Marefat Khah Alireza, Reinholdt Peter, Nuernberger Patrick, Kongsted Jacob, Hättig Christof
Quantum Chemistry Group, Ruhr University of Bochum, D-44780 Bochum, Germany.
Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense, Denmark.
J Chem Theory Comput. 2020 Aug 11;16(8):5203-5211. doi: 10.1021/acs.jctc.0c00489. Epub 2020 Jul 9.
The effects of biomolecular embedding on the photoinduced relaxation process of the DNA-minor-groove binder berenil, diminazene aceturate, are studied with quantum mechanics/molecular mechanics, QM/MM, calculations that employ the algebraic diagrammatic construction through second-order, ADC(2), for the quantum mechanical part and an atomistic polarizable embedding for the classical part. The lowest singlet excitation to the S state is a bright transition with a ππ* character and a perichromatic red shift, due to the interactions with the solvent and DNA. The excited-state relaxation pathway is a two-step mechanism, an N═N azo-bond stretch followed by a volume-conserving bicycle-pedal twist. The DNA confinement and the coupling to solvent molecules via hydrogen bonds lead, for the excited-state relaxation process, only to small deviations from the ideal bicycle-pedal relaxation. Because of its volume-conserving character, the S excited-state relaxation proceeds almost unhindered, even in a fully rigid minor-groove confinement. With a fully frozen DNA minor groove and solvent, the energy gap for deexcitation from S to the ground state increased to 2.0 eV compared to 0.16 eV in aqueous solution. When the relaxation of the first solvation shell is included, the relaxation process on the S potential energy surface proceeds to a region on the potential energy surface, where only a small gap to the ground-state potential energy surface remains, 0.43 eV. These results show that the solvent relaxation has a significant effect in controlling the energy gap between the ground and S electronically excited states, which explains the experimental observations of the fluorescence characteristics of berenil in DNA confinement.
采用量子力学/分子力学（QM/MM）计算方法研究了生物分子嵌入对DNA小沟结合剂贝尼尔（berenil）和乙酰马啉（diminazene aceturate）光诱导弛豫过程的影响。该计算方法在量子力学部分采用二阶代数图示构建法（ADC(2)），在经典部分采用原子可极化嵌入法。由于与溶剂和DNA的相互作用，最低单重激发到S态是一个具有ππ*特征和近色红移的明亮跃迁。激发态弛豫途径是一个两步机制，先是N═N偶氮键拉伸，然后是体积守恒的自行车踏板扭转。对于激发态弛豫过程，DNA限制以及通过氢键与溶剂分子的耦合仅导致与理想自行车踏板弛豫的小偏差。由于其体积守恒的特性，即使在完全刚性的小沟限制中，S激发态弛豫也几乎不受阻碍地进行。与水溶液中的0.16 eV相比，当DNA小沟和溶剂完全冻结时，从S态到基态去激发的能隙增加到2.0 eV。当包括第一溶剂化层的弛豫时，S势能面上的弛豫过程会进行到势能面上的一个区域，此时与基态势能面的能隙仅为0.43 eV。这些结果表明，溶剂弛豫在控制基态和S电子激发态之间的能隙方面具有显著作用，这解释了贝尼尔在DNA限制中荧光特性的实验观察结果。
