Centro de Química e Bioquímica, DQB, Faculdade de Ciências, Universidade de Lisboa , Campo Grande, 1749-016 Lisboa, Portugal.
Centro ALGORITMI, Universidade do Minho , 4710-057 Braga, Portugal.
J Chem Theory Comput. 2015 Jun 9;11(6):2714-28. doi: 10.1021/ct5006104.
The effects of phenanthroline (phen) intercalation on the structure, energetics, and bonding of adenine-thymine and guanine-cytosine tetramers (A-T/T-A and G-C/C-G) were studied through density functional theory (DFT) using functionals that were recently improved to consider the effect of dispersion forces. Our results given by energy decomposition analysis show that the dispersion contribution, ΔEdisp, is the most important contribution to the interaction energy, ΔEint. However, it is not enough to compensate the Pauli repulsion term, ΔEPauli, and the roles of the orbital contribution, ΔEorb, and, in particular, the electrostatic contribution, ΔEelstat, become crucial for the stabilization of the structures in the intercalation process. On the other hand, for G-C/C-G systems, hydrogen-bonding (HB) interactions are more important than stacking (S) interactions, whereas for A-T/T-A systems, HB and S become competitive. Moreover, intercalation produces important changes not only in the hydrogen bonds of base pairs, because S and HB are deeply connected, but also in other characteristic geometric parameters of the base pairs.
通过使用最近改进的考虑色散力影响的泛函，运用密度泛函理论（DFT）研究了菲咯啉（phen）嵌入对腺嘌呤-胸腺嘧啶和鸟嘌呤-胞嘧啶四聚体（A-T/T-A 和 G-C/C-G）结构、能量和键合的影响。我们通过能量分解分析得到的结果表明，色散贡献ΔEdisp 是相互作用能ΔEint 的最重要贡献。然而，这不足以补偿泡利排斥项ΔEPauli，轨道贡献ΔEorb 的作用，特别是静电贡献ΔEelstat 的作用，对于在嵌入过程中稳定结构变得至关重要。另一方面，对于 G-C/C-G 体系，氢键（HB）相互作用比堆积（S）相互作用更重要，而对于 A-T/T-A 体系，HB 和 S 变得具有竞争性。此外，嵌入不仅会对碱基对的氢键产生重要影响，因为 S 和 HB 是紧密相连的，而且会对碱基对的其他特征几何参数产生重要影响。
