Structures and interaction energies of stacked graphene–nucleobase complexes

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 C(150)H(30)). Large Gaussian basis sets of at least polarized triple-zeta 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 C(54)H(18) 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 C(96)H(24) 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 pi-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 pi-systems of that size. The relatively short equilibrium inter-plane distance (about 3 A) 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 C(96)H(24). Hydrogen bonds themselves are merely affected by binding on graphene.

Graphene nanodevices for DNA sequencing

“…The interaction strengths of the different bases with graphene vary as it depends on the polarizability of the DNA bases [93,95]. Both theoretical and experimental studies report that guanine binds most strongly to graphene while A, T and C have lower and similar interaction strengths [93,[96][97][98][99][100].…”

Adsorption and Desorption of DNA on Graphene Oxide Studied by Fluorescently Labeled Oligonucleotides

“…31 Previous work has focused on characterization of the adsorption of single nucleotides or nucleosides by atomic force microscopy (AFM), 32 isothermal titration calorimetry, 33 and theoretical calculations. [34][35][36] It was concluded that non-electrostatic interactions dominate the binding, 32 and the purine bases bind more strongly than the pyrimidines. 33,35,36 The adsorption of DNA on carbon nanotubes has also been studied.…”

“…[34][35][36] It was concluded that non-electrostatic interactions dominate the binding, 32 and the purine bases bind more strongly than the pyrimidines. 33,35,36 The adsorption of DNA on carbon nanotubes has also been studied. [37][38][39][40][41][42][43] GO and nanotubes, however, are fundamentally different and the adsorption/desorption of oligonucleotides on GO have not been systematically tested as a function of solution conditions.…”

Electronic structure of charged bilayer and trilayer phosphorene

“…Van der Waals interactions are accounted for by using an empirical correction method 29 . This method has been proven to be effective in describing layered materials [30][31][32] . We have checked that the atomic displacements due to extra doped charges or vertical external electric fields considered in our work are less than 0.5 % of the bond lengths (since the material is not polar).…”