BACKGROUND Partial atomic charges are a well-established concept, useful in understanding and modeling the chemical behavior of molecules, from simple compounds, to large biomolecular complexes with many reactive sites. RESULTS This paper introduces AtomicChargeCalculator (ACC), a web-based application for the calculation and analysis of atomic charges which respond to changes in molecular co...

Assigning effective atomic charges that properly reproduce the electrostatic fields of molecules is a crucial step in the construction of accurate interatomic potentials. We propose a new approach to calculate these charges, which as previous approaches are, is based on the idea of charge equilibration. However, we only allow charge to flow between covalently bonded neighbors by using the conce...

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...

Theoretical arguments and calculations are presented concerning atomic orbital-based population analyses, as well as the way they are affected by rigid rotation of the molecule. It was recently shown that the Löwdin distribution of atomic charges (atomic populations computed in a Löwdin-orthogonalized basis) is, in general, not rotationally invariant unless an initial atom-centered basis of pur...

We present the AMBER ff15ipq force field for proteins, the second-generation force field developed using the Implicitly Polarized Q (IPolQ) scheme for deriving implicitly polarized atomic charges in the presence of explicit solvent. The ff15ipq force field is a complete rederivation including more than 300 unique atomic charges, 900 unique torsion terms, 60 new angle parameters, and new atomic ...

The Pipek-Mezey scheme for generating chemically intuitive, localized molecular orbitals is generalized to incorporate various ways of estimating the atomic charges, instead of the ill-defined Mulliken charges used in the original formulation, or Löwdin charges, which have also been used. Calculations based on Bader, Becke, Voronoi, Hirshfeld, and Stockholder partial charges, as well as intrins...

The use of macroscopic electrostatic models to calculate the relative energetics of protonation states and the pH-titration properties of ionizable groups in proteins is described. These methods treat the protein as an irregularly-shaped low-dielectric object containing embedded atomic charges immersed in a high-dielectric (solvent) medium. The energetics of altering protonation states then inv...