Van der Waals volume fragmental constants

Van der Waals (vdW) volumes (V_w,x) of 117 molecular fragments (X) have been calculated by numerical integration of the van der Waals envelope using the hard-sphere approximation, standard geometries, and effective atomic van der Waals radii which were determined by comparison of their effects on the predicted sterically allowed conformations of peptides with observed crystal structures. vdW volume fragmental constants give accurate estimates of molecular, vdW volume as sum of approximate V_w,xs.     

Van der Waals surface graphs and molecular shape

A van der Waals surface graph is the graph defined on a van der Waals surface by the intersections of the atomic van der Waals spheres. A van der Waals shape graph has a vertex for each atom with a visible face on the van der Waals surface, and edges between vertices representing atoms with adjacent faces on the van der Waals surface. These are discrete invariants of three‐dimensional molecular shape. Some basic properties of van der Waals surface graphs are studied, including their relationship with the Voronoi diagram of the atom centres, and a class of molecular embeddings is identified for which the dual of the van der Waals surface graph coincides with the van der Waals shape graph. This revised version was published online in July 2006 with corrections to the Cover Date.     

Anisotropy of the van der Waals Configuration of Atoms in Complex,Condensed, and Gas-Phase Molecules

Anisotropic van der Waals (vdW) radii of 5b–7bsubgroup elements were determined from structures of gas-phase van der Waals complexes and crystal molecular compounds. The anisotropy of the van der Waals configuration of atoms was shown to decrease when going from isolated molecules to the condensed state. Variations in intermolecular distances, which are usually explained in terms of the formation of hydrogen bonds, are substantially governed by the anisotropic effect.     

Molecular Modeling for Mobile Phase Optimization in RP-HPLC

Abstract

The applicability of molecular parameters calculated on the bases of molecular mechanics have been investigated for the prediction of reversed-phase retention behavior of structurally unrelated series of drug molecules. Non-polar, non-polar unsaturated and polar surface areas, surface energies, dipole moments, van der Waals radii and hydrophobicity values expressed by the logarithm of the octanol/water partition coefficients have been calculated from the molecular structure. The reversed-phase retention behavior was described by the slope and the intercept of the straight lines obtained by plotting the log k¹ values against the acetonitrile concentration of the mobile phase. The acetonitrile concentration (OP%₀) which was needed for the log k¹ = 0 retention was also calculated from the slope and intercept values. Step-wise linear regression analyses have been applied for revealing the correlations between the investigated parameters. The slope values could be described by the difference of the non-polar and non-polar accessible surface areas or by the total surface energy values and the van der Waals radii. The intercept values could be described by the hydrophobicity parameter, the slope and the reciprocal values of dipole moment. The acetonitrile concentration for the log k'=O retention (OP%₀) could have been calculated from the hydrophobicity and the non-polar unsaturated surface area values of the investigated compounds.     

Ionic Liquids: Dissecting the Enthalpies of Vaporization

We calculate the heats of vaporisation for imidazolium‐based ionic liquids [C_nmim][NTf₂] with n=1, 2, 4, 6, 8 by means of molecular dynamics (MD) simulations and discuss their behavior with respect to temperature and the alkyl chain length. We use a force field developed recently. The different cohesive energies contributing to the overall heats of vaporisations are discussed in detail. With increasing alkyl chain length, the Coulomb contribution to the heat of vaporisation remains constant at around 80 kJ mol^?1, whereas the van der Waals interaction increases continuously. The calculated increase of about 4.7 kJ mol^?1 per CH₂‐group of the van der Waals contribution in the ionic liquid exactly coincides with the increase in the heats of vaporisation for n‐alcohols and n‐alkanes, respectively. The results support the importance of van der Waals interactions even in systems completely composed of ions.     

Molecular modeling of wine polyphenols

Due to wide range of health effects of wine polyphenols, it is important to investigate the relationship between their structure and physical properties (quantitative structure–property relationship, QSPR). We have investigated linear, nonlinear (polynomial), and multiple linear relationships between given topological indices and molecular properties of main pharmacological active components of wine, such as molecular weight (MW), van der Waals volume (Vw), molar refractivity (MR), polar molecular surface area (PSA) and lipophilicity (log P). Partition coefficient (log P) was calculated using three different computer program (CLOGP, ALOGPS and MLOGP). The best models were achieved using the MLOGP program. Topological indices used for correlation analysis include: the Wiener index, W(G); connectivity indices, χ(G); the Balaban index, J(G); information-theoretic index, I(G); and the Schultz index, MTI(G). QSPR was performed on the set of 19 polyphenols and, particularly, on the group of phenolic acids, and on the group of flavonoids with resveratrol. The connectivity index has been successfully used for describing almost all parameters. Significant correlations were achieved between the Wiener index and van der Waals volume, as well as molecular weight.     

A new equation of state for metal alloys

A perturbed hard-trimer (PHT) equation of state (EOS) has been employed to model volumetric properties of molten metals and their alloys considering a trimer expression obtained from the statistical associating fluid theory. The van der Waals dispersion forces were applied as perturbation term. Two parameters appeared in the PHT EOS, reflecting the dispersive energy among trimers, ε and the hard-core diameter σ were determined based on the molecular scaling parameters. The performance of the proposed PHT EOS has been evaluated by predicting the saturated and isobaric densities of 16 molten metals including alkali metals, alkali earth and refractory metals over the temperature range within 234–7400 K and pressures up to 436 MPa. From 677 data points examined, the average absolute deviation (AAD) of the predicted densities from the experimental ones was found to be 1.60%. Furthermore, the estimated uncertainties of predicted densities of alloys were ±3.00%.     

Shape group theory of van der Waals surfaces

In this article we present a method for the study of shapes of general, asymmetric van der Waals surfaces. The procedure is simple to apply and it consists of two steps. First, the surface is decomposed into spherical domains, according to the interpenetration of the van der Waals atomic spheres. Each domain defines a topological object that is either a 2-manifold or some truncated 2-manifold. Second, we compute the homology groups for all the objects into which the surface is divided. These groups are topological and homotopical invariants of the domains, hence they remain invariant to conformational changes that preserve the essential features of these domains of decomposition. In particular, these homology groups do not depend explicitly on the molecular symmetry. Major rearrangements of the nuclear configurations, however, do alter the decomposition into spherical domains, and the corresponding variation of the homology groups can be followed easily under conformational rearrangements. We discuss a partitioning of the metric internal configuration spaceM into shape regions of van der Waals surfaces, which allows one to identify those rearrangements which introduce an essential change in shape and to distinguish them from those which do not alter the fundamental shape of the molecular surface. The dependence of the shape group partitioning ofM on the symmetry under permutation of nuclear changes is discussed briefly, considering a simple illustrative example.     

Apparent molar heat capacities and volumes,van der Waals volumes and accessible surface areas of alkylated derivatives of cytosine and uracil in aqueous solutions at 25°C.

Densities and specific heat capacities of aqueous solutions: 1,3,5,6-tetramethyluracil, 1,6-dimethyl-3-ethyluracil, 1,6-dimethyl-3-propyluracil, 1,6-dimethyl-3-butyluracil, 1,N⁴-trimethylcytosine, 1,N⁴-dimethyl-5-ethylcytosine, 1,N⁴ dimethyl-5-propylcytosine, 1,N⁴-dimethyl-5-butylcytosine were determined using flow calorimetry and flow densimetry at 25°C. Apparent molar volumes and heat capacities, van der Waals volumes and accessible surface areas were determined. It was stated that for alkylcytosines and alkyluracils partial molar volumes and heat capacities correlate linearly with the number of substituted methylene groups-CH₂-as well as with the van der Waals volumes and accessible surface areas of the compounds studied; for cyclooligouracils the cyclization effect was discussed.     

Resonances of triatomic van der Waals molecules by the complex discrete variable representation

Summary The results of Light and co-workers [J. Chem. Phys. 85:4594 (1986); 86:3065 (1987); 92:2129 (1990)] for the Hamiltonian matrix of a triatomic van der Waals molecule in the discrete variable representation, DVR, is extended to complex-scaled Hamiltonians. As an illustrative numerical example theJ=1 resonances positions and widths of a van der Waals model system were obtained by the calculation of the complex-scaled Hamiltonian matrix in the DVR formalism.Supported in part by the Albert Einstein Research Fund, and the Fund for the Promotion of Research at the Technion     

Benzonitrile and its van der waals complexes studied in a free jet. III. Enhancement of the intersystem crossing rate in the benzonitrile dimer and other complexes

By using the sensitized phosphorescence spectroscopy, the intensity of the phosphorescence has been recorded upon excitation of the benzonitrile dimer to the S₁ vibronic states in a free jet. The results indicate that the strong vibrational energy dependence of the fluorescence quantum yield, reported previously, is attributable to the increasing rate of intersystem crossing with increasing vibrational energy. Similar behavior is also observed in other van der Waals complexes of benzonitrile though the increase is less obvious. The enhancement of the intersystem crossing can be correlated with the state density of van der Waals modes in the S₁ electronic state. In case of the benzonitrile trimer and benzonitrile-Kr complex, intersystem crossing is found to be fully efficient even without vibrational excitation.     

用DVR方法研究Ar-HF和Ar-DF的振转光谱

本文用离散变量表示(DVR)方法研究了Ar-HF和Ar-DF体系的振转光谱。对这两个体系的已观测到的振转能级, 用DVR方法得到的计算值与实验结果十分吻合, 误差一般小于0.1cm^-^1, 最大偏差为0.24cm^-^1对Ar-HF的(1113)态。该研究结果与Hutson等用耦合孔道法得到的计算结果基本一致, 但对(3210)振动能级和对(3002)-(3110)态的能级分裂值, 本文计算结果更接近观测值。     

AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling

We have developed an implicit solvent effective potential (AGBNP) that is suitable for molecular dynamics simulations and high-resolution modeling. It is based on a novel implementation of the pairwise descreening Generalized Born model for the electrostatic component and a new nonpolar hydration free energy estimator. The nonpolar term consists of an estimator for the solute-solvent van der Waals dispersion energy designed to mimic the continuum solvent solute-solvent van der Waals interaction energy, in addition to a surface area term corresponding to the work of cavity formation. AGBNP makes use of a new parameter-free algorithm to calculate the scaling coefficients used in the pairwise descreening scheme to take into account atomic overlaps. The same algorithm is also used to calculate atomic surface areas. We show that excellent agreement is achieved for the GB self-energies and surface areas in comparison to accurate, but much more expensive, numerical evaluations. The parameter-free approach used in AGBNP and the sensitivity of the AGBNP model with respect to large and small conformational changes makes the model suitable for high-resolution modeling of protein loops and receptor sites as well as high-resolution prediction of the structure and thermodynamics of protein-ligand complexes. We present illustrative results for these kinds of benchmarks. The model is fully analytical with first derivatives and is computationally efficient. It has been incorporated into the IMPACT molecular simulation program.     

Van der Waals radii of metals from spectroscopic data

The lack of information about the van der Waals radii of metals can be compensated for by using the results of spectroscopic investigations of van der Waals molecules. It has been shown that the interatomic distances in these molecules obey an additive scheme if one allows for the polarization effects. The van der Waals radii of the alkali metals, Ag, Mg, Zn, Cd, Hg, B, Al, In, and Si, have been determined from the interatomic distances in their heteroatomic molecules with atoms of noble gases. Use of the obtained radii for crystal chemistry is discussed.Translated fromIzyestiya Akademil Nauk. Seriya Khimicheskaya, No. 8, pp. 1374–1378, August, 1994.     

Determination of van der Waals forces in monolayer films of lipids & biopolymers. Equation of state for two-dimensional films

Amphiphile molecules are characterized by the dual property arising from the interactions between the apolar [alkyl] and the polar part and the surrounding solvent, i.e., water. In assemblies which amphiphiles form in diverse systems, e.g., micelles, soap bubbles, monolayers or bilayers at interfaces, the attractive forces are attributed to the van der Waals forces. It is not easy to estimate the magnitude of van der Waals forces in some of these systems by any direct method.The magnitude of van der Waals forces in spread monolayers of lipids and biopolymers has been reported to be estimated from experimental data. The magnitude of these forces has been estimated by using an equation of state of a very general form, as delineated herein. In the current literature no such attempt has been reported in the analyses of these monolayers spread on aqueous surfaces. These analyses suggest that the predominant surface forces arise from van der Waals interactions, if the magnitude of electrostatic charge repulsions is weak. The equation-of-state as derived indicates that it is useful in providing information about the molecular interaction in monolayers, for both lipids and biopolymers.     

Collisional energy-transfer processes involving van der waals bonds

Collisional energy transfer to van der Waals complexes is studied via trajectory calculations. Efficient build-up of energy in the van der Waals bond and its subsequent fragmentation is a result of the flow of energy from translation through the chemically bonded molecular unit. Despite such an efficient energy flow, migration of the vibrational energy initially present in the molecular unit into the van der Waals bond is not important. V-V energy transfer between the excited molecular unit and the incident molecule is very inefficient. O₂ is chosen for the model calculations.     

Assessing Density Functionals for Describing Methane Dissociative Chemisorption on Pt(110)-(2×1) Surface

In this work, we explore the suitability of several density functionals with the generalized gradient approximation (GGA) and beyond for describing the dissociative chemisorption of methane on the reconstructed Pt(110)-(2\begin{document}$ \times $\end{document}1) surface. The bulk and surface structures of the metal, methane adsorption energy, and dissociation barrier are used to assess the functionals. A van der Waals corrected GGA functional (optPBE-vdW) and a meta-GGA functional with van der Waals correction (MS PBEl-rVV10) are selected for ab initio molecular dynamics calculations of the sticking probability. Our results suggest that the use of these two functionals may lead to a better agreement with existing experimental results, thus serving as a good starting point for future development of reliable machine-learned potential energy surfaces for the dissociation of methane on the Pt(110)-(2\begin{document}$ \times $\end{document}1) surface.     

Adsorption and dissociation of the methanethiol (CH3SH) molecule on the Fe(100) surface

These contributions explore interaction modes between the methanethoil (CH₃SH) molecule and the Fe(100) surface via implementing accurate density functional theory (DFT) calculations with the inclusion of van der Waals corrections. We consider three adsorption sites over the Fe(100) surface, namely, top(T), bridge (B), and hollow (H) sites as potential catalytic active sites for the molecular and dissociative adsorption of the CH₃SH molecule. The molecular adsorption structures are found to occupy either B or T sites with former sites holding higher stability by 0.17 eV. The inclusion of van der Waals corrections refound to slightly alter adsorption energies. For instance, adsorption energies increased by ~ 0.18 and ~ 0.21 eV for B and T structure, respectively, in reference to values obtained by the plain generalized gradient approximation (GGA) functional. A stability ordering of the dissociation products was found to follow the sequence (CH₄, S) > (CH₃, S, H) > (─SCH_3, H) > (─CH₃, SH). The differential charge density distributions were examined to underpin prominent electronic contributing factors. Direct fission of C─S bond in the CH₃SH molecule attains exothermic values in the range 2.0 to 2.1 eV. The most energetically favorable sites for the surface-mediated fission of the thiol's S─H bond correspond to the structure where the ─SCH₃ and H are both situated on hollow sites with an adsorption energy of −2.43 eV. Overall, we found that inclusion of van der Waals functional to change the binding energies more noticeably in case of dissociative adsorption structures. The results presented herein should be instrumental in efforts that aim to design stand-alone Fe desulfurization catalysts.     

Direct numerical simulation of aerosol coagulation with van der Waals forces

The van der Waals interaction energy has been computed for a large number of silver and water particle pairs in the range of 1 to 15 nm radius by first calculating the exact, retarded Hamaker factor for semi-infinite bodies and then applying a geometric correction for sphericity. The enhancement of particle collision rates has been deduced from these calculations. These values for the collisional enhancement were used in a direct numerical simulation of the coagulation of silver and water aerosols. Despite the size dependence of the van der Waals enhancement factors, the aerosol size distributions quickly attained nearly self-preserving forms.     

Determination of vibrational level spacings of van der waals molecules from the Lennard-Jones potential

An approximate expression for the eigenvalues for van der Waals molecules by use of the Lennard-Jones (12-6) potential in the WKB approximation is presented. The expression is applied to the rare gas molecules. Ar₂, Kr₂, and Xe₂ by fitting the potential function to the observed potential parameters. Calculated results of vibrational energy spacings for these molecules agree well with the experiment and other calculations which are based on numerical integration of the Schrödinger equation. For Xe₂, the energy spacing expression is used to determine the thermodynamic functions of the van der Waals bond.