Structures and interaction energies of stacked graphene–nucleobase complexes
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- 5 March 2008
- journal article
- research article
- Published by Royal Society of Chemistry (RSC) in Physical Chemistry Chemical Physics
- Vol. 10 (19), 2722-2729
- https://doi.org/10.1039/b718788b
Abstract
The noncovalent interactions of nucleobases and hydrogen-bonded (Watson–Crick) base-pairs on graphene are investigated with the DFT-D method, i.e., all-electron density functional theory (DFT) in generalized gradient approximation (GGA) combined with an empirical correction for dispersion (van der Waals) interactions. Full geometry optimization is performed for complexes with graphene sheet models of increasing size (up to C150H30). Large Gaussian basis sets of at least polarized triple-ζ quality are employed. The interaction energies are extrapolated to infinite lateral size of the sheets. Comparisons are made with B2PLYP-D and SCS-MP2 single point energies for coronene and C54H18 substrates. The contributions to the binding (Pauli exchange repulsion, electrostatic and induction, dispersion) are analyzed. At a frozen inter-fragment distance, the interaction energy surface of the rigid C96H24 and base monomers is explored in three dimensions (two lateral and one rotational). Methodologically and also regarding the results of an energy decomposition analysis, the complexes behave like other π-stacked systems examined previously. The sequence obtained for the interaction energy of bases with graphene (G > A > T > C > U) is the same for all methods and supports recent experimental findings. The absolute values are rather large (about −20 to −25 kcal mol−1) but in the expected range for π-systems of that size. The relatively short equilibrium inter-plane distance (about 3 Å) is consistent with atomic force microscopy results of monolayer guanine and adenine on graphite. In graphene⋯Watson–Crick pair complexes, the bases lie differently from their isolated energy minima leading to geometrical anti-cooperativity. Together with an electronic contribution of 2 and 6%, this adds up to total binding anti-cooperativities of 7 and 12% for AT and CG, respectively, on C96H24. Hydrogen bonds themselves are merely affected by binding on graphene.Keywords
This publication has 47 references indexed in Scilit:
- Organic molecule adsorption on solid surfaces: chemical bonding, mutual polarisation and dispersion interactionApplied Physics A, 2006
- Molecular orbital interpretation of thymine/graphite nc-AFM imagesSurface and Interface Analysis, 2001
- Self-programmable, self-assembling two-dimensional genetic matter.Origins of Life and Evolution of Biospheres, 2000
- Self-assembled monolayer of adenine base on graphite studied by noncontact atomic force microscopyPhysical Review B, 1999
- Molecular mechanics study of hydrogen bonded self-assembled adenine monolayers on graphiteSurface Science, 1998
- Scanning tunneling microscopy of uracil monolayers self-assembled at the solid|liquid interfaceJournal of Electroanalytical Chemistry, 1997
- Structure determination of two-dimensional adenine crystals on graphitePhysical Review B, 1997
- Monolayer Guanine and Adenine on Graphite in NaCl Solution: A Comparative STM and AFM StudyThe Journal of Physical Chemistry, 1994
- Order and stability of an electrochemically condensed adenine layer on graphiteThe Journal of Physical Chemistry, 1993
- Two-dimensional ordering of the DNA base guanine observed by scanning tunneling microscopy.Proceedings of the National Academy of Sciences, 1991