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
Structure of complex dication containing
3 molecules of 15-crown-5, 2 Li cations
and 2 water molecules.
X-ray diffraction data
and calculations by B3LYP/6-311G(d,p)
method
O.V.Shishkin, R.I.Zubatyuk, O.Yu.Zhovtyak,
A.V.Kiriyak, S.A.Kotlyar, G.L.Kamalov.
Struct.Chem., 2009, 20, 139.
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 WatsonCrick 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
Case of pyridine monohydrate
OH
H
H
OH
pi(N)...H-O
Lp(N)...H-O
N
OH
H
H
O
H
?????...H-O
Experimental observation of
mixed O-H…N/O-H… H-bonds
NH2
COCH3
H
N
COCH3
N
H
O
H
E.M.Opozda,
W.Lasocha,
B.Wlodarczyk-Gajda,
J. Mol. Struct., 2006,
784, 149
Geometrical parameters of hydrogen bond:
N…H 2.430 Å
O-H…N 163.1o
C-C-N…H -113.0o
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)
N
N
N
NH2
NH2
Contribution into total
hydrogen bonding:
Lone pair: 45 %
π-system: 55 %
d, Ǻ
N6-Н…N3 2.46(1)
(r), a. e. 2(r), a. e. Econt, kcal/mol
0.0070
0.0328
-1.32
I.S.Konovalova, Yu.V.Nelyubina, K.A.Lyssenko, B.V.Paponov, O.V.Shishkin, in preparation
Competition between the O-H…N and OH… H-bonds in polyhydrates of guanine
Complex with 17 H2O
B3LYP/6-311G(d,p)
O. S. Sukhanov, O. V. Shishkin. L. Gorb, J.
Leszczynski, Struct. Chem., 2008, 19, 171
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
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
LP(N)*(H-O)
8.66
97
(N-C)*(H-O)
0.29
3
LP(N)*(H-O)
2.45
58
(N-C)*(H-O)
1.75
42
(C-C)*(H-O)
0.22
100
N(3)…H-O(W4)
N(3)…H-O(W5)
C(6)…H-O(W16)
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
Geometrical parameters of the N-H…O hydrogen
bond:
H…O 2.12 Å; N-H…O 166 o С-С=O…H -69o
O
H3C
HN
NH2
Contribution to total
energy of hydrogen
bonding from NBO
analysis (M062X/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)?
O
OH
HO
Case of relatively strong hydrogen
bonds
O
Adipinic acid
Crystal packing is packing of hydrogen bonded chains
What is the main motif of crystal packing
(supramolecular architecture of molecular
crystals)?
11
11
10
12 14
10
12
13
9
8
1O
7
6
2
5
2
O
14
1
3
15 O
4
18 O
8
16
7
16
O
3
13 O
2
17
4O
6
2
1
O
5
3
1
17
4
3
4
9
15
18
5
O
19
20
2
1
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
O2N
N
N
H3C
CH3
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
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
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
Layered structure of crystals of
bicyclic aziridines
Energy of interactions (kcal/mol) of basic
molecules with molecules within the same
layer and from neighboring layer
(MP2/6-311G(d,p) data)
Comp. Inside
Neighbor
1
-33.76 -7.33
2
-38.80 -6.36
3
-30.05 -7.34
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
I
N
N
2-(4-Iodophenyl)-1,10-phenanthroline
Eint=-10.3 kcal/mol
MP2/6-311G(d,p) data
Eint=-21.8 kcal/mol
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
2
3
-12.3
-12.0
-12.0
O.V.Shishkin, V.V.Dyakonenko, A.V.Maleev, D. Schollmeyer, M.Vysotsky, CrystEngComm, in press
Supramolecular architecture of
hydrogen bonded crystals
monoclinic
Crystals structure of two polymorphic modifications
of crystals of 3,4-diamino-1,2,4-triazole
orthorhombic
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/mol
To 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/mol
To 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. Konovalova
Viktoriya V. Dyakonenko Dr.
Svitlana V. Shishkina
Gennady V. Palamarchuk
Especially very special
thanks:
for your attention