Potential derived charges using a geodesic point selection scheme

Abstract

Potential derived (PD) atomic charges, obtained by fitting to molecular electrostatic potentials, are widely used in molecular modeling and simulation calculations. These charges are known to depend on the sample of points chosen for the fit, on the particular point selection algorithm, on molecular translations and rotations in many instances, and even on molecular conformation. Following a critique of currently available methods, a novel point selection scheme is described which results in a highly isotropic array of points located on a series of fused‐sphere van der Waals surfaces. The pattern of points is based on tesselations of the icosahedron, and these are discussed in some detail along with their connection with virus morphology, geodesic domes, and symmetric fullerene structures. Using methanol as a test case, it is shown that the new method leads to PD charges which are independent of translation and display minimal rotational dependence, and are hence far better suited to the determination of PD charges from electrostatic potentials obtained from both theory and experimental X‐ray diffraction data. The conformation dependence of the newly derived PD charges for alanyl dipeptide is found to be substantially less than obtained earlier by Williams [Biopolymers 29, 1367 (1990)]. © 1996 by John Wiley & Sons, Inc.

Reduction of CO2 to Methanol Catalyzed by a Biomimetic Organo-Hydride Produced from Pyridine

“…Similar results are found for HTPT to formaldehyde. Panels: (a) energy (E0K, not ZPE-corrected); R denotes the reactant complex, TS the transition state, i, ii, and iii are structures in the exit channel, and P, the product complex, (b) bond length, and (c) structures and charges q (calculated with the CHELPG method 141 and in the units of e) of important moieties along the reaction coordinate (corresponding to structures of R, TS, i, ii, iii and P in (a)). Both bond length and charge analyses show that the TS is dominated by HT (which is similar to the case of CO2 reduction by PyH2).…”

Electrostatic Potential Charge including Spatial Electron Density Distribution (SEDD): Application to Biosystems

“…15 To pass these criteria, many charge models have been proposed. 18 ESP charge, which is one of the choices for atomic charges, 1,3,4,6,9 is designed so that the criterion (ii) is satisfied. Moreover, previous studies have shown that the ESP charge is not sensitive to basis sets.…”

“…Because the number of grid points is finite and the positions greatly depend on the molecular conformation and orientation, it is difficult to remove the grid artifacts in the fitting process. To improve this weak point, some algorithms have been proposed, such as restrained electrostatic potential (RESP), 11 ESP charges with geodesic scheme (GEO), 4 CHelpG scheme, 3 and Merz-Singh-Kollman scheme. 1 In previous studies, we proposed a different ESP charge by including spatial electron density distribution (SEDD).…”

Fast Screening of Solvents for Simultaneous Extraction of Furfural, 5-Hydroxymethylfurfural and Levulinic Acid from Aqueous Solution Using SMD Solvation Free Energies

“…The charges were determined by the geodesic method of Spackman, 21 based on charges fitted to reproduce the electrostatic potential, and using the X3LYP/TZVPP electronic density (Scheme 2). The values of charges are very negative on the oxygens of the MIBK and the tributyl phosphate, suggesting strong hydrogen bond with the solutes.…”