Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects

This article describes a number of algorithms that are designed to improve both the efficiency and accuracy of finite difference solutions to the Poisson-Boltzmann equation (the FDPB method) and to extend its range of application. The algorithms are incorporated in the DelPhi program. The first algorithm involves an efficient and accurate semianalytical method to map the molecular surface of a molecule onto a three-dimensional lattice. This method constitutes a significant improvement over existing methods in terms of its combination of speed and accuracy. The DelPhi program has also been expanded to allow the definition of geometrical objects such as spheres, cylinders, cones, and parallelepipeds, which can be used to describe a system that may also include a standard atomic level depiction of molecules. Each object can have a different dielectric constant and a different surface or volume charge distribution. The improved definition of the surface leads to increased precision in the numerical solutions of the PB equation that are obtained. A further improvement in the precision of solvation energy calculations is obtained from a procedure that calculates induced surface charges from the FDPB solutions and then uses these charges in the calculation of reaction field energies. The program allows for finite difference grids of large dimension; currently a maximum of 571(3) can be used on molecules containing several thousand atoms and charges. As described elsewhere, DelPhi can also treat mixed salt systems containing mono- and divalent ions and provide electrostatic free energies as defined by the nonlinear PB equation.     

Effects of Adsorbed Polyaniline on Redox Processes on As(2)O(3) Surfaces

Polyaniline deposited on As(2)O(3) surface resulted in a new material, which was characterized by infrared spectoscopy, thermogravimetry, differential scanning calorimetry, scanning electron microscopy, X-ray diffraction, and cyclic voltammetry. The mass percentage of polymer deposited on oxide surface is approximately 13%. The scanning electron microscopy images as well as the X-ray diffraction patterns provided conclusive evidence that the oxide surface is coated by the polymer. The cyclic voltammograms of the polyaniline adsorbed on As(2)O(3) surface showed that the adsorbate exerts remarkable effects on redox processes on this oxide. The pure oxide exhibited two oxidation/reduction peaks at 0.25/-0.06 and 0.47/-0.25 V attributed tentatively to the processes As(2)O(3)(s)+6H(+)+6e(-)=2As(s)+3H(2)O and As(s)+3H(+)+3e(-)=AsH(3)(g), respectively. The polyaniline-coated sample exhibited a better-defined voltammogram in which the first oxidation peak of the oxide had its intensity increased about four times. Copyright 2000 Academic Press.     

ON THE MECHANISM OF WAVELENGTH REGULATION IN VISUAL PIGMENTS

Abstract— The contributions of different factors that might be responsible for the 500 nm absorption maximum of bovine rhodopsin are evaluated in detail. These include: (1) electrostatic interactions between the chromophore and a charged amino acid on the apoprotein; (2) exciton interactions with aromatic amino acids; (3) twisting about single bonds which have considerable double bond character; (4) weak interactions between the Schiff base and a putative counter-ion. Analysis of these mechanisms in terms of theoretical and experimental results suggests that(2–4) are all capable of contributing to the protein induced spectral shifts. However, the "external point charge" model proposed previously, i.e. mechanism (1), appears to provide the crucial interaction. In this paper, the theoretical basis for this model is discussed in detail. The model is briefly evaluated in light of the amino-acid sequence of bovine rhodopsin and possible implications for other visual pigments are considered.     

Natural orbitals of s-cis-butadiene and their relation to photochemical cyclization

Natural orbitals of the three lowest single states of s-cis-butadiene are calculated by CNDO/S. Under the disrotatory closure of s-cis-butadiene to cyclobutene, the 2 ¹A₁ natural orbitals are correlated differently from that described by the usual orbital diagram. The natural orbital correlations account for the main features of the potential surface.