Thiol SAM's

Studied by DFT

David Karhánek

Computational Materials Physics

University of Vienna

ICIQ Tarragona, May 8th, 2009

2

Outline

1. SAM's – Overview

2. Thiols as SAM's

3. Methane Thiol on Ni, Pd, Pt

4. Conclusions, Outlook

3

SAM may refer to:

* SAM (vehicles), a Greek truck manufacturer

* American Samoa (IOC and FIFA country code: SAM)

* Southern Annular Mode, a mode of atmospheric variability of the southern

hemisphere

* S-adenosyl methionine

* Scanning acoustic microscope

* Seattle Art Museum

* Secure Access Module

* Security Account Manager, the accounts database used by Microsoft Windows NT

* Self-assembled monolayer

* Sequential access memory, a class of storage devices that are read sequentially

* Small article monitor

* Sociedad Aeronáutica de Medellín, a Colombian airline

* Society of American Magicians

* Software Automatic Mouth

* Student Association of Missouri

* Surface-to-air missile, a missile designed to be launched from the ground to

destroy aircraft

* System Administration Manager, HP-UX System Administration Manager

* Sympathetic adrenal medullary system, related to the sympathetic nervous system

SAM's

www.wikipedia.org

4

SAM's

C11H23S @ Au(111)

5

Preparation of SAM's

A. Ulman, Chem. Rev. 96, 1533 (1996)

6

SAM's

SAM's (Self-Assembled Monolayers):

1. Fatty acids R-COOH

2. Organosilicium derivatives R-SiH3

3. Multilayers of diphosphates R(PO32-)2

4. Alkyls on silicium

5. Organosulfur adsorbates on metals and semiconductors R-SH, R2S

7

(1) Carboxylic Acids

Adsorptives:

CnH2n+1COOH („fatty acids“)

Substrates:

● Ag

● AgO

● Al2O3

● CuO

Acid-Base reactions

8

(2) Organosilicium Derivatives

Adsorptives:

● R-SiCl3

● R-Si(OR)Cl2

● R-Si(NH2)Cl2

Substrates:

● SiO2, Al2O3, quartz,

glass, GeO2, Au

Hydrolysis reactions

9

(3) Multilayers of Diphosphates

Adsorptives:

● Diphosphonic acids

● Zr4+ salt as a linker

Substrates:

● SiO2

● Silicium

● Au

Acid-Base reaction

10

(4) Alkyl Monolayers on Silicium

Adsorptives:

● Alkyl radicals R˙

Substrates:

● H-terminated silicium

11

(5) Organosulfurs on Metals

Adsorptives:

Substrates:

● Au, Ag, Ni, Pd, Pt, Cu,

Fe, Mo, W, Ru, Rh, Al

● GaAs, InP

12

SAM's – Study Techniques

● STM

● AFM (up to C12-chainlength)

● LEED

● IR – SFG, Raman

● HREELS

● TPD

● DFT calculations

13

From SAM's to Multilayers

Methyl 23-(trichlorosilyl)tricosanoate

multilayers on SiO2

Linkers:

● -O-Si- bonds

● -CO-NH- amidic

● -N=N- diazo-group

● ...

A. Ulman, An Introduction to Ultrathin Organic Films; Academic Press, Boston, 1991

14

Thiols as SAM's

15

Thiols as SAM's

● Optimal adsorption site for Au(111)

– local minima ~ hollow sites

– local maxima ~ on-top sites

16

Thiols as SAM's

● Thermal stability (TPD)

– methane thiol on Pt(111)

17

Methane Thiol

● CH3SH methane thiol

(methyl mercaptan)

● b.p. 6 °C

● „rotten cabbage“ smell → natural gas additive

● dehydrogenates on

metal surfaces

18

Methane Thiol, Methane Thiolate

● 10 Angstrom cubic cell

● Brillouin-zone

integration over Γ-point

● Gaussian smearing

Methane Thiol

19

Methane Thiolate

20

CH3SH DOS

CH3S DOS

CH3SH IR

23

CH3S IR

24

25

Bulk Metals: Ni, Pd, Pt

● 20x20x20 k-points

● energy cutoff 270 eV

● GGA-PAW functional

● orthorhombic cell

1 atom / cell

VASP input:

26

Bulk Metals: Ni, Pd, PtMurnaghan equation of state:

Cohesion energy:

27

Surfaces of Ni, Pd, Pt

● 6x6x1 k-points

● energy cutoff 400 eV

● GGA-PAW functional

● 5-layer slab, (111) surface

● superstructure

28

Methane Thiol on Ni, Pd, Pt

Adsorption energies:

29

Methane Thiol on Ni, Pd, Pt

30

Methane Thiolate on Ni, Pd, Pt

31

Methane Thiol on Ni, Pd, Pt

32

Conclusions

● SAM's are spontaneously formed organic

monolayers

● Uses as surface corrosion proof,

greasing/lubrication of surfaces, functional

surfaces – nanoelectronic devices, ...

● SAM's have a good, however limited thermal

and chemical stability

33

Outlook

● Electronic devices on molecular level

(„nanomachines“)

● Molecular sensing

● Perfectly adhesive lubes

● Stabilization of nanoparticles

34

Acknowledgement

● o.Univ.Prof. Dr. Jürgen Hafner

● Dr. Florian Mittendorfer

● Dr. Michal Jahnátek

● Dr. Martin Zelený

Ústav organické technologie, VŠCHT Praha

David Karhánek

Surface Complexes in Catalysis

Institut für Materialphysik, Universität Wien

Research Methodologies:

Competitive kinetic measurements

relative adsorptivities (KA/KB) a reactivities (rA/rB) of the substrates

Physical-Chemical methods

FT-IR, MAS-NMR, TPD, LEED,SEM, TEM, STM, XRD, …

properties of the catalyst surface

Molecular modeling

estimation of geometry, IR vibrations, adsorption enthalpybinding energies, transition state structurea) molecular dynamics (stat. thermodynamics)b) quantum mechanics (Schrödinger eqn.)

Catalytic Hydrogenation

Pt(111), Au(100)

CH2=CH2 @ Pt(111)37

1

3

2

4 5

Mechanism: Hoiruti - Polanyi (1934)

Surface complex:• changes of adsorptive geometry:

• distortion of substituents from the C=C bond plane

• elongation of C=C bond

• changes of adsorbent geometry:

• relaxation and reconstruction at the “active site”

• changes in hybridization, IR, NMR parameters

• el. density shifted from p-bond towards the metal surface

reaction mixture

catalyst surface

reactants

catalyst surface

Catalytic Hydrogenations: Adsorption

38

Metalsurface

Catalytic Hydrogenations: Adsorption

39

Application of the Quantum Mechanics

Gaussian® 03W Vienna Ab-initio Simulation Package (VASP)

Molecular Structures

(cluster):

Periodical Structures

(slab):

Schrödinger equation

DFT Methods

i

40

Model Compounds

ethylene-bis(phosphin)platinumdi-s-ethylene @ c(3x3)-Pt(111)

C38H34P2Pt

OH

OH

OH

OH

ethyleneprop-2-en-1-ol(allylalcohol) 2-methylbut-3-en-2-ol

hex-1-en-3-ol hept-1-en-4-ol

[C2H4Pt36]∞ C2H10P2Pt

41

Platinum Crystal and Surface

100 plane

FCC cell

Description of the periodical structure:

FCC Pt bulk3.9865

0.5 0.5 0.00.0 0.5 0.50.5 0.0 0.5

1cartesian0 0 0

110 plane 111 plane

s = 0.1145 eV/A2 s = 0.1150 eV/A2 s = 0.0943 eV/A2

Surface energy:

Lattice constanta = 3.9865 Å (calc.)a = 3.9242 Å (exp.)

42

Geometries of the Adsorbed ComplexesEthene Prop-2-en-1-ol 2-Methylbut-3-en -2-ol Hex-1-en-3-ol Hept-1-en-4-ol

Dd(C=C)* [Å] 0.1377 0.1432 0.1496 0.1552 0.1380

Dd(C=C)** [Å] 0.0943 0.0944 0.0971 0.0925 0.0966

di-s adsorbed state:

*

**

di-scoordinated state:

Absolutní prodloužení vazeb C=C

0,1250,13

0,1350,14

0,1450,15

0,1550,16

Ethen Prop-2-en-1-ol 2-Methylbut-3-en -2-ol Hex-1-en-3-ol Hept-1-en-4-ol

d*

[Å]

0,09

0,092

0,094

0,096

0,098

d**

[Å

]

Dd* [Å]

Dd** [Å]

Absolute elongation of the C=C bonds

Ethene

43

(111) (100)Freely exposed

crystallographic planes

(110)

Energetics of the Surface Complex

Organometallic compound Surface complex

CH2=CHR RH

* *

HH

CH3-CH

2R

EA1

EA2

EA3

TS1

TS2

TS3

DHads

+ 2*

DHads = Ecomplex - (Emetal + Eolefin)

H2

Energy Profile of Hydrogenation

44

Adsorption vs. Dissociation Energies

0,0

50,0

100,0

150,0

200,0

250,0

E [

kJ/m

ol]

0,0

5,0

10,0

15,0

20,0

K [

-]

E(ads) [kJ/mol] E(diss) [kJ/mol] K(rel) [-]

OH

OH OH

OH

Eads

[kJ/mol] Ediss

[kJ/mol] Krel

[-]

Ethene -203.6 116.8 -

Prop-2-en-1-ol -232.1 107.6 15.0

2-Methylbut-3-en-2-ol -216.1 110.9 1.0

Hex-1-en-3-ol -235.5 114.8 2.9

Hept-1-en-4-ol -193.6 98.9 1.9

Eads … adsorption enthalpy of the di-s adsorbate at c(3x3) surface of platinum Pt(111) cellEdiss … dissociation energy of the di-s bond in (olefin)Pt(PH3)2 complexKrel … relative adsorption coefficient of the adsorptive with respect to standard on 5%-Pt/C catalyst

OH

O

H2 / Pt

45

Impact of the Level of Theory on the Calculation Accuracy

Coordinated olefin Ediss

[kJ/mol] Ediss

[kJ/mol] Eads

[kJ/mol] Eads

[kJ/mol]

B3LYP / 6-31G(d) MP2 / 6-31G(d) GGA-PAW / -point

GGA-PAW /

k(2x2x1)

Ethene 51.8 116.8 -203.6 -123.4

Prop-2-en-1-ol 29.7 107.6 -232.1 -97.9

2-Methylbut-3-en-2-ol 29.5 110,9 -216.1 -85.4

Hex-1-en-3-ol 37.1 114,8 -235.5 -94.5

Hept-1-en-4-ol 26.3 98.9 -193.6 -68.4

Coordinated olefin

(C=C) [cm-1]

B3LYP / 6-31G(d)

(C=C) [cm-1]

GGA-PAW / -point

Ethene 1212.7 1187.5

Prop-2-en-1-ol 1216.2 1173.0

2-Methylbut-3-en-2-ol 1229.9 1169.5

Hex-1-en-3-ol 1220.6 1185.4

Hept-1-en-4-ol 1220.5 1199.1

Adsorption / dissociation energies

Stretch-vibrational wavenumber of the coordinated C=C bond

46

Correlation of the Applied MethodsDissociation Energies vs. Adsorption Energies

Coordinated olefin Ediss

[kJ/mol] Eads

[kJ/mol]

MP2 / 6-31G(d) GGA-PAW / k(2x2x1)

Ethene 116.8 -123.4

Prop-2-en-1-ol 107.6 -97.9

2-Methylbut-3-en-2-ol 110.9 -85.4

Hex-1-en-3-ol 114.8 -94.5

Hept-1-en-4-ol 98.9 -68.4

OH

O

H2 / Pt

Solution:

Correlation coefficientafter neglection ofallylalcohol:

R2 = 0.9873

Disociační vs. adsorpční energie

R2 = 0,6209

80

90

100

110

120

-110 -90 -70 -50

Disociační vs.

adsorpční en.

Lineární regrese

Eads

EdisDissociation vs.adsorption en.

Linear regression

Dissociation vs. Adsorption Energy

47

Charge Density Profile

48

Conclusions• Geometries of adsorbed structures of unsaturated compounds

on Pt(111) surface were described.

• Enthalpy changes of the chemisorption reactions were evaluated.

• Group of organometallics, suitable for good approximativedescription of surface adsorbates was found.

• Raising the level of theory more reliable geometries of adsorbates and adsorption enthalpy values.

• Applied methods may enable to predict the chemisorption of a mixture of substances and estimate the selectivity of the catalytic reaction.

• Calculation of entire reaction heats, activation energies and IR vibrational spectra rate constants real reaction kinetics.

• Comparison with experimental data formulation of LFER equation

(Linear Free Energy Relationship).

49

Acknowledgements

My Supervisors and Colleagues:

Assist.Prof. Petr Kačer

Dr. Marek Kuzma

Prof. Libor Červený

Prof. Jürgen Hafner

Dr. Florian Mittendorfer

50

51

Thank You for Your Attention!