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Electron density is not spherical: the many applications of the transferable aspherical atom model.

ABSTRACT: In the simplest approach and at low resolution, the electron density of an atom can be approximated by a sphere. However, the resolutions currently achieved in X-ray macromolecular crystallography reach atomic resolutions, where a more sophisticated approach is inevitable. This review summarizes the available electron density and scattering factor models and their applications with emphasis on the transferable aspherical atom model (TAAM).

SUBMITTER: Kulik M

PROVIDER: S-EPMC9676208 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Electron density is not spherical: the many applications of the transferable aspherical atom model.

Kulik Marta M Dominiak Paulina M PM

Computational and structural biotechnology journal 20221025

In the simplest approach and at low resolution, the electron density of an atom can be approximated by a sphere. However, the resolutions currently achieved in X-ray macromolecular crystallography reach atomic resolutions, where a more sophisticated approach is inevitable. This review summarizes the available electron density and scattering factor models and their applications with emphasis on the transferable aspherical atom model (TAAM). ...[more]

PMID: 36420158

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Project description:Accurate and fast evaluation of electrostatic interactions in molecular systems is one of the most challenging tasks in the rapidly advancing field of macromolecular chemistry and drug design. Electrostatic interactions are of crucial importance in biological systems. They are well represented by quantum mechanical methods; however, such calculations are computationally expensive. In this study, we have evaluated the University of Buffalo Pseudoatom Databank (UBDB)1,2 approach for approximation of electrostatic properties of macromolecules and their complexes. We selected the S663 and JSCH-20054 data sets (208 molecular complexes in total) for this study. These complexes represent a wide range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Reference electrostatic energies were obtained directly from wave functions at the B3LYP/aug-cc-pVTZ level of theory using the SAPT (Symmetry-Adapted Perturbation Theory) scheme for calculation of electrostatic contributions to total intermolecular interaction energies. Electrostatic energies calculated on the basis of the UBDB were compared with corresponding reference results. Results were also compared with energies computed using a point charge model from popular force fields (AM1-BCC and RESP used in AMBER and CGenFF from CHARMM family). The energy trends are quite consistent (R2 ≈ 0.98) for the UBDB method as compared to the AMBER5 and CHARMM force field methods6(R2 ≈ 0.93 on average). The RSMEs do not exceed 3.2 kcal mol-1 for the UBDB and are in the range of 3.7-7.6 kcal mol-1 for the point charge models. We also investigated the discrepancies in electrostatic potentials and magnitudes of dipole moments among the tested methods. This study shows that estimation of electrostatic interaction energies using the UBDB databank is accurate and reasonably fast when compared to other known methods, which opens potential new applications to macromolecules.

Dataset Information

Electron density is not spherical: the many applications of the transferable aspherical atom model.

Publications

Electron density is not spherical: the many applications of the transferable aspherical atom model.

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