We describe a three-stage procedure to analyze the dependence of Poisson Boltzmann calculations on the shape, size and geometry of the boundary between solute and solvent. Our study is carried out within the boundary element formalism, but our results are also of interest to finite difference techniques of Poisson Boltzmann calculations. At first, we identify the critical size of the geometrica...

Einstein’s unified field theory is extended by the addition of matter terms in the form of a symmetric energy tensor and of two conserved currents. From the field equations and from the conservation identities emerges the picture of a gravoelectrodynamics in a dynamically polarizable Riemannian continuum. Through an approximate calculation exploiting this dynamical polarizability it is argued t...

We present the theory and implementation for computing the (free) energy and its analytical gradients with the Brueckner doubles (BD) coupled cluster method in solution, in combination with the polarizable continuum model of solvation (PCM). The complete model, called PTED, and an efficient approximation, called PTE, are introduced and tested with numerical examples. Implementation details are ...

An interface between semi-empirical methods and the polarized continuum model (PCM) of solvation successfully implemented into GAMESS following the approach by Chudinov et al (Chem. Phys. 1992, 160, 41). The interface includes energy gradients and is parallelized. For large molecules such as ubiquitin a reasonable speedup (up to a factor of six) is observed for up to 16 cores. The SCF convergen...

Theoretical calculations have been performed on three model reactions representing the reduction of hydrogen peroxide by ebselen, ebselen selenol, and ebselen diselenide. The reaction surfaces have been investigated at the B3PW91/6-311G(2df,p) level, and single-point energies were calculated using the 6-311++G(3df,3pd) basis set. Solvent effects were included implicitly with the conductor-like ...

Density Functional Theory (DFT) calculations have been carried out using a Polarizable Continuum Model (PCM) in an attempt to investigate the electro-molecular properties of branched-chain glucoside (C14C10-D-glucoside) isomers. The results showed that αconfiguration of pyranoside form is thermodynamically the most stable, while the solution should contain much more β...

A polarizable empirical force field based on the classical Drude oscillator is presented for the hexopyranose form of selected monosaccharides. Parameter optimization targeted quantum mechanical (QM) dipole moments, solute-water interaction energies, vibrational frequencies, and conformational energies. Validation of the model was based on experimental data on crystals, densities of aqueous-sug...

The temperature dependence of the solvent reorganization energy for intramolecular electron transfer (ET) in acetonitrile is measured experimentally and calculated theoretically. The Stokes shifts for the charge transfer, optical transitions of (tetrahydro-4H-thiopyran-4-ylidene)propanedinitrile indicate that the solvent reorganization energy for ET decreases with temperature, whereas dielectri...

An effective polarizable bond (EPB) model has been developed for computer simulation of proteins. In this partial polarizable approach, all polar groups of amino acids are treated as polarizable, and the relevant polarizable parameters were determined by fitting to quantum calculated electrostatic properties of these polar groups. Extensive numerical tests on a diverse set of proteins (includin...

Langevin described a model for the interaction between an ion and a neutral nearly a century ago and since then, many modifications have been introduced to adjust for specific circumstances. This work discusses the induced dipole–induced dipole interaction between an ion and a neutral without a permanent dipole and introduces an anisotropic adjustment. A point polarizable ion model (PPI) and an...