Related Experiment Video
Updated: Aug 20, 2026

Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
Published on: April 8, 2020
The key role of atom types, reference states, and interaction cutoff radii in the knowledge-based method: new
1Force Field Lab., Algodign, LCC, Sadovaya, Moscow, Russia. anatoly.ruvinsky@algodign.com
Abstract:
We present a variational method to derive knowledge-based potentials. The method is based on an optimization procedure of objective variables: atom types, reference states, and interaction cutoff radii. We suggest and apply new unsymmetrical reference states. The cutoff radii and atom types are optimized to improve docking accuracy of the corresponding potentials. The atom types are varied along an atom type tree, with 6 root and 49 top atom types, and the set of 18 optimal atom types is obtained. We demonstrate strong dependence between the choice of atom types and the docking accuracy of the potentials derived with these atom types. The averaged root-mean square deviations (RMSDs) of the ligand docked positions relative to the experimentally determined positions decrease when the elements C, N, O are split into the optimal types.
Related Concept Videos
The Quantum-Mechanical Model of an Atom
Electronic Structure of Atoms
An atom comprises protons and neutrons, which are contained inside the dense, central core called the nucleus, with electrons present around the nucleus. Taking into account the wave–particle duality of electrons and the uncertainty in position around the nucleus, quantum mechanics provides a more accurate model for the atomic structure. It describes atomic orbitals as the regions around the nucleus where electrons of discrete energy exist, characterized by four quantum numbers: n, l, ml, and...
Valence Bond Theory and Hybridized Orbitals
A σ bond (single bond in a Lewis structure) is a covalent bond in which the electron density is...
Atomic Absorption Spectroscopy: Atomization Methods
MO Theory and Covalent Bonding
Hybridization of Atomic Orbitals I

