About: Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface

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About: Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface Goto Sponge NotDistinct Permalink

An Entity of Type : http://linked.opendata.cz/ontology/domain/vavai/Vysledek, within Data Space : linked.opendata.cz associated with source document(s)

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rdf:type	skos:Concept http://linked.opendata.cz/ontology/domain/vavai/Vysledek
Description	It has been demonstrated by molecular modeling and experiments that free nucleic acid bases form hydrogen-bonded complexes in vacuum but prefer pi-pi stacking in partially and fully solvated systems. Here we show using molecular dynamics simulations and metadynamics that the addition of a surface (in this case a nanographene monolayer) reverts the situation from stacking back to hydrogen bonding. Watson-Crick as well as several non-Watson-Crick base pairs lying on a graphene surface are significantly more stable in a water environment than a pi-pi-pi stacked graphene-base-base assembly. It illustrates that the thermodynamics of nucleobase interactions results from a fine balance among hydrogen bonding, stacking, and solvation, and that these effects must be considered in molecular design. It has been demonstrated by molecular modeling and experiments that free nucleic acid bases form hydrogen-bonded complexes in vacuum but prefer pi-pi stacking in partially and fully solvated systems. Here we show using molecular dynamics simulations and metadynamics that the addition of a surface (in this case a nanographene monolayer) reverts the situation from stacking back to hydrogen bonding. Watson-Crick as well as several non-Watson-Crick base pairs lying on a graphene surface are significantly more stable in a water environment than a pi-pi-pi stacked graphene-base-base assembly. It illustrates that the thermodynamics of nucleobase interactions results from a fine balance among hydrogen bonding, stacking, and solvation, and that these effects must be considered in molecular design. (en)
Title	Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface (en)
skos:prefLabel	Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface (en)
skos:notation	RIV/61388963:_____/11:00367779!RIV12-AV0-61388963
http://linked.open...avai/riv/aktivita	P Z
http://linked.open...avai/riv/aktivity	P(ED2.1.00/03.0058), P(LC512), Z(AV0Z40550506), Z(MSM6046137305), Z(MSM6198959216)
http://linked.open...iv/cisloPeriodika	40
http://linked.open...vai/riv/dodaniDat	2012
http://linked.open...aciTvurceVysledku	Řezáč, Jan 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	Ústav organické chemie a biochemie AV ČR, v. v. i.
http://linked.open...dnocenehoVysledku	200381
http://linked.open...ai/riv/idVysledku	RIV/61388963:_____/11:00367779
http://linked.open...riv/jazykVysledku	eng - angličtina
http://linked.open.../riv/klicovaSlova	nucleobases; graphene; stacking (en)
http://linked.open.../riv/klicoveSlovo	nucleobases stacking graphene
http://linked.open...odStatuVydavatele	US - Spojené státy americké
http://linked.open...ontrolniKodProRIV	[D16D2F912CF0]
http://linked.open...i/riv/nazevZdroje	Journal of Physical Chemistry C
http://linked.open...in/vavai/riv/obor	CF
http://linked.open...ichTvurcuVysledku	2 (xsd:int)
http://linked.open...cetTvurcuVysledku	3 (xsd:int)
http://linked.open...vavai/riv/projekt	Regional Centre of Advanced Technologies and Materials Center for biomolecules and complex molecular systems
http://linked.open...UplatneniVysledku	2011
http://linked.open...v/svazekPeriodika	115
http://linked.open...iv/tvurceVysledku	Hobza, Pavel Řezáč, Jan Spiwok, V.
http://linked.open...ain/vavai/riv/wos	000295546100001
http://linked.open...n/vavai/riv/zamer	Regulace biologických procesů: Chemické modulátory vybraných systémů významných pro medicínu a zemědělství Teoretické základy potravinářských a biochemických technologií Modulation of signalling and regulatory pathways in normal and cancer cells
issn	1932-7447
number of pages	8 (xsd:int)
http://bibframe.org/vocab/doi	10.1021/jp202491J

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