arXiv subjects

Dietmar Paschek

Publications and source records attributed to Dietmar Paschek.

14 recordsLinked to original sources

arXiv2026

Computing Shear Viscosities from Molecular Dynamics Simulation: Comparing the OrthoBoXY Approach with the Green-Kubo Method

We calculated shear viscosities of 15 neat molecular liquids from equilibrium molecular dynamics (MD) simulations using the OrthoBoXY approach and compare them to viscosities calculated via the Green-Kubo method. Data from both methods agree very well. Here, we show how to avoid pitfalls while computing the OrthoBoXY-data to obtain optimal results. From simulations of multiple system sizes, we could verify that the viscosity of molecular liquids is not influenced by finite size effects down to systems as small as 250 molecules. Moreover, we demonstrate that also the standard error of the viscosity is nearly independent of the system size. This is shown to be a consequence of a compensation effect of an increasing accuracy of the self-diffusion coefficients with increasing systems-size and the system-size dependent weighting according to the OrthoBoXY-equation. As a consequence, we suggest that it is preferable to run simulations of smaller systems with longer simulation times rather than larger systems with shorter simulation runs. In addition, we discuss a refinement of the recently introduced "recipe" for OrthoBoXY simulations block-lengths $\tau_\mathrm{block}$. Based on data from simulations with varying run-lengths, we suggest the following modification: for highly viscous systems, the value of $\tau_\mathrm{block}$ might safely be scaled by a factor of $1/8$, significantly reducing the computational resources needed. For less viscous systems, the value of $\tau_\mathrm{block}$ might safely be scaled by a factor of $1/4$. For systems with high fluidity, the value of $\tau_\mathrm{block}$ should not be scaled down in order to achieve reliable results. When using a smaller system size of 250 molecules, these refinements are leading up to a 24-fold reduction in computational cost compared to the previous recommended set-up without sacrificing numerical accuracy.

cond-mat.stat-mech↗

arXiv2024

When Theory Meets Experiment: What Does it Take to Accurately Predict $^1$H NMR Dipolar Relaxation Rates in Neat Liquid Water from Theory?

In this contribution, we compute the $^1$H nuclear magnetic resonance (NMR) relaxation rate of liquid water at ambient conditions. We are using structural and dynamical information from Coupled Cluster Molecular Dynamics (CCMD) trajectories generated at CCSD(T) electronic structure accuracy while considering also nuclear quantum effects in addition to consulting information from X-ray and neutron scattering experiments. Our analysis is based on a recently presented computational framework for determining the frequency-dependent NMR dipole-dipole relaxation rate of spin $1/2$ nuclei from Molecular Dynamics (MD) simulations, which allows for an effective disentanglement of its structural and dynamical contributions, and is including a correction for finite-size effects inherent to MD simulations with periodic boundary conditions. A close to perfect agreement with experimental relaxation data is achieved if structural and dynamical informations from CCMD trajectories are considered including a re-balancing of the rotational and translational dynamics, according to the product of the self-diffusion coefficient and the reorientational correlation time of the H-H vector $D_0\timesτ_\mathrm{HH}$. The simulations show that this balance is significantly altered when nuclear quantum effects are taken into account. Our analysis suggests that the intermolecular and intramolecular contribution to the $^1$H NMR relaxation rate of liquid water are almost similar in magnitude, unlike to what was predicted earlier from classical MD simulations.

physics.chem-ph↗

arXiv2023

Computing the Frequency-Dependent NMR Relaxation of $^1$H Nuclei in Liquid Water

It is the purpose of this paper to present a computational framework for reliably determining the frequency-dependent intermolecular and intramolecular NMR dipole-dipole relaxation rate of spin $1/2$ nuclei from MD simulations. The approach avoids alterations caused by well-known finite-size effects of the translational diffusion. Moreover, a procedure is derived to control and correct for effects caused by fixed distance-sampling cutoffs and periodic boundary conditions. By construction, this approach is capable of accurately predicting the correct low-frequency scaling behavior of the intermolecular NMR dipole-dipole relaxation rate and thus allows the reliable calculation of the frequency-dependent relaxation rate over many orders of magnitude. Our approach is based on the utilisation of the theory of Hwang and Freed for the intermolecular dipole-dipole correlation function and its corresponding spectral density [J. Chem. Phys. 63, 4017 (1975)] and its combination with data from molecular dynamics (MD) simulations. The deviations from the Hwang and Freed theory caused by periodic boundary conditions and sampling distance cutoffs are quantified by means of random walker Monte Carlo simulations. An expression based on the Hwang and Freed theoryis also suggested for correcting those effects. As a proof of principle, our approach is demonstrated by computing the frequency-dependent inter- and intramolecular dipolar NMR relaxation rate of the $^1$H nuclei in liquid water at $273\,\mbox{K}$ and $298\,\mbox{K}$ based on simulations of the TIP4P/2005 model. Our calculations are suggesting that the intermolecular contribution to the $^1$H NMR relaxation rate of the TIP4P/2005 model in the extreme narrowing limit has previously been substantially underestimated.

cond-mat.soft↗

arXiv2023

An OrthoBoXY-Method for Various Alternative Box Geometries

We have shown in a recent contribution [J. Phys. Chem.B 127, 7983-7987 (2023)] that for molecular dynamics (MD) simulations of isotropic fluids based on orthorhombic periodic boundary conditions with "magic" box length ratios of $L_z/L_x\!=\!L_z/L_y\!=\!2.7933596497$, the computed self-diffusion coefficients $D_x$ and $D_y$ in $x$- and $y$-direction become system size independent. They thus represent the true self-diffusion coefficient $D_0\!=\!(D_x+D_y)/2$, while the shear viscosity can be determined from diffusion coefficients in $x$-, $y$-, and $z$-direction, using the expression $η\!=\!k_\mathrm{B}T\cdot 8.1711245653/[3πL_z(D_{x}+D_{y}-2D_z)]$. Here we present a more generalized version of this "OrthoBoXY"-approach, which can be applied to any orthorhombic MD box. We would like to test, whether it is possible to improve the efficiency of the approach by using a shape more akin to the cubic form, albeit with different box-length ratios $L_x/L_z\!\neq\! L_y/L_z$ and $L_x\!<\!L_y\!<\!L_z$. We use simulations of systems of 1536 TIP4P/2005 water molecules as a benchmark and explore different box-geometries to determine the influence of the box shape on the computed statistical uncertainties for $D_0$ and $η$. Moreover, another "magical" set of box-length ratios is discovered with $L_y/L_z\!=\!0.57804765578$ and $L_x/L_z\!=\!0.33413909235$, where the self-diffusion coefficient in $x$-direction becomes system size independent, such that $D_0\!=\!D_x$.

cond-mat.soft↗

arXiv2023

OrthoBoXY: A Simple Way to Compute True Self-Diffusion Coefficients from MD Simulations with Periodic Boundary Conditions Without Prior Knowledge of the Viscosity

Recently, an analytical expression for the system size dependence and direction-dependence of self-diffusion coefficients for neat liquids due to hydrodynamic interactions has been derived for molecular dynamics (MD) simulations using orthorhombic unit cells. Based on this description, we show that for systems with a "magic" box length ratio of $L_z/L_x\!=\!L_z/L_y\!=\!2.7933596497$ the computed self-diffusion coefficients $D_x$ and $D_y$ in $x$- and $y$-direction become system-size independent and represent the true self-diffusion coefficient $D_0\!=\!(D_x+D_y)/2$. Moreover, by using this particular box geometry, the viscosity can be determined with a reasonable degree of accuracy from the difference of components of the diffusion coefficients in $x$-,$y$- and $z$-direction using the simple expression $η\!=\!k_\mathrm{B}T\cdot 8.1711245653/[3πL_z(D_{x}+D_{y}-2D_z)]$, where $k_\mathrm{B}$ denotes Boltzmann's constant, and $T$ represents the temperature. MD simulations of TIP4P/2005 water for various system-sizes using both orthorhombic and cubic box geometries are used to test the approach.

cond-mat.soft↗

arXiv2017

Revisiting Imidazolium Based Ionic Liquids: Effect of the Conformation Bias of the [NTf$_{2}$] Anion Studied By Molecular Dynamics Simulations

We study ionic liquids composed 1-alkyl-3-methylimidazolium cations and bis(trifluoromethyl-sulfonyl)imide anions ([C$_n$MIm][NTf$_2$]) with varying chain-length $n\!=\!2, 4, 6, 8$ by using molecular dynamics simulations. We show that a reparametrization of the dihedral potentials as well as charges of the [NTf$_2$] anion leads to an improvment of the force field model introduced by Köddermann {\em et al.} [ChemPhysChem, \textbf{8}, 2464 (2007)] (KPL-force field). A crucial advantage of the new parameter set is that the minimum energy conformations of the anion ({\em trans} and {\em gauche}), as deduced from {\em ab initio} calculations and {\sc Raman} experiments, are now both well represented by our model. In addition, the results for [C$_n$MIm][NTf$_2$] show that this modification leads to an even better agreement between experiment and molecular dynamics simulation as demonstrated for densities, diffusion coefficients, vaporization enthalpies, reorientational correlation times, and viscosities. Even though we focused on a better representation of the anion conformation, also the alkyl chain-length dependence of the cation behaves closer to the experiment. We strongly encourage to use the new NGKPL force field for the [NTf$_2$] anion instead of the earlier KPL parameter set for computer simulations aiming to describe the thermodynamics, dynamics and also structure of imidazolium based ionic liquids.

cond-mat.soft↗

arXiv2015

A Simple Guiding Principle for the Temperature Dependence of the Solubility of Light Gases in Imidazolium-based Ionic Liquids Derived from Molecular Simulations

We have determined the temperature dependence of the solvation behavior of a large collection of light gases in imidazolium-based Ionic Liquids (ILs) with the help of extensive molecular dynamics simulations. The solubility of molecular hydrogen, oxygen, nitrogen, methane, krypton, argon, neon and carbon dioxide in the imidazolium based ILs of type 1-n-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C$_n$mim][NTf$_2$]) with varying chain lengths $n\!=\!2,4,6,8$ are computed for a temperature range between $300\,\mbox{K}$ and $500\,\mbox{K}$ at $1\,\mbox{bar}$. By applying Widom's particle insertion technique and Bennet's overlapping distribution method, we are able to determine the temperature dependent solvation free energies for those selected light gases in simulated imidazolium based ILs with high statistical accuracy. Our simulations show that the magnitude of the solvation free energy of a gas molecule at a chosen reference temperature and its temperature-derivatives are intimately related with respect to oneanother. We conclude that this "universal" behavior is rooted in a solvation entropy-enthalpy compensation effect, which seems to be a defining feature of the solvation of small molecules in Ionic Liquids. We argue that this feature is based on a hypothesized funnel-like shape of the free energy landscape of a solvated gas molecule. The observations lead to simple analytical relations, determining the temperature dependence of the solubility data based on the absolute solubility at a certain reference temperature, which we call "solvation funnel" model. By comparing our results with available experimental data from many sources, we can show that the "solvation funnel" model is particularly helpful for providing reliable estimates for the solvation behavior of very light gases, such as hydrogen, where conflicting experimental data exist.

physics.chem-ph↗

arXiv2008

The Solvophobic Solvation and Interaction of Small Apolar Particles in Imidazolium-Based Ionic Liquids is Characterized by Enthalpy-/Entropy-Compensation

We report results of molecular dynamics simulations characterizing the solvation and interaction of small apolar particles such as methane and Xenon in imidazolium-based ionic liquids (ILs). The simulations are able to reproduce semi-quantitatively the anomalous temperature dependence of the solubility of apolar particles in the infinite dilution regime. We observe that the ``solvophobic solvation'' of small apolar particles in ILs is governed by compensating entropic and enthalpic contributions, very much like the hydrophobic hydration of small apolar particles in liquid water. In addition, our simulations clearly indicate that the solvent mediated interaction of apolar particles dissolved in ILs is similarly driven by compensating enthalpic/entropic contributions, making the ``solvophobic interaction'' thermodynamically analogous to the hydrophobic interaction.

cond-mat.soft↗

arXiv2006

Adding Salt to an Aqueous Solution of t-Butanol: Is Hydrophobic Association Enhanced or Reduced?

Recent neutron scattering experiments on aqueous salt solutions of amphiphilic t-butanol by Bowron and Finney [Phys. Rev. Lett. {\bf 89}, 215508 (2002); J. Chem. Phys. {\bf 118}, 8357 (2003)] suggest the formation of t-butanol pairs, bridged by a chloride ion via ${O}-{H}...{Cl}^-$ hydrogen-bonds, and leading to a reduced number of intermolecular hydrophobic butanol-butanol contacts. Here we present a joint experimental/theoretical study on the same system, using a combination of molecular dynamics simulations and nuclear magnetic relaxation measurements. Both theory and experiment clearly support the more intuitive scenario of an enhanced number of hydrophobic contacts in the presence of the salt, as it would be expected for purely hydrophobic solutes [J. Phys. Chem. B {\bf 107}, 612 (2003)]. Although our conclusions arrive at a structurally completely distinct scenario, the molecular dynamics simulation results are within the experimental errorbars of the Bowron and Finney work.

cond-mat.soft↗

arXiv2005

Characterizing the stepwise transformation from a low-density to a very-high-density form of supercooled liquid water

We explore the phase diagram of TIP4P-Ew [J. Chem. Phys. {\bf 120}, 9665 (2004)] liquid model water from the boiling-point down to $150 {K}$ at densities ranging from $0.950 {g} {cm}^{-3}$ to $1.355 {g} {cm}^{-3}$. In addition to the low-density/high-density (LDL/HDL) liquid-liquid transition, we observe a high-density/very-high-density (HDL/VHDL) transformation for the lowest temperatures at $1.30 {g} {cm}^{-3}$. A Van der-Waals type loop suggest the presence of a first order HDL/VHDL transition. In addition, we identify a pre-transition at $1.24 {g} {cm}^{-3}$, suggesting the experimentally detected HDA/VHDA-transformation to be a two-step process. For both pre- and main- HDA/VHDA-transition we observe a step-wise increase of the oxygen coordination number for interstitial water molecules.

cond-mat.stat-mech↗

arXiv2005

Low-Temperature and High-Pressure Induced Swelling of a Hydrophobic Polymer-Chain in Aqueous Solution

We report molecular dynamics simulations of a hydrophobic polymer-chain in aqueous solution between $260 {K}$ and $420 {K}$ at pressures of $1 {bar}$, $3000 {bar}$, and $4500 {bar}$. The simulations reveal a hydrophobically collapsed state at low pressures and high temperatures. At $3000 {bar}$ and about $260 {K}$ and at $4500 {bar}$ and about $260 {K}$, however, a transition to a swelled state is observed. The transition is driven by a smaller volume and a remarkably strong lower enthalpy of the swelled state, indicating a steep positive slope of the corresponding transition line. The swelling is stabilized almost completely by the energetically favorable state of water in the polymers hydrophobic first hydration shell at low temperatures. Although surprising, this finding is consistent with the observation of a positive heat capacity of hydrophobic solvation. Moreover, the slope and location of the observed swelling transition for the collapsed hydrophobic chain coincides remarkably well with the cold denaturation transition of proteins.

cond-mat.soft↗

arXiv2005

How the Liquid-Liquid Transition Affects Hydrophobic Hydration in Deeply Supercooled Water

We determine the phase diagram of liquid supercooled water by extensive computer simulations using the TIP5P-E model [J. Chem. Phys. {\bf 120}, 6085 (2004)]. We find that the transformation of water into a low density liquid in the supercooled range strongly enhances the solubility of hydrophobic particles. The transformation of water into a tetrahedrally structured liquid is accompanied by a minimum in the hydration entropy and enthalpy. The corresponding change in sign of the solvation heat capacity indicates a loss of one characteristic signature of hydrophobic hydration. The observed behavior is found to be qualitatively in accordance with the predictions of the information theory model of Garde et al. [Phys. Rev. Lett. {\bf 77}, 4966 (1996)].

cond-mat.stat-mech↗

arXiv2004

Heat Capacity Effects Associated with the Hydrophobic Hydration and Interaction of Simple Solutes: A Detailed Structural and Energetical Analysis Based on MD Simulations

We examine the SPCE and TIP5P water models to study heat capacity effects associated with the hydrophobic hydration and interaction of Xenon particles. We calculate the excess chemical potential for Xenon employing the Widom particle insertion technique. The solvation enthalpy and excess heat capacity is obtained from the temperature dependence of the chemical potentials and, alternatively, directly by Ewald summation, as well as a reaction field based method. All three different approaches provide consistent results. The reaction field method allows a separation of the individual components to the heat capacity of solvation into solute/solvent and solvent/solvent parts, revealing the solvent/solvent part as the dominating contribution. A detailed spacial analysis of the heat capacity of the water molecules around a pair of Xenon particles at different separations reveals that the enhanced heat capacity of the water molecules in the bisector plane between two Xenon atoms is responsible for the maximum of the heat capacity observed at the desolvation barrier, recently reported by Shimizu and Chan ({\em J. Am. Chem. Soc.},{\bf 123}, 2083--2084 (2001)). The about 60% enlarged heat capacity of water in the concave part of the joint Xenon-Xenon hydration shell is the result of a counterplay of strengthened hydrogen bonds and an enhanced breaking of hydrogen bonds with increasing temperature. Differences between the two models concerning the heat capacity in the Xenon-Xenon contact state are attributed to the different water model bulk heat capacities, and to the different spacial extension of the structure effect introduced by the hydrophobic particles. Similarities between the different states of water in the joint Xenon-Xenon hydration shell and the properties of stretched water are discussed.

cond-mat.soft↗

arXiv2004

Temperature Dependence of the Hydrophobic Hydration and Interaction of Simple Solutes: An Examination of Five Popular Water Models

We examine five different popular rigid water models (SPC, SPCE, TIP3P, TIP4P and TIP5P) using MD simulations in order to investigate the hydrophobic hydration and interaction of apolar Lennard-Jones solutes as a function of temperature in the range between $275 {K}$ and $375 {K}$. For all investigated models and state points we calculate the excess chemical potential for the noble gases and Methane.All water models exhibit too small hydration entropies, but show a clear hierarchy. TIP3P shows poorest agreement with experiment whereas TIP5P is closest to the experimental data at lower temperatures and SPCE is closest at higher temperatures. A rescaling procedure inspired by information theory model of Hummer et al. ({\em Chem.Phys.}258, 349-370 (2000)) suggests that the differences between the different models and real water can be explained on the basis of the density curves at constant pressure. In addition, the models that give a good representation of the water structure at ambient conditions (TIP5P, SPCE and TIP4P) show considerably better agreement with the experimental data than SPC and TIP3P. We calculate the hydrophobic interaction between Xenon particles directly from a series of 60 ns simulation runs.We find that the temperature dependence of the association is related to the strength of the solvation entropy. Nevertheless, differences between the models seem to require a more detailed molecular picture.The TIP5P model shows by far the strongest temperature dependence.The suggested density-rescaling is also applied to the Xenon-Xenon contact-pair configuration, indicating the presence of a temperature where the hydrophobic interaction turns into purely repulsive.The predicted association for Xenon in real water suggest the presence a strong variation with temperature.

cond-mat.soft↗