Post on 16-Dec-2015
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