INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR...
-
Upload
kaleb-callicott -
Category
Documents
-
view
221 -
download
5
Transcript of INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR...
![Page 1: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/1.jpg)
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
![Page 2: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/2.jpg)
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
![Page 3: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/3.jpg)
Aromatic fragments in supramolecular systems
![Page 4: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/4.jpg)
Aromatic fragments in supramolecular systems
![Page 5: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/5.jpg)
Aromatic fragments in supramolecular systems
![Page 6: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/6.jpg)
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
![Page 7: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/7.jpg)
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
![Page 8: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/8.jpg)
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
![Page 9: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/9.jpg)
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
![Page 10: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/10.jpg)
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.
![Page 11: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/11.jpg)
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 %
![Page 12: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/12.jpg)
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)
![Page 13: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/13.jpg)
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
![Page 14: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/14.jpg)
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
![Page 15: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/15.jpg)
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
![Page 16: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/16.jpg)
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
![Page 17: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/17.jpg)
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
![Page 18: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/18.jpg)
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
![Page 19: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/19.jpg)
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
![Page 20: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/20.jpg)
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
![Page 21: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/21.jpg)
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
![Page 22: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/22.jpg)
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
![Page 23: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/23.jpg)
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
![Page 24: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/24.jpg)
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
![Page 25: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/25.jpg)
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
![Page 26: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/26.jpg)
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
![Page 27: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/27.jpg)
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
![Page 28: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/28.jpg)
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
![Page 29: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/29.jpg)
Very special thanks
Department of X-Ray Diffraction Studies and Quantum Chemistry
Irina S. KonovalovaViktoriya V. Dyakonenko Dr.
Svitlana V. ShishkinaGennady V. Palamarchuk
![Page 30: INTERMOLECULAR INTERACTIONS WITH PARTICIPATION OF -SYSTEM IN SUPRAMOLECULAR COMPLEXES AND MOLECULAR CRYSTALS Oleg V. Shishkin STC “Institute for Single.](https://reader036.fdocuments.us/reader036/viewer/2022062713/56649cc25503460f94989609/html5/thumbnails/30.jpg)
Especially very special thanks:
for your attention