Centre for Advanced Computational Chemistry: Centre of Excellence of the SAS Comenius University, Faculty of Natural Sciences Slovak Academy of Sciences, Institute of Inorganic Chemistry The 9-th Central European Symposium on Theoretical Chemistry BOOK OF ABSTRACTS http://www.qch.fns.uniba.sk/cestc Nový Smokovec, Slovakia, September 12-15, 2010 Bratislava 2010 ISBN 978-80-223-2907-1 Editors: Jozef Noga, Miroslav Melicherčík, Ivan Černušák
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Centre for Advanced Computational Chemistry: Centre of Excellence of the SASComenius University, Faculty of Natural Sciences Slovak Academy of Sciences, Institute of Inorganic Chemistry
The 9-th Central European Symposium on Theoretical Chemistry
BOOK OF ABSTRACTS
http://www.qch.fns.uniba.sk/cestcNový Smokovec, Slovakia, September 12-15, 2010
Bratislava 2010
ISBN 978-80-223-2907-1
Editors: Jozef Noga, Miroslav Melicherčík, Ivan Černušák
Centre for Advanced Computational Chemistry: Centre of Excellence of the SASComenius University, Faculty of Natural Sciences Slovak Academy of Sciences, Institute of Inorganic Chemistry
Organizing Committee
Jozef Noga, chairman
Ivan Černušák
Vladimír Kellö
Miroslav Urban
Advisory committee:
Stanislav Biskupič Petr ČárskyIvan Hubač
Bogumił Jeziorski Stanislaw Kucharski
Hans LischkaPeter SurjánPeter Szalay
Miroslav Urban
Centre for Advanced Computational Chemistry: Centre of Excellence of the SASComenius University, Faculty of Natural Sciences Slovak Academy of Sciences, Institute of Inorganic Chemistry
The symposium was supported by
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Contents
PLENARY LECTURES
Roman Čurík: A message to quantum chemists: What we learned about DFT by modelling electron-molecule collisions 10
Christoph Flamm: In silico Evolution of Early Metabolism 11
Thomas S. Hofer, Bernd M. Rode, Bernhard R. Randolf: Characterisation of anisotropic ion hydration via QM/MM models 12
Florent Louis, Romain Vandeputte, Sébastien Canneaux, Marc Ribaucour: Thermochemical data calculation by quantum chemistry methods: application to ten species involved in low-temperature oxidation mechanism of o-xylene 13
Miroslav Medveď, Šimon Budzák, Jozef Noga, Ivan Černušák, Denis Jacquemin, Eric A. Perpète: Study and design of nonlinear optical materials: from molecules, through oligomers to polymers 15
Matthew K. MacLeod, Josef Michl: Trying to Understand the Mysterious Fluorescence of σ Systems: Oligosilanes 16
Monika Musiał: Fock space coupled cluster theory for two-valence sectors 17
Ágnes Nagy: Pair density functional theory 18
Katarzyna Pernal: Treating static and dynamic correlation with range-separated density and density matrix functionals 20
Piotr Piecuch, Wei Li: Local correlation coupled-cluster methods exploiting cluster-inmolecule ansatz and their multi-level generalizations 21
András Stirling: Reaction mechanism from quantum chemistry: unbiased and biased simulations 23
SHORT LECTURES
Prokopis Andrikopoulos, Stepan Sklenak, Zdenek Sobalik: Periodic DFT study of N2O decomposition over Fe-ferrierite 25
Alexei V. Arbuznikov, Hilke Bahmann, Martin Kaupp: Local hybrids: conceptually simple hyper-GGA exchange-correlation functionals for the Kohn-Sham density functional calculation of a wide range of properties 27
Kiran Bhaskaran-Nair, Ondrej Demel, Jir Pittner: Multireference State-Specic Mukherjee’s Coupled Cluster Methods With Triexcitations 29
Petr Čársky: Prospects of using MP2 for electron scattering 31
Kalju Kahn, Bernard Kirtman, Jozef Noga, Seiichiro Ten-no: Anharmonic Vibrational Analysis with Traditional and Explicitly Correlated Coupled Cluster Methods 32
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Dariusz Kędziera, Lukasz Mentel: Wave function in the relativistic two componet methods 34
Tatiana Korona: Local treatment of electron correlation for first-order molecular properties from expectation-value CCSD theory 35
Katarzyna Kulczycka, Joanna Trylska, Joanna Sadlej: Internal flexibility of clindamycin 36
István Mayer: The promotion energy of an atom in a molecule 38
Leszek Meissner: An extension of the coupled-cluster corrected configuration interaction method 39
Mariusz P. Mitoraj, Artur Michalak, Tom Ziegler: A Combined Charge and Energy Decomposition Scheme for Analysis of Chemical Bonds and Reaction Paths 40
Dana Nachtigallová, Mario Barbatti, Jaroslaw J. Szymczak, Hans Lischka: Photodynamics of pyrimidine-based molecules: Effect of substitution and initial energy 41
László Nyulászi, Oldamur Hollóczki: Some predictions on stable molecules: failure and success 42
Ivana Paidarová, Philippe Durand: Kinetic equations and dissipation 43
Łukasz Piękoś, Artur Michalak: Molecular dynamics modeling of half-metallocene titanium(IV) ethylene polymerization catalysts 45
Konrad Piszczatowski, Grzegorz Łach, Michał Przybytek, Jacek Komasa, Krzysztof Pachucki, Robert Moszyński, Bogumił Jeziorski: Relativistic, QED and nonadiabatic effects in the interaction of hydrogen atoms 46
Michał Przybytek, Trygve Helgaker: Gaussian and Finite-Element method for the calculation of Coulomb integrals 48
Dorota Rutkowska-Zbik, Malgorzata Witko: DFT Studies on Catalytic Oxidation of Cyclohexene on Manganese Porphyrins 50
Ján Šimunek, Jozef Noga: Orbital Optimized Second-Order Many-Body Perturbation Theory Via Coupled Cluster Ansatz 52
L. Skala, V. Kapsa: Quantum mechanics and mathematical statistics 54
Ágnes Szabados: The problem of small coefficients in SS-MRPT 55
Péter Szakács, Péter R. Surján: Jahn-Teller distortion and zero-field-splitting in carbon nanotubes 56
Štefan Varga: The Brillouin zone integration problem in density fitting of extended systems 57
Libor Veis, Jiří Pittner: Quantum chemical computations on quantum computers 58
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Aleš Vítek, Lenka Ličmanová, Ivana Paidarová, René Kalus: Structural changes in the water tetramer and hexamer. A combined Monte Carlo and DFT study 60
Zoboki Tamás, Mayer István, Surján R. Péter: Electron Correlation Calculations with Strictly Localized Orbitals 62
POSTERS
Dóra Barna, Gyula Tasi: Energy decomposition of alkyl-substituted furan molecules 64
L. Bucinsky, J. Kozisek, S. Biskupic, D. Jayatilaka, M. Gall: Relativistic effects vs. X-ray constrained Hartree Fock 66
Šimon Budzák, Ivan Černušák, Miroslav Medveď: Weak interactions between air pollutants 67
Sébastien Canneaux, Catherine Hammaecher, Florent Louis, Laurent Cantrel: A Theoretical Study of the H-abstraction Reactions of H2, H2O, HI, and OH by the IO (2Π3/2) Radicals 69
Aleksandra Chmielowska, Maria Jaworska, Piotr Lodowski: Structure and electronic properties of A-cluster in Acetyl-CoA synthase: insight from DFT 72
Ondřej Demel, Kiran Bhaskaran Nair, Jan Šmydke, Jiří Pittner: Noniterative triples correction in Mukherjee’s coupled cluster method via uncoupled approach 73
Jozef Federič, Ivan Černušák: MD modelling of tungsten carbide slab 75
R. W. Gora, R. Zalesny, W. Bartkowiak, J. M. Luis, B. Kirtman, H. Reis, M. G. Papadopoulos: Nonlinear optical properties of endohedral fullerene complexes 77
Ireneusz Grabowski, Andrew Teale, Szymon Śmiga, Karol Jankowski: Correlation potentials and electron densities obtained from correlated Optimized Effective Potential method and ab initio Wave Function Theory methods 79
Péter Jeszenszki, Ágnes Szabados, Péter R.Surján: Exact diagonalization of bosonic Hamiltonians 80
Anna Kaczmarek-Kędziera: Properties of encapsulated organic molecules 81
Stanislav Kedžuch, Ondřej Demel, Jiří Pittner, Jozef Noga: Multireference R12 Coupled Cluster Theory 82
Hyungrae Kim, Stepan Sklenak: ONIOM study of the catalytic mechanism of Dihydroneopterin Aldolase 83
Katarzyna Kowalska-Szojda, Monika Musiał, Stanisław A. Kucharski: The factorized quadruple excitations for potential energy surfaces with Λ functional 85
Anežka Křístková, Olga L. Malkina: The use of perturbation-stable localization in calculation and analysis of SO-correction to NMR chemical shifts 86
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Anežka Křístková, Olga L. Malkina, Stanislav Komorovský, Elena Malkin, Vladimir G. Malkin: NMR spin-spin couplings and overlap of densities of localized molecular orbitals 87
Piotr Kubisiak, Andrzej Eilmes: Relative Complexation Energies for Li+ Ion in Solution: Molecular Level Solvation Versus Polarizable Continuum Model Study 88
Mojmír Kývala: Secon-dorder Douglas–Kroll–Heß (DKH2) spin–orbit and parity-violating Hamiltonians 89
Piotr Lodowski, Maria Jaworska, Paweł M. Kozłowski, Tadeusz Andruniów: Quantum chemical calculations of photophysical properties of Methyl- and Adenosylcobalamin 90
Jakub Malohlava, Aleš Vítek, René Kalus: Protonated water clusters – structures and thermodynamics 91
Gergely Matisz, Walter M.F. Fabian, Sándor Kunsági-Máté: Hydrogen bonded clusters around aromatic π-systems 93
Gergely Matisz, Walter M.F. Fabian, Sándor Kunsági-Máté: Liquid structure of primary alcohols (methanol, ethanol, 1-propanol, 1-butanol) within the QCE theory 94
Katarína Mečiarová, Lukáš Demovič, Ivan Černušák: Effect of spin-orbit coupling on potential curves and spectroscopic properties of IO and I2 95
Miroslav Melicherčík, Lukáš Demovič, Michal Pitoňák, Pavel Neogrády: Applicability of Graphical Processing Units to Coupled Clusters Calculations 97
Balázs Nagy, József Csontos, Mihály Kállay, Gyula Tasi: Accurate ab initio heats of formation and standard molar entropies for several atmospherically important formyl derivatives 99
Péter Nagy, Imre Pápai: Catalytic hydrogenation of Quinolines via frustrated Lewis pairs: Mechanistic insight from theory 101
Jana Páleniková, Vladimír Kellö: Electric properties of 2-cyclopenten-1-on 103
Ewa Pastorczak, Katarzyna Pernal, Krzysztof Szalewicz: Long-range corrected dispersionless density functional 104
Lukáš F. Pašteka, Miroslav Urban: Electric properties of low-lying excited states of acetone and their interaction with water 105
Mariusz Pawlak, Mirosław Bylicki, Prasanta K. Mukherjee: Muonic systems with Debye-screened Coulomb interactions 107
Marek Pederzoli, Jiří Pittner: A non-adiabatic molecular dynamics study of azobenzene isomerization after excitation to the S1 state based on overlaps of CASSCF wave functions 108
Robert Ponec, Lukáš Bučinský, Carlo Gatti: Relativistic effects on metal-metal bonding. Comparison of the performance of ECP and scalar DKH description on the picture of metal-metal bonding in Re2Cl8(2-) 109
Mariusz Radoń, Ewa Brocławik, Kristine Pierloot: High Valent Iron-Oxo Complexes with Organic Macrocycles: DFT and Ab Initio Study 110
J. Rimarčík, M. Ilčin, L. Rottmannová, E. Klein, V. Lukeš:
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Quantum Chemical Study of the Energetics of Phenolic Compounds 112
Agnieszka Rogowska, Artur Michalak, Monika Srebro, Mariusz Mitoraj: The Influence of Substituents on the Activity of Half-Titanocene Catalysts for Ethylene Polymerization: Theoretical Study 114
Zoltán Rolik, Mihály Kállay: A local Coupled Cluster algorithm 116
Lenka Rottmannová, Ján Rimarčík, Erik Klein, Vladimír Lukeš: Thermodynamics of homolytic S–H bond dissociation in mono-substituted thiophenols 117
Eva Scholtzová, Pavel Mach: Computational study of weak interactions in the biologically active compounds 119
Jakub Šebera, Stanislav Záliš, Pavel Kubát, Kamil Lang, Tomáš Polívka: TD-DFT investigation of S1 and S2 singlet states of TMPyP(n) and complexes of TMPyP4 with sulfonated calix[m]arenes 121
Lucia Šimová, Pavel Neogrády, Miroslav Urban: Application of OVOS technique in calculations of small semiconductor clusters 123
R. Słupski, J. Komasa, K. Jankowski, J. Wasilewski: Benchmark electron density calculations on Be-like atoms 125
Szymon Śmiga, Ireneusz Grabowski: Comparison of the several correlated OEP methods in KS-DFT with correct asymptotic behavior 127
Jan Šmydke, Petra Ruth Kaprálová: Theoretical Study of Ionization and Excitation of He Gas Exposed to Intense XUV Radiation 129
Lukáš Sobek, Jiří Pittner: Femtosecond non-adiabatic molecular dynamics: a study of photochemical deactivation of indole 131
Roland Šolc, Daniel Tunega, Martin H. Gerzabek, Hans Lischka: Theoretical study of radical sites in gallic and protocatechuic acids 133
Anna Stachowicz, Jacek Korchowiec: Charge Sensitivity Analisys in Force Field Atoms Resolution 135
Miroslav Šulc, Roman Čurík: Cold electron collisions with nonpolar molecules 137
Martin Šulka, Michal Pitoňák, Miroslav Urban, Pavel Neogrády: OVOS technique with controlled accuracy in noniterative triples calculations 139
Nargis Sultana, Walter M. F. Fabian: Substituent effect on OH- addition to substituted benzocyclobutene-1, 2-diones: A DFT study 141
Robert Toboła, Fabien Dumouchel, Jacek Kłos, François Lique: Calculations of fine-structure resolved collisional rates for NH(X3Σ−)-He system 142
Daniel Tunega, Roland Šolc, Hasan Pašalić, Martin H. Gerzabek, Hans Lischka: Wetting of clay mineral surfaces – molecular dynamics simulation 143
Lucie Zárubová, Karel Oleksy: Optimalizations of the molecular clusters by the evolutional algorithms method 145
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PLENARY LECTURES
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A message to quantum chemists: What we learned about DFT by modelling electron-molecule collisions
Roman Čurík
J. Heyrovský Institute of Physical Chemistry ASCR Doleškova 3
While most mono-atomic ions exhibit a uniform potential in each direction of
space, some species do not follow this example leading to ansiotropic solvation
structures. This behaviour is observed in the case of main group as well as for transition
metal ions. While the presence of stereo-chemically active lone pairs is well-studied in
the case of crystals (e.g. of SnO), experimental and theoretical examinations of the
solvation of these compounds is a challenging and complex task. The construction of
classical interaction potentials enabling an accurate description of the ion-solvent
interaction has to be considered a difficult and challenging task and hence, a quantum
chemical treatment appears to be most practical approach. In particular hybrid
approaches, treating the chemical most relevant region at a quantum mechanical level
while the interactions in the remaining part are evaluated via classical potentials, appear
to be the method of choice. The recently formulated quantum mechanical charge field
molecular dynamics (QMCF MD) approach [1,2] proved to be a versatile tool for the
study of solvated species.
Applications of the QMCF MD framework to anisotropically hydrated ions are
presented. The system covered are Pd2+, Pt2+, Ge2+, Sn2+ and Pb2+.
[1] B. M. Rode, T. S. Hofer, B. R. Randolf, C. F. Schwenk, D. Xenides,
V. Vchirawongkwin, Theor. Chem. Acc. 2006, 115(2-3), 77-85
[2] T. S. Hofer, A. B. Pribil, B. R. Randolf, B. M. Rode,
Adv. Quant. Chem. 2010, 59 213-246
Acknowledgement
Financial support for this work provided by the Austrian Science Fund (FWF) is
gratefully acknowledged.
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Thermochemical data calculation by quantum chemistry methods: application to ten species involved in low-temperature oxidation
mechanism of o-xylene
Florent LOUIS, Romain VANDEPUTTE, Sébastien CANNEAUX, Marc RIBAUCOUR
PhysicoChimie des Processus de Combustion et de l’Atmosphère (PC2A) UMR 8522 CNRS/Lille1, Université Lille 1 Sciences et Technologies, Cité scientifique, Bât C11/C5, 59655 Villeneuve d’Ascq Cedex, France
Thermokinetic modeling studies of surrogate fuel combustion are carried out to
understand the mechanisms of formation of pollutants and toxic compounds in automotive
engines. A surrogate fuel is composed of molecules representative of each family of compounds
included in a commercial fuel: alkanes, aromatic compounds, cyclanes, alkenes, oxygenated
compounds. Among aromatic compounds, xylenes are good representative of alkylbenzenes.
Their percentages in mass in an European gasoline are 3.06, 5.70, and 1.96% for o-, m-, and p-
xylene, respectively. A low-temperature oxidation thermokinetic model of o-xylene is currently
elaborated in our laboratory. Thermochemical data of species involved in the mechanism are
usually estimated using the THERM software based on Benson group additivity theory. However,
due to missing groups in THERM group database, thermochemical data of many species cannot
be estimated. The aim of this work was to determine thermochemical data of ten species (see
Table 1) using quantum chemistry methods.
Quantum chemistry calculations were performed using the GAUSSIAN03 program suite.
ΔfH°(298 K) were calculated using four composite methods (G3, G3MP2, G3B3, and CBS-QB3)
and isodesmic reaction technique to cancel the systematic error in the molecular orbital
calculations. Sets of five isodesmic reactions were used for each target species. Total energies
were corrected by ZPVE and vibration frequencies were scaled using appropriate scaling factors.
Final values of ΔfH°(298 K) were obtained by averaging the values obtained from each isodesmic
reaction and then by averaging the averaged values given by each calculation method. They are
reported in Table 1. For species 4-7 owing many conformers, ΔfH°(298 K) was calculated by a
population-weighted average of each conformer ΔfH°(298 K). The mole fraction of each
conformer was determined using a Boltzmann distribution based on the energy difference
between conformers. For species 1, 2, 5-8 ΔfH°(298 K) values are available in the literature.
Except for species 2, the differences between our determination and the literature value are less
The 9th Central European Symposium on Theoretical Chemistry
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than 5 kJ.mol-1. ΔfH°(298 K) of species 3, 4, 9, and 10 has been determined for the first time to
our knowledge.
Table 1: Values of ΔfH°(298 K) in kJ.mol-1 calculated in this work for the ten species.
(from oligomeric values to polymeric limit) techniques and others. Possibilities of
investigation of NLO properties of infinite periodic systems will also be outlined.
This work has been supported by the Grant Agency of the Slovak Republic VEGA
(projects No. 1/0356/09 and No. 1/0428/09).
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Trying to Understand the Mysterious Fluorescence of ó Systems: Oligosilanes
Matthew K. MacLeod and Josef Michl
University of Colorado, Boulder, CO, USA, and Academy of Sciences of the Czech Republic,Prague, Czech Republic
Saturated hydrocarbons absorb in the vacuum UV part of the spectrum but produce verybroad and weak fluoresce bands at much longer wavelengths. The huge Stokes shifts suggestprofound differences between the equilibrium geometries of the ground and the singlet excited state.That should not be surprising, since electronic excitation in saturated systems involves electrons ofthe bonds that hold the molecule together. The nature of the geometry changes that take place uponexcitation is not known.
We have been examining the silicon analogs of saturated hydrocarbons, the peralkylated
n 2n+2oligosilanes Si R . Like hydrocarbons, they contain saturated and tetravalent tetrahedral atomsin the main chain or cycle (Si instead of C), only single bonds, and no lone pairs. Oligosilaneshowever are easier to study since they absorb throughout the near UV region, and their spectra aremuch simpler, although they, too, contain fairly numerous closely spaced transitions. The differenceoriginates in the lower electronegativity of the backbone Si atoms relative to the lateral alkylsubstituent atoms, and in some ways the oligosilanes resemble fluorocarbons more thanhydrocarbons.
Like hydrocarbons, short-chain peralkylated oligosilanes (n < 8) generally fluoresce atstrikingly long wavelengths, with huge Stokes shifts. A compound with no observable absorptionabove 250 nm can emit in the blue or even in the green part of the visible spectrum. Remarkably,some oligosilanes fluoresce in two different spectral regions. In contrast, longer-chain peralkylatedoligosilanes (n > 6) generally exhibit Franck-Condon allowed fluorescence with a minimal Stokesshift and apparently very little difference between ground state and excited state equilibriumgeometries. The behavior of these more normal emitters can be understood in terms of extensiveó-electron delocalization, and has been dealt with elsewhere (some conformers of the chain with n= 7 show Stokes-shifted fluorescence and others fluoresce with no Stokes shift).
We shall report the results of calculations at several levels of theory (CC2, CASPT2, TD-DFT) that we have performed to answer the following questions: (i) What are the equilibriumgeometries of the highly distorted first excited states of peralkylated oligosilanes? (ii) Can oneunderstand the nature of the geometrical distortion from the ground state in simple intuitive terms?
The 9th Central European Symposium on Theoretical Chemistry
It is well known that static and long-range correlation effects are not well treated by local or semilocal density functionals. They are accurate, however, for systems where dynamic correlation dominates. On the other hand, recently proposed functionals of one-electron reduced density matrix (density matrix) proved capable of treating static correlation effects correctly.
We propose a new method, based on range-separation of Coulomb electron-electron interaction. It employs density and density matrix functionals in the short- and long-range regimes, respectively.
The method has been successfully applied to the homogeneous electron gas. The long-range correlation energy of the electron gas is excellently reproduced by a modified Buijse-Baerends density matrix functional [1].
The same functional combined with a short-range PBE (Perdew-Burke-Ernzerhof) density functional reproduces accurately dissociation curves of simple molecules. Therefore, the new approach corrects the deficiency of the density functional in the dissociation limit, where static correlation effects are present.
The new method scales with the 4th power of the number of basis set functions. An efficient projected gradient algorithm is employed in the optimization process [2]. The total computational cost is comparable to that of DFT methods.
[1] K. Pernal, Phys. Rev. A 81, 052511 (2010).[2] E. Canc?s and K. Pernal, J. Chem. Phys. 128, 134108 (2008).
Acknowledgement This work was supported by Polish Ministry of Science and Higher Education grant No. N N204 159036
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Local correlation coupled-cluster methods exploiting cluster-in-molecule ansatz and their multi-level generalizations
Piotr Piecuch and Wei Li
Department of Chemistry, Michigan State University
Coupled-cluster (CC) methods have greatly impacted modern quantum chemistry,
but, as all electronic structure approaches that aim at the accurate description of many-
electron correlation effects, they face significant challenges when dealing with the in-
creasingly complex molecular problems chemists are interested in. This includes prohibi-
tive costs of CC calculations for larger molecular systems. To help to address this chal-
lenge, we have extended [1,2] a number of CC methods, including CCSD, CCSD(T), and
the completely renormalized extension of CCSD(T), abbreviated CR-CC(2,3) [3], to lar-
ger systems with hundreds of atoms through the use of the local correlation, cluster-in-
molecule (CIM) ansatz [1,2,4]. The resulting CIM-CCSD, CIM-CCSD(T), and CIM-CR-
CC(2,3) methods are characterized by (i) the linear scaling of the CPU time with the
system size when the same level of theory is applied to all CIM subsystems, (ii) the use
of orthonormal orbitals in subsystem calculations, (iii) the natural coarse-grain par-
allelism, which can be further enhanced by the additional fine-grain parallelism of each
subsystem calculation, (iv) the high computational efficiency, enabling calculations for
large molecular systems at high levels of CC theory, (v) the purely non-iterative character
of local triples corrections to CCSD energies, and (vi) the applicability to the covalently
and weakly bound molecular systems. In addition, one can use the flexibility of the CIM
local correlation ansatz to mix different CC or CC and non-CC methods within a single
calculation, enabling the rigorous formulation of multi-level local correlation theories [2]
that combine the high-level CC methods, such as CR-CC(2,3), to treat, for example, the
reactive part of a large molecular system with the lower-order ab initio (e.g., MP2)
scheme(s) to handle the chemically inactive regions without splitting it into ad hoc
fragments and saturating dangling bonds. By comparing the results of the canonical CC
calculations with the single- and multi-level CIM-CC calculations for normal alkanes
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[1,2], water clusters [1], the diffusion of atomic oxygen on the silicon surface [5], and the
proton transfer in the aggregates of dithiophosphinic acids with water [2], we de-
monstrate that the CIM-CCSD, CIM-CCSD(T), and CIM-CR-CC(2,3) approaches, and
their multi-level extensions accurately reproduce the corresponding canonical CC corre-
lation and relative energies, including chemical reaction pathways, while offering savings
in the computer effort by orders of magnitude.
[1] (a) W. Li, P. Piecuch, J. R. Gour, and S. Li, J. Chem. Phys. 131, 114109 (2009). (b) W. Li, P. Piecuch, and J. R. Gour, in: Theory and Applications of Computational Chemistry - 2008, AIP Conference Proceedings, Vol. 1102, edited by D.-Q. Wei and X.-J. Wang (AIP, Melville, NY, 2009), p. 68. (c) W. Li, P. Piecuch, and J. R. Gour, in: Progress in Theoretical Chemistry and Physics, Vol. 19, Advances in the Theory of Atomic and Molecular Systems: Conceptual and Computational Advances in Quantum Chemistry, edited by P. Piecuch, J. Maruani, G. Delgado-Barrio, and S. Wilson (Springer, Dordrecht, 2009), p. 131. (d) W. Li and P. Piecuch, J. Phys. Chem. A, in press; Articles ASAP; Publication Date (Web): April 7, 2010. [2] W. Li and P. Piecuch, J. Phys. Chem. A 114, 6721 (2010). [3] (a) P. Piecuch and M. Włoch, J. Chem. Phys. 123, 224105 (2005). (b) P. Piecuch, M. Włoch, J. R. Gour, and A. Kinal, Chem. Phys. Lett. 418, 467 (2006). [4] (a) S. Li, J. Ma, and Y. Jiang, J. Comput. Chem. 23, 237 (2002). (b) S. Li, J. Shen, W. Li, and Y. Jiang, J. Chem. Phys. 125, 074109 (2006). [5] P. Arora, W. Li, P. Piecuch, J. W. Evans, M. Albao, and M. S. Gordon, J. Phys. Chem. C, in press; Articles ASAP; Publication Date (Web): July 6, 2010.
Supported by the Chemical Sciences, Geosciences and Biosciences Division, Office of
Basic Energy Sciences, Office of Science, U.S. Department of Energy (Grant No. DE-
FG02-01ER15228; P.P).
The 9th Central European Symposium on Theoretical Chemistry
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Reaction mechanism from quantum chemistry:
unbiased and biased simulations
Andras Stirling
Chemical Research Center of the Hungarian Academy of Sciences
The standard coupled-cluster (CC) approach for correlation energy calculations provides a
set of nonlinear equations for cluster amplitudes and the energy expression. The set of CC
equations is usually solved using Jacobi-type iterative schemes combined with additional pro-
cedures for speeding up the convergence. An alternative route leading to the coupled-cluster
method can be obtained by introducing a modification of the configuration interaction (CI)
matrix. While the first approaches of this type have been called Coupled-Cluster Corrected
CI methods or, more frequently, Coupled Electron Pair Approximations (CEPAs), their
quite recent reformulation using intermediate Hamiltonian formalism is known as the size-
consistent self-consistent CI method ((SC)2 CI). Within the scheme the CC wave function
is partitioned into the linear and nonlinear components and contributions from the latter
one are incorporated through modification of the CI matrix. The solution is obtained by
diagonalization of the dressed CI matrix that must be done in a self-consistent manner since
the dressing depends on the matrix eigenvector. A possible generalization of this approach
can be obtained by treating the problem in a more formal way. The standard set of CC
amplitude equations does not depend on the CC energy that is calculated after determin-
ing the cluster amplitudes, however, simple manipulations can make the equations energy
dependent. A further rearrangement of the equations shows that diagonalization techniques
can be used to solve them. The scheme is quite flexible so even Newton-Raphson algorithm
can be used within this framework. Some numerical examples showing the convergence of
different iterative methods are presented.
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A Combined Charge and Energy Decomposition Scheme for Analysis of Chemical Bonds and Reaction Paths
Mariusz P. Mitoraja,b, Artur Michalaka, Tom Zieglerb
a Jagiellonian University, R.Ingardena 3, 30-060 Cracow, Poland. b Department of Chemistry, University of Calgary, 2500 University Dr NW, Calgary, Alberta Canada.
In the present work we have introduced a new scheme for the electronic structure analysis
by combining the Extended Transition State (ETS) method1 with the Natural Orbitals for
Chemical Valence (NOCV)2. The ETS-NOCV3 charge and energy decomposition scheme makes
it not only possible to decompose the deformation density, Δρ, into the different components
(such as σ, π, δ, etc.) of the chemical bond, but it also provides the corresponding energy
contributions to the total bond energy. Thus, the ETS-NOCV scheme offers a compact,
qualitative and quantitative, picture of the chemical bond formation within one common
theoretical framework. The applicability of the ETS-NOCV scheme is demonstrated for various
types of covalent and donor-acceptor bonds. We also included the applications involving inter-
and intra-molecular (agostic) hydrogen bonding (see Figure below). Finally, we will show that
ETS-NOCV can be used not only to analyze the stationary points on PES, but its is also able to
describe the changes in electronic structure along the reaction paths. Decomposition of energetic
reaction barrier into the stabilizing (electronic and electrostatic) and destabilizing (Pauli repulsion
and geometry reorganization) components will be discussed in a detailed way for the examples
of reactions of industrial importance (activation of B-H bond of ammonia borane, β-hydride
eliminations, Diels-Alder cycloadditions).
Figure. The contours of relevant deformation density contributions describing the bonding between the cationic nickel based fragment and the n-propyl group together with the corresponding energies obtained from ETS-NOCV scheme3.
agosticorborb ρρσ ΔΔ ,1
[1] Ziegler, T., Rauk, A. Theor. Chim. Acta 46, 1, (1977). [2] Nalewajski, R.F.; Mrozek, J.; Michalak, A. International Journal of Quantum Chemistry 61,589,(1997); Michalak, A.; Mitoraj, M.; Ziegler, T. J. Phys. Chem. A. 112(9), 1933, (2008). [3] Mariusz P. Mitoraj, Artur Michalak and Tom Ziegler J. Chem. Theory Comput. 5 (4), 962.
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Photodynamics of pyrimidine-based molecules: Effect of substitution and initial energy
Dana Nachtigallová1, Mario Barbatti2, Jaroslaw J. Szymczak2 and Hans Lischka1,2
1Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech
Republic, Flemingovo nam. 2, CZ-16610 Prague 6, Czech Republic 2Institute for Theoretical Chemistry – University of Vienna,
Waehrinegrstrasse 17, A 1090 Vienna, Austria
Substitution on the hetero-aromatic ring of the nucleic acid bases and their analogues can
significantly influence their excited state lifetime by changing the location of conical
intersections and/or due to the increasing of barriers on the trajectory towards them.
Consequently a relaxation mechanism responsible for a very rapid internal conversion to the
electronic ground state becomes inefficient.
In this study we present the results of an ab initio on-the-fly surface-hopping dynamics
simulation study of 2,4-diamino-pyrimidine for which the lifetime of the order of picoseconds
was measured.[1] Effect of substitution is discussed by comparison with the excited state
behavior of 4-amino-pyrimidine. Dynamics simulations are performed with different initial
energies to discuss the effect of pump energy used in the experiment.
The substitution on the pyrimidine ring of uracil changes its excited state lifetime
dramatically. Exploring the PES helps to explain this effect caused by changes of reaction
paths towards conical intersections.[2]
[1] Z. Gengeliczki, M. P. Callahan, C. I. Pongor, B. Sztára, D. Nachtigallová, P. Hobza, M.Barbatti, H. Lischka, M. S. de Vries; Phys. Chem. Chem. Phys. 12 (2010), 5375.
[2] D. Nachtigallová, H. Lischka, J.J. Szymczak, M. Barbatti, P. Hobza, Z. Gengeliczki, G. Pino, M. P. Callahan, M. S. de Vries; Phys. Chem. Chem. Phys. 12 (2010), 4924.
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Some predictions on stable molecules: failure and success.
László Nyulászi, Oldamur Hollóczki, ...
Budapest University of Technology and Economics Department of Inorganic and Analytical Chemistry
In the present work results of molecular dynamics simulations of half-metallocene titanium(IV) catalysts are presented. Molecular systems under consideration include non-bridged half-metallocene titanium(IV) complexes with aryloxo ligand acting as catalysts in ethylene polymerization process. Catalysts with various ligands and at various catalytic process stages are considered.
Methodology includes Car-Parinello molecular dynamics on the ab initio DFT level (CPMD software package) and Born-Oppenheimer molecular dynamics on the semiempirical level (MSINDO software package). Despite lower accuracy semiempirical approach is still useful due to ca. 3.5 orders of magnitude difference in performance comparing to DFT approach. Such performance allows for simulations on the timescale far beyond ab initio methods. Free molecular dynamics is used to study spontaneous transitions (including conformational changes and ethylene insertion reactions). Constrained molecular dynamics in slow-growth approach is used to obtain free energy profiles of ethylene insertion reaction.
Presented results include spontaneous conformational transitions affecting catalyst reactivity. Example where six stable conformations (including several transitions between them) can be observed on one simulation is also presented. Spontaneous insertion of ethylene is observed, followed by conformational changes which make catalytic cycle in one simulation.
Projections of presented trajectories (i.e. plots of selected coordinates) as well as animated visualizations are presented.
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Relativistic, QED and nonadiabatic effects in the
interaction of hydrogen atoms
Konrad Piszczatowski†, Grzegorz �Lach†, Micha�l Przybytek†, Jacek Komasa§,
Krzysztof Pachucki‡, Robert Moszynski†, Bogumi�l Jeziorski†
†Faculty of Chemistry, University of Warsaw
Pasteura 1
02-093 Warszawa, Poland
§ Faculty of Chemistry, A. Mickiewicz University
Grunwaldzka 6
60-780 Poznan, Poland
‡ Institute of Theoretical Physics, University of Warsaw
This study is presenting the relativistic effects and the effects of the X-ray constrained
Hartree-Fock/DFT (XC-HF) approach [1] for the mer,trans-[Ru(Cl)3(Hind)2(NO)]
complex. The quasirelativistic infinite order two component (IOTC) [2,3] and Douglas-
Kroll-Hess 2nd order (DKH2) [4,5] calculations were carried out at both 1-component
(scalar relativistic effects) and 2-component (scalar relativistic effects + SO coupling)
level of theory. The experimentally determined (X-ray refinement) charge density is
compared with XC-HF and XC-BLYP electron density. The X-ray constraint and
relativistic effects in electron densities as well as the difference of the DKH2 and IOTC
electron densities are presented. Picture change effects [6,7] in the DKH2 and IOTC
electron density and structure factors of the studied compound are investigated by
analytical means. The relativistic effects and PCE is considered also for radial
distribution of (NR, DKH2, IOTC, DCH)electron densities of the radon atom. The PCE
correction of DKH2 and IOTC electron densities and structure factors was performed
using the Tonto software package [8].
[1] Jayatilaka, D. & Grimwood, D. J. (2001). Acta Cryst. A57, 76-86.
[2] Barysz, M. & Sadlej, A. J. (2002) J. Chem. Phys. 116, 2696.
[3] Kędziera, D., Barysz, M. (2007) Chem. Phys. Lett. 446, 176.
[4] Wolf, A., Reiher, M. & Hess, B. A. (2002). J. Chem. Phys. 117, 9215-9226.
[5] Reiher, M. & Wolf, A. (2004a). J. Chem. Phys. 121, 2037-2047.
[6] Wolf, A. & Reiher, M. (2006a). J. Chem. Phys. 124, 064102.
[7] Mastarlez, R., Lindth, R. & Reiher, M. (2008). Chem. Phys. Lett. 465, 157-164.
[8] Jayatilaka, D. & Grimwood, D. J. (2000). TONTO. A Research Tool for Quantum
Chemistry. The University of Western Australia, Nedlands, Western Australia, Australia.
see at: http://www.theochem.uwa.edu.au/tonto
Acknowledgement
The support from the grants: APVV (contract No. APVV-0093-07) and VEGA (contracts
No. 1/0817/08 and 1/0127/09) is gratefully acknowledged.
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Weak interactions between air pollutants
Šimon Budzák1, Ivan Černušák2, Miroslav Medveď1
1 Department of Chemistry, Faculty of Natural Sciences, Matej Bel University, Tajovského 40, SK-97400 Banská Bystrica, Slovakia, [email protected],
2 Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, SK-842 15 Bratislava, Slovakia,
Carbon monoxide belongs to important air pollutants. It constitutes substantial part of the fuel emissions, represents non-negligible part of the cigarette-smoke and is also present in volcanic gases [1]. In this contribution we investigate the intermolecular interactions of neutral H2O, SO2 species and important atmospheric ion NO+ with CO.
Weak interactions in this dimers were studied with standard ab initio methods including MP2 and CCSD(T) method, using augmented correlation corrected polarized series of basis sets. Due to large computational demands the OVOS (Optimized virtual orbital space) approach was used. Interaction energy and its components, vibrational spectra and dipole moments for local minima are reported. In order to find in which layer of atmosphere is formation of such complexes possible, the dependence of Gibbs energy of their formation on temperature was studied.
In the most stable conformations the carbon atom of CO is oriented towards the partner molecule (see Figure 1). The interaction energies are: -32.3 kJ/mol for NO+...CO, -8.2 kJ/mol for CO...H2O and -7.0 kJ/mol for CO...SO2, while the Gibbs energies are -10.5 kJ/mol for NO+...CO, 14.3 kJ/mol for CO...H2O and 6.4 kJ/mol for CO...SO2 at 200 K during the night in the troposphere.
Figure 1 Most stable conformations of studied dimmers
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[1] Barbara J, Pitts F, Pitts JN. Chemistry of the Upper and Lower Atmosphere, Amsterdam: Elsevier, 2000.
AcknowledgementWe appreciate the financial support from Slovak Grant Agency VEGA (grant 1/0428/09) and Matej Bel University Grant Agency (grant 02/02/2010)
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A Theoretical Study of the H-abstraction Reactions of H2, H2O, HI,and OH by the IO (2Π3/2) Radicals
a PhysicoChimie des Processus de Combustion et de l’Atmosphère (PC2A) UMR 8522 CNRS/Lille1, Université Lille 1 Sciences et Technologies, Cité scientifique, Bât C11/C5, 59655 Villeneuve d’Ascq Cedex, France b Université Catholique de Louvain, Bâtiment Lavoisier, Place L. Pasteur 1, B-1348 Louvain-la-Neuve, Belgiumc Institut de Radioprotection et de Sûreté Nucléaire, DPAM, Centre de Cadarache, BP3, 13115 Saint Paul Lez Durance, Cedex, Franced Laboratoire de Recherche Commun IRSN-CNRS-Lille1 "Cinétique Chimique, Combustion, Réactivité" (C3R), Centre de Cadarache, BP3, 13115 Saint Paul Lez Durance, Cedex, France
During a loss-of-coolant accident due to a break in the Reactor Coolant System
(RCS) of a nuclear Pressurized Water Reactors (PWR), part of the nuclear fuel could
melt and release fission products which will be transported through the RCS and its break
to the reactor containment building, and then possibly to the environment. Radioiodine is
one of the most radiotoxic fission products released from the damaged fuel due to its
ability to form volatile species, and the potential accidental release of volatile iodine to
the environment is a key safety issue for emergency response planning. The gaseous part
of iodine at the RCS break has a great impact on the potential iodine outside releases, and
kinetic limitations occuring in gaseous phase are suspected to promote gaseous iodine
species. To better predict the iodine speciation reaching the containment building,
depending on accident scenarios, the thermokinetic parameters of the main gaseous
reactions which govern the overall iodine behavior in the RCS have to be determined.
Such kinetic reactions could be later implemented in the ASTEC severe accident
simulation software.
In a first step, the reactions of iodine atoms I (2P3/2) with H2, H2O, HI, and OH have
been studied theoretically [1]. The aim of this methodological work was to demonstrate
that standard theoretical methods are adequate to obtain quantitative rate constants for the
reactions involving iodine-containing species.
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In a second step, the computational procedure has been extended to some relevant
reactions involving the iodine oxide radical IO in its ground state (2Π3/2) and the same
species (H2, H2O, HI, and OH). Quantum chemistry calculations and TST kinetic models
are used in this work to compute the temperature dependence of the rate constants for the
abstraction reactions by iodine oxide radicals. Results will be presented and discussed in
this poster.
[1] Canneaux, S.; Xerri, B.; Louis, F. ; Cantrel, L. J. Phys. Chem. A, 2010, in press.
The 9th Central European Symposium on Theoretical Chemistry
a PhysicoChimie des Processus de Combustion et de l’Atmosphère (PC2A) UMR 8522 CNRS/Lille1 , Université Lille 1 Sciences et Technologies, Cité scientifique, Bât C11/C5, 59655 Villeneuve d’Ascq Cedex, France b Institut de Radioprotection et de Sûreté Nucléaire, DPAM, Centre de Cadarache, BP3, 13115 Saint Paul Lez Durance, Cedex, Francec Laboratoire de Recherche Commun IRSN-CNRS-Lille1 "Cinétique Chimique, Combustion, Réactivité" (C3R), Centre de Cadarache, BP3, 13115 Saint Paul Lez Durance, Cedex, France
The French Institut de Radioprotection et de Sûreté Nucléaire (IRSN) and the
German Gesellschaft für Anlagen und Reaktorsicherheit mbH (GRS) are jointly
developing the ASTEC (Accident Source Term Evaluation Code) software to simulate
severe accidents, which can arise in a pressured-water nuclear reactor (PWR), from
initiating event up to the possible radiological release of fission products (FP) outside.
IODE module of ASTEC is devoted to model the FP behavior inside the nuclear
containment building and more especially the iodine radiochemistry. The FP modeling, in
terms of physical chemistry processing, need the knowledge of numerous properties
which some cannot be experimentally determined. Thus, cooperation began with the
laboratory PC2A from University of Lille 1 to determine some data with a theoretical
chemistry approach.
At the instigation of IRSN, a new molecular dynamics program, named SPyDERS,
is in the making. The initial objective of this code is to calculate energetic values related
to the solvation, such as Henry's law constants (HLC), for compounds of nuclear interest
such as iodine oxides and iodine nitroxides whose volatilities are still questionable.
In this poster, the approach will be detailed and the first operating tests of
SPyDERS will be discussed.
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Structure and electronic properties of A-cluster in Acetyl-CoA synthase: insight from DFT
Aleksandra Chmielowska, Maria Jaworska, Piotr Lodowski
Institute of Chemistry, University of Silesia Szkolna 9
40-006 Katowice, Poland
Acetyl-CoA synthase (ACS) is a bacterial enzyme which catalyses the synthesis of
Acetyl-CoA from coenzyme-A (CoASH), CO and methyl group coming from corrinoid-
iron-sulfur protein (CoFeSP):
CH3-Co(III)FeSP + CO + CoASH ↔ CH3CO-SCoA + Co(I)FeSP + H+ The active centre of ACS consists of A-cluster, dinuclear nickel complex bounded
to the sulfur-iron cubane: Fe4S4 – NipNid. Nip and Nid denote nickel atoms proximal and
distal to the cubane, respectively.
The geometry of A-cluster was optimized with use of DFT/OLYP method and two
main structural conformations were found, closed (I) and open (II) ones. Similar
calculations were performed for A-cluster with ligands (CH3, H, CO, H2O) linked to Nip.
The influence of polar solvent on the structures was taken into account by PCM model.
Atomic charges and spin densities for all structures of A-cluster were analyzed.
Acknowledgement: Calculations were performed at the Wrocław Centre for Networking
and Supercomputing, WCSS, Wrocław, Poland, under calculational Grant No. 51/96.
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Noniterative triples correction in Mukherjee’s
coupled cluster method via uncoupled approach
Ondrej Demel, Kiran Bhaskaran Nair, Jan Smydke, Jirı Pittner
J. Heyrovsky Institute of Physical Chemistry, v.v.i., Academy of Sciences of the
Direct comparison of the correlation potentials, electron densities and correlation energies, generated from few variants of correlated Optimized Effective Potential Method (OEP), standard Density Functional Theory (DFT) and from ab intio Wave Function Theory Methods (WFT), has been employed for analyzing the impact of the correlation effects on those quantities. These methods have been applied to a few atomic and molecular systems. The correlation potentials, energies and densities generated from orbital-dependent OEP (OEP2-sc [1], OEP-ccpt2 [2]) and from WFT methods - Coupled Cluster (CCSD, CCSD(T) ) and second-order Many Body Perturbation Theory (MP2) show very similar and systematic behaviour, reconfirming the correctness of the ab initio DFT (OEP2) methods [3]. In a contrast it has been demonstrated that the VWN5 and LYP correlation functionals do not represent any substantial dynamical correlation effects on the KS-correlation potentials [3] and electron density [4].
[1] R. J. Bartlett, I. Grabowski, S. Hirata, S. Ivanov J. Chem. Phys. 122, 034104 (2005) [2] I. Grabowski, V. Lotrich, R.J. Bartlett J. Chem. Phys. 127, 154111 (2007) [3] I. Grabowski, A. Teale, Sz. Śmiga, K. Jankowski, R.J. Bartlett, In preparation 2010 [4] K. Jankowski, K. Nowakowski, I. Grabowski, J. Wasilewski J. Chem. Phys. 130, 164102 (2009)
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Exact diagonalization of bosonic Hamiltonians
Peter Jeszenszki, Agnes Szabados, Peter R.Surjan
Eotvos Lorand University, Institute of Chemistry, Laboratory of Theoretical
Analytical expressions have been derived for the one-electron DKH2 spin–orbitHamiltonian and for the one-electron DKH2 parity-violating Hamiltonian through the free-particle Foldy–Wouthuysen (fpFW) transformation followed by the Douglas–Kroll–Heßtransformation of the one-electron Dirac Hamiltonian and of the nuclear spin-independentpart of the one-electron 4-component parity-violating Hamiltonian respectively.
Matrix elements of the one-electron Breit–Pauli (approximate Foldy–Wouthuysen,aFW), fpFW (DKH1) and DKH2 spin–orbit Hamiltonians have been evaluated betweenthe components of the ground scalar pseudo-relativistic (DKH2 CASSCF) state 3Pg ofatoms C, Si, Ge, Sn and Pb to estimate the error introduced by using lower-order spin–orbit Hamiltonians in ab initio all-electron quasi-relativistic calculations of, e.g., zero-field splittings or spin-forbidden transition probabilities in molecules containing heavyelements.
Similarly, matrix elements of the one-electron aFW, fpFW and DKH2 parity-violatingHamiltonians have been evaluated between the components of the two lowest scalarpseudo-relativistic (DKH2 CASSCF) states 2Pu and 4Pg of atoms B, Al, Ga, In andTl to estimate the error introduced by using lower-order parity-violating Hamiltoniansin ab initio all-electron quasi-relativistic calculations of, e.g., electronic energy shifts orelectronic excitation frequency shifts due to parity violation in molecules containing heavyelements.
The active spaces contained 4 (3) electrons in the 4 valence atomic orbitals sp3 or14 (13) electrons in the 14 atomic orbitals (n − 1)d5sp3d5. Different orbitals wereoptimized for different states. Instead of the true atomic (spherical) symmetry, a bit lowersymmetry of the largest binary subgroup of SO(3), the point group D2h, was exploited forconvenience.
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Quantum chemical calculations of photophysical propertiesof Methyl- and Adenosylcobalamin
Piotr Lodowski1
, Maria Jaworska1, Paweł M. Kozłowski2, Tadeusz Andruniów3
1University of Silesia, Institute of Chemistry, Szkolna 9, 40-006 Katowice, Poland, 2Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, USA, 3Department of Molecular Modelling and Quantum Chemistry, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
Two B12 dependent human enzymes, methylmalonyl-CoA mutase and methionine synthase, incorporate active alkylcobalamins derived from cyanocobalamin (vitamin B12, CNCbl). Methylcobalamin (MeCbl) functions as methyl donor in methionine synthase, with heterolytic cleavage of the cobalt – carbon bond to form cob(I)alamin. Adenosylcobalamin (AdoCbl or coenzyme B12) is the cofactor of enzymes, which catalyze the rearrangement reactions that proceed via mechanisms involving organic radicals generated by homolysis of the coenzyme cobalt – carbon bond to produce an adenosyl radical and cob(II)alamin.
Over the past few years transient absorption spectroscopy has been applied by Sension and co-workers [1] to investigate nature of electronically excited states and photochemistry of alkylcobalamins. While these recent spectroscopic studies provided a new insight into the electronic structure of cob(III)alamins, the nature of their excited states remains largely unexplained.
The analysis of the electronic structure of methyl- and adenosylcobalamin has been performed by means of time-dependent density functional theory (TDDFT). Calculations were carried out using the gradient corrected Becke–Perdew (BP86) functional together with the TZVPP basis set and COSMO solvent model. In the calculations a simplified cobalamin model was used, in which all the corrin side chains were replaced by hydrogen atoms and the 5,6-dimethylbenzimidazole trans axial base was replaced by an imidazole. The calculations were carried out with the use of TURBOMOLE program.
Full geometry optimization was performed for the ground state (S0) and the first singlet excited state (S1). The S1 excited state for both investigated cobalamins is characterized as a MLCT(SBLCT) type and is derived from the d/π → π* excitation, where π and π* orbitals are localized on the corrin ring. For the ground and excited S1 state, potential energy curves were determined as a function of Co-CMe and Co-CAdo bond lengths. The bond length was repeatedly stretched with the step size of 0.05 Ǻ, and the geometries of S0 and S1 states were reoptimized at every point. At each optimized point the manifold of singlet and triplet states were calculated at the TDDFT/BP86/TZVPP level of theory.
[1] D.A. Harris, A.B. Stickrath, E.C. Carroll and R.J. Sension, J. Am. Chem. Soc, 129, 24 (2007) 7583 Acknowledgement: This work was supported by Ministry of Science and Higher Education (Poland) under grant No. N204 028336. The TURBOMOLE calculations were carried out in the Wrocław Centre for Networking and Supercomputing, WCSS, Wrocław, Poland, under calculational Grant No. 51/96. and in the Academic Computer Centre CYFRONET of the University of Science and Technology in Cracow, ACC CYFRONET AGH, Kraków, Poland,under grant No. MNiSW/SGI3700/UŚląski/111/2007.
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Protonated water clusters – structures and thermodynamics
Jakub Malohlava, Aleš Vítek, René Kalus
Department of Physics, Faculty of Science, University of Ostrava 30. dubna 22
Potential energy curves (PEC‘s), spectroscopic constants, equilibrium geometries and dissociation energies were calculated for the ground and excited states of iodine oxide and iodine molecule using the complete active space second-order perturbation theory (CASSCF/CASPT2) and coupled cluster theory through quasiperturbative triple excitations (CCSD(T)), implemented in the moLcas 7.3 program package [2]. The ground state of IO(X2Π) and I2 (X 1Σ+) were computed at the CCSD(T) level. Potential energy curves for excited states of IO (a4Σ-, A2Π) and I2 (A
3Π), which have multi-configuration nature, were computed at the CASSCF/CASPT2 level. The second order spin-free Douglas-Kroll-Hess Hamiltonian was applied to calculate relativistic effects within the spin-adapted CCSD(T) and the CASPT2 method. To include spin-orbit effects, which are important for both ground and excited state of IO and I2 due to the presence of the heavy I, we employed the Restricted Active Space State Interaction method (CASPT2/RASSI-SO), introduced by Roos and Malmqvist [1].
For energy predictions, relativistic basis set ANO-RCC with large contraction (for iodine (22s19p13d5f3g)/[10s9p8d5f3g] and for oxygen (14s9p4d3f2g)/[8s7p4d3f2g]) has been used in all the calculations. C2 symmetry with averaging the degenerate pairs of electronic states was used. Two active spaces were used in the CASPT2 spin-free calculations for IO: the first consisted of 9 valence electron in 6 orbitals (16a/10b inactive and 2a/4b active), followed by CASPT2 calculations with 17 correlated electrons; the second included 9 valence electron in 12 orbitals (16a/10b inactive and 6a/6b active). Two active space were used for I2 molecule: 10 valence electron in 6 orbitals (28a/20b inactive and 2a/4b active) and 10 valence electron in 16 orbitals (28a/20b inactive and 8a/8b active).
Spectroscopic constants (equilibrium bond lengths Re, harmonic frequencies ωe, anharmonicity constants ωexe and ro-vibrational constants αe) and equilibrium geometries were determined by fourth-fifth-order polynomial fit and VIBROT program. Calculated spectroscopic constants, geometries and dissociation energies were compared with existing experimental and theoretical data from the literature.
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[1] B. Roos and P.-A. Malmqvist, Phys. Chem. Chem. Phys., 6, 2919 (2004) [2] Aquilante, F; De Vico, L; Ferre, N, et al., Journal of computational chemistry, 31, 224-247 (2010)
Acknowledgment This work was supported by Slovak Research and Development Agency under the contract No. LPP-0110-07, grant APVV-20-018405, VEGA (1/0428/09) and EUROATOM, contract No. N° FU07-CT-2007-00051. Computational support from the Centre of Excellence program of the Slovak Academy of Sciences (COMCHEM, Contract no. II/1/2007) is gratefully acknowledged.
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Applicability of Graphical Processing Units to Coupled Clusters Calculations
Miroslav Melicherčík, Lukáš Demovič, Michal Pitoňák, Pavel Neogrády
Comenius University, Faculty of Natural Sciences Department of Physical and Theoretical Chemistry
In the past few years, there has been considerable interest in exploring the reactivity of bulky Lewis acid/base pairs towards small molecule activation. Following the concept of frustrated Lewis pairs (FLPs) introduced by Stephan and coworkers, a number of intermolecular and intramolecularly linked donor/acceptor pairs have been identified that cleave molecular H2 heterolytically under mild conditions.1
Based on a theoretical investigation, a mechanistic model have been proposed that provides a rationale for the unique reactivity of FLPs.2 The model has been built upon density functional theory based identification of the stationary points and single point vibrational analysis or polarisable continuum model calculations. From the calculated gas-phase and solution-phase Gibbs free energies one may conclude that the reactivity is associated with transient intermediates formed between the FLP components, which offer cooperative acid-base interactions with a hydrogen molecule.
However, the scope of synthetic applications of FLPs as hydrogenation catalyst is fairly limited, because these pairs add readily to olefins and acetylenes hampering the hydrogenation process. To bypass that undesirable reactivity, a novel intermolecular FLP has been designed that involves a sterically more demanding mesityl borane combined with small-size bases.3 These pairs show enhanced selectivity in catalytic hydrogenation of a variety of organic compounds.
Quinoline and mesityl borane can also act as an FLP towards hydrogen cleavage, however, the reaction yields tetrahydro products. Consequently, the recently developed borane can be used as an efficient catalyst in the hydrogenation of heteroaromatic rings. Our DFT calculations focusing on the mechanism of these reactions reveal the details of possible reaction pathways. The species depicted in the figure was identified as a key intermediate.
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B(C6F5)2Mes / Quinoline / H2 system
[1] D. W. Stephan and G. Erker, Angew. Chem. Int. Ed. 2010, 49, 46.
[2] T. A. Rokob, A. Hamza, A. Stirling, T. Soós and I. Pápai, Angew. Chem., Int. Ed., 2008, 47, 2435.
[3] G. Erős, H. Mehdi, I. Pápai, T. A. Rokob, P. Király, G. Tárkányi and T. Soós, Angew. Chem. Int. Ed 2010, 49, 1.
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Electric properties of 2-cyclopenten-1-on
Jana Páleniková, Vladimír Kellö
Department of Physical and Theoretical Chemistry, Faculty of Natural SciencesComenius UniversityMlynska Dolina CH-1
The aim of this study is to compare behavior of dipole moments and dipole polarisabilities of organic molecule 2-cyclopenten-1-one (2CP) in the ground state S0 and three electronic excited states S1 (n→π*), T1 (n→π*) and T2 (π→π*). The geometry of 2-cyclopenten-1-one in its ground state S0 was optimized using the CASPT2 method, including ALASKA for analytical gradients, with the 6-311+G(d,p) basis set. Calculations of the electric properties were carried out using coupled cluster methods CCSD and CCSD(T), in conjunction with the Pol [1] basis set and the Z2Pol [2] basis set. The two-determinant CCSD method [3] was used for open-shell singlet. All calculations were performed using the system of quantum chemical programs MOLCAS.
The order of vertical excitation energies 2CP computed using CCSD method with Pol basis set is T1 (3,62 eV), S1 (3,96 eV) and T2 (3,98 eV). There is a large change in dipole moment of the 2CP molecule due to excitation to the T1 and S1 states. Total dipole moment decreased by about 60%. This change is due to excitation in n (nonbonding) orbital located on oxygen atom to π* (π-antibonding) orbital located mainly along the C-C bond. Polarisabilities of the T1 and S1 excited states are much less affected by the excitation from the ground state. The largest change occurs by excitation in the z axis.
[1] A.J. Sadlej, Coll. Czech. Chem. Commun. 53, 1995 (1988).[2] Z. Benková, A.J. Sadlej, R.E. Oakes, S.E. Bell: J. Comput. Chem. 26, 145 (2005).[3] P. Neogrady, P. G. Szalay, W. P. Kraemer, et al.: Collect. Czech. Chem. Commun.
70, 951 (2005).
This work was supported by the Slovak Grant Agency VEGA under the contract No. 1/0520/10. The support is gratefully acknowledged.
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Long-range corrected dispersionless density
functional
Ewa Pastorczak1, Katarzyna Pernal2, Krzysztof Szalewicz3
1 Technical University of Lodz, Institute of Applied Radiation Chemistry
Wrblewskiego 15
93-590 Lodz, Poland
[email protected] Technical University of Lodz, Institute of Physics
Wolczanska 219
90-924 Lodz, Poland3 Department of Physics and Astronomy, University of Delaware
Newark, Delaware 19716, USA
A new density functional, based on dispersionless density functional (DL09) [1]
and Hirao’s long-range correction scheme [2], is proposed.
The DL09 functional is known to predict very accurately the dispersionless parts
of intermolecular interactions, whereas the dispersion part can be computed ab initio
or by a function fitted to computed ab initio values. However, its long-range sepa-
ration performance for a number of systems (e.g. C6H6) dimer could be improved.
Also, DL09 is not suitable for the problems involving forming or breaking chemical
bonds.
The new, long-range corrected DL09, where the exchange part consists of short-
range density functional part and long- and short-range parts of Hartree-Fock ex-
change (given with different coefficients), with reoptimized parameters is expected
to perform as well as, or better, than DL09 for all the systems with intermolecular
interactions and additionally calculate accurately the reaction barrier energies.
References
[1] Pernal K., Podeszwa R.,Patkowski K., Szalewicz K., Phys. Rev. Lett. 103,
263201 (2009).
[2] Iikura H., Tsuneda T., Yanai T., Hirao K., J. Chem. Phys. 115, 3540 (2001).
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Electric properties of low-lying excited states of acetone and their interaction with water
L. F. Pašteka1, M. Urban1,2
1Department of physical and theoretical chemistry, Faculty of natural Sciences,Comenius University, Mlynská dolina, 842 15 Bratislava, Slovakia
2Slovak University of Technology in Bratislava, Faculty of Materials Science and Technology, Institute of Materials Science, J. Bottu 25, 917 24 Trnava, Slovakia
Dipole moments, polarizabilities and hyperpolarizabilities are important molecular properties, for example in connection with optical shifts resulting from the rearrangement of the solvent upon the excitation of the solute molecule. Acetone, investigated in this paper, serves as a prototype of a variety of carbonyl compounds. Their electric properties affect the intermolecular interactions of molecules with the environment in organic and biochemical systems, in which chemiexcitation can occur easily.
The present work focuses on computing the electric properties of low lying singlet and triplet valence states as well as the ground state of acetone. Structures of these states were optimized at the aug-cc-pVTZ/CASPT2 level of the theory. Geometry of the ground state is in the C2v symmetry and geometry of the excited states is in Cs symmetry, since the oxygen leans out of the carbon plane during the excitation, except for 1,3σ-π* state, which is in C2v symmetry with the methyl groups twisted by 180°.
Subsequently, the same method was used in numerical derivatives of energy with respect to the strength of an external electric field (the FFPT approach). In this scheme the 3, 5, 7, 9, 11 and 13-point central differentiation formulae with equidistant step of size of 0.001 a.u., 0.002 a.u., 0.004 a.u., and 0.008 a.u. were used. We also differenciated the polynomial fit through all of the points with various degrees of the polynomes. This approach gave us enough results to be able to enumerate the accuracy of the resulting value in terms of an interval to which all the results belong. For each state the first four energy derivatives are calculated, which allows obtaining the dipole moment, dipole polarizability and first two hyperpolarizabilities.
Dipole moment expectation values obtained from CASSCF computations were also used to calculate higher derivatives and some of the off-diagonal terms of the tensor of polarizability and hyperpolarizability.
Vertical and adiabatic excitation energies are also presented. They primarily serve as a toll for justification of methods used in our computations, since these are the only available experimental data for excited states of acetone.
Significant changes of the geometry and electronic structure upon excitation substantially affect all these molecular properties of acetone.
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We were also interested how interaction with water may affect properties and geometries of the studied states. Monosolvated geometries of each of the studied states were optimized at CASPT2/aug-cc-pVDZ level of theory. Water binds through the H-bond to the oxygen atom in the acetone molecule. There are four such CS configurations for the excited states (see figure below), of which one is by ~2 kcal/mol lower in energy than the other three. This is due to the antiparallel orientation of the acetone and water dipole moments (d), thus total dipole is almost zero and there is small charge separation.
Monosolvatation energies were also computed. BBSE for water-acetone interaction energies is quite large (1-3 kcal/mol) so all energies were counterpoise corrected with inclusion of geometry relaxation effect.
c)
a) b) d)
Acknowledgements: This research was supported by the Slovak Grant Agency, grant VEGA-1/0520/10 and by the Slovak Research and Development Agency APVV, contract No. LPP-0155-09. and by Comenius University, grant UK/294/2010.
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Muonic systems with Debye-screened Coulomb
interactions
Mariusz Pawlakab, Miros�law Bylickia and Prasanta K. Mukherjeec
aInstitute of Physics, Nicolaus Copernicus University
The mechanism of azobenzene photoisomerization has been debated for decades
and various mechanisms have been proposed for photoisomerization after excitation
to S1 and S2 excited states. We carried out ab initio non-adiabatic dynamical
simulations of cis-to-trans isomerization upon S1 excitation employing the Tully’s
surface hopping method with potential-energy surfaces and couplings determined
”on the fly”. The non-adiabatic couplings have been computed based on overlap of
CASCSF wavefunction.
We confirmed that the azobenzene photoisomerization after n-π excitation occurs
purely as an torsional motion via a S0/S1 conical intersection located near the
midpoint of this rotational pathway.
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Relativistic effects on metal-metal bonding. Comparison of the performance of ECP and scalar DKH description on the picture of
metal-metal bonding in Re2Cl8(2-)
Robert Ponec,a Lukáš Bučinský,b Carlo Gattic aInstitute of Chemical Process Fundamentals, Academy of Sciences of the Czech Republic v.v.i., Prague 6, Suchdol 2, 165 02 Czech Republic bInstitute of Physical Chemistry and Chemical Physics, Slovak University of Technology in Bratislava, Bratislava, Slovakia cIstituto di Scienze e Tecnologie Molecolari del CNR (CNR-ISTM) e Dipartimento di Chimica Fisica ed Elettrochimica, Università di Milano, Via Golgi 19, I-20133, Milano, Italy
The picture of the metal-metal bonding in the Re2Cl8(2-) anion is analyzed using the
so-called domain averaged Fermi holes (DAFH) []. Besides the comparison of scalar
DKH2/B3LYP and ECP/B3LYP DAFH bonding analysis, the systematic comparison of
the “exact” atoms in molecules (AIM) [] generalized form of DAFH analysis with the
approximate Mulliken-like approach is presented. Furthermore the geometry of the
Re2Cl8(2-) anion has been reoptimized at the all-electron (AE) non-relativistic and 1-
component (scalar) and 2-component DKH2 level of theory.
The DAFH bonding analysis based on the AE-DKH2/B3LYP calculations yields
quantitatively the same conclusions as the ECP/B3LYP calculation using the AIM
population analysis. The DAFH analysis at the AE-DKH2/B3LYP level but using the
Mulliken population analysis on the other hand fails. The scalar and spin-orbit relativistic
effects at the AE-DKH2/B3LYP are not significant for the Re-Re, Re-Cl bond distances
Many methods use localized orbitals to reduce the calculation cost of electron cor-
relation for large molecules utilizing the weak interaction between orbitals localized
far away from each other. In addition, our Coupled Cluster (CC) approach applies
the idea behind the optimized virtual orbitals [1, 2]. Unlike many methods which
divide the molecules into molecular fragments, we divide the CC energy among the
localized occupied orbitals [3]. The partial CC energy contributions belonging to
the occupied orbitals are the quantities that we estimate. For each occupied orbital
a small optimized basis set is determined [4]. Each partial CC energy contribution
is approximated using the optimized basis sets.
The presentation also shows some promising preliminary numerical results.
References
[1] Ludwik Adamowicz, Rodney J. Bartlett, and Andrej J. Sadlej J. Chem. Phys.
88, 5749 (1988).
[2] Pavel Neogrady, Michal Pitonak and Miroslav Urban, Mol. Phys. 103, 2141
(2005).
[3] Wei Li, Piotr Piecuch, Jeffrey R. Gour, and Shuhua Li J. Chem. Phys. 131,
114109 (2009).
[4] Frank Neese, Frank Wennmohs, and Andreas Hansen J. Chem. Phys. 130,
114108 (2009).
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Thermodynamics of homolytic S–H bond dissociation in mono-substituted thiophenols
Lenka Rottmannová, Ján Rimarčík, Erik Klein, Vladimír Lukeš
Institute of Physical Chemistry and Chemical Physics, Slovak University of Technology in Bratislava, Radlinského 9, SK-812 37 Bratislava, Slovak republic
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TD-DFT investigation of S1 and S2 singlet states of TMPyP(n) and complexes of
TMPyP4 with sulfonated calix[m]arenes
Jakub Šebera1, Stanislav Záliš1, Pavel Kubát1, Kamil Lang2, Tomáš Polívka3
[email protected] J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic,
Dolejškova 3, CZ 18223, Prague, Czech Republic 2 Institute of Inorganic Chemistry, v.v.i., Academy of Sciences of the Czech Republic, 250 68
Řež, Czech Republic3 Institute of Physical Biology, University of South Bohemia, Zámek 136, Nové Hrady 37333,
Czech Republic
Photophysical and binding properties predetermine tetrakis (4-N-methylpyridyl)
porphyrin (TMPyP4) as efficient photosensitizer in many artificial light-harvesting systems as
well as in medicine for photodynamic therapy of tumors or bacteria/virus inactivation.
Organizing TMPyP4 molecules through noncovalent host−guest interaction with a range of
guests like nucleic acids/proteins, calixarenes, cyclodextrins, carbon nanotubes, PAMAM
dendrimers, graphene, cucurbituril or their incorporation into micelles, methyl viologen-
hybrid and nafion films, semiconductors, layered silicates, laponite, hydrogels and other solid
materials finds immense importance in creating ordered structures of specific functionality.
Isoelectronic TMPyP2 and TMPyP3 can modulate properties of resulting supramolecular
complexes due to rotational barrier of N-methylpyridyl groups.
Water-soluble p-sulfonatocalixarenes clxm possess the three-dimensional, flexible,
π-electron rich cavities that can adopt different conformations, form complexes with many
compounds and have diverse biomedical applications e.g they can serve as transportation
vehicles for porphyrin drugs. The number of conformations increases with the number of
4-hydroxy-benzenesulfonate units in the system, although this also depends on the solvent
and the nature of the guest.
We have used TD-DFT and DFT calculations to study (photoinduced) charge transfer
in tetrakis(n-N-methylpyridyl)porphyrins TMPyPn (n=2,3,4) and TMPyP4/p-
sulfonatocalix[m]arenes clxm (m=4,6) complexes and to interpret transient absorption
spectroscopy, cyclic voltametry experiments and UV-Vis absorption spectra. Density
functionals MPW1B95 and B3LYP were used. The effect of solvent (water) was described by
Conductor-like Screening Model (COSMO). Excitation of TMPyPn into S1 state is
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accompanied by increasing of electron density at methylpyridyl groups in the following order:
TMPyP2 < TMPyP3 < TMPyP4. Further results on characterization of S1 and S2 singlet states
will be presented. The examples of the investigated complexes are depicted in Figure 1.
Figure 1. DFT optimized geometries of TMPyP4-clx4 (left) and TMPyP4-clx6 (right). Both
systems have partly ionized OH groups.
Acknowledgement: The access to the METACentrum supercomputing facilities is highly
acknowledged. This research was supported by the Czech Science Foundation (No.
P208/10/1678).
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Application of OVOS technique in calculations of small semiconductor clusters.
L. Šimováa, P. Neográdya and M. Urbana,b
aDepartment of Physical and Theoretical chemistry, Faculty of Natural
Sciences,Comenius University, Mlynská dolina, 842 15 Bratislava, Slovakia bSlovak University of Technology in Bratislava, Faculty of Materials Science and Technology, Institute of Materials Science, J. Bottu 25, 917 24 Trnava, Slovakia
[5] Giannakopoulos, E., Stathi, P., Dimos, K., Gournis, D., Sanakis, Y., Deligiannakis,
Y., Langmuir, 22, 6863, (2006).
Acknowledgment - We are grateful for the financial support from the Austrian Sciences Fund (project P20893-N19), and the German Research Foundation, the priority program SPP 1315 (project GE1676/1-1). The authors also acknowledge the technical support and computer time at the Vienna Scientific Cluster.
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Charge Sensitivity Analisys in Force Field Atoms Resolution
Anna Stachowicz and Jacek Korchowiec
Jagiellonian University, Department of Theoretical Chemistry ul. R. Ingardena 3, 30-060, Kraków, Poland
This work focuses on searching for suitable parametrs in our computer programme
based on genetic algorithms. We tested various parameters – for Lennard-Jones clusters with
10 and 30 molecules we tested dependence of number of optimizations on the number of
processors used; for water clusters (H2O)n of n = 2-13 molecules we tested dependence of
energy evolution during the program progress, which was confronted with [1]; and for water
cluster with 11 molecules we tested suitability of various evolution operators (probability of
genotype mutation, phenotype mutation, cut by plane, crossover coordination, crossover
cluster) used.
0 10 20 30 40
4,30
4,32
4,34
4,36
4,38
4,40
4,42
4,44
4,46
Optimalization number
Ene
rgy
[eV]
0.2 1.0 0.8 0.6 0.4
Figure: Dependence of energy for water cluster (H2O)11 on probability of cut by plane (0.2-1.0) used
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[1] Wales, D.J. a Hodges, M.P. Chem. Phys. Lett., 286, 65. 1998. [2] Hartke, B. Global Geometry Optimalization of Molecular Clusters: TIP4P Water Zeitschrift für Phys. Chemie, 214, 9 1251-1264. 2000. [3] Cartwright, H. M. An introduction to Evolutionary Computation and Evolutionary Algorithms Springer-Verlag Berlin Heidelberg. 2004. Acknowledgement
Grant Agency of the Academy of Sciences of the Czech Republic, grant No. IAA401870702;
University of Ostrava, Students Grant Competition, grant No. SGS7/PřF/2010.