Pál Jedlovszky

Analysis of the hydrogen-bonded structure of water from ambient to supercritical conditions

The structure of water has been analyzed at eight different thermodynamic states from ambient to supercritical conditions both by molecular dynamics (MD) and Reverse Monte Carlo (RMC) simulation. MD simulations have been carried out with two different potential models, a polarizable potential and one of the most successful nonpolarizable models, i.e., the well known Simple Point Charge potential in its revised version labeled by E (SPC/E). It has been found that, although the polarizable model can reproduce the experimental partial pair correlation functions at the high temperature states better than the nonpolarizable one, it still cannot account for all the features of the measured functions. The experimental partial pair correlation functions have been well reproduced by the RMC simulations at every state point. The resulting structures have been analyzed in detail. It has been found that the tetrahedral orientation of the hydrogen bonded neighbors is already lost at 423k, whereas the hydrogen bonds th...

A new method for determining the interfacial molecules and characterizing the surface roughness in computer simulations. Application to the liquid–vapor interface of water

A new method is presented to identify the truly interfacial molecules at fluid/fluid interfaces seen at molecular resolution, a situation that regularly occurs in computer simulations. In the new method, the surface is scanned by moving a probe sphere of a given radius along a large set of test lines that are perpendicular to the plane of the interface. The molecules that are hit by the probe spheres are regarded as interfacial ones, and the position of the test spheres when they are in contact with the interfacial molecules give an estimate of the surface. The dependence of the method on various parameters, in particular, on the size of the probe sphere is discussed in detail. Based on the list of molecules identified as truly interfacial ones, two measures of the molecular scale roughness of the surface are proposed. The bivariate distribution of the lateral and normal distances of two points of the interface provides a full description of the molecular scale morphology of the surface in a statistical sense. For practical purposes two parameters related to the dependence of the average normal distance of two surface points on their lateral distance can be used. These two parameters correspond to the frequency and amplitude of the surface roughness, respectively. The new method is applied for the analysis of the molecular level structure of the liquid–vapor interface of water. As an immediate result of the application of the new method it is shown that the orientational preferences of the interfacial water molecules depend only on the local curvature of the interface, and hence the molecules located at wells of concave curvature of the rippled surface prefer the same orientations as waters located at the surface of small apolar solutes. The vast majority of the truly interfacial molecules are found to form a strongly percolating two‐dimensional hydrogen bonded network at the surface, whereas no percolation is observed within the second molecular layer beyond the surface.

New insight into the orientational order of water molecules at the water/1,2-dichloroethane interface: A Monte Carlo simulation study

The preferential orientation of the water molecules near the water/1,2-dichloroethane interface is analyzed in detail at different distances from the interface on the basis of a grand canonical ensemble Monte Carlo simulation. The orientation of the individual water molecules is described by the angular polar coordinates of the interface normal vector in a local coordinate frame fixed to the particular water molecule, and the bivariate joint distribution of the two polar angles is calculated. It is found that water molecules have two distinct orientational preferences, and these two preferences exist simultaneously among the water molecules penetrating farthest into the organic phase. In the first preferred orientation the plane of the molecule is parallel to the interface, whereas in the second the molecular plane is aligned perpendicularly to the interface and the molecular dipole vector declines from the plane parallel to the interface by about 30° pointing toward the organic phase. The first of the two preferred orientations is found to be present in the entire interfacial region and also, to a smaller extent, in the subsurface water layer adjacent to the interface. The second orientational preference is only present among the water molecules penetrating farthest into the organic phase. The two orientations correspond to the alignment of a hydrogen bonded pair of water molecules, in which the molecule located toward the aqueous phase has the first, whereas the one on the organic side the second of the two preferred orientations. The obtained picture is in a clear contrast with the findings of previous studies, in which the orientation of the water molecules was described by monovariate distributions of the alignment of one or more selected molecule-fixed vectors. In order to understand the origin of the difference between the present results and earlier findings we also calculate the monovariate distributions of the direction of three of such molecular vectors, i.e., the dipole vector of the water molecule, the vector joining the two H atoms, and the vector perpendicular to the molecular plane. The comparison of the obtained monovariate distributions with the bivariate joint distribution of the two polar angles reveals that the averaging of the bivariate distribution over any of its two angles completely obscures the dual orientational preference. The present study clearly points out the importance of choosing appropriate statistical distributions in the analysis of simulation results and demonstrates the pitfalls of averaging over too many variables.

Comparison of different water models from ambient to supercritical conditions: A Monte Carlo simulation and molecular Ornstein–Zernike study

Structural, thermodynamic, and dielectric properties of three polarizable and two nonpolarizable water models are compared with experimental data at four different thermodynamic states from ambient to supercritical conditions. Pair-correlation functions and thermodynamic data are obtained from Monte Carlo simulations, performed both on the (N,V,T) and (N,p,T) ensembles. The dielectric constants are determined with the molecular Ornstein–Zernike theory. It is found that the polarizable models can reproduce the experimental structure considerably better than the nonpolarizable ones at the high-temperature states. In particular, the elongation of the hydrogen bonds with increasing temperature, which is observed by neutron diffraction measurements, in only seen in the simulations with the polarizable potential models. On the other hand, the polarizable models fail to describe the correct temperature dependence of the thermodynamic properties. Although at ambient conditions they overestimate both the density a...

Monte Carlo simulation of liquid acetone with a polarizable molecular model

A Monte Carlo simulation of liquid acetone was performed in the NVT ensemble. The dielectric polarizability of the molecules was taken into account by induced point dipoles. A reference simulation on a system of non-polarizable molecules was also carried out. The induced polarization of the molecules lowered the total energy of the system, while the sum of the pair interaction energies was increased. The structural analysis of the resulting configurations revealed that the average coordination number in the first coordination shell is about 12, and the first one or two nearest neighbours tend to be in an antiparallel orientation relative to the central molecule while the orientation of the rest of the neighbours is random. The predominant interaction in determining the structure of liquid acetone was found to be steric rather than electrostatic. The induced dipole moments of the molecules and the electric field strength at the location of the molecular centres were also examined. The induced dipole moment...

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.

Investigation of the uniqueness of the reverse Monte Carlo method: Studies on liquid water

Reverse Monte Carlo (RMC) simulation of liquid water has been performed on the basis of experimental partial pair correlation functions. The resulted configurations were analyzed in various aspects; the hydrogen bond angle distribution, three body correlation and orientational correlation were calculated. The question of the uniqueness of the RMC method was also examined. In order to do this, two conventional computer simulations of liquid water with different potential models were performed, and the resulted pair correlation function sets were fitted by RMC simulations. The resulted configurations were then compared to the original configurations to study how the RMC method can reproduce the original structure. We showed that the configurations produced by the RMC method are not uniquely related to the pair correlation functions even if the interactions in the original system were pairwise additive. Therefore the difference between the original simulated and the RMC configurations can be a measure of the uncertainty of the RMC results on real water. We found that RMC produces less ordered structure than the original one from various aspects. However, the orientational correlations were reproduced rather successfully. The RMC method exaggerates the amount of the close packed patches in the structure, although these patches certainly exist in liquid water.

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.

Computer simulations of liquid HF by a newly developed polarizable potential model

A new polarizable potential model of liquid HF is developed. The model is tested by comparing simulated thermodynamic and structural properties of liquid HF with experimental and ab initio molecular dynamics results. Properties of the isolated HF dimer obtained with this model are also compared with both ab initio and experimental data. It turns out that this model can describe the thermodynamic properties of liquid HF with a good accuracy in the entire temperature range of the liquid state at atmospheric pressure, and also give the energy and geometry of the isolated HF dimer in a good agreement with experimental and ab initio results. The obtained pair correlation functions of liquid HF agree also reasonably well with experimental and ab initio molecular dynamics findings, although the position of the peaks describing hydrogen bonding appears to be at 0.1–0.3 A higher distances. Such a deviation is opposite to what has been observed with our previous nonpolarizable model, which resulted in peak position...

The generalized identification of truly interfacial molecules (ITIM) algorithm for nonplanar interfaces

We present a generalized version of the ITIM algorithm for the identification of interfacial molecules, which is able to treat arbitrarily shaped interfaces. The algorithm exploits the similarities between the concept of probe sphere used in ITIM and the circumsphere criterion used in the α-shapes approach, and can be regarded either as a reference-frame independent version of the former, or as an extended version of the latter that includes the atomic excluded volume. The new algorithm is applied to compute the intrinsic orientational order parameters of water around a dodecylphosphocholine and a cholic acid micelle in aqueous environment, and to the identification of solvent-reachable sites in four model structures for soot. The additional algorithm introduced for the calculation of intrinsic density profiles in arbitrary geometries proved to be extremely useful also for planar interfaces, as it allows to solve the paradox of smeared intrinsic profiles far from the interface.