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Pál Jedlovszky

Publications and source records attributed to Pál Jedlovszky.

13 recordsLinked to original sources

Determination of the adsorption isotherm of methanol on the surface of ice. An experimental and grand canonical Monte Carlo simulation study.

The adsorption isotherm of methanol on ice at 200 K has been determined both experimentally and by using the Grand Canonical Monte Carlo computer simulation method. The experimental and simulated isotherms agree well with each other; their deviations can be explained by a small (about 5 K) temperature shift in the simulation data and, possibly, by the non-ideality of the ice surface in the experimental situation. The analysis of the results has revealed that the saturated adsorption layer is monomolecular. At low surface coverage, the adsorption is driven by the methanol-ice interaction; however, at full coverage, methanol-methanol interactions become equally important. Under these conditions, about half of the adsorbed methanol molecules have one hydrogen-bonded water neighbor, and the other half have two hydrogen-bonded water neighbors. The vast majority of the methanols have a hydrogen-bonded methanol neighbor, as well.

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Development of a new polarizable potential model of hydrogen fluoride and comparison with other effective models in liquid and supercritical states.

Development of a new polarizable potential of hydrogen fluoride through the reparametrization of the JV-P model is presented: The length of the H-F bond has been shortened and the other parameters of the model have been readjusted accordingly. The structural, thermodynamic, and liquid-vapor equilibrium properties of the new model are compared with those of other effective potential models of HF as well as with experimental data in a broad range of thermodynamic states, from near-freezing to supercritical conditions. It is found that although the reparametrization does not change the structural properties of the HF model noticeably at the level of the pair correlations, it improves the reproduction of the thermodynamic properties of hydrogen fluoride over the entire range of existence of a thermodynamically stable liquid phase and also that of the vapor-liquid coexistence curve. However, the new model, which still overestimates the close-contact separation of the HF molecules, underestimates the density of the coexisting liquid phase and overestimates the saturation pressure, probably due to the too steep repulsion of the potential function.

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Structure of the liquid-vapor interface of water-methanol mixtures as seen from Monte Carlo simulations.

Monte Carlo simulation of the vapor-liquid interface of water-methanol mixtures of different compositions, ranging from pure water to pure methanol, have been performed on the canonical (N, V, T) ensemble at 298 K. The analysis of the systems simulated has revealed that the interface is characterized by a double layer structure: methanol is strongly adsorbed at the vapor side of the interface, whereas this adsorption layer is followed at its liquid side by a depletion layer of methanol of lower concentration than in the bulk liquid phase of the system. The dominant feature of the interface has been found to be the adsorption layer in systems of methanol mole fractions below 0.2, and the depletion layer in systems of methanol mole fractions between 0.25 and 0.5. The orientation of the molecules located at the depletion layer is found to be already uncorrelated with the interface, whereas the methanol molecules of the adsorption layer prefer to align perpendicular to the interface, pointing straight toward the vapor phase by their methyl group. Although both the preference of the molecular plane for a perpendicular alignment with the interface and the preference of the methyl group for pointing straight to the vapor phase are found to be rather weak, the preference of the methyl group for pointing as straight toward the vapor phase as possible within the constraint imposed by the orientation of the molecular plane is found to be fairly strong. One of the two preferred orientations of the interfacial water molecules present in the neat system is found to disappear in the presence of methanol, because methanol molecules aligned in their preferred orientation can replace these water molecules in the hydrogen-bonding pattern of the interface.

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Computer simulation investigation of the water-benzene interface in a broad range of thermodynamic States from ambient to supercritical conditions.

The dependence of the properties of the water-benzene system on the thermodynamic conditions in a broad range of temperatures and pressures has been investigated by computer simulation methods. For this purpose, Monte Carlo simulations have been performed at 23 different thermodynamic states, ranging from ambient to supercritical conditions. The density profiles of the water and benzene molecules have been determined at each of the thermodynamic states investigated. Information on the dependence of the mutual solubility of the two components in each other as well as of the width of the interface on the temperature and pressure has been extracted from these profiles. The width of the interface has been found to increase with increasing temperature up to a certain point, where it diverges. The temperature of this divergence corresponds to the mixing of the two phases. The determination of the critical mixing temperature at various pressures allowed us to estimate the upper critical curve, separating the two-phase and one-phase liquid systems, of the phase diagram of the simulated water-benzene system. In analyzing the preferential orientation of the interfacial molecules relative to the interface, it has been found that the main orientational preference of the benzene molecules is to lie parallel with the plane of the interface, and the water molecules penetrated deepest into the benzene phase prefer to stay perpendicular to the interface, pointing by one of their O-H bonds almost straight toward the benzene phase, whereas the waters located at the aqueous side of the interface are preferentially aligned parallel with the interfacial plane. Although the strength of the observed orientational preferences decreases rapidly with increasing temperature, the preferred orientations themselves are found to be independent of the thermodynamic conditions. Remains of the orientational preferences of the molecules are found to be present up to temperatures as high as 650 K. The analysis of the relative orientation of the neighboring water-benzene pairs has revealed that the radius of the first hydration shell of the benzene molecules is independent of the thermodynamic conditions, even if the system consists of one single phase. It has been found that the nearest water neighbors of the benzene molecules are preferentially located above and below the benzene ring, whereas more distant water neighbors, belonging still to the first hydration shell, prefer to stay within the plane of the benzene molecule. In the two-phase systems the dipole vector of the nearest waters has been found to be preferentially perpendicular to the vector pointing from the center of the benzene molecule to the water O atom.

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Line of percolation in supercritical water.

The percolation transition of the hydrogen-bonded clusters of molecules is investigated in supercritical water by Monte Carlo computer simulations. Simulations have been performed at four thermodynamic state points located above the supercritical extension of the vapor-liquid coexistence curve on the p-T phase diagram and at four state points located below this curve. It is found in a temperature range of a few hundred Kelvin that the extension of the vapor-liquid coexistence curve separates the supercritical thermodynamic states in which the water molecules form infinite hydrogen-bonded clusters from those in which the hydrogen-bonded clusters are isolated oligomers. However, the difference between the size of the hydrogen-bonded clusters at thermodynamic states located at the two sides of the extension of the coexistence curve is found to decrease with increasing temperature, and the present results suggest that this difference is likely to vanish at high enough temperatures.

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Structure of the acetone liquid-vapor interface as seen from Monte Carlo simulations.

The orientational order of the molecules at the liquid-vapor interface of acetone has been investigated by computer simulation. To fully describe the orientational preferences of the acetone molecules, the bivariate joint distribution of two independent orientational parameters has been determined at different layers of the interface. The strength of the orientational ordering of the interfacial molecules has been found to be liquid-like rather than crystal-like. The obtained results have revealed that the interfacial acetone molecules have dual orientational preferences. The main symmetry axis of the molecules declines by about 50-70 degrees from the interface normal axis, pointing toward the liquid phase in both of the preferred orientations. However, the plane of the molecules in the orientation preferred on the liquid side of the interface is perpendicular to the interfacial plane, whereas the other preferred orientation, which is present on the vapor side of the interface, corresponds to the alignment obtained from this orientation by an almost 90 degrees rotation around the main symmetry axis. Because the population of the liquid side is higher than that of the vapor side of the interface, the first of the two preferred orientations is the dominant alignment over the entire interface, in good agreement with recent experimental findings (Chen, H.; Gan, W.; Wu, B. H.; Wu, D.; Zhang, Z.; Wang, H. F. Chem. Phys. Lett. 2005, 408, 284).

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Structure of the nonionic surfactant triethoxy monooctylether C8E3 adsorbed at the free water surface, as seen from surface tension measurements and Monte Carlo simulations.

The adsorption layer of the nonionic surfactant triethoxy monooctylether C8E3 has been investigated at the free water surface by means of both experimental and computer simulation methods. The surface tension of the aqueous solution of C8E3 has been measured by pendant drop shape analysis in the entire concentration range in which C8E3 is soluble in water. The data obtained from these measurements are used to derive the adsorption isotherm. The critical micellar concentration and the surface excess concentration of the saturated adsorption layer are found to be 7.48 mM and 4.03 micromol/m2, respectively, the latter value corresponding to the average area per molecule of 41 A2. In order to analyze the molecular level structure of the unsaturated adsorption layer, Monte Carlo simulations have been performed at four different surface concentration values, i.e., 0.68, 1.36, 2.04, and 2.72 micromol/m2, respectively. It has been found that the water surface is already almost fully covered at the lowest surface density value investigated, and the adsorbed molecules show a strong preference for lying parallel with the interface in elongated conformations. No sign of the penetration of the hydrophilic triethoxy headgroups into the aqueous phase to any extent has been observed. With increasing surface densities the preferential orientation of the apolar octyl tails gradually turns from lying parallel with the interface to pointing toward the vapor phase by their CH3 end, whereas the conformation of the adsorbed molecules becomes gradually less elongated. Both of these changes lead to the increase of the number of C8E3 molecules being in a direct contact (i.e., forming hydrogen bonds) with water. However, the increasing number of the C8E3 molecules hydrogen bonded to water is found to be accompanied by the weakening of this binding, i.e., the decrease of both the number of hydrogen bonds a bound C8E3 molecule forms with water and the magnitude of the average binding energy of the adsorbed C8E3 molecules.

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Liquid-vapor and liquid-liquid phase equilibria of the Brodholt-Sampoli-Vallauri polarizable water model.

Liquid-vapor and liquid-liquid phase equilibria of the polarizable Brodholt-Sampoli-Vallauri water model have been investigated by Gibbs ensemble Monte Carlo computer simulations. The coexisting liquid and vapor densities and energy of vaporization of the model is found to be in a reasonable agreement with experimental data in the entire temperature range of liquid-vapor coexistence. The critical temperature and density of the model are found to be 615 K and 0.278 gcm(3), respectively, close to the experimental values of 647.1 K and 0.322 gcm(3). In the supercooled state two distinct liquid-liquid coexistence regions are observed. The existence of liquid-liquid phase separation of a polarizable water model is demonstrated for the first time.

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Orientational order of the water molecules at the vicinity of the water-benzene interface in a broad range of thermodynamic states, as seen from Monte Carlo simulations.

Monte Carlo simulation of the water/benzene liquid-liquid interfacial system has been performed at six different thermodynamic state points, ranging from ambient conditions up to the vicinity of the critical point of water. The system has been found to consist of two immiscible liquid phases at every state point studied. The orientational preferences of the interfacial water molecules have been analysed in detail using the simulated configurations. The results obtained at ambient conditions are in agreement with previous results on various different water/apolar interfaces. Thus, interfacial water molecules have been found to have dual orientational preferences: the molecules located nearest to the organic phase prefer to stay perpendicular to the interface, pointing flatly toward the apolar phase by their dipole vectors, whereas the waters located somewhat farther from the organic phase prefer the parallel alignment with the interface. The observed orientational preferences are found to be rather stable with changing thermodynamic conditions: although the increase of the temperature has led, due to the increasing thermal motion of the molecules, to a gradual weakening of the orientational preferences, both preferences are found to exist up to at least 450 K, and found to be completely washed out at 575 K only. The pressure has not been found to influence the orientation of the water molecules noticeably.

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Free volume properties of a linear soft polymer: a computer simulation study.

Molecular dynamics simulation of a linear soft polymer has been performed and the free volume properties of the system have been analyzed in detail in terms of the Voronoi polyhedra of the monomers. It is found that there are only small density fluctuations present in the system. The local environment of the monomers is found to be rather spherical, even in comparison with liquids of atoms or small molecules. The monomers are found to be, on average, eight coordinated by their nearest geometric neighbors, including intra-chain and inter-chain ones. The packing of the monomers is found to be rather compact, in a configuration of 1900 monomers there are, on average, only three voids large enough to incorporate a spherical particle as large as a monomer, indicating that the density of the large vacancies in the system is considerably, i.e., by a few orders of magnitude lower than in molecular liquids corresponding to roughly the same reduced densities.

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Adsorption of 1-octanol at the free water surface as studied by Monte Carlo simulation.

The adsorption of 1-octanol at the free water surface has been investigated by Monte Carlo computer simulation. Six different systems, built up by an aqueous and a vapor phase, the latter also containing various number of octanol molecules, have been simulated. The number of the octanol molecules has been chosen in such a way that the octanol surface density varies in a broad range, between 0.27 and 7.83 micromol/m(2) in the six systems simulated. For reference, the interfacial system containing bulk liquid octanol in the apolar phase has also been simulated. The results have shown that the formation of hydrogen bonds between the interfacial water and adsorbed octanol molecules is of key importance in determining the properties of the adsorbed layer. At low octanol surface concentration values all the octanol molecules are strongly (i.e., by hydrogen bonds) bound to the aqueous phase, whereas their interaction with each other is negligibly small. Hence, they are preferentially oriented in such a way that their own binding energy (and thus their own free energy) is minimized. In this preferred orientation the O-H bond of the octanol molecule points flatly toward the aqueous phase, declining by about 30 degrees from the interfacial plane, irrespectively from whether the octanol molecule is the H-donor or the H-acceptor partner in the hydrogen bond. Hence, in its preferred orientation the octanol molecule can form at least two low energy hydrogen bonds with water: one as a H-donor and another one as a H-acceptor. Moreover, the preferred orientation of the hydrogen bonded water partners is close to one of the two preferred interfacial water alignments, in which the plane of the water molecule is parallel with the interface. When increasing the octanol surface density, the water surface gets saturated with hydrogen bonded octanols, and hence any further octanol molecule can just simply condense to the layer of the adsorbed octanols. The surface density value at which this saturation occurs is estimated to be about 1.7 micromol/m(2). Above this surface density value the hydrogen bonded octanols and their water partners are oriented in such a way that the number of the water-octanol hydrogen bonds is maximized. Hence, the preferred alignment of the O...O axes of these hydrogen bonds is perpendicular to the interface. This orientation is far from the optimal alignment of the individual octanol molecules, which is also reflected in the observed fact that, unlike in the case of many other adsorbents, the average molecular binding energy of the adsorbed octanol molecules increases (i.e., becomes less negative) with increasing octanol surface density.

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Temperature of maximum density line of a polarizable water model.

Monte Carlo simulations of liquid water were performed with a polarizable model in a narrow range of temperatures around the temperature of maximum density (TMD) and a broad pressure range, extended also to negative pressures. In order to infer features of the phase diagram relevant for the explanation of the anomalous behavior of water the pressure dependence of the TMD line was analyzed. The TMD is found to increase with decreasing pressure up to 274.8 K at -32 bar, and decrease upon further stretching. This behavior excludes the possibility of a reentrant liquid-gas spinodal line.

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Role of base flipping in specific recognition of damaged DNA by repair enzymes.

DNA repair enzymes induce base flipping in the process of damage recognition. Endonuclease V initiates the repair of cis, syn thymine dimers (TD) produced in DNA by UV radiation. The enzyme is known to flip the base opposite the damage into a non-specific binding pocket inside the protein. Uracil DNA glycosylase removes a uracil base from G.U mismatches in DNA by initially flipping it into a highly specific pocket in the enzyme. The contribution of base flipping to specific recognition has been studied by molecular dynamics simulations on the closed and open states of undamaged and damaged models of DNA. Analysis of the distributions of bending and opening angles indicates that enhanced base flipping originates in increased flexibility of the damaged DNA and the lowering of the energy difference between the closed and open states. The increased flexibility of the damaged DNA gives rise to a DNA more susceptible to distortions induced by the enzyme, which lowers the barrier for base flipping. The free energy profile of the base-flipping process was constructed using a potential of mean force representation. The barrier for TD-containing DNA is 2.5 kcal mol(-1) lower than that in the undamaged DNA, while the barrier for uracil flipping is 11.6 kcal mol(-1) lower than the barrier for flipping a cytosine base in the undamaged DNA. The final barriers for base flipping are approximately 10 kcal mol(-1), making the rate of base flipping similar to the rate of linear scanning of proteins on DNA. These results suggest that damage recognition based on lowering the barrier for base flipping can provide a general mechanism for other DNA-repair enzymes.

Base Pair Mismatch↗