DNA介导的长程电荷转移速率常数的计算

The present study aims at establishing a programmatic way which quantitatively predicts the electronic conductivity of a given DNA fragmentation. Generally, DNA-mediated charge transfer (DNA CT) is controlled by whether consecutive hopping or superexchange mechanism. The former can transport a charge to a remote distance while the latter can be valid just within a few base pairs. Both of them are considered here. Concretely, for the given DNA fragmentation, firstly all possible single-step charge transfer rates via hopping or superexchange are calculated, and then the most probable transport path can be determined by kinetic Monte Carlo method, and finally the characteristic current through the DNA, which implicates the conductivity of this DNA fragmentation, can be evaluated. Since the rates are obtained by Marcus electron transfer theory, necessary parameters are treated as follows: (1) About reorganization energy, only the contributions of the bases themselves are considered. The effects from the environment are assumed to be equal on an average and so have no significant affect on relative rates. In fact, what we concerned through this whole work are relative conductivities. (2) About the site energy, its dependences on the π-stacked effect and the base sequence are considered. (3) About charge transfer integrals, we perform molecular dynamics in advance to reflect the conformational fluctuation of DNA so the charge transfer integrals are obtained by dynamic average values.

本研究旨在建立一套可对任意DNA片段上发生的长程电荷转移速率进行定量评估的可执行的程序化方法。一般来说，由DNA介导的电荷转移可通过连续跳跃或超交换机制进行传输，前者可在长距离内传输电荷，而后者只在短距离内有效。本方法中，在一段DNA序列给定后，首先对其所有可能通过单步跳跃或超交换发生电荷转移的区间进行判断，计算出单步转移速率，然后用动力学蒙特卡洛方法确定最可能的传输路径，最后估算出电荷通过这段DNA时产生的电流，而这个电流可用来表征其固有导电性质。其中，速率常数的计算基于Marcus电子转移理论，在获取所需参数时做了如下处理：(1) 对重组能的计算假定环境的贡献平均下来对所有碱基是一样的；(2) 计算位点能时考虑了相邻碱基的差异性和堆积作用的影响；(3) 对电荷转移积分的计算取的是考虑DNA波动效应后的动态平均值。这样一套方案是可程序化的，对于任意DNA序列标准相同而且是可执行的。

本工作主要分两部分:.• DNA 电荷传输动力学的建立.结合经典分子动力学、量子化学、半古典电子转移理论和动态蒙特卡洛方法，可模拟出一段 DNA 上的电荷动力学。此方法对通过弱相互作用堆积在一起的软物质体系中的电荷传输过程具有普适性。.• π 堆积体系电荷离域结构的表征.像 DNA 这样的 π 堆积体系，碱基对之间是通过弱相互作用堆积在一起。如果一个电荷在碱基上，那么电荷的离域/定域性质很难直接用像分子中的原子之间的电子离域一样处理。为了表征这种分子间的电荷离域性质,我们定义了轨道离域指数、π 堆积离域指数、离域域、离域图等概念，并结合机器学习中的分类方法，可以对任一给出的 π 堆积构象所具有的离域结构给出一个定量的分析。此方法对 π堆积体系电荷传输性质的解析具有普适性。