Maps of the electrostatic potentials at the basal plane of talc and pyrophyllite, computed using a two-dimensional Ewald lattice-sum, reveal the effects caused by structural distortion of the phyllosilicate layer. Rotation and tilting of basal tetrahedra in phyllosilicates dramatically perturb the electrostatic potential near the (001) surface. A potential high exists at the center of each six-fold ring of the talc (001) surface. Concerted counter-rotations of basal tetrahedra by 10°, as are typical in pyrophyllite, cause the potential lows above basal oxygens rotated into the ring to overlap, eliminating the ring-centered potential highs. Expansion of the vacant site in dioctahedral minerals tilts the basal tetrahedra by 4° and moves one-third of the basal oxygens about 0.2 Å toward the center of each phyllosilicate layer and away from the (001) surface, thereby producing corrugations of the basal surface. This shift dramatically reduces the contribution of these displaced basal oxygens to the (001) surface potential. Rotation and tilting of basal tetrahedra may influence the arrangement of interlayer water molecules on smectites and other swelling phyllosilicates by the effect that these distortions have on the (001) surface potential.

A fundamental property of electrostatic potentials is their additivity. This study demonstrates that the electrostatic potential of a negatively charged, cation-substituted phyllosilicate layer can be represented as the sum of two potentials. Viewing cation substitution as a defect, one potential is derived from the atoms in a charge-neutral, unsubstituted layer such as pyrophyllite or talc. The “neutral-layer” potential rapidly decays to zero with distance from the layer and is determined primarily by the atoms in the first two atomic planes parallel to the (001) surface, i.e., the basal oxygens and tetrahedral cations. The second component, characterized as a “defect” potential, is a long-range potential derived from cation-substitution. The model used to compute the electrostatic potentials, a two-dimensional Ewald lattice sum, represents the atoms of a single phyllosilicate layer as point charges.

This paper describes structural models of four pyrophyllite edge faces: {010}, {110}, {100}, and {130}. Water molecules chemisorbed to Lewis acid sites stabilize edge faces both crystallochemically and electrostatically. The detailed assignment of protons to surface oxygens and the orientation of OH bond-vectors both influence the surface Coulomb energy.

The geometry chosen for the electrostatic calculations was infinite pyrophyllite ribbon the thickness of a single phyllosilicate layer and the width of 50 to 70 unit cells. Such a phyllosilicate ribbon has only two edges, a top and bottom, which were simulated using the edge-face models mentioned above. About 94% of the surface Coulomb energy is confined to the edge-face repeat unit. The surface Coulomb energies of the four edge faces are on the order of 2–3 nJ/m, varying ± 1 nJ/m with proton assignment. The Coulomb potential, measured either within the layer or parallel to the layer, has a distinct negative trend near the edge face that can be traced to chemisorbed water molecules. Finally, the correlation between proton Coulomb potentials at the edge face and the coordination environment of the protons is poor, obscured by long-range interactions.

The self-consistent propagation of electrical impulses and of the accompanying distortions of the electron surface in the framework of a cold plasma model with a sharp boundary has been described with help of a derived system of two equations. The method of ‘shallow water theory’ has been applied for the case of bounded plasma and deriving an equation with which to link the spatial and temporal structures and evolution of the boundary curvature and the surface charge. Under certain conditions, such perturbations can propagate along the boundary without changing their shape for a long distance. An approximate analytical solution has been found, and numerical calculations have been performed. Mutual connections between basic parameters of the considered perturbations (velocity components, electrostatic field, etc.) have been presented.

Here we report a web server, the DelPhi web server, which utilizes DelPhi program to calculate electrostatic energies and the corresponding electrostatic potential and ionic distributions, and dielectric map. The server provides extra services to fix structural defects, as missing atoms in the structural file and allows for generation of missing hydrogen atoms. The hydrogen placement and the corresponding DelPhi calculations can be done with user selected force field parameters being either Charmm22, Amber98 or OPLS. Upon completion of the calculations, the user is given option to download fixed and protonated structural file, together with the parameter and Delphi output files for further analysis. Utilizing Jmol viewer, the user can see the corresponding structural file, to manipulate it and to change the presentation. In addition, if the potential map is requested to be calculated, the potential can be mapped onto the molecule surface. The DelPhi web server is available from http://compbio.clemson.edu/delphi_webserver.

Pasteuria penetrans is a bacterium with the potential to control plant-parasitic nematode populations; the mechanism of spore adhesion, however, is poorly understood. Attachment assays were performed in media supplemented with various concentrations of fibronectin and in the presence and absence of KSCN which modulates hydrophobic interactions. A reduction in the strength of the hydrophobic effect prevented spores from binding to the cuticle as did 20 μg/ml fibronectin. It was also shown directly utilizing a newly-developed technique which utilizes 3-hexadecanoyl-7-hydro-coumarin as an indicator of the fibronectin binding to the spore surface that the presence of KSCN prohibited binding. This effect was interpreted to indicate that the reduction of binding was the direct result of the influence of hydrophobic interactions between the fibronectin and the spore surface. Western blot analysis of cuticle extracts of Meloidogyne incognita and Caenorhabditis elegans revealed small amounts of fibronectin to be present. Fibronectin, or a similar receptor, present in the cuticle could be responsible for the adhesion of P. penetrans by hydrophobic interactions.

Amorphous 1–2-nm-wide intergranular films in ceramics dictate many of their properties. The detailed investigation of structure and chemistry of these films pushes the limits of today's transmission electron microscopy. We report on the reconstruction of the one-dimensional potential profile across the film from an experimentally acquired tilt series of energy-filtered electron diffraction patterns. Along with the potential profile, the specimen thickness, film orientation with respect to the grain lattice and specimen surface, and the absolute specimen orientation with respect to the laboratory frame of reference are retrieved.

Off-axis electron holography is used to measure electrostatic potential profiles across a silicon p-n junction, which has been prepared for examination in the transmission electron microscope (TEM) in two different specimen geometries using focused ion beam (FIB) milling. Results are obtained both from a conventional unbiased FIB-milled sample and using a novel sample geometry that allows a reverse bias to be applied to an FIB-milled sample in situ in the TEM. Computer simulations are fitted to the results to assess the effect of TEM specimen preparation on the charge density and the electrostatic potential in the thin sample.

Specific aminoacylation by aminoacyl-tRNA synthetases requires accurate recognition of cognate tRNA substrates. In the case of alanyl-tRNA synthetase (AlaRS), RNA duplexes that mimic the acceptor stem of the tRNA are efficient substrates for aminoacylation in vitro. It was previously shown that recognition by AlaRS is severely affected by a simple base pair transversion of the G2:C71 pair at the second position in the RNA helix. In this study, we determined the aminoacylation efficiencies of 50 variants of the tRNAAla acceptor stem containing substitutions at the 2:71 position. We find that there is not a single functional group of the wild-type G2:C71 base pair that is critical for positive recognition. Rather, we observed that base-pair orientation plays an important role in recognition. In particular, pyrimidine2:purine71 combinations generally resulted in decreased aminoacylation efficiency compared to the corresponding purine:pyrimidine pair. Moreover, the activity of a pyrimidine:purine variant could be partially restored by the presence of a major groove amino group at position 71. In an attempt to understand this result further, dielectric continuum electrostatic calculations were carried out, in some cases with additional inclusion of van der Waals interaction energies, to determine interaction potentials of the wild-type duplexAla and seven 2:71 variants. This analysis revealed a positive correlation between major groove negative electrostatic potential in the vicinity of the 3:70 base pair and measured aminoacylation efficiency.

Blue copper proteins are type-I copper-containing redox proteins whose role is to shuttle electrons from an electron donor to an electron acceptor in bacteria and plants. A large amount of experimental data is available on blue copper proteins; however, their functional characterization is hindered by the complexity of redox processes in biological systems. We describe here the application of a semiquantitative method based on a comparative analysis of molecular interaction fields to gain insights into the recognition properties of blue copper proteins. Molecular electrostatic and hydrophobic potentials were computed and compared for a set of 33 experimentally-determined structures of proteins from seven blue copper subfamilies, and the results were quantified by means of similarity indices. The analysis provides a classification of the blue copper proteins and shows that (1) comparison of the molecular electrostatic potentials provides useful information complementary to that highlighted by sequence analysis; (2) similarities in recognition properties can be detected for proteins belonging to different subfamilies, such as amicyanins and pseudoazurins, that may be isofunctional proteins; (3) dissimilarities in interaction properties, consistent with experimentally different binding specificities, may be observed between proteins belonging to the same subfamily, such as cyanobacterial and eukaryotic plastocyanins; (4) proteins with low sequence identity, such as azurins and pseudoazurins, can have sufficient similarity to bind to similar electron donors and acceptors while having different binding specificity profiles.