Van Der Waals Molecular Surface Research Articles

Phosphorus-Enhanced and Calcium-Retarded Transport of Ferrihydrite Colloid: Mechanism of Electrostatic Potential Changes Regulated via Adsorption Speciation.

The transport of ferrihydrite colloid (FHC) through porous media is influenced by anions (e.g., PO43-) and cations (e.g., Ca2+) in the aqueous environment. This study investigated the cotransport of FHC with P and P/Ca in saturated sand columns. The results showed that P adsorption enhanced FHC transport, whereas Ca loaded onto P-FHC retarded FHC transport. Phosphate adsorption provided a negative potential on the FHC, while Ca added to P-FHC led to electrostatic screening, compression of the electric double layer, and formation of Ca5(PO4)3OH followed by heteroaggregation at pH ≥ 6.0. The monodentate and bidentate P surface complexes coexisted, and Ca mainly formed a ternary complex with bidentate P (≡(FeO)2PO2Ca). The unprotonation bidentate P at the Stern 1-plane had a considerable negative potential at the Van der Waals molecular surface. Extending the potential effect to the outer layer of FHC, the potential at the Stern 2-plane and zeta potential exhibited a corresponding change, resulting in a change in FHC mobility, which was validated by comparison of experimental results, DFT calculations, and CD-MUSIC models. Our results highlighted the influence of P and Ca on FHC transport and elucidated their interaction mechanisms based on quantum chemistry and colloidal chemical interface reactions.

A BOX-MODEL APPROACH TO MOLECULAR SHAPE

In this work, using the length-width-height ratios of a rectangular box in which the molecule under study is enclosed, two descriptors for the characterization of molecular shape are introduced. The molecular shape analysis of the set of molecules under study is facilitated by the introduction of a diagram where the extreme cases (i.e. cubic-box, prolate-box and oblate-box) are clearly located. The method is illustrated by the analysis of fifty molecules including normal alkanes, acenes, alkynes, oblate molecules and the eighteen octane isomers. The geometry of each molecule was optimized by AM1 semiempirical method, and van der Waals molecular surface was used to define the molecular shape contour. The length, the width, and the height of the enclosing box were extracted using VEGA ZZ software. A regular behaviour of the shape descriptors for homologous series was observed. Finally, using the present descriptors, a molecular shape similarity analysis of the octane isomer molecules was included.

Quantitative relationships for the prediction of the vapor pressure of some hydrocarbons from the van der Waals molecular surface

A quantitative structure - property relationship (QSPR) modeling of vapor pressure at 298.15 K, expressed as log (VP / Pa) was performed for a series of 84 hydrocarbons (63 alkanes and 21 cycloalkanes) using the van der Waals (vdW) surface area, SW/Å2, calculated by the Monte Carlo method, as the molecular descriptor. The QSPR model developed from the subset of 63 alkanes (C1-C16), deemed as the training set, was successfully used for the prediction of the log (VP / Pa) values of the 21 cycloalkanes, which was the external prediction (test) subset. A QSPR model was also developed for a series composed of all 84 hydrocarbons. Both QSPR models were statistically tested for their ability to fit the data and for prediction. The results showed that the vdW molecular surface used as molecular descriptor (MD) explains the variance of the majority of the log (VP / Pa) values in this series of 84 hydrocarbons. This MD describes very well the intermolecular forces that hold neutral molecules together. The clear physical meaning of the molecular surface values, SW/Å2, could explain the success of the QSPR models obtained with a single structural molecular descriptor.

QSPR Studies on Impact Sensitivities of High Energy Density Molecules

Impact sensitivity, one of the most important screening factors for novel high energy density materials (HEDMs), was predicted by use of quantitative structure-property relationship (QSPR) based on the electrostatic potential (ESP) values calculated on the van der Waals molecular surface (MSEP). Among various 3D descriptors derived from MSEP, we utilized total and positive variance of MSEP, and devised a new QSPR equation by combining three other parameters. We employed 37 HEDMs bearing a benzene scaffold and nitro substituents, which were also utilized by Rice and Hare. All the molecular structures were optimized at the B3LYP/6-31G(d) level of theory and confirmed as minima by the frequency calculations. Our new QSPR equation provided a good result to predict the impact sensitivities of the molecules in the training set including zwitterionic molecules.

Molecular recognition of polycyclic aromatic hydrocarbons by pyrene-imprinted microspheres

Pyrene-imprinted microbeads that display molecular recognition towards polyaromatic hydrocarbons (PAHs) were obtained by the aqueous suspension thermopolymerization of a mixture of template, 4-vinylpyridine and divinylbenzene in the molar ratio of 1:8:40. The microbeads were packed into an HPLC column and the retention behaviour of pyrene in the presence of eluents of increasing polarity was investigated by measuring the binding capacity and the imprinting factor. Selectivity was evaluated by eluting pyrene and 22 other related PAHs in the HPLC column when equilibrated with acetonitrile-dichloromethane 4:1 (v/v). Twelve molecular descriptors were calculated for each PAH molecule: MW, the molecular weight; SAS, the solvent-accessible molecular surface area; Svdw, the van der Waals molecular surface area; Vol, the van der Waals molecular volume; MOv, the molecular ovality; RG, the radius of gyration; B/L, the breadth-to-length ratio; micro(2), the square of the total dipole moment; HOMO, the highest occupied molecular orbital; LUMO, the lowest unoccupied molecular orbital; Deltaorb, the absolute value of the difference between the HOMO and LUMO; log P, the logarithm of the n-octanol-water partition coefficient. Quantitative structure-retention relationships between the logarithm of the capacity factors and these descriptors were searched for using a multiple linear regression (MLR) method. The best regression models obtained showed that the capacity factor correlated well with those molecular descriptors which had structural character, such as logP, while the effect of the molecular descriptors with electronic character was negligible. The results obtained indicate that the molecular recognition of PAHs by the imprinted polymer is controlled by the shape and dimension of the binding sites through hydrophobic interactions.

Theoretical study of antagonists and inhibitors of mammalian adenosine deaminase. II. Isomeric aza-deazaanalogues of adenosine

Isomeric aza-deazaanalogues of adenosine and their N1-protonated forms (except for that of 8-aza-1-deazaadenosine) were studied by computer modeling to find a relationship between their molecular structures and the properties as substrates for the mammalian adenosine deaminase. The atomic charge distribution and maps of the electrostatic potential around their van der Waals molecular surface were calculated using the ab initio STO-3G method. The conformational studies were carried out by the MM+ method of molecular mechanics. The previously proposed mechanism of the substrate acceptance in the active site of mammalian adenosine deaminase was refined, and the potential substrate properties were predicted for two previously unstudied adenosine analogues, 5-aza-9-deazaadenosine and 8-aza-3-deazaadenosine.

Theoretical study of antagonists and inhibitors of mammalian adenosine deaminase. I. Adenosine and its aza- and deaza-analogs

Aza- and deazaanalogues of adenosine, including their 1-protonated forms (except for that of 1-deazaadenosine), were studied by computer computation to find a relationship between their molecular structures and substrate properties for the mammalian adenosine deaminase. The atomic charge distribution and maps of the electrostatic potential around their van der Waals molecular surface were calculated for these compounds using the ab initio STO-3G method. The conformational studies were carried out by the MM+ method of molecular mechanics. The mechanism that determines the substrate selectivity of mammalian adenosine deaminase is discussed. The English version of the paper: Russian Journal of Bioorganic Chemistry, 2002, vol. 28, no. 4; see also http://www.maik.ru.

Occluded molecular surface analysis of ligand-macromolecule contacts: application to HIV-1 protease-inhibitor complexes.

Herein is described a method of quantifying and visualizing ligand-macromolecule contacts with the occluded surface algorithm by utilizing Connolly's van der Waals molecular surface dots together with the associated normals, to scoop out surrounding macromolecule atoms within a distance of 6.4 A from any ligand atom. On the basis of the intersections of surface normals with the van der Waals spheres of surrounding macromolecule atoms, the van der Waals molecular surface area for each atom is divided into occluded and nonoccluded surface areas. Also, we calculate a packing parameter for each occluded surface, measuring the closeness of the occluded surface against the macromolecule atom in contact. From the partial charges of ligand and macromolecule atoms and the occluded and nonoccluded surface areas due to the contact, we were able to identify favorable and unfavorable contacts. From the value of occluded surface constant, nonoccluded surface constant, and solvent-exposed constant for ligands, we qualitatively rank order the binding of ligands to the same target. From the individual parameters, group parameters for groups of atoms in a ligand or for each residue in a ligand-binding pocket of a macromolecule could be calculated. The group and the residue-based parameters could be used in structure-based ligand design and protein engineering experiments. In this paper, we present our analysis of ligand-macromolecule contacts, using five X-ray crystal structures of HIV-1 protease-ligand complexes.

Hydrogen Bonding and Molecular Surface Shape Complementarity as a Basis for Protein Docking

A geometric docking algorithm based upon correlation analysis for quantification of geometric complementarity between protein molecular surfaces in close interfacial contact has been developed by a detailed optimization of the conformational search of the algorithm. In order to reduce the entire conformation space search required by the method a physico-chemical pre-filter of conformation space has been developed based upon the a prioriassumption that two or more intermolecular hydrogen bonds are intrinsic to the mechanism of binding within protein complexes. Donor sites are defined spatially and directionally by the positions of explicitly calculated donor hydrogen atoms, and the vector space within a defined range about the donor atom-hydrogen atom bond vector. Acceptor sites are represented spatially and directionally by the van der Waals molecular surface points having normal vectors within a predefined range of vector space about the acceptor atom covalent bond vector(s). Geometric conditions necessary for the simultaneous hydrogen bonding interaction between both sites of functionally congruent hydrogen bonding site pairs, located on the individual proteins, are then tested on the basis of a transformation invariant parameterization of the site pair spatial and directional properties. Sterically acceptable conformations defined by interaction of functionally, spatially, and directionally compatable site pairs are then refined to a maximum contact of complementary contact surfaces using the simplex method for the angular search and correlation techniques for the translational search. The utility of the spatial and directional properties of hydrogen bonding donor and acceptor sites for the identification of candidate docking conformations is demonstrated by the reliable preliminary reduction of conformation space, the improved geometric ranking of the minimum RMS conformations of some complexes and the overall reduction of CPU time obtained.

Reproduction of ab initio electrostatic potential with classical fractional point charges.

New additional charge sets, which were added to correct the electrostatic potential (ESP) values on the van der Waals molecular surface using Mulliken net atomic charges, were found to reproduce ab initio ESP with the STO-3G basis set. The charge sets were obtained for fundamental small molecules (water, ammonia. methane. ethane, and benzene). Lone pair regions of oxygen and nitrogen atoms show remarkable improvement, while pi electrons do not contribute much to ESP. The present work opens a way for treating large molecules of biological interest.