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.     

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.     

Neutron scattering from a deformed “vander Waals chain”-quasi Gaussian approximation

We calculate the neutron scattering form of an affinely deformed van der Waals chain, i.e., a labeled chain embedded in a network, whose deformation behavior can be described by an effective van der Waals equation in an effective Gaussian approximation. This provides microscopic information about the deformation behavior of van der Waals networks and complements the macroscopic information given by stress-strain relations.dedicated to Prof H.-G. Kilian on occasion of his 66th birthday     

On the decisive role of finite chain extensibility and global interactions in networks

The stress-strain dependence of dry networks at unidirectional extension and compression is studied. The phenomenological van der Waals equation of state is compared with different molecular models in order to provide an interpretation of the van der Waals corrections. It is shown that the stress-strain behavior predicted by the phantom, Langevin, and constrained junction fluctuation models are altogether covered by the van der Waals approach. The relationship between the suppression of junction fluctuation parameter introduced by Dossin and Graessley and the van der Waals corrections has been worked out. The effect of junction functionality on the small strain modulus as well as on the second Mooney-Rivlin coefficient is also presented.     

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.     

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.     

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.     

二维材料范德华间隙的利用

Since their discovery, two-dimensional (2D) materials have attracted significant research attention owing to their excellent and controllable physical and chemical properties. These materials have emerged rapidly as important material system owing to their unique properties such as electricity, optics, quantum properties, and catalytic properties. 2D materials are mostly bonded by strong ionic or covalent bonds within the layers, and the layers are stacked together by van der Waals forces, thereby making it possible to peel off 2D materials with few or single layers. The weak interaction between the layers of 2D materials also enables the use of van der Waals gaps for regulating the electronic structure of the system and further optimizing the material properties. The introduction of guest atoms can significantly change the interlayer spacing of the original material and coupling strength between the layers. Also, interaction between the guest and host atom also has the potential to change the electronic structure of the original material, thereby affecting the material properties. For example, the electron structure of a host can be modified by interlayer guest atoms, and characteristics such as carrier concentration, optical transmittance, conductivity, and band gap can be tuned. Organic cations intercalated between the layers of 2D materials can produce stable superlattices, which have great potential for developing new electronic and optoelectronic devices. This method enables the modulation of the electrical, magnetic, and optical properties of the original materials, thereby establishing a family of 2D materials with widely adjustable electrical and optical properties. It is also possible to introduce some new properties to the 2D materials, such as magnetic properties and catalytic properties, by the intercalation of guest atoms. Interlayer storage, represented by lithium-ion batteries, is also an important application of 2D van der Waals gap utilization in energy storage, which has also attracted significant research attention. Herein, we review the studies conducted in recent years from the following aspects: (1) changing the layer spacing to change the interlayer coupling; (2) introducing the interaction between guest and host atoms to change the physico-chemical properties of raw materials; (3) introducing the guest substances to obtain new properties; and (4) interlayer energy storage. We systematically describe various interlayer optimization methods of 2D van der Waals gaps and their effects on the physical and chemical properties of synthetic materials, and suggest the direction of further development and utilization of 2D van der Waals gaps.     

On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy

Implicit solvent hydration free energy models are an important component of most modern computational methods aimed at protein structure prediction, binding affinity prediction, and modeling of conformational equilibria. The nonpolar component of the hydration free energy, consisting of a repulsive cavity term and an attractive van der Waals solute-solvent interaction term, is often modeled using estimators based on the solvent exposed solute surface area. In this paper, we analyze the accuracy of linear surface area models for predicting the van der Waals solute-solvent interaction energies of native and non-native protein conformations, peptides and small molecules, and the desolvation penalty of protein-protein and protein-ligand binding complexes. The target values are obtained from explicit solvent simulations and from a continuum solvent van der Waals interaction energy model. The results indicate that the standard surface area model, while useful on a coarse-grained scale, may not be accurate or transferable enough for high resolution modeling studies of protein folding and binding. The continuum model constructed in the course of this study provides one path for the development of a computationally efficient implicit solvent nonpolar hydration free energy estimator suitable for high-resolution structural and thermodynamic modeling of biological macromolecules.