A systematic approach to calibrate a transferable polarizable force field parameter set for primary alcohols

In this work, parameters are optimized for a charge‐on‐spring based polarizable force field for linear alcohols. We show that parameter transferability can be obtained using a systematic approach in which the effects of parameter changes on physico‐chemical properties calculated from simulation are predicted. Our previously described QM/MM calculations are used to attribute condensed‐phase polarizabilities, and starting from the non‐polarizable GROMOS 53A5/53A6 parameter set, van der Waals and Coulomb interaction parameters are optimized to reproduce pure‐liquid (thermodynamic, dielectric, and transport) properties, as well as hydration free energies. For a large set of models, which were obtained by combining small perturbations of 10 distinct parameters, values for pure‐liquid properties of the series methanol to butanol were close to experiment. From this large set of models, we selected 34 models without special repulsive van der Waals parameters to distinguish between hydrogen‐bonding and non‐hydrogen‐bonding atom pairs, to make the force field simple and transparent. © 2017 Wiley Periodicals, Inc.     

Theoretical characterization of the (H2O)21 cluster: application of an n-body decomposition procedure

Two low-energy minima of (H2O)21 with very different H-bonding arrangements have been investigated with the B3LYP density functional and RIMP2 methods, as well as with the TIP4P, Dang-Chang, AMOEBA, and TTM2-F force fields. The AMOEBA and TTM2-F model potentials give an energy ordering that agrees with the results of the electronic structure calculations, while the TIP4P and Dang-Chang models give the opposite ordering. Insight into the role of many-body polarization for establishing the relative stability of the two isomers is provided by an n-body decomposition of the energies calculated using the various theoretical methods.     

Molecular thermodynamics of fluid mixtures containing molecules differing in size and potential energy

Recent computer-simulation work by Shing and Gubbins (1983) for binary mixtures has shown that common semiempirical models (van der Waals n-fluid models) are in error when the molecules of the two components differ appreciably in size; the error is most severe in the dilute region. While perturbation theories are much better, they (like computer simulations) are not as yet useful for engineering work because of prohibitive computer requirements.This work proposes an algebraic expression for the Helmholtz energy of a mixture which gives results in very good agreement with those reported by Shing and Gubbins. This expression, using the local-composition concept, is based on a simplified but realistic picture of a fluid mixture: short-range order and long-range disorder. The proposed expression uses the Mansoori-Carnahan-Starling-Leland equation for the contribution of repulsive forces. For the contribution of attractive forces, it uses a new expression based on not one but several radii for the first-neighbor shell, one radius for each component.With reasonable simplifications, the resulting equation for the Helmholtz energy indicates that the van der Waals “constant” a is a strict quadratic function of mole fraction only at very low densities; at advanced densities, there are small deviations from the quadratic mixing rule. For practical calculations, the computer requirements are nearly the same as those for conventional engineering models.     

Review article: ion pair potentials for alkali halides and some applications to liquids and defect studies

Abstract

We review the basis on which interionic potentials for alkali halides are obtained. We find that the sizes of the van der Waals terms are known poorly and that the polarizable ion models lack the necessary thermodynamic corrections, however small they may be, to fit low temperature properties of the solid. Although the quantum statistical calculations indicated some damping of van der Waals interactions due to ionic overlap, a systematic study of the basic and modified approaches shows them to be unsatisfactory.     

Peculiarities of long-range interaction between the nucleotides after DNA damage.

In this work, the long-range interaction between the pairs of nucleotides situated on the opposite ends of a double broken DNA helix have been studied theoretically. The long-range energy was considered as a sum of electrodynamics Van der Waals and electrostatic Coulomb interactions. The most important region for the problem under consideration is about 5-15 A between the nucleotides. The calculations of the energy of long-range interaction have shown that during the interaction between the pairs CG-CG, there is a potential repulsive barrier with the amplitude of about 4 kT at the distance of 7-9 A, and during the interaction between the pairs TA-TA, there is a potential repulsive barrier with the amplitude of about 1.5 kT at the same distance, which can prevent DNA from enzyme selfrepairing after a double DNA break. This barrier vanishes as the pH of intracellular medium increases. The remainder pairs of nucleotides do not have such barrier, and there is always an attraction like interaction.     

The combined simulation approach of atomistic and continuum models for the thermodynamics of lysozyme crystals

We have studied the thermodynamic properties of hen egg white lysozyme crystals using a novel simulation method combining atomistic Monte Carlo simulation to calculate van der Waals interactions and the boundary element method to solve the Poisson-Boltzmann equation for the electrostatic interactions. For computational simplicity, we treat the protein as a rigid body, using the crystallographic coordinates of all non-hydrogen atoms of the protein to describe the detailed shape. NVT Monte Carlo simulations are carried out for tetragonal and orthorhombic crystals to obtain the van der Waals energy, incorporating an implicit solvation effect. For crystal phases, an optimally linearized Poisson-Boltzmann equation is used to include the effect of the Donnan equilibrium of the salt ions. The Helmholtz energy is obtained from expanded ensemble Monte Carlo simulations. By using the force field parameters that had previously been tuned for the solution properties, reasonable agreement with experiment is found for the crystallization energy of the tetragonal form. The prediction of the entropy is also reasonable with a slight underestimation suggesting the release of a few water molecules per protein during the crystallization. However, the predictions of the properties of the orthorhombic crystal are poor, probably due to differences in the solvation structure as indicated by experiments, and also as a result of the approximate force field used.     

Electron-gas interaction potentials for collisions of CaCl(X 2Σ+) and KCl(X 1Σ+) with Ar

Interaction potentials for CaCl(X ²Σ⁺)-Ar and KCl(X ¹Σ⁺)-Ar have been determined. They include a Gordon-Kim electron-gas repulsive part smoothly joined to the long-range van der Waals potential. The van der waals potential for KClAr was taken from Meyer and Toennies. For CaClAr, the necessary molecular parameter were estimated from the Rittner model, which predicts both the dipole and quadrupole moments fairly accurately. The CaClAr interaction potential is quite different from that of KClAr. Due to the outer 4s electron on the Ca⁺ ion. the CaClAr potential exhibits a deep minimum in the odd-order Legendre terms which is expected to have a large effect on the cross sections for collisional rotational excitation. The KClAr potential determined here also shows significant differences in the repulsive and well regions from that predicted by Meyer and Toennies using a site-site model for the repulsive contribution.     

Long-Range van der Waals Interactions in Density Functional Theory

The early difficulties in accounting for long-range van der Waals interactions in the framework of density functional theory (DFT) have been overcome to a certain extent in recent works by several groups, and those interactions can be computed numerically. In this paper a derivation of the analytical form of the attractive van der Waals interaction between two neutral atoms with polarizabilities α₁ and α₂ at large distance R, namely E _int=−C ₆ α₁ α₂/R ⁶ is performed within the context of DFT. Use is made of the properties of the Coulomb correlation hole, and it is shown that nonlocal Coulomb correlations are responsible for long-range dispersion interactions.     

An Extension of the Consistent Valence Force Field (CVFF) with the Aim to Simulate the Structures of Vanadium Phosphorus Oxides and the Adsorption of n‐Butane and of 1‐Butene on their Crystal Planes

A specific force field of Consistent Valence Force Field type was developed with the aim to simulate the structures of catalysts of vanadium phosphorus oxide type and the reversible adsorption of organic compounds on specific crystallographic planes of such catalysts by molecular modeling. The appropriate parameters were derived for the bonded (stretching, bending, and torsional deformations) and nonbonded (attractive and repulsive van der Waals and Coulomb forces) atomic interactions for V—O and P—O bonds in typical fragments of these catalysts with the vanadium atom in the oxidation state IV. The parameters for bonded interactions were computed from Hessian matrices, supplied by the program DMol for performing Density Functional Theory, by means of a program for non‐linear regression. The DMol program was applied to energy minimize structures of known vanadium phosphorus oxides, which were compared with X‐ray structures, and to obtain their Hessian matrices as a basis for the force constants needed. Some hypothetical structural models had to be added. The van der Waals parameters were estimated by means of correlations between van der Waals radii and the repulsive parameters and between polarizabilities and the dispersive parameters from the literature. The force field obtained was applied to simulate the crystal structure of vanadyl pyrophosphate and to compute the heat of adsorption of n‐butane and of 1‐butene on its (100) plane (computer codes of company Biosym/MSI/Accelrys). The experimental crystal structure and the adsorption energies were fairly well reproduced, except that the a lattice constant proves somewhat too large.     

Specific and nonspecific interaction forces between Escherichia coli and silicon nitride, determined by poisson statistical analysis

The nature of the physical interactions between Escherichia coli JM109 and a model surface (silicon nitride) was investigated in water via atomic force microscopy (AFM). AFM force measurements on bacteria can represent the combined effects of van der Waals and electrostatic forces, hydrogen bonding, steric interactions, and perhaps ligand-receptor type bonds. It can be difficult to decouple these forces into their individual components since both specific (chemical or short-range forces such as hydrogen bonding) and nonspecific (long-range colloidal) forces may be present in the overall profiles. An analysis is presented based on the application of Poisson statistics to AFM adhesion data, to decouple the specific and nonspecific interactions. Comparisons with classical DLVO theory and a modified form of a van der Waals expression for rough surfaces were made in order to help explain the nature of the interactions. The only specific forces in the system were due to hydrogen bonding, which from the Poisson analysis were found to be -0.125 nN. The nonspecific forces of 0.155 nN represent an overall repulsive interaction. These nonspecific forces are comparable to the forces calculated from DLVO theory, in which electrostatic-double layer interactions are added to van der Waals attractions calculated at the distance of closest approach, as long as the van der Waals model for "rough" spherical surfaces is used. Calculated electrostatic-double layer and van der Waals interactions summed to 0.116 nN. In contrast, if the classic (i.e., smooth) sphere-sphere model was used to predict the van der Waals forces, the sum of electrostatic and van der Waals forces was -7.11 nN, which appears to be a large overprediction. The Poisson statistical analysis of adhesion forces may be very useful in applications of bacterial adhesion, because it represents an easy way to determine the magnitude of hydrogen bonding in a given system and it allows the fundamental forces to be easily broken into their components.     

A note on excess Gibbs energy models,equations of state and the local composition concept

A density-dependent local composition expression for the residual energy is derived from a generalized NRTL expression for the excess energy and the van der Waals fluid theory. Integration of this expression yields a volume-dependent expression for the Helmholtz energy from which equations of state utilizing the local composition concept are derived and which in the high-density limit contain the well-known activity coefficient models.The local composition versions of the Carnahan—Starling—van der Waals, the Redlich—Kwong—Soave and the Peng—Robinson equations of state are derived. It is further shown that the group contribution versions of the NRTL, the Wilson and the UNIQUAC excess models may be derived from the generalized NRTL expression for the residual energy when applied to groups instead of molecules.It is thus demonstrated that all current local composition activity-coefficient models can be derived from a local composition version of the van der Waals equation of state using different sets of assumptions. In the same way the van Laar, the Scatchard—Hildebrand and the Flory—Huggins activity coefficient models are obtained from the van der Waals equation of state using the original mixing rules.     

Nonmonotoic fluctuation-induced interactions between dielectric slabs carrying charge disorder

We investigate the effect of monopolar charge disorder on the classical fluctuation-induced interactions between randomly charged net-neutral dielectric slabs and discuss various generalizations of recent results [A. Naji et al., Phys. Rev. Lett. 104, 060601 (2010)] to highly inhomogeneous dielectric systems with and without statistical disorder correlations. We shall focus on the specific case of two generally dissimilar plane-parallel slabs, which interact across vacuum or an arbitrary intervening dielectric medium. Monopolar charge disorder is considered to be present on the bounding surfaces and/or in the bulk of the slabs, may be in general quenched or annealed and may possess a finite lateral correlation length reflecting possible "patchiness" of the random charge distribution. In the case of quenched disorder, the bulk disorder is shown to give rise to an additive long-range contribution to the total force, which decays as the inverse distance between the slabs and may be attractive or repulsive depending on the dielectric constants of the slabs. By contrast, the force induced by annealed disorder in general combines with the underlying van der Waals forces in a nonadditive fashion, and the net force decays as an inverse cube law at large separations. We show, however, that in the case of two dissimilar slabs, the net effect due to the interplay between the disorder-induced and the pure van der Waals interactions can lead to a variety of unusual nonmonotonic interaction profiles between the dielectric slabs. In particular, when the intervening medium has a larger dielectric constant than the two slabs, we find that the net interaction can become repulsive and exhibit a potential barrier, while the underlying van der Waals force is attractive. On the contrary, when the intervening medium has a dielectric constant between that of the two slabs, the net interaction can become attractive and exhibit a free energy minimum, while the pure van der Waals force is repulsive. Therefore, the charge disorder, if present, can drastically alter the effective interaction between net-neutral objects.     

Analysis of the crystal binding and the Anderson-Gruneisen parameters in the halides of copper(I), silver(I) and thallium(I)

An analysis of the crystal binding for the halides of copper(I), silver(I) and thallium(I) has been performed using the Born model. The van der Waals dipole-dipole and dipole-quadrupole potentials are calculated from an interpolation scheme based on the Slater-Kirkwood variational method. Three different forms for the short range repulsive energy are adopted to calculate the binding energies of the crystals under study. The Born-Mayer exponential law is found to yield best agreement with experiment. The analysis has been extended to evaluate the Anderson-Gruneisen parameters which are related to the thermoelastic behaviour of crystals.     

van der Waals interaction between internal aqueous droplets and the external aqueous phase in double emulsions

A mathematical model for analyzing the van der Waals interaction between the internal aqueous droplets (W(1)) and the external aqueous phase (W(2)) of double emulsions has been established. The effects of Hamaker constants of the materials forming the system, especially those of the two different adsorbed surfactant layers with uniform density (A(1) and A(2)), on the van der Waals interaction were investigated. The overall van der Waals interaction across the oil film is a combined result of four individual parts, that is, W(1)-W(2), A(1)-A(2), W(1)-A(1), and A(2)-W(2) van der Waals interaction, and it may be either attractive or repulsive depending on many factors. It was found that the overall van der Waals interaction is dominated by the W(1)-W(2) interaction at large separation distances between the W(1)/O and O/W(2) interfaces, while it is mostly determined by the A(1)-A(2) interaction when the two interfaces are extremely close. Specifically, in the cases when the value of the Hamaker constant of the oil phase is intermediate between those of W(1) and W(2) and there is a thick oil film separating the two interfaces, a weak repulsive overall van der Waals interaction will prevail. If the Hamaker constant of the oil phase is intermediate between those of A(1) and A(2) and the two interfaces are very close, the overall van der Waals interaction will be dominated by the strong repulsive A(1)-A(2) interaction. The repulsive van der Waals interaction at such cases helps stabilize the double emulsions.     

Generalized van der Waals Theory of Interfaces in Simple Fluid Mixtures

An efficient implementation of the generalized van der Waals theory of fluids is presented for the calculation of surface tension in simple fluid mixtures. While detailed correlation analysis is avoided the dominant binding energy contribution and the negative contribution due to the nonlocal entropy are accounted for in the free energy density functional by simple physical approximations of the type originally introduced by van der Waals. Efficient computation is achieved by the use of a single-parameter optimization of a tanh-shaped profile representing the total density as well as the composition variation across the interface. This simple profile nevertheless incorporates the expected adsorption to the interface of the volatile component. Application is made to argon/krypton mixtures represented by Lennard-Jones potentials and Lorentz-Berthelot combining rules. Surface tension predictions compare well with both experimental observations and computer simulation results which also indicated close agreement in particle density profiles, especially if the Berthelot rule is amended with a binary interaction parameter slightly (3%) less than unity. Copyright 2001 Academic Press.     

A novel equation of state for the prediction of thermodynamic properties of fluids

This work proposes a new equation of state (EOS) based on molecular theory for the prediction of thermodynamic properties of real fluids. The new EOS uses a novel repulsive term, which gives the correct hard sphere close packed limit and yields accurate values for hard sphere and hard chain virial coefficients. The pressure obtained from this repulsive term is corrected by a combination of van der Waals and Dieterici potentials. No empirical temperature functionality of the parameters has been introduced at this stage. The novel EOS predicts the experimental volumetric data of different compounds and their mixtures better than the successful EOS of Peng and Robinson. The prediction of vapor pressures is only slightly less accurate than the results obtained with the Peng-Robinson equation that is designed for these purposes. The theoretically based parameters of the new EOS make its predictions more reliable than those obtained from purely empirical forms.     

Second-order MS-MA calculations for the triplet state of H2 in the van der Waals region

Second-order MS-MA calculations by the variation-perturbation method for the triplet state of H₂ show that in the van der Waals region induction including exchange is practically negligible and the depth and position of the potential minimum are determined by the competition between repulsive first-order exchange and attractive Coulomb dispersion. Accurate interaction energies are obtained in second order only if all non-expanded multipoles up to the dipole-octupole term are properly accounted for.     

Electron impact ionization efficiency curves of van der Waals clusters

The study of van der Waals clusters is an area of growing interest and is being widely studied for a number of reasons. The measurement of the ionization efficiency (IE) curves have yielded a wealth of information by enabling ionization and appearance energies of ions to be determined which are essential for the calculation of thermochemical data. In the case of van der Waals clusters, the measurement ofIE curves enables one to determine the qualitative trends in the ionization potentials as a function of cluster size. In additionIE curves have also offered valuable insight into ionization related processes occurring in clusters. This paper will cover some of the more recent studies of Penning ionization, exciton induced decay and Coulomb explosion in van der Waals clusters through the use of electron impactIE curves.