DNA骨架在介导B-DNA电子激发跃迁起源中的重要作用——来自长程校正TDDFT与定量化NTO分析的启示
Significant Role of DNA Backbone in Mediating the Transition Origin of Electronic Excitations of B-DNA - Implication from Long Range Corrected TDDFT and Quantified NTO Analysis
AI总结：
本研究结合长程校正TDDFT与QNTO分析，揭示DNA骨架、周围核碱基及构象变化会显著影响B-DNA中胸腺嘧啶相关电子激发的跃迁起源。
摘要：
我们利用近期提出的QNTO分析[J.-H. Li, J.-D. Chai, G. Y. Guo and M. Hayashi, Chem. Phys. Lett., 2011, 514, 362]，结合长程校正含时密度泛函理论（TDDFT）计算，系统研究了巨型分子体系电子激发可能具有的复杂跃迁起源。随后，以生物分子B-DNA中与胸腺嘧啶（Thy）相关的激发作为示例进行研究；这些模型体系提取自理想的或X射线晶体（PDB编号3BSE）的B-DNA结构，并至少包含一个Thy。在第一部分中，我们考虑由核心分子片段（如Thy、di-Thy）和所关注的周围物理/化学环境（如骨架、相邻堆叠核碱基）组成的体系，考察核心的激发性质如何随环境变化。我们发现，来自DNA骨架和周围核碱基的轨道经常参与Thy相关激发的跃迁，从而影响其组成、吸收能和振子强度。在第二部分中，我们考虑了不同来源（理想结构和3BSE）获得的各种B-DNA片段（如di-Thy、dTpdT等）激发性质由几何结构引起的变化。结果表明，这些片段中若干Thy相关激发的跃迁起源对微小构象变化十分敏感，这意味着细胞中受热运动影响的DNA可能不时表现出非常不同的光致物理和/或化学过程。
英文摘要：
We systematically investigate the possible complex transition origin of electronic excitations of giant molecular systems by using the recently proposed QNTO analysis [J.-H. Li, J.-D. Chai, G. Y. Guo and M. Hayashi, Chem. Phys. Lett., 2011, 514, 362.] combined with long-range corrected TDDFT calculations. Thymine (Thy) related excitations of biomolecule B-DNA are then studied as examples, where the model systems have been constructed extracting from the perfect or a X-ray crystal (PDB code 3BSE) B-DNA structure with at least one Thy included. In the first part, we consider the systems composed of a core molecular segment (e.g. Thy, di-Thy) and a surrounding physical/chemical environment of interest (e.g. backbone, adjacent stacking nucleobases) and examine how the excitation properties of the core vary in response to the environment. We find that the orbitals contributed from DNA backbone and surrounding nucleobases often participate in a transition of Thy-related excitations affecting their composition, absorption energy, and oscillator strength. In the second part, we take into account geometrically induced variation of the excitation properties of various B-DNA segments, e.g. di-Thy, dTpdT etc., obtained from different sources (ideal and 3BSE). It is found that the transition origin of several Thy-related excitations of these segments is sensitive to slight conformational variations, suggesting that DNA with thermal motions in cells may from time to time exhibit very different photo-induced physical and/or chemical processes.
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