Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB

Abstract

A fast and accurate operational model of electron density is crucial in many scientific disciplines including crystallography, molecular biology, pharmaceutical, and structural chemistry. In quantum crystallography, the aspherical refinement of crystal structures is becoming increasingly popular because of its accurate description in terms of physically meaningful properties. The transferable aspherical atom model (TAAM) is quick and precise, though it requires a robust algorithm for atom typing and coverage of the most popular atom types present in small organic molecules. Thus, the University at Buffalo Databank (UBDB) has been renamed to the Multipolar Atom Types from Theory and Statistical clustering (MATTS) data bank, broadened, restructured, and implemented into the software DiSCaMB with 651 atom types obtained from 2316 small-molecule crystal structures containing C, H, N, O, P, S, F, Cl, and Br atoms. MATTS2021 data bank now covers most of the small molecules, peptides, RNA, DNA, and some frequently occurring cations and anions in biological, pharmaceutical, and organic materials, including the majority of known crystal structures composed of the above elements. The multipole model parameters ( P val , κ, κ′, P lm ) obtained for different atom types were greatly influenced by neighboring atom types, hybridization, geometrical strain in the ring system, and charges on the molecule. Contrary to previous findings, the atoms showing variable oxidation states and ions deviate from the linear dependence of monopole-derived charges on the expansion–contraction κ parameter.

Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Impact of Surrounding Atoms on Electron Density from Cluster Analysis

“…In the original MATTS2021 data bank, 11% of atom types has at least one sample standard deviation for P lm larger than 0.05 e, which was allowed only in the case of either low transferability of electron density expected due to chemical factors or rarity of atom type occurrence. 11 After rotations, 3298 out of 11 064 data points had at least one sample standard deviation for P lm larger than 0.05, which makes up 29.81% of the data set. In terms of atom types, 205 of them were marked inconsistent, which makes up 31.5% of the data bank.…”

“… 11 For more details, especially regarding the procedure of defining atom types and bank making, see previous publications about the UBDB 10 , 31 and MATTS data bank. 11 The current version of the MATTS data bank can be downloaded from .…”

“…Data. All analyses were carried out using the MATTS2021 data bank that contains entries for 651 atom types 11 of chemical elements including C, H, N, O, S, P, F, Cl, and Br. The atom types in the MATTS2021 data bank give information about their topology (chemical elements, numbers and types of neighbors, ring membership, the orientation of the coordinate system for the MM, etc.)…”

“… 7 − 10 Lately, the UBDB was superseded by the multipolar atom types from theory and statistical clustering (MATTS) data bank. 11 Pseudoatom data banks allow the replacement of independent atom model (IAM) scattering factors, typically used for refining crystal structures, with aspherical ones calculated from the transferable aspherical atom model (TAAM). In effect, the TAAM refinement increases the accuracy and precision of defining thermal atomic displacement parameters and molecular geometry, particularly for hydrogen atoms.…”

“…Intending to get past limitations with the experimental approach, the idea of transferability of parameters describing electron density between chemically related molecules was introduced to crystallography by Brock et al in 1991 and has since been used to create data banks of aspherical atom parameters . There are three well-established databases: the Invariom database, , the experimental library of multipolar atom model (ELMAM), , and the University at Buffalo Data Bank (UBDB). − Lately, the UBDB was superseded by the multipolar atom types from theory and statistical clustering (MATTS) data bank . Pseudoatom data banks allow the replacement of independent atom model (IAM) scattering factors, typically used for refining crystal structures, with aspherical ones calculated from the transferable aspherical atom model (TAAM).…”