A new method for the characterization of molecules based on the model approach of molecular surfaces is presented. We use the topographical properties of the surface as well as the electrostatic potential, the local lipophilicity/hydrophilicity, and the hydrogen bond density on the surface for characterization. The definition and the calculation method for these properties are reviewed shortly....

The equilibrium geometry and harmonic frequencies of the 6-methylnicotinic acid, were determined and analyzed at DFT level employing the basis set 6-311+G(d,p). The skeleton of the optimized molecule is non-planar. In general, a good agreement between experimental and calculated normal modes of vibrations has been observed. The molecular electrostatic potential surface has been used along with ...

UNLABELLED PreDs is a WWW server that predicts the dsDNA-binding sites on protein molecular surfaces generated from the atomic coordinates in a PDB format. The prediction was done by evaluating the electrostatic potential, the local curvature and the global curvature on the surfaces. Results of the prediction can be interactively checked with our original surface viewer. AVAILABILITY PreDs is...

The major features of a scalar property P defined on a molecular surface can be captured in the form of a directed graph derived from the gradient flow of P . These molecular surface property graphs (MSPG) have vertices at the critical points (maxima, minima and saddles) of P and edges formed by the trajectories of the gradient flow that pass through the saddles. Techniques developed for the co...

Electrostatics plays a fundamental role in virtually all processes involving biomolecules in solution. The Poisson-Boltzmann equation constitutes one of the most fundamental approaches to treat electrostatic effects in solution. The theoretical basis of the Poisson-Boltzmann equation is reviewed and a wide range of applications is presented, including the computation of the electrostatic potent...

This work concerns electrostatic properties of an ionic solution with multiple ionic species of possibly different ionic sizes. Such properties are described by the minimization of an electrostatic free-energy functional of ionic concentrations. Bounds are obtained for ionic concentrations with low electrostatic free energies. Such bounds are used to show that there exists a unique set of equil...

In this study adsorption of Cr(VI) from aqueous solution by Fe3O4 nanoparticles was investigated. Desorption process and recovery of nanoparticles using different solutions were then carried out, and it was observed that NaOH (0.5M) can remove 90% of adsorbed chromium ions. Following the completion of adsorption/ desorption cycles, it was determined that nanoparticles have still had a high abil...

We introduce a method of molecular dynamics in shape space aimed at metal clusters. The ionic degrees of freedom are described via a dynamically deformable jellium with inertia parameters derived from an incompressible, irrotational flow. The shell correction method is used to calculate the electronic potential energy surface underlying the dynamics. Our finite-temperature simulations of Ag14 a...

Crystalline surface layer proteins (S-layer proteins) have considerable potential for the crystalline arrays in biotechnology, biomimetics and nonlife applications, including areas such as microelectronics and molecular nanotechnology. The extensive application potential of surface layers in nanobiotechnology is according to the particular inherent attributes of the single molecular arrays cons...

A novel analysis and representation of the protein surface in terms of electrostatic binding complementarity and selectivity is presented. The charge optimization methodology is applied in a probe-based approach that simulates the binding process to the target protein. The molecular surface is color coded according to calculated optimal charge or according to charge selectivity, i.e., the bindi...