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Multipolar Atom Types from Theory and Statistical Clustering (MATTS) Data Bank: Restructurization and Extension of UBDB
Journal of Chemical Information and Modeling ( IF 5.6 ) Pub Date : 2022-08-09 , DOI: 10.1021/acs.jcim.2c00144
Kunal Kumar Jha 1 , Barbara Gruza 1 , Aleksandra Sypko 1 , Prashant Kumar 1 , Michał Leszek Chodkiewicz 1 , Paulina Maria Dominiak 1
Affiliation  

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 (Pval, κ, κ′, Plm) 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.

中文翻译:

来自理论和统计聚类 (MATTS) 数据库的多极原子类型:UBDB 的重组和扩展

快速准确的电子密度操作模型在许多科学学科中都至关重要,包括晶体学、分子生物学、药物学和结构化学。在量子晶体学中,晶体结构的非球面细化正变得越来越流行,因为它可以准确地描述物理上有意义的特性。可转移非球面原子模型 (TAAM) 快速而精确,但它需要一种强大的算法来进行原子分型和覆盖有机小分子中最流行的原子类型。因此,布法罗大学数据库 (UBDB) 已重命名为来自理论和统计聚类 (MATTS) 数据库的多极原子类型,扩展、重组、并实施到软件 DiSCaMB 中,从包含 C、H、N、O、P、S、F、Cl 和 Br 原子的 2316 个小分子晶体结构中获得 651 种原子类型。MATTS2021数据库现在涵盖了生物、药物和有机材料中的大部分小分子、多肽、RNA、DNA以及一些经常出现的阳离子和阴离子,包括由上述元素组成的大部分已知晶体结构。多极模型参数 (P val , κ, κ', P lm ) 得到的不同原子类型受到相邻原子类型、杂化、环系统中的几何应变和分子上的电荷的很大影响。与先前的发现相反,显示可变氧化态和离子的原子偏离了单极子衍生电荷对膨胀 - 收缩 κ 参数的线性依赖性。
更新日期:2022-08-09
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