glasses having

pore sizes usually in nm to μm range With increasing environmental concerns worldwide porous

materials have become a suitable choice for separation of polluting gases storage and transport of

energy carriers etc Synthesis of open structures has advanced this area5-7 especially since the

invention of MCM-41 (Mobil Composition of Matter No 41) by Mobil scientists89 Furthermore

there are many templating pathways in making nanoporous materials10-13 Currently it is possible to

engineer the internal geometry at molecular scales

3

For more than a decade chemists are able to synthesize extended structures from well-defined and

rigid molecular building units Such designed and controlled extensions provide porosity which can

be scaled and modified by selecting appropriate building blocks The first realization of this kind was

a class of materials known as Metal-Organic Frameworks (MOFs) in which metal-oxides are stitched

together by organic molecules Synthesis of molecules into predicted frameworks have led to the

emergence of a discipline called reticular chemistry14 The new design-based synthetic approaches

have produced large number of nanoporous materials in comparison to the discovery-based

synthetic chemistry

22 Reticular Chemistry

The discipline of designed (rational) synthesis of materials is known as reticular chemistry Desired

materials can be realized by starting with well-defined and rigid molecular building blocks that will

maintain their structural integrity throughout the construction process The extended structures

adopt high symmetry topologies The synthetic approach follows well-defined conditions which

provide general control over the character of solids In short it is the chemistry of linking molecular

building blocks by strong bonds into predetermined structures

The knowledge about how atoms organize themselves during synthesis is essential for the design

The principal possibilities rely on the starting compounds and the reaction mechanisms Porosity is

almost an inevitable outcome of reticular synthesis Solvents may be used in most cases as space-

filling agents and in cases of more than one possibility as structure-directing agents

Thousands of materials in large varieties have been synthesized using the reticular chemistry

principles Reticular Chemistry Structure Resource (RCSR) is a searchable database for nets a project

initiated by of Omar M Yaghi and Michael OrsquoKeeffe15 They define nets as the collection of vertices

and edges that form an irreducible network in which any two vertices are connected through at least

one continuous path of edges Building units are finite nets as in the case of a polyhedron Periodic

structures have one two or three-periodic nets An example case of 3D diamond net (dia) is shown in

Figure 1 Graph-theoretical aspects together with explicative terminology and definitions can be

found in the literature16-18

Figure 1 a) ldquoAdamantinerdquo unit of diamond structure and b) diamond (dia) net

4

In other words a framework can be deconstructed into one or more fundamental building blocks

each of them assigned by a vertex in the net The vertices are the branching points and edges are

joining them The realization of the net in space by representing the vertices and lattice parameters

by co-ordinates and a matrix respectively is called embedding of the net Underlying topology of an

extended structure is the structure of the net inherited from the crystal structure that is invariant

under different embeddings For example Cu-BTC MOF has paddlewheels and benzene rings as

fundamental blocks The MOF structure can be simplified into its underlying topology as shown in

Figure 2

Figure 2 CU-BTC MOF and the corresponding tbo net

Alternatively the topology of a framework can be defined using the convention of so-called

secondary building units (SBUs) The shapes of SBUs are defined by points of extension of the

fundamental building blocks SBUs are invariant for building units of identical connectivity Based on

the number of connections with the adjacent blocks (4 for paddlewheel and 3 for the benzene) SBUs

of Cu-BTC can be represented as shown in Figure 3a Assembly of SBUs following the network

topology and insertion of the fundamental building blocks give the crystal structure (see Figure 3b for

the extension of SBUs to the topology of Cu-BTC)

In addition to MOFs Metal-Organic Polyhedra (MOP)19 Zeolite Imidazolate Frameworks (ZIFs)20 and

Covalent-Organic Frameworks (COFs)2122 are developing classes of materials within reticular

chemistry the first members of all of them were synthesized by the group of Yaghi MOPs are nano-

sized polyhedra achieved by linking transition metal ions and either nitrogen or carboxylate donor

organic units ZIFs are aluminosilicate zeolites with replacements of tetrahedral Si (Al) and bridging

oxygen by transition metal ion and imidazolate link respectively COFs are extended organic

5

structures constructed solely from light elements (H B C and O) The materials synthesized under

the reticular scheme are largely crystalline

Figure 3 a) Fundamental building blocks and SBUs of Cu-BTC and b) extension of SBUs following

crystal structure

23 Metal-Organic Frameworks

MOFs are porous crystalline materials consisting of metal complexes (connectors) linked together by

rigid organic molecules (linkers) MOFs are analogues to a class of materials called coordination

polymers (CPs) However there are primary differences between them CPs are inorganic or

organometallic polymer structures containing metal ions linked by organic ligands A ligand is an

atom or a group of atoms that donate one or more lone pairs of electrons to the metal cations and

thereby participate in the formation of a coordination complex In MOFs typically metal-oxide

centers are used instead of single metal ions as they provide strong bonds with organic linkers This

provides not only high stability but also high directionality because multiple bonds are involved

6

between metal-centers and organic linkers Predictability lies in the pre-knowledge about the

connector-linker interactions Thus the reticular design of MOFs derives from the precise

coordination geometry between metal centers and the linkers Figure 4a shows a schematic diagram

of MOFs By varying the chemical composition of nodes and linkers thousands of different MOF

structures with a large variety in pore size and structure have been synthesized Figure 4b shows

MOF-5 that consists of zinc-oxide tetrahedrons and benzene linkers

Figure 4 a) Schematic diagram of the single pore of MOF b) An example of a simple cubic MOF in

which zinc-oxide tetrahedron are linked together by benzene linkers Atom colors blue ndash Zn red ndash

O grey ndash C white ndash H

The synthesis of MOFs differs from organic polymerizations in the degree of reversible bond

formation Reversibility allows detachment of incoherently matched monomers followed by their

attachment to form defect-free crystals Assembly of monomers occurs as single step hence

synthetic conditions are of high importance The strength of the metal-organic bond is an obstacle

for reversible bond formation however solvothermal techniques are found out to be a convenient

solution23 Solvothermal synthesis generally allows control over size and shape distribution Using

post-synthetic methods further changes on cavity sizes and chemical affinities can be made

Materials that are stable with open pores after removal of guest molecules are termed as open-

frameworks The stability of guest-free materials is usually examined by Powder X-ray diffraction

(PXRD) analysis Thermogravimetric analysis may be performed to inspect the thermal stability of the

material Elemental analysis can detail the elemental composition of the material Physical

techniques such as Fourier transform infrared (FTIR) spectra and nuclear magnetic resonance (NMR)

may be used to verify the condensation of monomers to the desired topology Porosity can be

evidenced from adsorption isotherms of gases or mercury porosimetry

7

The number of linkers that are allowed to bind to the metal-center and the orientations of the linkers

depend exclusively on the coordination preferences of the metal The organic linkers are typically

ditopic or polytopic They are essential in determining the topology and providing porosity Longer

linkers provide larger pore size A series of compounds with the same underlying topology and

different linker sizes are called iso-reticular series The structure of MOFs in principle can be formed

into the requirement of prominent applications such as gas storage gas separation sensing and

catalysis The structural divergence and performance can be further increased by functionalizing the

organic linkers Hence several attempts are on-going in purpose to come up with the best material

possible in each application

Interpenetration of frameworks is an inevitable outcome of large pore volume Interpenetrated nets

are periodic equivalents of mechanically interlocked molecules rotaxanes and catenanes Depending

on topology they are either maximally separated termed as interpenetration or minimally separated

termed as interweaving (see Figure 5) Interpenetration can be beneficial to some porous structures

protecting from collapse upon removal of solvents

Figure 5 Schematic diagram of interpenetrated and interwoven frameworks

Controlled growth of MOFs on organic surfaces is achieved by R A Fischer and C Woumlll24 The then

named SURMOFs allow to fabricate structures possibly not achievable by bulk synthesis The growth

is achieved through liquid phase epitaxy (LPE) of MOF reactants on the surface (nucleation site) A

step-by-step approach which is alternate immersion of the substrate in metal and ligand precursors

supplies control of the growth mechanism

8

Figure 6 Schematic diagram of SURMOF

24 Covalently-bound Organic Frameworks

As a result of the long-term struggle for complete covalent crystallization in the year 2005 Cocircte et

al21 synthesized porous crystalline extended 2D Covalent-Organic Frameworks (COFs) using

reticular concepts The success was followed by the design and synthesis of 3D COFs in the year

200722 By now there are about 50 COFs reported in the literature COFs are made entirely from

light elements and the building blocks are held together by strong covalent bonds Most of them

were formed by solvothermal condensation of boronic acids with hydroxyphenyl compounds

Tetragonal building blocks were used for the formation of 3D COFs Alternate synthetic methods

were also used for producing COFs COFs are generally studied for gas storage applications However

they have also shown potentialities in photonic and catalytic applications

Alternative synthesis methods paved the way to new covalently bound organic frameworks

Trimerization of polytriazine monomers in ionothermal conditions gives rise to Covalent Triazine

Frameworks (CTFs)25 Similarly coupling reactions of halogenated monomers produced Porous

Aromatic Frameworks (PAFs) Albeit the short-range order one of the PAFs showed very high surface

area (5600 m2 g-1) and gas uptake capacity26

Due to low weight the covalently-bound materials show very high gravimetric capacities

Suggestions such as metal-doping functionalization and geometry modifications can be found in the

literature for the general improvement of the functionalities There are also various studies of their

structure and properties

A review on the synthesis structure and applications of covalently bound organic frameworks has

been prepared for publication

Article 1 Covalently-bound organic frameworks

Binit Lukose Thomas Heine

9

See Appendix A for the article

My contributions include collecting data and preparing a preliminary manuscript

Figure 7 SBUs and topologies of 2D COFs

10

3 Methodology and Validation

31 Methods and Codes

The Density-Functional based Tight Binding (DFTB) method2728 is an approximate Kohn-Sham DFT29-31

scheme It avoids any empirical parameterization by calculating the Hamiltonian and overlap matrix

elements from DFT-derived local orbitals (atomic orbitals) and atomic potentials The Kohn-Sham

orbitals are represented with the linear combination of atomic orbitals (LCAO) scheme The matrix

elements of Hamiltonian are restricted to include only one- and two-center contributions Therefore

they can be calculated and tabulated in advance as functions of the distance between atomic pairs

The remaining contributions to the total energy that is the nucleus-nucleus repulsion and the

electronic double counting terms are grouped in the so-called repulsive potential This two-center

potential is fitted to results of DFT calculations of properly chosen reference systems The accuracy

and transferability can be improved with the self-consistent charge (SCC) extension to DFTB32 This

method is based on the second-order expansion of the Kohn-Sham total energy with respect to

charge density fluctuations which are estimated by Mulliken charge analysis In order to account for

London dispersion empirical dispersion energy can be added to the total energy3334 Various reviews

are available on DFTB notably the recent ones by Oliveira et al35 and by Seifert et al36

DFTB is implemented in a large number of computer codes For this work we employed the codes

deMonNano37 and DFTB+38 as they allow DFTB calculations on periodic and finite structures

Typically dispersion corrected (DC) SCC-DFTB calculations were carried out Periodic boundary

conditions were used to represent the crystalline frameworks and as the unit cells are large the

standard approach used the point approximation Electronic density of states (DOS) have been

calculated using the DFTB+ code using k-point sampling where the k space was determined by

reaching convergence for the total energy according to the scheme proposed by Monkhorst and

Pack39

For DFT calculations of finite and periodic structures ADF40 Turbomole41 and Crystal0942 were used

For studies of finite models of COFs the calculations were performed at PBEDZP level However for

extensive calculations on SURMOF-2 models we used B3LYP-D The copper atoms were described

using the basis set associated with the Hay-Wadt43 relativistic effective core potentials44 which

include polarization f functions45 Carbon oxygen and hydrogen atoms were described using the

Pople basis set 6-311G

Details of the individual calculations are given in the individual articles in the appendix of this thesis

11

32 DFTB Validation

Figure 8 Deconstructed building units their schematic diagrams and final geometries of HKUST-1

(Cu-BTC) MOF-5 MOF-177 MOF-205 and MIL-53

12

In the literature MOFs and COFs are largely studied for applications such as gas storage using

classical force field methods46-48 First principles based studies of several hundreds of atoms are

computationally expensive Hence they are generally limited to cluster models of the periodic

structures Contrarily DFTB paves the way to model periodic structures involving large numbers of

atoms Being an approximate method DFTB holds less accuracy hence comparisons to experimental

data or higher level methods should be performed for validation

As MOFs contain metal centers andor metal oxides as well as organic elements the DFTB

parameters for both heavy and light elements as well as their mixtures are required Thus we have

chosen MOFs such as Cu-BTC (HKUST-1) MOF-5 MOF-177 MOF-205 and MIL-53 as our model

structures which contain Cu Zn and Al atoms apart from C O and H The MOFs comprising three

common connector units copper paddlewheels (HKUST-1) zinc oxide Zn4O tetrahedron (MOF-5

MOF-177 DUT-6 (MOF-205)) and aluminum oxide AlO4(OH)2 octahedron (MIL-53) Figure 8 shows

the schematic diagram of the MOFs

The validation calculations have been published

Article 2 Structural properties of metal-organic frameworks within the density-functional based

tight-binding method

Binit Lukose Barbara Supronowicz Petko St Petkov Johannes Frenzel Agnieszka B Kuc Gotthard

Seifert Georgi N Vayssilov and Thomas Heine Phys Status Solidi B 2012 249 335ndash342 DOI

101002pssb201100634

See Appendix B for the article

In this article DFTB has been validated against full hybrid density-functional calculations for model

clusters against gradient corrected density-functional calculations for supercells and against

experiment Moreover the modular concept of MOF chemistry has been discussed on the basis of

their electronic properties Our results show that DC-SCC-DFTB predicts structural parameters with a

good accuracy (with less than 5 deviation even for adsorbed CO and H2O on HKUST-1) while

adsorption energies differ by 12 kJ mol-1 or less for CO and water compared to DFT benchmark

calculations

My contributions to this article include performing DFTB based calculations on the MOFs (HKUST-1

MOF-5 MOF-177 and MOF-205) that is optimizing the geometries simulating powder X-ray

diffraction patterns and calculating density of states and bulk modulus Additional involvement is in

comparing structural parameters such as bond lengths bond angles dihedral angles and bulk

modulus with experimental data or data derived from DFT calculations and preparing the manuscript

13

4 2D Covalent Organic Frameworks

41 Stacking

Condensation of planar boronic acids and hydroxyphenyl compounds leads to the formation of two-

dimensional covalent organic frameworks (2D COFs) The layers are held together by London

dispersion interactions The first synthesized COFs COF-1 and COF-5 were reported to have AB

(P63mmc staggered as in graphite) and AA (P6mmm eclipsed as in boron nitride) stackings

respectively (see Figure 9)21 The synthesis of several further 2D COFs then followed49-51 all of them

were inspected for only two stacking possibilities ndash P6mmm or P63mmc and it was reported that

they aggregate in P6mmm symmetry As framework materials possess framework charges the

interlayer interactions significantly include Coulomb interactions P6mmm symmetry is the face-to-

face arrangement where the overlap of the stacked structures is maximized (maximization of the

London dispersion energy) however atom types of alike charges are facing each other in the closest

possible way With the interlayer separation similar to that in graphite or boron nitride the Coulomb

repulsion should be high in such arrangements One should notice that in the example case of boron

nitride the facing atom types are different We therefore assumed that a stable stacking should

possess layer-offset

Figure 9 AA and AB layer stacks of hexagonal layers

We considered two symmetric directions for layer shift and studied their total energies (see Figure

10) The stable geometries are found to have a layer-shift of ~14 Aring a value corresponding to the

shift of AA to AB stacking in graphite and compatible with the bond length between two 2nd row

atoms This stability-supported stacking arrangement as revealed from our calculations was

14

supported by good agreement between simulated and experimental PXRD patterns Hence

independent of the elementary building blocks any 2D COF should expose a layer-offset Based on

the direction of the shift we proposed two stacking kinds serrated and inclined (Figure 10) In the

former the layer-offset is back and forth while in the latter the layer-offset followed single direction

As serrated and inclined stackings have no significant change in stacking energy our calculations

cannot predict the long-range stacking in the crystal However this problem is known from other

layered compounds and the ultimate answer is yet to be revealed by analyzing high-quality

crystalline phases at low temperature

Figure 10 Stacking energy Es vs shift of adjacent layers for COF-5 Different stacking possibilities

and their energies are also shown

We published our analysis of the stacking in 2D COFs

Article 3 The Structure of Layered Covalent-Organic Frameworks

Binit Lukose Agnieszka Kuc Thomas Heine Chem Eur J 2011 17 2388 ndash 2392 DOI

101002chem201001290

See Appendix C for the article

15

My contributions to this article include performing the shift calculations simulating XRDs and partly

preparing the manuscript The article has made certain impact in the literature Most of the 2D COFs

synthesized afterwards were inspected for their stacking stability The instability of AA stacking was

also suggested by the studies of elastic properties of COF-1 and COF-5 by Zhou et al52 The shear

modulus shows negative signs for the vertical alignment of COF layers while they are small but

positive for the offset of layers Detailed analysis performed by Dichtel53 et al using DFT was

confirming the instability of AA stacking and suggesting shifts of about 13 to 25 Aring

42 Concept of Reticular Chemistry

Reticular chemistry means that (functional) molecules can be stitched together to form regular

networks The structural integrity of these molecules we also speak of building blocks remains in the

crystal lattices Consequently also the electronic structure and hence the functionality of these

molecules should remain similar

2D COFs are formed by condensation of well-defined planar building blocks With the usage of linear

and triangular building blocks hexagonal networks are expected The properties of each COF may

differ due to its unique constituents However the extent of the relationship of the properties of

building blocks in and outside the framework has not been studied in the literature

Reticular chemistry allows the design of framework materials with pre-knowledge of starting

compounds and reaction mechanisms Reverse of this is finding reactants for a certain topology We

intended to propose some building units suitable to form layered structures (see Figure 11) The

building units obey the regulations of reticular chemistry and offer a variety of structural and

electronic parameters

Our strategic studies on a set of designed COFs have been published

Article 4 On the reticular construction concept of covalent organic frameworks

Binit Lukose Agnieszka Kuc Johannes Frenzel Thomas Heine Beilstein J Nanotechnol 2010 1

60ndash70 DOI103762bjnano18

See Appendix D for the article

16

Figure 11 Schematic diagram of different building units forming 2D COFs

Various hexagonal 2D COFs with different building blocks have been designed and investigated

Stability calculations indicated that all materials have the layer offset as reported in our earlier

work54 (see Appendix C) We show that the concept of reticular chemistry works as the Density-Of-

States (DOS) of the framework materials vary with the the DOS of the molecules involved in the

frameworks However the stacking does have some influence on the band gap

My contributions to this article include performing all the calculations and preparing the manuscript

17

5 3D Frameworks


First 3D COFs were reported in 2007 by the group of Yaghi22 Although the number of 3D COFs

synthesized so far has not been crossed half a dozen they are of particular interest for their very low

mass density Similar to 2D COFs condensation of boronic acids and hydroxyphenyl compounds led

to the formation of COF-102 103 105 108 and 202 Usage of tetragonal boronic acids leads to the

formation of 3D networks (Figure 12) All of them possessed ctn topology while COF-108 which has

the same material composition as COF-105 crystallized in bor topology COF-300 which was formed

from tetragonal and linear building units possessed diamond topology and was five-fold

interpenetrated55 COF-108 has the lowest mass density of all materials known today Unlike most of

the MOFs the connectors in COFs are not metal oxide clusters but covalently bound molecular

moieties In the synthesized COFs the centers of the tetragonal blocks were either sp3 carbon or

silicon atoms

Schmid et al56 have analyzed the two different topologies and developed force field parameters for

COFs The mechanical stability of COFs was also reported However no further study that details the

inherent energetic stability and properties of COFs was found in the literature Using DFTB we

performed a collective study of all 3D COFs in their known topologies with C and Si centers

Figure 12 Schematic diagram of tetragonal and triangular building blocks forming lsquoctnrsquo or lsquoborrsquo

topologies

Our studies of3D COFs have been prepared for publication

Article 5 Stability and electronic properties of 3D covalent organic frameworks

Binit Lukose Agnieszka Kuc Thomas Heine

18

See Appendix E for the article


We discussed the energetic and mechanical stability as well as the electronic properties of COFs in

the article All studied 3D COFs are energetically stable materials with formation energies of 76 ndash

403 kJ mol-1 The bulk modulus ranges from 29 to 206 GPa Electronically all COFs are

semiconductors with band gaps vary with the number of sp2 carbon atoms present in the linkers

similar to 3D MOFs

52 Porous Aromatic Frameworks

Porous Aromatic Frameworks (PAFs) are purely organic structures where linkers are connected by sp3

carbon atoms (see Appendix A) Tetragonal units were coupled together to form diamond-like

networks The synthesis follows typically a Yamamoto-type Ullmann cross-coupling reaction those

reactions are known to be much simpler to be carried out than the condensation reactions necessary

to form COFs However as the coupling reactions are irreversible a lower degree of crystallinity is

achieved and the materials formed were amorphous The first PAF was reported in 2009 and

showed a very high BET surface area of 5600 m2g-1 The geometry of PAF-1 was equal to diamond

with the C-C bonds replaced by biphenyl Subsequent PAFs may be synthesized with longer linkers

between carbon tetragonal nodes Nevertheless synthesis of a PAF with quaterphenyl linker

provided an amorphous material of very low surface area due to the short range order

Synthetic complexities aside the diamond-like PAFs are interesting for their special geometries from

the viewpoint of the theorist It is interesting to see to what extent they follow the properties of

diamond Additionally the large surface area and high polarizability of aromatic rings are auxiliary for

enhanced hydrogen storage Thus we have explored the possibilities of diamond topology by

inserting various organic linkers in place of C-C bonds (Figure 13)

Figure 13 Diamond structure and various organic linkers to build up PAFs

Our studies of PAFs have been prepared for publication

19

Article 6 Structure electronic structure and hydrogen adsorption capacity of porous aromatic

frameworks

Binit Lukose Mohammad Wahiduzzaman Agnieszka Kuc Thomas Heine

See Appendix F for the article

In this article we have discussed the correlations of properties with the structures Exothermic

formation energies of PAFs calculated from the dehydrogenation of the linkers with CH4 indicate the

strong coordination of linkers in the diamond topology The studied PAFs exhibited bulk moduli much

smaller than diamond however in line with related MOFs and COFs The PAFs are semi-conductors

with their band gaps decrease with the increasing number of benzene rings in the linkers

Using Quantized Liquid Density Functional Theory (QLDFT) for hydrogen57 a method to compute

hydrogen adsorption that takes into account inter-particle interactions and quantum effects we

predicted a large choice of hydrogen uptake capacities in PAFs At room temperature and 100 bar

the predicted uptake in PAF-qtph was 732 wt which exceeds the 2015 DOE (US) target We

further discussed the structural impacts on the adsorption capacities

My contributions to this article include designing the materials performing calculations of stability

and electronic properties describing the adsorption capacities and preparing the manuscript

20

6 New Building Concepts

61 Isoreticular Series of SURMOFs

The growth of MOFs on substrates using liquid phase epitaxy (LPE) opened up a controlled way to

construct frameworks This is achieved by alternate immersion of the substrates in metal and ligand

precursors for several cycles Such MOFs named as SURMOFs can avoid interpenetration because

the degeneracy is lifted58 and are suited for conventional applications This is an advantage as

solvothermally synthesized MOFs with larger pore size suffer from interpenetration and the large

pores are hence not accessible for guest species

MOF-259 is a simple 2D architecture based on paddlewheel units formed by attaching four

dicarboxylic groups to Cu2+ or Zn2+ dimers yielding planar sheets with 4-fold symmetry The

arrangement of MOF layers possessed P2 or C2 symmetry Recently the group of C Woumlll at KIT has

synthesized an isoreticular series of SURMOFs derived from MOF-2 which has a homogeneous series

of linkers with different lengths (Figure 14) XRD comparisons suggest that these MOFs possess P4

symmetry The cell dimensions that correspond to the length of the pore walls range from 1 to 28

nm The diagonal pore-width of one of the SURMOFs (PPDC) accounts to 4 nm The symmetry of

SURMOFs as determined to be different from bulk MOF-2 should be understood by means of theory

As collaborators we simulated the structures and inspected each stacking corresponding to the

symmetries in order to understand the difference

Figure 14 The building units and schematic diagram of the formation of iso-reticular SURMOF

series

21

This collaborated work has been submitted for publication

Article 7 A novel series of isoreticular metal organic frameworks realizing metastable structures

by liquid phase epitaxy

Jinxuan Liu Binit Lukose Osama Shekhah Hasan Kemal Arslan Peter Weidler Hartmut Gliemann

Stefan Braumlse Sylvain Grosjean Adelheid Godt Xinliang Feng Klaus Muumlllen Ioan-Bogdan Magdau

Thomas Heine Christof Woumlll

See Appendix G for the article

The main contribution of this article was the experimental proof backed up by our computer

simulations that SURMOFs with exceptionally large pore sizes of more than 4 nm can be prepared in

the laboratory and they offer the possibility to host large materials such as clusters nanoparticles or

small proteins The most important contribution of theory was to show that while MOF-2 in P2

symmetry shows the highest stability the P4 symmetry as obtained using LPE for SURMOF-2

corresponds to a local minimum

My contribution to this article includes performing and analyzing the calculations Our theoretical

study went significantly beyond and will be published as separate article (Appendix H)

62 Metastability of SURMOFs

Following the difference in stability of SURMOFs-2 in comparison with MOF-2 we identified the role

of linkers as a constituent of the framework that provides the metastability to SURMOFs-2 (Figure

15) In MOFs linkers are essential in determining the topology as well as providing porosity Linkers

typically contain single or multiple aromatic rings and are ditopic and polytopic The orientation of

them normally undergoes lowest repulsion from the coordinated metal-oxide clusters and provides

high stability In the case of 2D MOFs non-covalent interlayer interactions lead to the most stable

arrangements Paddlewheels are identified as the reasons for the stability of bulk MOF-2 as they

form metal-oxide bridges across the MOF layers In the case of SURMOFs-2 the linkers are rotated in

a tightly-packed environment of layers and each linker in bulk MOF-2 is rotated in such a way that

any attempt of shifting is obstructed by repulsion between the neighboring linkers The energy

barrier for leaving P4 increases with the length of organic linkers Moreover SURMOF-2 derivatives

with extremely large linkers are energetically stable due to the increased London dispersion

interaction between the layers in formula units Thus we encountered a rare situation in which the

linkers guarantee the persistence of a series of materials in an otherwise unachievable state

22

Figure 15 Energy diagram of the metastable P4 and stable P2 structures

Our results on the linker guided stability of SUMORs-2 have been prepared for publication

Article 8 Linker guided metastability in templated Metal-Organic Framework-2 derivatives

(SURMOFs-2)

Binit Lukose Gabriel Merino Christof Woumlll Thomas Heine

See Appendix H for the article

This article is based solely on my scientific contributions

23

7 Summary

Nanotechnology is the way of ingeniously controlling the building of small and large structures with

intricate properties it is the way of the future a way of precise controlled building with incidentally

environmental benignness built in by design - Roald Hoffmann Chemistry Nobel Laureate 1981

Currently it is possible to design new materials rather than discovering them by serendipity The

design and control of materials at the nanoscale requires precise understanding of the molecular

interactions processes and phenomena In the next level the characteristics and functionalities of

the materials which are inherent to the material composition and structure need to be studied The

understanding of the materials properties may be put into the design of new materials

Computational tools to a large extend provide insights into the structures and properties of the

materials They also help to convert primary insights into new designs and carry out stability analysis

Our theoretical studies of a variety of materials have provided some insights on their underlying

structures and properties The primary differences in the material compositions and skeletons

attributed a certain choice in properties The contents of the articles discussed in the thesis may be

summarized into the following three parts

71 Validation of Methods

Simulations of nanoporous materials typically include electronic structure calculations that describe

and predict properties of the materials Density functional theory (DFT)30 is the standard and widely-

used tool for the investigation of the electronic structure of solids and molecules Even the optical

properties can be studied through the time-dependent generalization of DFT MOFs and COFs have

several hundreds of atoms in their unit cells DFT becomes inappropriate for such large periodic

systems because of its necessity of immense computational time and power Molecular force field

calculations60 on the other hand lack transferable parameterization especially for transition metal

sites and are hence of limited use to cover the large number of materials to be studied Apparently

a non-orthogonal tight-binding approximation to DFT called density functional tight-binding

(DFTB)28323561 has proven to be computationally feasible and sufficiently accurate This method

computes parameters from DFT calculations of a few molecules per pair of atom types The

parameters are generally transferable to other molecules or solids With self-consistent charge (SCC)

extension DFTB has improved accuracy In order to account weak forces the London dispersion

energy can be calculated separately using empirical potentials and added to total energy Successful

realizations of DFTB include the studies of large-scale systems such as biomolecules62

24

supramolecular compounds63 surfaces64 solids65 liquids and alloys66 Being an approximate method

DFTB needs validation Often one compares DFTB results of selected reference systems with those

obtained with DFT

Before electronic structure calculations of framework materials can be carried out it is necessary to

compute the equilibrium configurations of the atoms Geometry optimization (or energy

minimization) employs a mathematical procedure of optimization to move atoms so as to reduce the

net forces on them to negligible values We adopted the conjugate gradient scheme for the

optimizations using DFTB A primary test for the validation of these optimizations is the comparison

of cell parameters bond lengths bond angles and dihedral angles with the corresponding known

numbers We compared the DFTB optimized MOF COF and PAF geometries with the experimentally

determined or DFT optimized geometries and found that the values agree within 6 error

The angles and intensities of X-ray diffraction patterns can produce three-dimensional information of

the density of electrons within a crystal This can provide a complete picture of atomic positions

chemical bonds and disorders if any Hence simulating powder X-ray diffraction (PXRD) patterns of

optimized geometries and comparing them with experimental patterns minimize errors in the crystal

model Our focus on this matter directed us to identify the layer-offsets of 2D COFs for the first time

In the case of 3D COFs excellent correlations were generally observed between experimental and

simulated patterns Slight differences in the intensities of some of them were due to the presence of

solvents in the crystals as they were reported in the experimental articles PAFs as experimentally

being amorphous do not possess XRD comparisons MOFs within DFTB optimization have

undergone some changes especially in the dihedral angles in comparison with experimental

suggestion or DFT optimization This was verified from the differences in the simulated PXRD

patterns Another interesting outcome of XRD comparison was the discovery of P4 symmetry of

templated MOF-2 derivatives (SURMOFs-2) made by Woumlll et al

Bulk moduli which may be expressed as the second derivative of energy with respect to the unit cell

volume can give a sense of mechanical stability Our calculations provide the following bulk moduli

for some materials MOF-5 1534 (1537)67 Cu-BTC 3466 (3517)68 COF-102 206 (170)69 COF-

103 139 (118)69 COF-105 79 (57)69 COF-108 37 (29)69 COF-202 153 (110)69 The data in the

parenthesis give corresponding values found in the literature calculated using force-field methods

The bulk moduli of MOFs are comparable with the results in the literature however COFs show

significant differences Albeit the differences in values each type of calculation shows the trend that

bulk modulus decreases with decreasing mas density increasing pore volume decreasing thickness

of pore walls and increasing distance between connection nodes

25

Formation of framework materials from condensation of reactants may be energetically modeled

COFs are formed from dehydration reactions of boronic acids and hydroxyphenyl compounds The

formation energy calculated from the energies of the products and reactants can indicate energetic

stability Both DFTB for periodic structures and DFT for finite structures predict exothermic formation

of 3D COFs Likewise for 2D COFs such as COF-1 and 5 the formation of monolayers is found to be

endothermic within both the periodic model calculation using DFTB and finite model calculation

using DFT The stacking of layers provides them stability

72 Weak Interactions in 2D Materials

AB stacked natural graphite and ABC stacked rhombohedral graphite are found to be in proportions

of 85 and 15 in nature respectively whereas AA stacking has been observed only in graphite

intercalation compounds On the other hand boron nitride (h-BN) the synthetic product of boric

acid and boron trioxide exists with AA stacking 2D COFs were believed to have high symmetric AA

(eclipsed ndash P6mmm symmetry) stacking as boron nitride (h-BN) An exception was COF-1 which was

considered to have AB (staggered ndash P63mmc) stacking as graphite The AA stacking maximizes the

attractive London dispersion interaction between the layers a dominating term of the stacking

energy At the same time AA stacking always suffers repulsive Coulomb force between the layers

due to the polarized connectors It should be noted that in boron nitride oppositely charged boron

atoms and nitrogen atoms are facing each other The Coulomb interaction has ruled out possible

interlayer eclipse between atoms of alike charges This gave us the notion that 2D COFs cannot

possess layer-eclipsing Based on these facts we have suggested a shift of ~14 Aring between adjacent

layers at which one or two of the edge atoms of the hexagonal rings are situated perpendicular to

the center of adjacent rings In other words some or all of the hexagonal rings in the pore walls

undergo staggering with that of adjacent layers These lattice types were found to be very stable

compared to AA or AB analogues AA stacking was found to have the highest Coulombic repulsion in

each COF Within an error limit the bulk COFs may be either serrated or inclined The interlayer

separations of all the COF stacks are in the range of 30 to 36 Aring and increase in the order AB

serratedinclined AA70 The motivation for proposing inclined stacking for COFs is that the

rhombohedral graphite (ABC stacking) is the inclined version of the layer-offset in natural graphite

(AB stacking) The instability of AA stacking was also suggested by the studies of elastic properties of

COF-1 and COF-5 by Zhou et al52 The shear modulus show negative signs for the vertical alignment of

COF layers while they are small but positive for the offset of layers

The change of stacking should be visible in their PXRD patterns because each space group has a

distinct set of symmetry imposed reflection conditions We simulated the XRD patterns of COFs in

their known and new configurations and on comparison with the experimental spectrum the new as

26

well as AA stacking showed good agreement5470 The slight layer-offsets are only able to make a few

additional peaks in the vicinity of existing peaks and some changes in relative intensities The

relatively broad experimental data covers nearly all the peaks of the simulated spectrum In other

words the broad experimental peaks are explainable with layer-offset

A detailed analysis on the interlayer stacking of HHTP-DPB COF made by Dichtel et al53 is very

complementary53 This work uses molecular mechanics extensively to define potential energy

surfaces of stacking of two layers from eclipsed to staggered covering all possible layer offsets Low

energy region was near to the eclipsed stacking which was then zoomed in to examine using DFT for

higher accuracy The far-eclipsed regions encounter no energy barriers with the near-eclipsed regions

which suggest the unlikeness of forming near-staggered layering Within DFT the eclipsed

geometries are at high energy compared to the slight offsets around AA (~ 13 ndash 25 Aring away) For a

hexagonal COF the energetically preferred offset could be in one of the six hexagonal sectors (or

circle sectors) of central angle 60 The preference of falling into one sector over the others is

arbitrary and may be determined by symmetry set by nature or external parameters Hence the

layering order in bulk could be serrated inclined spiral or purely by random The latter case better

known as turbostratic disorder is then more like a rule for 2D COFs rather than an exception caused

by external forces This also explains why the experimental PXRD patters have relatively broad peaks

The layer-offset not only change the internal pore structure but also affect interlayer exciton and

vertical charge transport in opto-electronic applications

About stacking stability the square COFs are expected not to be different from hexagonal COFs

because the local environment causing the shifts is nearly the same The DFTB based calculations

reported along with the synthesis of electron-transporting 2D-NiPc-BTDA COF supports this notion71

Two shifted configurations ndash at 07 and 14 Aring away from AA ndash appeared to be energetically preferred

over the AA stacking It appears that AA stacking is only possible for boron nitride-like structures

were adjacent layers have atoms with opposite charges in vertical direction

SURMOFs-2 a series of paddlewheel-based 2D MOFs possess a different symmetry than

solvothermally synthesized MOF-2 due to the differences in interlayer interactions Typically the

interaction between the paddlewheels favors P2 or C2 symmetry of bulk MOF-2 rather than the P4

symmetry of SURMOFs-2 Bader charge analysis reveals that electron distribution between the Cu-

paddlewheels is the lowest when they follow P4 symmetry This indicates the smallest possibility of

having a direct Cu-Cu bond between the paddlewheels In monolayer organic linkers undergo no

rotation with respect to metal dimers

27

X-ray diffraction of SURMOFs-2 made by Woumlll et al indicated P4 symmetry and a relatively small

interlayer separation This increases the repulsion between the linkers and enforces them to rotate

The rotations of each linker in a layer are controlled globally The rotated linkers in adjacent layers

increase London dispersion however a paddlewheel-led shift towards any side increases repulsion

thereby locking SURMOF-2 in P4 packing Hence with the special arrangement of rotated linkers the

linker-linker interaction overcomes the paddlewheel-paddlewheel interaction

P4 symmetry opens up the pores more clearly than P2 or C2 Additionally the metal sites that

typically host solvents are inaccessible Furthermore improvements such as functionalizing the linker

may be easily carried out

Based on our calculations on 2D materials we emphasize the role of van der Waals interactions in

determining the layer-to-layer arrangements The promise of reticular chemistry which is the

maintainability of structural integrity of the building blocks in the construction process is partly

broken in the case of SURMOFs-2 This is because due to repulsion the linkers undergo rotation with

respect to the carboxylic parts albeit keeping the topology

73 Structure-Property Relationships

We have studied a variety of materials from the classes of MOFs COFs and PAFs The structural

differences arise from the differences in the constituents andor their arrangements Properties in

general are interlinked with structural specifications Therefore it is beneficial to know the

relationship between the structural parameters and properties

The mass density is an intensive property of a material In the area of nanoporous materials a crystal

with low mass density has advantages in applications involving transport Definitely the mass density

decreases with increasing pore volume Still the number of atoms in the wall and their weights are

important factors The pore size does not relate directly to the atom counts The volume per atom

(inverse of atom density) another intensive property of a material obliquely gives porosity Figure

16 shows the variation of mass density with volume per atom (including the volume of the atom) for

MOFs COFs and PAFs MOFs show higher mass density compared to other materials of identical

atom density implying the presence of heavy elements It is to be noted that Cu-BTC has mass

density 184 times higher than COF-102 The presence of metals in the form of oxide clusters in MOFs

increases the mass density and decreases the volume per atom Note that the low-weighted MOF in

the discussion (MOF-205) is heavier than many of the PAFs and COFs The relatively high mass

density and small volume per atom of COF-300 is due to its 5-fold interpenetration whereas COF-202

has additional tert-butyl groups which do not contribute to the system shape but affect the mass

density and the volume per atom COF-102 and 103 have same topology but different centers (C and

28

Si respectively) The Si centers increases the cell volume and decreases mass density COF-105 (Si

centers) and COF-108 (C centers) additionally differ in their topologies (ctn and bor respectively) It

appears that bor topology expands the material compared to ctn PAFs hold the extreme cases PAF-

phnl has the highest atom and mass densities whereas PAF-qtph has the smallest atom and mass

densities

Figure 16 Mass density as a function of volume per atom for MOFs COFs and PAFs

The bulk modulus indicates the materialsrsquo resistance towards compression which should in principle

decrease with increasing porosity At the same time larger number of atoms making covalent

networks in unit volume should supply larger bulk moduli Thus differences in molecular contents

and architectures give rise to different bulk moduli It is interesting to see how the mechanical

stability of nanoporous materials is related with the atom density We have obtained a correlation

between bulk modulus (B) and volume per atom (VA) in the case of the studied MOFs COFs and PAFs

as follows

29

where k is a constant (see Figure 17) The inverse-volume correlation indicates that the materials

close to the fitting curve have average bond strengths (interaction energy between close atoms)

identical to each other independent of number of bonds bond order and branching Only Cu-BTC

COF-202 and COF-300 show significant differences from the fitted curve Cu-BTC has 17 times larger

bulk modulus compared to COF-102 of similar volume per atom which implies the substantially

higher strength of the bond network resulting from paddlewheel units and tbo topology

Interpenetration decreased the volume per atom however increased bulk modulus through

interlayer interactions in the case of COF-300 The tert-butyl groups in COF-202 do not transmit its

inherent stability to the COF significantly however decreases the volume per atom Comparison

between COF-102 (C centers) and COF-103 (Si centers) discloses that Si centers decrease the

mechanical stability Comparison between COF-105 (ctn) and COF-108 (bor) suggests that ctn

topology possess higher stability This indicates that local angular preferences can amend the

strength of the bulk material

Figure 17 Bulk modulus as a function of volume per atom for MOFs COFs and PAFs

Band gaps of all the studied materials show that they are semiconductors except of Cu-BTC which

has unpaired electrons at the Cu centers Our studies of the density of states (DOS) of bulk MOFs and

the cluster models that have finite numbers of connectors and linkers show that electronic structure

30

stays unchanged when going from cluster to periodic crystal In the case of 2D COFs the DOS of

monolayers and bulk materials were identical Interpenetrated COF-300 showed no difference in the

electronic structure in comparison with the non-interpenetrated structure Based on these results

we may reach into a premature conclusion that electronic structure of a solid is determined by its

constituent bonded network sufficiently large to include all its building units

HOMO-LUMO gap of the building units determine the band gap of a framework material We have

observed that PAFs nearly reproduced the HOMO-LUMO gaps of the linkers 3D COFs that are made

of more than one building unit show that the band gap is slightly smaller than the smallest of the

HOMO-LUMO gaps of the building units For example

TBPM (43 eV) + HHTP (34 eV) COF-105COF-108 (32 eV)

TBPM (43 eV) + TBST (139 eV) COF-202 (42 eV)

TAM (41 eV) + TA (26 eV) COF-300 (23 eV)

The compound names are taken from appendix E Additionally the band gaps decrease with

increasing number of conjugated rings similar to HOMO-LUMO gaps of the linkers

I believe that the studies in the thesis have helped to an extent to understand the structure

stability and properties of different classes of framework materials The benchmark structures we

studied have the essential features of the classes they represent Ab-initio based computational

studies of several periodic structures are exceptional and thus have its place in the literature

31

List of Abbreviations

ADF Amsterdam Density Functional code

BLYP Becke-Lee-Yang-Parr functional

B3LYP Becke 3-parameter Lee Yang and Parr functional

COF Covalent-Organic Framework

CP Coordination Polymer

CTF Covalent-Triazine Framework

DC Dispersion correction

DFT Density Functional Theory

DFTB Density Functional Tight-Binding

DOS Density of States

DOE (US) Department of Energy (United States)

DZP Double-Zeta Polarized basis set

GGA Generalized Gradient Approximation

LCAO Linear Combination of Atomic Orbitals

LPE Liquid Phase Epitaxy

MOF Metal-Organic Framework

PAF Porous Aromatic Framework

PBE Perdew-Burke-Ernzerhof functional

PXRD Powder X-ray Diffraction Pattern

QLDFT Quantized Liquid Density Functional Theory

RCSR Reticular Chemistry Structure Resource

SBU Secondary Building Unit

SCC Self-Consistent Charge

TZP Triple-Zeta Polarized basis set

SURMOF Surface-Metal-Organic Framework

32

List of Figures

Figure 1 ldquoAdamantinerdquo unit of diamond structure and diamond (dia) net 3

Figure 2 CU-BTC MOF and the corresponding tbo net 4

Figure 3 Fundamental building blocks and SBUs of Cu-BTC and extension of SBUs following crystal

structure 5

Figure 4 Schematic diagram of the single pore of MOF and An example of a simple cubic MOF in

which zinc-oxide tetrahedron are linked together by benzene linkers Atom colors blue ndash Zn red ndash O

grey ndash C white ndash H 6

Figure 5 Schematic diagram of interpenetrated and interwoven frameworks 7

Figure 6 Schematic diagram of SURMOF 8

Figure 7 SBUs and topologies of 2D COFs 9

Figure 8 Deconstructed building units their schematic representations and final geometries of

HKUST-1 (Cu-BTC) MOF-5 MOF-177 MOF-205 and MIL-53 11

Figure 9 AA and AB layer stacks of hexagonal layers 13

Figure 10 Stacking energy Es vs shift of adjacent layers for COF-5 Different stacking possibilities and

their energies are also shown 14

Figure 11 Schematic diagram of different building units forming 2D COFs 16


topologies 17

Figure 13 Diamond structure and various organic linkers to build up PAFs 18

Figure 14 The building units and schematic diagram of the formation of iso-reticular SURMOF series

20

Figure 15 Energy diagram of the metastable P4 and stable P2 structures 22

Figure 16 Mass density as a function of volume per atom for MOFs COFs and PAFs 28

Figure 17 Bulk modulus as a function of volume per atom for MOFs COFs and PAFs 29

33

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37

Appendix A

Review Covalently-bound organic frameworks

Binit Lukose and Thomas Heine

To be submitted for publication after revision

Contents

1 Introduction

2 Synthetic achievements

21 Covalent Organic Frameoworks (COFs)

22 Covalent-Triazine Frameworks (CTFs)

23 Porous Aromatic Frameworks (PAFs)

24 Schemes for synthesis

25 List of materials

3 Studies of the underlying structure and properties of COFs

4 Applications

41 Gas storage

411 Porosity of COFs

412 Experimental measurements

413 Theoretical preidctions

414 Adsorption sites

415 Hydrogen storage by spillover

42 Diffusion and selectivity

43 Suggestions for improvement

431 Geometry modifications

432 Metal doping

433 Functionalization

5 Conclusions

6 List and pictures of chemical compounds

38

1 Introduction

Nanoporous materials have perfectly ordered voids to accommodate to interact with and to

discriminate molecules leading to prominent applications such as gas storage separation and sieving

catalysis filtration and sensoring1-4 They are defined as porous materials with pore diameters less

than 100 nm and are classified as micropores of less than 2 nm in diameter mesopores between 2

and 50 nm and macropores of greater than 50 nm The internal geometry that determines pore size

and surface area can be precisely engineered at molecular scales Reticular synthetic methods

suggested by Yaghi and co-workers5-7 can accomplish pre-designed frameworks The procedure is to

select rigid molecular building blocks prudently and assemble them into destined networks using

strong bonds

Several types of materials have been synthesized using reticular chemistry concepts One prominent

group which is much appreciated for its credentials is the Metal-Organic Frameworks (MOFs)8-13 in

which metal-oxide connectors and organic linkers are judiciously selected to form a large variety of

frameworks The immense potential of MOFs is facilitated by the fact that all building blocks are

inexpensive chemicals and that the synthesis can be carried out solvothermally The progress in MOF

synthesis has reached the point that some of the MOFs are commercially available Several MOFs of

ultrahigh porosity have also been successfully synthesized notably the non-interpenetrated IRMOF-

74-XI which has a pore size of 98 Aring Scientists are also able to synthesize MOFs from cheap edible

natural products14 Since the discovery of MOFs many other crystalline frameworks have been

synthesized using reticular chemistry such as Metal-Organic Polyhedra (MOP)15-19 Zeolite

Imidazolate Frameworks (ZIFs)20-22 and Covalent Organic Frameworks (COFs)23-29

COFs are composed of covalent building blocks made of boron carbon oxygen and hydrogen in

many cases also including nitrogen or silicon stitched together by organic subunits The atoms are

held together by strong covalent bonds Depending on the selection of building blocks the COFs may

form in two (2D) or three (3D) dimensions Planar building blocks are the constituents of 2D COFs

whereas for the formation of 3D COFs typically tetragonal building blocks are involved High

symmetric covalent linking as it is perceived in reticular chemistry was confirmed for the end

products5

Unlike the case of supramolecular assemblies the absence of noncovalent forces between the

molecular building units endorses exceptional rigidity and stability for COFs They are in general

thermally stable above 4000 C Also in COFs the stitching of molecular building units guarantees an

39

increased order and allows control over porosity and composition Without any metals or other

heavy atoms present they exhibit low mass densities This gives them advantages over MOFs in

various applications for example higher gravimetric capacities for gas storage3031 The lowest

density crystal known until today is COF-10824 In addition COFs exhibit permanent porosity with

specific surface areas that are comparable to MOFs and hence larger than in zeolites and porous

silicates

MOF and COF crystals possess long range order although COFs have been achieved so far only at the

μm scale Reversible solvothermal condensation reactions are credited for the high order of

crystallinity Other new framework materials such as Covalent Triazine Frameworks (CTFs) and

Porous Aromatic Frameworks (PAFs) differed in ways of synthesis The former was prepared by

ionothermal polymerization while the latter was produced by coupling reactions PAFs lack long

range order in the crystals as a result of the irreversible synthesis Nevertheless many of the

materials are promisingly good for applications In this review we intend to discuss the synthetic

achievements of COF CTFs and PAFs and studies on their structure properties and prominent

applications

For easy understanding of the atomic geometry of a material the reader is referred to Table 1 which

gives the names of the framework materials the reactants and the synthesis scheme Figure 5 shows

the reactants and Figure 4 shows the reaction schemes Example reactions are given in Figure 1-3

Abbreviations of each chemical compound are given in Section 6


21 Covalent Organic Frameworks (COFs)

In the year 2005 Yaghi et al23 achieved the crystallization of covalent organic molecules in the form

of periodic extended layered frameworks The condensation of discrete molecules of different sizes

enabled the synthesis of micro- and mesoporous crystalline COFs27 The selection of molecules with 2

and 3 connection sites for synthesis led to the formation of hexagonal layered geometries32 Yaghi et

al have synthesized half a dozen three-dimensional crystalline COFs solvothermally using tetragonal

building blocks containing 4 connection sites since 2007242829 Figure 1 shows a few examples of 2D

and 3D COFs formed by the self-condensation of boronic acids such as BDBA TBPM and TBPS and co-

condensation of the same boronic acids with HHTP

40

Figure 1 Solvothermal condensation (dehydration) of monomers to form 2D and 3D COFs Atom colors are boron yellow oxygen red yellow (big) silicon grey carbon

Alternate synthetic procedures were also exploited for production and functionalization of COFs

Lavigne et al33 showed that the synthesis of COFs using polyboronate esters is facile and high-yielded

41

Boronate esters often contain multiple catechol moieties which are prone to oxidation and are

insoluble in organic solvents Dichtel et al3435 presented Lewis acid-catalysis procedures to form

boronate esters of catechols and arylboronic acids without subjecting to oxidation Cooper et al36

successfully utilized microwave heating techniques for rapid production (~200 times faster than

solvothermal methods) of both 2D and 3D COFs The syntheses of phthalocyanine3437 or porphyrin38

based square COFs have been reported in literature The latter was noticed for its time-dependent

crystal growth which also affects its pore parameters

Abel et al39 reported the ability to form COFs on metallic surfaces COF surfaces (SCOFs) have been

formed by molecular dehydration of boroxine and triphenylene on a silver surface Albeit with some

defects the materials showed high temperature stability allowing to proceed with functionalization

Lackinger et al40 realized the role of substrates on the formation of surface COFs from the surface-

generated radicals Halogen substituted polyaromatic monomers can be sublimed onto metal

substrates and ultimately turned into a COF after homolysis and intermolecular colligation

Chemically inert graphite surfaces cannot support the homolysis of covalent carbon-halogen bonds

and thus cannot initiate the subsequent association of radicals COF layers can be formed onto

Cu(111)40 and Au(111)41 surfaces but with lower crystal ordering Beton et al41 deposited the

monomers on annealed Au(111) surfaces which supplied surface mobility for the monomers and

subsequently increased porosity and surface coverage of the covalent networks Unlike the bulk form

at the surface the monomers were self-organized onto polygons with 4 to 8 edges Such a template

was able to organize a sublimed layer of C60 fullerenes the number of C60 molecules adsorbed in a

cavity was correlated to the size of the polygon

In 2009 Sassi et al42 studied the problem of crystal growth of COFs on substrates They calculated

the reaction mechanism of 14-benzenediboronic acid (BDBA) on Ag(111) surface self-condensation

of BDBA molecules in solvents leads to the formation of two-dimensional (the planar) stacked COF-1

For the surface COFs the study using Density Functional Theory reveals that there are neither

preferred adsorption sites for the molecules nor a charge transfer between the molecules and the

surface Hence the electronic structure of the molecules remains unchanged and the role of the

metal surface is limited in providing the planar nature for the polymer The free reaction enthalpy

(Gibbs free energy) difference of the reaction ∆G = ∆H ndash T∆S is approximated using the harmonic

approximation taking into account the geometrical restrictions of the metal surface and the entropic

contributions of the released water molecules As result the formation of SCOF-1 has been found to

be exothermic if more than six monomers are involved Ourdjini et al43 reported the polymerization

of 14-benzenediboronic acid (BDBA) on different substrates (Ag(111) Ag(100) Au(111) and Cu(111))

and at different source and substrate temperatures to follow how molecular flux and adsorption-

42

diffusion environments should be controlled for the formation of polymers with the smallest number

of structural defects High flux is essential to avoid H-bonded supramolecular assemblies of

molecules and the substrate temperature needs to be optimized to allow the best surface diffusion

and longest residential time of the reactants Achieving these two contradictory conditions together

is a limitation for some substrates eg for copper Silver was found to be the best substrate for

producing optimum quality polymers Controlling the growth parameters is important since

annealing cannot cure defects such as formation of pentagons heptagons and other non-hexagonal

shapes which involved strong covalent bonds

Ditchel et al44 successfully grew COF films on monolayer graphene supported by a substrate under

operationally simple solvothermal conditions The films have better crystallinity compared to COF

powders and can facilitate photoelectronic applications straightaway Zamora et al45 have achieved

exfoliation of COF layers by sonication The thin layered nanostructures have been isolated under

ambient conditions on surfaces and free-standing on carbon grids

A noted characteristic of COFs is its organic functionality Judiciously selected organic units ndash pyrene

and triphenylene (TP) ndash for the production of TP COF can not only harvest photons over a wide range

but also facilitate energy migration over the crystalline solid25 Polypyrene (PPy)-COF that consists of

a single aromatic entity ndash pyrene- is fluorescent upon the formation of excimers and hence undergo

exciton migration across the stacked layers26 A nickel(II)-phthalocyanine based layered square COF

that incorporates phenyl linkers and forms cofacially stacked H-aggregates was reported to absorb

photons over the solar spectrum and transport charges across the stacked layers37 COF-366 and

COF-66 showed excellent hole mobility of 81 and 30 cm2 V-1s-1 surpassing that of all polycrystalline

polymers known until today46 A first example of an electron-transporting 2D COF was reported

recently47 This square COF was built from the co-condensation of nickel(II) phthalocyanine and

electron-deficient benzothiadiazole With the nearly vertical arrangement of its layers it exhibits an

electron mobility of 06 cm2 V-1s-1 The enhanced absorbance is over a wide range of wavelengths up

to 1000 nm In addition it exhibits panchromatic photoconductivity and high IR sensitivity

Lavigne et al48 achieved the condensation of alkyl (methyl ethyl and propyl) substituted organic

building units with boronic acids forming functionalized COFs The alkyl groups contribute for higher

molar adsorption of H2 however the increased mass density of the functionalized COFs cause for

decreased gravimetric storage capacities Boronate ester-linked COFs are stable in organic solvents

however undergo rapid hydrolysis when exposed in water49 In particular the instability of COF-1

upon H2O adsorption shall be mentioned here50 Lanni et al claimed that alkylation could bring

hydrolytic stability into COFs49

43

Functionalization and pore surface engineering in 2D COFs can be improved if azide appended

building blocks are stitched together in click reactions with alkynes51 Control over the pore surface

is made possible by the use of both azide appended and bare organic building units the ratios of

which is matching with the final amount of functionalization in the pore walls The click reactions of

azide groups with alkynes within the pores lead to the formation of triazole-linked groups on the

pore surfaces This strategy also gives the relief of not condensing the already functionalized building

units Jiang et al have asserted eclipsed layering for most of the final COFs using powder X-ray

diffraction pattern Exceptions are the hexagonal functionalized COFs with relatively high azide-

content (ge 75) Their weak XRD signals suggest possible layer-offset or de-lamellation Although

functionalization on pore surfaces exhibits the nature of lowering the surface area the possibility to

add reactive groups within the pores can be utilized for gas-sorption selectivity The authors have

claimed a 16 fold selectivity of CO2 over N2 using 100 acetyl-rich COF-5 compared to the pure COF-5

The range of the click reaction approach is so wide that relatively large chromophores can be

accommodated in the pores thereby making COF-5 fluorescent

Functionalization of 3D COFs has just reported in 201252 Dichtel et al used a monomer-truncation

strategy where one of the four dihydroxyborylphenyl moieties of a tetrahedral building unit was

replaced by a dodecyl or allyl functional group Condensation of the truncated and the pure

tetrahedral blocks in a certain ratio created a functionalized 3D COF The degree of functionalization

was in proportion with the ratio The crystallinity was maintained except for high loading (gt 37) of

truncated monomers The pore volume and the surface area were decreased as a function of loading

level

A heterogeneous catalytic activity of COFs is achieved with an imine-linked palladium doped COF by

enabling Suzuki-Miyaura coupling reaction within the pores53 The COF-LZU1 has a layered geometry

that has the distance between nitrogen atoms in the neighboring linkers in a level (~37 Aring) sufficient

to accommodate metal ions Palladium was incorporated by a post-treatment of the COF PdCOF-

LZU1 was applied to catalyze Suzuki-Miyaura coupling reaction This coupling reaction is generally

used for the facile formation of C-C bonds54 The increased structural regularity and high insolubility

in water and organic solvents are adequate qualities of imine-linked COFs to perform as catalysts

Experiments with the above COF show a broad scope of the reactants excellent yields of the

products and easy recyclability of the catalyst

The comparatively higher thermal stability of COFs is often noted and is explainable with their strong

covalent bonds The reversible dehydrations for the formation of most of the COFs point to their

instability in the presence of water molecules This has been tested and verified for some layered

COFs with boronate esters49 Such COFs are stable as hosts for organometallic molecules55 COF-102

44

framework was found to be stable and robust even in the presence of highly reactive cobaltocenes

The highly stable ferrocenes appear to have an arrangement within the framework led by π-π

interactions

22 Covalent Triazine Frameworks (CTFs)

In the year 2008 Thomas et al56 synthesized a crystalline extended porous nanostructure by

trimerization of polytriazine monomers in ionothermal conditions With the catalytic support of ZnCl2

three aromatic nitrile groups can be trimerized to form a hexagonal C3N3 ring The resulting structure

known as Covalent Triazine-based Frameworks (CTFs) is similar to 2D COFs in geometry and atomic

composition (see Figure 2) Usage of larger non-planar monomers at higher amounts of ionic salts

however led to the formation of contorted structures Interestingly those structures showed

enhanced surface area and pore volume The trimerization of monomers that lack a linear

arrangement of nitrile groups ended up as organic polymer networks Later the same group

introduced mesoporous channels onto a CTF (CTF-2)57 by increasing temperature and ion content

The resulting structure however was amorphous It is concluded that the reaction parameters and

the amount of salt play a crucial role for tuning the porosity and controlling the order of the material

respectively58

Figure 2 Trimerization of nitrile monomers to form CTF-1 Atom colors blue N grey C white H

Ben et al59 followed ionothermal conditions for the targeted synthesis of a 3D framework using

tetraphenylmethane block and a triangular triazine ring The end product was amorphous thermally

stable up to 400 0C and could be applied for the selective sorption of benzene over cyclohexane On a

later synthetic study Zhang et al60 reported that this polymerization could be accomplished in short

45

reaction times under microwave enhanced conditions The template-free high temperature dynamic

polymerization reactions constitute irreversible carbonization reactions coupled with reversible

trimerization of nitriles The irreversibility encounter in these condensation reactions is responsible

for the production of frameworks as amorphous solids6162

An amorphous yet microporous CTF was found to be able to catalyze the oxidation of glycerol with

Pd nanoparticles that are dispersed in the framework63 This solid catalyst appears to be strong

against deactivation and selective toward glycerate compared to Pd supported activated carbon This

is attributed to the relatively high stability of Pd nanoparticles that benefit from the presence of

nitrogen functionalities in CTF An advancement on selective oxidation of methane to methanol at

low temperature is accomplished by using an amorphous bipyridyl-rich platinum-coordinated CTF as

catalyst64


a notably high surface area (BET surface area of 5600 m2g-1 Langmuir surface area of 7100 m2g-1)65

PAF-1 has been synthesized in a rather simple way using a nickel(0)-catalyzed Yamamoto-type66

Ullmann cross-coupling reaction67(see Figure 3) The material is thermally (up to 520 0C in air) and

hydrothermally (in boiled water for a minimum of seven days) stable The framework exposes all

faces and edges of the phenyl rings to the pores and hence the high surface area can be achieved

while its high stability is inherited from the parent diamond structure The synthesized material was

verified as disordered and amorphous yet with uniform pore diameters The excess H2 uptake

capacity of PAF-1 was measured as 70 wt at 48 bar and 77 K It can adsorb 1300 mg g-1 CO2 at 40

bar and room temperature PAF-1 was also tested for benzene and toluene adsorption

Figure 3 Coupling reaction using halogenated tetragonal blocks for the formation of diamond-like PAF-1 Atom colors red Br grey C white H

46

An attempt to synthesize a diamondoid with quaterphenyl as linker is described recently68 A

tetrahedral unit and a linear linker each of them has two phenyl rings were polymerized using the

Suzuki-Miyaura coupling reaction54 The product (PAF-11) however stayed behind theoretical

predictions and performed poorly pointing to its shortcomings such as short-range order distortion

and interpenetration of phenyl rings Nevertheless the amorphous solid displayed high thermal and

chemical stabilities proneness for adsorbing methanol over water and usability for eliminating

harmful aromatic molecules

PAF-569 is a two-dimensional hexagonal organic framework synthesized using the Yamamoto-type

Ullmann reaction This material is composed only of phenyl rings however lack long range order

because of the distortion of the phenyl rings and kinetics controlled irreversible coupling reaction It

retains a uniform pore diameter and provides high thermal and chemical stability despite its

amorphous nature PAF-5 was suggested for adsorbing organic pollutants at saturated vapour

pressure and room temperature

Co-condensation reactions with piperazine enabled nucleophilic substitution of cyanuric chloride to

form a covalently linked porous organic framework PAF-670 The synthesis in mild conditions yields a

product with uniform morphology and a certain degree of structural regularity Being nontoxic this

material was tested for drug delivery thereby stepping into biomedical applications of covalently

linked organic frameworks Primary tests suggest that PAF-6 could be promoted for drug release for

its permanent porosity and facile functionalization In comparison with MCM-4171 a widely tested

inorganic framework PAF-6 performed equally or even superiorly


The majority of the COFs were synthesized using solvothermal step-by-step condensation

(dehydration) reactions The method incorporates reversibility and is applicable for supplying long

range order in COF materials The reactants generally consist of boronic acids and hydroxy-

polyphenyl (catechol) compounds Extended porous networks are obtained when O-B or O-C bonds

are formed into 5 or 6-membered rings after dehydration (scheme 1) Dehydration may also be

carried out using microwave synthesis Alternately boronic acid can react with catechol acetonide in

presence of a Lewis acid catalyst The molecules link to each other after the liberation of acetone and

water (scheme 2) The utilization of phenyl-attached formyl and amino groups as building units

results in the formation of imines after dehydration (scheme 3) A desired arrangement of molecular

arrays on surfaces can be fulfilled by depositing planar molecules on metallic surfaces followed by

covalent linking using annealing

47

Isocyanate groups follow trimerization to form poly-isocyanurate rings (scheme 4) Cyclotrimerization

of monomers containing nitrile groups or cyanate groups is prone to generate C3N3 rings (scheme 5)

However the ionothermal synthesis of them resulted with amorphous materials Unique bond

formation is often not achieved throughout the material and thus the crystal lacks long-range order

Analogously coupling reactions such as Ullmann and Suzuki-Miyaura give rise to amorphous

products However they are adequate in producing C-C bonds when halogen-substituted compounds

are reacted (scheme 6) Nucleophilic substitution may also be used for framing networks in cases

like reactants are formed into nucleophiles and ions after release of their end-groups (scheme 7)

48

Figure 4 Different schemes reported for the synthesis of covalently-bound organic frameworks

49

25 List of synthesized materials

Table 1 List of synthesized materials in the literature their building blocks synthesis methods measured surface area [m

2 g

-1] pore volume [cm

3 g

-1] and pore size [Aring]

COF Names Reactants Synthesis Surface

Area

Pore

volume

Pore

size

COF-1 BDBA Solvothermal condensation235072

scheme 1

711 62850 032

03650

9

COF-5 BDBA HHTP Solvothermal condensation23

scheme 1

1590 0998 27

Microwave3673 scheme 1 2019

BDBA TPTA Lewis acid catalysis35 TPTA

COF-6 BTBA HHTP Solvothermal condensation27

scheme 1

980 (L) 032 64

COF-8 BTPA HHTP Solvothermal condensation27

scheme 1

1400 (L) 069 187

COF-10 BPDA HHTP Solvothermal condensation27

scheme 1

2080 (L) 144 341

BPDA TPTA Lewis acid catalysis35 scheme 2

COF-18Aring BTBA THB Facile dehydration3348 scheme 1 1263 069 18

COF-16Aring BTBA alkyl-THB

(alkyl = CH3)

Facile dehydration48 scheme 1 753 039 16


(alkyl = C2H5)



(alkyl = C3H7)


50

SCOF-1 BDBA Substrate-assisted synthesis39

scheme 1

SCOF-2 BDBA HHTP Substrate-assisted synthesis39

scheme 1

TP COF PDBA HHTP Solvothermal condensation25

scheme 1

868 079 314

PPy-COF PDBA Solvothermal condensation26

scheme 1

923 188

TBB COF TBB (on Cu(111) and

Ag(110) surfaces)

Surface polymerisation40 scheme

6

TBPB COF TBB (on Au(111)

surface)


6

BTP COF BTPA THDMA Solvothermal condensation72

scheme 1

2000 163 40

HHTP-DPB COF DPB HHTP Solvothermal condensation73

scheme 1

930 47

PICU-A DMBPDC Cyclotrimerization74 scheme 4

PICU-B DCF Cyclotrimerization74 scheme 4

COF-LZU1 DAB TFB Solvothermal condensation53

scheme 3

410 054 12

PdCOF-LZU1 COF-LZU1 PdAc Facile post-treatment53 146 019 12

XN3-COF-5 X N3-BDBA (100-X)

BDBA HHTP

Solvothermal condensation51

scheme 1

2160

(X=5)

1865 (25)

1722 (50)

1641 (75)

1421

(100)

1184

1071

1016

0946

0835

295

276

259

258

227

51

XAcTrz-COF-5 XN3-COF-5 PAc Click reaction51 2000

(X=5)

1561 (25)

914 (50)

142 (75)

36 (100)

1481

0946

0638

0152

003

298

243

156

153

125

XBuTrz-COF-5 XN3-COF-5 HP Click reaction51

XPhTrz-COF-5 XN3-COF-5 PPP Click reaction51

XEsTrz-COF-5 XN3-COF-5 MP Click reaction51

XPyTrz-COF-5 XN3-COF-5 PyMP Click reaction51

COF-42 DETH TFB Solvothermal condensation75

scheme 3

710 031 23

COF-43 DETH TFPB Solvothermal condensation75

scheme 3

620 036 38

CTF-1 DCB Ionothermal trimerization56

scheme 5

791 040 12

CTF-2 DCN Ionothermal trimerization57

scheme 5

90 8

mp-CTF-2 2255 151 8

CTF (DCP) DCP Ionothermal trimerization64

scheme 5

1061 0934 14

K2[PtCl4]-CTF DCP K2[PtCl4] Trimerization (scheme 5) +

coordination64

Pt-CTF DCP Pt Trimerization (scheme 5) +

coordination64

PAF-5 TBB Yamamoto-type Ullmann cross-

coupling reaction69 scheme 6

1503 157 166

52

PAF-6 PA CA Nucleophilic substitution70

scheme 7

1827 118

Pc-PBBA COF PcTA BDBA Lewis acid catalysis34 scheme 2 506 (L) 0258 217

NiPc-COF OH-Pc-Ni BDBA Solvothermal condensation37

scheme 1

624 0485 190

XN3-NiPc-COF OH-Pc-Ni X N3-BDBA

(100-X) BDBA


scheme 1

XEsTrz-NiPc-

COF

XN3-NiPc-COF MP Click reaction51

ZnP COF TDHB-ZnP THB Solvothermal condensation38

scheme 1

1742 1115 25

NiPc-PBBA COF NiPcTA BDBA Lewis acid catalysis35 scheme 2 776

2D-NiPc-BTDA

COF

OHPcNi BTDADA Solvothermal condensation47

scheme 1

877 22

ZnPc-Py COF OH-Pc-Zn PDBA Solvothermal condensation

scheme 1

420 31

ZnPc-DPB COF OH-Pc-Zn DPB Solvothermal condensation

scheme 1

485 31

ZnPc-NDI COF OH-Pc-Zn NDI Solvothermal condensation

scheme 1

490 31

ZnPc-PPE COF OH-Pc-Zn PPE Solvothermal condensation

scheme 1

440 34

COF-366 TAPP TA Solvothermal condensation46

scheme 3

735 032 12

COF-66 TBPP THAn Solvothermal condensation46

scheme 1

360 020 249

53

COF-102 TBPM Solvothermal condensation24

scheme 1

3472 135 115

Microwave36

scheme 1

2926

COF-102-C12 TBPM trunk-TBPM-R

(R=dodecyl)


scheme 1

12

COF-102-allyl TBPM trunk-TBPM-R

(R=allyl)


scheme 1

COF-103 TBPS Solvothermal condensation24

scheme 1

4210 166 125

COF-105 TBPM HHTP Solvothermal condensation24

scheme 1


scheme 1

COF-202 TBPM TBST Solvothermal condensation28

scheme 1

2690 109 11

COF-300 TAM TA Solvothermal condensaion29

scheme 3

1360 072 72

PAF-1 TkBPM-X (X=C) Yamamoto-type Ullmann cross-


5600

PAF-2 TCM cyclotrimerization59 scheme 5 891 054 106

PAF-3 TkBPM-X (X=Si) Yamamoto-type Ullmann cross-


2932 154 127

PAF-4 TkBPM-X (X=Ge) Yamamoto-type Ullmann cross-


2246 145 118

PAF-11 TkBPM-X (X=C) BPDA Suzuki coupling reaction68 704 0203 166

54

scheme 6

3 Studies of structure and properties of COFs

31 2D COFs

Following the literature of the years 2005-2010 2D COFs were believed to have high symmetric AA

(eclipsed ndash P6mmm symmetry) stacking as boron nitride (h-BN) [REF] An exception was COF-1

which was considered to have AB (staggered ndash P63mmc) stacking as graphite[REF] The AA stacking

maximizes the attractive London dispersion interaction between the layers an important

contribution to the stacking energy At the same time AA stacking always suffers repulsive Coulomb

force between the layers due to the polarized connectors as the distance between atoms exposing

the same charge is closest It should be noted that in boron nitride boron atoms serve as nearest

neighbors to nitrogen atoms in adjacent layers The Coulomb interaction has ruled out possible

interlayer eclipse between atoms of alike charges Based on these facts we modeled77 a set of 2D

COFs with different possible stacks Each layer was drifted with respect to the neighboring layers in

directions symmetric to the hexagonal pore and we calculated the total energies and their Coulombic

contributions The AA stacking version was found to have the highest Coulombic repulsion in each

COF The lattice types with the layers shifted to each other by ~14 Aring approximately the bond length

between two atoms in a 2D COF were found to be more stable compared to AA or AB In this low-

symmetry configuration the hexagonal rings in the pore walls undergo staggering with that of

adjacent layers Within an error limit the bulk COFs may be either serrated or inclined as shown in

Figure 5 The interlayer separations of all the COF stacks are in the range of 30 to 36 Aring and increase

in the order AB serratedinclined AA32 The motivation for proposing inclined stacking for COFs is

that the rhombohedral graphite (ABC stacking) is the inclined version of the layer-offset in natural

graphite (AB stacking) The instability of AA stacking was also suggested by the studies of elastic

properties of COF-1 and COF-5 by Zhou et al78 The shear modulus show negative signs for the

vertical alignment of COF layers while they are small but positive for the offset of layers

55

Figure 5 Different stacks of a 2D covalent organic framework COF-1 The atoms are shown as Van der Waals spheres

The different stacking modes should in principle be visible in their PXRD patterns as each space

group has a distinct set of symmetry imposed reflection conditions We simulated the XRD patterns

of COFs in their known and new configurations and on comparison with the experimental spectrum

the new as well as AA stacking showed good agreement3279 However the slight layer-offsets in

conjunction with the large number of atoms in the unit cells change the PXRD spectrum only by the

appearance of a few additional peaks all of them in the vicinity of existing signals and by changes in

relative intensities Unfortunately the low resolution of the experimental data does now allow

distinguishing between the different stackings as the broad signals cover all the peaks of the

simulated spectrum

A detailed analysis on the interlayer stacking of HHTP-DPB COF has been made by Dichtel et al73 is

very complementary73 This work uses molecular mechanics extensively to define potential energy

surfaces of stacking of two layers from eclipsed to staggered covering all possible layer offsets The

low energy region was near to the eclipsed stacking which was then zoomed in to examine using DFT

for higher accuracy The far-eclipsed regions encounter no energy barriers with the near-eclipsed

regions which suggest the unlikeness of forming near-staggered layering Within DFT the eclipsed








The layer-offset may not only change the internal pore structure but also affect interlayer exciton

and vertical charge transport in opto-electronic applications

56

Concerning the stacking stability the square 2D COFs are expected not to be different from

hexagonal COFs because the local environment causing the shifts is nearly the same DFTB based

calculations reported along with the synthesis of electron-transporting 2D-NiPc-BTDA COF supports

this notion47 Two shifted configurations ndash at 07 and 14 Aring away from AA ndash appeared to be

energetically preferred over the AA stacking It appears that AA stacking is only possible for boron

nitride-like structures were adjacent layers have atoms with opposite charges in vertical direction In

analogy to BN layers it might be possible to force AA stacking by the introduction of alkalis in

between the layers

32 3D COFs

3D COFs in general are composed of tetragonal and triangular building blocks So far that their

synthesis leads to two high symmetry topologies ndash ctn and bor - in high yields24 The two topologies

differ primarily in the twisting and bulging of their components at the molecular level The

thermodynamic preference of one topology over the other may result from the kinetic entropic and

solvent effects and the relative strain energies of the molecular components It is straight-forward to

state that the effects at the molecular level crucial crucial in the bulk state since transformation from

one net to the other is impossible without bond-breaking There has not been any detailed study on

this matter experimentally or theoretically

Schmid et al8182 have developed force-field parameters from first principles calculations using

Genetic Algorithm approach The parameters developed for cluster models of COF-102 can

reproduce the relative strain energies in sufficient accuracies and be extended to calculations on

periodic crystals The internal twists of aromatic rings within the tetragonal units are different for ctn

and bor nets which lead to stable S4 and unstable D2d symmetries respectively This together with

the bulging of triangular units in the bor net reasoned for energetic preference of ctn over bor for all

boron-based 3D COFs79

The connectivity-based atom contribution method (CBAC) developed by Zhong et al80 can

significantly reduce computational time needed for quantum chemical calculation for framework

charges when screening a large number of MOFs or COFs in terms of their adsorption properties The

basic assumption is that atom types with same bonding connectivity in different MOFsCOFs have

identical charges a statement that follows from the concept of reticular chemistry where the

properties of the molecular building blocks keep their properties in the bulk After assigning the

CBAC charges to the atom types slight adjustment (usually less than 3 ) is needed to make the

frameworks neutral Simulated adsorption isotherms of CO2 CO and N2 in MOFs and COFs show that

CBAC charges reproduce well the results of the QM charges8384 The CBAC method still requires a

57

well-parameterized force field in order to account correctly for adsorption isotherms as the second

important contribution to the host-guest interaction is the London dispersion energy between

framework and adsorbed moleculesG

The elastic constants calculated for the 3D COFs COF-102 and COF-108 show that COF-102 is nearly

five times stronger than COF-10878 While the bulk modulus (B) of COF-102 (B = 216 GPa) exceeds

that of known MOFs such as MOF-5 MOF-177 and MOF-205 (B = 153 101 107 GPa respectively81)

the least dense COF-108 is at the edge of structural collapse (B = 49 GPa) The calculations were

made using Density Functional Tight-Binding (DFTB) method Another report82 based on the same

level of theory possibly with a different parameter set however reveals lower bulk moduli for both

COFs 177 GPa for COF-102 and 005 GPa for COF-108 The bulk moduli for COF-103 and COF-105 are

110 and 33 GPa respectively Recently we have reported the structural properties of 3D COFs The

calculations were made using self-consistent charge (SCC) DFTB method The bulk modulus of each

COF is as follows COF-102 ndash 206 COF-103 ndash 139 COF-105 ndash 79 COF-108 ndash 37 COF-202 ndash 153 and

COF-300 ndash 144 GPa Force field calculations79 provide slightly different values COF-102 ndash 170 COF-

103 ndash 118 COF-105 ndash 57 COF-108 ndash 29 COF-202 ndash 110 GPa Albeit the differences in values each

type of calculation shows the trend that bulk modulus decreases with decreasing mas density and

increasing pore volume and distance between connection nodes One has to note that the high

mechanical stabilities of 3D COFs as suggested by the calculations correspond always to defect-free

crystals Theory is expected therefore to overestimate experimental mechanical stability for real

materials

COFs in general have semiconductor-like band gaps (~ 17 to 40 eV)32 Layer-offset from eclipsed

layering slightly increases the band gap However the Density-Of-States (DOS) of a monolayer is

similar to that of bulk COF The band gap is generally smaller for a COF with larger number conjugate

rings

The thermal influence on the crystal structure of 3D COFs is also intriguing as negative thermal

expansion (NTE) the contraction of crystal volume on heating has been reported for COF-10283 The

studies were performed using molecular dynamics with the force field parameters by Schmid et al84

However the thermal expansion coefficient α = -151 times 10-6 K-1 is much smaller compared to that of

some of the reported MOFs that also show NTE behavior85 The volume-contraction upon the

increase of temperature arises from the tilt of phenyl linkers between B3O3 rings and sp3 carbon

atom in TBPM (figure ) Later Schmid et alreported that COF-102 103 105 108 exhibit NTE

behavior both in ctn and bor topologies whereas COF-202 only in ctn topology79 A typical

application is the realization of controllable thermal expansion composites made of both negative

and positive thermal expansion materials

58

4 Applications

41 Gas storage

The success in the synthesis of COFs was certainly the result of a long-term struggle for complete

covalent crystallization The discovery of COFs coincided with the time when world-wide effort was

paid to develop new materials for gas storage in particular for the development hydrogen tanks for

mobile applications Materials made exclusively from light-weight atoms and with large surface

areas were obviously excellent candidates for these applications The gas storage capacity of porous

materials relies on the success of assembling gas molecules in minimum space This is achieved by

the interaction energy exerted by storage materials on the gas molecules Because the interactions

are noncovalent no significant activation is required for gas uptake and release and hence the so-

called physical adsorption or physisorption is reversible The other type of adsorption ndash chemical

adsorption or chemisorption ndash binds dissociated hydrogen covalently or interstitially at the risk of

losing reversibility As it requires the chemical modification of the host material chemisorption is not

a viable route for COFs and might become possible only through the introduction of reactive

components into the lattice The total amount of gas adsorbed in the pores gives rise to what is

referred to as lsquototal adsorption capacityrsquo This quantity is hard to be assessed experimentally as a

measurement is always subjected to influence of the materials surface and gas present in all parts of

the experimental setup Therefore the lsquoexcess adsorption capacityrsquo is reported in experiment Here

the gas stored in the free accessible volume is subtracted from the total adsorption In experiment

this volume includes the voids in the material as well as any empty space between the sample

crystals This volume is typically determined by measuring the uptake of inert gas molecules (He for

H2 adsorption N2 or Ar for adsorption studies of larger molecules) at room temperature with the

assumption that the host-guest interaction between the material and He can be neglected The

different definitions of adsorption is given in Figure 6

Typically experiments measure excess values and simulations provide total values Quantities of

adsorbed molecules are usually expressed as gravimetric and volumetric units The former gives the

amount per unit mass of the adsorbent while the latter gives the amount per unit volume of the

adsorbent Explicative definitions and terminologies related to gas adsorption can be found

elsewhere86

59

Figure 6 Hydrogen density profile in a pore A denotes the excess A+B the absolute and A+B+C the total adsorption The skeletal volume corresponds to the volume occupied by the framework atomsCourtesy of Dr Barbara Streppel and Dr Michael Hirscher MPI for intelligent systems Stuttgart Germany


It is common to inspect the porosity of synthesized nanoporous materials using some inert or simple

gas adsorption measurements Distribution of pore size can be sketched from the

adsorptiondesorption isotherm N2 and Ar isotherms provide an approximation of the pore surface

area pore volume and pore size over the complete micro and mesopore size range Usually the

surface area is calculated using the Brunauer-Emmet-Teller (BET) equation or Langmuir equation

Total pore volume (volume of the pores in a pre-determined range of pore size) can be determined

from either the adsorption or desorption phase The Dubinin-Radushkevic method the T-plot

method or the Barrett-Joyner-Halenda (BJH) method may also be employed for calculating the pore

volume The pore size is often corroborated by fitting non-local density functional theory (NLDFT)

based cylindrical model to the isotherm90-93 In some cases the desorption isotherm is affected by

the pore network smaller pores with narrower channels remain filled when the pressure is lowered

This leads to hysteresis on the adsorption-desorption isotherms The different methods employed for

pore structure analysis are characteristic for micropore filling monolayer and multilayer formations

capillary condensation and capillary filling

For any adsorbate in order to form a layer on pore surface the temperature of the surface must

yield an energy (kBT) much less than adsorbate-surface interaction energy Additionally the absolute

value of the adsorbate-surface binding energy must be greater than the absolute value of the

adsorbate-adsorbate binding energy This avoids clustering of the adsorbate into its three-

dimensional phase

60

At high pressure the adsorption isotherm shows saturation which means that no more voids are left

for further occupation The isotherms show different behaviors characteristic of the pore structure of

the materials There are known classifications based on these differences type I II III IV and V For

COFs and the related materials discussed in this review type I II and IV have been observed (see

Figure 7) As more adsorbate is attracted to the surface after the first surface layer completion one

can expect a bend in the isotherm Type I implies monolayer formation which is typical of

microporosity If the surface sites have significantly different binding energies with the adsorbate

type II behavior is resulted In type IV each ldquokneerdquo where the isotherm bends over and the vapor

pressure corresponds to a different adsorption mechanisms (multiple layers different sites or pores)

and represents the formation of a new layer

Figure 7 Different types of adsorptions in Covalently-bound Organic Frameworks

Argon and nitrogen adsorption measurements at respectively 87 and 77 K exhibit type I isotherms

for COF-1 6 102 and 103 and type IV isotherms for COF-5 8 10 102 and 10387 Smaller pore

diameters of COF-1 and 6 (~ 9 Aring each) are characteristic of monolayer gas formation on the internal

pore surface The same reasons are responsible for the type I character of COF-102 and COF-103

(pore size = 12 Aring each) isotherms albeit with some unusual steps at low pressure The type IV

isotherms of COF-5 8 10 102 and 103 show formation of monolayers followed by their

multiplication within their relatively larger pores (sizes are approximately 27 16 32 12 and 12 Aring

respectively) Other COFs that exhibit type I isotherms for N2 adsorption are the 3D COFs COF-202 (11

Aring) COF-300 (72 Aring) and COF-102-C12 (12 Aring) the alkylated 2D COF series COF-18Aring COF-16Aring COF-14Aring

COF-11Aring (the nomenclature includes their pore sizes) and a 2D square COF NiPc COF (19 Aring)

Isotherms like Type-II were observed for PPy-COF (188 Aring) COF-366 (176 Aring) COF-66 (249 Aring) Pc-

PBBA COF (217 Aring) ZnP-COF (25 Aring) COF-LZU1 (12 Aring) PdCOF-LZU1 (12 Aring) and some of the azide-

appended COFs 50AcTrz-COF-5 (156 Aring) 75AcTrz-COF-5 (153 Aring) 100AcTrz-COF-5 (125 Aring)

50BuTrz-COF-5 (232 Aring) 50PhTrz-COF-5 (212 Aring) 50EsTrz-COF-5 (212 Aring) and 25PyTrz-COF-5

(221 Aring) The majority of the COFs with mesopores exhibit type-IV isotherms They are TP-COF (314

Aring) BTP-COF (40 Aring) COF-42 (23 Aring) COF-43 (38 Aring) HHTP-DPB COF (47 Aring) CTC-COF (226 Aring) NiPc-PBBA

COF ZnPc-Py-COF (31 Aring) ZnPc-DPB-COF (31 Aring) ZnPc-NDI-COF (31 Aring) ZnPc-PPE-COF (34 Aring) 5N3-

61

COF (295 Aring) 25N3-COF (276 Aring) 50N3-COF (259 Aring) 75N3-COF (258 Aring) 100N3-COF (227 Aring)

5AcTrz-COF-5 (298 Aring) 25AcTrz-COF-5 (243 Aring) 5PyTrz-COF-5 (289 Aring) and 10PyTrz-COF-5

(242 Aring)

The synthesized microporous amorphous materials CTF-1 (12 Aring) CTF-DCP (14 Aring) PAF-1 and PAF-2

(106 Aring) exhibit type-I isotherms with N2 adsorption PAF-3 (127 Aring) PAF-4(118 Aring) PAF-5 (157 Aring)

PAF-6 (118 Aring) and PAF-11 showed surprisingly not the typical type I behavior in spite of their

microporosity but type-II isotherms

Many of the mesoporous COFs showed small hysteresis in the adsorption-desorption isotherm

pointing the possibility of capillary condensation Hysteresis was observed for the amorphous

materials in both mirco and meso-pore range Various reasons have been attributed for the observed

hysteresis including the softness of the material and guest-host interactions

412 Gas adsorption experiments

Hydrogen uptake capacities of some boron-based COFs were measured by Yaghi et al87 The excess

gravimetric saturation capacities of COF-1 -5 -6 -8 -10 -102 and -103 at 77 K were found to be 148

358 226 350 392 724 and 705 mg g-1 respectively The saturation pressure increases with an

increase in pore size similar to MOFs88 Pore walls of 2D COFs consist only of edges of connectors

and linkers The fact that faces and edges are largely available for interactions with H2 in 3D

geometries is a reason for their enhanced capacity Total adsorption generally increases without

saturation upon pressure because the difference between the total and the excess capacities

corresponds to the situation in bulk (or in a tank) COFs show in particular good gravimetric

capacities because of their low mass density while volumetric capacities typically do not exceed

those of MOFs The gravimetric hydrogen storage capacities of COF-102 and -103 exceeds 10 wt at

a pressure of 100 bar

COF-18 and its alkylated versions COF-16 -14 and -1 have H2 excess gravimetric capacities 155 144

123 and 122 wt respectively at hellipK and hellipbar

Excess uptake of methane in COFs at room temperature and at 70 bar pressure is as follows COF-1

and -6 up to10 wt COF-5 -6 and -8 between 10 and 15 wt and COF-102 and -103 above 20

wt 87 Isosteric heat of adsorption Qst calculated by fitting the isotherms to virial expansion with

the same temperature are relatively weaker (lt 10 kJmol) for COF-102 and COF-103 at low

adsorption which implies weaker adsorbate-adsorbent interactions In comparison COF-1 and 6

exhibit twice the enthalpy however the overall hydrogen storage capacity was very limited due to

62

the smaller pore volume High Qst at zero-loading is not desirable because the primary excess amount

adsorbed at very low pressures cannot be desorbed practically89

COF-102 and 103 outperform 2D COFs for CO2 storage87 The saturation uptakes at room

temperature were 1200 and 1190 mg g-1 for COF-102 and 103 respectively

A type IV isotherm has been observed for ammonia adsorption in COF-10 inherent to its mesoporous

nature90 The material showed an uptake of 15 mol kg-1 at room temperature and 1 bar the highest

of any nanoporous materials The repeated adsorption-desorption cycles were reported to disrupt

the layer arrangement of this 2D COF Yaghi et al90 were also able to make a tablet of COF-10 crystal

which performed nearly up to the crystalline powder

Not many COFs have been experimentally studied for gas storage applications in spite of high

expectations This has to be understood together as a result of the powder-like polycrystallization of

COFs The enthalpy Qst at low-loading accounted to only 46 kJmol

The excess and total hydrogen uptake capacity of PAF-1 at 48 bar and 77 K reached 7 wt and 10

wt respectively65 PAF-3 and PAF-478_ENREF_73 follow the same diamond topology as PAF-1 the

difference accounts in the central atoms of the tetragonal blocks PAF-1 3 and 4 have C Si and Ge

atoms at the centers respectively At 1 bar the respective adsorption capacities were 166 207 and

150 wt The highest value being found for PAF-3 is attributed to its relatively high enthalpy (66 kJ

mol-1) compared to PAF-1 (54 kJ mol-1) and PAF- 4 (66 kJ mol-1) At high pressure the surface area is

a key factor and because of the lower BET surface area PAF-3 and PAF-4 performs poor At 60 bar

their respective adsorption capacities were 55 and 42 wt For PAF-11 hydrogen uptake was 103

wt at 1 bar68

Methane uptakes of PAF-1 3 and 4 at 1 bar are 13 19 and 13 wt respectively76 Their enthalpies

are respectively 14 15 and 232 kJ mol-1 This suggests that Ge moiety have strong interactions with

methane

CO2 adsorption in PAF-1 at 40 bar and room temperature was 1300 mg g-1 which was slightly more

than the capacity of COF-102 and 10365 PAF-1 3 and 4 at 1 atm pressure could store 48 80 and 51

wt respectively At 273 K and 1 atm they stored 91 153 and 107 wt respectively The storage

capacities at 273 K and 298 K lead to the following zero-loading isosteric enthalpies 156 192 162

kJ mol-1 for PAF-1 3 and 4 respectively The higher uptake of PAF-3 may also be explained by its

relatively higher surface area with CO2 molecules

The selective adsorption of greenhouse gases in PAFs was discussed by Ben et al76 At 273 K and 1

atm pressure PAF-1 selectively adsorbes CO2 and CH4 respectively 38 and 15 times more in

63

amounts than N2 PAF-3 showed extraordinary selectivity of 871 for CO2 over N2 and 301 for CH4

over N2 For PAF-4 the selectivity was 441 for CO2 over N2 and 151 for CH4 over N2 Generally the

uptake of N2 Ar H2 O2 are significantly lower compared to CO2 and NH4 which makes these PAFs

suitable for separating them

Harmful gases like benzene and toluene can be stored in PAF-1 in amounts 1306 mg g-1 (1674 mmol

g-1) and 1357 mg g-1 (1473 mmol g-1) respectively at saturated pressures and room temperature65

In PAF-11 their adsorptions were in amounts of 874 mg g-1 and 780 mg g-1 respectively68 PAF-2 was

accounted to a much lower benzene adsorption (138 mg g-1) at the same conditions59 Adsorption of

cyclohexane vapor in PAF-2 was only 7 mg g-1 While PAF-11 exhibited hydrophobicity it could

accommodate significant amount of methanol (654 mg g-1 or 204 mmol g-1) at room temperature

and saturated pressure68 PAF-5 has been tested for storing organic pollutants69 At room

temperature and saturated pressure PAF-5 adsorbed methanol benzene and toluene in amounts

6531 cm3 g-1 (292 mmol g-1) 26296 cm3 g-1 (117 mmol g-1) and 2582 cm3 g-1 (115 mmol g-1)

respectively Their adsorptions in PAF-5 were deviated from the typical type-I behavior Methanol

exhibited a large slope at the high pressure region corresponding to the relative size of it Zhu G et

al dedicated PAF-6 for biomedical applications With no toxicity observed for PAF-6 over a range of

concentrations adsorption of ibuprofen was measured in it PAF-6 showed an uptake of 350 mg g-1

The release of ibuprofen was also tested in simulated body fluid which showed a release rate of 50

in 5 hours 75 in 10 hours and 100 in almost 46 hours

413 Theoretical predictions

Grand canonical Monte Carlo (GCMC) is a widely used method for the simulation of gas uptakes in

nanoporous materials In GCMC the number of adsorbates and their motions are allowed to change

at constant volume temperature and chemical potential to equilibrate the adsorbate phase The

motions are random guided by Monte Carlo methods and the energies are calculated by force field

methods The details of it may be found in the literature91

Goddart III WA et al92 simulated the uptake capacities of boron-based COFs using force fields derived

from the interactions of H2 and COFs calculated at MP2 level of theory The saturated excess uptakes

of both COF-105 (at 80 bar) and 108 (at 100 bar) were accounted to 10 wt at 77 K which are more

than the uptakes measured in ultrahigh porous MOF-200 205 and 21093 The predictions for other

COFs include 38 wt for COF-1 (AB stacking) 34 wt for COF-5 (AA stacking) 88 wt for COF-102

and 91 wt for COF-103 At 01 bar COF-1 in AB stacking showed highest excess uptake (17 wt )

compared to other COFs in the present discussion Total uptake capacities of the COFs are in the

following order COF-108 (189 wt ) COF-105 (183 wt ) COF-103 (113 wt ) COF-102 (106

64

wt ) COF-5 (55 wt ) and COF-1 (38 wt ) It is worth noticing the higher gravimetric capacities of

COF-108 and 105 which were not measured experimentally They benefit from their lower mass and

higher pore volume In case of volumetric capacity COF-102 (404 gL excess) surpasses the others at

high pressures The total volumetric capacities of the COFs are 499 498 399 395 361 and 338

gL for COF-102 103 108 105 1 and 5 respectively Their additional calculations predicted benzene

rings as favorite locations for H2 molecules

Similar values and trends have been reported by Garberoglio G94 who also reasoned poor solid-fluid

interactions in a large part of free volume for the low volumetric capacity of COF-108 and 105 A

room temperature excess gravimetric uptake of approximately 08 wt was obtained for COF-108

and 105 Quantum diffraction effects were added to the interaction energies of H2 with itself and the

material which were calculated using universal force-field (UFF) With possible overestimation

Klontzas et al30 and Bassem et al95 have reported total gravimetric uptake of 45 and 417 wt

respectively at 300 K for the same COFs Among the boron-based 3D COFs COF-202 exhibited much

smaller uptake capacity at high pressures due to its smaller pore volume95 Lan et al96 predicted a

very small H2 uptake of 152 wt COF-202 at 300K and 100 bar Studies of Yang et al97 clarifies that

pore filling with H2 in 2D COFs is a gradual process rather than being in steps of layer formation

Garberoglio and Vallauri98 pointed out that the relatively higher mass density and lower surface area

per unit volume of 2D COFs are the reasons for their lower uptakes in comparison with 3D COFs The

surface area of hexagonal 2D COFs (AA stacking) averaged around 1000 m2 cm-3 while that of 3D

COFs were about 1500 m2 cm-3

Simulations of H2 adsorption in the perfect crystalline form of PAF-1 and PAF-11 also known as PAF-

302 and PAF-304 respectively are carried out by Zhu et al99 At 77 K H2 excess uptake of PAF-302 (7

wt ) is slightly higher than COF-102 (684 wt )87 and slightly lower than MOF-177 (740 wt )100 At

room temperature PAF-302 exhibited a poor uptake (221 wt at 100 bar) PAF-304 showed

excellent total uptakes 2238 wt at 77 K and 100 bar 653 wt at 298 K and 100 bar These are

highest among all nanoporous materials

Babarao and Jiang studied room-temperature CO2 adsorption in COFs101 At low pressures COFs with

smaller pore volume exhibit a steep rise in their isotherm while at high pressures COF-105 and 108

(82 and 96 mmol g-1 respectively at 30 bar) dominate the others COF-6 has the highest isosteric heat

of adsoption (328 kJmol) hence it made the first steep rise in the volumetric isotherm followed by

COF-8 102 103 10 105 and 108 Correlations of gravimetric and volumetric capacities with mass

density pore volume porosity and surface area have been excellently manifested in this article101

With increasing framework-density gravimetric uptake falls inversely while volumetric capacity

decreases linearly The former rises with free volume while the latter rises and then drops slightly

65

Both of them rise with porosity and surface area Choi et al102 predicted 45 times more CO2 uptake in

COF-108 (3D) compared to COF-5 (2D) Recently Schmid et al79 also have predicted CO2 adsorption

especially for 3D COFs The uptake of COF-202 was almost half of COF-102 and 103 at room

temperature Type IV isotherm has been found for CO2 adsorption in COF-8 and 10 at low

temperatures (lt 200 K)97 Yang and Zhong97 excluded capillary condensation and dissimilar

adsorption sites but multilayer formation as reasons of the stepped behavior (Yang and Zhong

explained this as a consequence of multilayer formation rather than a result of capillary

condensation or dissimilar adsorption sites)

Methane adsorption in 2D and 3D COFs was first calculated by Garberoglio et al Among COF-6 8 and

10 the former which has smaller pore size and higher binding energy with CH4 shows better

volumetric adsorption (~ 120 cm3cm3 at 20 bar) than the others at room temperature at low

pressure region (lt 25 bar) Larger pore size favors COF-10 for higher volumetric adsorption (~ 160

cm3cm3 at 70 bar) at high pressures COF-8 with intermediate pore size shows largest excess amount

of methane adsorbed upon saturation however still lower than two 3D COFs COF-102 and 103

show excess volumetric adsorption of about 180 cm3cm3 at 35 bar This is significantly higher than

the uptake of two other 3D COFs COF-105 and 108 Entropic effects which primarily arise from the

change of dimensionality when the bulk phase of adsorbate transforms to adsorbed phase are

crucial in adsorption Garberoglio94 shows that solid-fluid interaction potential in large part of volume

of COF-105 and 108 is not strong enough to overcome the entropic loss On the other hand these

two COFs exhibit relatively higher gravimetric uptake (720 and 670 cm3g respectively) Goddard III et

al89 predicted total methane uptakes in the following amounts 415 wt in COF108 405 wt in

COF-105 31 wt in COF-103 284 wt in COF-102 196 wt in COF-10(AA) 169 wt in COF-

5(AA) 159 wt in COF-8(AA) 123 wt in COF-6(AA) and 109 wt in COF-1(AB) Yang and Zhong97

have shown that even at low temperatures (100 K) the pore filling of COF-8 with CH4 is rather

gradual than by step-by-step whereas for COF-10 multilayer formation provides a stepped behavior

in the isotherm Alternately Goddard et al pointed out that layer formation coexists with pore-filling

at room temperature89


First principle calculations on cluster models are typically employed to find favorite adsorption sites

and binding energies of adsorbates within frameworks Benzene rings are found to be a usual

location for H2 where it prefers to orient in perpendicular fashion3086110 Other favorite locations

include B3O3 and C2O2B rings110111 where H2 orients horizontally on the face as well as on the

edge3086 The central ring of HHTP does not provide enough binding to H2 atoms because of small

amount of charges There are some differences in the adsorption energies and favorite sites

66

calculated at different levels of theory Overall the reported binding energies between H2 and any

COF fragment are less than 6 kJ mol-1 In comparison to MOFs COFs do not offer any stronger binding

energy with H2 The advantage of COFs is their low mass density Lan et al103 reported that CO2 is

more preferred to be adsorbed on B3O3 or C2O2B rings than benzene rings Choi et al102 reported that

the oxygen sites are the primary locations for CO2 and CO2 bound COFs are the second strong binding

sites


Hydrogen spillover is an alternate way to store hydrogen113114 It involves dissociation of hydrogen

gas by supported metal catalysts subsequent migration of atomic hydrogen through the support

material and final adsorption in a sorbent Here surface-diffusion of H atoms over the support is

known as primary spillover Secondary spillover is the further diffusion to the sorbent Bridging the

metal part with the sorbent is a practice to enhance the uptake It increases the contact between the

source and receptor and reduces the energy barriers especially in the secondary spillover As the

final sorption is chemisorption surface area of the sorbent is more important than pore volume

Yang and Li measured H2 storage in COF-1 by spillover They used Pt supported on active carbon

(PtAC) as source for hydrogen dissociation Active carbon was the primary receptor and COF-1 the

secondary receptor COF-1 showed much low uptake 128 wt at 77 K and 1 atm 026 wt at 298

K and 100 bar In comparison to MOFs these are very low104 However they have found that the

uptake could be scaled up by a factor of 26 by bridging COF-1 with PtAC by applying carbonization

They also report that heat of adsorption between H and surface sites is more important than surface

area and pore volume in enhancing the net adsorption by spillover

Ganz et al theoretically predicted that the uptake capacities in COFs by hydrogen spillover can be

higher than the measured value116117 Based on ab initio quantum chemistry calculations and

counting the active storage sites they predicted 45 wt for COF-1 in AB stacking and 55 wt for

COF-5 in AA stacking at room temperature and 100 bar

42 Diffusion and Selectivity

Computed self-diffusion coefficients for H2 and CH4 adsorbates in 2D COFs (in AA stacking) are up to

one order of magnitude higher than that in 3D MOFs such as MOF-598 In comparison to nanotubes

the diffusion of H2 molecules in 2D COFs is one order of magnitude slower The differences in

diffusion coefficients are attributed to different pore structures Interactions of the corners of the

hexagonal pore with the fluid present potential barriers along the cylindrical pore axis Diffusion

occurs with jumps after long waiting The height of the barrier is still smaller than in MOFs

67

Homogeneous pore walls and absence of pore corners in nanotubes contribute much less

corrugation to the solid-fluid potential energy surface Increase of self-diffusivities of H2 and CH4 with

increase in pore size of 2D COFs is also shown by Keskin[Ref] Due to the smaller size of H2 its

diffusivity is higher than that of CH4 in any material For reasons of their relative size In a mixture of

the two the self-diffusivity of CH4 increases while that of H2 decreases

Molecular dynamics simulation studies of the diffusion of gas molecules within a 2D COF performed

by Krishna et al105 revealed its relatively lower binding energy of hydrogen molecules within the pore

walls compared to argon CO2 benzene ethane propane n-butane n-pentane and n-hexane

Binding energy prevents the molecules from diffusing through the pore channels They tested if

Knudsen diffusion is applicable to COFs Knudsen diffusion occurs when the molecules frequently

collide with the pore wall This generally happens when the mean free path is larger than the pore

diameter The simulations had been carried out in BTP-COF which accounts a pore diameter of 4 nm

It is found out that the ratio of zero-loading diffusivity with the Knudsen diffusivity has a significant

correlation with isosteric heat of adsorption the stronger the binding energy of the molecules with

the walls the lower the ratio Hydrogen being an exception among the investigated molecules

exhibited the ratio close to unity while others with their isosteric heat of adsorption higher than 10

kJmol-1 have a value close to 01 For a mixture of two gases with significant differences in binding

energies the ratio of self-diffusivities affirms high diffusion selectivity

Selectivity of CH4 over H2 in COF-5 6 and 10 is studied by Keskin106 Narrow pores support the

selective adsorption of CH4 over H2 however they suffer from entropic effects at high pressures

which favor H2 adsorption Liu et al107 have reported that the adsorption selectivity of COFs and

MOFs are in general similar up to 20 bar Delta loading or working capacity (usually expressed in

molkg) is an important term often used to show the economics of the selective adsorption This is

defined as the difference in loadings of the preferred gas at adsorption and desorption pressures

Adsorption is usually in the range 1 to 100 bar while desorption in 01 to 1 bar High selectivity and

high working capacity are preferential for practical use COF-6 has higher selectivity among the three

studied COFs but lower working capacity106 Best selectivity-working capacity combination is shown

by COF-5106 Nonetheless it is not better than CuBTC or CPO-27-X (X = Zn Mg)121122 Liu et al107

attributed the high isosteric heat of adsorption of COF-6 and Cu-BTC for their high adsorption

selectivity They also pointed out that the electrostatic contribution of framework charges in COFs

are smaller than in MOFs however needs to be taken into account

While CH4 is strongly adsorbed H2 undergoes faster diffusion Hence the product of adsorption

selectivity (gt1) and diffusion selectivity (gt0 lt1) which is membrane selectivity is smaller than

adsorption selectivity Keskin106 has compared the selectivity of COF-membranes with known

68

membranes The selectivity of COF-10 is similar to MOF-177 and IRMOFs COF-5 and 6 outperform

them It is to be noted that COF-5 is CH4 selective while COF-10 is H2 selective although their

topologies are similar CH4 permeability of COF membranes is much higher than several MOFs and

ZIFs COF-5 and 6 exhibited high membrane selectivity together with high membrane permeability

Some discussions on the adsorption and membrane based selectivity of COF-102 in comparison with

IRMOFs and Cu-BTC for CH4CO2H2 mixtures can be found in ref108 Adsorption selectivity of COF-6

and Cu-BTC in CH4H2 and CH4CO2 mixtures surpass other COFs and MOFs107 sdfalf


The level of achievement made by COFs and related materials yet do not practically meet the

practical requirements of several applications Hence thoughts for improvement primarily focused

on overcoming their limitations and enhancing characteristic parameters Some theoretical

suggestions for improved performances are mainly discussed here

431 Geometric modifications

Functionalities may be improved by utilizing the structural divergence of framework materials

Several examples may be found in the literature for MOFs etc Klontzas et al suggested replacement

of phenyl linkers in COF-102 by multiple aromatic moieties while keeping the topology unchanged to

increase surface area and pore volume109 They used biphenyl triphenyl naphthalene and pyrene

linkers in the new COFs All of them showed enhanced gravimetric capacity compared to the parent

COF One of the modified COF-102 with triphenyl linker showed 267 and 65 wt at 77 K and 300 K

respectively at 100 bar This kind of replacement may affect the adsorption of each adsorbate

differently leading to the alteration of the selective adsorption of one component over the other110

Following the reticular construction scheme we modeled some new 2D COFs by cross-linking some

of the familiar and unfamiliar building blocks in the COF literature32 This showed the structural

divergence of COFs however they exhibited structural and electronic properties analogues to other

2D COFs

Similar modifications in 2D and 3D COFs for high CO2 uptake were made by Choi et al102 DPABA

(diphenylacetylene-44ʹ-diboronic acid) and its tetrahedral version TBPEPM (tetra[4-(4-

dihydroxyborylphenyl)ethynyl]phenyl) in place of BDBA in COF-5 and TBPMTBPS in COF-108COF-

105 respectively were used for new COF designs The new 2D COF promised a saturated CO2 uptake

higher than in COF-102 because of its large pore volume The new 3D COFs were worth for an uptake

twice more than in COF-105 and 108

69

Goddard et al also designed about 14 new COFs by substituting the aromatic rings in the tetragonal

part (TBPM or TBPS) of COF-102 COF-103 COF-105 COF-108 and COF-202 with vinyl groups or alkyl-

functionalized extended or fused aromatic rings111 The new designs adopted their parent topology

and their structural stability was confirmed by analyzing molecular dynamics (MD) simulations at

room temperature Fused aromatic rings and vinyl groups provided relatively lower and the highest

zero-loading isosteric heat of adsorption (Qst) respectively however the room-temperature delivery

amounts of methane in the respective COFs crossed the DOE target at 35 bar111 In the latter

methane-methane interaction compensated Qst on high-loading

Lino M A et al112 theoretically inspected the ability of layered COFs to exhibit structural variants of

layered materials The hexagonal 2D COF layers may be rolled into the form of nanotubes (NT) or

may exist in the form of fullerenes with the inclusion of pentagons One could think of a formula unit

which resembles the carbon atoms in carbon nanotubes (CNT) or fullerenes The NTs in general can

have any chirality although the study included only armchair and zigzag NTs Density Functional

Theory based calculations reveal that COF-1 NTs of diameter greater than 15 Aring is energetically

favored This was concluded from the comparison of strain-energy per formula unit of the COF-1 NTs

with that of small diameter CNTs The strain energies of zigzag and armchair nanotubes show similar

quadratic functions of tube-diameter The Youngrsquos modulus of COF-1 (22) NT is found out to be 120

GPa This is much smaller compared to typical CNTs which have Youngrsquos modulus average around

1100 GPa113 Band gaps of COF layers remain unchanged when they roll up into nanotubes A COF-1-

fullerene built by scaling C60 molecule has large diameter and hence much less strain energy

compared to C60 Babarao and Jiang reported that the predicted CO2 adsorption capacity of COF-1 NT

is similar to that of CNTs101

Balance between mass density and surface area and hence high gravimetric and volumetric

capacities can be achieved by proper utilization of pore volume or proper distribution of pores Choi

et al theoretically predicted high gravimetric and volumetric capacities for H2 in a pillared COF114 A

pyridine molecule vertically placed above a boron atom in the boroxine ring of COF-1 layer is found

energetically favorable however with wrinkling of the layer115 Here nitrogen atom in pyridine forms

a covalent bond with the boron atom This pillaring increases the separation between the layers

exposes the buried faces of boroxine and aromatic rings to pores and hence increases surface area

and free volume Accessible surface area and free volume have been tripled and gravimetric and

volumetric capacities were calculated to be 10 wt and 60 g L-1 respectively at 77 K and 100 bar114

This volumetric capacity is higher than in NU-100116 and MOF-21093 which show ultrahigh surface

area

70

432 Metal doping

Miao Wu et al studied doping of COF-10 with Li and Ca atoms for hydrogen storage117 The metal

dopants transferred charges to substrate which in turn provided large polarization to hydrogen

molecules Similar observation has been made by Lan et al96 for Li atoms in COF-202 However they

showed the tendency to aggregate at high concentration Lan et al extensively studied doping of

positively charged alkali (Li Na and K) alkaline-earth (Be Mg Ca) and transition (Sc and Ti) metals in

COF-102 and 105 for enhanced CO2 capture103 They found that benzene rings and the three outer

rings of HHTP are the favorite sites for all the metal dopants Other interested locations are edges of

benzene rings and oxygen atoms B3O3 C2O2B rings and the central ring of HHTP were the unwanted

areas Lithium showed stability on the favorite locations while sodium and potassium tended to

cluster even at low concentrations Alkaline-earth metals only weakly interacted with the COFs

whereas transition metals chemisorbed in them which would possibly damage the substrate Lithium

is found out to be a good dopant for enhanced gas storage

Doping electropositive metals would be of advantage because they provide stronger binding with H2

(~ 4 kcalmol)103125133134 The effect of counterions in COFs is studied by Choi et al118 They found out

that although the binding energy of LiF is smaller than Li ion F counterion can hold one hydrogen

atom Additionally Li+ and Mg2+ ions preferred to be isolated than aggregated A step further

Goddard et al119 have recently shown that in presence of tetrahydrofuran (THF a solvent) an

electron is transferred from Li to the benzene ring whereas in the case of gas phase the electron

remained in the atom Additionally they suggested ways to remove solvents which are weakly

coordinated to the material Zhu et al110 suggested doping Li+ after replacement of hydrogen atom by

oxygen ion in COF-102 Another suggestion was the replacement of hydrogen atom by O--Li+ group

Both the cases exhibited higher CO2 adsorption than in the case of Li doping below 10 bar At 10 bar

the three cases exhibited almost the same uptake capacity Below 1 bar the doped Li+ provided

stronger interaction with quadrupolar CO2 in comparison with the substituted O--Li+ group The

differences at low pressures are attributed to the differences in the magnitude of the charge of Li

The doped Li+ remained to hold nearly +1 charge whereas the inclusion of O--Li+ to the framework

diminished the charge of Li+ to a moderate amount Doping Li atom added only relatively small

amount of charge to Li

Doping with Li+ could increase the H2 binding energies up to 28 kJmol118 With properly distributed

metal ion dopants the H2 uptake capacity in COF-108 is predicted to be 65 wt Cao et al also

predicted 684 and 673 wt of H2 uptake in Li-doped COF-105 and 108 respectively at room

temperature and 100 bar120 In Li-doped COF-202 the predicted uptake was 438 wt for the same

conditions96 Goddard et al119 observed that high performance of Li doped COFsMOFs at low

71

pressures (1 ndash 10 bar) is a disadvantage when calculating delivery uptake capacity Na doping could

overcome this difficulty as its heat of adsorption is lower than in Li doped materials Their predicted

delivery gravimetric capacities from 1 to 100 bar at room temperature for Li and Na doped COF-102

and 103 were higher than the 2010 DOE target of 45 wt at room temperature

Lan et al described that CO2 is polarized in presence of Li cation and the polarization increases when

Li cation is physisorbed in COF103 Their calculated uptake capacities of lithium-doped COF-102 and

COF-105 at low loading is about eight and four times higher than that of nondoped ones respectively

Also a very high uptake of 2266 mgg was predicted in the doped COF-105 at 40 bar Li-doped COF-

102 and COF-103 also showed higher uptakes of methane ndash almost double the amount ndash compared

to nondoped COFs at room temperature and low pressures (lt 50 bar)121 Binding energy between

doped Li cation and CH4 was calculated to be 571 kcalmol

Li-functionalized COF-105 realized by inserting alkoxide groups provided very high volumetric uptake

of H2 Klontzas et al122 replaced three hydrogen atoms in HHTP by oxygen atoms in order to achieve

the functionalization In spite of the increased weight due to the additional oxygen atoms the COF

exhibited gravimetric capacity of 6 wt at 300 K

Incorporation of lithium tetrazolide group into a new PAF having diamond topology and triphenyl

linkers for enhanced hydrogen adsorption is suggested by Sun et al123 The tetrazolide anion (CHN4-)

interacts with the lithium cation via ionic bonds The anion and the cation together can bind upto 14

hydrogen molecules Two lithium tetrazolide groups were introduced in the middle phenyl ring of

each triphenyl linker and GCMC calculations predicted 45 wt for the network at 233 K and 100 bar

With the intention of increasing the H2 binding energy Li et al chemically implanted metals in the

place of light atoms in COF-108124 They replaced the C2O2B rings in COF-108 by C2O2Al C2N2Al and

C2Mg2N and each new COF showed stability within DFT This kind of doping does not allow

aggregation of metal clusters Their GCMC simulations showed that the replacement strategy could

improve the hydrogen storage capacity at room temperature by a factor of up to three124 Zou et al

suggested that para-substitution of two carbon atoms in benzene rings by two boron atoms can

facilitate charge transfer between the rings and metal dopants125 Their work revealed that

dispersion of metals forbid any clustering and the doping could enhance the H2 uptake capacity

significantly


Functionalization of porous frameworks with ether groups for selective CO2 capture is suggested by

Babarao et al126 The electropositive C atom of CO2 interacts mainly with the electronegative O or N

72

atom of the functional groups They studied PAF-1 functionalized with ndashOCH3 ndashNH2 and ndashCH2OCH2ndash

groups in its biphenyl linkers The latter one which is the tetrahydrofuran-like ether-functionalized

PAF-1 showed high adsorption capacity for CO2 and high selectivity for CO2CH4 CO2N2 and CO2H2

mixtures at ambient conditions

5 Conclusions

Successful covalent crystallization resulted as a class of materials Covalent Organic Frameworks This

review portrays different synthetic schemes successful realizations and potential applications of

COFs and related materials The growth in this area is relatively slow and thus promotions are

needed in order to achieve its potential


alkyl-THB Alkyl-1245-tetrahydroxybenzene

BDBA 14-benzenediboronic acid

BPDA 44ʹ-biphenyldiboronic acid

BTBA 135-benzene triboronic acid

BTDADA 14-benzothiadiazole diboronic acid

BTPA 135-benzenetris(4-phenylboronic acid)

CA Cyanuric acid

DAB 14-diaminobenzene

DCB 14-dicyanobenzene

DCF 27-diisocyanate fluorine

DCN 26-dicyanonaphthalene

DCP 26-dicyanopyridine

DETH 25-diethoxyterephthalohydrazole

DMBPDC 33ʹ-dimethoxy-44ʹ-biphenylene diisocyanate

DPB Diphenyl butadyenediboronic acid

73

HP 1-hexyne propiolate

HHTP 23671011-hexahydroxytriphenylene

MP Methyl propiolate

N3-BDBA Azide-appended benzenediboronic acid

NDI Naphthalenediimide diboronic acid

NiPcTA Nickel-phthalocyanice tetrakis(acetonide)

OH-Pc-Ni 2391016172324-octahydroxyphthalocyaninato)nickel(II)

OH-Pc-Zn 2391016172324-octahydroxyphthalocyaninato)zinc

PA Piperazine

Pac 2-propenyl acetate

PcTA Phthalocyanine tetra(acetonide)

PdAc Palladium acetate

PDBA Pyrenediboronic acid

PPE Phenylbis(phenylethynyl) diboronic acid

PPP 3-phenyl-1-propyne propiolate

PyMP (3α13α2-dihydropyren-1-yl)methyl propionate

TA Terephthaldehyde

TAM tetra-(4-anilyl)methane

TAPP Tetra(p-amino-phneyl)porphyrin

TBB 135-tris(4-bromophenyl)benzene

TBPM tetra(4-dihydroxyboryl-phenyl)methane

TBPP Tetra(p-boronic acid-phenyl)porphyrin

TBPS tetra(4-dihydroxyboryl-phenyl)silane

TBST tert-butylsilane triol

74

TCM Tetrakis(4-cyanophenyl)methane

TDHB-ZnP Zinc(II) 5101520-tetrakis(4-(dihydroxyboryl)phenyl)porphyrin

TFB 135-triformylbenzene

TFPB 135-tris-(4-formyl-phenyl)-benzene

THAn 2345-Tetrahydroxy anthracene

THB 1245-tetrahydroxybenzene

THDMA Polyol 2367-tetrahydroxy-910-dimethyl-anthracene

TkBPM Tetrakis(4-bromophenyl)methane

TPTA Triphenylene tris(acetonide)

trunc-TBPM-R R-functionalized truncated TBPM

75

Figure 8 Reactants of Covalently-bound Organic Frameworks

76

Figure 9 (Figure 8 continued)

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(33) Tilford R W Gemmill W R zur Loye H C Lavigne J J Chemistry of Materials 2006 18 5296 (34) Spitler E L Dichtel W R Nature Chemistry 2010 2 672 (35) Spitler E L Giovino M R White S L Dichtel W R Chemical Science 2011 2 1588 (36) Campbell N L Clowes R Ritchie L K Cooper A I Chemistry of Materials 2009 21 204 (37) Ding X Guo J Feng X Honsho Y Guo J Seki S Maitarad P Saeki A Nagase S Jiang D Angewandte Chemie-International Edition 2011 50 1289 (38) Feng X A Chen L Dong Y P Jiang D L Chemical Communications 2011 47 1979 (39) Zwaneveld N A A Pawlak R Abel M Catalin D Gigmes D Bertin D Porte L Journal of the American Chemical Society 2008 130 6678 (40) Gutzler R Walch H Eder G Kloft S Heckl W M Lackinger M Chemical Communications 2009 4456 (41) Blunt M O Russell J C Champness N R Beton P H Chemical Communications 2010 46 7157 (42) Sassi M Oison V Debierre J-M Humbel S Chemphyschem 2009 10 2480 (43) Ourdjini O Pawlak R Abel M Clair S Chen L Bergeon N Sassi M Oison V Debierre J-M Coratger R Porte L Physical Review B 2011 84 (44) Colson J W Woll A R Mukherjee A Levendorf M P Spitler E L Shields V B Spencer M G Park J Dichtel W R Science 2011 332 228 (45) Berlanga I Ruiz-Gonzalez M L Gonzalez-Calbet J M Fierro J L G Mas-Balleste R Zamora F Small 2011 7 1207 (46) Wan S Gandara F Asano A Furukawa H Saeki A Dey S K Liao L Ambrogio M W Botros Y Y Duan X Seki S Stoddart J F Yaghi O M Chemistry of Materials 2011 23 4094 (47) Ding X Chen L Honsho Y Feng X Saenpawang O Guo J Saeki A Seki S Irle S Nagase S Parasuk V Jiang D Journal of the American Chemical Society 2011 133 14510 (48) Tilford R W Mugavero S J Pellechia P J Lavigne J J Advanced Materials 2008 20 2741 (49) Lanni L M Tilford R W Bharathy M Lavigne J J Journal of the American Chemical Society 2011 133 13975 (50) Li Y Yang R T Aiche Journal 2008 54 269 (51) Nagai A Guo Z Feng X Jin S Chen X Ding X Jiang D Nature Communications 2011 2 (52) Bunck D N Dichtel W R Angewandte Chemie-International Edition 2012 51 1885 (53) Ding S-Y Gao J Wang Q Zhang Y Song W-G Su C-Y Wang W Journal of the American Chemical Society 2011 133 19816 (54) Miyaura N Suzuki A Chemical Reviews 1995 95 2457 (55) Kalidindi S B Yusenko K Fischer R A Chemical Communications 2011 47 8506 (56) Kuhn P Antonietti M Thomas A Angewandte Chemie-International Edition 2008 47 3450 (57) Bojdys M J Jeromenok J Thomas A Antonietti M Advanced Materials 2010 22 2202 (58) Kuhn P Forget A Su D Thomas A Antonietti M Journal of the American Chemical Society 2008 130 13333 (59) Ren H Ben T Wang E Jing X Xue M Liu B Cui Y Qiu S Zhu G Chemical Communications 2010 46 291 (60) Zhang W Li C Yuan Y-P Qiu L-G Xie A-J Shen Y-H Zhu J-F Journal of Materials Chemistry 2010 20 6413 (61) Trewin A Cooper A I Angewandte Chemie-International Edition 2010 49 1533 (62) Mastalerz M Angewandte Chemie-International Edition 2008 47 445

79

(63) Chan-Thaw C E Villa A Katekomol P Su D Thomas A Prati L Nano Letters 2010 10 537 (64) Palkovits R Antonietti M Kuhn P Thomas A Schueth F Angewandte Chemie-International Edition 2009 48 6909 (65) Ben T Ren H Ma S Q Cao D P Lan J H Jing X F Wang W C Xu J Deng F Simmons J M Qiu S L Zhu G S Angewandte Chemie-International Edition 2009 48 9457 (66) Yamamoto T Bulletin of the Chemical Society of Japan 1999 72 621 (67) Zhou G Baumgarten M Muellen K Journal of the American Chemical Society 2007 129 12211 (68) Yuan Y Sun F Ren H Jing X Wang W Ma H Zhao H Zhu G Journal of Materials Chemistry 2011 21 13498 (69) Ren H Ben T Sun F Guo M Jing X Ma H Cai K Qiu S Zhu G Journal of Materials Chemistry 2011 21 10348 (70) Zhao H Jin Z Su H Jing X Sun F Zhu G Chemical Communications 2011 47 6389 (71) Mortera R Fiorilli S Garrone E Verne E Onida B Chemical Engineering Journal 2010 156 184 (72) Dogru M Sonnauer A Gavryushin A Knochel P Bein T Chemical Communications 2011 47 1707 (73) Spitler E L Koo B T Novotney J L Colson J W Uribe-Romo F J Gutierrez G D Clancy P Dichtel W R Journal of the American Chemical Society 2011 133 19416 (74) Zhang Y Tan M Li H Zheng Y Gao S Zhang H Ying J Y Chemical Communications 2011 47 7365 (75) Uribe-Romo F J Doonan C J Furukawa H Oisaki K Yaghi O M Journal of the American Chemical Society 2011 133 11478 (76) Ben T Pei C Zhang D Xu J Deng F Jing X Qiu S Energy amp Environmental Science 2011 4 3991 (77) Lukose B Kuc A Heine T Chemistry-a European Journal 2011 17 2388 (78) Zhou W Wu H Yildirim T Chemical Physics Letters 2010 499 103 (79) Amirjalayer S Snurr R Q Schmid R Journal of Physical Chemistry C 2012 116 4921 (80) Xu Q Zhong C Journal of Physical Chemistry C 2010 114 5035 (81) Lukose B Supronowicz B St Petkov P Frenzel J Kuc A B Seifert G Vayssilov G N Heine T Physica Status Solidi B-Basic Solid State Physics 2012 249 335 (82) Assfour B Seifert G Chemical Physics Letters 2010 489 86 (83) Zhao L Zhong C L Journal of Physical Chemistry C 2009 113 16860 (84) Schmid R Tafipolsky M Journal of the American Chemical Society 2008 130 12600 (85) Han S S Goddard W A III Journal of Physical Chemistry C 2007 111 15185 (86) Suh M P Park H J Prasad T K Lim D-W Chemical Reviews 2012 112 782 (87) Furukawa H Yaghi O M Journal of the American Chemical Society 2009 131 8875 (88) Wong-Foy A G Matzger A J Yaghi O M Journal of the American Chemical Society 2006 128 3494 (89) Mendoza-Cortes J L Han S S Furukawa H Yaghi O M Goddard III W A Journal of Physical Chemistry A 2010 114 10824 (90) Doonan C J Tranchemontagne D J Glover T G Hunt J R Yaghi O M Nature Chemistry 2010 2 235 (91) Getman R B Bae Y-S Wilmer C E Snurr R Q Chemical Reviews 2012 112 703 (92) Han S S Furukawa H Yaghi O M Goddard III W A Journal of the American Chemical Society 2008 130 11580 (93) Furukawa H Ko N Go Y B Aratani N Choi S B Choi E Yazaydin A O Snurr R Q OKeeffe M Kim J Yaghi O M Science 2010 329 424 (94) Garberoglio G Langmuir 2007 23 12154 (95) Assfour B Seifert G Microporous and Mesoporous Materials 2010 133 59

80

(96) Lan J Cao D Wang W Journal of Physical Chemistry C 2010 114 3108 (97) Yang Q Zhong C Langmuir 2009 25 2302 (98) Garberoglio G Vallauri R Microporous and Mesoporous Materials 2008 116 540 (99) Lan J H Cao D P Wang W C Ben T Zhu G S Journal of Physical Chemistry Letters 2010 1 978 (100) Furukawa H Miller M A Yaghi O M Journal of Materials Chemistry 2007 17 3197 (101) Babarao R Jiang J Energy amp Environmental Science 2008 1 139 (102) Choi Y J Choi J H Choi K M Kang J K Journal of Materials Chemistry 2011 21 1073 (103) Lan J Cao D Wang W Smit B Acs Nano 2010 4 4225 (104) Wang L Yang R T Energy amp Environmental Science 2008 1 268 (105) Krishna R van Baten J M Industrial amp Engineering Chemistry Research 2011 50 7083 (106) Keskin S Journal of Physical Chemistry C 2012 116 1772 (107) Liu Y Liu D Yang Q Zhong C Mi J Industrial amp Engineering Chemistry Research 2010 49 2902 (108) Keskin S Sholl D S Langmuir 2009 25 11786 (109) Klontzas E Tylianakis E Froudakis G E Nano Letters 2010 10 452 (110) Zhu Y Zhou J Hu J Liu H Hu Y Chinese Journal of Chemical Engineering 2011 19 709 (111) Mendoza-Cortes J L Pascal T A Goddard W A III Journal of Physical Chemistry A 2011 115 13852 (112) Lino M A Lino A A Mazzoni M S C Chemical Physics Letters 2007 449 171 (113) Krishnan A Dujardin E Ebbesen T W Yianilos P N Treacy M M J Physical Review B 1998 58 14013 (114) Kim D Jung D H Kim K-H Guk H Han S S Choi K Choi S-H Journal of Physical Chemistry C 2012 116 1479 (115) Kim D Jung D H Choi S-H Kim J Choi K Journal of the Korean Physical Society 2008 52 1255 (116) Farha O K Yazaydin A O Eryazici I Malliakas C D Hauser B G Kanatzidis M G Nguyen S T Snurr R Q Hupp J T Nature Chemistry 2010 2 944 (117) Wu M M Wang Q Sun Q Jena P Kawazoe Y Journal of Chemical Physics 2010 133 (118) Choi Y J Lee J W Choi J H Kang J K Applied Physics Letters 2008 92 (119) Mendoza-Cortes J L Han S S Goddard W A III Journal of Physical Chemistry A 2012 116 1621 (120) Cao D Lan J Wang W Smit B Angewandte Chemie-International Edition 2009 48 4730 (121) Lan J H Cao D P Wang W C Langmuir 2010 26 220 (122) Klontzas E Tylianakis E Froudakis G E Journal of Physical Chemistry C 2009 113 21253 (123) Sun Y Ben T Wang L Qiu S Sun H Journal of Physical Chemistry Letters 2010 1 2753 (124) Li F Zhao J Johansson B Sun L International Journal of Hydrogen Energy 2010 35 266 (125) Zou X Zhou G Duan W Choi K Ihm J Journal of Physical Chemistry C 2010 114 13402 (126) Babarao R Dai S Jiang D-e Langmuir 2011 27 3451

81

Appendix B

Structural properties of metal-organic frameworks within the density-functional based tight-binding method

Binit Lukose Barbara Supronowicz Petko St Petkov Johannes Frenzel Agnieszka Kuc

Gotthard Seifert Georgi N Vayssilov and Thomas Heine

Phys Status Solidi B 2012 249 335ndash342

DOI 101002pssb201100634

Abstract Density-functional based tight-binding (DFTB) is a powerful method to describe large

molecules and materials Metal-organic frameworks (MOFs) materials with interesting catalytic

properties and with very large surface areas have been developed and have become commercially

available Unit cells of MOFs typically include hundreds of atoms which make the application of

standard density-functional methods computationally very expensive sometimes even unfeasible

The aim of this paper is to prepare and to validate the self-consistent charge-DFTB (SCC-DFTB)

method for MOFs containing Cu Zn and Al metal centers The method has been validated against

full hybrid density-functional calculations for model clusters against gradient corrected density-

functional calculations for supercells and against experiment Moreover the modular concept of

MOF chemistry has been discussed on the basis of their electronic properties We concentrate on

MOFs comprising three common connector units copper paddlewheels (HKUST-1) zinc oxide Zn4O

tetrahedron (MOF-5 MOF-177 DUT-6 (MOF-205)) and aluminum oxide AlO4(OH)2 octahedron (MIL-

53) We show that SCC-DFTB predicts structural parameters with a very good accuracy (with less than

82

5 deviation even for adsorbed CO and H2O on HKUST-1) while adsorption energies differ by 12 kJ

mol1 or less for CO and water compared to DFT benchmark calculations

1 Introduction In reticular or modular chemistry molecular building blocks are stitched together to

form regular frameworks [1] With this concept it became possible to construct framework

compounds with interesting structural and chemical composition most notably metal-organic

frameworks (MOFs) [1ndash10] and covalent organic frameworks (COFs) [11ndash17] The interest in MOFs

and COFs is not limited to chemistry these crystalline materials are also interesting for applications

in information storage [18] sieving of quantum liquids [19] hydrogen storage [20] and for fuel cell

membranes [21ndash23]

Covalent organic framework and MOF frameworks are composed by combining two types of building

blocks the so-called connectors typically coordinating in four to eight sites and linkers which have

typically 2 sometimes also three or four connecting sites Fig 1 illustrates a simplified representation

of the topology of connectors and linkers by using secondary building units (SBUs) (see Fig 1)

Figure 1 The connector and the linker of the frameworks CuBTC (HKUST-1) MOF-177 MOF-5 DUT-6 (MOF-205) and MIL-53 and their respective secondary building units (SBUs) The arrows indicate the connection points of the fragments Red oxygen green carbon white hydrogen yellow copperzinc and blue aluminum

Linkers are organic molecules with carboxylic acid groups at their connection sites which form

bonds to the connectors (typically in a solvothermal condensation reaction) They can carry

functional groups which can make them interesting for applications in catalysis [24] Connectors are

83

either metal organic units as for example the well-known Zn4O(CO2)6 unit of MOF-5 [8] the

Cu2(HCOO)4 paddle wheel unit of HKUST-1 [10] or covalent units incorporating boron oxide linking

units for COFs [11] As the building blocks of MOFs and COFs comprise typically some ten atoms unit

cells quickly get very large In particular if adsorption or dynamic processes in MOFs and COFs are of

interest (super)cells of some 1000 atoms need to be processed While standard organic force fields

show a reasonable performance for COFs [25] the creation of reliable force fields is not

straightforward for MOFs as transferable parameterization of the transition metal sites is an issue

even though progress has been achieved for selected materials [26 27] The difficulty to describe

transition metals in particular if they are catalytically active as in HKUST-1 limits the applicability of

molecular mechanics (MM) even for QMMM hybrid methods [28]

On the other hand the density-functional based tight-binding (DFTB) method with its self-consistent

charge (SCC) extension to improve performance for polar systems is a computationally feasible

alternative This non-orthogonal tight-binding approximation to density-functional theory (DFT)

which has been developed by Seifert Frauenheim and Elstner and their groups [29ndash32] (for a recent

review see Ref [30]) has been successfully applied to a large-scale systems such as biological

molecules [33ndash36] supramolecular systems [37 38] surfaces [39 40] liquids and alloys [41 42] and

solids [43] Being a quantum-mechanical method and hence allowing the description of breaking and

formation of chemical bonds the method showed outstanding performance in the description of

processes such as the mechanical manipulation of nanomaterials [44ndash46] It is remarkable that the

method performs well for systems containing heavier elements such as transition metals as this

domain cannot be covered so far with acceptable accuracy by traditional semi-empirical methods [47

48] DFTB covers today a large part of the elements of the periodic table and parameters and a

computer code are available from the DFTBorg website

Recently we have validated DFTB for its application for COFs [16 17] and have shown that structural

properties and formation energies of COFs are well described within DFTB Kuc et al [49] have

validated DFTB for substituted MOF-5 frameworks where connectors are always the Zn4O(CO2)6 unit

which has been combined with a large variety of organic linkers In this work we have revised the

DFTB parameters developed for materials science applications and validated them for HKUST-1 and

being far more challenging for the interaction of its catalytically active Cu sites with carbon

monoxide (CO) and water The Cu2(HCOO)4 paddle wheel units are electronically very intriguing on a

first note the electronic ground state of the isolated paddle wheel is an antiferromagnetic singlet

state which cannot be described by one Slater determinant and which is consequently not accessible

for KohnndashSham DFT However the energetically very close triplet state correctly describes structure

and electronic density of the system and also adsorption properties agree well with experiment [32

84

50 51] We therefore use DFT in the B3LYP hybrid functional representation as benchmark for DFTB

validations for HKUST-1 added by DFT-GGA calculations for periodic unit cellsWewill show that the

general transferability of the DFTB method will allow investigating structural electronic and in

particular dynamic properties

2 Computational details All calculations of the finite model and periodic crystal structures of MOFs

were carried out using the dispersion-corrected self-consistent density functional based tight-binding

(DC-SCC-DFTB in short DFTB) method [30 52ndash54] as implemented in the deMonNano code [55] Two

sets of parameters have been used the standard SCC-DFTB parameter set developed by Elstner et al

[53] for Zn-containing MOFs for Cu- and Al-containing materials we have extended our materials

science parameter set which has been developed originally for zeolite materials to include Cu For

this element we have used the standard procedure of parameter generation we have used the

minimal atomic valence basis for all atoms including polarization functions when needed Electrons

below the valence states were treated within the frozen-core approximation The matrix elements

were calculated using the local density approximation (LDA) while the short-range repulsive pair-

potential was fitted to the results from DFT generalized gradient approximation (GGA) calculations

For more details on DFTB parameter generation see Ref [30] Periodic boundary conditions were

used to represent frameworks of the crystalline solid state The conjugate-gradient scheme was

chosen for the geometry optimization An atomic force tolerance of 3x10-4 eV Aring-1 was applied

The reference DFT calculations of the equilibrium geometry of the investigated isolated MOF models

were performed employing the Becke three-parameter hybrid method combined with a LYP

correlation functional (B3LYP) [56 57] The basis set associated with the HayndashWadt [58] relativistic

effective core potentials proposed by Roy et al [59] was supplemented with polarization ffunctions

[60] and was employed for description of the electronic structure of Cu atoms The Pople 6-311G(d)

basis sets were applied for the H C and O atoms The calculations were performed with the

Gaussian09 program suite [61] For optimization of the periodic structure of CuBTC at DFT level the

electronic structure code Quickstep [62] which is a part of the CP2K package [63] was used

Quickstep is an implementation of the Gaussian plane wave method [64] which is based on the

KohnndashSham formulation of DFT

We have used the generalized gradient functional PBE [65] and the GoedeckerndashTeterndashHutter

pseudopotentials [64 66] in conjunction with double-z basis sets with polarization functions DZVP-

MOLOPT-SR-GTH basis sets obtained as described in Ref [67] but using two less diffuse primitives

Due to the large unit cell sampling of Brillouin zone was limited only to the G-point Convergence

85

criterion for the maximum force component was set to 45 x 10-3 Hartree Bohr1 The plane wave

basis with cutoff energy of 400 Ry was used throughout the simulations

The initial crystal structures were taken from experiment (powder X-ray diffraction (PXRD) data) The

cell parameters and the atomic positions were fully optimized using conjugate-gradient method at

the DFTB level For the reference DFT calculations only the atomic positions of experimental crystal

structures were minimized The cluster models were cut from the optimized structures and saturated

with hydrogen atoms (see Fig 2 for exemplary systems of Cu-BTC)

3 Results and discussion

31 Cu-BTC We have optimized the crystal structure of Cu-BTC (HKUST-1) [10] using cluster and the

periodic models The structural properties were compared to DFT results (see Table 1) The

geometries were obtained for the activated form (open metal sites) and in the presence of axial

water ligands (see Table 2) as the synthesized crystals often have H2O molecules attached to the

open metal sites of Cu (Fig 2b) We have also studied changes of the cluster model geometry in the

presence of CO (Fig 2c) and the results are also shown in Table 2 We have obtained good agreement

with experimental data as well as with DFT results

Figure 2 (a) Periodic and cluster models of Cu-BTC MOF as used in the computer simulations (b) cluster model with adsorbed H2O and (c) CO molecules

We have also simulated the XRD patterns of Cu-BTC which show very good structural agreement for

peak positions between the experimental and calculated structures The XRD pattern of DFT

optimized structure is nearly a copy of that of the experimental geometry However for DFTB

optimized patterns the relative intensities of some of the peaks notably that of the peaks at 2θ =

138 and 2θ = 158 are different from the experimental XRDs (see Fig 3) The differences in bond

angles between simulation and experiment may affect the sharpness of the signals and hence the

86

intensity To support this argument we have calculated the radial pair distribution function (g(r))

which details the probabilities of all atomndashatom distances in a given cell volume Figure S3 in the

Supporting Information shows g(r) of CundashCu CundashC CundashO CndashC and CndashO atom pairs of DFTB

optimized DFT optimized and experimentally modeled Cu-BTC unit cells The peaks of DFT as well as

DFTB optimized geometries are much broadened whereas the experimentally modeled geometry

has single peaks at the most predicted atomndashatom distances However it is to be noted that DFTB

optimized geometries give slightly shifted peaks compared to those of the DFT optimized geometry

They are broadened around the experimental values The distances between Cu and C atoms which

are not direct neighbors have the largest deviations from the experiment what indicates

shortcomings of the bond angles

Table 1 Selected bond lengths (Aring ) bond angles (⁰) and dihedral angles (⁰) of Cu-BTC optimized at DFTB and DFT level

Bond Type Cluster Model Periodic Model Exp

Cu-Cu 250 (257) 250 (250) 263 Cu-O 205 (198) 202 (198) 195 O-C 134 (133) 133-138 (128) 125

OCuO 836-971 (898) 892-907 (873-937)

891 896

Cu-O-O-Cu plusmn56 ˗ plusmn62 (plusmn02) plusmn04 (plusmn47 ˗ plusmn131) 0

O-C-C-C plusmn38 - plusmn50 (0) plusmn03 - plusmn05 (plusmn06 - plusmn105) 063

Cell paramet a=b=c=27283 (26343)

α=β=γ=90 (90) a=b=c=26343

α=β=γ=90

In detail the bond lengths and bond angles do not change significantly when going from the cluster

to the periodic model confirming the reticular chemistry approach The only exception is the OndashCundash

O bond angle that differs by 4ndash78 between the two systems at both levels of theory

87

Figure 3 Simulated XRD patterns of Cu-BTC MOF with the experimental unit cell parameters and optimized at the DFTB and DFT level of theory

The bond length between Cu atoms is slightly underestimated comparing with experimental (by

maximum 5) and DFT (maximum by 3) results while all other bond lengths are somewhat larger

at DFTB

All bond lengths stay unchanged or become longer in the presence of water molecules The most

striking example is the CundashCu bond where the change reaches 012ndash017 Aring compared with the

structure with activated Cu sites Also bond angles increase by up to 28 when the H2O is present

The CundashO bond length with the oxygen atom from the carboxylate groups is shorter than that with

the oxygen atoms from the water molecules indicating that the latter is only weakly bound to the

copper ions The OndashC distances (~133 Aring) correspond to values between that for the typical single

(142 Aring ) and double (122 Aring) oxygenndashcarbon bond The calculated CringndashCcarboxyl bond lengths of

146A deg indicate that these are typical single sp2ndashsp2 CndashC bonds while experimental findings give a

slightly longer value (15 Aring) for this MOF When comparing dihedral angles CundashOndashOndashCu and OndashCndashCndashC

of the clusters fairly large deviations between DFTB and DFT calculations and experiment are visible

due to the softer potential energy surface associated with these geometrical parameters In periodic

models however the agreement of DFT and DFTB with experiment and with each other is

significantly improved

The unit cell parameters with and without water molecules obtained at the DFTB level overestimate

the experimental data by less than 4 which gives a fairly good agreement if we take into account

high porosity of the material These lattice parameters increase only slightly from 27283 to 27323 Aring

in the presence of water

We have calculated the binding energies of H2O molecules attached to the Cu-metal sites within the

cluster model At the DFTB level Ebind of 40 kJ mol-1 was obtained in a good agreement with the DFT

results (52 kJ mol-1) as well as results from the literature (47 kJ mol-1 [50]) We have also calculated

88

the binding energy of CO which was twice smaller than that of H2O (165 and 28 kJ mol-1 for DFTB

and DFT respectively) suggesting much stronger binding of O atom (from H2O) than C atom (from

CO) While the bond lengths in the MOF structure do not change in the presence of either H2O or CO

the differences in the binding energy come from much longer bond distances (by around 07 Aring) for

CundashC than for CundashO in the presence of CO and water molecules respectively

Furthermore we have studied the electronic properties of periodic and cluster model Cu-BTC by

means of partial density-of-states (PDOS)We have compared especially the Cu-PDOS for s- p- and d-

orbitals (see Fig 4) The results show that the electronic structure stays unchanged when going from

the cluster models to the fully periodic crystal of Cu-BTC Since the copper atoms are of Cu(II) the d-

orbitals are just partially occupied what results in the metallic states at the Fermi level This is a very

interesting result as other ZnndashO-based MOFs are either semiconductors or insulators [49]

Table 2 Selected bond lengths (Aring) bond angles (˚) and dihedral angles (˚) of Cu-BTC optimized at DFTB and DFT levels with water molecules in the axial positions Cluster models are calculated using water and carbon monoxide molecules The adsorption energies Eads (kJ mol-1) of the guest molecules are given as well The DFT data are given in parenthesis

Bond Type Cluster Model +

H2O Periodic

Model+ H2O Cluster Model +

CO

Cu-Cu 267 (266) 262 (260) 250 (260)

Cu-O 205 (197-206) 210 (196-200) 206 (199)

O-C 134 (127) 133 (128) 134 (127)

OCuO 843-955 (889-905)

871-921 (842-930) 842-967 (896)

Cu-O-O-Cu plusmn59 - plusmn76 (plusmn06 ˗ plusmn10)

plusmn02 ˗ plusmn18 (plusmn40 ˗ plusmn136)

plusmn51 - plusmn58 (plusmn70)

O-C-C-C plusmn39 - plusmn53 (plusmn05 - plusmn11)

plusmn03 - plusmn05 (plusmn06 - plusmn105)


Cu-O(H2O) Cu-C(CO) 237 (219) 244 (233-

255) 307 (239)

Eads -4045 (-5200) -1648

(-2800)

32 MOF-5 -177 DUT-6 (MOF-205) and MIL- 53 We have also studied the structural properties

of MOF structures with large surface areas using the SCC-DFTB method Very good agreement with

the experimental data shows that this method is applicable for MOFs of large structural diversity as

well as for coordination polymers based on the MOF-5 framework which has been reported earlier

[49] Tables 3 and 4 show selected bond lengths and bond angles of MOF-5 [68] MOF-177 [69] DUT-

6 (MOF-205) [70 71] and MIL-53 [72] respectively

89

MOFs-5 -177 and DUT-6 (MOF-205) are built of the same connector which is Zn4O(CO2)6

octahedron The difference is in the organic linker 14-benzenedicarboxylate (BDC) 135-

benzenetribenzoates (BTB) and BTB together with 26-naphtalenedicarboxylate (NDC) for MOF-5 -

177 andDUT-6 (MOF-205) respectively (see Fig 5)

Figure 4 DFTB calculations of PDOS of (top left) Cu in Cu-BTC and Zn in MOF-5 (top right) MOF-177 (bottom left) and DUT-6 (MOF-205) (bottom right) In each plot s-orbitals (top) p-orbitals (middle) and d-orbitals (bottom) are shown as computed from periodic (black) and cluster (red) models Cluster models are given in Fig S4

All three MOFs have different topologies due to the organic linkers where the number of

connections is varied or where two different linker types are present MOF-5 is the most simple and

it is the prototype in the isoreticular series (IRMOF-1) [68] it is a simple cubic topology with

threedimensional pores of the same size and the linkers have only two connection points In the

case of MOF-177 the linker is represented by a triangularSBU that means three connection points

are present This results in the topology with mixed (36)-connectivity [69] DUT-6 (MOF-205) has a

much more complicated topology due to two types of linkers The first one (NDC) has just two

90

connection points while the second is the same as in MOF-177 with three connection points One

ZnndashO-based connector is connected to two NDC and four BTB linkers The topology is very interesting

all rings of the underlying nets are fivefold and it forms a face-transitive tiling of dodectahedra and

tetrahedra with a ratio of 13 [73]

Figure 5 The crystal structures in the unit cell representations of (a) MOF-5 (b) MOF-177 (c) DUT-6 (MOF-205) and (d) MIL-53 red oxygen gray carbon white hydrogen and blue metal atom (Zn Al)

MIL-53 is a MOF structure with one-dimensional pores The framework is built up of corner-sharing

AlndashO-based octahedral clusters interconnected with BDC linkers The linkers have again two

connection points MIL-53 shows reversible structural changes dependent on the guest molecules

[74] It undergoes the so-called breathing mode depending on the temperature and the amount of

adsorbed molecules

In this case also the bond lengths and bond angles are slightly overestimated comparing with the

experimental structures but the error does not exceed 3

91

Table 3 Selected bond lengths (Aring) and bond angles (˚) of MOF-5 (424 atoms in unit cell) MOF-177 (808 atoms in unit cell) and DUT-6 (MOF-205) (546 atoms in unit cell) optimized at DFTB level The available experimental data is given in parenthesis [70-73+ Orsquo denotes the central O atom in the Zn-O-octahedron

Bond Type MOF-5 MOF-177 DUT-6

(MOF-205)

Zn-Zn 330 (317) 322-336 (306-330)

325-331 (318)

Zn-Orsquo 202 (194) 202 (193) 202 (194) Zn-O 204 (192) 202-206

(190-199) 202 205 (193)

O-C 128 (130) 128 (131) 128 (125) ZnOrsquoZn 1095 (1095) 1056-1124

(1055 1092) 107-1118 (1084 1100)

OZnO 1083 1108 (1061)

1048 1145 (981-1281)

1046-1112 (1062 1085)

Zn-O-O-Zn 0 (0 plusmn17 plusmn20) plusmn122 - plusmn347 (plusmn176 - plusmn374)

05 - plusmn62 (0 plusmn29)

O-C-C-C 00 (0 - plusmn24) (plusmn 35 - plusmn 336) (plusmn65 - plusmn374)

plusmn04 plusmn22 (0 plusmn174)

Cell paramet a=b=c=26472 (25832) α=β=γ=90 (90)

a=b=37872 (37072) c=3068 (30033) α=β=90 (90) γ=120 (120)

a=b=c=31013 (30353) α=β=γ=90 (90)

We have calculated PDOS for MOF-5 MOF-177 and DUT-6 (MOF-205) (see Fig 4) Their band gaps

calculated to be 40 35 and 31 eV respectively indicate that they are either semiconductors or

insulators We have calculated it for both periodic crystal structure and a cluster containing a metal-

oxide connector and all its carboxylate linkers

Table 4 Selected bond lengths (Aring) and bond angles (˚) of MIL-53 (152 atoms in unit cell) optimized at DFTB level

Bond Type DFTB Exp

Al-Al 341 331 Al-O 189 183-191 O-C 133 129 130 O-Al-O 884 912 886 898 Al-O-Al 1289 1249 Al-O-O-Al 0 0 O-C-C-O 06 03 Cell paramet a=1246

b=1732 c=1365 α=β=γ=90

a=1218 b=1713 c=1326 α=β=γ=90

4 Mechanical properties Due to the low-mass density the elastic constants of porous materials

are a very sensitive indicator of their mechanical stability For crystal structures like MOFs we have

92

studied these by means of bulk modulus (B) B can be calculated as a second derivative of energy

with respect to the volume of the crystal (here unit cell)

The result shows that CuBTC has bulk modulus of 3466 GPa what is in close agreement with

B=3517 GPa obtained using force-field calculations [73 74] and experiment [75] Bulk moduli for the

series of MOFs resulted in 1534 1010 and 1073 GPa for MOF-5 -177 and DUT-6 (MOF-205)

respectively For MOF-5 B=1537 GPa was reported from DFTGGA calculations using plane-waves

[76 77] The results show that larger linkers give mechanically less stable structures what might be

an issue for porous structures with larger voids For MIL-53 we have obtained the largest bulk

modulus of 5369 GPa keeping the angles of the pore fixed

5 Conclusions We have validated the DFTB method with SCC and London dispersion corrections for

various types of MOFs The method gives excellent geometrical parameters compared to experiment

and for small model systems also in comparison with DFT calculations Importantly this statement

holds not only for catalytically inactive MOFs based on the Zn4O(CO2)6 octahedron and organic linkers

which are important for gas adsorption and separation applications but also for catalytically active

HKUST-1 (CuBTC) This is remarkable as the Cu atoms are in the Cu2+ state in this framework DFTB

parameters have been generated and validated for Cu and the electronic structure contains one

unpaired electron per Cu atom in the unit cell which makes the electronic description technically

difficult but manageable within the SCC-DFTB method SCC-DFTB performs well for the frameworks

themselves as well as for adsorbed CO and water molecules

Partial density-of-states calculations for the transition metal centers reveal that the concept of

reticular chemistry ndash individual building units keep their electronic properties when being integrated

to the framework ndash is also valid for the MOFs studied in this work in agreement with a previous

study of COFs [16] The electronic properties computed using the cluster models and the periodic

structure contains the same features and hence cluster models are good models to study the

catalytic and adsorption properties of these materials This is in particular useful if local quantum

chemical high-level corrections shall be applied that require to use finite structures

We finally conclude that we have now a high-performing quantum method available to study various

classes of MOFs of unit cells up to 10000 atoms including structural characteristics the formation

and breaking of chemical and coordination bonds for the simulation of diffusion of adsorbate

molecules or lattice defects as well as electronic properties The parameters can be downloaded

from the DFTBorg website

93

References

[1] E A Tomic J Appl Polym Sci 9 3745 (1965)

2+ M Eddaoudi D B Moler H L Li B L Chen T M Reineke M OrsquoKeeffe and O M Yaghi Acc Chem Res

34 319 (2001)

[3] M Eddaoudi H L Li T Reineke M Fehr D Kelley T L Groy and O M Yaghi Top Catal 9 105 (1999)

[4] B F Hoskins and R Robson J Am Chem Soc 111 5962 (1989)

[5] K Schlichte T Kratzke and S Kaskel Microporous Mesoporous Mater 73 81 (2004) [6] J L C Rowsell A

R Millward K S Park and O M Yaghi J Am Chem Soc 126 5666 (2004)

7+ O M Yaghi M OrsquoKeeffe N W Ockwig H K Chae M Eddaoudi and J Kim Nature 423 705 (2003)

[8] M Eddaoudi J Kim N Rosi D Vodak J Wachter M OrsquoKeeffe and O M Yaghi Science 295 469 (2002)

9+ M OrsquoKeeffe M Eddaoudi H L Li T Reineke and O M Yaghi J Solid State Chem 152 3 (2000)

[10] S S Y Chui SM F Lo J P H Charmant A G Orpen and I D Williams Science 283 1148 (1999)

11+ A P Cote A I Benin N W Ockwig M OrsquoKeeffe A J Matzger and O M Yaghi Science 310 1166 (2005)

[12] A P Cote H M El-Kaderi H Furukawa J R Hunt and O M Yaghi J Am Chem Soc 129 12914 (2007)

[13] H M El-Kaderi J R Hunt J L Mendoza-Cortes A P Cote R E Taylor M OrsquoKeeffe and O M Yaghi

Science 316 268 (2007)

[14] S Wan J Guo J Kim H Ihlee and D L Jiang Angew Chem 120 8958 (2008)


[16] B Lukose A Kuc J Frenzel and T Heine Beilstein J Nanotechnol 1 60 (2010)

[17] B Lukose A Kuc and T Heine Chem Eur J 17 2388 (2011)

[18] D S Marlin D G Cabrera D A Leigh and A M Z Slawin Angew Chem Int Ed 45 77 (2006)

[19] I Krkljus and M Hirscher Microporous Mesoporous Mater 142 725 (2011)

[20] M Hirscher Handbook of Hydrogen Storage (Wiley-VCH Weinheim 2010)

[21] H Kitagawa Nature Chem 1 689 (2009)

[22] M Sadakiyo T Yamada and H Kitagawa J Am Chem Soc 131 9906 (2009)

[23] T Yamada M Sadakiyo and H Kitagawa J Am Chem Soc 131 3144 (2009)

94

[24] K S Jeong Y B Go S M Shin S J Lee J Kim O M Yaghi and N Jeong Chem Sci 2 877 (2011)

[25] R Schmid and M Tafipolsky J Am Chem Soc 130 12600 (2008)

[26] M Tafipolsky S Amirjalayer and R Schmid J Comput Chem 28 1169 (2007)

[27] M Tafipolsky S Amirjalayer and R Schmid J Phys Chem C 114 14402 (2010)

[28] A Warshel and M Levitt J Mol Biol 103 227 (1976)

[29] G Seifert D Porezag and T Frauenheim Int J Quantum Chem 58 185 (1996)

[30] A F Oliveira G Seifert T Heine and H A Duarte J Braz Chem Soc 20 1193 (2009)

[31] D Porezag T Frauenheim T Koumlhler G Seifert and R Kaschner Phys Rev B 51 12947 (1995)

[32] T Frauenheim G Seifert M Elstner Z Hajnal G Jungnickel D Porezag S Suhai and R Scholz Phys

Status Solidi B 217 41 (2000)

[33] M Elstner Theor Chem Acc 116 316 (2006)

Supporting Information

Figure S4 Cluster models as used for the P-DOS calculations in Fig 4 MOF-5 MOF-177 and DUT-6 (MOF-205) (from left to right)

95

Figure S3 Radial pair distribution function (g(r)) of Cu-Cu Cu-C Cu-O C-C and C-O atom-pairs in a Cu-BTC MOF unit cell

96

Appendix C

The Structure of Layered Covalent-Organic Frameworks

Binit Lukose Agnieszka Kuc and Thomas Heine

Chem Eur J 2011 17 2388 ndash 2392

DOI 101002chem201001290

Abstract Covalent-Organic Frameworks (COFs) are a new family of 2D and 3D highly porous and

crystalline materials built of light elements such as boron oxygen and carbon For all 2D COFs an AA

stacking arrangement has been reported on the basis of experimental powder XRD patterns with the

exception of COF-1 (AB stacking) In this work we show that the stacking of 2D COFs is different as

originally suggested COF-1 COF-5 COF-6 and COF-8 are considerably more stable if their stacking

arrangement is either serrated or inclined and layers are shifted with respect to each other by ~14 Aring

compared with perfect AA stacking These structures are in agreement with to date experimental

data including the XRD patterns and lead to a larger surface area and stronger polarisation of the

pore surface

Introduction In 2005 Cocircteacute and co-workers introduced a new class of porous crystalline materials

Covalent Organic Frameworks (COFs)[1] where organic linker molecules are stitched together by

connectors covalent entities including boron and oxygen atoms to a regular framework These

materials have the genuine advantage that all framework bonds represent strong covalent

interactions and that they are composed of light-weight elements only which lead to a very low

mass density[2] These materials can be synthesized solvothermally in a condensation reaction and

97

are composed of inexpensive and non-toxic building blocks so their large-scale industrial production

appears to be possible

Figure 1 Calculated and experimental XRD patterns of all studied COFs (COF-1 top left COF-5 top right COF-6 bottom left COF-8 bottom right)

To date a number of different COF structures have been reported[1ndash3] From a topological

viewpoint we distinguish two- and three-dimensional COFs In two-dimensional (2D) COFs the

covalently bound framework is restricted to 2D layers The crystal is then similar as in graphite or

hexagonal boron nitride composed by a stack of layers which are not connected by covalent bonds

but held together primarily by London dispersion interactions

98

The COF structures have been analyzed by powder X-ray diffraction (PXRD) experiments The

topology of the layers is determined by the structure of the connector and linker molecules and

typically a hexagonal pattern is formed due to the 2m (D3h) symmetry of the connector moieties

The individual layers are then stacked and form a regular crystal lattice With one exception (COF-

1)[1] for all 2D-COFs AA (eclipsed P6mmm) interlayer stacking has been reported[3andashd f g] This

geometrical arrangement maximizes the proximity of the molecular entities and results in straight

channels orthogonal to the COF layers which are known from the literature[1 3a]

The connectors of 2D-COFs include oxygen and boron atoms which cause an appreciable polarization

The AA stacking arrangement maximizes the attractive London dispersion interaction between the

layers which is the dominating term of the stacking energy At the same time AA stacking always

results in a repulsive Coulomb force between the layers due to the polarized connectors It should be

noted that the eclipsed hexagonal boron nitride (h-BN)[4] has boron atoms in one layer serving as

nearest neighbours to nitrogen atoms in adjacent layers (AB stacking) The Coulomb interaction has

ruled out possible interlayer eclipse between atoms of alike charges In this article we aim at

studying the layer arrangements of solvent-free COFs based on the interlayer interactions and the

minimum variance Various lattice types have been considered all significantly more stable than the

reported AA stacked geometry In all 2D COFs we have studied the Coulomb interaction between the

layers leads to a modification of the stacking and shifts the layers by about one interatomic distance

(~14 Aring) with respect to each other (see Figure 1)

Breaking of the highly symmetric layer arrangement has been observed for COF-1 and COF-10 after

removal of guest molecules from pores leading to a turbostratic repacking of pore channels[1 5]

The authors have confirmed the disorder either by the changes in the PXRD spectrum taken before

and after adsorptionndashdesorption cycle[1] or by the changes in the adsorption behavior[5] The

disruption of layer arrangement is attributed to the force exerted by the guest molecules Formation

of poly disperse pores has also been verified[5] The lattice types that we discuss in this article on

the other hand are neither the result of the pressure from any external molecule in the pore nor

having more than one type of pores They are the resultant of minimum variance guided by Coulomb

and London dispersion interactions For the COF models under investigation perfect crystallinity has

been considered

Methods We have studied the experimentally known structures of COF-1 COF-5 COF-6 and COF-8

Structure calculations were carried out using the Dispersion-Corrected Self-Conistent-Charge

Density-Functional-Based Tight-Binding method (SCC-DFTB)[6] DFTB is based on a second-order

expansion of the KohnndashSham total energy in DFT with respect to charge density fluctuations This

does not require large amounts of empirical parameters however maintains all qualities of DFT The

99

accuracy is very much improved by the SCC extension The DFTB code (deMonNano[6a]) has

dispersion correction[6d] implemented to account for weak interactions and was used to obtain the

layered bulk structure of COFs and their formation energies The performance for interlayer

interactions has been tested previously for graphite[6d] All structures correspond to full geometry

optimizations (structure and unit cell) XRD patterns have been simulated using the Mercury

software[7] To allow best comparison with experiment for PXRD simulations we used the calculated

geometry of the layer and of the relative shifts between the layers but experimental interlayer

distances The electrostatic potential has been calculated using Crystal 09[8] at the DFTVWN level

with 6-31G basis set

Results and Discussion

In order to see the favorite stacking arrangement of the layers we have shifted every second layer in

two directions along zigzag and armchair vertices of the hexagonal pores (see Figure 2) The initial

stacking is AA (P6mmm) and the final zigzag shift gives AB stacking (P63mmc) Considering that the

attractive interlayer dispersion forces and repulsive interlayer orbital interactions are different we

have optimized the interlayer separation for each stacking Figure 2 show their total energies

calculated per formula unit that is per established bond between linkers and connectors with

reference to AA stacking for COF-5 and COF-1 In each direction the energy minimum is found close

to the AA stacking position shifted only by about one aromatic C-C bond length (~14 Aring) so that

either connector or linker parts become staggered with those in the adjacent layers leading to a

stacking similar to that of graphite for either connector (armchair shift) or linker (zigzag shift) For

COF-5 the staggering at the connector or linker depends whether the shift is armchair or zigzag

respectively while for COF-1 the zigzag shift alone can give staggering in both the aromatic and

boron-oxygen rings

The low-energy minima in the two directions are labeled following the common nomenclature as

zigzag and armchair respectively Both shifts result in a serrated stacking order (orthorhombic

Cmcm) which shows a significantly more attractive interlayer Coulomb interaction than AA stacking

(see Table 1) while most of the London dispersion attraction is maintained and consequently

stabilizes the material Still this configuration can be improved if we consider inclined stacking

(Figure 1) that is the lattice vector pointing out of the 2D plane is not any longer rectangular

reducing the lattice symmetry from Cmcm (orthorhombic) to C2m (monoclinic)

Besides we have calculated the monolayer formation energy (condensation energy Ecb) from the

total energies of the monolayer and of the individual building blocks and the stacking formation

energy from the total energies of the bulk structure and of the monolayer for four selected COFs The

100

COF building blocks are the same as those used for their synthesis[1 3a] (BDBA for COF-1 BDBA and

HHTP for COF-5 BTBA and HHTP for COF-6 BTPA and HHTP for COF-8) The final energies given per

formula unit that is per condensed bond are given in Table 1 The serrated and inclined stacking

structures are energetically more stable than AA and AB Interestingly within our computational

model zigzag and armchair shifting is energetically equivalent

Figure 2 Change of the total energy (per formula unit) when shifting COF-5 even layers in zigzag (top) and armchair (middle) directions and COF-1 in zigzag (bottom) direction The vector d shows the shift direction The low-energy minima in the two directions are labelled as zigzag and armchair respectively The equilibrium structures are shown as well

The formation energies of the individual COF structures are in agreement with full DFT calculations

We have calculated using ADF[9] the condensation energy of COF-1 and COF-5 using first-principles

DFT at the PBE[10]DZP[11] level to qualitatively support our results For simplicity we have used a

finite structure instead of the bulk crystal Their calculated Ecb energies are 77 and 15 kJmol-1

respectively for COF-1 and COF-5 These values support the endothermic nature of the condensation

101

reaction and are in excellent agreement with our DFTB results (91 and 21 kJmol-1 respectively see

Table 1)

The change of stacking should be visible in X-ray diffraction patterns because each space group has a

distinct set of symmetry imposed reflection conditions Powder XRD patterns from experiments are

available for all 2D COF structures[1 3andashd f g] We have simulated XRD patterns for AA AB serrated

Table 1 Calculated formation energies for the studied COF structures Ecb = condensation Esb = stacking energy EL = London dispersion energy Ee = electronic energy Energies are per condensed bond and are given in [kJ mol

-1+ lsquoarsquo and lsquozrsquo stand for armchair and zigzag respectively Note that the electronic energy Ee=Esb-EL

includes the electronic interlayer interaction and the formation energy of the monolayer and that the formation of the monolayers is endothermic

Structure Stacking Esb EL Ee

COF-5 AA -2968 -3060 092

AB -2548 -2618 070

serrated z -3051 -3073 022

serrated a -3052 -3073 021

inclined z -3297 -3045 -252

inclined a -3275 -3044 -231

Monolayer Ecb= 211

COF-1 AA -2683 -2739 056

AB -2186 -2131 -055

serrated z -2810 -2806 -004

inclined z -2784 -2788 004

Monolayer Ecb= 906

COF-6 AA -2881 -2963 082

AB -2127 -2146 019

serrated z -2978 -2996 018

serrated a -2978 -2995 017

inclined z -2946 -2975 029

inclined a -2954 -2974 021

Monolayer Ecb= 185

COF-8 AA -4488 -4617 129

102

AB -2477 -2506 029

serrated z -4614 -4646 032

serrated a -4615 -4647 032

inclined z -4578 -4612 035

inclined a -4561 -4591 030

Monolayer Ecb= 263

and inclined stacking forms for COF-5 COF-1 COF-6 and COF-8 (see Figure 1for their comparison

with experimental spectrum) For completeness we have studied XRD patterns of optimized COFs

using the experimentally determined[1 3a] interlayer separations this means we have kept the

layer geometry the same as the optimized structures and different stackings were obtained by

shifting adjacent layers accordingly

COF-1 was reported as having different powder spectra for samples before (as-synthesized) and after

removal of guest molecules with a particular mentioning about its layer shifting after removal We

have compared the two spectra with our simulated XRDs in order to see the stacking in the pure

form and how the stacking is changed at the presence of mesitylene guests Except that we have only

a vague comparison at angles (2θ) 11ndash15 the powder spectrum after guest removal is more similar

to the XRDs of serrated and inclined stacking structures A notable difference from AB is the absence

of high peaks at angles ~12 ~15 and ~19 This gives rise to the suggestion that COF-1 is not a

notable exception among the 2D COFs it follows the same topological trend as all other frameworks

of this class having one-dimensional (1D) pores as soon as the solvent is removed from the pores

This suggestion is supported by the experimental fact that the gas adsorption capacity of COF-1 is

only slightly lower than that of COF-6 for even as large gas molecules as methane and CO2[12] It is

not obvious how these molecules would enter an AB stacked COF-1 framework where the pores are

not connected by 1D channels (see Figure 1) Moreover our calculations suggest that the serrated

and inclined stackings are energetically favorable (see Table 1)

Indeed all the new stackings discussed in this article yield XRD patterns which are in agreement with

the currently available experimental data (see Figure 1) The inclined stackings have more peaks but

those are covered by the broad peaks in the experimental pattern The same is observed for the (002)

peaks of serrated stackings At present 2D COF synthesis methods are not yet capable to produce

crystals of sufficient quality to allow more detailed PXRD analysis in particular for the solvent-free

materials Microwave synthesis of COF-5 by rapid heating is reported[13] as much faster (~200 times)

compared with solvothermal methods however the structural details (XRD etc) remained

103

ambiguous We are confident that better crystals will be produced in future which will allow the

unambiguous determination of COF structures and can be compared to our simulations

Finally we want to emphasize that the suggested change of stacking is not only resulting in a

moderate change of geometry and XRD pattern The functional regions of COFs are their pores and

the pore geometry is significantly modified in our suggested structures compared to AA and AB

stackings First the inclined and serrated structures account for an increase of the surface area by 6

estimated for the interaction of the COFs with helium (3 for N2 5 for Ar 56 for Ne) Moreover

the shift between the layers exposes both boron and oxygen atoms to the pore surface leading to a

much stronger polarity than it can be expected for AA stacked COFs This difference is shown in

Figure 3 which plots the electrostatic potential of COF-5 in AA serrated and inclined stacking

geometries While the pore surface of AA stacked COF-5 shows a positively and negatively charged

stripes the other stacking arrangements show a much stronger alternation of charges indicating the

higher polarity of the surface The surface polarity can also be expressed in terms of Mulliken charges

of oxygen and boron atoms calculated at the DFT level which are COF-5 AA qB = 048 and qO = -048

COF-5 serrated qB = 047 and qO = -049 COF-5 inclined qB = 045 and qO = -048

Figure 3 Calculated electrostatic potential of COF-5 AA (left) serrated (middle) and inclined (right) stacking forms Blue - negative and red-positive values of the 005 isosurface

Conclusion We have studied 2D COF layer stackings energetically and found that energy minimum

structures have staggering of hexagonal rings at the connector or linker parts This can be achieved if

the bulk structure has either serrated or inclined order These newly proposed orders have their

simulated XRDs matching well with the available experimental powder spectrum Hence we claim

that all reported 2D COF geometries shall be re-examined carefully in experiment Due to the change

of the pore geometry and surface polarity the envisaged range of applications for 2D COFs might

change significantly We believe that these results are of utmost importance for the design of

functionalized COFs where functional groups are added to the pore surfaces

104

References

[1] A P Cocircteacute A I Benin N W Ockwig M OKeeffe A J Matzger O M Yaghi Science 2005 310 1166

[2] H M El-Kaderi J R Hunt J L Mendoza-Cortes A P Cote R E Taylor M OKeeffe O M Yaghi Science

2007 316 268

[3] a) A P Cocircteacute H M El-Kaderi H Furukawa J R Hunt O M Yaghi J Am Chem Soc 2007 129 12914 b) J

R Hunt C J Doonan J D LeVangie A P Cocircte O M Yaghi J Am Chem Soc 2008 130 11872 c) R W

Tilford W R Gemmill H C zur Loye J J Lavigne Chem Mater 2006 18 5296 d) R W Tilford S J Mugavero

P J Pellechia J J Lavigne Adv Mater 2008 20 2741 e) F J Uribe-Romo J R Hunt H Furukawa C Klock M

OKeeffe O M Yaghi J Am Chem Soc 2009 131 4570 f) S Wan J Guo J Kim H Ihee D L Jiang Angew

Chem 2008 120 8958 Angew Chem Int Ed 2008 47 8826 g) S Wan J Guo J Kim H Ihee D L Jiang

Angew Chem 2009 121 5547 Angew Chem Int Ed 2009 48 5439

[4] R T Paine C K Narula Chem Rev 1990 90 73

[5] C Doonan D Tranchemontagne T Glover J Hunt O Yaghi Nat Chem 2010 2 235

[6] a) T Heine M Rapacioli S Patchkovskii J Frenzel A M Koester P Calaminici S Escalante H A Duarte R

Flores G Geudtner A Goursot J U Reveles A Vela D R Salahub deMon deMonnano edn Mexico DF

Mexico and Bremen (Germany) 2009 b) A F Oliveira G Seifert T Heine H A Duarte J Braz Chem Soc

2009 20 1193 c) G Seifert D Porezag T Frauenheim Int J Quantum Chem 1996 58 185 d) L Zhechkov T

Heine S Patchkovskii G Seifert H A Duarte J Chem Theory Comput 2005 1 841

[7] a) httpwwwccdccamacukproductsmercury b) C F Macrae P R Edgington P McCabe E Pidcock

G P Shields R Taylor M Towler J Van de Streek J Appl Crystallogr 2006 39 453

[8] R Dovesi V R Saunders C Roetti R Orlando C M Zicovich- Wilson F Pascale B Civalleri K Doll N M

Harrison I J Bush P DrsquoArco M Llunell Crystal 102 ed

[9] a) httpwwwscmcom ADF200901 Amsterdam The Netherlands b) G te Velde F M Bickelhaupt S J

A van Gisbergen C Fonseca Guerra E J Baerends J G Snijders T Ziegler J Comput Chem 2001 22 931

[10] J P Perdew K Burke M Ernzerhof Phys Rev Lett 1996 77 3865

[11] E Van Lenthe E J Baerends J Comput Chem 2003 24 1142

[12] H Furukawa O M Yaghi J Am Chem Soc 2009 131 8875

[13] N L Campbell R Clowes L K Ritchie A I Cooper Chem Chem Mater 2009 21 204

105

Appendix D

On the reticular construction concept of covalent organic frameworks

Binit Lukose Agnieszka Kuc Johannes Frenzel and Thomas Heine

Beilstein J Nanotechnol 2010 1 60ndash70

DOI103762bjnano18

Abstract

The concept of reticular chemistry is investigated to explore the applicability of the formation of

Covalent Organic Frameworks (COFs) from their defined individual building blocks Thus we have

designed optimized and investigated a set of reported and hypothetical 2D COFs using Density

Functional Theory (DFT) and the related Density Functional based tight-binding (DFTB) method

Linear trigonal and hexagonal building blocks have been selected for designing hexagonal COF layers

High-symmetry AA and AB stackings are considered as well as low-symmetry serrated and inclined

stackings of the layers The latter ones are only slightly modified compared to the high-symmetry

forms but show higher energetic stability Experimental XRD patterns found in literature also

support stackings with highest formation energies All stacking forms vary in their interlayer

separations and band gaps however their electronic densities of states (DOS) are similar and not

significantly different from that of a monolayer The band gaps are found to be in the range of 17ndash

40 eV COFs built of building blocks with a greater number of aromatic rings have smaller band gaps

Introduction

In the past decade considerable research efforts have been expended on nanoporous materials due

to their excellent properties for many applications such as gas storage and sieving catalysis

106

selectivity sensoring and filtration [1] In 1994 Yaghi and co-workers introduced ways to synthesize

extended structures by design This new discipline is known as reticular chemistry [23] which uses

well-defined building blocks to create extended crystalline structures The feasibility of the building

block approach and the geometry preservation throughout the assembly process are the key factors

that lead to the design and synthesis of reticular structures

One of the first families of materials synthesized using reticular chemistry were the so-called Metal-

Organic Frameworks (MOFs) [4] They are composed of metal-oxide connectors which are covalently

bound to organic linkers The coordination versatility of constituent metal ions along with the

functional diversity of organic linker molecules has created immense possibilities The immense

potential of MOFs is facilitated by the fact that all building blocks are inexpensive chemicals and that

the synthesis can be carried out solvothermally MOFs are commercially available and the scale up of

production is continuing Since the discovery of MOFs many other crystalline frameworks have been

synthesized using reticular chemistry such as Metal-Organic Polyhedra (MOP) [5] Zeolite

Imidazolate Frameworks (ZIFs) [6] and Covalent Organic Frameworks (COFs) [7]

In 2005 Cocircteacute and co-workers introduced COF materials [7-14] where organic linker molecules are

stitched together by covalent entities including boron and oxygen atoms to form a regular

framework These materials have the distinct advantage that all framework bonds represent strong

covalent interactions and that they are composed of light-weight elements only which lead to a very

low mass density [7-9] These materials can be synthesized by wet-chemical methods by

condensation reactions and are composed of inexpensive and non-toxic building blocks so their

large-scale industrial application appears to be possible From a topological viewpoint we distinguish

two- and three-dimensional COFs In two-dimensional (2D) COFs the covalently bound framework is

restricted to layers The crystal is then similar as in graphite composed of a stack of layers which

are not connected by covalent bonds

COFs compared with MOFs have lower mass densities due to the absence of heavy atoms and

therefore might be better for many applications For example the gravimetric uptake of gases is

almost twice as large as that of MOFs with comparable surface areas [1516] Because COFs are fairly

new materials many of their properties and applications are still to be explored

Recently we have studied the structures of experimentally well-known 2D COFs [17] We have found

that commonly accepted 2D structures with AA and AB kinds of layering are energetically less stable

than inclined and serrated forms This is because AA stacking maximises the Coulomb repulsion due

to the close vicinity of charge carrying atoms alike (O B atoms) in neighbouring layers The serrated

and inclined forms are only slightly modified (layers are shifted with respect to each other by asymp14 Aring)

107

and experience less Coulomb forces between the layers compared to AA stacking This is equivalent

to the energetic preference of graphite for an AB (Bernal) over an AA form (simple hexagonal) if we

ignore the fact that interlayer ordering in serrated and inclined forms are not uniform everywhere A

known example of this is that in eclipsed hexagonal boron nitride (h-BN) boron atoms in one layer

serve as nearest neighbours to nitrogen atoms in adjacent layers (AB stacking) The Coulomb

interaction rules out possible interlayer eclipse between atoms with similar charges in this case

In the present work we aim to explore how far the concept of reticular chemistry is applicable to the

individual building units which define COFs For this purpose we have investigated a set of reported

and hypothetical 2D COFs theoretically by exploring their structural energetic and electronic

properties We have compared the properties of the isolated building blocks with those of the

extended crystal structures and have found that the properties of the building units are indeed

maintained after their assembly to a network


Structures and nomenclature

We have considered four connectors (IndashIV) and five linkers (andashe) for the systematic design of a

number of 2D COFs (Figure 1) Each COF was built from one type of connector and one type of linker

thus resulting in the design of 20 different structures Moreover we have considered two

hypothetical reference structures which are only built from connectors I and III (no linker is present)

REF-I and REF-III Properties of other COFs were compared with the properties of these two

structures Some of the studied COFs are already well known in the literature [781314] and we

continue to use their traditional nomenclature while hypothetical ones are labelled in the

chronological order with an M at the end which stands for modified

Figurel 1 The connector (IndashIV) and linker (andashe) units considered in this work The same nomenclature is used in the text Carbon ndash green oxygen ndashred boron ndash magenta hydrogen ndash white

108

Using the secondary building unit (SBU) approach we can distinguish the connectors between

trigonal [T] (connectors I II III) and hexagonal [H] (connector IV) and the linkers between linear [l]

(linkers a b e) and trigonal [t] (linkers c d) Topology of the layer is determined by the geometries

of the connector and linker molecules and typically a hexagonal pattern is formed due to the D3h

symmetry of the connector moieties Based on these topologies of the constituent building blocks

we have classified the studied COFs into four groups Tl Tt Hl and Ht (Figure 2) Hereafter we will

use this nomenclature to describe the COF topologies

Figurel 2 Topologies of 2D COFs considered in this work (from the left) Tl Tt Hl and Ht Red and blue blocks are secondary building units corresponding to connectors and linkers respectively

We have considered high-symmetry AA and AB kinds of stacking (hexagonal) and low-symmetry

serrated (orthorhombic) and inclined (monoclinic) kinds of stacking of the layers The latter two were

discussed in a previous work on 2D COFs [17] As an example the structure of COF-5 [7] in different

kinds of stacking of layers is shown in Figure 3 In eclipsed AA stacking atoms of adjacent layers lie

directly on top of each other whilst in staggered AB stacking three-connected vertices lie directly on

top of the geometric center of six-membered rings of neighbouring layers In both serrated and

inclined kinds of stacking the layers are shifted with respect to each other by approximately 14 Aring

resulting in hexagonal rings in the connector or linker being staggered with those in the adjacent

layers In serrated stacking alternate layers are eclipsed In inclined stacking layers lie shifted along

one direction and the lattice vector pointing out of the 2D plane is not rectangular For COFs made of

connector I due to the absence of five-membered C2O2B rings a zigzag shift leads to staggering in

both connector and linker parts For those made of other connectors staggering at the connector or

linker depends on whether the shift is armchair or zigzag respectively [17]

Structural properties

We have compared structural properties of isolated building blocks with those of the extended COF

structures Negligible differences have been found in the bond lengths and bond angles of the

building blocks and the corresponding crystal structures This indicates that the structural integrity of

the building blocks remains unchanged while forming covalent organic frameworks confirming the

109

principle of reticular chemistry In addition the CndashB BndashO and OndashC bond lengths are almost the same

when different COF structures are compared (see Table S1 in Supporting Information File 1) The

experimental bond lengths are asymp154 Aring for CndashB asymp138 Aring for OndashC and 137ndash148 Aring for BndashO However

in the case of COF-1 the experimental values are slightly larger (160 Aring for CndashB and 151 Aring for BndashO)

This could be the reason why our calculated bond lengths for COF-1 are much shorter than the

experimental values while all the other structures agree within 5 error The calculated CndashC bond

lengths vary in the range from 136ndash147 Aring (Figure S2 in Supporting Information File 1) and are the

same for the COFs and their constituent building blocks at the respective positions of the carbon

atoms In addition the reference structures REF-I and REF-III have direct BndashB bond lengths of 167 Aring

and 166 Aring respectively which is shorter by 014 Aring than a typical BndashB bond length The calculated

bond angles OBO in B3O3 and C2O2B rings are 120deg and 113deg respectively

Figure 3 Layer stackings considered AA AB serrated and inclined

Interlayer distances (d) which is the shortest distance between two layers (equivalent to c for AA

c2 for AB and serrated) are different in all kinds of stacking AB stacked 2D COFs have shorter

interlayer distances than the corresponding AA serrated and inclined stacked structures Among the

latter three AA stacked COFs have higher values for d because of the higher repulsive interlayer

orbital interactions resulting from the direct overlap of polarized alike atoms between the adjacent

layers This results in higher mass densities for AB stacked COF analogues Serrated and inclined

stacks have only slightly higher mass densities compared to AA The differences in mass densities for

all kinds of stacking are attributed to the differences in their interlayer separations The d values of

most of the COFs are larger than that of graphite in AA stacking but smaller in AB stacking

Cell parameters (a) and mass densities (ρ) of all the COFs constructed from the considered

connectors and linkers are shown in Table 1 (and in Table S3 in Supporting Information File 1) Mass

densities of all the COFs are much lower than that of graphite (227 gmiddotcmminus3) and diamond (350

gmiddotcmminus3) AAserratedinclined stacked COF-10s have the lowest mass densities (045046046

gmiddotcmminus3) which is lower than that of MOF-5 (059 gmiddotcmminus3) [4] and comparable to that of highly porous

MOF-177 (042 gmiddotcmminus3) [18]

110

In order to identify the stacking orders we have analyzed X-ray diffraction (XRD) patterns of the well-

known COFs (COF-10 TP COF PPy-COF see Figure 4) in all the above discussed stacking kinds The

change of stacking should be visible in XRDs because each space group has a distinct set of symmetry

imposed reflection conditions The XRD patterns of AA serrated and inclined stacking kinds which

differ within a slight shift of adjacent layers to specific directions are in agreement with the presently

available experimental data [81314] Their peaks are at the same angles as in the experimental

spectrum whereas AB stacking clearly shows differences The slight differences in the (001) angle

between each stacking resemble the differences in their interlayer separations The inclined

stackings have more peaks however they are covered by the broad peaks in the experimental

patterns Similar results for COF-1 COF-5 COF-6 and COF-8 have been discussed in our previous

work [17]

Figure 4 The calculated and experimental [81314] XRD patterns of PPy-COF (top) COF-10 (middle) and TP COF (bottom)

111

Table 1 The calculated unit cell parameter a [Aring] interlayer distance d [Aring] and mass density ρ [gmiddotcmminus3

] for AA and AB stacked COFs Note that the cell parameter a is the same for all stacking types Experimental data [719] is given in parentheses

COF Building

Blocks

a d ρ

AA AB AA AB

COF-1 I-a 1502 (15620) 351 313 (332) 094 106

COF-1M I-b 2241 349 304 068 078

COF-2M I-c 1492 347 312 095 106

COF-3M I-d 0747 349 327 153 164

PPy-COF I-e 2232 (22163) 349 (3421) 297 084 099

COF-5 II-a 3014 (30020) 347 (3460) 326 056 060

COF-10 II-b 3758 (37810) 347 (3476) 318 045 (045) 050

COF-8 II-c 2251 (22733) 346 (3476) 320 071 (070) 077

COF-6 II-d 1505 (15091) 346 (3599) 327 104 110

TP COF II-e 3750 (37541) 348 (3378) 320 051 056

COF-4M III-a 2171 350 318 073 080

COF-5M III-b 2915 350 318 055 061

COF-6M III-c 1833 345 318 083 090

COF-7M III-d 1083 350 330 129 136

TP COF-1M III-e 2905 349 310 065 074

COF-8M IV-a 1748 359 329 140 148

COF-9M IV-b 2176 349 330 117 174

COF-10M IV-c 2254 342 336 127 128

COF-11M IV-d 1512 346 338 168 172

TP COF-2M IV-e 2173 347 332 134 140

REF-I I 0773 359 336 144 148

REF-III III 1445 353 336 104 121

Graphite 247 343 335 220 227

112

Energetic stability

We have considered dehydration reactions the basis of experimental COF synthesis to calculate

formation energies of COFs in order to predict their energetic stability Molecular units 14-

phenylenediboronic acid (BDBA) 11rsquo-biphenyl]-44-diylboronic acid (BPDA) 5rsquo-(4-boronophenyl)-

11rsquo3rsquo1rdquo-terphenyl]-44rdquo-diboronic acid (BTPA) benzene-135-triyltriboronic acid (BTBA) and

pyrene-27-diylboronic acid (PDBA) were considered as linkers andashe respectively with -B(OH)2 groups

attached to each point of extension (Figure 5) Self-condensation of these building blocks result in

the formation of B3O3 rings and the resultant COFs are those made of connector I and the

corresponding linkers This process requires a release of three or six water molecules in case of t or l

topology respectively

Figure 5 The reactants participating in the formation of 2D COFs

Co-condensation of the above molecular units with compounds such as 23671011-

hexahydroxytriphenylene (HHTP) hexahydroxybenzene (HHB) and dodecahydroxycoronene (DHC)

(Figure 5) gives rise to COFs made of connectors II III and IV respectively and the corresponding

linkers Self-condensation of tetrahydroxydiborane (THDB) and co-condensation of HHB with THDB

result in the formation of the reference structures REF-I and REF-III respectively In relation to the

corresponding connectorlinker topologies these building blocks satisfy the following equations of

the co-condensation reaction for COF formation

2 2 3 COF 12 H O Tl T l (1)

113

2 1 1 COF 6 H O Tt T t (2)

2 1 3 COF 12 H O Hl H l (3)

2 1 2 COF 12 H O Ht H t (4)

with a stochiometry appropriate for one unit cell The number of covalent bonds formed between

the building blocks is equivalent to the number of released water molecules we refer to it as

ldquoformula unitrdquo and will give all energies in the following in kJmiddotmolminus1 per formula unit

Table 2 The calculated energies [kJ molminus1

] per bond formed between building blocks for AA and AB stacked COFs Ecb is the condensation energy Esb is the stacking energy and Efb is the COF formation energy (Efb = Ecb

+ Esb) The calculated band gaps Δ eV+ are given as well

COF Building

Blocks

Mono-

layer

AA AB

Ecb Esb Efb ∆ Esb Efb ∆

COF-1 I-a 906 -2683 -1777 33 -2187 -1280 36

COF-1M I-b 949 -4266 -3366 27 -2418 -1469 31

COF-2M I-c 956 -5727 -4771 28 -4734 -3778 30

COF-3M I-d 763 -2506 -1742 38 -2801 -2037 40

PPy-COF I-e 858 -5723 -4866 24 -3855 -2998 26

COF-5 II-a 211 -2968 -2756 24 -2548 -2337 28

COF-10 II-b 317 -3766 -3448 23 -1344 -1026 26

COF-8 II-c 263 -4488 -4224 25 -2477 -2213 28

COF-6 II-d 185 -2881 -2695 28 -2127 -1942 31

TP COF II-e 231 -4453 -4222 24 -1480 -1250 27

COF-4M III-a -033 -1730 -1763 26 -880 -913 26

COF-5M III-b 007 -2533 -2526 25 -972 -965 25

COF-6M III-c 014 -3231 -3217 26 -2134 -2120 28

114

COF-7M III-d -170 -1635 -1805 30 -1607 -1777 32

TP COF-1M III-e -014 -3226 -3240 24 -1277 -1291 24

COF-8M IV-a -787 -2756 -3543 18 -2680 -3467 21

COF-9M IV-b -836 -3577 -4414 17 -3003 -3839 21

COF-10M IV-c -947 -4297 -5244 18 -4192 -5140 22

COF-11M IV-d -403 -2684 -3087 21 -2833 -3236 24

TP COF-2M IV-e 030 -4345 -4315 18 -4117 -4087 21

We have calculated the condensation energy of a single COF layer formed from monomers (building

blocks hereafter called bb) according to the above reactions as follows

tot tot tot totcb m H2O 1 bb1 2 bb2E E n E ndash m E m E (5)

where Emtot ndash total energy of the monolayer EH2O

tot is the total energy of the water molecule Ebb1tot

and Ebb2tot are the total energies of interacting building blocks and n m1 m2 are the corresponding

stoichiometry numbers

We have also calculated the stacking energy Esb of layers

tot totsb nl s mE E n E (6)

where Enltot is the total energy of ns number of layers stacked in a COF Finally the COF formation

energy can be given as a sum of Ecb and Esb (see Table 1 and Table S1)

Electronic properties

All COFs including the reference structures are semiconductors with their band gaps lying between

17 eV and 40 eV (Table 2 and Table S4 in Supporting Information File 1) The largest band gaps are

of the reference structures while the lowest values are of COFs built from connector IV The band

gaps are different for different stacking kinds This difference can be attributed to the different

optimized interlayer distances Generally AB serrated and inclined stacked COFs have band gaps

comparable to or larger than that of their AA stacked analogues

115

We have calculated the electronic total density of states (TDOS) and the individual atomic

contributions (partial density of states PDOS) The energy state distributions of COFs and their

monolayers are studied and a comparison for COF-5 is shown in Figure 6 In all stacking kinds

negligible differences are found for the densities at the top of valence band and the bottom of

conduction band These slight differences suggest that the weak interaction between the layers or

the overlap of π-orbitals does not affect the electronic structure of COFs significantly Hence there is

almost no difference between the TDOS of AA AB serrated and inclined stacking kinds Therefore in

the following we discuss only the AA stacked structures

Figure 6 Total densities of states (DOS) (black) of AA (top left) AB (top right) serrated (bottom left) and inclined (bottom right) comparing stacked COF-5 with a monolayer (red) of COF-5 The differences between the TDOS of bulk and monolayer structures are indicated in green The Fermi level EF is shifted to zero

Figure 7 Partial density of states of carbon (left) boron (center) and oxygen (right) atoms of COFs built from type-I connectors and different linkers The vertical dashed line in each figure indicates the Fermi level EF

116

It is of interest to see how the properties of COFs change depending on their composition of different

secondary building units that is for different connectors and linkers PDOS of COFs built from type-I

connectors and different linkers are plotted in Figure 7 The PDOS of carbon atoms is compared with

that of graphite (AA-stacking) while PDOS of boron and oxygen atoms are compared with that of

REF-I a structure which is composed solely of connector building blocks Going from top to bottom

of the plots the number of carbon atoms per unit cell increases It can be seen that this causes a

decrease of the band gap Figure 8 shows the PDOS of COFs built from type-a linkers and different

connectors where the COFs are arranged in the increasing number of carbon atoms in their unit cells

from top to the bottom Again the C PDOS is compared with that of graphite while both REF-I and

REF- III are taken in comparison to O and B PDOS The observed relation between number of carbon

atoms and band gap is verified

Figure 8 Partial density of states of carbon (left) boron (center) and oxygen (right) atoms of COFs built from type-a linkers The vertical dashed line in each figure indicates the Fermi level EF

Conclusion

In summary we have designed 2D COFs of various topologies by connecting building blocks of

different connectivity and performed DFTB calculations to understand their structural energetic and

electronic properties We have studied each COF in high-symmetry AA and AB as well as low-

symmetry inclined and serrated stacking forms The optimized COF structures exhibit different

interlayer separations and band gaps in different kinds of layer stackings however the density of

states of a single layer is not significantly different from that of a multilayer The alternate shifted

layers in AB serrated and inclined stackings cause less repulsive orbital interactions within the layers

which result in shorter interlayer separation compared to AA stacking All the studied COFs show

117

semiconductor-like band gaps We also have observed that larger number of carbon atoms in the

unit cells in COFs causes smaller band gaps and vice versa Energetic studies reveal that the studied

structures are stable however notable difference in the layer stacking is observed from

experimental observations This result is also supported by simulated XRDs

Methods

We have optimized the atomic positions and the lattice parameters for all studied COFs All

calculations were carried out at the Density Functional Tight-Binding (DFTB) [2021] level of theory

DFTB is based on a second-order expansion of the KohnndashSham total energy in the Density-Functional

Theory (DFT) with respect to charge density fluctuations This can be considered as a non-orthogonal

tight-binding method parameterized from DFT which does not require large amounts of empirical

parameters however maintains all the qualities of DFT The main idea behind this method is to

describe the Hamiltonian eigenstates with an atomic-like basis set and replace the Hamiltonian with

a parameterized Hamiltonian matrix whose elements depend only on the inter-nuclear distances and

orbital symmetries [21] While the Hamiltonian matrix elements are calculated using atomic

reference densities the remaining terms to the KohnndashSham energy are parameterized from DFT

reference calculations of a few reference molecules per atom pair The accuracy is very much

improved by the self-consistent charge (SCC) extension Two computational codes were used

deMonNano code [22] and DFTB+ code [23] The first code has dispersion correction [24]

implemented to account for weak interactions and was used to obtain the layered bulk structure of

COFs and their formation energies The performance for interlayer interactions has been tested

previously for graphite [24] The second code which can perform calculations using k-points was

used to calculate the electronic properties (band structure and density of states) Band gaps have

been calculated as an additional stability indicator While these quantities are typically strongly

underestimated in standard LDA- and GGA-DFT calculations they are typically in the correct range

within the DFTB method For validation of our method we have calculated some of the structures

using Density Functional Theory (DFT) as implemented in ADF code [2526]

Periodic boundary conditions were used to represent frameworks of the crystalline solid state The

conjugatendashgradient scheme was chosen for the geometry optimization The atomic force tolerance of

3 times 10minus4 eVAring was applied The optimization using Γ-point approximation was performed with the

deMon-Nano code on 2times2times4 supercells Some of the monolayers were also optimized using the

DFTB+ code on elementary unit cells in order to validate the calculations within the Γ-point

approximation The number of k-points has been determined by reaching convergence for the total

energy as a function of k-points according to the scheme proposed by Monkhorst and Pack [27]

118

Band structures were computed along lines between high symmetry points of the Brillouin zone with

50 k-points each along each line XRD patterns have been simulated using Mercury software [2829]

We have also performed first-principles DFT calculations at the PBE [30] DZP [31] level to support

our results quantitatively For simplicity we have used finite structures instead of bulk crystals


Table S1 The calculated bond lengths and angles of all studied COFs Corresponding experimental values found from the literature are shown in brackets

COF Building

Blocks

C-B B-O O-C OBO

COF-1 I-a 1498 (1600) 1393 (1509) 1203 (1200)

COF-1M I-b 1497 1393 1203

COF-2M I-c 1497 1392 1203

COF-3M I-d 1496 1392 1201

PPy-COF I-e 1498 1393 1202 (1190)

COF-5 II-a 1496 (1530) 1399 (1367) 1443 (1384) 1135dagger (1139)

COF-10 II-b 1495 (1553) 1399 (1465) 1443 (1385) 1135dagger (1120)

COF-8 II-c 1495 (1548) 1399 (1479) 1443 1135dagger

COF-6 II-d 1496 1399 1443 1135dagger

TP COF II-e 1496 (1542) 1399 (1396) 1444 (1377) 1135dagger (1182)

COF-4M III-a 1496 1398 1449 1135dagger

COF-5M III-b 1496 1398 1449 1136dagger

COF-6M III-c 1496 1399 1451 1134dagger

COF-7M III-d 1496 1398 1449 1136dagger

TP COF-1M III-e 1496 1398 1450 1136dagger

COF-8M IV-a 1496 1398 1445 1131dagger

COF-9M IV-b 1495 1398 1444 1131dagger

119

COF-10M IV-c 1495 1391 1418 1126dagger

COF-11M IV-d 1498 1399 1450 1134dagger

TP COF-2M IV-e 1499 1399 1447 1134dagger

B3O3 connectivity dagger C2B2O connectivity

It can be noticed that the bond lengths of experimentally known COF-1 is much larger compared to

our optimized bond lengths as well as that of other synthesized COFs

Figure S2 Calculated C-C bond lengths in connectors and linkers Hydrogen atoms are omitted for clarity

Table S3 The calculated unit cell parameters a interlayer distance d Aring+ and mass density ρ gcm-3

] for serrated (Sa serrated armchair Sz serrated zigzag) and inclined (Ia inclined armchair Iz inclined zigzag) stacked COFs

COF Building

Blocks

a d ρ

Sa Sz Ia Iz Sa Sz Ia Iz

COF-1 I-a 1502 343 343 097 097

COF-1M I-b 2241 341 342 069 069

COF-2M I-c 1492 340 339 097 097

COF-3M I-d 0747 341 342 157 156

PPy-COF I-e 2232 341 341 086 086

120

COF-5 II-a 3014 342 342 341 340 057 057 058 058

COF-10 II-b 3758 341 341 342 340 046 046 046 046

COF-8 II-c 2251 341 341 342 342 073 073 072 072

COF-6 II-d 1505 342 341 340 340 105 106 106 106

TP COF II-e 3750 342 341 342 342 052 052 052 052

COF-4M III-a 2171 344 344 345 344 074 074 074 074

COF-5M III-b 2915 343 342 343 343 056 056 056 056

COF-6M III-c 1833 341 341 342 341 084 084 084 084

COF-7M III-d 1083 344 343 340 344 131 131 132 131

TP COF-1M III-e 2905 343 342 343 342 066 067 066 066

COF-8M IV-a 1748 341 341 342 342 142 142 142 142

COF-9M IV-b 2176 341 341 341 342 119 119 119 119

COF-10M IV-c 2254 340 340 340 340 128 128 128 128

COF-11M IV-d 1512 341 341 340 340 171 171 171 171

TP COF-2M IV-e 2173 340 340 340 340 137 137 137 137

REF-I I 0773 349 345 148 15

REF-III III 1445 348 349 106 106

Table S4 The calculated energies [kJ mol-1

] per bond formed between building blocks for serrated (Sa serrated armchair Sz serrated zigzag) and inclined (Ia inclined armchair Iz inclined zigzag) stacked COFs Ecb ndash condensation energy Esb ndash stacking energy and Efb ndash COF formation energy (Efb = Ecb + Esb) The calculated band gaps ∆ eV+ are given as well

COF Sa Sz Ia Iz

Esb Efb Δ Esb Efb Δ Esb Efb Δ Esb Efb Δ

-1 -2810 -1904 36 -2786 -1880 36

-1M -4426 -3477 30 -4389 -3440 30

-2M -5967 -5011 30 -5833 -4877 30

121

-3M -2667 -1904 40 -2591 -1828 40

PPy- -5916 -5058 26 -5865 -5007 26

-5 -3052 -2841 27 -3051 -2840 26 -3275 -3064 26 -3297 -3086 26

-10 -3868 -3551 26 -3869 -3552 25 -3830 -3513 26 -4293 -3976 25

-8 -4615 -4352 27 -4614 -4351 27 -4571 -4308 27 -4573 -4310 27

-6 -2978 -2793 30 -2978 -2793 30 -3117 -2932 30 -3090 -2905 30

TP -4557 -4326 26 -4562 -4331 26 -4511 -4280 26 -4511 -4280 26

-4M -1811 -1844 28 -1813 -1846 28 -1769 -1802 28 -1880 -1913 28

-5M -2626 -2619 27 -2630 -2623 26 -2597 -2590 26 -2600 -2593 26

-6M -3375 -3361 28 -3381 -3367 28 -3487 -3473 28 -3349 -3335 28

-7M -1724 -1894 32 -1726 -1896 31 -2333 -2503 32 -1866 -2036 31

TP -1M -3327 -3341 26 -3334 -3348 26 -3340 -3354 26 -3353 -3367 26

-8M -2897 -3684 21 -2895 -3682 21 -2971 -3758 21 -2983 -3770 21

-9M -3732 -4568 20 -3733 -4569 20 -3684 -4520 20 -3706 -4542 20

-10M -4512 -5459 21 -4513 -5460 21 -4491 -5438 21 -4495 -5442 21

-11M -2831 -3234 24 -2834 -3237 24 -2816 -3219 24 -2830 -3233 24

TP -2M -4500 -4470 20 -4505 -4475 20 -4495 -4465 20 -4496 -4466 20

122

Appendix E

Stability and electronic properties of 3D covalent organic frameworks



Abstract Covalent Organic Frameworks (COFs) are a class of covalently linked crystalline nanoporous

materials versatile for nanoelectronic and storage applications 3D COFs in particular have very

large pores and low-mass densities Extensive theoretical studies of their energetic and mechanical

stability as well as their electronic properties are discussed in this paper All studied 3D COFs are

energetically stable materials though mechanical stability does not exceed 20 GPa Electronically all

COFs are semiconductors with band gaps depending on the number of sp2 carbon atoms present in

the linkers similar to 3D MOF family

Introduction

Covalent Organic Frameworks (COFs)1-3 comprise an emerging class of crystalline materials that

combines organic functionality with nanoporosity COFs have organic subunits stitched together by

covalent entities including boron carbon nitrogen oxygen or silicon atoms to form periodic

frameworks with the faces and edges of molecular subunits exposed to pores Hence their

applications can range from organic electronics to catalysis to gas storage and sieving4-7 The

properties of COFs extensively depend on their molecular constituents and thus can be tuned by

rational chemical design and synthesis289 Step by step reversible condensation reactions pave the

123

way to accomplish this target Such a reticular approach allows predicting the resulting materials and

leads to long-range ordered crystal structures

Since their first mentioning in the literature13 COFs are under theoretical investigation10-17 mainly for

gas storage applications Methods such as doping18-24 and organic linker functionalization2526 have

been suggested to improve their storage capacities In addition to the moderate pore size and

internal surface area COFs have the privileges of a low-weight material as they are made of light

elements Hence their gravimetric adsorption capacity is remarkably high10 The lowest mass density

ever reported for any crystalline material is that for COF-108 (018 gcm-3) Also their stronger

covalent bonds compared to related Metal-Organic Frameworks (MOFs)27 endorse thermodynamic

strength These genuine qualities of COFs make them attractive for hydrogen storage investigations

Crystallization of linked organic molecules into 2D and 3D forms was achieved in the years 20051 and

20073 respectively by the research group of O M Yaghi Several COFs have been synthesized since

then and some of the 2D COFs has been proven good for electronic or photovoltaic applications428-33

However the growth in this area appears to be slow compared to rapidly developing MOFs albeit

the promising H2 adsorption measurements53435 and a few synthetic improvements736-42

COF-102 and COF-103 were synthesized3 by the self-condensation of the non-planar tetra(4-

dihydroxyborylphenyl)methane (TBPM) and tetra(4-dihydroxyborylphenyl)silane (TBPS) respectively

(see Fig 1 for the building blocks and COF geometries) The co-condensation of these compounds

with triangular hexahydroxytriphenylene (HHTP) results in COF-108 and COF-105 respectively with

different topologies Yaghi et al3 have reported the formation of highly symmetric topologies ctn

(carbon nitride dI 34 ) and bor (boracite mP 34 ) when tetrahedral building blocks are linked

together with triangular ones The topology names were adopted from reticular chemistry structure

resource (RCSR)43 Simulated Powder X-ray diffraction in comparison with experimental powder

spectrum suggested ctn topology for COF-102 103 and 105 and bor topology for COF-108 The

condensation of tert-butylsilanetriol (TBST) and TBPM leads to the formation of COF-20244 This was

reported as ctn topology The COF reactants and schematic diagrams of ctn and bor topologies are

given in Figure1 The assembly of tetrahedral and linear units is very likely to result in a diamond-like

form COF-300 was formed according to the condensation of tetrahedral tetra-(4-anilyl)methane

(TAM) and linear terephthaldehyde (TA)45 However the synthesized structure was 5-fold

interpenetrated dia-c5 topology43

In this work we present theoretical studies of 3D COFs using density functional based methods to

explore their structural electronic energetic and mechanical properties Our previous studies on 2D

COFs4647 had resulted in questioning the stability of eclipsed arrangement of layers (AA stacking) and

124

suggesting energetically more stable serrated and inclined packing In this paper we attempt to

explore the stability and electronic properties of the experimentally known 3D COFs namely COF-

102 103 105 108 202 and 300 In the present studies we follow the reticular assembly of the

molecular units that form low-weight 3D COFs Considering the structural distinction from MOFs

COFs lack the versatility of metal ingredients what results in diverse properties48 A collective study is

then carried out to understand the characteristics and drawbacks of COFs

Figure 1 (Upper panel) Building blocks for the construction of 3D COFs (Lower panel) lsquoctnrsquo and lsquoborrsquo

networks formed by linking tetrahedral and triangular building units

Methods

COF structures were fully optimized using Self-consistent Charge -Density Functional based Tight-

Binding (SCC-DFTB) level of theory4950 Two computational codes were used deMonNano51 and

125

DFTB+52 The first code which has dispersion correction53 implemented to account for weak

interactions was used for the geometry optimization and stability calculations The second code

which can perform calculations using k-point sampling was used to calculate the electronic

properties (band structure and density of states) The number of k-points has been determined by

reaching convergence for the total energy as a function of k-points according to the scheme

proposed by Monkhorst and Pack54 Periodic boundary conditions were used to represent

frameworks of the crystalline solid state Conjugatendashgradient scheme was chosen for the geometry

optimization Atomic force tolerance of 3 times 10minus4 eVAring was applied The optimization using Γ-point

approximation was performed on rectangular supercells containing more than 1000 atoms For

validation of our method we have calculated energetic stability using Density Functional Theory (DFT)

at the PBE55DZP56 level as implemented in ADF code5758 using cluster models The cluster models

contain finite number of building units and correspond to the bulk topology of the COFs XRD

patterns have been simulated using Mercury software5960

In this work we continued to use the traditional nomenclature of the experimentally known COFs All

of the structures have the same tetrahedral blocks and differ only in the central sp3 atom (carbon or

silicon) that is included in our nomenclature

Bulk modulus (B) of a solid at absolute zero can be calculated as

(1) B = 2

2

dV

EdV

where V and E are the volume and energy respectively

Owing to the dehydration reactions we have calculated the formation (condensation) energy of each

COF formed from monomers (building blocks) as follows

(2) EF = Etot + n EH2Otot ndash (m1 Ebb1

tot + m2 Ebb2tot)

where Etot -- total energy of the COF EH2Otot -- total energy of water molecule Ebb1

tot and Ebb2tot -- total

energies of interacting building blocks n m1 m2 -- stoichiometry numbers

Results and Discussions

Structure and Stability

We have optimized the atomic positions and cell dimensions of the COFs in the experimentally

determined topologies Cell parameters in comparison with experimental values are given in Table 1

The calculated bond lengths are C-B = 150 C-C = 139-144 (COF-300) C(sp3)-C = 156 C-O = 142 B-

126

O = 140 Si-C = 188 Si-O = 186 C-N = 131-136 Aring These values agree within 6 error with the

experimental values34445

Mass densities (see Table 1) of COFs range between 02 to 05 g cm-3 and are smaller for the silicon at

the tetrahedral centers This implies that the presence of silicon atoms impacts more on the cell

volume than on the total mass That means the replacement of sp3 C with Si in COF-108 can change

its mass density to a slightly lower value To our best knowledge among all the natural or

synthesized crystals COF-108 has the lowest mass-weight

In order to validate our optimized structures we have simulated X-ray Diffraction of each COF and

compared them with the available experimental spectra (see Figure2) Almost all of the simulated

XRDs have excellent correlation in the peak positions with the experiment Only COF-300 shows

somehow significant differences in the intensities These differences may be attributed to the

presence of guest molecules in the synthesized COF-30045

Table 1 The calculated cell parameters [Aring] mass density ρ gcm-3

+ band gap Δ eV+ bulk modulus B GPa+

and formation energy EF [kJ mol-1

] for all the studied 3D COFs Experimental values are given in brackets

along with the cell parameters HOMO-LUMO gaps [eV] of the building blocks are also given in brackets

along with the band gaps

Structure Building

Blocks

Cell

parameters

ρ Δ B EF

COF-102 (C) TBPM 2707 (2717) 043 39 (43) 206 -14995

COF-103 (Si) TBPS 2817 (2825) 039 38 (41) 139 -14547

COF-105-C TBPM HHTP 4337 019 33 (43 34) 80 -18080

COF-105 (Si) TBPS HHTP 4444 (4489) 018 32 (41 34) 79 -17055

COF-108 (C) TBPM HHTP 2838 (2840) 017 32 (43 34) 37 -17983

COF-108-Si TBPS HHTP 2920 016 30 (41 34) 29 -18038

COF-202 (C) TBPM TBST 3047 (3010) 050 42 (43 139) 143 -7954

COF-202-Si TBPS TBST 3157 046 39 (41 139) 153 -7632

COF-300 (C) TAM TA 2932 925 049 23 (41 26) 144 -40286

127

(2828 1008)

COF-300-Si TAS TA 3039 959 044 23 (40 26) 133 -39930

tetra-(4-anilyl)silane

Figure 2 Simulated XRDs are compared with the experimental patterns from the literature COF-300

exhibits some differences between the simulated and experimental XRDs while others show reasonably

good match

The bulk modulus (B) is a measure of mechanical stability of the materials The calculated values of B

are given in Table 1 Compared to the force-field based calculation of bulk modulus by Schmid et

al61 these values are larger The bulk modulus of COF-105 and COF-108 are relatively small

compared with other COFs Considering that the two COFs differ only in the topology it may be

concluded that ctn nets are mechanically more stable compared to bor COFs with carbon atoms in

the center are mechanically more stable than those with silicon atoms Bulk modulus of COF-102

103 COF-202 and interpenetrated COF-300 are higher than many of the isoreticular MOFs62 and

comparable to IRMOF-6 (1241 GPa) MOF-5 (1537 GPa)63 bNon-interpenetrated COF-300 (single

framework dia-a topology43) has much lower bulk modulus of only 317 GPa

Calculated formation energies (Table 1) are given in terms of reaction energies according to Eq 2

Condensation of monomers to form bulk 3D structures is exothermic in all the cases supporting

reticular approach The presence of C or Si at the vertex center does not show any particular trend in

the formation energies We have calculated the formation energy of non-interpenetrated COF-300

(dia-a) to be -39346 kJ mol-1 which is comparable to the interpenetrated cases For a quantitative

comparison we have performed DFT calculations at the PBEDZP level as implemented in ADF code

on finite structures The obtained formation energies for COF-105-C COF-105 (Si) COF-108 (C) COF-

108-Si are -9944 -9968 -1245 -12436 respectively They are in a reasonable agreement with the

128

DFTB results A comparison between COF-105 and COF-108 suggests that bor nets are energetically

more favored than ctn nets

Electronic Properties

Band gaps (Δ) calculated for the 3D COFs are in the range of 23-42 eV (see Table 1) which show

their semiconducting nature similar to the hexagonal 2D COFs47 and MOFs62 The band gap

decreases with the increase of conjugated rings in the unit cell relative to the number of other atoms

Si atoms in comparison with carbon atoms at the tetrahedral centers give a relatively smaller Δ This

is evident from the partial density of states of C (sp3) in COF-102 and Si in COF-103 plotted in Figure3

Carbon atoms define the band edges of the PDOS (see Figure4) The band gaps of COF-105 and COF-

108 differ only slightly (see Figure5) which means that the band gap is nearly independent of the

topology This is because for each atom the coordination number and the neighboring atoms remain

the same in both ctn and bor networks albeit the topology difference DOS of non-interpenetrated

(dia-a) and 5-fold interpenetrated (dia-c5) COF-300 are plotted in Figure6 It may be concluded from

their negligible differences that interpenetration does not alter the DOS of a framework We have

shown similar results for 2D COFs47

Figure 3 Partial density of states (DOS) of sp3 C in COF-102 (top) and Si in COF-103 (bottom) The latter is

inverted for comparison The Fermi level EF is shifted to zero

129

Figure 4 Partial and total density of states of COF-103 The Fermi level EF is shifted to zero

Figure 5 Density of states of COF-108 (bor) and COF-105 (ctn) The two COFs differ only in the topology

130

Figure 6 Density of states of non-interpenetrated (dia-c1) and 5-interpenetrated (dia-c5) COF-300

We also have calculated HOMO-LUMO gaps of the molecular building blocks (see Table 1) In

comparison band gaps of COFs are slightly smaller than the smallest of the HOMO-LUMO gaps of the

building units

Conclusion

In summary we have calculated energetic mechanical and electronic properties of all the known 3D

COF using Density Functional Tight-Binding method Energetically formation of 3D COFs is favorable

supporting the reticular chemistry approach Mechanical stability is in line with other frameworks

materials eg MOFs and bulk modulus does not exceed 20 GPa Also all COFs are semiconducting

with band gaps ranging from 2 to 4 eV Band gaps are analogues to the HOMO-LUMO gaps of the

molecular building units We believe that this extensive study will define the place of COFs in the

broad area of nanoporous materials and the information obtained from the work will help to

strategically develop or modify porous materials for the targeted applications

131

Appendix F

Structure electronic structure and hydrogen adsorption capacity of porous aromatic frameworks

Binit Lukose Mohammad Wahiduzzaman Agnieszka Kuc and Thomas Heine


Abstract

Diamond-like porous aromatic frameworks (PAFs) form a new family of materials that contain only

carbon and hydrogen atoms within their frameworks These structures have very low mass densities

large surface area and high porosity Density-functional based calculations indicate that crystalline

PAFs have mechanical stability and properties similar to those of Covalent Organic Frameworks Their

exceptional structural properties and stability make PAFs interesting materials for hydrogen storage

Our theoretical investigations show exceptionally high hydrogen uptake at room temperature that

can reach 7 wt a value exceeding those of well-known metal- and covalent-organic frameworks

(MOFs and COFs)

Introduction

Porous materials have been widely investigated in the fields of materials science and technology due

to their applications in many important fields such as catalysis gas storage and separation template

materials molecular sensors etc1-3 Designing porous materials is nowadays a simple and effective

strategy following the approach of reticular chemistry4 where predefined building blocks are used to

132

predict and synthesize a topological organization in an extended crystal structure The most famous

and striking examples of such materials are Metal- and Covalent-Organic Frameworks (MOFs and

COFs)56 These new nanoporous materials have many advantages high porosity and large surface

areas lowest mass densities known for crystalline materials easy functionalization of building blocks

and good adsorption properties

Gas storage and separation by physical adsorption are very important applications of such

nanoporous materials and have been major subjects of science in the last two decades These

applications are based on certain physical properties namely presence of permanent large surface

area and suitable enthalpy of adsorption between the host framework and guest molecules

Attempts to produce materials with large internal surface area have been successful and some of the

notable accomplishments include the synthesis of MOF-2107 (BET surface area of 6240 m2 g-1 and

Langmuir surface area of 10400 m2 g-1) NU-1008 (BET surface area 6143 m2 g-1) or 3D COFs9 (BET

surface area 4210 m2 g-1 for COF-103)

More recently a new family of porous materials emerged So-called porous-aromatic frameworks

(PAFs) have surface areas comparable to MOFs eg PAF-110 has a BET surface area of 5640 m2 g-1 and

Langmuir surface area of 7100 m2 g-1 Since they are composed of carbon and hydrogen only they

have several advantages over frameworks containing heavy elements MOFs with coordination bonds

often suffer from low thermal and hydrothermal stability what might limit their applications on the

industrial scale The coordination bonds can be substituted with stronger covalent bonds as it was

realized in the case of COFs6 however this lowers significantly their surface areas comparing with

MOFs

Besides its exceptional surface area PAF-110 has high thermal and hydrothermal stability and

appears to be a good candidate for hydrogen and carbon dioxide storage applications PAFs have

topology of diamond with C-C bonds replaced by a number of phenyl rings (see Figure 1)

Experimentally obtained PAF-110 and PAF-1111 have eg one and four phenyl rings respectively

connected by tetragonal centers (carbon tetrahedral nodes) The simulated and experimental

hydrogen uptake capacities of such PAFs exceed the DOE target12

In this paper we have studied structural electronic and adsorption properties of PAFs using Density

Functional based Tight-Binding (DFTB) method1314 and Quantized Liquid Density Functional Theory

(QLDFT)15 We have found exceptionally high storage capacities at room temperature what makes

PAFs very good materials for hydrogen storage devices beyond well-known MOFs and COFs We have

compared our results to widely-used classical Grand Canonical Monte-Carlo (GCMC) calculations

reported in the literature We have also studied other properties of these materials such as

133

structural energetic electronic and mechanical We explored the structural variance of diamond

topology by individually placing a selection of organic linkers between carbon nodes This generally

changes surface area mass density and isosteric heat of adsorption what is reflected in the

adsorption isotherms

Methods

Using a conjugate-gradient method we have fully optimized the crystal structures (atomic positions

and unit cell parameters) of PAFs The calculations were performed using Dispersion-corrected Self-

consistent Charge density-functional based tight-binding (DFTB) method as implemented in the

deMonNano code1617 Periodic boundary conditions were applied to a (3x3x3) supercell thus

representing frameworks of the crystalline solid state Electronic density of states (DOS) have been

calculated using the DFTB+ code18 with k-point sampling where the k space was determined by


Pack19

Hydrogen adsorption calculations have been carried out using QLDFT within the LIE-0 approximation

thus including many-body interparticle interactions and quantum effects implicitly through the

excess functional The PAF-H2 non-bonded interactions were represented by the classical Morse

atomic-pair potential Force field parameters were taken from Han et al20 who originally developed

them for studying hydrogen adsorption in COFs that incorporate similar building blocks as PAFs The

authors adopted the approach to the shapeless particle approximation of QLDFT These PAF-H2

parameters have been determined by fitting first-principles calculations at the second-order Moslashllerndash

Plesset (MP2) level of theory using the quadruple-ζ QZVPP basis set with correction for the basis set

superposition error (BSSE) QLDFT calculations use a grid spacing of 05 Bohr radii and a potential

cutoff of 5000 K


Design and Structure of PAFs

We have designed a set of PAFs by replacing C-C bonds in the diamond lattice by a set of organic

linkers phenyl biphenyl pyrene para-terphenyl perylenetetracarboxylic acid (PTCDA)

diphenylacetylene (DPA) and quaterphenyl (see Figure 1) We label the respective crystal structures

as PAF-phnl (PAF-301 in Ref 12) PAF-biph (PAF-302 in Ref 12) PAF-pyrn PAF-ptph(PAF-303 in Ref

12) PAF-PTCDA PAF-DPA and PAF-qtph (PAF-304 in Ref 12) respectively Such a design of

frameworks should result in materials with high stability due to the parent diamond-topology and

pure covalent bonding of the network The selected linkers differ in their length width and the

134

number of aromatic rings These should play an important role for hydrogen adsorption properties

aromatic systems exhibit large polarizabilities and interact with H2 molecules via London dispersion

forces Long linkers introduce high pore volume and low mas-weight to the network while wide

linkers offer large internal surface area and high heat of adsorption Hence long linkers are of

advantage for high gravimetric capacity while wide linkers enhance volumetric capacity Proper

optimization of the linker size should result in a perfect candidate for hydrogen storage applications

Figure 1 a) Schematic diagram of the topology of PAFs blue spheres and grey pillars represent carbon

tetragonal centers and organic linkers respectively b) Linkers used for the design of PAFs i) phenyl ii)

biphenyl iii) pyrene iv) DPA v) para-Terphenyl vi) PTCDA and vii) quaterphenyl

Selected structural and mechanical properties of the investigated PAF structures are given in Table 1

Frameworks created with the above mentioned linkers have mass densities that range from 085 g

cm-3 (for phenyl) to 01 g cm-3 (for quaterphenyl) The lowest mass-density obtained for a crystal

structure was for COF-108 with = 0171 g cm-39 Our results show that PAF-DPA and PAF-ptph have

mass densities close to the one of COF-108 while PAF-qtph with = 01 g cm-3 exhibits the lowest

for all the PAFs investigated in this study

While the large cell size and the small mass density of PAF-qtph are an advantage for high

gravimetric hydrogen storage capacity other PAFs (eg PAF-pyrn with wide linker) would

compromise gravimetric for high volumetric capacity As both of them are important for practical

applications a balance between them is crucial

Table 1 Calculated cell parameters a (a=b=c α=β=γ=60⁰) mass densities () formation energies (EForm) band

gaps () bulk moduli (B) and H2 accessible free volume and surface area of PAFs studied in the present work

In parenthesis are given HOMU-LUMO gaps of the corresponding saturated linkers

PAFs

a

(Aring)

ρ

(g cm-3)

EForm

(kJ mol-1)

Δ

(eV)

B

(GPa)

H2 accessible

free volume

H2 accessible

surface area

135

() (m2 g-1)

PAF-phnl 97 085 -121 47 (55) 360 35 2398

PAF-biphl 167 032 -122 36 (40) 132 73 5697

PAF-pyrn 166 042 -124 26 (28) 192 66 5090

PAF-DPA 210 019 -122 35 (37) 87 84 7240

PAF-ptph 237 016 -119 32 (33) 56 86 6735

PAF-PTCDA 236 024 -122 18 (19) 95 81 5576

PAF-qtphl 308 010 -119 29 (30) 35 91 7275

Energetic and Mechanical Properties

We have investigated energetic stability of PAFs by calculating their formation energies We regarded

the formation of PAFs as dehydrogenation reaction between saturated linkers and CH4 molecules

For a unit cell containing n carbon nodes and m organic linkers the formation energy (EForm) is given

by

( )

where Ecell EL and

are the total energies of the unit cell saturated linkers CH4 and H2

molecules respectively This excludes the inherent stability of linkers and represents the energy for

coordinating linkers with sp3 carbon atoms during diamond-topology formation All the formation

energies calculated in the present work are given in Table 1 Negative values indicate that the

formation of PAFs is exothermic The values per formula unit do not deviate significantly for different

PAF sizes and shapes

Although diamond is the hardest known material insertion of longer linkers diminishes its

mechanical strength to some extent In order to study the mechanical stability of PAFs we have

calculated their bulk moduli which is the second derivative of the cell energy with respect to the cell

volume (see Table 1) The highest value that we have obtained is for PAF-phnl with B = 36 GPa This is

over ten times smaller than the bulk modulus of pure diamond 514 GPa (calculated at the DFTB

level)21 and 442 GPa (experimental value)22 Bulk modulus should scale as 1V (V - volume) if all

bonds have the same strength We have plotted such a function for PAFs and other framework

136

materials23 in Figure 2 As PAFs have various types of CmdashC bonds there are minor deviations from

the perfect trend

Figure 2 Calculated bulk modulus B as function of the volume per atom PAFs are highlighted in blue and

compared with other framework materials Red curve denotes the fitting to 1V function (V - volume)

The stability of PAF-phnl is similar to that of Cu-BTC MOF and much higher than for other MOFs such

as MOF-5 -177 and -20524 and 3D COFs23 Subsequent addition of phenyl rings decreases B the

lowest value of 35 GPa has been found for PAF-qtph which is in the same order as for COF-108 In

general all the studied PAFs except for PAF-phnl have bulk moduli in line with 3D COFs25 When the

organic linker is extended in the width (cf PAF-biph and PAF-pyrn) the mechanical stability increases


All PAF structures are semiconductors similar to COFs The band gaps of PAFs range from 18 to 47

eV (see Table 1) Interesting trends may be observed from the band gaps of this iso-reticular series

In comparison with diamond which has a band gap of 55 eV it may be understood that subsequent

insertion of benzene groups between carbon atoms in diamond decreases the band gap This is easily

understood as the sp3 responsible for the semiconducting character become far apart with large

number of π-electrons in between which tend to close the gap More importantly the values of

band gaps are directly related to the HOMO-LUMO gaps of the corresponding saturated linkers

which are just slightly larger Also more extended linkers (cf PAF-biph and PAF-pyrn or PAF-ptph and

PAF-PTCDA) reduce the band gap

In general conjugated rings reduce the band gap more effectively than CmdashC bond networks (cf PAF-

DPA PAF-ptph or PAF-qtphl) The extreme cases for this behaviour are graphene which is metallic

137

and diamond which is an insulator Overall the band gap may be tuned by placing suitable linkers in

the diamond network Similar results have been reported for MOFs2627

We have calculated the electronic density of states (DOS) for all the PAF structures Figure 3 a shows

carbon DOS of PAFs arranged in such a way that the band gaps decrease going from the top to the

bottom of the figure PAFs with larger band gaps have larger population of energy states at the top of

valence band and bottom of conduction band whereas for linkers with smaller band gaps the

distribution of energy states is rather spread In order to study the impact of sp3 carbon atoms in the

DOS we plotted their contributions against the total carbon DOS in the cases of PAF-phnl and PAF-

pyrn as examples (see Figure 3 b and c) In both cases the sp3 carbons exhibit no energy states in the

band gap and in the close vicinity of band edges

Figure 3 (a) Carbon density of states of all calculated PAFs From top to bottom the value of band gap

decreases (b) and (c) projected DOS on sp3 C atoms of PAF-phnl and PAF-pyrn respectively The vertical

dashed line indicates Fermi level EF

Hydrogen Adsorption Properties

One of the potential applications of PAFs is hydrogen adsorption We have calculated the gravimetric

and volumetric capacities and analyzed them to understand the contributions of the linkers on the

138

hydrogen uptake in different range of temperatures and pressures H2 accessible free volume and

surface area of the PAFs are given in Table 1 In order to assess the excess adsorption capacity the

free pore volume is necessary In our simulation the free pore volume is defined to be that where

the H2-host interaction energy is less than 5000K This covers all sites where H2 is attracted by the

host structure and excludes the repulsion area close to the framework The solvent accessible surface

areas of the PAFs were determined by rolling a probe molecule along the van der Waals spheres of

the atoms A probe molecule of radius 148 Aring was used which is consistent with the Lennard-Jones

sphere of hydrogen and commonly used in various H2 molecular simulations28

Very large surface areas per mass unit have been observed for all PAFs except for PAF-phnl PAF-DPA

and PAF-qtph for example have 7240 and 7274 m2 g-1 H2 accessible surface area respectively For

comparison highly porous MOF-210 and NU-100 give values of 6240 and 6143 m2 g-1 BET surface

areas respectively determined from the experimental adsorption isotherms78 It is worth

mentioning that longer linkers expand the pore and increase the surface area per unit volume and

unit mass Wider linkers provide a higher surface area per unit volume however they possess larger

mass density and hence the surface area per unit mass gets lower

Figure 4 shows the gravimetric and volumetric total and excess adsorption isotherms of PAFs at 77K

The results show that the gravimetric (total and excess) H2 uptake is dependent on the linker length

The longest linker in the PAF-qtph structure gives the total and excess gravimetric capacity of 32 and

128 wt respectively which is larger than for highly porous crystalline 3D COFs29 These numbers

are calculated for the limit pressure of 100 bar For the shortest linker in PAF-phnl we have obtained

only around 25 wt for the same pressure Using grand canonical Monte-Carlo methods (GCMC)

Lan et al12 have predicted total and excess adsorption capacities of PAF-qtph of 224 and 84 wt

respectively The deviations in results are attributed to the differences in both methods where

different force fields are used to describe atom-atom interactions

The volumetric adsorption capacities lower with the size of the linker and the largest uptake we have

found for the PAF-pyrn (46 and 35 kg m-3 total and excess respectively) while very low values were

found for PAF-qtph (30 and 145 kg m-3 total and excess respectively) at 35-bar pressure It could be

predicted that for PAF-phnl the volumetric adsorption reaches the larges values however due to its

very compact crystal structure it reaches saturation at the low-pressure region and does not exceed

30 kg m-3 for the total uptake From the excess adsorption isotherms however PAF-phnl is the best

adsorbing system for low-pressure application as it gets saturated at 11 bar by adsorbing 266 kg m-3

of H2 Generally we have observed that PAFs with lower pore sizes exhibited saturation of volumetric

capacities at lower pressures

139

Figure 4 Calculated H2 uptake of PAFs at 77 K (a)-(b) gravimetric and (c)-(d) volumetric total (upper panel)

and excess (lower panel) respectively

We have also calculated the adsorption performance of PAFs at room temperature The gravimetric

total adsorption isotherms are shown in Figure 5 Similar to the results obtained for T=77 K PAF-

qtph exhibits the highest total gravimetric capacity at room temperature which is as high as 732 wt

at 100 bar Lan et al12 have predicted the uptake of 653 wt at 100 bar using GCMC simulations

These results exceed the 2015 DOE target of 55 wt 3031 On the other hand at more applicable

pressure of 5 bar the uptake reaches only 05 wt This suggests however that the delivery amount

(approximately the difference between the uptakes at 100 and 5 bar) is still more than the DOE

target Phenyl linker at room temperature does not exceed the gravimetric uptake of 1 wt at 100

bar

Figure 5 Calculated gravimetric total (left) and excess (right) H2 uptake of PAFs at 300 K

140

At 300K excess gravimetric capacity is rather low and does not exceed 075 wt even for large

pressure (see Figure 5)

Effects of interpenetration

Very often frameworks with large pores crystallize as interpenetrated lattices In most cases this is

an undesired fact due to reduction of the pore size and free volume For instance COF-300 which

has diamond topology was found to have 5-interpenetrated frameworks32

We have studied the effect of interpenetration in the case of PAF-qtph which has the largest pore

volume among the materials in this study Without any steric hindrance PAF-qtph may be

interpenetrated up to the order of four The two three and four interpenetrated networks are

named as PAF-qtph-2 PAF-qtph-3 and PAF-qtph-4 respectively and in each case the interpenetrated

structures possess translational symmetry Table 2 shows calculated mass densities and H2 accessible

free volume and surface area of non-interpenetrated and n-fold penetrated PAF-qtph Obviously the

mass density increases by one unit for each degree of interpenetration PAF-qtph has 91 of its

volume accessible for H2 which means that 9 of volume is occupied by the skeleton of the PAF

Hence each degree of interpenetration decreases the free volume by 9 H2 accessible surface area

per unit mass remains the same up to 3-fold interpenetration However PAF-qtph-4 results in much

less accessibility for H2

Table 2 Calculated mass densities () and H2 accessible free volume and surface area of non-interpenetrated

and n-fold interpenetrated PAF-qtph where n = 2 3 4

PAF

(g cm-3)

H2 accessible

free volume ()

H2 accessible

surface area

(m2 g-1)

PAF-qtph 010 91 7275

PAF-qtph-2 020 82 7275

PAF-qtph-3 030 73 7275

PAF-qtph-4 040 64 5998

Figure 6 shows the excess and total adsorption isotherms (gravimetric and volumetric) of non-

interpenetrated and interpenetrated PAF-qtph at 77 K With the increasing degree of

141

interpenetration saturation occurs at lower values of pressure This is due to the smaller pore size

resulted from the high-fold interpenetration The excess gravimetric capacity decreases by 18 - 2 wt

per each n-fold interpenetration a result of the decreasing free space around the skeleton It is to be

noted that the difference between the total and the excess adsorption capacities of PAF-qtph is quite

large however it decreases less for interpenetrated structures This is because the interpenetrated

frameworks occupy the free space that otherwise would be taken by hydrogen to increase the total

capacity but not the excess

Figure 6 Calculated H2 uptake at 77 K of non-interpenetrated and n-fold interpenetrated PAF-qtph with n = 2

3 4 (a)-(b) gravimetric and (c)-(d) volumetric total (lower panel) and excess (upper panel) respectively

On the other hand the interpenetrated frameworks have larger volumetric capacity what is easily

understandable due to the volume reduction Significant increase in excess volumetric capacity has

been obtained for PAF-qtph-2 in comparison with PAF-qtph whereas only slightly lower increase was

obtained for PAF-qtph-3 in comparison with PAF-qtph-2 (see Figure 6) PAF-qtph-4 exhibited even

lower increase compared to PAF-qtph-3 suggesting that only a certain degree of interpenetration is

appreciable Although non-interpenetrated PAF has a large amount of H2 gas in the bulk phase due

to the high pore volume its total volumetric uptake does not exceed that of the interpenetrated

PAFs

Almost linear gravimetric isotherms were obtained at room temperature for all studied PAFs

including the interpenetrated cases (see Figure 7) Large decrease of gravimetric capacity was noted

142

when the PAF was interpenetrated from around 7 wt down to 2 wt for 4-fold interpenetrated

PAF-qtph The excess gravimetric capacity however is the same independent of the n-fold

interpenetration and maximum of 06 wt was found for 100-bar pressure (see Figure 7)

Figure 7 Calculated gravimetric total (left) and excess (right) H2 uptake of non-interpenetrated and n-fold

interpenetrated PAF-qtph (n = 2 3 4) at 300 K

Conclusions

Following diamond-topology we have designed a set of porous aromatic frameworks PAFs by

replacing CmdashC bonds by various organic linkers what resulted in remarkably high surface area and

pore volume

Exothermic formation energies of PAFs calculated from the dehydrogenation of the linkers with CH4

indicate strong coordination of linkers in the diamond topology The studied PAFs exhibit bulk moduli

that are much smaller than diamond however in the same order as other porous frameworks such

as MOFs and COFs PAFs are semi-conductors with their band gaps dependent on the HOMO-LUMO

gaps of the linking molecules

Using quantized liquid density functional theory which takes into account inter-particle interactions

and quantum effects we have predicted hydrogen uptake capacities in PAFs At room temperature

and 100 bar the predicted uptake in PAF-qtph was 732 wt which exceeded the 2015 DOE target

At the same conditions other PAFs showed significantly lower uptakes At 77 K the PAFs with similar

pore sizes exhibited similar gravimetric uptake capacities whereas smaller pore size and larger

number of aromatic rings result in higher volumetric capacities In smaller pores saturation of excess

capacities occurred at lower pressures Interpenetrated frameworks largely decrease the amount of

hydrogen gas in the pores and increase the weight of the material however they are predicted to

have high volumetric capacities

143

References

(1) Eddaoudi M Moler D B Li H L Chen B L Reineke T M OKeeffe M Yaghi O M

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(3) Ferey G Mellot-Draznieks C Serre C Millange F Accounts of Chemical Research 2005 38

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(4) Yaghi O M OKeeffe M Ockwig N W Chae H K Eddaoudi M Kim J Nature 2003 423

705

(5) Eddaoudi M Kim J Rosi N Vodak D Wachter J OKeeffe M Yaghi O M Science 2002

295 469

(6) Cote A P Benin A I Ockwig N W OKeeffe M Matzger A J Yaghi O M Science 2005

310 1166

(7) Furukawa H Ko N Go Y B Aratani N Choi S B Choi E Yazaydin A O Snurr R Q

OKeeffe M Kim J Yaghi O M Science 2010 329 424

(8) Farha O K Yazaydin A O Eryazici I Malliakas C D Hauser B G Kanatzidis M G

Nguyen S T Snurr R Q Hupp J T Nature Chemistry 2010 2 944

(9) El-Kaderi H M Hunt J R Mendoza-Cortes J L Cote A P Taylor R E OKeeffe M Yaghi

O M Science 2007 316 268

(10) Ben T Ren H Ma S Cao D Lan J Jing X Wang W Xu J Deng F Simmons J M Qiu

S Zhu G Angewandte Chemie-International Edition 2009 48 9457

(11) Yuan Y Sun F Ren H Jing X Wang W Ma H Zhao H Zhu G Journal of Materials

Chemistry 2011 21 13498

(12) Lan J Cao D Wang W Ben T Zhu G Journal of Physical Chemistry Letters 2010 1 978


2009 20 1193

(14) Seifert G Porezag D Frauenheim T International Journal of Quantum Chemistry 1996 58

185


(16) Heine T Rapacioli M Patchkovskii S Frenzel J Koester A M Calaminici P Escalante S

Duarte H A Flores R Geudtner G Goursot A Reveles J U Vela A Salahub D R deMon-nano edn ed

deMon 2009

(17) Zhechkov L Heine T Patchkovskii S Seifert G Duarte H A Journal of Chemical Theory

and Computation 2005 1 841

(18) BCCMS Bremen DFTB+ - Density Functional based Tight binding (and more)


(20) Han S S Furukawa H Yaghi O M Goddard III W A Journal of the American Chemical

Society 2008 130 11580

(21) Kuc A Seifert G Physical Review B 2006 74

(22) Cohen M L Physical Review B 1985 32 7988

(23) Lukose B Kuc A Heine T manuscript in preparation 2012

(24) Lukose B Supronowicz B Petkov P S Frenzel J Kuc A Seifert G Vayssilov G N

Heine T physica status solidi (b) 2011


(26) Gascon J Hernandez-Alonso M D Almeida A R van Klink G P M Kapteijn F Mul G

Chemsuschem 2008 1 981

(27) Kuc A Enyashin A Seifert G Journal of Physical Chemistry B 2007 111 8179

(28) Dueren T Millange F Ferey G Walton K S Snurr R Q Journal of Physical Chemistry C

2007 111 15350

(29) Furukawa H Yaghi O M Journal of the American Chemical Society 2009 131 8875

144

(30) US DOE Office of Energy Efficiency and Renewable Energy and The FreedomCAR and

Fuel Partnership 2009

httpwww1eereenergygovhydrogenandfuelcellsstoragepdfstargets_onboard_hydro_storage_explanatio

npdf

(31) US DOE USCAR Shell BP ConocoPhillips Chevron Exxon-Mobil T F a F P Multi-Year

Research Development and Demonstration Plan 2009

httpwww1eereenergygovhydrogenandfuelcellsmypppdfsstoragepdf

(32) Uribe-Romo F J Hunt J R Furukawa H Klock C OKeeffe M Yaghi O M Journal of the


145

Appendix G

A novel series of isoreticular metal organic frameworks realizing metastable structures by liquid phase epitaxy

Jinxuan Liu Binit Lukose Osama Shekhah Hasan Kemal Arslan Peter Weidler Hartmut


Bogdan Magdau Thomas Heine and Christof Woumlll


Highly crystalline molecular scaffolds with nm-sized pores offer an attractive basis for the fabrication

of novel materials The scaffolds alone already exhibit attractive properties eg the safe storage of

small molecules like H2 CO2 and CH41-4 In addition to the simple release of stored particles changes

in the optical and electronic properties of these nanomaterials upon loading their porous systems

with guest molecules offer interesting applications eg for sensors5 or electrochemistry6 For the

construction of new nanomaterials the voids within the framework of nanostructures may be loaded

with nm-sized objects such as inorganic clusters larger molecules and even small proteins a

process that holds great potential as for example in drug release7-8 or the design of novel battery

materials9 Furthermore meta-crystals may be prepared by loading metal nanoparticles into the

pores of a three-dimensional scaffold to provide materials with a number of attractive applications

ranging from plasmonics10-12 to fundamental investigations of the electronic structure and transport

properties of the meta-crystals13

146

In the last two decades numerous studies have shown that MOFs also termed porous coordination

polymers (PCPs) fulfill many of the aforementioned criteria Although originally developed for the

storage of hydrogen eg in tanks of automobiles MOFs have recently found more technologically

advanced applications as sensors5 matrices for drug release7-8 and as membranes for enantiomer

separation14 and for proton conductance in fuel cells15 Although pore-sizes available within MOFs1

are already sufficiently large to host metal-nanoclusters such as Au5516-17 the actual realization of

meta-crystals requires in addition to structural requirements a strategy for the controlled loading

of the nanoparticles (NPs) into the molecular framework Simply adding NPs to the solutions before

starting the solvothermal synthesis of MOFs has been reported18 but this procedure does not allow

for controlled loading The layer-by-layer growing process of SUFMOFs allows the uptake of

nanosized objects during synthesis including the fabrication of compositional gradients of different

NPs Those guest NPs can range from pure metal metal oxide or covalent clusters over one-

dimensional objects such as nanowires carbon or inorganic nanotubes to biological molecules such

as drugs or even small proteins If the loading happens during synthesis alternating layers of

different NPs can be realized

The introduction of procedures for epitaxial growth of MOFs on functionalized substrates19 was a

major step towards controlled functionalization of frameworks Epitaxial synthesis allowed the

preparation of compositional gradients20-21 and provided a new strategy to load nano-objects into

predefined pores

Unfortunately the LPE process has so far been only demonstrated for a fairly small number of

MOFs141922-23 none of which exhibits the required pore sizes In addition for the fabrication of meta-

crystals the architecture of the network should be sufficiently adjustable to realize pores of different

sizes There should also be a straightforward way to functionalize the framework itself in order to

tailor the interaction of the walls with the targeted guest objects Ideally such a strategy would be

based on an isoreticular series of MOFs in which the pore size can be determined by a choice from a

homologous series of ligands with different lengths1

Here we present a novel isoreticular MOF series with the required flexibility as regards pore-sizes

and functionalization which is well suited for the LPE process This class denoted as SURMOF-2 is

derived from MOF-2 one of the simplest framework architectures24-25 MOF-2 is based on paddle-

wheel (pw) units formed by attaching 4 dicarboxylate groups to Cu++ or Zn++-dimers yielding planar

sheets with 4-fold symmetry (see Fig 1) These planes are held together by strong

carboxylatemetal- bonds26 Conventional solvothermal synthesis yields stacks of pw-planes shifted

relative to each other with a corresponding reduction in symmetry to yield a P2 or C2 symmetry2427-

28

147

The relative shifts between the pw-planes can be avoided when using the recently developed liquid

phase epitaxy (LPE) method22 As demonstrated by the XRD-data shown in Fig 2 for a number of

different dicarboxylic acid ligands the LPE-process yields surface attached metal organic frameworks

(SURMOFs) with P4 symmetry29 except for the 26-NDC ligand which exhibits a P2 symmetry as a

result of the non-linearity of the carboxyl functional groups on the ligand The ligand PPDC

pentaphenyldicarboxylic acid with a length of 25 nm is to our knowledge the longest ligand which

has so far been used successfully for a MOF synthesis303030 A detailed analysis of the diffraction data

allowed us to propose the structures shown in Fig 1 This novel isoreticular series of MOFs hereafter

termed SURMOF-2 also consists of pw-planes which ndash in contrast to MOF-2 ndash are stacked directly

on-top of each other This absence of a lateral shift when stacking the pw-planes yields 1d-pores of

quadratic cross section with a diagonal up to 4 nm (see Fig 2) Importantly for the SURMOF-2 series

interpenetration is absent For many known isoreticular MOF series the formation of larger and

larger pores is limited by this phenomenon if the pores become too large a second or even a third

3d-lattice will be formed inside the first lattice yielding interpenetrated networks which exhibit the

expected larger lattice constant but with rather small pore sizes31-33 the hosting of NPs thus becomes

impossible For SURMOF-2 the particular topology with 1d-pores of quadratic cross section is not

compatible with the presence of a second interwoven network and as a result interpenetration is

suppressed

Although the solubility of some the long dicarboxylic acids ligands used for the SURMOF-2 fabrication

(TPDC QPDC and PPDC see Fig 1) is fairly small we encountered no problems in the LPE process

since already small concentrations of dicarboxylic acids are sufficient for the formation of a single

monolayer on the substrate the elementary step of the LPE synthesis process34-35 Even with the

longest dicarboxylic acid available to us PPDC growth occurred in a straightforward fashion and

optimization of the growth process was not necessary

The P4 structures proposed for the SURMOF-2 series except for the 26-NDC ligand differ markedly

from the bulk MOF-2 structures obtained from conventional solvothermal synthesis2427-28 To

understand this unexpected difference and in particular the absence of relative shifts between the

pw-planes in the proposed SURMOF-2 structure we performed extensive quantum chemical

calculations employing approximate density-functional theory (DFT) in this case London dispersion-

corrected self-consistent charge density-functional based tight-binding (DFTB)36-38 to a periodic

model of MOF-2 and its SURMOF derivatives

Periodic structure DFTB calculations (Fig S1) confirmed that the P2m structure proposed by Yaghi

et al for the bulk MOF-2 material24 is indeed the energetically favorable configuration for MOF-2

while the C2m structure that has also been reported for bulk MOF-227-28 is slightly higher in energy

148

(41 meV per formula unit see Table 1) The optimum interlayer distance between the pw-planes in

the P4 structure is 58 Aring in very good agreement with the experimental value of 56 Aring (as obtained

from the in-plane XRD-data see Fig S2) It is important to note that at that distance the linkers

cannot remain in rectangular position as in MOF-2 but are twisted in order to avoid steric hindrance

and to optimize linker-linker interactions

The P4mmm structure as proposed for SURMOF-2 is less stable by 200 meV per formula unit as

compared to the P2m configuration Although the crystal energy for the P4 stacking is substantially

smaller than for P2 packing simulated annealing (DFTB model using Born-Oppenheimer Molecular

Dynamics) carried out at 300K for 10 ps demonstrated that the P4mmm structure corresponds to a

local minimum This observation is confirmed by the calculation of the stacking energy of MOF-2

where a shifting of the layers is simulated along the P2-P4-C2 path (Figure 3) On the basis of these

calculations we thus propose that SURMOF-2 adopts this metastable P4 structure

In Table 1 the interlayer interaction energies are summarized They range from 590 meV per formula

unit with respect to fully dissociated MOF-2 layers for Cu2(bdc)2 and successively increase for longer

linkers of the same type reaching 145 eV per formula unit for Cu2(ppdc)2 indicating that the linkers

play an important role in the overall stabilization of SURMOF-2 with large pore sizes Even stronger

interlayer interactions are found for different linker topologies (PPDC) A detailed computational

analysis of the role of the individual building blocks of SURMOF-2 for the crystal growth and

stabilization will be published elsewhere

The flat well-defined organic surfaces used as the templating (or nucleating) substrate in the LPE

growth process provide a satisfying explanation for why SURMOF-2 grows with the highly

symmetrical P4 structure instead of adopting the energetically more favorable bulk P2 symmetry3439

The carboxylic acid groups exposed on the surface force the first layer of deposited Cu-dimers into a

coplanar arrangement which is not compatible with the bulk P2 (or C2) structure but rather

nucleates the P4 packing In turn the carboxylate-groups in the first layer of deposited dicarboxylic

acids provide the same constraints for the next layer (see Fig 1) As a result of the layer-by-layer

method employed for further SURMOF-2 growth the same boundary conditions apply for all

subsequent layers The organic surface thus acts as a seed structure to yield the metastable P4

packing not an unusual motif in epitaxial growth40

The calculations allow us to predict that it will be possible to grow SURMOF structures with even

larger linker molecules as used here The stacking will further stabilize the P4 symmetry as the

interaction energy per formula unit is more and more dominated by the linkers (Table 1) At present

149

we cannot predict the maximum possible size of the pores but linker PPDC (see Fig 2) is thus far

unmatched as a component in non-interpenetrated framework structures

Acknowledgement

We thank Ms Huumllsmann Bielefeld University for the preparation of P(EP)2DC Financial support by

Deutsche Forschungsgemeinschaft (DFG) within the Priority Program Metal-Organic Frameworks

(SPP 1362) is gratefully acknowledged

Methods

Computational Details

All structures were created using a preliminary version of our topological framework creator

software which allows the creation of topological network models in terms of secondary building

units and their replacement by individual molecules to create the coordinates of virtually any

framework material The generated starting coordinates including their corresponding lattice

parameters have been hierarchically fully optimized using the Universal Force Field (UFF)41 followed

by the dispersion-corrected self-consistent-charge density-functional based tight-binding (DFTB)

method36-3842-43 that we have recently validated against experimental structures of HKUST-1 MOF-5

MOF-177 DUT-6 and MIL-53(Al) as well as for their performance to compute the adsorption of

water and carbon monoxide37 For all calculations we employed the deMonNano software44444444

We have chosen periodic boundary conditions for all calculations and the repeated slab method has

been employed to compute the properties of the single layers in order to evaluate the stacking

energy A conjugate-gradient scheme was employed for geometry optimization of atomic

coordinates and cell dimensions The atomic force tolerance was set to 3 x 10-4 eVAring

The confined conditions at the SURMOF-substrate interface was modeled by fixing the corresponding

coordinate in the computer simulations All calculated structures have been substantiated by

simulated annealing calculations where a Born-Oppenheimer Molecular Dynamics trajectory at 300K

has been computed for 10 ps without geometry constrains All structures remained in P4 topology

Experimental methods

The SURMOF-2 samples were grown on Au substrates (100-nm Au5-nm Ti deposited on Si wafers)

using a high-throughput approach spray method45 The gold substrates were functionalized by self-

assembled monolayers SAMs of 16-mercaptohexadecanoic acid (MHDA) These substrates were

mounted on a sample holder and subsequently sprayed with 1 mM of Cu2 (CH3COO)4middotH2O ethanol

solution and ethanolic solution of SURMOF-2 organic linkers (01 mM of BDC 26-NDC BPDC and

150

saturated concentration of TPDC QPDC PPDC P(EP)2DC) at room temperature After a given

number of cycles the samples were characterized with X-ray diffraction (XRD)

Figure 1 Schematic representation of the synthesis and formation of the SURMOF-2 analogues

151

Figure 2 Out of plane XRD data of Cu-BDC Cu-26-NDC Cu-BPDC Cu-TPDC Cu-QPDC Cu-P(EP)2DC and Cu-PPDC (upper left) schematic representation (upper right) and proposed structures of SURMOF-2 analogues (lower panel) All the SURMOF-2 are grown on ndashCOOH terminated SAM surface using the LPE method

152

Figure 3 Energy for the relative shift of each layer in two different directions horizontal (P4 to P2) and diagonal (P4 to C2) at a fixed interlayer distance of 56 Aring Structures have been partially optimized and energies are given per formula unit with respect to fully dissociated planes

Supporting information

Synthesis of organic linkers

(1) para-terphenyldicarboxylic acid (TPDC)

To a solution of para-terphenyl (1500 g 651 mmol 1 eq) and oxalyl chloride (3350 mL 3900 mmol

6 eq) in carbon disulfide (30 mL) at 0degC (ice bath) was added aluminium chloride (1475 g 1106

mmol 17 eq) After 1h stirring additional aluminium chloride (0870 g 651 mmol 1 eq) was added

the ice bath was removed and the reaction mixture was stirred at room temperature for 24h The

mixture was poured into crushed ice and stirred until the dark-brown mixture turned to yellow

Carbon disulfide was removed under reduced pressure and the resulting aqueous suspension was

filtered The solid was washed with diluted hydrochloric acid then with diethyl ether and dried

under vacuum overnight with an oil bath at 50degC Pale yellow solid yield 2028 g (98)

(2) para-quaterphenyldicarboxylic acid (QPDC)

153

To a solution of para-quaterphenyl (1000 g 326 mmol 1 eq) and oxalyl chloride (1680 mL 1956

mmol 6 eq) in carbon disulfide (20 mL) at 0degC (ice bath) was added aluminium chloride (0740 g 555






under vacuum overnight with an oil bath at 50degC Yellow solid yield 1186 g (92)

(3) P(EP)2DC

The synthesis of the P(EP)2DC-linker has been described in Ref 46

(4) para-pentaphenly dicarboxylic acid (PPDC)

Scheme 1 Synthesis of para-pentaphenly dicarboxylic acid i) Pd(PPh3)4 Na2CO3 toluenedioxane H2O 85oC ii) MeOH 6M NaOH HCl

para-pentaphenly dicarboxylic acid (H2L) was synthesized via Suzuki coupling of 44rdquo-dibromo-p-

terphenyl and 4-methoxycarbonylphenylboronic acid (Scheme 1) 44rdquo-dibromo-p-terphenyl (776 mg

200 mmol) 4-methoxycarbonylphenylboronic acid (108 g 60 mmol) and Na3CO3 (170 g 160 mmol)

were added to a degassed mixture of toluene14-dioxane (50 mL 221) under Ar [Pd(PPh3)4] (116

mg 010 mmol) was added to the mixture and heated to 85 degC for 24 hours under Ar The reaction

mixture was cooled to room temperature The precipitate was collected by filtration washed with

water methanol and used for next reaction without further purification The final product H4L was

obtained by hydrolysis of the crude product under reflux in methanol (100 mL) overnight with 6M

aqueous NaOH (20 mL) followed by acidification with HCl (conc) After removal of methanol the

final product was collected by filtration as a grey solid (078 g 83 yield) 1H NMR (d6-DMSO

250MHz 298K) δ (ppm) 805 (d J = 75Hz 4H) 789-783 (m 12H) 750 (d J = 75Hz 4H) 13C NMR

cannot be clearly resolved due to poor solubility MALDI-TOF-MS (TCNQ as matrix) mz 47002

cacld 47051 Elemental analysis Calculated C 8169 H 471 Found C 8163 H 479

Br Br MeOOC B

OH

OH

+

COOMe

COOMe

COOH

COOH

i ii

154

Figure S1 MOF-2 in P4 (as reported) P2 and C2 symmetry

155

Figure S2 In-plane XRD data of Cu-BDC Cu-26-NDC Cu-BPDC Cu-TPDC Cu-QPDC and Cu-P(EP)2DC All the

SURMOF-2 are grown on ndashCOOH terminated SAM surface using the LPE method The position of (010) plane

represents the layer distance

Table 1 Stacking energy and geometries of P4 SURMOF-2 derivatives

Symmetry a= c b Stacking Energy

Cu2(bdc)2 C2 1119 50 -076

Cu2(bdc)2 P2 1119 54 -08

Cu2(bdc)2 P4 1119 58 -059

156

Cu2(ndc)2 P2 1335 56 -04

Cu2(bpdc)2 P4 1549 59 -068

Cu2(tpdc)2 P4 1984 59 -091

Cu2(qpdc)2 P4 2424 59 -121

Cu2(P(EP)2DC)2 P4 2512 52 -173

Cu2(ppdc)2 P4 2859 59 -145

Stacking energies (DFTB level in eV) of SURMOFs The energies were calculated within periodic

boundary conditions and are given per formula unit

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in MOF-200 amounts to 18 nm by 28 nm clearly smaller than the 1d-channels in the PPDC

SURMOF-2 that are 28 nm by 28 nm

31 Batten S R amp Robson R Interpenetrating nets Ordered periodic entanglement


32 Snurr R Q Hupp J T amp Nguyen S T Prospects for nanoporous metal-organic materials in

advanced separations processes Aiche Journal 50 1090-1095 (2004)

33 Yaghi O M A tale of two entanglements Nature Materials 6 92-93 (2007)

34 Shekhah O Liu J Fischer R A amp Woumlll C MOF thin films existing and future applications

Chemical Society Reviews 40 1081-1106 (2011)

35 Zacher D Shekhah O Woumlll C amp Fischer R A Thin films of metal-organic frameworks


36 Elstner M et al Self-consistent-charge density-functional tight-binding method for

simulations of complex materials properties Physical Review B 58 7260-7268 (1998)

37 Lukose B et al Structural properties of metal-organic frameworks within the density-

functional based tight-binding method Physica Status Solidi B-Basic Solid State Physics 249

335-342 (2012)

38 Zhechkov L Heine T Patchkovskii S Seifert G amp Duarte H A An efficient a Posteriori

treatment for dispersion interaction in density-functional-based tight binding Journal of

Chemical Theory and Computation 1 841-847 (2005)

159

39 Zacher D Schmid R Woumlll C amp Fischer R A Surface Chemistry of Metal-Organic

Frameworks at the Liquid-Solid Interface Angewandte Chemie-International Edition 50 176-

199 (2011)

40 Prinz G A Stabilization of bcc Co via Epitaxial Growth on GaAs Physical Review Letters 54

1051-1054 (1985)

41 Rappe A K Casewit C J Colwell K S Goddard W A amp Skiff W M UFF a full periodic

table force field for molecular mechanics and molecular dynamics simulations Journal of the

American Chemical Society 114 10024-10035 (1992)

42 Seifert G Porezag D amp Frauenheim T Calculations of molecules clusters and solids with a

simplified LCAO-DFT-LDA scheme International Journal of Quantum Chemistry 58 185-192

(1996)

43 Oliveira A F Seifert G Heine T amp Duarte H A Density-Functional Based Tight-Binding an

Approximate DFT Method Journal of the Brazilian Chemical Society 20 1193-1205 (2009)

44 deMonNano v 2009 (Bremen 2009)

45 Arslan H K et al High-Throughput Fabrication of Uniform and Homogenous MOF Coatings

Adv Funct Mater 21 4228-4231 (2011)

46 Schaate A et al Porous Interpenetrated Zirconium-Organic Frameworks (PIZOFs) A

Chemically Versatile Family of Metal-Organic Frameworks Chemistry-a European Journal 17

9320-9325 (2011)

160

Appendix H

Linker guided metastability in templated Metal-Organic Framework-2 derivatives (SURMOFs-2)

Binit Lukose Gabriel Merino Christof Woumlll and Thomas Heine


INTRODUCTION

The molecular assembly of metal-oxides and organic struts can provide a large number of network

topologies for Metal-Organic Frameworks (MOFs)1-3 This is attained by the differences in

connectivity and relative orientation of the assembling units Within each topology replacement of a

building unit by another of same connectivity but different size leads to what is known as isoreticular

alteration of pore size The structure of MOFs in principle can be formed into the requirement of

prominent applications such as gas storage4-8 sensing910 and catalysis11-13 The structural

divergence and the performance can be further increased by functionalizing the organic linkers1415

In MOFs linkers are essential in determining the topology as well as providing porosity A linker

typically contains single or multiple aromatic rings the orientation of which normally undergoes

lowest repulsion from the coordinated metal-oxide clusters providing the most stable symmetry for

the bulk material We encounter for the first time a situation that the orientation of the linker

provides metastability in an isoreticular series of MOFs Templated MOF-2 derivatives (surface-MOF-

2 or simply SURMOFs-2)16 show this extraordinary phenomenon While bulk MOF-2 is determined to

be stable in P217 or C218-20 symmetry we found the existence of SURMOFs-2 in P4 symmetry

161

(Figure 1)16 Our theoretical approach to this problem identifies the role of the linkers in providing

P4 geometry the status of a local energy-minimum

MOF-2 derivatives are two-dimensional lattice structures composed of dimetal-centered four-fold

coordinated paddlewheels and linear organic linkers Solvothermally synthesized archetypal MOF-2

had transition metal (Zn or Cu) centers in the connectors and benzenedicarboxylic acid linkers17 The

derivatives under our investigation contain paddlewheels with Cu dimers and benzenedicarboxylic

acid (BDC) naphthalenedicarboxylic acid (NDC) biphenyldicarboxylic acid (BPDC)

triphenyldicarboxylic acid (TPDC) quaterphenyldicarboxylic acid (QPDC) P(EP)2DC21 and

pentaphenyldicarboxylic acid (PPDC) linkers pertaining to isoreticular expansion of pore size16 The

four-fold connectivity of the Cu dimers together with linearity of the linkers gives rise to layers with

quadratic (square) topology The interlayer separation d is typically much more than that of

graphite or 2D COFS22-24 because all the atoms in one layer do not lie in one plane

In bulk form the nearest layers are shifted to each other either towards one of the four linkers

(P2)171920 or diagonally towards one of the four surrounding pores (C2)18-20 in effort to reduce

the repulsion of alike charges in the adjacent paddlewheels when they are in eclipsed form (P4)

(Figure 1) The metal-dimers often show high reactivity which results in attracting water or

appropriate solvents in their axial positions The stacking along the third axis is typically through

interlayer interactions and through hydrogen bonds established between the solvents or between

the solvents and oxygen atoms in the paddlewheel The lateral shift of layers is inevitable without

additional supports Coordination of pillar molecules such as 14-diazabicyclo[222]octane (dabco) or

bipyridine in the axis of metal dimers between the adjacent layers25 is a practical mean to avoid

layer-offset however with the change of MOF dimensionality

Figure 1 Monolayer of MOF-2 and three kinds of layer packing -P4 P2 and C2- of periodic MOF-2

162

Alternate to solvothermal synthesis a step-by-step route may be enabled for the synthesis of

MOFs26-28 It adopts liquid phase epitaxy (LPE) of MOF reactants on substrate-assisted self-assembled

monolayers This is achieved by alternate immersion of the template in metal and ligand precursors

for several cycles This allows controlled growth of MOFs on surfaces The latest outcomes of this

method are the surface-standing MOF-2 derivatives (SURMOF-2s) This isoreticular SURMOF series

has linkers of different lengths (as given above) The cell dimensions that correspond to the length of

the pore walls range from 1 to 28 nm The diagonal pore-width of one of the MOFs (PPDC) accounts

to 4 nm

After evacuation of solvents (water in the present case) X-ray diffraction patterns were taken in

directions both perpendicular (scans out of plane) and parallel (scans in-plane) to the substrate

surface The presence of only one peak -(010)- in the perpendicular scan implies that the layers

orient perpendicular to the surface and the corresponding angle gives the cell parameter a (or c) In

the latter case the peaks - (100) and (001) ndash are identical and this rules out the possibility of layer-

offset Hence the symmetry of the MOFs was determined to be P4 These peaks give rise to the cell

parameter c which is nothing but the interlayer distance d This value (56 Aring) is relatively small for

P4 geometry to have water molecules in the axial position of paddlewheels Presence of some water

molecules observed using Infrared Reflection Absorption Spectroscopy (IRRAS) might be located near

paddlewheels but exposed to the pore The new observations with the SURMOFs are very intriguing

in the context that P4 symmetry appears to be impossible for solvothermally produced MOF-2

We have primarily reported that the P4 geometry of SURMOF-2 exists as a local energy-minimum16

The verification was made using an approximate method of density functional theory (DFT) which is

London dispersion-corrected self-consistent charge density-functional based tight-binding (DFTB) In

the bulk form absolute energies of P2 and C2 are 210 and 170 meV respectively higher than P4 per

a formula unit which is equivalent to the unit cell For SURMOF the barrier for leaving P4 was nearly

50 meV per formula unit It requires further analysis to unravel the reasons for this unusual

metastability We therefore performed an extensive set of quantum chemical calculations on the

composition of the constituent building units The procedure involves defining SURMOF geometry

and analyzing the translations of individual layers

The major individual contributions to the total energy are the interaction between the paddlewheel

units (favouring P2) London dispersion interaction between tilted linkers (favouring P4) and energy

to tilt the linkers In the iso-reticular series of SURMOF-2 the differences arise only in the

163

contributions from the linkers Hence we performed an extensive study only on the smallest of all

linkers- BDC A scaling might be appropriate for other linkers

RESULTS AND DISCUSSION

In solvothermal synthesis of layered MOFs it is assumed that the nucleation process is associated

with the interaction between two connectors This is rationalized by the fact that two paddlewheels

show the strongest possible noncovalent interaction between the individual MOF building blocks

present in MOF-2 As the orientation of the paddlewheels is restricted by the linkers we studied the

stacking of adjacent layers by determining the attraction of two adjacent interacting paddlewheels

upon their respective offsets Thus we investigated the geometries corresponding to lateral

displacements between the known stable arrangements of the bulk structure ie P4-to-P2 and P4-

to-C2 (Figure 2) In the model calculation the two paddlewheels were shifted from D4h symmetry to

two directions that respectively correspond to P2 and C2 symmetries in the bulk The minima along

the two shifts are referred as min-I and min-II and are having C2h symmetry It is interesting to note

that the interaction is in all cases attractive If only the paddlewheels are studied the D4h

configuration where both axes are concentric can be interpreted as transition state between the

two minima configurations P2 or C2 Comparing the two minima min-I corresponding to MOF-2 in

P2 symmetry indicates the formation of two CuO bonds while for min-II the reactive Cu centers do

not participate in the interlayer bonding

Formation of the diagonally shifted C2 bulk geometry for Zn and Cu based MOF-2 as reported in the

literature18-20 possibly is due to the presence of large solvent molecules such as DMF that

coordinate to the free Cu centers the paddlewheels

Figure 2 Displacements of two paddlewheels from D4h symmetry (corresponding to P4) towards minima that correspond to P2 and C2 bulk symmetries

164

To gain further insight on type of interactions for the three paddlewheel arrangements as found in

the bulk (Figure 3) we performed the topological analysis of the electron density for each

structure2930 An inspection of the paddlewheel shows that the electron density of the Cu-O bond has

a (relatively small) value of 0042 au thus showing only weak character In the forms related to P4

and C2 bulk symmetries all (3-1) critical points between the two paddlewheels show very small

density values (0004 au and less) In the P2 structure it is apparent the formation of a four-

membered Cu-O-Cu-O ring across the paddlewheel Note that the Cu-O interactions inside the

paddlewheel weaken (from 0042 to 0031 au) and two intermolecular Cu-O interactions with a

density value of 0024 au stabilize the P2 orientation These links if formed during nucleation will

be regularly repeated during the MOF-2 formation in solvothermal synthesis and due to its strong

binding of -08 eV they are the main reason for the stabilization of the P2 phase If the paddlewheels

are packed in P4 symmetry there must be additional means of stabilization present and that may

only arise from the linkers Moreover one should note that in order to reach the P4 symmetry a

layer-by-layer growth process is required as otherwise the linkers will readily stack as in the P2 bulk

form

165

Figure 3 Topological analysis of the electron density of fully optimized P4 (top left) C2 (top right) and P4 (bottom) structures Atom (grey) (3-1) (red) and (3+1) (green) critical points along with their charge densities are shown

The optimized geometry of a single-layer MOF-2 is shown in Figure 1 Note that the phenyl rings of

the linkers are oriented perpendicular to the MOF plane Contrary to graphene or 2D COFs the more

complex structure of MOF-2 layers may become subject to change upon the interlayer interactions

This is in particular important for the P4 stacking as reported for SURMOF-2 The interaction energy

of two linkers and two benzene rings as oriented in the monolayer has been computed as function

of the interlayer distance (Figure 4) At the experimental interlayer distance of 56 Aring the linkers are

so close that they repel each other strongly and stacking the monolayer structure at the

experimental interlayer distance would introduce an energy penalty of 08 eV per linker

It would not be exotic if we assume that the anchoring of layers on the substrate plays an important

role in setting d A supporting argument is the fact that all the SURMOFs in the iso-reticular series

have the same d An additional point is that the comparatively wider linkers NDC and LM do not

create any difference in the interlayer distance

166

Figure 4 Energy as a function of interlayer distance [d] in case of two paddlewheels and two benzene molecules The energies are given with respect to the complete dissociation of the building blocks

The best adaptation for the linkers in a closer alignment to avoid the repulsion is to partially rotate

the phenyl rings This reduces the Pauli repulsion and at the same time increases the attractive

London dispersion between the linkers However the rotation is energetically penalized by 06 eV as

accordance with similar calculations found in the literature31 and is with the same order of Zn4O-

tetrahedron clusters of the IRMOFs3233

Figure 5 Energy as a function of rotation of linker between two saturated paddlewheels The dihedral angle O-C1-C2-C3 θ between the linker and the carboxylic part in the paddlewheel Values are with respect to the ground state θ = 0⁰

To model the conditions in SURMOF-2 we need to combine the intermolecular interaction of the

linkers with the barrier associated to the rotation of the linker between two paddlewheel units as

given in Figure 5 We may consider a system of three linkers placed as if they are in three adjacent

layers of bulk P4 SURMOF-2 The linkers are undergoing a rotation along their C2 axis that would be

aligned to the Cu-Cu axes in the paddlewheels (see system-I in Figure 6) The dissociation energy of

167

the system includes four times the repulsion from one adjacent linker If we neglect the interaction

between the end-linkers which is only -35 meV the system represents the situation in bulk P4 MOF-

2 The gain of intermolecular energy due to twisting the stacked linkers is partially compensated by

the energy penalty arising from rotation of the linker between the paddlewheels and the resulting

energy shows a minimum at 22deg (Figure 6)

Figure 6 Model of the linker orientation in SURMOF-2 The stabilization of a linker inbetween two layers is approximated in System-I the arrows indicating the rotation while the energy penalty due to breaking the p conjugation of Figure 5 is given in System-II The resulting energy is the black line showing a minimum at 22deg The energy in System-I is with respect to its dissociation limit

Each linker may undergo rotation either clockwise or anti-clockwise with equal preferences in the

local environment However there may be a global control over the preference of each linker The

most stable structure can be figured out from the total energies of each possible arrangement Since

there are only two choices for each linker it may orient either in same fashion or alternate fashion

along X and Y directions If we expect a regular pattern the total number of possibilities are only

three as shown in Figure 8 where rotation of linkers (violet lines) are marked with lsquo+rsquo signs in one of

its two sides which means that facing (outer)-edges of linkers are tilted towards these sides The

three orderings may be verbalized as follows

(i) projection of the facing edges of oppositely placed linkers are either within the square or outside

(P4nbm) (ii) projection of the facing edge of only one of the oppositely placed linkers is within the

square (P4mmm) (iii) projection of the facing edges of all four linkers are either within the square

or outside (P4nmm)

The adjacent layers follow the same linker-orientations The unit cells of (i) and (iii) are four times

bigger than (ii) The stacking energies calculated at the DFTB level suggest P4nbm as the most stable

168

geometry The energies are respectively -048 -032 and -029 eV per formula unit for P4nbm

P4mmm and P4nmm respectively Within P4nbm symmetry the linker edges undergo lowest

repulsion compared to others It is to be noted that only P4nbm has four-fold rotational symmetry

along Z-axis about the Cu-dimer in any paddlewheel

Figure 7 Three possible arrangements of tilted linkers in the periodic SURMOF-2 Paddlewheels are shown as red diamonds and the linkers as violet lines Facing (outer) edges of the linkers are rotated towards the side with + signs The symmetries and calculated stacking energies (per formula unit) of the arrangements are also given

To quantify the different stacking energies we performed periodic DFT calculations on the structure

of Cu2(bdc)2 MOF-2 As the most stable P4nbm geometry demands high computational resources in

each calculation we used P4mmm geometry which has four times less atoms in unit cell We

explored tight-packing with rotated linkers and loose-packing with un-rotated linkers Two energy-

minima have been found as shown in Figure 8a at 58 and 65 Aring corresponding to rotated and un-

rotated states of linkers respectively The latter is 40 meV more stable than the former which

means that SURMOF-2 exists in a metastable state along the perpendicular axis The relative shift of

adjacent layers in the direction of the lattice vector (or ) represents the transition from P2 to P4

and back to P2 symmetry We shifted the adjacent layers parallel to and calculated the relative

energies Since the shift of adjacent layers in P4mmm geometry is not symmetric for positive and

negative directions of averages of the energies of the shift in both directions are plotted (see

Figure 9b) P4 is a local minimum while P2 is the global minimum and the energy barrier separating

the two minima accounts to 23 meV per formula unit Hence the P4 geometry of SURMOF-2 can be

taken as metastable state of MOF-2

169

Figure 8 a) Energy as function of interlayer separation d and b) Energy as a function of relative shift of adjacent layers for periodic MOF-2 Energies are given in eV per formula unit

The role of linkers in creating a local minimum at P4 is now apparent However when undergoing the

transition from P4 to P2 the relative motions of the horizontal and vertical linkers are different from

each other Hence a qualitative study is essential to accurately determine the role of each building

block for holding SURMOFs-2 in a metastable state We thus resolved the shift of entire adjacent

layers with respect to each other into relative motions of individual building blocks The experimental

interlayer distance (56 Aring) has been fixed and the energy-profiles have been calculated using DFT

The scans include the shift of

i) a paddlewheel over other

ii) a horizontal linker over other

iii) a vertical linker over other

iv) a paddlewheel over a horizontal linker

v) a paddlewheel over a vertical linker

Here vertical and horizontal linkers are the linkers vertical and horizontal to the shift directions

respectively A complete picture of individual shifts of the MOF-2 SBU including their energy-profiles

is given in Figure 9 The shift of the vertical over the horizontal linker was found insignificant and was

omitted A note of warning is that the tilted vertical linker meets different neighborhoods when

shifted to the left and right However an average energy of these two shifts seems sensible because

the nearest vertical linker in the same layer of P4nbm geometry has opposite orientation This

averaging also makes sense in a case that alternate layers undergo shifting to the same direction

leading to a zigzag (or serrated) packing of layers in the bulk As is readily seen in Figure 9 the

formation of the Cu-O-Cu-O rings between the paddlewheels (see Figure 3) is the key reasons for the

layer shift in P2 MOF-2 A support is obtained from the shifting of the paddlewheel over the

170

horizontal linker (Shift IV) A major objection is made by the vertical linkers (Shift III) The total

interaction becomes repulsive when a vertical linker shifts with respect to the other for about 05 Aring

This may alter the tilt of the linker however a minimum is already established The vertical linkers of

a layer in a way are trapped between those of adjacent layers The shift to either side from P4 most

probably decreases the interlayer separation However this demands further rotation of the vertical

linkers in order to reduce their mutual Pauli repulsion Overall the sharp minimum at P4 may be

taken as an inheritance from the lower interlayer distance of P4 geometry fixed by the anchoring on

the substrate

Figure 9 Shift of individual building blocks in the adjacent layers correspond to the situation in bulk The energies of each shifted arrangement and their total energy are given in the graph

The total energy involved in the shifting of two building blocks (one building block over the other) is

equivalent to the energy per one building block when it feels shift from two neighbors Only the

vertical linker is sensitive to the shift-direction of the two neighbors However since averages were

taken as discussed earlier the total energy becomes independent of the direction Besides the

relative motion of the SBU facing each other in P4 symmetry (Shifts I II and III) for strong distortions

we also have to consider the interaction of adjacent linker-connector interactions as represented in

Shifts IV and V The former stabilizes P2 while the latter support P4 Overall the total energy for all

the shifts shows a local minimum at P4 (see figure 9) in agreement with the periodic calculation

shown in Figure 8 Indeed the relative energy between P2 and P4 stackings estimated by the

171

superposition of individual contributions is 43 meV in close agreement to the 40 meV obtained by

the periodic calculations

Our finite-component model successfully provides adequate information on the individual

contributions of building blocks Vertical linkers play crucial role in holding the SURMOF with P4

symmetry which was never achieved with solvothermally synthesized MOF-2 Paddlewheels are

held most responsible for lateral shift The vertical linkers winningly establish a local minimum at P4

for the SURMOF

Recently we have reported SURMOF-2 derivatives with very large pore sizes(Ref) This has been

achieved by increasing the length of the linker units In view of our analysis of the stacking and

stability of MOF-2 we can now safely state that it will be possible to generate SURMOF-2 derivatives

with even larger pores with pore sizes essentially limited by the availability of stiff long organic

linker molecules This is exemplified by a calculation of the stacking energy of a series of phenyl

oligomers that is SURMOF-2 derivatives incorporating chains with 1 to 10 benzene rings in the

linkers The stacking energies per formula unit are -041 -067 -091 -121 -145 -168 -192 -215

-237 and -26 eV respectively Each benzene ring adds more than 02 eV into the stacking energy per

formula unit This energy is due to the London dispersion interaction between the linkers in the

neighboring layers

The drop of SURMOFs into the local minimum perhaps is blended with some parameters related to

synthetic environments This was beyond the scope of this work however we suggest that studies of

the mechanism of substrate-assisted layer-by-layer deposition of metal and ligand precursors may

give some primary insights into it

CONCLUSION

We have analyzed the reason for the different stackings observed for MOF-2 In the traditional

solvothermal synthesis MOF-2 is likely to crystallize in P2 symmetry determined by the strong

interaction between the paddlewheel units The coordination of large solvent molecules to the free

metal centers may lead to MOF-2 in C2 symmetry In contrast the formation of SURMOFs using

Liquid Phase Epitaxy (LPE) allows the formation of high-symmetry P4 MOF-2 This structure requires

a structural modification in terms of the orientation of the linkers with respect to the free monolayer

and the stacking is stabilized by London dispersion interactions between the linkers Increasing the

linker length is a straightforward way for the linear expansion of pore size and according to our

computations the pore size is only limited by the availability of linker molecules showing the desired

length Thus we presented a rare situation in which the linkers guarantee the persistence of a series

of materials in an otherwise unachievable state

172

COMPUTATIONAL DETAILS

The Becke three-parameter hybrid method combined with Lee-Yang-Par correlational functional

(B3LYP)34-37 and augmented with a dispersion term38 as implemented in Turbomole39 has been used

for DFT calculations The copper atoms were described using the basis set associated with the Hay-

Wadt40 relativistic effective core potentials41 which include polarization f functions42 This basis set

was obtained from the EMSL Basis Set Library4344 Carbon oxygen and hydrogen atoms were

described using the Pople basis set 6-311G Geometry optimizations of the MOF fragments were

performed using internal redundant co-ordinates45 A triplet spin state was assigned for each Cu-

paddlewheel46

Periodic structure calculations at the BLYP47 level were performed using the ADF BAND 2012

code4849 Dispersion correction was implemented based on the work by Grimme50 Triple-zeta basis

set was used The crystalline state of MOFs was computationally described using periodic boundary

conditions Bader charge analysis of paddlewheel-pairs was also performed using ADF 2012 code

The analysis was made at the level of B3LYP-D using an all-electron triple-zeta basis set

The non-orthogonal tight-binding approximation to DFT called Density Functional Tight-Binding

(DFTB)51 is computationally feasible for unit cells of several hundreds of atoms Hence this method

was used for extensive calculations on periodic structures This method computes a transferable set

of parameters from DFT calculations of a few molecules per pair of atom types The more accurate

self-consistent charge (SCC) extension of DFTB52-54 has been used for the study of bulk MOFs Validity

of the Slater-Koster parameters of Cu-X (X = Cu C O H) pairs were reported before55 The

computational code deMonNano56 which has dispersion correction implemented57 was used

If not stated otherwise the energies of the periodic structure are given per a formula unit (FU) of the

MOF which includes one paddlewheel and two linkers (one vertical linker and one horizontal linker)

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(52) Elstner M Porezag D Jungnickel G Elsner J Haugk M Frauenheim T Suhai S Seifert G

Physical Review B 1998 58 7260

(53) Frauenheim T Seifert G Elstner M Hajnal Z Jungnickel G Porezag D Suhai S Scholz R

Physica Status Solidi B-Basic Research 2000 217 41

(54) Oliveira A F Seifert G Heine T Duarte H A Journal of the Brazilian Chemical Society 2009 20

1193

(55) Lukose B Supronowicz B Petkov P S Frenzel J Kuc A Seifert G Vayssilov G N Heine T

physica status solidi (b) 2011

(56) Heine T Rapacioli M Patchkovskii S Frenzel J Koester A M Calaminici P Escalante S Duarte

H A Flores R Geudtner G Goursot A Reveles J U Vela A Salahub D R deMon-nano edn ed deMon

2009

(57) Zhechkov L Heine T Patchkovskii S Seifert G Duarte H A Journal of Chemical Theory and

Computation 2005 1 841

Statutory Declaration

I Binit Lukose hereby declare that I have written this PhD thesis independently

unless where clearly stated otherwise I have used only the sources the data

and the support that I have clearly mentioned This PhD thesis has not been

submitted for conferral of degree elsewhere

Bremen 2012

Signature _________________________

i

List of Articles



DOI103762bjnano18



















publication

ii

Acknowledgment











iii










iv

Abstract


















reasoning








metastability









2 Introduction 2









41 Stacking 13


5 3D Frameworks 17






7 Summary 23





List of Figures 32

References 33









1

1 Outline






information






















2

2 Introduction































3








synthetic chemistry





















4








Figure 2















5




crystal structure










6
























7





















8

























9




10
























Pack39








11

32 DFTB Validation



12



















101002pssb201100634








calculations






13


41 Stacking




















14














101002chem201001290


15



























16








17

5 3D Frameworks












silicon atoms






topologies




18







similar to 3D MOFs



















19


frameworks















20




















series

21































22




(SURMOFs-2)




23

7 Summary































24



obtained with DFT































25



































26

































27


































28





densities








as follows

29


















30












TAM (41 eV) + TA (26 eV) COF-300 (23 eV)







31



























32

List of Figures




structure 5














topologies 17



20




33

References













56





423 705


2008 41 1782








501


2005 310 1166





2007 19 2168

34


3450




51 12947


58 185










2001 114 5149


2009 20 1193


2012 2 456








2011 2007






1029

35




13094


1460





47 8826


48 5439












1998 120 8571








2007 111 5648




36


437




15133





37

Appendix A




Contents

1 Introduction








4 Applications

41 Gas storage









432 Metal doping


5 Conclusions


38

1 Introduction









strong bonds


















products5




39






silicates









applications















40




41



































42


































43





















level














44



interactions













respectively58






45











catalyst64












46

































47









48


49



2 g

-1] pore volume [cm

3 g



Area

Pore

volume

Pore

size


scheme 1

711 62850 032

03650

9


scheme 1

1590 0998 27




scheme 1

980 (L) 032 64


scheme 1

1400 (L) 069 187


scheme 1

2080 (L) 144 341




(alkyl = CH3)



(alkyl = C2H5)



(alkyl = C3H7)


50


scheme 1


scheme 1


scheme 1

868 079 314


scheme 1

923 188


Ag(110) surfaces)


6


surface)


6


scheme 1

2000 163 40


scheme 1

930 47




scheme 3

410 054 12



BDBA HHTP


scheme 1

2160

(X=5)

1865 (25)

1722 (50)

1641 (75)

1421

(100)

1184

1071

1016

0946

0835

295

276

259

258

227

51


(X=5)

1561 (25)

914 (50)

142 (75)

36 (100)

1481

0946

0638

0152

003

298

243

156

153

125






scheme 3

710 031 23


scheme 3

620 036 38


scheme 5

791 040 12


scheme 5

90 8

mp-CTF-2 2255 151 8


scheme 5

1061 0934 14


coordination64


coordination64



1503 157 166

52


scheme 7

1827 118



scheme 1

624 0485 190


(100-X) BDBA


scheme 1

XEsTrz-NiPc-

COF



scheme 1

1742 1115 25


2D-NiPc-BTDA

COF


scheme 1

877 22


scheme 1

420 31


scheme 1

485 31


scheme 1

490 31


scheme 1

440 34


scheme 3

735 032 12


scheme 1

360 020 249

53


scheme 1

3472 135 115

Microwave36

scheme 1

2926


(R=dodecyl)


scheme 1

12


(R=allyl)


scheme 1


scheme 1

4210 166 125


scheme 1


scheme 1


scheme 1

2690 109 11


scheme 3

1360 072 72



5600




2932 154 127



2246 145 118


54

scheme 6


31 2D COFs























55










simulated spectrum
















56








between the layers

32 3D COFs

























57




















materials




rings











58

4 Applications

41 Gas storage



























elsewhere86

59





















dimensional phase

60





























61



(242 Aring)





























62





















wt at 1 bar68



methane









63


































64



































65



































66






sites



























67



































68

























2D COFs







69

































area

70

432 Metal doping


































71





























significantly




72





5 Conclusions












CA Cyanuric acid









73









PA Piperazine








TA Terephthaldehyde








74











75


76



77


78


79


80


81

Appendix B





DOI 101002pssb201100634














82


















83



































84

































85























86













Cu-Cu 250 (257) 250 (250) 263 Cu-O 205 (198) 202 (198) 195 O-C 134 (133) 133-138 (128) 125

OCuO 836-971 (898) 892-907 (873-937)

891 896




α=β=γ=90 (90) a=b=c=26343

α=β=γ=90




87




at DFTB





















88














H2O Periodic


CO

Cu-Cu 267 (266) 262 (260) 250 (260)

Cu-O 205 (197-206) 210 (196-200) 206 (199)

O-C 134 (127) 133 (128) 134 (127)

OCuO 843-955 (889-905)

871-921 (842-930) 842-967 (896)







Cu-O(H2O) Cu-C(CO) 237 (219) 244 (233-

255) 307 (239)

Eads -4045 (-5200) -1648

(-2800)







89













90










adsorbed molecules



91



(MOF-205)

Zn-Zn 330 (317) 322-336 (306-330)

325-331 (318)

Zn-Orsquo 202 (194) 202 (193) 202 (194) Zn-O 204 (192) 202-206

(190-199) 202 205 (193)

O-C 128 (130) 128 (131) 128 (125) ZnOrsquoZn 1095 (1095) 1056-1124

(1055 1092) 107-1118 (1084 1100)

OZnO 1083 1108 (1061)

1048 1145 (981-1281)

1046-1112 (1062 1085)






a=b=37872 (37072) c=3068 (30033) α=β=90 (90) γ=120 (120)

a=b=c=31013 (30353) α=β=γ=90 (90)






Bond Type DFTB Exp


b=1732 c=1365 α=β=γ=90

a=1218 b=1713 c=1326 α=β=γ=90



92
































93

References



34 319 (2001)












Science 316 268 (2007)











94














95


96

Appendix C



Chem Eur J 2011 17 2388 ndash 2392

DOI 101002chem201001290









pore surface







97









98





























been considered






99























boron-oxygen rings











100












101


Table 1)








COF-5 AA -2968 -3060 092

AB -2548 -2618 070

serrated z -3051 -3073 022

serrated a -3052 -3073 021

inclined z -3297 -3045 -252

inclined a -3275 -3044 -231

Monolayer Ecb= 211

COF-1 AA -2683 -2739 056

AB -2186 -2131 -055

serrated z -2810 -2806 -004

inclined z -2784 -2788 004

Monolayer Ecb= 906

COF-6 AA -2881 -2963 082

AB -2127 -2146 019

serrated z -2978 -2996 018

serrated a -2978 -2995 017

inclined z -2946 -2975 029

inclined a -2954 -2974 021

Monolayer Ecb= 185

COF-8 AA -4488 -4617 129

102

AB -2477 -2506 029

serrated z -4614 -4646 032

serrated a -4615 -4647 032

inclined z -4578 -4612 035

inclined a -4561 -4591 030

Monolayer Ecb= 263



























103

























104

References



2007 316 268

























105

Appendix D




DOI103762bjnano18

Abstract













Introduction



106


































107
























108



























109




























110











work [17]


111



COF Building

Blocks

a d ρ

AA AB AA AB

COF-1 I-a 1502 (15620) 351 313 (332) 094 106

COF-1M I-b 2241 349 304 068 078

COF-2M I-c 1492 347 312 095 106

COF-3M I-d 0747 349 327 153 164

PPy-COF I-e 2232 (22163) 349 (3421) 297 084 099

COF-5 II-a 3014 (30020) 347 (3460) 326 056 060

COF-10 II-b 3758 (37810) 347 (3476) 318 045 (045) 050

COF-8 II-c 2251 (22733) 346 (3476) 320 071 (070) 077

COF-6 II-d 1505 (15091) 346 (3599) 327 104 110

TP COF II-e 3750 (37541) 348 (3378) 320 051 056

COF-4M III-a 2171 350 318 073 080

COF-5M III-b 2915 350 318 055 061

COF-6M III-c 1833 345 318 083 090

COF-7M III-d 1083 350 330 129 136

TP COF-1M III-e 2905 349 310 065 074

COF-8M IV-a 1748 359 329 140 148

COF-9M IV-b 2176 349 330 117 174

COF-10M IV-c 2254 342 336 127 128

COF-11M IV-d 1512 346 338 168 172

TP COF-2M IV-e 2173 347 332 134 140

REF-I I 0773 359 336 144 148

REF-III III 1445 353 336 104 121

Graphite 247 343 335 220 227

112

Energetic stability


















2 2 3 COF 12 H O Tl T l (1)

113

2 1 1 COF 6 H O Tt T t (2)

2 1 3 COF 12 H O Hl H l (3)

2 1 2 COF 12 H O Ht H t (4)







COF Building

Blocks

Mono-

layer

AA AB


COF-1 I-a 906 -2683 -1777 33 -2187 -1280 36

COF-1M I-b 949 -4266 -3366 27 -2418 -1469 31

COF-2M I-c 956 -5727 -4771 28 -4734 -3778 30

COF-3M I-d 763 -2506 -1742 38 -2801 -2037 40

PPy-COF I-e 858 -5723 -4866 24 -3855 -2998 26

COF-5 II-a 211 -2968 -2756 24 -2548 -2337 28

COF-10 II-b 317 -3766 -3448 23 -1344 -1026 26

COF-8 II-c 263 -4488 -4224 25 -2477 -2213 28

COF-6 II-d 185 -2881 -2695 28 -2127 -1942 31

TP COF II-e 231 -4453 -4222 24 -1480 -1250 27

COF-4M III-a -033 -1730 -1763 26 -880 -913 26

COF-5M III-b 007 -2533 -2526 25 -972 -965 25

COF-6M III-c 014 -3231 -3217 26 -2134 -2120 28

114

COF-7M III-d -170 -1635 -1805 30 -1607 -1777 32

TP COF-1M III-e -014 -3226 -3240 24 -1277 -1291 24

COF-8M IV-a -787 -2756 -3543 18 -2680 -3467 21

COF-9M IV-b -836 -3577 -4414 17 -3003 -3839 21

COF-10M IV-c -947 -4297 -5244 18 -4192 -5140 22

COF-11M IV-d -403 -2684 -3087 21 -2833 -3236 24

TP COF-2M IV-e 030 -4345 -4315 18 -4117 -4087 21



















115











116













Conclusion









117





Methods





























118







COF Building

Blocks

C-B B-O O-C OBO

COF-1 I-a 1498 (1600) 1393 (1509) 1203 (1200)

COF-1M I-b 1497 1393 1203

COF-2M I-c 1497 1392 1203

COF-3M I-d 1496 1392 1201

PPy-COF I-e 1498 1393 1202 (1190)

COF-5 II-a 1496 (1530) 1399 (1367) 1443 (1384) 1135dagger (1139)

COF-10 II-b 1495 (1553) 1399 (1465) 1443 (1385) 1135dagger (1120)

COF-8 II-c 1495 (1548) 1399 (1479) 1443 1135dagger

COF-6 II-d 1496 1399 1443 1135dagger

TP COF II-e 1496 (1542) 1399 (1396) 1444 (1377) 1135dagger (1182)

COF-4M III-a 1496 1398 1449 1135dagger

COF-5M III-b 1496 1398 1449 1136dagger

COF-6M III-c 1496 1399 1451 1134dagger

COF-7M III-d 1496 1398 1449 1136dagger


COF-8M IV-a 1496 1398 1445 1131dagger

COF-9M IV-b 1495 1398 1444 1131dagger

119

COF-10M IV-c 1495 1391 1418 1126dagger

COF-11M IV-d 1498 1399 1450 1134dagger








COF Building

Blocks

a d ρ


COF-1 I-a 1502 343 343 097 097

COF-1M I-b 2241 341 342 069 069

COF-2M I-c 1492 340 339 097 097

COF-3M I-d 0747 341 342 157 156

PPy-COF I-e 2232 341 341 086 086

120

COF-5 II-a 3014 342 342 341 340 057 057 058 058

COF-10 II-b 3758 341 341 342 340 046 046 046 046

COF-8 II-c 2251 341 341 342 342 073 073 072 072

COF-6 II-d 1505 342 341 340 340 105 106 106 106

TP COF II-e 3750 342 341 342 342 052 052 052 052

COF-4M III-a 2171 344 344 345 344 074 074 074 074

COF-5M III-b 2915 343 342 343 343 056 056 056 056

COF-6M III-c 1833 341 341 342 341 084 084 084 084

COF-7M III-d 1083 344 343 340 344 131 131 132 131

TP COF-1M III-e 2905 343 342 343 342 066 067 066 066

COF-8M IV-a 1748 341 341 342 342 142 142 142 142

COF-9M IV-b 2176 341 341 341 342 119 119 119 119

COF-10M IV-c 2254 340 340 340 340 128 128 128 128

COF-11M IV-d 1512 341 341 340 340 171 171 171 171

TP COF-2M IV-e 2173 340 340 340 340 137 137 137 137

REF-I I 0773 349 345 148 15

REF-III III 1445 348 349 106 106



COF Sa Sz Ia Iz


-1 -2810 -1904 36 -2786 -1880 36

-1M -4426 -3477 30 -4389 -3440 30

-2M -5967 -5011 30 -5833 -4877 30

121

-3M -2667 -1904 40 -2591 -1828 40

PPy- -5916 -5058 26 -5865 -5007 26

-5 -3052 -2841 27 -3051 -2840 26 -3275 -3064 26 -3297 -3086 26

-10 -3868 -3551 26 -3869 -3552 25 -3830 -3513 26 -4293 -3976 25

-8 -4615 -4352 27 -4614 -4351 27 -4571 -4308 27 -4573 -4310 27

-6 -2978 -2793 30 -2978 -2793 30 -3117 -2932 30 -3090 -2905 30

TP -4557 -4326 26 -4562 -4331 26 -4511 -4280 26 -4511 -4280 26

-4M -1811 -1844 28 -1813 -1846 28 -1769 -1802 28 -1880 -1913 28

-5M -2626 -2619 27 -2630 -2623 26 -2597 -2590 26 -2600 -2593 26

-6M -3375 -3361 28 -3381 -3367 28 -3487 -3473 28 -3349 -3335 28

-7M -1724 -1894 32 -1726 -1896 31 -2333 -2503 32 -1866 -2036 31

TP -1M -3327 -3341 26 -3334 -3348 26 -3340 -3354 26 -3353 -3367 26

-8M -2897 -3684 21 -2895 -3682 21 -2971 -3758 21 -2983 -3770 21

-9M -3732 -4568 20 -3733 -4569 20 -3684 -4520 20 -3706 -4542 20

-10M -4512 -5459 21 -4513 -5460 21 -4491 -5438 21 -4495 -5442 21

-11M -2831 -3234 24 -2834 -3237 24 -2816 -3219 24 -2830 -3233 24

TP -2M -4500 -4470 20 -4505 -4475 20 -4495 -4465 20 -4496 -4466 20

122

Appendix E











Introduction








123


































124









Methods



125


















(1) B = 2

2

dV

EdV





tot + m2 Ebb2tot)









126



















Structure Building

Blocks

Cell

parameters

ρ Δ B EF

COF-102 (C) TBPM 2707 (2717) 043 39 (43) 206 -14995

COF-103 (Si) TBPS 2817 (2825) 039 38 (41) 139 -14547

COF-105-C TBPM HHTP 4337 019 33 (43 34) 80 -18080

COF-105 (Si) TBPS HHTP 4444 (4489) 018 32 (41 34) 79 -17055

COF-108 (C) TBPM HHTP 2838 (2840) 017 32 (43 34) 37 -17983

COF-108-Si TBPS HHTP 2920 016 30 (41 34) 29 -18038

COF-202 (C) TBPM TBST 3047 (3010) 050 42 (43 139) 143 -7954

COF-202-Si TBPS TBST 3157 046 39 (41 139) 153 -7632

COF-300 (C) TAM TA 2932 925 049 23 (41 26) 144 -40286

127

(2828 1008)

COF-300-Si TAS TA 3039 959 044 23 (40 26) 133 -39930




good match


















128


















129



130




building units

Conclusion









131

Appendix F




Abstract








(MOFs and COFs)

Introduction





132





















MOFs













133





Methods








Pack19










cutoff of 5000 K










134























PAFs

a

(Aring)

ρ

(g cm-3)

EForm

(kJ mol-1)

Δ

(eV)

B

(GPa)

H2 accessible

free volume

H2 accessible

surface area

135

() (m2 g-1)

PAF-phnl 97 085 -121 47 (55) 360 35 2398

PAF-biphl 167 032 -122 36 (40) 132 73 5697

PAF-pyrn 166 042 -124 26 (28) 192 66 5090

PAF-DPA 210 019 -122 35 (37) 87 84 7240

PAF-ptph 237 016 -119 32 (33) 56 86 6735

PAF-PTCDA 236 024 -122 18 (19) 95 81 5576

PAF-qtphl 308 010 -119 29 (30) 35 91 7275





by

( )

where Ecell EL and














136


the perfect trend




















137

















138


































139











bar


140




















PAF

(g cm-3)

H2 accessible

free volume ()

H2 accessible

surface area

(m2 g-1)

PAF-qtph 010 91 7275

PAF-qtph-2 020 82 7275

PAF-qtph-3 030 73 7275

PAF-qtph-4 040 64 5998



141

















PAFs



142






Conclusions



pore volume















143

References





217


705


295 469


310 1166






O M Science 2007 316 268




Chemistry 2011 21 13498



2009 20 1193


185




deMon 2009






Society 2008 130 11580











2007 111 15350


144




npdf






145

Appendix G


















146



















predefined pores















28

147


















suppressed

















148

































149



Acknowledgement




Methods

























150




151


152














153









(3) P(EP)2DC

















Br Br MeOOC B

OH

OH

+

COOMe

COOMe

COOH

COOH

i ii

154


155






Cu2(bdc)2 C2 1119 50 -076

Cu2(bdc)2 P2 1119 54 -08

Cu2(bdc)2 P4 1119 58 -059

156

Cu2(ndc)2 P2 1335 56 -04

Cu2(bpdc)2 P4 1549 59 -068

Cu2(tpdc)2 P4 1984 59 -091

Cu2(qpdc)2 P4 2424 59 -121

Cu2(P(EP)2DC)2 P4 2512 52 -173

Cu2(ppdc)2 P4 2859 59 -145



References




1127-1129 (2003)






Reviews 112 1105-1124 (2012)



(2012)









(2010)



157



Society 132 7832-7833 (2010)






(2012)



























158






























335-342 (2012)




159



199 (2011)


1051-1054 (1985)






(1996)





Adv Funct Mater 21 4228-4231 (2011)



9320-9325 (2011)

160

Appendix H




INTRODUCTION















161
























162








to 4 nm
























163























164















form

165














166













167


















or outside (P4nmm)



168




















169
























170








the substrate











171







for the SURMOF










neighboring layers





CONCLUSION












172









paddlewheel46















REFERENCES







173




1127


112 1105



38 1450




126 5666


Science 2010 327 846







Chemistry 2005 178 3342


7 5168


2011 17 9320


1166


174




2009 48 5038














11623










175



13 2025












1193





2009



i

List of Articles



DOI103762bjnano18



















publication

ii

Acknowledgment











iii










iv

Abstract


















reasoning








metastability









2 Introduction 2









41 Stacking 13


5 3D Frameworks 17






7 Summary 23





List of Figures 32

References 33









1

1 Outline






information






















2

2 Introduction































3








synthetic chemistry





















4








Figure 2















5




crystal structure










6
























7





















8

























9




10
























Pack39








11

32 DFTB Validation



12



















101002pssb201100634








calculations






13


41 Stacking




















14














101002chem201001290


15



























16








17

5 3D Frameworks












silicon atoms






topologies




18







similar to 3D MOFs



















19


frameworks















20




















series

21































22




(SURMOFs-2)




23

7 Summary































24



obtained with DFT































25



































26

































27


































28





densities








as follows

29


















30












TAM (41 eV) + TA (26 eV) COF-300 (23 eV)







31



























32

List of Figures




structure 5














topologies 17



20




33

References













56





423 705


2008 41 1782








501


2005 310 1166





2007 19 2168

34


3450




51 12947


58 185










2001 114 5149


2009 20 1193


2012 2 456








2011 2007






1029

35




13094


1460





47 8826


48 5439












1998 120 8571








2007 111 5648




36


437




15133





37

Appendix A




Contents

1 Introduction








4 Applications

41 Gas storage









432 Metal doping


5 Conclusions


38

1 Introduction









strong bonds


















products5




39






silicates









applications















40




41



































42


































43





















level














44



interactions













respectively58






45











catalyst64












46

































47









48


49



2 g

-1] pore volume [cm

3 g



Area

Pore

volume

Pore

size


scheme 1

711 62850 032

03650

9


scheme 1

1590 0998 27




scheme 1

980 (L) 032 64


scheme 1

1400 (L) 069 187


scheme 1

2080 (L) 144 341




(alkyl = CH3)



(alkyl = C2H5)



(alkyl = C3H7)


50


scheme 1


scheme 1


scheme 1

868 079 314


scheme 1

923 188


Ag(110) surfaces)


6


surface)


6


scheme 1

2000 163 40


scheme 1

930 47




scheme 3

410 054 12



BDBA HHTP


scheme 1

2160

(X=5)

1865 (25)

1722 (50)

1641 (75)

1421

(100)

1184

1071

1016

0946

0835

295

276

259

258

227

51


(X=5)

1561 (25)

914 (50)

142 (75)

36 (100)

1481

0946

0638

0152

003

298

243

156

153

125






scheme 3

710 031 23


scheme 3

620 036 38


scheme 5

791 040 12


scheme 5

90 8

mp-CTF-2 2255 151 8


scheme 5

1061 0934 14


coordination64


coordination64



1503 157 166

52


scheme 7

1827 118



scheme 1

624 0485 190


(100-X) BDBA


scheme 1

XEsTrz-NiPc-

COF



scheme 1

1742 1115 25


2D-NiPc-BTDA

COF


scheme 1

877 22


scheme 1

420 31


scheme 1

485 31


scheme 1

490 31


scheme 1

440 34


scheme 3

735 032 12


scheme 1

360 020 249

53


scheme 1

3472 135 115

Microwave36

scheme 1

2926


(R=dodecyl)


scheme 1

12


(R=allyl)


scheme 1


scheme 1

4210 166 125


scheme 1


scheme 1


scheme 1

2690 109 11


scheme 3

1360 072 72



5600




2932 154 127



2246 145 118


54

scheme 6


31 2D COFs























55










simulated spectrum
















56








between the layers

32 3D COFs

























57




















materials




rings











58

4 Applications

41 Gas storage



























elsewhere86

59





















dimensional phase

60





























61



(242 Aring)





























62





















wt at 1 bar68



methane









63


































64



































65



































66






sites



























67



































68

























2D COFs







69

































area

70

432 Metal doping


































71





























significantly




72





5 Conclusions












CA Cyanuric acid









73









PA Piperazine








TA Terephthaldehyde








74











75


76



77


78


79


80


81

Appendix B





DOI 101002pssb201100634














82


















83



































84

































85























86













Cu-Cu 250 (257) 250 (250) 263 Cu-O 205 (198) 202 (198) 195 O-C 134 (133) 133-138 (128) 125

OCuO 836-971 (898) 892-907 (873-937)

891 896




α=β=γ=90 (90) a=b=c=26343

α=β=γ=90




87




at DFTB





















88














H2O Periodic


CO

Cu-Cu 267 (266) 262 (260) 250 (260)

Cu-O 205 (197-206) 210 (196-200) 206 (199)

O-C 134 (127) 133 (128) 134 (127)

OCuO 843-955 (889-905)

871-921 (842-930) 842-967 (896)







Cu-O(H2O) Cu-C(CO) 237 (219) 244 (233-

255) 307 (239)

Eads -4045 (-5200) -1648

(-2800)







89













90










adsorbed molecules



91



(MOF-205)

Zn-Zn 330 (317) 322-336 (306-330)

325-331 (318)

Zn-Orsquo 202 (194) 202 (193) 202 (194) Zn-O 204 (192) 202-206

(190-199) 202 205 (193)

O-C 128 (130) 128 (131) 128 (125) ZnOrsquoZn 1095 (1095) 1056-1124

(1055 1092) 107-1118 (1084 1100)

OZnO 1083 1108 (1061)

1048 1145 (981-1281)

1046-1112 (1062 1085)






a=b=37872 (37072) c=3068 (30033) α=β=90 (90) γ=120 (120)

a=b=c=31013 (30353) α=β=γ=90 (90)






Bond Type DFTB Exp


b=1732 c=1365 α=β=γ=90

a=1218 b=1713 c=1326 α=β=γ=90



92
































93

References



34 319 (2001)












Science 316 268 (2007)











94














95


96

Appendix C



Chem Eur J 2011 17 2388 ndash 2392

DOI 101002chem201001290









pore surface







97









98





























been considered






99























boron-oxygen rings











100












101


Table 1)








COF-5 AA -2968 -3060 092

AB -2548 -2618 070

serrated z -3051 -3073 022

serrated a -3052 -3073 021

inclined z -3297 -3045 -252

inclined a -3275 -3044 -231

Monolayer Ecb= 211

COF-1 AA -2683 -2739 056

AB -2186 -2131 -055

serrated z -2810 -2806 -004

inclined z -2784 -2788 004

Monolayer Ecb= 906

COF-6 AA -2881 -2963 082

AB -2127 -2146 019

serrated z -2978 -2996 018

serrated a -2978 -2995 017

inclined z -2946 -2975 029

inclined a -2954 -2974 021

Monolayer Ecb= 185

COF-8 AA -4488 -4617 129

102

AB -2477 -2506 029

serrated z -4614 -4646 032

serrated a -4615 -4647 032

inclined z -4578 -4612 035

inclined a -4561 -4591 030

Monolayer Ecb= 263



























103

























104

References



2007 316 268

























105

Appendix D




DOI103762bjnano18

Abstract













Introduction



106


































107
























108



























109




























110











work [17]


111



COF Building

Blocks

a d ρ

AA AB AA AB

COF-1 I-a 1502 (15620) 351 313 (332) 094 106

COF-1M I-b 2241 349 304 068 078

COF-2M I-c 1492 347 312 095 106

COF-3M I-d 0747 349 327 153 164

PPy-COF I-e 2232 (22163) 349 (3421) 297 084 099

COF-5 II-a 3014 (30020) 347 (3460) 326 056 060

COF-10 II-b 3758 (37810) 347 (3476) 318 045 (045) 050

COF-8 II-c 2251 (22733) 346 (3476) 320 071 (070) 077

COF-6 II-d 1505 (15091) 346 (3599) 327 104 110

TP COF II-e 3750 (37541) 348 (3378) 320 051 056

COF-4M III-a 2171 350 318 073 080

COF-5M III-b 2915 350 318 055 061

COF-6M III-c 1833 345 318 083 090

COF-7M III-d 1083 350 330 129 136

TP COF-1M III-e 2905 349 310 065 074

COF-8M IV-a 1748 359 329 140 148

COF-9M IV-b 2176 349 330 117 174

COF-10M IV-c 2254 342 336 127 128

COF-11M IV-d 1512 346 338 168 172

TP COF-2M IV-e 2173 347 332 134 140

REF-I I 0773 359 336 144 148

REF-III III 1445 353 336 104 121

Graphite 247 343 335 220 227

112

Energetic stability


















2 2 3 COF 12 H O Tl T l (1)

113

2 1 1 COF 6 H O Tt T t (2)

2 1 3 COF 12 H O Hl H l (3)

2 1 2 COF 12 H O Ht H t (4)







COF Building

Blocks

Mono-

layer

AA AB


COF-1 I-a 906 -2683 -1777 33 -2187 -1280 36

COF-1M I-b 949 -4266 -3366 27 -2418 -1469 31

COF-2M I-c 956 -5727 -4771 28 -4734 -3778 30

COF-3M I-d 763 -2506 -1742 38 -2801 -2037 40

PPy-COF I-e 858 -5723 -4866 24 -3855 -2998 26

COF-5 II-a 211 -2968 -2756 24 -2548 -2337 28

COF-10 II-b 317 -3766 -3448 23 -1344 -1026 26

COF-8 II-c 263 -4488 -4224 25 -2477 -2213 28

COF-6 II-d 185 -2881 -2695 28 -2127 -1942 31

TP COF II-e 231 -4453 -4222 24 -1480 -1250 27

COF-4M III-a -033 -1730 -1763 26 -880 -913 26

COF-5M III-b 007 -2533 -2526 25 -972 -965 25

COF-6M III-c 014 -3231 -3217 26 -2134 -2120 28

114

COF-7M III-d -170 -1635 -1805 30 -1607 -1777 32

TP COF-1M III-e -014 -3226 -3240 24 -1277 -1291 24

COF-8M IV-a -787 -2756 -3543 18 -2680 -3467 21

COF-9M IV-b -836 -3577 -4414 17 -3003 -3839 21

COF-10M IV-c -947 -4297 -5244 18 -4192 -5140 22

COF-11M IV-d -403 -2684 -3087 21 -2833 -3236 24

TP COF-2M IV-e 030 -4345 -4315 18 -4117 -4087 21



















115











116













Conclusion









117





Methods





























118







COF Building

Blocks

C-B B-O O-C OBO

COF-1 I-a 1498 (1600) 1393 (1509) 1203 (1200)

COF-1M I-b 1497 1393 1203

COF-2M I-c 1497 1392 1203

COF-3M I-d 1496 1392 1201

PPy-COF I-e 1498 1393 1202 (1190)

COF-5 II-a 1496 (1530) 1399 (1367) 1443 (1384) 1135dagger (1139)

COF-10 II-b 1495 (1553) 1399 (1465) 1443 (1385) 1135dagger (1120)

COF-8 II-c 1495 (1548) 1399 (1479) 1443 1135dagger

COF-6 II-d 1496 1399 1443 1135dagger

TP COF II-e 1496 (1542) 1399 (1396) 1444 (1377) 1135dagger (1182)

COF-4M III-a 1496 1398 1449 1135dagger

COF-5M III-b 1496 1398 1449 1136dagger

COF-6M III-c 1496 1399 1451 1134dagger

COF-7M III-d 1496 1398 1449 1136dagger


COF-8M IV-a 1496 1398 1445 1131dagger

COF-9M IV-b 1495 1398 1444 1131dagger

119

COF-10M IV-c 1495 1391 1418 1126dagger

COF-11M IV-d 1498 1399 1450 1134dagger








COF Building

Blocks

a d ρ


COF-1 I-a 1502 343 343 097 097

COF-1M I-b 2241 341 342 069 069

COF-2M I-c 1492 340 339 097 097

COF-3M I-d 0747 341 342 157 156

PPy-COF I-e 2232 341 341 086 086

120

COF-5 II-a 3014 342 342 341 340 057 057 058 058

COF-10 II-b 3758 341 341 342 340 046 046 046 046

COF-8 II-c 2251 341 341 342 342 073 073 072 072

COF-6 II-d 1505 342 341 340 340 105 106 106 106

TP COF II-e 3750 342 341 342 342 052 052 052 052

COF-4M III-a 2171 344 344 345 344 074 074 074 074

COF-5M III-b 2915 343 342 343 343 056 056 056 056

COF-6M III-c 1833 341 341 342 341 084 084 084 084

COF-7M III-d 1083 344 343 340 344 131 131 132 131

TP COF-1M III-e 2905 343 342 343 342 066 067 066 066

COF-8M IV-a 1748 341 341 342 342 142 142 142 142

COF-9M IV-b 2176 341 341 341 342 119 119 119 119

COF-10M IV-c 2254 340 340 340 340 128 128 128 128

COF-11M IV-d 1512 341 341 340 340 171 171 171 171

TP COF-2M IV-e 2173 340 340 340 340 137 137 137 137

REF-I I 0773 349 345 148 15

REF-III III 1445 348 349 106 106



COF Sa Sz Ia Iz


-1 -2810 -1904 36 -2786 -1880 36

-1M -4426 -3477 30 -4389 -3440 30

-2M -5967 -5011 30 -5833 -4877 30

121

-3M -2667 -1904 40 -2591 -1828 40

PPy- -5916 -5058 26 -5865 -5007 26

-5 -3052 -2841 27 -3051 -2840 26 -3275 -3064 26 -3297 -3086 26

-10 -3868 -3551 26 -3869 -3552 25 -3830 -3513 26 -4293 -3976 25

-8 -4615 -4352 27 -4614 -4351 27 -4571 -4308 27 -4573 -4310 27

-6 -2978 -2793 30 -2978 -2793 30 -3117 -2932 30 -3090 -2905 30

TP -4557 -4326 26 -4562 -4331 26 -4511 -4280 26 -4511 -4280 26

-4M -1811 -1844 28 -1813 -1846 28 -1769 -1802 28 -1880 -1913 28

-5M -2626 -2619 27 -2630 -2623 26 -2597 -2590 26 -2600 -2593 26

-6M -3375 -3361 28 -3381 -3367 28 -3487 -3473 28 -3349 -3335 28

-7M -1724 -1894 32 -1726 -1896 31 -2333 -2503 32 -1866 -2036 31

TP -1M -3327 -3341 26 -3334 -3348 26 -3340 -3354 26 -3353 -3367 26

-8M -2897 -3684 21 -2895 -3682 21 -2971 -3758 21 -2983 -3770 21

-9M -3732 -4568 20 -3733 -4569 20 -3684 -4520 20 -3706 -4542 20

-10M -4512 -5459 21 -4513 -5460 21 -4491 -5438 21 -4495 -5442 21

-11M -2831 -3234 24 -2834 -3237 24 -2816 -3219 24 -2830 -3233 24

TP -2M -4500 -4470 20 -4505 -4475 20 -4495 -4465 20 -4496 -4466 20

122

Appendix E











Introduction








123


































124









Methods



125


















(1) B = 2

2

dV

EdV





tot + m2 Ebb2tot)









126



















Structure Building

Blocks

Cell

parameters

ρ Δ B EF

COF-102 (C) TBPM 2707 (2717) 043 39 (43) 206 -14995

COF-103 (Si) TBPS 2817 (2825) 039 38 (41) 139 -14547

COF-105-C TBPM HHTP 4337 019 33 (43 34) 80 -18080

COF-105 (Si) TBPS HHTP 4444 (4489) 018 32 (41 34) 79 -17055

COF-108 (C) TBPM HHTP 2838 (2840) 017 32 (43 34) 37 -17983

COF-108-Si TBPS HHTP 2920 016 30 (41 34) 29 -18038

COF-202 (C) TBPM TBST 3047 (3010) 050 42 (43 139) 143 -7954

COF-202-Si TBPS TBST 3157 046 39 (41 139) 153 -7632

COF-300 (C) TAM TA 2932 925 049 23 (41 26) 144 -40286

127

(2828 1008)

COF-300-Si TAS TA 3039 959 044 23 (40 26) 133 -39930




good match


















128


















129



130




building units

Conclusion









131

Appendix F




Abstract








(MOFs and COFs)

Introduction





132





















MOFs













133





Methods








Pack19










cutoff of 5000 K










134























PAFs

a

(Aring)

ρ

(g cm-3)

EForm

(kJ mol-1)

Δ

(eV)

B

(GPa)

H2 accessible

free volume

H2 accessible

surface area

135

() (m2 g-1)

PAF-phnl 97 085 -121 47 (55) 360 35 2398

PAF-biphl 167 032 -122 36 (40) 132 73 5697

PAF-pyrn 166 042 -124 26 (28) 192 66 5090

PAF-DPA 210 019 -122 35 (37) 87 84 7240

PAF-ptph 237 016 -119 32 (33) 56 86 6735

PAF-PTCDA 236 024 -122 18 (19) 95 81 5576

PAF-qtphl 308 010 -119 29 (30) 35 91 7275





by

( )

where Ecell EL and














136


the perfect trend




















137

















138


































139











bar


140




















PAF

(g cm-3)

H2 accessible

free volume ()

H2 accessible

surface area

(m2 g-1)

PAF-qtph 010 91 7275

PAF-qtph-2 020 82 7275

PAF-qtph-3 030 73 7275

PAF-qtph-4 040 64 5998



141

















PAFs



142






Conclusions



pore volume















143

References





217


705


295 469


310 1166






O M Science 2007 316 268




Chemistry 2011 21 13498



2009 20 1193


185




deMon 2009






Society 2008 130 11580











2007 111 15350


144




npdf






145

Appendix G


















146



















predefined pores















28

147


















suppressed

















148

































149



Acknowledgement




Methods

























150




151


152














153









(3) P(EP)2DC

















Br Br MeOOC B

OH

OH

+

COOMe

COOMe

COOH

COOH

i ii

154


155






Cu2(bdc)2 C2 1119 50 -076

Cu2(bdc)2 P2 1119 54 -08

Cu2(bdc)2 P4 1119 58 -059

156

Cu2(ndc)2 P2 1335 56 -04

Cu2(bpdc)2 P4 1549 59 -068

Cu2(tpdc)2 P4 1984 59 -091

Cu2(qpdc)2 P4 2424 59 -121

Cu2(P(EP)2DC)2 P4 2512 52 -173

Cu2(ppdc)2 P4 2859 59 -145



References




1127-1129 (2003)






Reviews 112 1105-1124 (2012)



(2012)









(2010)



157



Society 132 7832-7833 (2010)






(2012)



























158






























335-342 (2012)




159



199 (2011)


1051-1054 (1985)






(1996)





Adv Funct Mater 21 4228-4231 (2011)



9320-9325 (2011)

160

Appendix H




INTRODUCTION















161
























162








to 4 nm
























163























164















form

165














166













167


















or outside (P4nmm)



168




















169
























170








the substrate











171







for the SURMOF










neighboring layers





CONCLUSION












172









paddlewheel46















REFERENCES







173




1127


112 1105



38 1450




126 5666


Science 2010 327 846







Chemistry 2005 178 3342


7 5168


2011 17 9320


1166


174




2009 48 5038














11623










175



13 2025












1193





2009



ii

Acknowledgment











iii










iv

Abstract


















reasoning








metastability









2 Introduction 2









41 Stacking 13


5 3D Frameworks 17






7 Summary 23





List of Figures 32

References 33









1

1 Outline






information






















2

2 Introduction































3








synthetic chemistry





















4








Figure 2















5




crystal structure










6
























7





















8

























9




10
























Pack39








11

32 DFTB Validation



12



















101002pssb201100634








calculations






13


41 Stacking




















14














101002chem201001290


15



























16








17

5 3D Frameworks












silicon atoms






topologies




18







similar to 3D MOFs



















19


frameworks















20




















series

21































22




(SURMOFs-2)




23

7 Summary































24



obtained with DFT































25



































26

































27


































28





densities








as follows

29


















30












TAM (41 eV) + TA (26 eV) COF-300 (23 eV)







31



























32

List of Figures




structure 5














topologies 17



20




33

References













56





423 705


2008 41 1782








501


2005 310 1166





2007 19 2168

34


3450




51 12947


58 185










2001 114 5149


2009 20 1193


2012 2 456








2011 2007






1029

35




13094


1460





47 8826


48 5439












1998 120 8571








2007 111 5648




36


437




15133





37

Appendix A




Contents

1 Introduction








4 Applications

41 Gas storage









432 Metal doping


5 Conclusions


38

1 Introduction









strong bonds


















products5




39






silicates









applications















40




41



































42


































43





















level














44



interactions













respectively58






45











catalyst64












46

































47









48


49



2 g

-1] pore volume [cm

3 g



Area

Pore

volume

Pore

size


scheme 1

711 62850 032

03650

9


scheme 1

1590 0998 27




scheme 1

980 (L) 032 64


scheme 1

1400 (L) 069 187


scheme 1

2080 (L) 144 341




(alkyl = CH3)



(alkyl = C2H5)



(alkyl = C3H7)


50


scheme 1


scheme 1


scheme 1

868 079 314


scheme 1

923 188


Ag(110) surfaces)


6


surface)


6


scheme 1

2000 163 40


scheme 1

930 47




scheme 3

410 054 12



BDBA HHTP


scheme 1

2160

(X=5)

1865 (25)

1722 (50)

1641 (75)

1421

(100)

1184

1071

1016

0946

0835

295

276

259

258

227

51


(X=5)

1561 (25)

914 (50)

142 (75)

36 (100)

1481

0946

0638

0152

003

298

243

156

153

125






scheme 3

710 031 23


scheme 3

620 036 38


scheme 5

791 040 12


scheme 5

90 8

mp-CTF-2 2255 151 8


scheme 5

1061 0934 14


coordination64


coordination64



1503 157 166

52


scheme 7

1827 118



scheme 1

624 0485 190


(100-X) BDBA


scheme 1

XEsTrz-NiPc-

COF



scheme 1

1742 1115 25


2D-NiPc-BTDA

COF


scheme 1

877 22


scheme 1

420 31


scheme 1

485 31


scheme 1

490 31


scheme 1

440 34


scheme 3

735 032 12


scheme 1

360 020 249

53


scheme 1

3472 135 115

Microwave36

scheme 1

2926


(R=dodecyl)


scheme 1

12


(R=allyl)


scheme 1


scheme 1

4210 166 125


scheme 1


scheme 1


scheme 1

2690 109 11


scheme 3

1360 072 72



5600




2932 154 127



2246 145 118


54

scheme 6


31 2D COFs























55










simulated spectrum
















56








between the layers

32 3D COFs

























57




















materials




rings











58

4 Applications

41 Gas storage



























elsewhere86

59





















dimensional phase

60





























61



(242 Aring)





























62





















wt at 1 bar68



methane









63


































64



































65



































66






sites



























67



































68

























2D COFs







69

































area

70

432 Metal doping


































71





























significantly




72





5 Conclusions












CA Cyanuric acid









73









PA Piperazine








TA Terephthaldehyde








74











75


76



77


78


79


80


81

Appendix B





DOI 101002pssb201100634














82


















83



































84

































85























86













Cu-Cu 250 (257) 250 (250) 263 Cu-O 205 (198) 202 (198) 195 O-C 134 (133) 133-138 (128) 125

OCuO 836-971 (898) 892-907 (873-937)

891 896




α=β=γ=90 (90) a=b=c=26343

α=β=γ=90




87




at DFTB





















88














H2O Periodic


CO

Cu-Cu 267 (266) 262 (260) 250 (260)

Cu-O 205 (197-206) 210 (196-200) 206 (199)

O-C 134 (127) 133 (128) 134 (127)

OCuO 843-955 (889-905)

871-921 (842-930) 842-967 (896)







Cu-O(H2O) Cu-C(CO) 237 (219) 244 (233-

255) 307 (239)

Eads -4045 (-5200) -1648

(-2800)







89













90










adsorbed molecules



91



(MOF-205)

Zn-Zn 330 (317) 322-336 (306-330)

325-331 (318)

Zn-Orsquo 202 (194) 202 (193) 202 (194) Zn-O 204 (192) 202-206

(190-199) 202 205 (193)

O-C 128 (130) 128 (131) 128 (125) ZnOrsquoZn 1095 (1095) 1056-1124

(1055 1092) 107-1118 (1084 1100)

OZnO 1083 1108 (1061)

1048 1145 (981-1281)

1046-1112 (1062 1085)






a=b=37872 (37072) c=3068 (30033) α=β=90 (90) γ=120 (120)

a=b=c=31013 (30353) α=β=γ=90 (90)






Bond Type DFTB Exp


b=1732 c=1365 α=β=γ=90

a=1218 b=1713 c=1326 α=β=γ=90



92
































93

References



34 319 (2001)












Science 316 268 (2007)











94














95


96

Appendix C



Chem Eur J 2011 17 2388 ndash 2392

DOI 101002chem201001290









pore surface







97









98





























been considered






99























boron-oxygen rings











100












101


Table 1)








COF-5 AA -2968 -3060 092

AB -2548 -2618 070

serrated z -3051 -3073 022

serrated a -3052 -3073 021

inclined z -3297 -3045 -252

inclined a -3275 -3044 -231

Monolayer Ecb= 211

COF-1 AA -2683 -2739 056

AB -2186 -2131 -055

serrated z -2810 -2806 -004

inclined z -2784 -2788 004

Monolayer Ecb= 906

COF-6 AA -2881 -2963 082

AB -2127 -2146 019

serrated z -2978 -2996 018

serrated a -2978 -2995 017

inclined z -2946 -2975 029

inclined a -2954 -2974 021

Monolayer Ecb= 185

COF-8 AA -4488 -4617 129

102

AB -2477 -2506 029

serrated z -4614 -4646 032

serrated a -4615 -4647 032

inclined z -4578 -4612 035

inclined a -4561 -4591 030

Monolayer Ecb= 263



























103

























104

References



2007 316 268

























105

Appendix D




DOI103762bjnano18

Abstract













Introduction



106


































107
























108



























109




























110











work [17]


111



COF Building

Blocks

a d ρ

AA AB AA AB

COF-1 I-a 1502 (15620) 351 313 (332) 094 106

COF-1M I-b 2241 349 304 068 078

COF-2M I-c 1492 347 312 095 106

COF-3M I-d 0747 349 327 153 164

PPy-COF I-e 2232 (22163) 349 (3421) 297 084 099

COF-5 II-a 3014 (30020) 347 (3460) 326 056 060

COF-10 II-b 3758 (37810) 347 (3476) 318 045 (045) 050

COF-8 II-c 2251 (22733) 346 (3476) 320 071 (070) 077

COF-6 II-d 1505 (15091) 346 (3599) 327 104 110

TP COF II-e 3750 (37541) 348 (3378) 320 051 056

COF-4M III-a 2171 350 318 073 080

COF-5M III-b 2915 350 318 055 061

COF-6M III-c 1833 345 318 083 090

COF-7M III-d 1083 350 330 129 136

TP COF-1M III-e 2905 349 310 065 074

COF-8M IV-a 1748 359 329 140 148

COF-9M IV-b 2176 349 330 117 174

COF-10M IV-c 2254 342 336 127 128

COF-11M IV-d 1512 346 338 168 172

TP COF-2M IV-e 2173 347 332 134 140

REF-I I 0773 359 336 144 148

REF-III III 1445 353 336 104 121

Graphite 247 343 335 220 227

112

Energetic stability


















2 2 3 COF 12 H O Tl T l (1)

113

2 1 1 COF 6 H O Tt T t (2)

2 1 3 COF 12 H O Hl H l (3)

2 1 2 COF 12 H O Ht H t (4)







COF Building

Blocks

Mono-

layer

AA AB


COF-1 I-a 906 -2683 -1777 33 -2187 -1280 36

COF-1M I-b 949 -4266 -3366 27 -2418 -1469 31

COF-2M I-c 956 -5727 -4771 28 -4734 -3778 30

COF-3M I-d 763 -2506 -1742 38 -2801 -2037 40

PPy-COF I-e 858 -5723 -4866 24 -3855 -2998 26

COF-5 II-a 211 -2968 -2756 24 -2548 -2337 28

COF-10 II-b 317 -3766 -3448 23 -1344 -1026 26

COF-8 II-c 263 -4488 -4224 25 -2477 -2213 28

COF-6 II-d 185 -2881 -2695 28 -2127 -1942 31

TP COF II-e 231 -4453 -4222 24 -1480 -1250 27

COF-4M III-a -033 -1730 -1763 26 -880 -913 26

COF-5M III-b 007 -2533 -2526 25 -972 -965 25

COF-6M III-c 014 -3231 -3217 26 -2134 -2120 28

114

COF-7M III-d -170 -1635 -1805 30 -1607 -1777 32

TP COF-1M III-e -014 -3226 -3240 24 -1277 -1291 24

COF-8M IV-a -787 -2756 -3543 18 -2680 -3467 21

COF-9M IV-b -836 -3577 -4414 17 -3003 -3839 21

COF-10M IV-c -947 -4297 -5244 18 -4192 -5140 22

COF-11M IV-d -403 -2684 -3087 21 -2833 -3236 24

TP COF-2M IV-e 030 -4345 -4315 18 -4117 -4087 21



















115











116













Conclusion









117





Methods





























118







COF Building

Blocks

C-B B-O O-C OBO

COF-1 I-a 1498 (1600) 1393 (1509) 1203 (1200)

COF-1M I-b 1497 1393 1203

COF-2M I-c 1497 1392 1203

COF-3M I-d 1496 1392 1201

PPy-COF I-e 1498 1393 1202 (1190)

COF-5 II-a 1496 (1530) 1399 (1367) 1443 (1384) 1135dagger (1139)

COF-10 II-b 1495 (1553) 1399 (1465) 1443 (1385) 1135dagger (1120)

COF-8 II-c 1495 (1548) 1399 (1479) 1443 1135dagger

COF-6 II-d 1496 1399 1443 1135dagger

TP COF II-e 1496 (1542) 1399 (1396) 1444 (1377) 1135dagger (1182)

COF-4M III-a 1496 1398 1449 1135dagger

COF-5M III-b 1496 1398 1449 1136dagger

COF-6M III-c 1496 1399 1451 1134dagger

COF-7M III-d 1496 1398 1449 1136dagger


COF-8M IV-a 1496 1398 1445 1131dagger

COF-9M IV-b 1495 1398 1444 1131dagger

119

COF-10M IV-c 1495 1391 1418 1126dagger

COF-11M IV-d 1498 1399 1450 1134dagger








COF Building

Blocks

a d ρ


COF-1 I-a 1502 343 343 097 097

COF-1M I-b 2241 341 342 069 069

COF-2M I-c 1492 340 339 097 097

COF-3M I-d 0747 341 342 157 156

PPy-COF I-e 2232 341 341 086 086

120

COF-5 II-a 3014 342 342 341 340 057 057 058 058

COF-10 II-b 3758 341 341 342 340 046 046 046 046

COF-8 II-c 2251 341 341 342 342 073 073 072 072

COF-6 II-d 1505 342 341 340 340 105 106 106 106

TP COF II-e 3750 342 341 342 342 052 052 052 052

COF-4M III-a 2171 344 344 345 344 074 074 074 074

COF-5M III-b 2915 343 342 343 343 056 056 056 056

COF-6M III-c 1833 341 341 342 341 084 084 084 084

COF-7M III-d 1083 344 343 340 344 131 131 132 131

TP COF-1M III-e 2905 343 342 343 342 066 067 066 066

COF-8M IV-a 1748 341 341 342 342 142 142 142 142

COF-9M IV-b 2176 341 341 341 342 119 119 119 119

COF-10M IV-c 2254 340 340 340 340 128 128 128 128

COF-11M IV-d 1512 341 341 340 340 171 171 171 171

TP COF-2M IV-e 2173 340 340 340 340 137 137 137 137

REF-I I 0773 349 345 148 15

REF-III III 1445 348 349 106 106



COF Sa Sz Ia Iz


-1 -2810 -1904 36 -2786 -1880 36

-1M -4426 -3477 30 -4389 -3440 30

-2M -5967 -5011 30 -5833 -4877 30

121

-3M -2667 -1904 40 -2591 -1828 40

PPy- -5916 -5058 26 -5865 -5007 26

-5 -3052 -2841 27 -3051 -2840 26 -3275 -3064 26 -3297 -3086 26

-10 -3868 -3551 26 -3869 -3552 25 -3830 -3513 26 -4293 -3976 25

-8 -4615 -4352 27 -4614 -4351 27 -4571 -4308 27 -4573 -4310 27

-6 -2978 -2793 30 -2978 -2793 30 -3117 -2932 30 -3090 -2905 30

TP -4557 -4326 26 -4562 -4331 26 -4511 -4280 26 -4511 -4280 26

-4M -1811 -1844 28 -1813 -1846 28 -1769 -1802 28 -1880 -1913 28

-5M -2626 -2619 27 -2630 -2623 26 -2597 -2590 26 -2600 -2593 26

-6M -3375 -3361 28 -3381 -3367 28 -3487 -3473 28 -3349 -3335 28

-7M -1724 -1894 32 -1726 -1896 31 -2333 -2503 32 -1866 -2036 31

TP -1M -3327 -3341 26 -3334 -3348 26 -3340 -3354 26 -3353 -3367 26

-8M -2897 -3684 21 -2895 -3682 21 -2971 -3758 21 -2983 -3770 21

-9M -3732 -4568 20 -3733 -4569 20 -3684 -4520 20 -3706 -4542 20

-10M -4512 -5459 21 -4513 -5460 21 -4491 -5438 21 -4495 -5442 21

-11M -2831 -3234 24 -2834 -3237 24 -2816 -3219 24 -2830 -3233 24

TP -2M -4500 -4470 20 -4505 -4475 20 -4495 -4465 20 -4496 -4466 20

122

Appendix E











Introduction








123


































124









Methods



125


















(1) B = 2

2

dV

EdV





tot + m2 Ebb2tot)









126



















Structure Building

Blocks

Cell

parameters

ρ Δ B EF

COF-102 (C) TBPM 2707 (2717) 043 39 (43) 206 -14995

COF-103 (Si) TBPS 2817 (2825) 039 38 (41) 139 -14547

COF-105-C TBPM HHTP 4337 019 33 (43 34) 80 -18080

COF-105 (Si) TBPS HHTP 4444 (4489) 018 32 (41 34) 79 -17055

COF-108 (C) TBPM HHTP 2838 (2840) 017 32 (43 34) 37 -17983

COF-108-Si TBPS HHTP 2920 016 30 (41 34) 29 -18038

COF-202 (C) TBPM TBST 3047 (3010) 050 42 (43 139) 143 -7954

COF-202-Si TBPS TBST 3157 046 39 (41 139) 153 -7632

COF-300 (C) TAM TA 2932 925 049 23 (41 26) 144 -40286

127

(2828 1008)

COF-300-Si TAS TA 3039 959 044 23 (40 26) 133 -39930




good match


















128


















129



130




building units

Conclusion









131

Appendix F




Abstract








(MOFs and COFs)

Introduction





132





















MOFs













133





Methods








Pack19










cutoff of 5000 K










134























PAFs

a

(Aring)

ρ

(g cm-3)

EForm

(kJ mol-1)

Δ

(eV)

B

(GPa)

H2 accessible

free volume

H2 accessible

surface area

135

() (m2 g-1)

PAF-phnl 97 085 -121 47 (55) 360 35 2398

PAF-biphl 167 032 -122 36 (40) 132 73 5697

PAF-pyrn 166 042 -124 26 (28) 192 66 5090

PAF-DPA 210 019 -122 35 (37) 87 84 7240

PAF-ptph 237 016 -119 32 (33) 56 86 6735

PAF-PTCDA 236 024 -122 18 (19) 95 81 5576

PAF-qtphl 308 010 -119 29 (30) 35 91 7275





by

( )

where Ecell EL and














136


the perfect trend




















137

















138


































139











bar


140




















PAF

(g cm-3)

H2 accessible

free volume ()

H2 accessible

surface area

(m2 g-1)

PAF-qtph 010 91 7275

PAF-qtph-2 020 82 7275

PAF-qtph-3 030 73 7275

PAF-qtph-4 040 64 5998



141

















PAFs



142






Conclusions



pore volume















143

References





217


705


295 469


310 1166






O M Science 2007 316 268




Chemistry 2011 21 13498



2009 20 1193


185




deMon 2009






Society 2008 130 11580











2007 111 15350


144




npdf






145

Appendix G


















146



















predefined pores















28

147


















suppressed

















148

































149



Acknowledgement




Methods

























150




151


152














153









(3) P(EP)2DC

















Br Br MeOOC B

OH

OH

+

COOMe

COOMe

COOH

COOH

i ii

154


155






Cu2(bdc)2 C2 1119 50 -076

Cu2(bdc)2 P2 1119 54 -08

Cu2(bdc)2 P4 1119 58 -059

156

Cu2(ndc)2 P2 1335 56 -04

Cu2(bpdc)2 P4 1549 59 -068

Cu2(tpdc)2 P4 1984 59 -091

Cu2(qpdc)2 P4 2424 59 -121

Cu2(P(EP)2DC)2 P4 2512 52 -173

Cu2(ppdc)2 P4 2859 59 -145



References




1127-1129 (2003)






Reviews 112 1105-1124 (2012)



(2012)









(2010)



157



Society 132 7832-7833 (2010)






(2012)



























158






























335-342 (2012)




159



199 (2011)


1051-1054 (1985)






(1996)





Adv Funct Mater 21 4228-4231 (2011)



9320-9325 (2011)

160

Appendix H




INTRODUCTION















161
























162








to 4 nm
























163























164















form

165














166













167


















or outside (P4nmm)



168




















169
























170








the substrate











171







for the SURMOF










neighboring layers





CONCLUSION












172









paddlewheel46















REFERENCES







173




1127


112 1105



38 1450




126 5666


Science 2010 327 846







Chemistry 2005 178 3342


7 5168


2011 17 9320


1166


174




2009 48 5038














11623










175



13 2025












1193





2009



iii










iv

Abstract


















reasoning








metastability









2 Introduction 2









41 Stacking 13


5 3D Frameworks 17






7 Summary 23





List of Figures 32

References 33









1

1 Outline






information






















2

2 Introduction































3








synthetic chemistry





















4








Figure 2















5




crystal structure










6
























7





















8

























9




10
























Pack39








11

32 DFTB Validation



12



















101002pssb201100634








calculations






13


41 Stacking




















14














101002chem201001290


15



























16








17

5 3D Frameworks












silicon atoms






topologies




18







similar to 3D MOFs



















19


frameworks















20




















series

21































22




(SURMOFs-2)




23

7 Summary































24



obtained with DFT































25



































26

































27


































28





densities








as follows

29


















30












TAM (41 eV) + TA (26 eV) COF-300 (23 eV)







31



























32

List of Figures




structure 5














topologies 17



20




33

References













56





423 705


2008 41 1782








501


2005 310 1166





2007 19 2168

34


3450




51 12947


58 185










2001 114 5149


2009 20 1193


2012 2 456








2011 2007






1029

35




13094


1460





47 8826


48 5439












1998 120 8571








2007 111 5648




36


437




15133





37

Appendix A




Contents

1 Introduction








4 Applications

41 Gas storage









432 Metal doping


5 Conclusions


38

1 Introduction









strong bonds


















products5




39






silicates









applications















40




41



































42


































43





















level














44



interactions













respectively58






45











catalyst64












46

































47









48


49



2 g

-1] pore volume [cm

3 g



Area

Pore

volume

Pore

size


scheme 1

711 62850 032

03650

9


scheme 1

1590 0998 27




scheme 1

980 (L) 032 64


scheme 1

1400 (L) 069 187


scheme 1

2080 (L) 144 341




(alkyl = CH3)



(alkyl = C2H5)



(alkyl = C3H7)


50


scheme 1


scheme 1


scheme 1

868 079 314


scheme 1

923 188


Ag(110) surfaces)


6


surface)


6


scheme 1

2000 163 40


scheme 1

930 47




scheme 3

410 054 12



BDBA HHTP


scheme 1

2160

(X=5)

1865 (25)

1722 (50)

1641 (75)

1421

(100)

1184

1071

1016

0946

0835

295

276

259

258

227

51


(X=5)

1561 (25)

914 (50)

142 (75)

36 (100)

1481

0946

0638

0152

003

298

243

156

153

125






scheme 3

710 031 23


scheme 3

620 036 38


scheme 5

791 040 12


scheme 5

90 8

mp-CTF-2 2255 151 8


scheme 5

1061 0934 14


coordination64


coordination64



1503 157 166

52


scheme 7

1827 118



scheme 1

624 0485 190


(100-X) BDBA


scheme 1

XEsTrz-NiPc-

COF



scheme 1

1742 1115 25


2D-NiPc-BTDA

COF


scheme 1

877 22


scheme 1

420 31


scheme 1

485 31


scheme 1

490 31


scheme 1

440 34


scheme 3

735 032 12


scheme 1

360 020 249

53


scheme 1

3472 135 115

Microwave36

scheme 1

2926


(R=dodecyl)


scheme 1

12


(R=allyl)


scheme 1


scheme 1

4210 166 125


scheme 1


scheme 1


scheme 1

2690 109 11


scheme 3

1360 072 72



5600




2932 154 127



2246 145 118


54

scheme 6


31 2D COFs























55










simulated spectrum
















56








between the layers

32 3D COFs

























57




















materials




rings











58

4 Applications

41 Gas storage



























elsewhere86

59





















dimensional phase

60





























61



(242 Aring)





























62





















wt at 1 bar68



methane









63


































64



































65



































66






sites



























67



































68

























2D COFs







69

































area

70

432 Metal doping


































71





























significantly




72





5 Conclusions












CA Cyanuric acid









73









PA Piperazine








TA Terephthaldehyde








74











75


76



77


78


79


80


81

Appendix B





DOI 101002pssb201100634














82


















83



































84

































85























86













Cu-Cu 250 (257) 250 (250) 263 Cu-O 205 (198) 202 (198) 195 O-C 134 (133) 133-138 (128) 125

OCuO 836-971 (898) 892-907 (873-937)

891 896




α=β=γ=90 (90) a=b=c=26343

α=β=γ=90




87




at DFTB





















88














H2O Periodic


CO

Cu-Cu 267 (266) 262 (260) 250 (260)

Cu-O 205 (197-206) 210 (196-200) 206 (199)

O-C 134 (127) 133 (128) 134 (127)

OCuO 843-955 (889-905)

871-921 (842-930) 842-967 (896)







Cu-O(H2O) Cu-C(CO) 237 (219) 244 (233-

255) 307 (239)

Eads -4045 (-5200) -1648

(-2800)







89













90










adsorbed molecules



91



(MOF-205)

Zn-Zn 330 (317) 322-336 (306-330)

325-331 (318)

Zn-Orsquo 202 (194) 202 (193) 202 (194) Zn-O 204 (192) 202-206

(190-199) 202 205 (193)

O-C 128 (130) 128 (131) 128 (125) ZnOrsquoZn 1095 (1095) 1056-1124

(1055 1092) 107-1118 (1084 1100)

OZnO 1083 1108 (1061)

1048 1145 (981-1281)

1046-1112 (1062 1085)






a=b=37872 (37072) c=3068 (30033) α=β=90 (90) γ=120 (120)

a=b=c=31013 (30353) α=β=γ=90 (90)






Bond Type DFTB Exp


b=1732 c=1365 α=β=γ=90

a=1218 b=1713 c=1326 α=β=γ=90



92
































93

References



34 319 (2001)












Science 316 268 (2007)











94














95


96

Appendix C



Chem Eur J 2011 17 2388 ndash 2392

DOI 101002chem201001290









pore surface







97









98





























been considered






99























boron-oxygen rings











100












101


Table 1)








COF-5 AA -2968 -3060 092

AB -2548 -2618 070

serrated z -3051 -3073 022

serrated a -3052 -3073 021

inclined z -3297 -3045 -252

inclined a -3275 -3044 -231

Monolayer Ecb= 211

COF-1 AA -2683 -2739 056

AB -2186 -2131 -055

serrated z -2810 -2806 -004

inclined z -2784 -2788 004

Monolayer Ecb= 906

COF-6 AA -2881 -2963 082

AB -2127 -2146 019

serrated z -2978 -2996 018

serrated a -2978 -2995 017

inclined z -2946 -2975 029

inclined a -2954 -2974 021

Monolayer Ecb= 185

COF-8 AA -4488 -4617 129

102

AB -2477 -2506 029

serrated z -4614 -4646 032

serrated a -4615 -4647 032

inclined z -4578 -4612 035

inclined a -4561 -4591 030

Monolayer Ecb= 263



























103

























104

References



2007 316 268

























105

Appendix D




DOI103762bjnano18

Abstract













Introduction



106


































107
























108



























109




























110











work [17]


111



COF Building

Blocks

a d ρ

AA AB AA AB

COF-1 I-a 1502 (15620) 351 313 (332) 094 106

COF-1M I-b 2241 349 304 068 078

COF-2M I-c 1492 347 312 095 106

COF-3M I-d 0747 349 327 153 164

PPy-COF I-e 2232 (22163) 349 (3421) 297 084 099

COF-5 II-a 3014 (30020) 347 (3460) 326 056 060

COF-10 II-b 3758 (37810) 347 (3476) 318 045 (045) 050

COF-8 II-c 2251 (22733) 346 (3476) 320 071 (070) 077

COF-6 II-d 1505 (15091) 346 (3599) 327 104 110

TP COF II-e 3750 (37541) 348 (3378) 320 051 056

COF-4M III-a 2171 350 318 073 080

COF-5M III-b 2915 350 318 055 061

COF-6M III-c 1833 345 318 083 090

COF-7M III-d 1083 350 330 129 136

TP COF-1M III-e 2905 349 310 065 074

COF-8M IV-a 1748 359 329 140 148

COF-9M IV-b 2176 349 330 117 174

COF-10M IV-c 2254 342 336 127 128

COF-11M IV-d 1512 346 338 168 172

TP COF-2M IV-e 2173 347 332 134 140

REF-I I 0773 359 336 144 148

REF-III III 1445 353 336 104 121

Graphite 247 343 335 220 227

112

Energetic stability


















2 2 3 COF 12 H O Tl T l (1)

113

2 1 1 COF 6 H O Tt T t (2)

2 1 3 COF 12 H O Hl H l (3)

2 1 2 COF 12 H O Ht H t (4)







COF Building

Blocks

Mono-

layer

AA AB


COF-1 I-a 906 -2683 -1777 33 -2187 -1280 36

COF-1M I-b 949 -4266 -3366 27 -2418 -1469 31

COF-2M I-c 956 -5727 -4771 28 -4734 -3778 30

COF-3M I-d 763 -2506 -1742 38 -2801 -2037 40

PPy-COF I-e 858 -5723 -4866 24 -3855 -2998 26

COF-5 II-a 211 -2968 -2756 24 -2548 -2337 28

COF-10 II-b 317 -3766 -3448 23 -1344 -1026 26

COF-8 II-c 263 -4488 -4224 25 -2477 -2213 28

COF-6 II-d 185 -2881 -2695 28 -2127 -1942 31

TP COF II-e 231 -4453 -4222 24 -1480 -1250 27

COF-4M III-a -033 -1730 -1763 26 -880 -913 26

COF-5M III-b 007 -2533 -2526 25 -972 -965 25

COF-6M III-c 014 -3231 -3217 26 -2134 -2120 28

114

COF-7M III-d -170 -1635 -1805 30 -1607 -1777 32

TP COF-1M III-e -014 -3226 -3240 24 -1277 -1291 24

COF-8M IV-a -787 -2756 -3543 18 -2680 -3467 21

COF-9M IV-b -836 -3577 -4414 17 -3003 -3839 21

COF-10M IV-c -947 -4297 -5244 18 -4192 -5140 22

COF-11M IV-d -403 -2684 -3087 21 -2833 -3236 24

TP COF-2M IV-e 030 -4345 -4315 18 -4117 -4087 21



















115











116













Conclusion









117





Methods





























118







COF Building

Blocks

C-B B-O O-C OBO

COF-1 I-a 1498 (1600) 1393 (1509) 1203 (1200)

COF-1M I-b 1497 1393 1203

COF-2M I-c 1497 1392 1203

COF-3M I-d 1496 1392 1201

PPy-COF I-e 1498 1393 1202 (1190)

COF-5 II-a 1496 (1530) 1399 (1367) 1443 (1384) 1135dagger (1139)

COF-10 II-b 1495 (1553) 1399 (1465) 1443 (1385) 1135dagger (1120)

COF-8 II-c 1495 (1548) 1399 (1479) 1443 1135dagger

COF-6 II-d 1496 1399 1443 1135dagger

TP COF II-e 1496 (1542) 1399 (1396) 1444 (1377) 1135dagger (1182)

COF-4M III-a 1496 1398 1449 1135dagger

COF-5M III-b 1496 1398 1449 1136dagger

COF-6M III-c 1496 1399 1451 1134dagger

COF-7M III-d 1496 1398 1449 1136dagger


COF-8M IV-a 1496 1398 1445 1131dagger

COF-9M IV-b 1495 1398 1444 1131dagger

119

COF-10M IV-c 1495 1391 1418 1126dagger

COF-11M IV-d 1498 1399 1450 1134dagger








COF Building

Blocks

a d ρ


COF-1 I-a 1502 343 343 097 097

COF-1M I-b 2241 341 342 069 069

COF-2M I-c 1492 340 339 097 097

COF-3M I-d 0747 341 342 157 156

PPy-COF I-e 2232 341 341 086 086

120

COF-5 II-a 3014 342 342 341 340 057 057 058 058

COF-10 II-b 3758 341 341 342 340 046 046 046 046

COF-8 II-c 2251 341 341 342 342 073 073 072 072

COF-6 II-d 1505 342 341 340 340 105 106 106 106

TP COF II-e 3750 342 341 342 342 052 052 052 052

COF-4M III-a 2171 344 344 345 344 074 074 074 074

COF-5M III-b 2915 343 342 343 343 056 056 056 056

COF-6M III-c 1833 341 341 342 341 084 084 084 084

COF-7M III-d 1083 344 343 340 344 131 131 132 131

TP COF-1M III-e 2905 343 342 343 342 066 067 066 066

COF-8M IV-a 1748 341 341 342 342 142 142 142 142

COF-9M IV-b 2176 341 341 341 342 119 119 119 119

COF-10M IV-c 2254 340 340 340 340 128 128 128 128

COF-11M IV-d 1512 341 341 340 340 171 171 171 171

TP COF-2M IV-e 2173 340 340 340 340 137 137 137 137

REF-I I 0773 349 345 148 15

REF-III III 1445 348 349 106 106



COF Sa Sz Ia Iz


-1 -2810 -1904 36 -2786 -1880 36

-1M -4426 -3477 30 -4389 -3440 30

-2M -5967 -5011 30 -5833 -4877 30

121

-3M -2667 -1904 40 -2591 -1828 40

PPy- -5916 -5058 26 -5865 -5007 26

-5 -3052 -2841 27 -3051 -2840 26 -3275 -3064 26 -3297 -3086 26

-10 -3868 -3551 26 -3869 -3552 25 -3830 -3513 26 -4293 -3976 25

-8 -4615 -4352 27 -4614 -4351 27 -4571 -4308 27 -4573 -4310 27

-6 -2978 -2793 30 -2978 -2793 30 -3117 -2932 30 -3090 -2905 30

TP -4557 -4326 26 -4562 -4331 26 -4511 -4280 26 -4511 -4280 26

-4M -1811 -1844 28 -1813 -1846 28 -1769 -1802 28 -1880 -1913 28

-5M -2626 -2619 27 -2630 -2623 26 -2597 -2590 26 -2600 -2593 26

-6M -3375 -3361 28 -3381 -3367 28 -3487 -3473 28 -3349 -3335 28

-7M -1724 -1894 32 -1726 -1896 31 -2333 -2503 32 -1866 -2036 31

TP -1M -3327 -3341 26 -3334 -3348 26 -3340 -3354 26 -3353 -3367 26

-8M -2897 -3684 21 -2895 -3682 21 -2971 -3758 21 -2983 -3770 21

-9M -3732 -4568 20 -3733 -4569 20 -3684 -4520 20 -3706 -4542 20

-10M -4512 -5459 21 -4513 -5460 21 -4491 -5438 21 -4495 -5442 21

-11M -2831 -3234 24 -2834 -3237 24 -2816 -3219 24 -2830 -3233 24

TP -2M -4500 -4470 20 -4505 -4475 20 -4495 -4465 20 -4496 -4466 20

122

Appendix E











Introduction








123


































124









Methods



125


















(1) B = 2

2

dV

EdV





tot + m2 Ebb2tot)









126



















Structure Building

Blocks

Cell

parameters

ρ Δ B EF

COF-102 (C) TBPM 2707 (2717) 043 39 (43) 206 -14995

COF-103 (Si) TBPS 2817 (2825) 039 38 (41) 139 -14547

COF-105-C TBPM HHTP 4337 019 33 (43 34) 80 -18080

COF-105 (Si) TBPS HHTP 4444 (4489) 018 32 (41 34) 79 -17055

COF-108 (C) TBPM HHTP 2838 (2840) 017 32 (43 34) 37 -17983

COF-108-Si TBPS HHTP 2920 016 30 (41 34) 29 -18038

COF-202 (C) TBPM TBST 3047 (3010) 050 42 (43 139) 143 -7954

COF-202-Si TBPS TBST 3157 046 39 (41 139) 153 -7632

COF-300 (C) TAM TA 2932 925 049 23 (41 26) 144 -40286

127

(2828 1008)

COF-300-Si TAS TA 3039 959 044 23 (40 26) 133 -39930




good match


















128


















129



130




building units

Conclusion









131

Appendix F




Abstract








(MOFs and COFs)

Introduction





132





















MOFs













133





Methods








Pack19










cutoff of 5000 K










134























PAFs

a

(Aring)

ρ

(g cm-3)

EForm

(kJ mol-1)

Δ

(eV)

B

(GPa)

H2 accessible

free volume

H2 accessible

surface area

135

() (m2 g-1)

PAF-phnl 97 085 -121 47 (55) 360 35 2398

PAF-biphl 167 032 -122 36 (40) 132 73 5697

PAF-pyrn 166 042 -124 26 (28) 192 66 5090

PAF-DPA 210 019 -122 35 (37) 87 84 7240

PAF-ptph 237 016 -119 32 (33) 56 86 6735

PAF-PTCDA 236 024 -122 18 (19) 95 81 5576

PAF-qtphl 308 010 -119 29 (30) 35 91 7275





by

( )

where Ecell EL and














136


the perfect trend




















137

















138


































139











bar


140




















PAF

(g cm-3)

H2 accessible

free volume ()

H2 accessible

surface area

(m2 g-1)

PAF-qtph 010 91 7275

PAF-qtph-2 020 82 7275

PAF-qtph-3 030 73 7275

PAF-qtph-4 040 64 5998



141

















PAFs



142






Conclusions



pore volume















143

References





217


705


295 469


310 1166






O M Science 2007 316 268




Chemistry 2011 21 13498



2009 20 1193


185




deMon 2009






Society 2008 130 11580











2007 111 15350


144




npdf






145

Appendix G


















146



















predefined pores















28

147


















suppressed

















148

































149



Acknowledgement




Methods

























150




151


152














153









(3) P(EP)2DC

















Br Br MeOOC B

OH

OH

+

COOMe

COOMe

COOH

COOH

i ii

154


155






Cu2(bdc)2 C2 1119 50 -076

Cu2(bdc)2 P2 1119 54 -08

Cu2(bdc)2 P4 1119 58 -059

156

Cu2(ndc)2 P2 1335 56 -04

Cu2(bpdc)2 P4 1549 59 -068

Cu2(tpdc)2 P4 1984 59 -091

Cu2(qpdc)2 P4 2424 59 -121

Cu2(P(EP)2DC)2 P4 2512 52 -173

Cu2(ppdc)2 P4 2859 59 -145



References




1127-1129 (2003)






Reviews 112 1105-1124 (2012)



(2012)









(2010)



157



Society 132 7832-7833 (2010)






(2012)



























158






























335-342 (2012)




159



199 (2011)


1051-1054 (1985)






(1996)





Adv Funct Mater 21 4228-4231 (2011)



9320-9325 (2011)

160

Appendix H




INTRODUCTION















161
























162








to 4 nm
























163























164















form

165














166













167


















or outside (P4nmm)



168




















169
























170








the substrate











171







for the SURMOF










neighboring layers





CONCLUSION












172









paddlewheel46















REFERENCES







173




1127


112 1105



38 1450




126 5666


Science 2010 327 846







Chemistry 2005 178 3342


7 5168


2011 17 9320


1166


174




2009 48 5038














11623










175



13 2025












1193





2009



iv

Abstract


















reasoning








metastability









2 Introduction 2









41 Stacking 13


5 3D Frameworks 17






7 Summary 23





List of Figures 32

References 33









1

1 Outline






information






















2

2 Introduction































3








synthetic chemistry





















4








Figure 2















5




crystal structure










6
























7





















8

























9




10
























Pack39








11

32 DFTB Validation



12



















101002pssb201100634








calculations






13


41 Stacking




















14














101002chem201001290


15



























16








17

5 3D Frameworks












silicon atoms






topologies




18







similar to 3D MOFs



















19


frameworks















20




















series

21































22




(SURMOFs-2)




23

7 Summary































24



obtained with DFT































25



































26

































27


































28





densities








as follows

29


















30












TAM (41 eV) + TA (26 eV) COF-300 (23 eV)







31



























32

List of Figures




structure 5














topologies 17



20




33

References













56





423 705


2008 41 1782








501


2005 310 1166





2007 19 2168

34


3450




51 12947


58 185










2001 114 5149


2009 20 1193


2012 2 456








2011 2007






1029

35




13094


1460





47 8826


48 5439












1998 120 8571








2007 111 5648




36


437




15133





37

Appendix A




Contents

1 Introduction








4 Applications

41 Gas storage









432 Metal doping


5 Conclusions


38

1 Introduction









strong bonds


















products5




39






silicates









applications















40




41



































42


































43





















level














44



interactions













respectively58






45











catalyst64












46

































47









48


49



2 g

-1] pore volume [cm

3 g



Area

Pore

volume

Pore

size


scheme 1

711 62850 032

03650

9


scheme 1

1590 0998 27




scheme 1

980 (L) 032 64


scheme 1

1400 (L) 069 187


scheme 1

2080 (L) 144 341




(alkyl = CH3)



(alkyl = C2H5)



(alkyl = C3H7)


50


scheme 1


scheme 1


scheme 1

868 079 314


scheme 1

923 188


Ag(110) surfaces)


6


surface)


6


scheme 1

2000 163 40


scheme 1

930 47




scheme 3

410 054 12



BDBA HHTP


scheme 1

2160

(X=5)

1865 (25)

1722 (50)

1641 (75)

1421

(100)

1184

1071

1016

0946

0835

295

276

259

258

227

51


(X=5)

1561 (25)

914 (50)

142 (75)

36 (100)

1481

0946

0638

0152

003

298

243

156

153

125






scheme 3

710 031 23


scheme 3

620 036 38


scheme 5

791 040 12


scheme 5

90 8

mp-CTF-2 2255 151 8


scheme 5

1061 0934 14


coordination64


coordination64



1503 157 166

52


scheme 7

1827 118



scheme 1

624 0485 190


(100-X) BDBA


scheme 1

XEsTrz-NiPc-

COF



scheme 1

1742 1115 25


2D-NiPc-BTDA

COF


scheme 1

877 22


scheme 1

420 31


scheme 1

485 31


scheme 1

490 31


scheme 1

440 34


scheme 3

735 032 12


scheme 1

360 020 249

53


scheme 1

3472 135 115

Microwave36

scheme 1

2926


(R=dodecyl)


scheme 1

12


(R=allyl)


scheme 1


scheme 1

4210 166 125


scheme 1


scheme 1


scheme 1

2690 109 11


scheme 3

1360 072 72



5600




2932 154 127



2246 145 118


54

scheme 6


31 2D COFs























55










simulated spectrum
















56








between the layers

32 3D COFs

























57




















materials




rings











58

4 Applications

41 Gas storage



























elsewhere86

59





















dimensional phase

60





























61



(242 Aring)





























62





















wt at 1 bar68



methane









63


































64



































65



































66






sites



























67



































68

























2D COFs







69

































area

70

432 Metal doping


































71





























significantly




72





5 Conclusions












CA Cyanuric acid









73









PA Piperazine








TA Terephthaldehyde








74











75


76



77


78


79


80


81

Appendix B





DOI 101002pssb201100634














82


















83



































84

































85























86













Cu-Cu 250 (257) 250 (250) 263 Cu-O 205 (198) 202 (198) 195 O-C 134 (133) 133-138 (128) 125

OCuO 836-971 (898) 892-907 (873-937)

891 896




α=β=γ=90 (90) a=b=c=26343

α=β=γ=90




87




at DFTB





















88














H2O Periodic


CO

Cu-Cu 267 (266) 262 (260) 250 (260)

Cu-O 205 (197-206) 210 (196-200) 206 (199)

O-C 134 (127) 133 (128) 134 (127)

OCuO 843-955 (889-905)

871-921 (842-930) 842-967 (896)







Cu-O(H2O) Cu-C(CO) 237 (219) 244 (233-

255) 307 (239)

Eads -4045 (-5200) -1648

(-2800)







89













90










adsorbed molecules



91



(MOF-205)

Zn-Zn 330 (317) 322-336 (306-330)

325-331 (318)

Zn-Orsquo 202 (194) 202 (193) 202 (194) Zn-O 204 (192) 202-206

(190-199) 202 205 (193)

O-C 128 (130) 128 (131) 128 (125) ZnOrsquoZn 1095 (1095) 1056-1124

(1055 1092) 107-1118 (1084 1100)

OZnO 1083 1108 (1061)

1048 1145 (981-1281)

1046-1112 (1062 1085)






a=b=37872 (37072) c=3068 (30033) α=β=90 (90) γ=120 (120)

a=b=c=31013 (30353) α=β=γ=90 (90)






Bond Type DFTB Exp


b=1732 c=1365 α=β=γ=90

a=1218 b=1713 c=1326 α=β=γ=90



92
































93

References



34 319 (2001)












Science 316 268 (2007)











94














95


96

Appendix C



Chem Eur J 2011 17 2388 ndash 2392

DOI 101002chem201001290









pore surface







97









98





























been considered






99























boron-oxygen rings











100












101


Table 1)








COF-5 AA -2968 -3060 092

AB -2548 -2618 070

serrated z -3051 -3073 022

serrated a -3052 -3073 021

inclined z -3297 -3045 -252

inclined a -3275 -3044 -231

Monolayer Ecb= 211

COF-1 AA -2683 -2739 056

AB -2186 -2131 -055

serrated z -2810 -2806 -004

inclined z -2784 -2788 004

Monolayer Ecb= 906

COF-6 AA -2881 -2963 082

AB -2127 -2146 019

serrated z -2978 -2996 018

serrated a -2978 -2995 017

inclined z -2946 -2975 029

inclined a -2954 -2974 021

Monolayer Ecb= 185

COF-8 AA -4488 -4617 129

102

AB -2477 -2506 029

serrated z -4614 -4646 032

serrated a -4615 -4647 032

inclined z -4578 -4612 035

inclined a -4561 -4591 030

Monolayer Ecb= 263



























103

























104

References



2007 316 268

























105

Appendix D




DOI103762bjnano18

Abstract













Introduction



106


































107
























108



























109




























110











work [17]


111



COF Building

Blocks

a d ρ

AA AB AA AB

COF-1 I-a 1502 (15620) 351 313 (332) 094 106

COF-1M I-b 2241 349 304 068 078

COF-2M I-c 1492 347 312 095 106

COF-3M I-d 0747 349 327 153 164

PPy-COF I-e 2232 (22163) 349 (3421) 297 084 099

COF-5 II-a 3014 (30020) 347 (3460) 326 056 060

COF-10 II-b 3758 (37810) 347 (3476) 318 045 (045) 050

COF-8 II-c 2251 (22733) 346 (3476) 320 071 (070) 077

COF-6 II-d 1505 (15091) 346 (3599) 327 104 110

TP COF II-e 3750 (37541) 348 (3378) 320 051 056

COF-4M III-a 2171 350 318 073 080

COF-5M III-b 2915 350 318 055 061

COF-6M III-c 1833 345 318 083 090

COF-7M III-d 1083 350 330 129 136

TP COF-1M III-e 2905 349 310 065 074

COF-8M IV-a 1748 359 329 140 148

COF-9M IV-b 2176 349 330 117 174

COF-10M IV-c 2254 342 336 127 128

COF-11M IV-d 1512 346 338 168 172

TP COF-2M IV-e 2173 347 332 134 140

REF-I I 0773 359 336 144 148

REF-III III 1445 353 336 104 121

Graphite 247 343 335 220 227

112

Energetic stability


















2 2 3 COF 12 H O Tl T l (1)

113

2 1 1 COF 6 H O Tt T t (2)

2 1 3 COF 12 H O Hl H l (3)

2 1 2 COF 12 H O Ht H t (4)







COF Building

Blocks

Mono-

layer

AA AB


COF-1 I-a 906 -2683 -1777 33 -2187 -1280 36

COF-1M I-b 949 -4266 -3366 27 -2418 -1469 31

COF-2M I-c 956 -5727 -4771 28 -4734 -3778 30

COF-3M I-d 763 -2506 -1742 38 -2801 -2037 40

PPy-COF I-e 858 -5723 -4866 24 -3855 -2998 26

COF-5 II-a 211 -2968 -2756 24 -2548 -2337 28

COF-10 II-b 317 -3766 -3448 23 -1344 -1026 26

COF-8 II-c 263 -4488 -4224 25 -2477 -2213 28

COF-6 II-d 185 -2881 -2695 28 -2127 -1942 31

TP COF II-e 231 -4453 -4222 24 -1480 -1250 27

COF-4M III-a -033 -1730 -1763 26 -880 -913 26

COF-5M III-b 007 -2533 -2526 25 -972 -965 25

COF-6M III-c 014 -3231 -3217 26 -2134 -2120 28

114

COF-7M III-d -170 -1635 -1805 30 -1607 -1777 32

TP COF-1M III-e -014 -3226 -3240 24 -1277 -1291 24

COF-8M IV-a -787 -2756 -3543 18 -2680 -3467 21

COF-9M IV-b -836 -3577 -4414 17 -3003 -3839 21

COF-10M IV-c -947 -4297 -5244 18 -4192 -5140 22

COF-11M IV-d -403 -2684 -3087 21 -2833 -3236 24

TP COF-2M IV-e 030 -4345 -4315 18 -4117 -4087 21



















115











116













Conclusion









117





Methods





























118







COF Building

Blocks

C-B B-O O-C OBO

COF-1 I-a 1498 (1600) 1393 (1509) 1203 (1200)

COF-1M I-b 1497 1393 1203

COF-2M I-c 1497 1392 1203

COF-3M I-d 1496 1392 1201

PPy-COF I-e 1498 1393 1202 (1190)

COF-5 II-a 1496 (1530) 1399 (1367) 1443 (1384) 1135dagger (1139)

COF-10 II-b 1495 (1553) 1399 (1465) 1443 (1385) 1135dagger (1120)

COF-8 II-c 1495 (1548) 1399 (1479) 1443 1135dagger

COF-6 II-d 1496 1399 1443 1135dagger

TP COF II-e 1496 (1542) 1399 (1396) 1444 (1377) 1135dagger (1182)

COF-4M III-a 1496 1398 1449 1135dagger

COF-5M III-b 1496 1398 1449 1136dagger

COF-6M III-c 1496 1399 1451 1134dagger

COF-7M III-d 1496 1398 1449 1136dagger


COF-8M IV-a 1496 1398 1445 1131dagger

COF-9M IV-b 1495 1398 1444 1131dagger

119

COF-10M IV-c 1495 1391 1418 1126dagger

COF-11M IV-d 1498 1399 1450 1134dagger








COF Building

Blocks

a d ρ


COF-1 I-a 1502 343 343 097 097

COF-1M I-b 2241 341 342 069 069

COF-2M I-c 1492 340 339 097 097

COF-3M I-d 0747 341 342 157 156

PPy-COF I-e 2232 341 341 086 086

120

COF-5 II-a 3014 342 342 341 340 057 057 058 058

COF-10 II-b 3758 341 341 342 340 046 046 046 046

COF-8 II-c 2251 341 341 342 342 073 073 072 072

COF-6 II-d 1505 342 341 340 340 105 106 106 106

TP COF II-e 3750 342 341 342 342 052 052 052 052

COF-4M III-a 2171 344 344 345 344 074 074 074 074

COF-5M III-b 2915 343 342 343 343 056 056 056 056

COF-6M III-c 1833 341 341 342 341 084 084 084 084

COF-7M III-d 1083 344 343 340 344 131 131 132 131

TP COF-1M III-e 2905 343 342 343 342 066 067 066 066

COF-8M IV-a 1748 341 341 342 342 142 142 142 142

COF-9M IV-b 2176 341 341 341 342 119 119 119 119

COF-10M IV-c 2254 340 340 340 340 128 128 128 128

COF-11M IV-d 1512 341 341 340 340 171 171 171 171

TP COF-2M IV-e 2173 340 340 340 340 137 137 137 137

REF-I I 0773 349 345 148 15

REF-III III 1445 348 349 106 106



COF Sa Sz Ia Iz


-1 -2810 -1904 36 -2786 -1880 36

-1M -4426 -3477 30 -4389 -3440 30

-2M -5967 -5011 30 -5833 -4877 30

121

-3M -2667 -1904 40 -2591 -1828 40

PPy- -5916 -5058 26 -5865 -5007 26

-5 -3052 -2841 27 -3051 -2840 26 -3275 -3064 26 -3297 -3086 26

-10 -3868 -3551 26 -3869 -3552 25 -3830 -3513 26 -4293 -3976 25

-8 -4615 -4352 27 -4614 -4351 27 -4571 -4308 27 -4573 -4310 27

-6 -2978 -2793 30 -2978 -2793 30 -3117 -2932 30 -3090 -2905 30

TP -4557 -4326 26 -4562 -4331 26 -4511 -4280 26 -4511 -4280 26

-4M -1811 -1844 28 -1813 -1846 28 -1769 -1802 28 -1880 -1913 28

-5M -2626 -2619 27 -2630 -2623 26 -2597 -2590 26 -2600 -2593 26

-6M -3375 -3361 28 -3381 -3367 28 -3487 -3473 28 -3349 -3335 28

-7M -1724 -1894 32 -1726 -1896 31 -2333 -2503 32 -1866 -2036 31

TP -1M -3327 -3341 26 -3334 -3348 26 -3340 -3354 26 -3353 -3367 26

-8M -2897 -3684 21 -2895 -3682 21 -2971 -3758 21 -2983 -3770 21

-9M -3732 -4568 20 -3733 -4569 20 -3684 -4520 20 -3706 -4542 20

-10M -4512 -5459 21 -4513 -5460 21 -4491 -5438 21 -4495 -5442 21

-11M -2831 -3234 24 -2834 -3237 24 -2816 -3219 24 -2830 -3233 24

TP -2M -4500 -4470 20 -4505 -4475 20 -4495 -4465 20 -4496 -4466 20

122

Appendix E











Introduction








123


































124









Methods



125


















(1) B = 2

2

dV

EdV





tot + m2 Ebb2tot)









126



















Structure Building

Blocks

Cell

parameters

ρ Δ B EF

COF-102 (C) TBPM 2707 (2717) 043 39 (43) 206 -14995

COF-103 (Si) TBPS 2817 (2825) 039 38 (41) 139 -14547

COF-105-C TBPM HHTP 4337 019 33 (43 34) 80 -18080

COF-105 (Si) TBPS HHTP 4444 (4489) 018 32 (41 34) 79 -17055

COF-108 (C) TBPM HHTP 2838 (2840) 017 32 (43 34) 37 -17983

COF-108-Si TBPS HHTP 2920 016 30 (41 34) 29 -18038

COF-202 (C) TBPM TBST 3047 (3010) 050 42 (43 139) 143 -7954

COF-202-Si TBPS TBST 3157 046 39 (41 139) 153 -7632

COF-300 (C) TAM TA 2932 925 049 23 (41 26) 144 -40286

127

(2828 1008)

COF-300-Si TAS TA 3039 959 044 23 (40 26) 133 -39930




good match


















128


















129



130




building units

Conclusion









131

Appendix F




Abstract








(MOFs and COFs)

Introduction





132





















MOFs













133





Methods








Pack19










cutoff of 5000 K










134























PAFs

a

(Aring)

ρ

(g cm-3)

EForm

(kJ mol-1)

Δ

(eV)

B

(GPa)

H2 accessible

free volume

H2 accessible

surface area

135

() (m2 g-1)

PAF-phnl 97 085 -121 47 (55) 360 35 2398

PAF-biphl 167 032 -122 36 (40) 132 73 5697

PAF-pyrn 166 042 -124 26 (28) 192 66 5090

PAF-DPA 210 019 -122 35 (37) 87 84 7240

PAF-ptph 237 016 -119 32 (33) 56 86 6735

PAF-PTCDA 236 024 -122 18 (19) 95 81 5576

PAF-qtphl 308 010 -119 29 (30) 35 91 7275





by

( )

where Ecell EL and














136


the perfect trend




















137

















138


































139











bar


140




















PAF

(g cm-3)

H2 accessible

free volume ()

H2 accessible

surface area

(m2 g-1)

PAF-qtph 010 91 7275

PAF-qtph-2 020 82 7275

PAF-qtph-3 030 73 7275

PAF-qtph-4 040 64 5998



141

















PAFs



142






Conclusions



pore volume















143

References





217


705


295 469


310 1166






O M Science 2007 316 268




Chemistry 2011 21 13498



2009 20 1193


185




deMon 2009






Society 2008 130 11580











2007 111 15350


144




npdf






145

Appendix G


















146



















predefined pores















28

147


















suppressed

















148

































149



Acknowledgement




Methods

























150




151


152














153









(3) P(EP)2DC

















Br Br MeOOC B

OH

OH

+

COOMe

COOMe

COOH

COOH

i ii

154


155






Cu2(bdc)2 C2 1119 50 -076

Cu2(bdc)2 P2 1119 54 -08

Cu2(bdc)2 P4 1119 58 -059

156

Cu2(ndc)2 P2 1335 56 -04

Cu2(bpdc)2 P4 1549 59 -068

Cu2(tpdc)2 P4 1984 59 -091

Cu2(qpdc)2 P4 2424 59 -121

Cu2(P(EP)2DC)2 P4 2512 52 -173

Cu2(ppdc)2 P4 2859 59 -145



References




1127-1129 (2003)






Reviews 112 1105-1124 (2012)



(2012)









(2010)



157



Society 132 7832-7833 (2010)






(2012)



























158






























335-342 (2012)




159



199 (2011)


1051-1054 (1985)






(1996)





Adv Funct Mater 21 4228-4231 (2011)



9320-9325 (2011)

160

Appendix H




INTRODUCTION















161
























162








to 4 nm
























163























164















form

165














166













167


















or outside (P4nmm)



168




















169
























170








the substrate











171







for the SURMOF










neighboring layers





CONCLUSION












172









paddlewheel46















REFERENCES







173




1127


112 1105



38 1450




126 5666


Science 2010 327 846







Chemistry 2005 178 3342


7 5168


2011 17 9320


1166


174




2009 48 5038














11623










175



13 2025












1193





2009



computational studies of structure, stability and

Documents