About: On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	Until recently, the description of halogen bonding by standard molecular mechanics has been poor, owing to the lack of the so-called sigma hole localized at the halogen. This region of positive electrostatic potential located on top of a halogen atom explains the counterintuitive attraction of halogenated compounds interacting with Lewis bases. In molecular mechanics, the sigma hole is modeled by a massless point charge attached to the halogen atom and referred to as an explicit sigma hole (ESH). Here, we introduce and compare three methods of ESH construction, which differ in the complexity of the input needed. The molecular mechanical dissociation curves of three model complexes containing bromine are compared with accurate CCSD(T)/CBS data. Furthermore, the performance of the Amber force field enhanced by the ESH on geometry characteristics is tested on the casein kinase 2 protein complex with seven brominated inhibitors. It is shown how various schemes depend on the selection of the ESH parameters and to what extent the energies and geometries are reliable. The charge of 0.2e placed 1.5 angstrom from the bromine atomic center is suggested as a universal model for the ESH. Until recently, the description of halogen bonding by standard molecular mechanics has been poor, owing to the lack of the so-called sigma hole localized at the halogen. This region of positive electrostatic potential located on top of a halogen atom explains the counterintuitive attraction of halogenated compounds interacting with Lewis bases. In molecular mechanics, the sigma hole is modeled by a massless point charge attached to the halogen atom and referred to as an explicit sigma hole (ESH). Here, we introduce and compare three methods of ESH construction, which differ in the complexity of the input needed. The molecular mechanical dissociation curves of three model complexes containing bromine are compared with accurate CCSD(T)/CBS data. Furthermore, the performance of the Amber force field enhanced by the ESH on geometry characteristics is tested on the casein kinase 2 protein complex with seven brominated inhibitors. It is shown how various schemes depend on the selection of the ESH parameters and to what extent the energies and geometries are reliable. The charge of 0.2e placed 1.5 angstrom from the bromine atomic center is suggested as a universal model for the ESH. (en)
Title	On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds (en)
skos:prefLabel	On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds On Extension of the Current Biomolecular Empirical Force Field for the Description of Halogen Bonds (en)
skos:notation	RIV/61989592:15310/12:33142587!RIV13-MSM-15310___
http://linked.open...avai/riv/aktivita	I P Z
http://linked.open...avai/riv/aktivity	I, P(ED2.1.00/03.0058), P(GBP208/12/G016), Z(AV0Z40550506)
http://linked.open...iv/cisloPeriodika	4
http://linked.open...vai/riv/dodaniDat	2013
http://linked.open...aciTvurceVysledku	Hobza, Pavel
http://linked.open.../riv/druhVysledku	J - Článek v odborném periodiku
http://linked.open...iv/duvernostUdaju	S - Úplné a pravdivé údaje nepodléhající ochraně podle zvláštních právních předpisů
http://linked.open...titaPredkladatele	Univerzita Palackého v Olomouci / Přírodovědecká fakulta
http://linked.open...dnocenehoVysledku	156231
http://linked.open...ai/riv/idVysledku	RIV/61989592:15310/12:33142587
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	sigma-hole; molecular mechanics; halogen bond (en)
http://linked.open.../riv/klicoveSlovo	halogen bond molecular mechanics sigma-hole
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[8F8F6B235CFF]
http://linked.open...i/riv/nazevZdroje	Journal of Chemical Theory and Computation
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	1 (xsd:int)
http://linked.open...cetTvurcuVysledku	2 (xsd:int)
http://linked.open...vavai/riv/projekt	Controlling structure and function of biomolecules at the molecular scale: theory meets experiment Regional Centre of Advanced Technologies and Materials
http://linked.open...UplatneniVysledku	2012
http://linked.open...v/svazekPeriodika	8
http://linked.open...iv/tvurceVysledku	Hobza, Pavel Kolář, Michal
http://linked.open...ain/vavai/riv/wos	000302487700018
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství
issn	1549-9618
number of pages	9 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/ct2008389
http://localhost/t...ganizacniJednotka	15310

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