Atomic partial charges for use in traditional force fields for biomolecular simulation are often fit to the electrostatic potentials of small molecules and, hence, neglect large-scale electronic polarization. On the other hand, recent advances in atoms-in-molecule charge derivation schemes show promise for use in flexible force fields but are limited in size by the underlying quantum mechanical...

The octanol-water partition coefficient (logPow) is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the logPow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. Howeve...

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 ...

A new viewpoint on iterative Hirshfeld charges is presented, whereby the atomic populations obtained from such a scheme are interpreted as such populations which reproduce themselves. This viewpoint yields a self-consistent requirement for the Hirshfeld-I populations rather than being understood as the result of an iterative procedure. Based on this self-consistent requirement, much faster algo...

We introduce a method for obtaining atomic point-charges that yield accurate representations of the electrostatic potentials (ESP) of large systems. The method relies on a decomposition of the density and subsequent projection of the multipole moments of the density components onto neighbouring atomic sites. The resulting local multipole-derived charges (LMDCs) are well-defined, do not require ...

We have improved a modified charge equilibration (MQEq) method for calculating the geometry-dependent distribution of atomic charges. In this paper, Ohno-Klopman, Ohno and DasGupta-Huzinaga equations are adopted to express the shielding effect, and the calculated atomic charges with these MQEq methods are in good agreement with those by the HF/6-31G(d,p) calculations for several organic molecul...

Quantum chemical (MNDo)caleulations have beenused toelucidate the molecular properties and structure - activity relationships of dihydropyridine (DHP) type calcium antagonists. There is a good corielation between the net atomic charges on various atoms of the 4 - phenyl ring of dihydropyridines and pharmacological activity. .Also, activity decreases with increasing free rotation of the phen...