Van der Waals Radii of Hydrogen in Gas-Phase and Condensed Molecules

Van der Waalsa radii of hydrogen in the different gas-phase and condensed molecules are determined and shown that a value of the van der Waals radius depends on the effective charge of the H atom. Is described also the van der Waals anisotropy of H in some molecules.     

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.     

A Novel Charge Distribution Method for the Numerical Solution of the Poisson-Boltzmann Equation

A charge distribution method to solve the linearized Poisson-Boltzmann equation numerically through use of the finite difference method is proposed, The molecules are mapped by 1 and 0.25 Å grid systems. Each atom is modeled as a point charge and a weighted sum of point charge of every atom that is within its van der Waals radius with a grid point is assigned to the grid point. Depending on a charge distribution factor determined, the charge/grid (q/g) ratio calculated for every grid point inside a molecule can be fixed to a certain value. A grid size of the I Å grid is often fixed for mapping a small or large molecular system. Solvation energies for a group of small molecules calculated by the method arc comparable with those calculated by other methods and the grid energy calculated by the method is also reduced.     

Method for Smoothing the Boundaries of the Van Der Waals Models of Molecules

A geometrical method is suggested for representing a molecule by a smoothed region. The effective volume and surface area are calculated, which results in more adequate proportionality of interactant molecules compared to the classical van der Waals models.     

Adsorption of square and rectangular plate-like molecules on a planar surface

A mean-field statistical thermodynamic analysis of monolayer adsorption of rigid square and rectangular plate-like molecules on a homogeneous planar surface is developed. The analysis is simplified by only considering facewise and edgewise modes of adsorption in restricted orthogonal orientations parallel to the surface. The free energy density, adsorbate population distribution and surface spreading pressure are obtained as a function of adsorbate density and compared for square plate molecules using three different sequences of adsorbate molecule placement on the surface to evaluate the configurational degeneracy. It is found that edgewise adsorbed molecules can be anisotropically ordered if the edge length of square and rectangular plate-like molecules exceeds three length units in the absence of anisotropic dispersion interactions. If intermolecular dispersion interactions are present and of sufficient strength, the spreading pressure-density isotherms can exhibit one or two van der Waals loops for square plate molecules with three van der Waals loops possible for rectangular plate adsorbate molecules. The phase transitions for the adsorbed monolayer corresponding to the appearance of these van der Waals loops are discussed.     

Importance of van der Waals Interactions in QM/MM Simulations

The importance of accurately treating van der Waals interactions between the quantum mechanical (QM) and molecular mechanical (MM) atoms in hybrid QM/MM simulations has been investigated systematically. First, a set of van der Waals (vdW) parameters was optimized for an approximate density functional method, the self-consistent charge-tight binding density functional (SCC-DFTB) approach, based on small hydrogen-bonding clusters. The sensitivity of condensed phase observables to the SCC-DFTB vdW parameters was then quantitatively investigated by SCC-DFTB/MM simulations of several model systems using the optimized set and two sets of extreme vdW parameters selected from the CHARMM22 forcefield. The model systems include a model FAD molecule in solution and a solvated enediolate, and the properties studied include the radial distribution functions of water molecules around the solute (model FAD and enediolate), the reduction potential of the model FAD and the potential of mean force for an intramolecular proton transfer in the enediolate. Although there are noticeable differences between parameter sets for gas-phase clusters and solvent structures around the solute, thermodynamic quantities in the condensed phase (e.g., reduction potential and potential of mean force) were found to be less sensitive to the numerical values of vdW parameters. The differences between SCC-DFTB/MM results with the three vdW parameter sets for SCC-DFTB atoms were explained in terms of the effects of the parameter set on solvation. The current study has made it clear that efforts in improving the reliability of QM/MM methods for energetical properties in the condensed phase should focus on components other than van der Waals interactions between QM and MM atoms.     

An electric field-based approach for quantifying effective volumes and radii of chemically affected space

Chemical shape and size play a critical role in chemistry. The van der Waals (vdW) radius, a familiar manifold used to quantify size by assuming overlapping spheres, provides rapid estimates of size in atoms, molecules, and materials. However, the vdW method may be too rigid to describe highly polarized systems and chemical species that stray from spherical atomistic environments. To deal with these exotic chemistries, numerous alternate methods based on electron density have been presented. While each boasts inherent generality, all define the size of a chemical system, in one way or another, by its electron density. Herein, we revisit the longstanding problem of assessing sizes of atoms and molecules, instead through examination of the local electric field produced by them. While conceptually different than nuclei-centered methods like that of van der Waals, the field assesses chemically affected volumes. This approach implicitly accounts for long-range fields in highly polar systems and predicts that cations should affect more space than neutral counterparts.

Computing atomic and molecular volumes from DFT and ab initio-based electric fields.     

The structure of phosphacymantrene

Proton NMR spectra of phosphacymantrene (π-phospholyl manganese tricarbonyl) orientated in the nematic phases of liquid crystals have been investigated. The derived H-H and H-P direct dipolar coupling constants have been used to determine the relative proton-proton and proton-phosphorus distances. A comparison of the geometrical data of various 5-membered aromatic heterocycles shows that the relative distances between the protons closest to the heteroatom increase with the van der Waals radius of the heteroatom. The results suggest that NMR spectroscopy of orientated molecules can be used to determine van der Waals radii.     

Orientation of a benzene molecule inside a carbon nanotube

Benzene molecules confined in carbon nanotubes of varying radii are employed as semiconductors in electronic nanodevices, and their orientation determines the electrical properties of the system. In this paper, we investigate the interaction energy of all the possible configurations of a benzene molecule inside various carbon nanotubes and then we determine the equilibrium configuration. We adopt the continuous approach together with the semi-empirical Lennard-Jones potential function to model van der Waals interaction between a benzene molecule and a carbon nanotube. This approach results in an analytical expression, which accurately approximates the interaction energy and can be readily used to generate numerical data. We find that horizontal, tilted and perpendicular configurations on the axis of the carbon nanotube are all possible equilibrium configurations of the benzene molecule when the radius of the carbon nanotube is less than 5.580 Å. However, when the radius of the carbon nanotube is larger than 5.580 Å an offset horizontal orientation is the only possible equilibrium configuration of the benzene molecule. In the limiting case, the orientation of a benzene molecule on a graphene sheet can be derived simply by letting the radius of the carbon nanotube tend to infinity.     

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.     

Multiscale Approach to the Study of the Electronic Properties of Two Thiophene Curcuminoid Molecules

We studied the electronic and conductance properties of two thiophene–curcuminoid molecules, 2‐thphCCM ( 1 ) and 3‐thphCCM ( 2 ), in which the only structural difference is the position of the sulfur atoms in the thiophene terminal groups. We used electrochemical techniques as well as UV/Vis absorption studies to obtain the values of the HOMO–LUMO band gap energies, showing that molecule 1 has lower values than 2 . Theoretical calculations show the same trend. Self‐assembled monolayers (SAMs) of these molecules were studied by using electrochemistry, showing that the interaction with gold reduces drastically the HOMO–LUMO gap in both molecules to almost the same value. Single‐molecule conductance measurements show that molecule 2 has two different conductance values, whereas molecule 1 exhibits only one. Based on theoretical calculations, we conclude that the lowest conductance value, similar in both molecules, corresponds to a van der Waals interaction between the thiophene ring and the electrodes. The one order of magnitude higher conductance value for molecule 2 corresponds to a coordinate (dative covalent) interaction between the sulfur atoms and the gold electrodes.     

Modeling van der Waals interactions between proteins and inorganic surfaces from time-dependent density functional theory calculations

In this work we show how the ab initio determination of van der Waals coefficients within time-dependent density functional theory can be used to build efficient and accurate atomistic models that describe the long-range interactions of proteins with other proteins and of proteins with semi-conducting surfaces. The model parameters are fitted so that they reproduce the ab initio van der Waals coefficients of amino acids and dipeptides. We then assess the quality of our results by comparing ab initio van der Waals coefficients for larger peptides with the coefficients yielded by the models. The different sets of parameters can be easily incorporated in current empirical force field methods, thus providing an essential ingredient for molecular dynamics simulations of proteins close to surfaces.     

The Effect of van der Waals Forces on the Deposition of Highly Dispersed Aerosol Particles on Ultrafine Fibers

The effect of van der Waals forces on the collection of highly dispersed aerosol particles with ultrafine fiber filters was studied theoretically. The capture coefficient was found from the numerical solution of the equation of convective diffusion with the account of the particle size, the effect of van der Waals forces acting between a particle and a fiber, and the gas slip effect at the surface of ultrafine fibers. It was shown that allowance being made for van der Waals forces markedly affects the capture coefficient within the maximal particle penetration range and that the radius of the most penetrating particles decreases with the rising effect of these forces.     

Modeling and conformation analysis of β-cyclodextrin complexes

Summary A series of -cyclodextrin complexes containing various guest molecules was studied using computer-aided molecular modeling and conformation analysis techniques. The geometry of each complex was studied using crystallographic data. The positions of the glycosidic O4 atoms indicate that the -cyclodextrin molecules are elliptically distorted. This distortion can be related to the van der Waals volume of the guest molecules. This correlation is different for aromatic and non-aromatic guest compounds. Rigid body docking experiments demonstrated that in crystal structures the guest molecule occupies a position in the cavity of nearly minimum interaction energy when there are no other molecules having interactions with the guest molecule. From the crystallographic data several rules could be deduced which seem to determine the conformation of -cyclodextrin molecules in complexes. A procedure was developed to construct -cyclodextrin molecules that are able to encompass guest molecules having a given van der Waals volume.     

Molecular polarizability of organic compounds and their complexes: LIX. Molar volumes, intrinsic atomic solvation radii, and spatial structures of certain conformationally flexible compounds in solutions

The molar volumes and structures in individual liquids and solutions of a series of conformationally flexible compounds, such as alkanes and diaryl-substituted systems with sp ³-hybridized bridging atoms, were analyzed in terms of intrinsic solvation radii of atoms constituting the molecule. Intrinsic solvation atomic radii were determined for various molecules to show that they are larger than the van der Waals radii of the same atoms. An approach to parametrization of the intrinsic solvation radii of atoms constituting a molecule, using appropriate model compounds, was proposed. From the resulting values of intrinsic atomic solvation radii, the possible conformations of a series of diphenylmethanes, diphenylsilanes, diphenyl sulfides, diphenyl sulfoxides, and diphenyl sulfones in solutions were assessed.     

Photodynamics of the excited states of trimethylamine in a supersonic beam

The photophysics of trimethylamine (TMA) and rare gas-TMA van der Waals molecules has been studied under supersonic beam conditions. Dual exponential fluorescence decays observed for excitation of the second excited singlet state (S₂) are attributed to a novel S₂-S₁ relaxation induced by the vibrational predissociation of van der Waals molecules.     

Simple model for DNA adsorption onto a mica surface in 1:1 and 2:1 electrolyte solutions

We propose a simple theory of interactions between like-charged polyelectrolyte and a surface based on a mean-field Derjaguin-Landau-Verwey-Overbeek approach. It predicts that the van der Waals attractive interactions are responsible for irreversible physisorption of polyelectrolytes onto charged surfaces. We show that monovalent salts contribute significantly to repulsive interactions, while enhancing the attraction very slightly. The effect of the divalent counterions is reverse. Therefore, to achieve the adsorption, the overall repulsion due to 1:1 electrolyte should be counterbalanced by the stronger van der Waals attraction due to the presence of doubly charged counterions in solution. The theory has been validated experimentally against its ability to predict the minimum polymer/surface interaction energy required for the adsorption using DNA/mica in NaCl, MgCl2, and NiCl2 solutions as a test system. The theory explains the mechanism of linear DNA adsorption to a mica surface for different solvent compositions and can be used as a tool for predicting the optimum conditions for AFM experiments on linear polymer systems. The model can also be used to make general conclusions on the conformation of polymer molecules on a surface. We have shown for the DNA/mica surface system that when the adsorption of DNA is mostly governed by long-range van der Waals forces the molecule adopts an ideal 2D conformation. When the adsorption is mostly due to short-range ion-correlation forces, DNA will appear 3D --> 2D projected in agreement with experimental data.     

Effects of pH on the interactions and conformation of bovine serum albumin: comparison between chemical force microscopy and small-angle neutron scattering

The conformation of bovine serum albumin (BSA), as well as its interactions with negatively charged mica surfaces in saline solutions of different pH values, have been studied by small-angle neutron scattering (SANS) and chemical force microscopy (CFM), respectively. A new approach to extract the contribution of elementary interactions from the statistically averaged force-extension curves through self-consistent fitting was proposed and used to understand the effects of pH on the interactions and conformation of BSA in saline solutions. When pH increases, the SANS results reveal that the sizes of BSA molecules increase slightly, while the statistical analysis of the CFM results shows that the averaged pull-off force for the elongation monotonously decreases. The decrease of pull-off force with the increase of pH results from the decrease in the strength of hydrogen bonding and the number of interaction pairs, as well as the slight increase of the strength of van der Waals interaction. When pH approaches the isoelectric point (pI) of BSA, results from both SANS and CFM suggest a loss of long-range interactions in BSA molecules. Our results also suggest that the force-extension curve is mainly contributed by the van der Waals interaction. The combination of SANS and CFM provides new insight to understand the interactions and conformation of BSA molecules.