supramolecular chemistry hydrogen-bonded networks · supramolecular chemistry –hydrogen-bonded...

Supramolecular Chemistry

– Hydrogen-Bonded Networks

Christoph Janiak

University of Düsseldorf, Germany

Email: [email protected]

Hydrogen-bonded frameworks

M

N

N D

A

MN

N

D

A

M

N

ND

A

M N

N

D

A

D = hydrogen donorA = hydrogen acceptor

Cl

Cl Cl

Cl

M HCl

Cl Cl

Cl

MHN N

Supramolecular interactions (hydrogen-bonding, p-stacking)

in metal-organic networks

MLx

MLx

MLx

LxM

LxM

LxM

hydrogen bonding p-p stacking van der Waals hydrophobic hydrophilic interactions

inter-polymer packing

MLx

LxM

MLx

LxM

intra-polymer packing

=polymer-solvent

MLx

MLx

MLx

-anion packing

(template)

Aromatic...aromatic interactions

3.3-3.8 Å > 4.8 Å

p-stacking, "p-p interaction" C-H...p interaction

face-to-face offset, slipped T-shaped

p-Stacking between metal-pyridine fragments

N

planenormal

N

P, plane 2

x

x

M

M

centroid-centroid distance

P, plane 1

intermolecular contact3.0 < centroid-centroid distance < 4.6 Å

Constraints:

J. Chem. Soc., Dalton Trans. 2000, 3885

CSD search setup:


centroid-centroid distance [Å] interplanar angle [°]

frequency



frequency

plane normal - centroid-centroid angle [°]

N

planenormal

N

x

x

M

M

centroid-centroiddistance



pla

ne n

orm

al -

centr

oid

-centr

oid

angle

[°]

centroid-centroid distance [Å]

N

planenormal

N

x

x

M

M

centroid-centroiddistance


p-Stacking between metal-ligand fragments

NM

N

M

OM

OO

M

M

M

M

X M

XM

x

x

~3.80 Å

>20°

plane-planedistance: ~3.6 Å

>1.30 Å

lateral shift


Aromatic...aromatic interactions

face-to-face offset, slipped T-shaped

p-p

repulsion

H

H

+

+

-p

attraction

H+-p

attraction

Hunter, Sanders, J. Am. Chem. Soc. 1990, 112, 5525

p...p or C-H...p ?

Type of weak bond Interaction type Interaction energy[kJ/mol]

O-H···ON-H···O

electrostatic

dispersive

16-60

cation···p

C-H···O

C-H···p

p···p

van der Waals

5-80

<16

<2-20

<4-10

<5

Desiraju, Steiner, The Weak Hydrogen Bond, Oxford, 1999

Nishio et al., The CH/p Interaction, Wiley-VCH, 1998

Steed, Atwood, Supramolecular Chemistry, Wiley, 2000

Schneider, Yatsimirski, Principles and Methods in Supramolecular Chemistry, Wiley, 2000

Janiak, (p-p stacking), J. Chem. Soc., Dalton Trans. 2000, 3885

Non-covalent supramolecular interactions

How do we analyze for non-covalent interactions?

http://www.cryst.chem.uu.nl/platon/

Program PLATON: A. L. Spek, Acta Crystallogr. A, 1990, 46, C34.

(current) PLATON Version 1.12, 29-10-07.

Windows implementation: L. J. Farrugia, University of Glasgow, Scotland, 2007.

How do we analyze for non-covalent interactions?

From metal-organic networks

to hydrogen-bonded Networks

M

N

N D

A

MN

N

D

A

M

N

ND

A

M N

N

D

A

D = hydrogen donorA = hydrogen acceptor

Metal-organic networks H-bonded networks

M M M M1D chains

M M M

M M M

M M M

2D nets

M M M

M M M

M M MM

M M M

M M M

MM3Dframeworks

covalent

less flexible

more directional

network

electrostatic

more flexible

less directional

network

Introduction

pyrazolylborate ligands

Trofimenko, Scorpionates, Imperial College Press, London 1999

N

B

N N

N

H

N

N

N

N

N

NB

HH

hydro-tris(pyrazolyl)borate dihydro-bis(pyrazolyl)borate

- molecular chelate complexes

KBH4 + n H-azolyl K[H4-nB(azolyl)n] + n H2

D

Modified poly(pyrazolyl)borate ligands

N

B

N N

N

H

N

N

N

NN

N

NN

B

HH

tris(pyrazolyl)borate

bis(triazolyl)borate

N

N

B

N

N

H

N

N

tris(indazolyl)borate

N

B

N N

NNN

H

N

NN

N

NN

N

NN

NN

B

HH

tris(triazolyl)borate

bis(tetrazolyl)borate

Chem. Commun. 1994, 545; Chem. Eur. J. 1995, 1, 637; Z. Anorg. Allg. Chem. 2000, 626, 2053

NB

N N

NNN

H

N

NN

B

N

NM

N

NN

N

H

N

NN

M2+ + 2 N3–H2O

M = Fe, Co, Ni, Zn

H2O·2H2O

2OH2·OH2

two-dimensional

water/ice substructure


with tris(triazolyl)borate N3

J. Am. Chem. Soc. 2002,

124, 14010

two-dimensional

complex layer

Polyhedron 2003,

22, 1123

Two-dimensional complex layer

CH···N bonds

Polyhedron 2003, 22, 1123


Two-dimensional complex layer

CH···N bonds

Fe-N3

spin crossover

NB

N N

NNN

H

N

NN

B

N

NFe

N

NN

N

H

N

NN

low-spin high-spin

1A1g5T2g

FeII, d6T1/2 ~ 62 °C

temperature variable magnetic measurements

Moessbauer spectroscopy

UV/Vis spectroscopy

DSC

magnetic dilution

2

4

6

8

10

12

20 40 60 80

Temperature [°C]T

1 [

s]

20

30

40

50

60

70

80

90

20 40 60 80

Temperature [°C]

T1

[s

]

temperature variable T1-measurements on H2O

NB

N N

NNN

H

N

NN

B

N

NFe

N

NN

N

H

N

NN

H2O in 99.8% D2O

+

[Fe]

in mmol/l

1.24

2.26

4.87

Fe-N3

spin crossover

NB

N N

NNN

H

N

NN

B

N

NFe

N

NN

N

H

N

NN

H2OOH2

OH2

H2O

H2O

outer-sphere relaxation mechanism

Fe-N3

spin crossover

Two-dimensional water/ice substructure

J. Am. Chem. Soc. 2002, 124, 14010(neutron diffraction)


J. Am. Chem. Soc. 2002, 124, 14010(neutron diffraction on [Ni(N3)2] · 6 D2O )

263 K

Pmnb

(Pmna)

20 K

P21nb

(Pna21)

DT

278 K

Cmce

(Cmca)

k2 t2


J. Am. Chem. Soc. 2002, 124, 14010

263 K 20 K

DT

= crystallographic disorder

(neutron diffraction on [Ni(N3)2] · 6 D2O )


J. Am. Chem. Soc. 2002, 124, 14010

(neutron diffraction)

263 K 20 K

DT

Other (modified) poly(pyrazolyl)borato ligands

N

B

N N

N

H

N

N

N

NN

N

NN

B

HH

tris(pyrazolyl)borate bis(triazolyl)borate

N

N

B

N

N

H

N

N

tris(indazolyl)borateN2inda

3-D coordination polymer

P212121

B

N

N N

H

chiral crystal structure

H

N

NN

Tl (Tl)

TlTl

NLO-effect


Main-group metal chemistry

(modified) poly(pyrazolyl)borato ligands

chiral crystal structure

NN

B

HNN

NN

Tl

N N

B

HN N

NN

Tl

C2 axis

p---p stacking, chiral pairs

C2

NLO-effect

Inorg. Chem. Commun. 2000, 3, 271





NB

N N

N

H

N

N

3D coordination polymer

P212121

TlB

N

N N

H

NB

NN

N

H

N

N

Tl

Tl+---p(azolyl) interactions

P21chiral crystal structure

Z. Anorg. Allg. Chem. 1998, 624, 755

H

N

NN

Tl (Tl)

Tl Tl

NN

BH

NN

NNTl

N N

BH

N N

N NTl

C2 axis

p---p stacking, chiral pairs

C2

Inorg. Chem. Commun. 2000, 3, 271


NLO-effectspontaneous resolution

N

N

B

N

N

H

N

N

Cu

N

N

B

N

N

H

N

N

crystallizationwith 2.5THF

5 Å

Supramolecular assemblies with MOF-type structures

based on modified poly(pyrazolyl)borate ligands

26% pot. solvent volume

Eur. J. Inorg. Chem. 2000, 1229

M = Fe,Co16 Å

2 Å 6 Å

N

N

B

N

N

H

N

N

M

N

N

B

N

N

H

N

N

crystallization

with 3.5CHCl3

38% pot. solvent volume




N

N

B

NN

H

N

N

M

N

N

B

NN

H

N

N

with 1.67 dioxane

crystallization

29% channel volume

M = Ni,Zn4 Å




Hydrogen-bonded framework

with isonicotinamide and Ag+: {Ag(INA)2(µ-NO3)}2

N

OH2N

isonicotinamideINA

Ag–Ag 3.1429(5) Å

Aust. J. Chem. 2006, 59, 22.

Bis(isonicotinamide)silver nitrate,

{Ag(INA)2(µ-NO3)}2

light-stability: after 30 min irradiation with a 15 W energy saving lamp at a distance of 5 cm

{Ag(INA)2

(µ-O3SCF3)}2

untreated

filter paper

{Ag(INA)2

(µ-NO3)}2

filter papers

impregnated

with 0.1 mol/l

solutions

AgNO3

INA

stabilization by

- hydrogen bonding

- NO3 clamping

- Ag-Ag contact

Aust. J. Chem. 2006, 59, 22.



dissolution behavior:

- pH dependent

- slower at more acidic pH

- faster at more basic pH

due to

- low base strength of INA

(pKa = 3.67)

- H-bonding network in

solid {Ag(INA)2(µ-NO3)}2

Aust. J. Chem. 2006, 59, 22.

0

500

1000

1500

2000

30 min 5 h

pp

m

pH = 4.1

pH = 7.0

H-Brücken-Gitter

mit Isonicotinamid und Ag+

– slow release of Ag+:



N

OH2N

isonicotinamideINA

Anion recognition

here: perchlorate, ClO4–

Chem. Commun. 2003, 902

Chiral building blocks for

supramolecular, hydrogen-bonded networks

N N

H2N NH2

5,5'-diamino-2,2'-bipyridineDABP

N

NNH2

H2N

NN

Fe

NH2

H2N

D-[Fe(DABP)3]2+

N

N

NH2

H2N 1,1'-bi-2-naphtholBINOL

OH

OH

–2H+

BINOLAT2–

R(S)

N

NNH2

H2N

NN

Fe

NH2

H2N

D-[Fe(DABP)3]2+

N

N

NH2

H2N

Tris(bipyridine)metal complexes

with diaminobipyridine, DABP

M = Fe, Ni, (Cu) Zn, Cd


Inorg. Chim. Acta 2003, 343, 366

Z. Anorg. Allg. Chem. 2004, 630, 1564

M2+ + 3 DABP

N

NNH2

H2N

O

O2N

NN

Fe

NH2

H2N

O

D-[Fe(DABP)3]2+

O2N

N

N

NH2

H2N

O

O2NO NO2

O

NO2

O

NO2

Second-sphere hydrogen bonding

with [Fe(DABP)3]2+

CrystEngComm 2004, 6, 126

Fe2+ + 3 DABPnitrophenolate

Molecular paneling through hydrogen-directed assembly




-[Fe(DABP)3]2+

D-

[Fe(DABP)3]2+

D-

[Fe(DABP)3]2+

polar space group: P31c

O

OP

O

OH

Hydrogen-bonded (and metal-organic) frameworks:

Our interest: Chiral, enantiomeric structures

OH

OHR(S)

1,1'-binaphthalene-

2,2'-diyl phosphoric acid

BNPPAH

rac or R

–H+

BNPPA–

- inexpensive ligand enantiomers

1,1'-bi-2-naphthol

BINOL

–2H+

BINOLAT2–

Hydrogen-bonded networks

with rac-BINOL

M = Cu, x = 5

Ni, Cd, x = 6

Zn, x = 4[M(NH3)x]

2+[BINOLAT]2–(BINOL)2M2+ + 3 BINOL

conc. NH3

MeOH

O

O

H

H

H

H

BINOLAT2–BINOL

HO

H

OH

H

O

O

O

O

O

O

Hydrogen-bonded strands

with rac-BINOL

M = Cu, x = 5

Ni, Cd, x = 6

Zn, x = 4[M(NH3)x]


conc. NH3

MeOH

c

strand

+

cavities

O

O

H

H

H

H

BINOLAT2–BINOL

M

H3N NH3

NH3H3N

NH3H3N

M = Ni, Cd

or

NH3

MH3N

NH3

NH3

M = Zn

2+

2+

HO

H

OH

H

O

O

O

O

O

O


with rac-BINOL

M = Cu, x = 5

Ni, Cd, x = 6

Zn, x = 4[M(NH3)x]


conc. NH3

MeOH


Hydrogen-bonded strands with rac-BINOL


strand+

cavities



strand

100 200 300 400 500 600

dm

/dT

, Dm

, DT

,

ion

ic f

low

in

arb

itra

ry u

nits

temperature [°C]

m/z=268

–27.4

–55.0

–6.3

endo

Tp=302

Tp=443

Tp=116

DTG

TG

DTA

m/z=17

m/z=44

m/z=286

Supramolecular M-BINOL Strands:

thermischal behavior of [M(NH3)6]2+[BINOLAT]2–(BINOL)2

–6NH3

– ~2OH

OH

O–

–CO2,

DTG, TG, DTA and MS-trend-scan



with rac-BINOL

S

R

R R

S

S

R

S


with rac- and S-BINOL

[Cd(S-BINOLAT)(NH3)4]0(S-BINOL)2(H2O)(MeOH)2

Cd2+ + 3 S-BINOL

conc. NH3

MeOH

chiral crystal structure: C2

[M(NH3)x]2+[rac-BINOLAT]2–(rac-BINOL)2

M2+ + 3 rac-BINOL

conc. NH3

MeOH

space group: C2/c



with rac-BINOL

c

R

RS

S

S

O

O

HH

HH

-BINOLAT2–-BINOL

HO

H

OH H

O

O

O

O

O

O

rac

O

O

H

H

-BINOLAT2–-BINOL

H

OH

O

O O

S

HH

O O

HOH

O


with S-BINOL

c

S

SS

S

S

[Cd(S-BINOLAT)(NH3)4]0(S-BINOL)2(H2O)(MeOH)2Cd2+ + 3 S-BINOL

conc. NH3

MeOH

no matchanymore inH-bonding


O

O

H

H

-BINOLAT2–-BINOL

H

OH

O

O O

S

HH

O O

HOH

O


with S-BINOL

c

S

SS

S

S


conc. NH3

MeOH

strand

+

cavities

translocation along c

O

O

H

H

-BINOLAT2–-BINOL

H

OH

O

O O

S

HH

O O

HOH

O

Cd

H3N NH3

NH3H3N

2+


with S-BINOL

c

S

SS

S

S


conc. NH3

MeOH


Metal coordination

with S-BINOL



with S-BINOL

strand

+

cavities


strand



with (S)-BINOL

[Ag(NH3)2]+[S-BINOLAT]–(S-BINOL)(EtOH)Ag+ + 2 S-BINOL

conc. NH3

EtOH

Ag+ + 2 rac-BINOL

conc. NH3

EtOH[Ag(NH3)2]

+[S(R)-BINOLAT]–(S(R)-BINOL)(EtOH)

spontaneous resolution, ~40%ee

chiral crystal structure: P1



BINOLAT – BINOL

Ag NH3H3N

+O

O

H

H

H

O

O

H

H

O

O

O

O

H

BINOLAT –BINOL

[Ag(NH3)2]+[S-BINOLAT]–(S-BINOL)(EtOH)Ag+ + 2 S-BINOL

conc. NH3

EtOH

strand


with (S)-BINOL


U-shaped channels


100 200 300 400 500 600

dm

/dT

, Dm

, DT

,

ionic

flo

w in a

rbitra

ry u

nits

temperature [°C]

Tp=323

Tp=211

Tp=116

Tp=319

Tp=114

–75.3

–8.9

DTG

TG

DTA

m/z=17

m/z=46

m/z=286

H-bonded strands

with (S)-BINOL and Ag+

–2NH3

–EtOHOH

OH

DTG, TG, DTA und MS-trend-scan


10 15 20 25 30 35 40 45 50

silver

heated to 130 °C

(S)-BINOL

calculated

inte

nsity

2 Theta (°)

H-bonded strands

with (S)-BINOL and Ag+

D

130 °C

CrystEngComm 2005, 7, 309CrystEngComm 2005, 7, 309

Hydrogen-bonded (and meta-organic) frameworks:


1,1'-binaphthalene-

2,2'-diyl phosphoric acid

BNPPAH

rac or R

–H+

BNPPA–

O

OP

O

OH


OH

OHR(S)

1,1'-bi-2-naphthol

BINOL

–2H+

BINOLAT2–


with bi-naphthol phosphate BNPPA

O

OP

O

O–

rac

BNPPA–

NH2H2N

NH2

+

CuH3N

H3N NH3

NH3

. HOCH3

. HOCH3

2+

CuH3CO

H

. HH3CO

HOCH3

OCH3H

OH2

OH2

2+

NiH2N

H2N OH2

OH2

NH2

NH2

2+

cations:

(compressed

octahedron !)

New J. Chem. 2006, 30, 156.


with bi-naphthol phosphate BNPPA

- common feature

hydrophobic layers

hydrophilic layers

New J. Chem. 2006, 30, 156.

inverse bilayer

hydrophilic interior

hydrophobic exterior


stacking

weak interactions thin plate

thin-plate crystal dimension= longest crystallographic axis

OO

POO –

Inverse bilayers through strong O/N–H···O hydrogen bonding

and very weak C–H···p interactions

New J. Chem. 2006, 30, 156.

inverse bilayer




stacking



OO

POO –

Inverse bilayers from BNPPA

"normal" bilayer

water

water water

liposome

H2O

- hydrophilic exterior- hydrophobic interior

inverse bilayer




stacking



OO

POO –

Inverse bilayers through strong O/N–H···O hydrogen bonding

and very weak C–H···p interactions

only very weak

C–H···p interactions,

no p-p interactions

New J. Chem. 2006, 30, 156.

Inverse bilayers from BNPPA

inverse bilayer




stacking



OO

POO –

New J. Chem. 2006, 30, 156.




- amino acid chiral pool

HO NH

O

Ph

N-phenylglycine =

2-(phenylamino)acetic acid

(*)HN

O

R

O

NH

R

*

*

HO

O

OH

O

R = -CH3 (L-Ala)

= -CH(CH3)2 (L-Val)

= -CH2-indol (L-Trp)

= -CH2CH(CH3)2 (L-Leu)

= -CH2Ph (L-Phe)

NH2

Rh

HO

Ph

S*

NH2

Rh

HO

O R

R = MeR = Ph

S*

–O2CMe

+

NH

Rh

O

O

R

R/S

*

Higher element of chirality

– homochiral helices

Chiral cod-Rh(aminocarboxylato) and chiral cod-Rh(amino alcohol) complexes:

- amino acids as chiral ligands

Dalton Trans. 2009, 3698.

Eur. J. Inorg. Chem. 2006, 2146.

HO NH

O

Ph



N-phenylglycine =


(*)

spontaneous

resolution

upon crystallization

(M) 43-helical chains

– homochiral –

R-complex →

chiral space group: P43

NH

Rh

O

O

Ph

(R/S)

*



Transfer of chirality?

N-H···O hydrogen bonding R complexes into 43-helical chain

intra-chain homochirality

Higher elements of chirality – homochiral helices

through hydrogen bonding and van der Waals interactions

Transfer of chirality?

43-helix

corrugated van der Waals surface homochiral assembly of 43-helices in crystal

inter-chain homochirality

Eur. J. Inorg. Chem. 2006, 2146.

only very weak C–H···p interactions,

no p-p interactions



R complex left-handed M-

43-helix

P43




43-helix

S complex right-handed P-

41-helix

P43 P41

Dalton Trans. 2009, 3698.Eur. J. Inorg. Chem. 2006, 2146.




43-helix

S complex right-handed P-

41-helix

P43 P41

crystal ensemble =

racemic mixture

Dalton Trans. 2009, 3698.Eur. J. Inorg. Chem. 2006, 2146.




- amino acid chiral pool

HO NH

O

Ph

N-phenylglycine =


(*)HN

O

R

O

NH

R

*

*

HO

O

OH

O

R = -CH3 (L-Ala)

= -CH(CH3)2 (L-Val)

= -CH2-indol (L-Trp)

= -CH2CH(CH3)2 (L-Leu)

= -CH2Ph (L-Phe)

Chiral, enantiomeric ligand for chiral coordination polymers,

molecular trigonal prism with Cu2 as SBU

Chirality

Porosity ?

trigonal space group R3


Molecular trigonal prism with Cu2 as SBU

Chirality

Porosity ?

~30 Ǻ


Chiral, enantiomeric molecular trigonal prism with three Cu2 units:

[Cu2(μ4-TBPhe)2(EtOH)(H2O)]3 · ~28(H2O/0.33EtOH)

~30 Ǻ

electron density in the interior

of the trigonal prism

cannot be clearly localized

- solvent of crystallization highly disordered

crystal solvent O atoms refined

- simultaneously with their occupancies

- isotropically

- with "anti-bumping"

restraints, BUMP in SHELXLCrystEngComm 2008, 10, 461

Chiral, enantiomeric molecular trigonal prism with three Cu2 units

23.4%

potential solvent area volume

calculated by

PLATON for WindowsTotal potential solvent area volume

3275 Å3

per unit cell volume

13955 Å3


Chirality

Porosity ?

solution study:

ESI-mass

UV/VIS

NMR

CD spectroscopy



solution study:

ESI-mass

UV/VIS

NMR

CD spectroscopy

light scattering

channels through

crystal lattice


channels through

crystal lattice

trigonal space group R3

a = b = 39.7978(3) Å

c = 10.1735(2) ÅCrystEngComm 2008, 10, 461


solution study:

ESI-mass

UV/VIS

NMR

CD spectroscopy

~30 Ǻ

= ~3 nm

TEM from MeOH solution:


solution study:

ESI-mass

UV/VIS

NMR

CD spectroscopy

~30 Ǻ

= ~3 nm

Light scattering in MeOH solution:

4.2–5.6 nm

av. 4.85 nm

Chiral molecular trigonal prism with Cu2 as SBU:

Magnetism

0 50 100 150 200 250 300T (K)

0

2

4

6

8

10

12

(m

em

u/a

sym

. unit)

g = 2,29

J = -214 K

= 4 %

TIP= 0.23 memu/asym. unit

C54H58.66Cu2N6O17.33

0 50 100 150 200 250 300T (K)

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

T (

em

uK

/asym

. unit)

C54H58.66Cu2N6O17.33


Type of weak bond Interaction type Interaction energy[kJ/mol]

O-H···ON-H···O

electrostatic

dispersive

16-60

cation···p

C-H···O

C-H···p

p···p

van der Waals

5-80

<16

<2-20

<4-10

<5

Desiraju, Steiner, The Weak Hydrogen Bond, Oxford, 1999

Nishio et al., The CH/p Interaction, Wiley-VCH, 1998

Steed, Atwood, Supramolecular Chemistry, Wiley, 2000

Schneider, Yatsimirski, Principles and Methods in Supramolecular Chemistry, Wiley, 2000

Janiak, (p-p stacking), J. Chem. Soc., Dalton Trans. 2000, 3885

Non-covalent supramolecular interactions:

From strong to weak hydrogen bonds

X-ray crystallography and solid state NMR:

Palladacycle pseudo-polymorphs and a vanishing polymorph

Chronology:

The first observation: 12 from toluene

2 symmetry independent molecules in the asymmetric unit, Z' = 2, P1

(Z' > 1 structure)

- the start: Short CH3···CH3 contact (3.256 Å) ?

CrystEngComm 2008, 1928



Chronology:

Why

2 symmetry independent molecules in the asymmetric unit, Z' = 2?

(Z' > 1 structure) – Conformational difference?

overlay of

molecule Pd1-Pd2

and

molecule Pd3-Pd4

NMe2

Pd

O NMe2

Pd

O

N




Chronology:

Why

2 symmetry independent molecules in the asymmetric unit, Z' = 2?

(Z' > 1 structure) – the full structure with disordered solvent

~2 x 0.25 = ~0.5 toluene per 2 Pd2 molecules (= 12)


Z' > 1 structures: A crystal "on the way"?

Matter of discussion

Desiraju: On the presence of multiple molecules in the crystal asymmetric unit (Z' > 1)

(CrystEngComm 2007, 9, 91-92)

Anderson and Steed: Comment on "On the presence of multiple molecules in the

aymmetric unit"

(CrystEngComm 2007, 9, 328-330)

Nichol and Clegg: Further thoughts on crystal structures with Z' > 1: analysis of ...

(CrystEngComm 2007, 9, 959-960)

Babu and Nangia: High Z' polymorphs have shorter C–H···O interactions and O–H···O

hydrogen bonds

(CrystEngComm 2007, 9, 980-983)

Gavezotti: Structure and energy in organic crystals with two molecules in the asymmetric

unit: causality of chance?

(CrystEngComm 2008, 10, 389-398)

Chronology:

Verification of Z' = 2 by CPMAS NMR

NMe2

Pd

O NMe2

Pd

O

N

1

12 · 0.5 C6H5-CH3

- each C-signal appears in pairs

- 16 out of 18 signals for the above non-aromatic C atoms of 12 are resolved

- two toluene positions in crystal




Chronology:

changing the solvent for verification

of toluene-CH3 assignment

NMe2

Pd

O NMe2

Pd

O

N

1

12 · 0.5 C6H5-CH3

12 · 0.5 C6D5-CD3

from C6H5CH3:

from C6D5CD3:




Chronology:

2 independent molecules in the asymmetric unit

because of solvent loss during crystal mounting?

~2 x 0.25 = ~0.5 toluene per 2 Pd2 (= 12)



Chronology:

2 independent molecules in the asymmetric unit

because of solvent loss during crystal mounting? Crystallization from C6D6: P1

~2 x 0.25 = ~0.5 toluene per 2 Pd2 (= 12) 1.5 benzene per Pd2 (= 1), Z' = 1




X-ray and CPMAS NMR:

Pd pseudo-polymorphs

Chronology:

verification from CPMAS: NMe2

Pd

O NMe2

Pd

O

N

1

12 · 0.5 C6H5-CH3

12 · 0.5 C6D5-CD3

1 · 1.5 C6D6

from C6H5CH3:

from C6D5CD3:

from C6D6 no splitting

Z' = 1

Chronology:

2 independent molecules in the asymmetric unit New X-ray data set of 1 from toluene,

because of solvent loss during crystal mounting? quick and careful crystal mounting

~2 x 0.25 = ~0.5 toluene per 2 Pd2 (= 12) 1.5 toluene per Pd2 (= 1), Z' = 1

P1






Chronology: attempted

verification from CPMAS: NMe2

Pd

O NMe2

Pd

O

N

1

12 · 0.5 C6H5-CH3

12 · 0.5 C6D5-CD3

1 · 1.5 C6D6

1 · 1.5 C6H5-CH3

from C6H5CH3:

crystals of 1 wet in rotor, clearly visible solvent in CPMAS 1H NMR

strong toluene smell after the experiment upon opening of rotor

splitting

Z' = 2


NMe2

Pd

O NMe2

Pd

O

N

tolueneP 1

1

1 · 1.5 C7H8

P 112 · 0.5 C7H8

toluene

P 11 · 1.5 C6H6

C6H6

CH2Cl2/hexane

P21/c1 · 1 C6H14



To obtain the structure of 1 · 1.5 C7H8 or 12 · 0.5 C7H8 depends on the crystallization technique

and crystal handling:


NMe2

Pd

O NMe2

Pd

O

N

tolueneP 1

1

1 · 1.5 C7H8

P 112 · 0.5 C7H8

toluene

P 11 · 1.5 C6H6

C6H6

CH2Cl2/hexane

P21/c1 · 1 C6H14



hexane

sample intoluene

technique B

hexane

sample intoluene

technique A

technique A

technique B



NMe2

Pd

O NMe2

Pd

O

N

tolueneP 1

1

1 · 1.5 C7H8

P 112 · 0.5 C7H8

toluene

P 11 · 1.5 C6H6

C6H6

CH2Cl2/hexane

P21/c1 · 1 C6H14



hexane

sample intoluene

technique B

hexane

sample intoluene

technique A

technique A

technique B

crystallization

and collection

within

3-4 days!

crystal-to-crystal transition






NMe2

Pd

O NMe2

Pd

O

N

1

1 · 1.5 C6H5-CH3

12 · 0.5 C6H5-CH3

from C6H5CH3,

technique A:

1 · 1.5 C6H5CH3

technique B:

12 ·0.5 C6H5CH3

crystal-to-crystal transition

after 30 min

after 10 h

quick

spectrum


Pd pseudo-polymorphs and solvent mobility from 2H static CPMAS

12 · ~0.5 C6D5-CD3

toluene-d8 is immobile



Pd pseudo-polymorphs and solvent mobility from 2H static CPMAS

1 · 1.5 C6D6

benzene-d6 rotates around C6-axis


NMe2

Pd

O NMe2

Pd

O

N

tolueneP 1

1

1 · 1.5 C7H8

P 112 · 0.5 C7H8

toluene

P 11 · 1.5 C6H6

C6H6

CH2Cl2/hexane

P21/c1 · 1 C6H14



1 · 1.5 C7H8 12 · 0.5 C7H8 1 · 1.5 C6H6 1 · C6H14

Independent reflections

Obs. reflect. [I > 2(I)]

Parameters refined

R1 / wR2 [I > 2(I)]

R1 / wR2 (all reflect.)

Goodness-of-fit on F2

7772

7089

452

0.0338 / 0.0793

0.0379 / 0.0814

1.082

11565

9237

757

0.0272 / 0.0598

0.0388 / 0.0618

1.008

7746

6641

473

0.0231 / 0.0519

0.0309 / 0.0548

1.034

7491

7157

422

0.0296 / 0.0717

0.0312 / 0.0725

1.135


recrystallization from

CHCl3red crystals

MeOHyellow crystals

THF and acetonitrile mixture of

red and yellowcrystals

N NPd

Br Br

Pd polymorphs originating from different Br···p and C–H···Br contacts

Two polymorphic forms (dimorphs) depending on the solvent:

monoclinic, P21/c

triclinic, P1


Conformational difference?




"Dimeric units" as common "building block"

red crystals yellow crystals



"Dimeric units" as common "building block"


Br2···N2 3.480(4) 3.780(8)

Difference in Br2···PdN2C2-heterocycle contact:


Different packing of the dimeric building blocks in dimorphs:


"herringbone" array



Different packing of the dimeric building blocks in dimorphs:


"herringbone" array parallel array


Difference in C–H···Br contacts (Å):




Statistiscal analysis of C–H···Br contacts, "data mining" in Cambridge Structure Data bank:

(histogram) (scattergram)

0

500

1000

1500

2000

2500

3000

2.50 2.60 2.70 2.80 2.90 3.00 3.10 3.20 3.30

H···Br (Å)

Nu

mb

er

of

exam

ple

s

H···Br (Å)


Can a single C–H···F–C hydrogen bond make a difference?

Assessing the H···F bond strength from 2D 1H-19F CP/MAS NMR

The observation: 2 symmetry independent molecules in the asymmetric unit (Z' > 1 structure)

Pd PF

F

F F

F

Pd PF

F

F F

F

molecule 1 molecule 2

asymmetric unit




The observation: 2 symmetry independent molecules in the asymmetric unit (Z' > 1 structure)

Pd PF

F

F F

F

Pd PF

F

F F

F


asymmetric unit

What is the reason?




Conformational difference?

overlay of

molecule 1

and

molecule 2




Conformational difference? No!

overlay of

molecule 1

and

molecule 2




Pd PF

F

F F

F

Pd PF

F

F F

F


asymmetric unit

Differentiating, strong intermolecular p-p or C–H···p interactions?




Pd PF

F

F F

F

Pd PF

F

F F

F


asymmetric unit

Differentiating, strong intermolecular p-p or C–H···p interactions? No!




Pd PF

F

F F

F

Pd PF

F

F F

F


asymmetric unit

Is the structure / space group correct? orthorhombic, Pbca

2 data sets: 100 K and 293 K

all R-values < 0.094




Pd PF

F

F F

F

Pd PF

F

F F

F


asymmetric unit

Test for correct observation: Solid-state 19F-NMR

10 different F-signals expected

-100 -105 -110 -115 -120 -125 -130 -135 -140 -145 -150 -155 -160 -165 ppm

-16

2.4

-16

0.5

-15

8.8

-15

7.8

-15

7.4

-10

9.0

-10

7.5

-10

4.3

-10

3.9



Pd PF

F

F F

F

Pd PF

F

F F

F


asymmetric unit

Test for correct observation: Solid-state 19F-NMR

10 different F-signals expected

9/10 found

ortho-F

4 signals

meta+para-F

5/6 signals



What about C–H···F–C hydrogen bonds?

D’Oria, Novoa: " neutral C–H···F interactions have an interaction energy

around 0.4 kcal mol–1 "

(E. D’Oria, J. J. Novoa, CrystEngComm 2008, 10, 423)

Hulliger et al.: "the role of fluorine in crystal engineering is not yet clear"

"except for phenyl-perfluorphenyl p-stacking,

other observed fluorine interactions are generally weak"

(K. Reichenbächer, H. I. Süss, J. Hulliger, Chem. Soc. Rev. 2005, 34, 22)

Boese, Nangia, Desiraju et al.: "relevant C–H···F–C interactions in fluorobenzenes C6H6–nFn"

(V. R. Thalladi, H.-C. Weiss, D. Bläser, R. Boese, A. Nangia, G. R. Desiraju,

J. Am. Chem. Soc. 1998, 120, 8702)

Dunitz and Taylor: "organic fluorine (C–F) hardly ever accepts hydrogen bonds"

(J. D. Dunitz, R. Taylor, Chem. Eur. J. 1997, 3, 89)



Differentiating C–H···F–C hydrogen bonds?

A lot of intermolecular C–H···F–C hydrogen bonds between Pd1 – Pd1, Pd2 – Pd2 and Pd1 – Pd2




Differentiating C–H···F–C hydrogen bonds?

shortest contact H40···ortho-F1 2.39 / 2.42 Å (100 K / 293 K),

second-shortest H44···para-F8 2.50 / 2.58 Å




shortest contact H40···ortho-F1 contact is between Pd1 – Pd2 !



-500010000 5000 0 Hz

PILGRIM experiment:

assesses the strength of the 1H–19F dipol–dipol coupling

–104

–162

ppm

o-F

m/p-F

width ~ coupling strength

strongest

coupling


Metal complexes for biopolymers

Biochemistry

Coordination

chemistry


N

N

N

N

RuN

NL

L

2+

L = -NH2

-CO2Et

-NHCO2Et

Ruthenium(II) complexes

– photophysical properties

– energy and electron transfer

– binding to proteins

Inorg. Chim. Acta 2001, 318, 103

metal complexes with bio relevance:

Z. Anorg. Allg. Chem. 2003, 629, 2282

Z. Anorg. Allg. Chem. 2003, 629, 2585

Z. Anorg. Allg. Chem. 2004, 631, 17

2+

(PF6–)2

L:

N

NH

N

NH

N

NH

N

NH

N

NH

Ph

Ph

N N

NRu

N

N

L

NNH

NNH

NNH


Model complexes:

Binding to cytochrome c:

+ cyt c [Ru(bipy)(terpy)(cyt c)]2+

– UV/VIS

– fluorescence

– ESI-MS

Dalton Trans. 2005, 256

– X-ray

– UV/VIS = f(pH, time)

– fluorescence

[Ru(bipy)(terpy)(cyt c)]2+

Histidin binding site:

His44 (His39)

– analysis of

trypsin digestion products

with HPLC-MS

(ESI-MS/MS)His44

His38

His31

His23

Dalton Trans. 2005, 256

NB

N N

NNN

H

N

NN

B

N

NM

N

NN

N

H

N

NN

H2O

OH2

Summary:


two-dimensional


NB

N N

NNN

H

N

NN

B

N

NM

N

NN

N

H

N

NN

H2O

OH2

two-dimensional


Summary:


N

OH2N

isonicotinamideINA

+ AgNO3

stabilizing formulation of solid AgNO3

Summary:


OH

OH

molecular

paneling

O

OP

O

O–

BNPPA–

inverse

bilayers

BINOL/BINOLAT2–

N

N

NN

FeN

N

NH2

NH2

NH2

H2NH2N

H2N

[Fe(DABP)3]2+

Summary:


spontaneous resolution molecular trigonal-prismatic hexamer

HO NH

O

Ph

HN

O

R

O

NH

R

*

*

HO

O

OH

O

Summary:

Recent case studies on non-covalent interactions

recrystallization from

CHCl3red crystals

MeOHyellow crystals

THF and acetonitrile mixture of

red and yellowcrystals

N NPd

Br Br

NMe2

Pd

O NMe2

Pd

O

N

tolueneP 1

1

1 · 1.5 C7H8

P 112 · 0.5 C7H8

toluene?

P 11 · 1.5 C6H6

C6H6

CH2Cl2/hexane

P21/c1 · 1 C6H14

?

Acknowledgements

Magnetism Prof. J. Sanchiz, Univ. La Laguna

Mössbauer Dr. H. Winkler, Univ. Lübeck

TG/MS PD Dr. C. Näther, Univ. Kiel

Neutron diffraction Dr. S. Mason, ILL Grenoble

Heat transformation S. Henninger, ISE Freiburg

Luminescence Dr. H. Höppe, Univ. Freiburg

special X-ray Prof. C. Röhr, Univ. Freiburg

NP-TEM Dr. R. Thomann, Univ. Freiburg

Au-NP Dr. M. Krüger, Dr. M. Walter, Univ. Freiburg

Finances: DFG, FCI, AvH

Dr. Khalid Abu-Shandi

Frederik Blank

Anne-Christine Chamayou

Stefan Deblon

Dr. Thomas Dorn

Prof. Dr. M. Enamullah (AvH)

Marie Genitrini

Jerôme Krämer

Dr. Paul G. Lassahn

Hesham Mena

Dr. Barbara Wisser (née Paul)

Engelbert Redel

Dr. Tobias Scharmann

Dr. Savas Temizdemir

Lars Uehlin

Jana Vieth

Christian Vollmer

Dr. Biao Wu

Dr. He-Ping Wu (AvH)

Dr. Xiao-Juan Yang

Dr. Cungen Zhang (AvH)

supramolecular chemistry hydrogen-bonded networks · supramolecular chemistry –hydrogen-bonded...

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