Noncovalent Interactions of DNA Bases with Naphthalene and Graphene

Abstract

The complexes of a DNA base bound to graphitic systems are studied. Considering naphthalene as the simplest graphitic system, DNA base-naphthalene complexes are scrutinized at high levels of ab initio theory including coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] at the complete basis set (CBS) limit. The stacked configurations are the most stable, where the CCSD(T)/CBS binding energies of guanine, adenine, thymine, and cytosine are 9.31, 8.48, 8.53, 7.30 kcal/mol, respectively. The energy components are investigated using symmetry-adapted perturbation theory based on density functional theory including the dispersion energy. We compared the CCSD(T)/CBS results with several density functional methods applicable to periodic systems. Considering accuracy and availability, the optB86b nonlocal functional and the Tkatchenko-Scheffler functional are used to study the binding energies of nucleobases on graphene. The predicted values are 18-24 kcal/mol, though many-body effects on screening and energy need to be further considered.

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

“…As shown in Figure 5 and in Tables 8-11 in the supplementary material, even in the case of hydrogen-bonded structures B3LYP shows the largest deviations for both binding energies and structural parameters with respect to the best theoretical estimates [137][138][139][140] , while B3LYP-D3 and B3LYP-DCP show very good performances and provide rather similar values, making both approaches of essentially equal accuracy. The slight differences between B3LYP-D3 and B3LYP-DCP results suggest that each method has its pros and cons and none of them can be considered clearly superior to the other.…”

“…Indeed, an overestimation within 0.6% of the reference, in the case of the uracil dimer, and an underestimation of 2%, in the case of adenine dimer, are observed. For stacked structures 137,139,140 , in most cases B3LYP-D3 and B3LYP-DCP underestimate interaction energies (exception: uracil dimer at the B3LYP-D3 level), and in all cases the difference from the reference is at most 2 % (see Table 8 in the supplementary material).…”

“…Counterpoise-corrected binding energies (ΔE bind ) of hydrogen-bonded and stacked dimer structures were calculated and compared to reference values [137][138][139][140] in Figure 5 (detailed data are reported in Table 8 in the supplementary material). The comparison between the optimized structures of the dimers and the reference ones is reported in Tables 9 in the supplementary material, while the percentage mean absolute errors (MAE, %) of rotational constants of dimer structures are shown in Figure 5.…”

Functional molecules and materials by π‐Interaction based quantum theoretical design

“…10) are predicted to be 18.4, 19.7, 21.7, and 19.8 kcal/mol at the PBE 1 TS level. [88] Boron nitride (BN) sheet is also a good alternative to graphene. The hexagonal BN sheet is an insulator (with $5-7 eV energy gap) with polar nature bond compared with gapless and semimetal graphene with nonpolar carbon-carbon bonds.…”

“…[5] Reproduced from Refs. [83] and [88], with permission from Nature Publishing Group and American Chemical Society, respectively). Schneebeli et al [95] designed and synthesized singly right/ left handed self-assemble helices of chiral triangular NDI-D redox prisms (macrocycle composed of linking three electrondeficient naphthalene diimides together using 1,2-diaminocyclohexane) with I 2 3 anion by using cooperative effects of space orbital interaction, p-p/anion-p interactions and electron transfer effects.…”