arXiv subjects

Ildikó Pethes

Publications and source records attributed to Ildikó Pethes.

At least 19 recordsLinked to original sources

arXiv2025

Comparison of water models for structure prediction

Describing the interactions of water molecules is one of the most common, yet critical, tasks in molecular dynamics simulations. Because of its unique properties, hundreds of attempts have been made to construct an ideal interaction potential model for water. In various studies, the models have been evaluated based on their ability to reproduce different properties of water. This work focuses on the atomic-scale structure in the liquid phase of water. Forty-four classical water potential models are compared to identify those that can accurately describe the structure in alignment with experimental results. In addition to some older models that are still popular today, new or re-parametrized classical models using effective pair-additive potentials that have appeared in recent years are examined. Molecular dynamics simulations were performed over a wide range of temperatures and the resulting trajectories were used to calculate the partial radial distribution functions. The total scattering structure factors were compared with data from neutron and X-ray diffraction experiments. Our analysis indicates that models with more than four interaction sites, as well as flexible or polarizable models with higher computational requirements, do not provide a significant advantage in accurately describing the structure. On the other hand, recent three-site models have made considerable progress in this area, although the best agreement with experimental data over the entire temperature range was achieved with four-site, TIP4P-type models.

physics.chem-ph↗

arXiv2024

Short range order and topology of Te-rich amorphous Ge-Sb-Te alloys

The structure of evaporated amorphous Ge$_x$Sb$_x$Te$_{100-2x}$ ($x =$ 6, 9, 13) alloys was investigated by neutron diffraction, X-ray diffraction and extended X-ray absorption spectroscopy (EXAFS) at the Ge, Sb and Te K-edges. Large scale structural models were generated by fitting the experimental datasets (5 for each composition) simultaneously in the framework of the reverse Monte Carlo simulation technique. It was found that the alloys are chemically ordered (Ge and Sb have predominantly Te neighbors) and within the experimental uncertainty each component satisfies the $8-N$ rule. A comparison with the pair correlation functions of melt quenched Ge$_{20}$Te$_{80}$ revealed that the first minimum of $g_{\mathrm{TeTe}}(r)$ is shallower in the ternary alloys than in Ge$_{20}$Te$_{80}$. On the other hand, the separation of the first and second coordination environments of Ge atoms is stronger in the Ge-Sb-Te alloys investigated.

cond-mat.mtrl-sci↗

arXiv2023

Evolution of the hydrogen-bonded network in methanol-water mixtures upon cooling

The hydrogen-bonded structure of methanol-water mixtures is investigated over the entire alcohol concentration range (from $x_{\mathrm{Methanol}}=$ 0.1 to 1.0) at several temperatures, from 300 K down to the freezing point of the given mixture. Classical molecular dynamics simulations have been carried out, using the all-atom OPLS-AA force field for methanol and the TIP4P/2005 model for water molecules. Simulation trajectories ('particle configurations') obtained have been analyzed, in order to characterize the hydrogen-bonded network in the mixtures. The temperature and concentration dependence of the average hydrogen bond (H-bond) numbers between different types of molecules, the donor/acceptor roles of water and methanol molecules, and hydrogen bond number distributions have been revealed. The topology of the total system, as well as that of the water and methanol subsystems, has been investigated by calculating the cluster size distributions, the number of primitive rings, and ring size and ring type distributions. It has been found that upon cooling, the average number of H-bonded water molecules increases at every concentration and temperature investigated. As far as the connectivity of the hydrogen-bonded network is concerned, the percolation threshold has been shown to be above $x_{\mathrm{M}}=$ 0.9 already at room temperature.

physics.chem-ph↗

arXiv2022

Short range order and topology of binary Ge-S glasses

Short range order and topology of Ge$_x$S$_{100-x}$ glasses over a broad composition range (20 $\le$ x $\le$ 42 in at%) was investigated by neutron diffraction, X-ray diffraction, and Ge K-edge extended X-ray absorption fine structure (EXAFS) measurements. The experimental data sets were fitted simultaneously in the framework of the reverse Monte Carlo simulation method. It was found that both constituents (Ge and S) satisfy the Mott-rule in all investigated glasses: Ge and S atoms have 4 and 2 neighbours, respectively. The structure of these glasses can be described with the chemically ordered network model: Ge-S bonds are preferred, S-S bonds are present only in S-rich glasses. Dedicated simulations showed that Ge-Ge bonds are necessary in Ge-rich glasses. Connections between Ge atoms (such as edge-sharing GeS$_{4/2}$ tetrahedra) in stoichiometric and S-rich glasses were analysed. The frequency of primitive rings was also calculated.

physics.chem-ph↗

arXiv2022

Towards the correct microscopic structure of aqueous CsCl solutions with a comparison of classical interatomic potential models

The structure of aqueous CsCl solutions was investigated by classical molecular dynamics simulations (MD) at three salt concentrations (1.5, 7.5, and 15 mol %). Thirty interatomic potential sets, based on the 12-6 Lennard-Jones model, parametrized for non-polarizable water solvent molecules were collected and tested. Some basic properties, such as density, static dielectric constant, and self-diffusion coefficients, predicted by the force fields (FF), were compared with available experimental data. The simulated particle configurations were used to calculate the partial radial distribution functions (PRDF) and the neutron and X-ray total scattering structure factors (TSSF). The TSSFs were compared with experimental data from the literature, to find the best FF models, which describe the structure correctly. It was found that, though several of the thirty models failed in the tests, some models are compatible with the measured data. Values of the structural parameters consistent with the experiments were determined (such as water-ion distances, the average number of water molecules around the ions, average number, and distance between anion-cation contact ion pairs, water-water hydrogen bonds). It was shown, that in addition to models in which the number of contact ion pairs is too high, models in which this number is too low are also unable to reproduce the experimental data.

physics.chem-ph↗

arXiv2021

Temperature-dependent structure of 1-propanol/water mixtures: X-ray diffraction experiments and computer simulations at low and high alcohol contents

Aqueous mixtures of 1-propanol have been investigated by high-energy synchrotron X-ray diffraction upon cooling. X-ray weighted total scattering structure factors of 6 mixtures, from 8 mol% to 89 mol% alcohol content, as well as that of pure 1-propanol are reported from room temperature down to the freezing points of the liquids. Molecular dynamics simulations have been performed, in order to interpret measured data. The all atom OPLS-AA potential model was used for 1-propanol, combined with both the SPC/E and the TIP4P/2005 water models: both combinations provide a semi-quantitative description of the measured total structure factors at low and high alcohol contents, while the agreement is qualitative for the mixture with 71 mol% of 1-propanol. From the simulated particle configurations, partial radial distribution functions were calculated. Furthermore, detailed description of the hydrogen bonded network is provided, in terms of hydrogen bond numbers, analysis of proton donor-acceptor ratios, size distributions of hydrogen bonded clusters and ring size statistics. Strong temperature dependence of the percolation threshold, as well as of the participation of the number of doubly hydrogen bonded molecules in cyclic entities, has been found for the mixture with 89 mol% of 1-propanol. Above an alcohol content of 20 mol%, 5-fold rings are the most frequent cyclic entities, with a strong temperature dependence in terms of the number of rings.

physics.chem-ph↗

arXiv2021

Properties of hydrogen bonded network in ethanol-water liquid mixtures as a function of temperature: diffraction experiments and computer simulations

New X-ray and neutron diffraction experiments have been performed on ethanol-water mixtures as a function of decreasing temperature, so that such diffraction data are now available over the entire composition range. Extensive molecular dynamics simulations show that the all-atom interatomic potentials applied are adequate for gaining insight of the hydrogen bonded network structure, as well as of its changes on cooling. Various tools have been exploited for revealing details concerning hydrogen bonding, like determining H-bond acceptor and donor sites, calculating cluster size distributions and cluster topologies, as well as computing the Laplace spectra and fractal dimensions of the networks. It is found that 5-membered hydrogen bonded cycles are dominant up to an ethanol content of 70% at room temperature, above which concentration ring structures nearly disappear. Percolation has been given special attention, so that it could be shown that at low temperature, close to the freezing point even the mixture with 90% ethanol possesses a 3D percolating network. Moreover, the water sub-network also percolates even at room temperature, with a percolation transition occurring around 50% ethanol.

cond-mat.soft↗

arXiv2020

Temperature-dependent structure of methanol-water mixtures on cooling: X-ray and neutron diffraction and molecular dynamics simulations

Methanol-water liquid mixtures have been investigated by high-energy synchrotron X-ray and neutron diffraction at low temperatures. We are thus able to report the first complete sets of both X-ray and neutron weighted total scattering structure factors over the entire composition range (at 12 different methanol concentrations (x$_M$) from 10 to 100 mol%) and at temperatures from ambient down to the freezing points of the mixtures. The new diffraction data may later be used as reference in future theoretical and simulation studies. The measured data are interpreted by molecular dynamics simulations, in which the all atom OPLS/AA force field model for methanol is combined with both the SPC/E and TIP4P/2005 water potentials. Although the TIP4P/2005 water model was found to be somewhat more successful, both combinations provide at least semi-quantitative agreement with measured diffraction data. From the simulated particle configurations, partial radial distribution functions, as well as various distributions of the number of hydrogen bonds have been determined. As a general trend, the average number of hydrogen bonds increases upon cooling. However, the number of hydrogen bonds between methanol molecules slightly decreases with lowering temperatures in the concentration range between ca. 30 and 60 mol % alcohol content. The same is valid for water-water hydrogen bonds above 70 mol % of methanol content, from room temperature down to 193 K.

physics.chem-ph↗

arXiv2020

Chloride ions as integral parts of hydrogen bonded networks in aqueous salt solutions: the appearance of solvent separated anion pairs

Hydrogen bonding to chloride ions has been frequently discussed over the past 5 decades. Still, the possible role of such secondary intermolecular bonding interactions in hydrogen bonded networks has not been investigated in any detail. Here we consider computer models of concentrated aqueous LiCl solutions and compute usual hydrogen bond network characteristics, such as distributions of cluster sizes and of cyclic entities, both for models that take and do not take chloride ions into account. During the analysis of hydrogen bonded rings, a significant amount of 'solvent separated anion pairs' have been detected at high LiCl concentrations. It is demonstrated that taking halide anions into account as organic constituents of the hydrogen bonded network does make the interpretation of structural details significantly more meaningful than when considering water molecules only. Finally, we compare simulated structures generated by 'good' and 'bad' potential sets on the basis of the tools developed here, and show that this novel concept is, indeed, also helpful for distinguishing between reasonable and meaningless structural models.

physics.chem-ph↗

arXiv2020

Short range order and topology of Ge$_{x}$Ga$_{x}$Te$_{100-2x}$ glasses

Chemical short range order and topology of Ge$_{x}$Ga$_{x}$Te$_{100-2x}$ glasses was investigated by neutron- and x-ray diffraction as well as Ge and Ga K-edge extended x-ray absorption fine structure (EXAFS) measurements. Large scale structural models were obtained by fitting experimental datasets simultaneously with the reverse Monte Carlo simulation technique. Models, relying only on experimental data and basic physical information without constraining the average coordination numbers, give 3.9 - 4.1 for the number of the atoms in the first coordination sphere of Ge atoms, while the average number of first neighbors of Ga atoms scatters around 3.8. The average coordination number of Te atoms is significantly higher than 2 for $x$ = 12.5 and 14.3. It is found that the vast majority of MTe$_4$ (M=Ge or Ga) tetrahedra have at least one corner sharing MTe$_4$ neighbor.

physics.chem-ph↗

arXiv2020

Hydrogen bonding and percolation in propan-2-ol -- water liquid mixtures: X-ray diffraction experiments and computer simulations

Synchrotron X-ray diffraction measurements have been conducted on aqueous mixtures of propan-2-ol (a.k.a. isopropanol, or 2-propanol), for alcohol contents between 10 and 90 molar %, from room temperature down to 230 K. Molecular dynamics simulations, by using an all-atom parametrization of the propan-2-ol molecule and the well-known TIP4P/2005 water model, were able to provide semi-quantitative descriptions of the measured total structure factors. Various quantities related to hydrogen bonding, like hydrogen bond numbers, size distribution of cyclic entities and cluster size distributions, have been determined from the particle co-ordinates obtained from the simulations. The percolation threshold at room temperature could be estimated to be between isopropanol concentrations of 62 and 74 molar %, whereas at very low temperature, calculations yielded a value above 90 molar %.

physics.chem-ph↗

arXiv2019

Structural, Rheological and Dynamic Aspects of Hydrogen-Bonding Molecular Liquids: Aqueous Solutions of Hydrotropic tert-Butyl Alcohol

Hypothesis: The structural details, viscosity trends and dynamic phenomena in t-butanol/water solutions are closely related on the molecular scales across the entire composition range. Utilizing the experimental small- and wide-angle x-ray scattering (SWAXS) method, molecular dynamics (MD) simulations and the complemented-system approach method developed in our group it is possible to comprehensively describe the structure-viscosity-dynamics relationship in such structurally versatile hydrogen-bonded molecular liquids, as well as in similar, self-assembling systems with pronounced molecular and supramolecular structures at the intra-, inter-, and supra-molecular scales. Experiments: The SWAXS and x-ray diffraction experiments and MD simulations were performed for aqueous t-butanol solutions at 25 °C. Literature viscosity and self-diffusion data were also used. Findings: The interpretive power of the proposed scheme was demonstrated by the extensive and diverse results obtained for aqueous t-butanol solutions across the whole concentration range. Four composition ranges with qualitatively different structures and viscosity trends were revealed. The experimental and calculated zero-shear viscosities and molecular self-diffusion coefficients were successfully related to the corresponding structural details. The hydrogen bonds, that were, along with hydrophobic effects, recognized as the most important driving force for the formation of t-butanol aggregates, show intriguing lifetime trends and thermodynamic properties of their formation.

cond-mat.soft↗

arXiv2018

X-ray diffraction and computer simulation studies of the structure of liquid aliphatic aldehydes: from propanal to nonanal

Synchrotron X-ray diffraction experiments and molecular dynamics simulations have been performed on simple aliphatic aldehydes, from propanal to nonanal. The performance of the OPLS all-atom interaction potential model for aldehydes has been assessed via direct comparison of simulated and experimental total scattering structure factors. In general, MD results reproduce the experimental data at least semi-quantitatively. However, a slight mismatch can be observed between the two datasets in terms of the position of the main diffraction maxima. Partial radial distribution functions have also been calculated from the simulation results. Clear differences could be detected between the various O-H partial radial distribution functions, depending on whether the H atom is attached to the carbon atom that is doubly bonded to the oxygen atom of the aldehyde group or not.

physics.chem-ph↗

arXiv2018

Unexpected composition dependence of the first sharp diffraction peak in an alcohol-aldehyde liquid mixture: n-pentanol and pentanal

The total scattering structure factors of pure liquid n-pentanol, pentanal, and 5 of their mixtures, as determined by high energy synchrotron X-ray diffraction experiments, are presented. For the interpretation of measured data, molecular dynamics computer simulations are performed, utilizing 'all-atom' type force fields. The diffraction signals in general resemble each other over most of the monitored Q range above 1 $Å^{-1}$, but the absolute values of the intensities of the small-angle scattering maximum ('pre-peak', 'first sharp diffraction peak'), around 0.6 $Å^{-1}$, change in an unexpected fashion, non-linearly with the composition. MD simulations are not able to reproduce this low-Q behavior; on the other hand, they do reproduce the experimental diffraction data above 1 $Å^{-1}$ rather accurately. Partial radial distribution functions are calculated based on the atomic coordinates in the simulated configurations. Inspection of the various O-O and O-H partial radial distribution functions clearly shows that both the alcoholic and the aldehydic oxygens form hydrogen bonds with the hydrogen atoms of the alcoholic OH-group.

physics.chem-ph↗

arXiv2018

Local order in binary Ge-Te glasses - an experimental study

The structure of $\mathrm{Ge}_x\mathrm{Te}_{100-x}$ (x = 14.5, 18.7, 23.6) glasses prepared by twin roller quenching technique was investigated by neutron diffraction, X-ray diffraction and Ge-K-edge X-ray absorption spectroscopy measurements. Large scale structural models were obtained for each composition by fitting the experimental datasets in the framework of the reverse Monte Carlo technique. It was found that the majority of Ge and Te atoms satisfy the 8-N rule. Simulation results indicate that Ge-Ge bonding is not significant for x = 14.5 and 18.7. The shape and position of the first peak of the Ge-Ge partial pair correlation function evidence the presence of corner sharing tetrahedra already in compositions (x = 14.5 and 18.7) where 'sharing' of a Te atom by two Ge atoms could be avoided due to the low concentration of Ge.

physics.chem-ph↗

arXiv2018

The structure of near stoichiometric Ge-Ga-Sb-S glasses: a reverse Monte Carlo study

The structure of Ge$_{22}$Ga$_3$Sb$_{10}$S$_{65}$ and Ge$_{15}$Ga$_{10}$Sb$_{10}$S$_{65}$ glasses was investigated by neutron diffraction (ND), X-ray diffraction (XRD), and extended X-ray absorption fine structure (EXAFS) measurements at the Ge, Ga and Sb K-edges. Experimental data sets were fitted simultaneously in the framework of the reverse Monte Carlo (RMC) simulation technique. Short range order parameters were determined from the obtained large-scale configurations. It was found that the coordination numbers of Ge, Sb and S are around the values predicted by the Mott-rule (4, 3 and 2, respectively). The Ga atoms have on average 4 nearest neighbors. The structure of these stoichiometric glasses can be described by the chemically ordered network model: Ge-S, Ga-S and Sb-S bonds are the most important. Long Sb-S distances (0.3 - 0.4 Å higher than the usual covalent bond lengths) are observed, suggesting that Sb atoms can be found in various local environments.

cond-mat.mtrl-sci↗

arXiv2018

Atomic level structure of Ge-Sb-S glasses: chemical short range order and long Sb-S bonds

The structure of Ge$_{20}$Sb$_{10}$S$_{70}$, Ge$_{23}$Sb$_{12}$S$_{65}$ and Ge$_{26}$Sb$_{13}$S$_{61}$ glasses was investigated by neutron diffraction (ND), X-ray diffraction (XRD), extended X-ray absorption fine structure (EXAFS) measurements at the Ge and Sb K-edges as well as Raman scattering. For each composition, large scale structural models were obtained by fitting simultaneously diffraction and EXAFS data sets in the framework of the reverse Monte Carlo (RMC) simulation technique. Ge and S atoms have 4 and 2 nearest neighbors, respectively. The structure of these glasses can be described by the chemically ordered network model: Ge-S and Sb-S bonds are always preferred. These two bond types adequately describe the structure of the stoichiometric glass while S-S bonds can also be found in the S-rich composition. Raman scattering data show the presence of Ge-Ge, Ge-Sb and Sb-Sb bonds in the S-deficient glass but only Ge-Sb bonds are needed to fit diffraction and EXAFS datasets. A significant part of the Sb-S pairs has 0.3-0.4 Å longer bond distance than the usually accepted covalent bond length (~2.45 Å). From this observation it was inferred that a part of Sb atoms have more than 3 S neighbors.

cond-mat.dis-nn↗

arXiv2018

The structure of aqueous lithium chloride solutions at high concentrations as revealed by a comparison of classical interatomic potential models

Highly concentrated aqueous lithium chloride solutions were investigated by classical molecular dynamics (MD) and reverse Monte Carlo (RMC) simulations. At first MD calculations were carried out applying twenty-nine combinations of ion-water interaction models at four salt concentrations. The structural predictions of the different models were compared, the contributions of different structural motifs to the partial pair correlation functions (PPCF) were determined. Particle configurations obtained from MD simulations were further refined using the RMC method to get better agreement with experimental X-ray and neutron diffraction data. The PPCFs calculated from MD simulations were fitted together with the experimental structure factors to construct structural models that are as consistent as possible with both the experimental results and the results of the MD simulations. The MD models were validated according to the quality of the fits. Although none of the tested MD models can describe the structure perfectly at the highest investigated concentration, their comparison made it possible to determine the main structural properties of that solution as well. It was found that four nearest neighbors (oxygen atoms and chloride ions together) are around a lithium ion at each concentration, while in the surroundings of the chloride ion hydrogen atom pairs are replaced by one lithium ion as the concentration increases. While in pure liquid water four water molecules can be found around a central water molecule, near the solubility limit nearly all water molecules are connected to two chloride ions (via their hydrogen atoms) and one lithium ion (by their oxygen atoms).

physics.chem-ph↗