Using a semiempirical quantum mechanical procedure (FCPAC) we have calculated the partial atomic charges of amino acids from 494 high-resolution protein structures. To analyze the influence of the protein's environment, we considered each residue under two conditions: either as the center of a tripeptide with PDB structure geometry (free) or as the center of 13-16 amino acid clusters extracted ...

Inspired by the idea of charge decomposition in calculation of the dipole preserving and polarization consistent charges (Zhang et al., J. Comput. Chem. 2011, 32, 2127), we have proposed a numerically stable restrained electrostatic potential (ESP)-based charge fitting method for protein. The atomic charge is composed of two parts. The dominant part is fixed to a predefined value (e.g., AMBER c...

The effective use of partial atomic charge models is essential for such purposes in molecular computations as a simplified representation of global charge distribution in a molecule and predicting its conformational behavior. In this work, ten of the most popular models of partial atomic charge are taken into consideration, and these models operate on the molecular wave functions/electron densi...

We report here a new and fast approach [Transferable Partial Atomic Charge Model (TPACM4)-upto four bonds] for deriving the partial atomic charges of small molecules for use in protein/DNA-ligand docking and scoring. We have created a look-up table of 5302 atom types to cover the chemical space of C, H, O, N, S, P, F, Cl, and Br atoms in small molecules together with their quantum mechanical RE...

An optimization of Rappe and Goddard's charge equilibration (QEq) method of assigning atomic partial charges is described. This optimization is designed for fast and accurate calculation of solvation free energies using the finite difference Poisson-Boltzmann (FDPB) method. The optimization is performed against experimental small molecule solvation free energies using the FDPB method and adjust...

We have recently developed a new class IV charge model for calculating partial atomic charges in molecules. The new model, called Charge Model 3 (CM3), was parameterized for calculations on molecules containing H, Li, C, N, O, F, Si, S, P, Cl, and Br by Hartree-Fock theory and by hybrid density functional theory (HDFT) based on the modified Perdew-Wang density functional with several basis sets...

recent studies have indicated that 1, 4-dihydropyridine-3, 5-dicarboxamidederivativesshow significant anti-tubercular activity. in this research, new derivatives of 1, 4-dihydropyridine were designed and synthesized using hantzsch condensation in which dicyclohexyl and different dicyclohexylcarbamoylwere substituted at c-3 and c-5 positions of the dhp ring.in addition, 4 (5)-chloro-2-methyl-5 (...

We explore the relationship between grand canonical (GC) ensemble and charge equilibration (CE), also known as electronegativity equalization, theories for describing charge flow in molecules. We introduce a new unifying approach to classical charge transfer theories based on valence bond (VB) theory and the maximum entropy (ME) method, which we call MEVB. We show how MEVB reduces to GC and CE ...

The (4, +) energy surface of blocked alanine (N-acetyl-N'-methyl alanineamide) was calculated at the Hartree-Fock (HF)/6-31G* level using ab initio molecular orbital theory. A collection of six electrostatic models was constructed, and the term electrostatic model was used to refer to (1) a set of atomic charge densities, each unable to deform with conformation; and (2) a rule for estimating th...

We optimize force fields for H3O(+) and OH(-) that reproduce the experimental solvation free energies and the activities of H3O(+) Cl(-) and Na(+) OH(-) solutions up to concentrations of 1.5 mol/l. The force fields are optimized with respect to the partial charge on the hydrogen atoms and the Lennard-Jones parameters of the oxygen atoms. Remarkably, the partial charge on the hydrogen atom of th...