厦门大学学报（自然科学版）2024，Vol.63Issue(1)：24-33,10.DOI:10.6043/j.issn.0438-0479.202303021
激发态DNA碱基对分子间相互作用的理论研究
Theoretical study on intermolecular interactions in DNA base pairs with excited states
摘要
Abstract
[Objective]Intermolecular interactions in DNA base pairs with excited states play the important roles in various processes such as photodamage,photoprotection and photoinduced gene mutation.Lately,an energy decomposition analysis method,termed time-dependent generalized Kohn-Sham based energy decomposition analysis[GKS-EDA(TD)],has been proposed for intermolecular interactions with excited states based on time-dependent density functional theory(TDDFT)calculations.As an extension of GKS-EDA,GKS-EDA(TD)divides the total interaction energy into electrostatic,exchange-repulsion,polarization,correlation and dispersion.In this study,using the GKS-EDA(TD)method,the physical origin of intermolecular interactions in two types of DNA base-pairs is explored.[Methods]The geometries of four kinds of base pairs are optimized with PBE0-D3 and 6-31+G*basis set by the Gaussian 16 program.The excited state properties of four complexes are calculated based on the equilibrium geometry.Atoms in molecules(AIM),independent gradient model based on Hirshfeld partition(IGMH)and hole-electron analyses are performed with the Multiwfn program.The GKS-EDA and GKS-EDA(TD)calculation are carried out by the XEDA program interfaced with the GAMESS program in PBE0-D3(BJ)/6-31++G**and LC-PBE-D3(BJ)/6-31++G**level of theory.The counterpoise(CP)method is applied for basis set superposition error(BSSE).[Results]GKS-EDA results show that in the ground state(S0),the intermolecular interactions in Waston-Crick type AT and GC base pairs[denoted as AT(WC)and GC(WC)in the following]are dominated by electrostatic and polarization,while those in two 兀-兀 stacked base pairs[denoted as AT(stacked)and GC(stacked)in the following]are mainly contributed by the dispersion and correlation terms.Regarding the excitation energy,the results of TDDFT calculations by LC-PBE are in good agreement the results of CC2 and EOM-CCSD(T)calculations.The first excited state(S1)of AT(WC)can be attributed by the n→π*transition of T,while the second excited state(S2)arises from the π→π*transition in T.GKS-EDA(TD)results show that from the S0 to the S1,the hydrogen bond in AT(WC)weakens,which can be interpreted as the dramatical decrease of the polarization term.This is because the orbitals involved in the n→π*excitation are related to the hydrogen bonding interaction between A and T.Therefore,in the S1,the origin of the interaction in AT(WC)changs,which is governed by dispersion and correlation term.The S1 and S2 of GC(WC)are π→π*transition on G and C,respectively.The GKS-EDA results reveal that the nature of intermolecular interactions remains almost unchanged because the transit orbitals are not involved in the hydrogen bonding interaction.The S1 and S2 of AT(stacked)are the n→π*transition,which are mainly local on T and A,respectively.The GKS-EDA(TD)results for the interaction in the two lowest-lying excited states are similar to that in the S0.As for GC(stacked),the S1 and S2 arise from the π→π*transition of C and G,respectively.GKS-EDA(TD)reveals that with the excitation,compared to the S0,the contribution of the electrostatic term decreases while that of correlation term increases.[Conclusion]In this work,the intermolecular interactions of DNA base-pairs in the two lowest lying excited states are explored using the GKS-EDA(TD)method.The relation between the geometrical configuration and the electron transition is revealed.It is found that the origin of the intermolecular interaction in the excited state can be quite different from the S0.In detail,for Waston-Crick type base-pair,the variation of the total interaction from the S0 to the excited state is sensitive to the n→π*transition,while for the π-π stacked based pair,the π→π*transition could obviously alter the origin of base pair interaction due to the enlargement of the correlation term.关键词
激发态/DNA碱基对/分子间相互作用/能量分解分析Key words
excited state/DNA base-pair/intermolecular interaction/energy decomposition analysis分类
化学化工引用本文复制引用
邵博孝,吴玮,苏培峰..激发态DNA碱基对分子间相互作用的理论研究[J].厦门大学学报（自然科学版）,2024,63(1):24-33,10.基金项目
国家自然科学基金(22173076,21973077) （22173076,21973077）
