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

0367779 - ÚOCHB 2012 RIV US eng J - Článek v odborném periodiku
Spiwok, V. - Hobza, Pavel - Řezáč, Jan
Free-Energy Simulations of Hydrogen Bonding versus Stacking of Nucleobases on a Graphene Surface.
Journal of Physical Chemistry C. Roč. 115, č. 40 (2011), s. 19455-19462. ISSN 1932-7447. E-ISSN 1932-7455
Grant CEP: GA MŠMT LC512
Výzkumný záměr: CEZ:AV0Z40550506
Klíčová slova: nucleobases * graphene * stacking
Kód oboru RIV: CF - Fyzikální chemie a teoretická chemie
Impakt faktor: 4.805, rok: 2011

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.
Trvalý link: http://hdl.handle.net/11104/0202332