The effect of off-center σ-hole on the atom-centered partial charges in halogenated molecules

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22340%2F22%3A43924045" target="_blank" >RIV/60461373:22340/22:43924045 - isvavai.cz</a>

Výsledek na webu

<a href="https://doi.org/10.1002/jcc.26841" target="_blank" >https://doi.org/10.1002/jcc.26841</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/jcc.26841" target="_blank" >10.1002/jcc.26841</a>

Jazyk výsledku

angličtina

Název v původním jazyce

The effect of off-center σ-hole on the atom-centered partial charges in halogenated molecules

Popis výsledku v původním jazyce

Partial atomic charges belong to key concepts of computational chemistry. In some cases, however, they fail in describing the electrostatics of molecules. One such example is the σ-hole, a region of positive electrostatic potential located on halogens and other atoms. In molecular mechanics, the σ-hole is often modeled as a pseudo-atom with a positive partial charge located off the halogen nucleus. Here we address a question, to what extent the pseudo-atom affects partial charges of other atoms in the molecule. To this aim, we have thoroughly analyzed partial charges of over 2300 halogenated molecules from the ZINC database calculated by the restricted electrostatic potential (RESP) method and compared them with the charges fitted by RESP including the pseudo-atom. We show that the pseudo-atom improves charge fitting for a vast majority of molecules. The σ-hole, modeled as the off-center charge, affects the atoms within three covalent bonds from the halogen.

Název v anglickém jazyce

The effect of off-center σ-hole on the atom-centered partial charges in halogenated molecules

Popis výsledku anglicky

Partial atomic charges belong to key concepts of computational chemistry. In some cases, however, they fail in describing the electrostatics of molecules. One such example is the σ-hole, a region of positive electrostatic potential located on halogens and other atoms. In molecular mechanics, the σ-hole is often modeled as a pseudo-atom with a positive partial charge located off the halogen nucleus. Here we address a question, to what extent the pseudo-atom affects partial charges of other atoms in the molecule. To this aim, we have thoroughly analyzed partial charges of over 2300 halogenated molecules from the ZINC database calculated by the restricted electrostatic potential (RESP) method and compared them with the charges fitted by RESP including the pseudo-atom. We show that the pseudo-atom improves charge fitting for a vast majority of molecules. The σ-hole, modeled as the off-center charge, affects the atoms within three covalent bonds from the halogen.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10301 - Atomic, molecular and chemical physics (physics of atoms and molecules including collision, interaction with radiation, magnetic resonances, Mössbauer effect)

Projekt

<a href="/cs/project/GJ19-06479Y" target="_blank" >GJ19-06479Y: Struktura a dynamika peptidového tunelu v ribozomu</a><br>

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2022

Kód důvěrnosti údajů

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Název periodika

Journal of Computational Chemistry

ISSN

0192-8651

e-ISSN

1096-987X

Svazek periodika

43

Číslo periodika v rámci svazku

12

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

6

Strana od-do

864-869

Kód UT WoS článku

000770032600001

EID výsledku v databázi Scopus

2-s2.0-85126378276