Ramos Pablo, Pavanello Michele
Department of Chemistry, Rutgers University , Newark, New Jersey 07102, United States.
J Chem Theory Comput. 2014 Jun 10;10(6):2546-56. doi: 10.1021/ct400921r.
In the past two decades, many research groups worldwide have tried to understand and categorize simple regimes in the charge transfer of such biological systems as DNA. Theoretically speaking, the lack of exact theories for electron-nuclear dynamics on one side and poor quality of the parameters needed by model Hamiltonians and nonadiabatic dynamics alike (such as couplings and site energies) on the other are the two main difficulties for an appropriate description of the charge transfer phenomena. In this work, we present an application of a previously benchmarked and linear-scaling subsystem density functional theory (DFT) method for the calculation of couplings, site energies, and superexchange decay factors (β) of several biological donor-acceptor dyads, as well as double stranded DNA oligomers composed of up to five base pairs. The calculations are all-electron and provide a clear view of the role of the environment on superexchange couplings in DNA-they follow experimental trends and confirm previous semiempirical calculations. The subsystem DFT method is proven to be an excellent tool for long-range, bridge-mediated coupling and site energy calculations of embedded molecular systems.
在过去二十年中，全球许多研究团队都试图理解并对诸如DNA等生物系统电荷转移中的简单机制进行分类。从理论上讲，一方面缺乏关于电子-核动力学的精确理论，另一方面模型哈密顿量和非绝热动力学所需参数的质量较差（如耦合和位点能量），这是恰当描述电荷转移现象的两个主要困难。在这项工作中，我们展示了一种先前经过基准测试的线性标度子系统密度泛函理论（DFT）方法的应用，用于计算几种生物供体-受体二元体系以及由多达五个碱基对组成的双链DNA寡聚物的耦合、位点能量和超交换衰减因子（β）。这些计算是全电子的，清晰地展现了环境对DNA中超交换耦合的作用——它们遵循实验趋势并证实了先前的半经验计算。子系统DFT方法被证明是用于嵌入式分子系统的远程、桥介导耦合和位点能量计算的优秀工具。
