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Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface
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SYSNO ASEP 0367779 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface Author(s) Spiwok, V. (CZ)
Hobza, Pavel (UOCHB-X) RID, ORCID
Řezáč, Jan (UOCHB-X) RID, ORCIDNumber of authors 3 Source Title Journal of Physical Chemistry C. - : American Chemical Society - ISSN 1932-7447
Roč. 115, č. 40 (2011), s. 19455-19462Number of pages 8 s. Language eng - English Country US - United States Keywords nucleobases ; graphene ; stacking Subject RIV CF - Physical ; Theoretical Chemistry R&D Projects LC512 GA MŠMT - Ministry of Education, Youth and Sports (MEYS) CEZ AV0Z40550506 - UOCHB-X (2005-2011) UT WOS 000295546100001 DOI 10.1021/jp202491J Annotation 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. Workplace Institute of Organic Chemistry and Biochemistry Contact asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Viktorie Chládková, Tel.: 232 002 434 Year of Publishing 2012
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