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Michal Ilčin, Martin Michalík, Klára Kováčiková, Lenka Káziková and Vladimír Lukeš

Abstract

The molecular dynamics simulations of the liquid-vapor equilibrium of water including both water phases — liquid and vapor — in one simulation are presented. Such approach is preferred if equilibrium curve data are to be collected instead of the two distinct simulations for each phase separately. Then the liquid phase is not restricted, e.g. by insufficient volume resulting in too high pressures, and can spread into its natural volume ruled by chosen force field and by the contact with vapor phase as vaporized molecules are colliding with phase interface. Averaged strongly fluctuating virial pressure values gave untrustworthy or even unreal results, so need for an alternative method arisen. The idea was inspired with the presence of vapor phase and by previous experiences in gaseous phase simulations with small fluctuations of pressure, almost matching the ideal gas value. In presented simulations, the first idea how to calculate pressure only from the vapor phase part of simulation box were applied. This resulted into very simple method based only on averaging molecules count in the vapor phase subspace of known volume. Such simple approach provided more reliable pressure estimation than statistical output of the simulation program. Contrary, also drawbacks are present in longer initial thermostatization time or more laborious estimation of the vaporization heat. What more, such heat of vaporization suffers with border effect inaccuracy slowly decreasing with the thickness of liquid phase. For more efficient and more accurate vaporization heat estimation the two distinct simulations for each phase separately should be preferred.

Open access

Vladimir Sladek and Michal Ilčin

Abstract

Strong correlation of stabilization energies of π-stacked pyridine and fluorinated pyridine dimers with various relative orientations is presented. Four possible orientations of the monomers were considered. A SAPT decomposition of the interaction energies is presented and briefly discussed. The dominant electrostatic contribution to the stabilization energy is found in some dimers and its possible origin is addressed in the discussion. An outline of possible future studies is introduced.

Open access

Adam Vagánek, Lenka Rottmannová and Michal Ilčin

Abstract

In this work, the substituent effect on the Se-H bond dissociation enthalpy (BDE) for benzeneselenol and ten para-substituted benzeneselenols was investigated. The set of various electron-donating and electron-withdrawing substituents was used. The gas-phase bond dissociation enthalpies were calculated using B3LYP/6-311++G** method. Obtained trends were compared with those found for para-substituted phenols and thiophenols for the same set of substituents. While the BDE = ƒ(σp) dependences for phenols and thiophenols exhibit very good linearity, for benzeneselenols, the linearity is rather insufficient. It was found for oxygen, sulphur and selenium that the larger the atom is, the weaker the substituent induced changes in corresponding BDE values are. It has been also observed that the larger the atom, the smaller corresponding BDEs.

Open access

Vladimir Sladek, Lenka Rottmannová, Peter Škorňa, Michal Ilčin and Vladimír Lukeš

Abstract

A systematic comparative theoretical study has been performed on a series of fourteen metasubstituted selenophenols. The optimal geometries were calculated using the density functional theory (DFT) and the Nuclear Magnetic Resonance parameters were computed by applying the Gauge Including Atomic Orbital (GIAO) method. The calculated NMR shifts were correlated with the Hammett constants. The obtained results were also compared with the theoretical data obtained for thiophenols and phenols. Our results indicate the linear dependence between the gas-phase NMR shifts and Hammett constants. However, the presence of large selenium atoms is able to suppress significantly the substituent effect in meta position. Therefore six substituents (Me, OH, MeCO, COOMe, COOEt and CF3 groups) were excluded from the data evaluation. Correlations with the fundamental stretching vibration frequencies of the mode with the dominant Se-H vibration have not been found.