A density functional theory (DFT) in the framework of cell model is proposed to calculate the structural and thermodynamic properties of aqueous DNA-electrolyte solution with finite DNA concentrations. The hard-sphere contribution to the excess Helmholtz energy functional is derived from the modified fundamental measure theory, and the electrostatic interaction is evaluated through a quadratic ...

A quantum chemical investigation was carried out to study the properties of intermolecular F•••F, Br•••Br and Br•••O interactions in crystalline 1-bromo-2,3,5,6-tetrafluoro-nitrobenzene (BFNB). This system was selected to mimic the halogen-halogen as well as halogen bonding interactions found within crystal structures as well as within biological systems. We found that fluorine atoms have weak ...

Single-molecule studies that allow to compute pKa values, proton affinities (gas-phase acidity/basicity) and the electrostatic energy of solvation have been performed for a heterogeneous set of 26 organic compounds. Quantum mechanical density functional theory (DFT) using the Becke-half&half and B3LYP functionals on optimized molecular geometries have been carried out to investigate the energet...

One of the underlying principles in drug discovery is that a biologically active compound is complimentary in shape and molecular recognition features to its receptor. This principle infers that molecules binding to the same receptor may share some common features. Here, we have investigated whether the electrostatic similarity can be used for the discovery of small molecule protein-protein int...

An ability to efficiently compute the electrostatic potential produced by molecular charge distributions under realistic solvation conditions is essential for a variety of applications. Here, the simple closed-form analytical approximation to the Poisson equation rigorously derived in Part I for idealized spherical geometry is tested on realistic shapes. The effects of mobile ions are included ...

In Computer-Aided-Drug-Design (CADD), the electrostatic interactions contribute strongly to the interaction between the drug-molecule and the target. Further, the Coulomb term is crucial for calculating the electrostatic contribution to the solvation energy. In spite of this, conventional Force Fields use the obsolete physical concept of point-monopoles (net atomic charges) and thus, are not ab...

This paper addresses the problem of determining the electrostatic potential of large proteins by the superposition of potentials calculated for small fragments. The use of different atomic and molecular fragments is considered for reproducing the molecular electrostatic potential of different conformations of N-acetylalanine methylamide (NAAMA) with an acceptable degree of error as measured by ...

Accurate and fast evaluation of electrostatic interactions in molecular systems is still one of the most challenging tasks in the rapidly advancing field of macromolecular chemistry, including molecular recognition, protein modeling and drug design. One of the most convenient and accurate approaches is based on a Buckingham-type approximation that uses the multipole moment expansion of molecula...

Recent experiments have shown that transport properties of molecular-scale devices can be reversibly altered by the surrounding solvent. Here, we use a combination of first-principles calculations and experiment to explain this change in transport properties through a shift in the local electrostatic potential at the junction caused by nearby conducting and solvent molecules chemically bound to...

Pyrazine derivatives are important class of compounds with diverse biological and cytotoxic activities and clinical applications. In this study, B3 p 86 / 6 - 31 (+ +) G * was used to compute and map the molecular surface electrostatic potentials of a group of substituted amides of pyrazine-2-carboxylic acids to identify common features related to their subsequent cytotoxicities. Several statis...