INTERMOLECULAR INTERACTIONS WITH

PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR

COMPLEXES AND MOLECULAR CRYSTALS

Oleg V. Shishkin

STC “Institute for Single Crystals”, National Academy of Science of Ukraine,

Kharkiv, Ukraine

Intermolecular interactions as the main factor stabilizing

supramolecular systems

O.V.Shishkin, R.I.Zubatyuk, O.Yu.Zhovtyak, A.V.Kiriyak, S.A.Kotlyar, G.L.Kamalov. Struct.Chem., 2009, 20, 139.

Structure of complex dication containing 3 molecules of 15-crown-5, 2 Li cations

and 2 water molecules.

X-ray diffraction dataand calculations by B3LYP/6-311G(d,p)

method

Aromatic fragments in supramolecular systems

Aromatic fragments in supramolecular systems

Aromatic fragments in supramolecular systems

Stacking interactions between π-systems

Structure of stacked dimer of N-methylated adenine-thymine Watson-Crick pairs of bases optimized by SCC-DFTB-D method

O.V.Shishkin, M.Elstner, T.Frauencheim, S.Suhai, Int.J.Mol.Sci., 2003, 4, 537

D-H…π hydrogen bonds in molecular complexes and crystals

Infinite chains formed by the O-H…π hydrogen bonds in crystals of tribromo substituted trityl alcohols

D. Schollmeyer, O.V.Shishkin, T.Ruhl, M. O. Vysotsky, CrystEngComm, 2008, 10, 715

Possible hydrogen bonds for aromatic azines

H OH

Lp(N)...H-O

H

OH

pi(N)...H-O

H

OH

?????...H-O

N

H

O

H

Case of pyridine monohydrate

Experimental observation of mixed O-H…N/O-H… H-bonds

N

NH2

HN

COCH3

COCH3

H

O

H

Geometrical parameters of hydrogen bond:N…H 2.430 ÅO-H…N 163.1o

C-C-N…H -113.0o

E.M.Opozda, W.Lasocha,

B.Wlodarczyk-Gajda, J. Mol. Struct., 2006,

784, 149

Competition of the O-H…N and O-H… H-bonds in monohydrate of pyridine

Contribution of lone pair and π-system into total energy of hydrogen bond obtained from NBO analysis. MP2/aug-cc-pvdz data

O-H…N bond

O-H… bond

O.V.Shishkin, I.S.Konovalova, L.Gorb, J.Leszczynski, Struct.Chem., 2009, 20, 37.

Mixed N-H…N/N-H…π hydrogen bonds in crystals of diaminotriazole (experimental

change density distribution)

NN

N

NH2

NH2

d, Ǻ (r), a. e. 2(r), a. e. Econt, kcal/molN6-Н…N3 2.46(1) 0.0070 0.0328 -1.32

I.S.Konovalova, Yu.V.Nelyubina, K.A.Lyssenko, B.V.Paponov, O.V.Shishkin, in preparation

Contribution into total hydrogen bonding:

Lone pair: 45 %π-system: 55 %

Competition between the O-H…N and O-H… H-bonds in polyhydrates

of guanine

H-bond H…A D-H…A

N(7)…H-O(W12)

2.059 151.1

N(7)…H-O(W13)

1.958 168.3

N(3)…H-O(W4) 2.016 179.3

N(3)…H-O(W5) 2.100 161.2

C(6)…H-O(W16)

2.635 135.9

O. S. Sukhanov, O. V. Shishkin. L. Gorb, J. Leszczynski, Struct. Chem., 2008, 19, 171

Complex with 17 H2OB3LYP/6-311G(d,p)

Competition between the O-H…N and O-H… H-bonds in polyhydrates of guanine

NBO analysis of contributions of individual interactions into hydrogen bonding

H-bond Interacting NO E(2), кcal/mol

Contrib., %

N(7)…H-O(W12) LP(N)*(H-O) 4.70 100

N(7)…H-O(W13) LP(N)*(H-O) 8.61 82

(N-C)*(H-O) 1.89 18

N(3)…H-O(W4) LP(N)*(H-O) 8.66 97

(N-C)*(H-O) 0.29 3

N(3)…H-O(W5) LP(N)*(H-O) 2.45 58

(N-C)*(H-O) 1.75 42

C(6)…H-O(W16) (C-C)*(H-O) 0.22 100

Mixed hydrogen bonds in hydrated nucleic acid

bases

Distribution of water hydrogens around adenine and cytosine during Car-Parrinello molecular dynamics simulation

A. Furmanchuk, O. Isayev, O. V. Shishkin, L.Gorb, J. Leszczynski, PCCP, 2010, 12, 3363

Mixed hydrogen bonds with participation of carbonyl group

H3C

O

HN NH2

Geometrical parameters of the N-H…O hydrogen bond:

H…O 2.12 Å; N-H…O 166 o С-С=O…H -69o

Contribution to total energy of hydrogen bonding from NBO

analysis (M06-2X/aug-cc-

pvdz):Lone pair: 60%π-system: 40 %

I.S.Konovalova, G.V.Palamarchuk, O.V.Hordienko, O.V.Shishkin, in preparation

What is the main motif of crystal packing (supramolecular architecture of molecular

crystals)?

HO

O

O

OH

Adipinic acid

Case of relatively strong hydrogen bonds

Crystal packing is packing of hydrogen bonded chains

What is the main motif of crystal packing (supramolecular architecture

of molecular crystals)?

OO

OO

12

3

4

5

67

89

10

11

12

13 1415 16

1718

1

23

4

1

O

O

O

O

O

1

2

3

4

5

67

89

10

11

12

13

1415

16

17

18

1920

1

23

4

5

2

S.V.Shishkina, O.V.Shishkin, R.Ya.Grygorash, A.V.Mazepa, I.M.Rakipov, V.V.Yakshin, S.A.Kotlyar, G.L.Kamalov,

J.Mol.Struct., 2007, 832, 199

Crystal packing of bicyclic aziridines

N N

H3C CH3

O2N

V.V.Dyakonenko, A.V.Zbruyev, V.A.Chebanov, S.M.Desenko, O.V.Shishkin, J.Struct.Chem.,

2005, 46, 1110

Approach for determination of real crystal packing pattern Accurate determination of crystal structure Determination of molecules belonging to

first coordination sphere of basic molecule using Dirichlet polyhedron

Accurate quantum chemical calculations of energy of intermolecular interactions of basic molecule and molecules from its first coordination sphere

Recognition of crystal fragments containing strongly bonded molecules

Dimer Symmetry Eint, kcal/mol

Structure 1

1_1 (-x, -y, 1-z) -11.26

1_2 (-x, 1-y, 1-z) -8.09

1_3 (-x, 1-y, -z) -5.73

1_4 (x-1, y, z) -1.08

1_5 (x+1, y, z) -1.08

1_6 (1-x, 1-y, -z) -3.06

1_7 (x, y, z-1) -2.90

1_8 (x, y, z+1) -2.90

1_9 (x, y-1, z+1) -0.53

1_10 (x, y+1, z-1) -0.53

1_11 (1+x, y, z-1) -2.98

1_12 (x-1, y, z+1) -2.98

1_13 (-1-x, -y, 2-z) -2.20

1_14 (1-x, -y, 1-z) -0.90

1_15 (-x, -y, 2-z) -1.82

1_16 (1-x, 1-y, 1-z) -0.38

Energy of interaction of basic molecule and molecules from its

first coordination sphere calculated by MP2/6-311G(d,p)

method

V.V.Dyakonenko, A.V.Maleev, A.I.Zbruyev, V.A.Chebanov, S.M.Desenko, O.V.Shishkin,

CrystEngComm, 2010, 6, 1816

Layered structure of crystals of bicyclic aziridines

Comp.

Inside Neighbor

1 -33.76

-7.33

2 -38.80

-6.36

3 -30.05

-7.34

Energy of interactions (kcal/mol) of basic molecules with molecules within the same

layer and from neighboring layer (MP2/6-311G(d,p) data)

V.V.Dyakonenko, A.V.Maleev, A.I.Zbruyev, V.A.Chebanov, S.M.Desenko, O.V.Shishkin,

CrystEngComm, 2010, 12, 1816

Supramolecular architecture of crystal with stacking interaction

N

N

I

2-(4-Iodophenyl)-1,10-phenanthroline

Eint=-21.8 kcal/mol

Eint=-10.3 kcal/mol

MP2/6-311G(d,p) data

O.V.Shishkin, V.V.Dyakonenko, A.V.Maleev, D. Schollmeyer, M.Vysotsky, CrystEngComm, in press

Supramolecular architecture of crystal with stacking interaction

Total energy of interactions (kcal/mol) of basic molecule to molecules belonging to

the same layer in the crystal MP2/6-311G(d,p) data

Layer Total in layer

1 -12.3

2 -12.0

3 -12.0

O.V.Shishkin, V.V.Dyakonenko, A.V.Maleev, D. Schollmeyer, M.Vysotsky, CrystEngComm, in press

Supramolecular architecture of hydrogen

bonded crystals

orthorhombic

monoclinicCrystals structure of two polymorphic modifications

of crystals of 3,4-diamino-1,2,4-triazole

I.S.Konovalova, S.V.Shishkina, B.V.Paponov, O.V.Shishkin, CrystEngComm, 2010, 12, 909

Layered structure of monoclinic polymorph of 3,4-diamino-1,2,4-triazole

Energy of interactions (MP2/aug-cc-pvdz):

Inside layer: -32.8 kcal/molTo neighboring layer: -3.6 kcal/mol

I.S.Konovalova, S.V.Shishkina, B.V.Paponov, O.V.Shishkin, CrystEngComm, 2010, 12, 909

Layered structure of orthorhombic polymorph of 3,4-diamino-1,2,4-triazole

Energy of interactions (MP2/aug-cc-pvdz):

Inside layer: -40.6 kcal/molTo neighboring layer: -1.5 kcal/mol

I.S.Konovalova, S.V.Shishkina, B.V.Paponov, O.V.Shishkin, CrystEngComm, 2010, 12, 909

Conclusions π-System of aromatic and heteroaromatic rings

represents very rich source of different types of weak intermolecular interactions influencing geometry and properties of supramolecular systems and molecular crystals.

Combination of reliable experimental methods of structure determination and modern ab initio quantum-chemical methods leads to successful recognition and investigation of various weak intermolecular interactions.

Application of reliable quantum-chemical methods of calculations of intermolecular interaction energy provides unambiguous recognition of main pattern of supramolecular architecture of molecular crystals and assemblies

Special thanks:

Synthesis and crystal growth Prof. G.L.Kamalov and

Dr.S.A.Kotlyar – A.V.Bogatsky Physico-Chemical Institute, Odessa, Ukraine.

Dr. O.V.Hordienko – T.G.Shevchenko Kyiv National University, Ukraine

Dr. M.O.Vysotsky – Mainz University,Germany

Prof. S.M.Desenko, Dr. V.A.Chebanov – Division of Functional Materials Chemistry, SSI “Institute for Single Crystals”, Kharkiv, Ukraine

Dr. B.V.Paponov – V.N.Karazin Kharkiv National University, Ukraine

Experimental charge density distribution analysis

Dr. K.A.Lyssenko, Dr. Yu.V.Nelyubina – A.N.Nesmeyanov Institute of Organoelement Compounds, Moscow, Russian Federation

Analysis of crystal packing Dr. A. V. Maleev – Vladimir

State Humanitarian University, Russian Federation

Quantum-chemical calculations

Prof. J. Leszczynski, Dr. L.Gorb, Dr. A.Furmanchuk, Dr. O Isayev – Jackson State University,USA

Very special thanks

Department of X-Ray Diffraction Studies and Quantum Chemistry

Irina S. KonovalovaViktoriya V. Dyakonenko Dr.

Svitlana V. ShishkinaGennady V. Palamarchuk

Especially very special thanks:

for your attention