Heck Alexander, Woiczikowski P Benjamin, Kubař Tomáš, Welke Kai, Niehaus Thomas, Giese Bernd, Skourtis Spiros, Elstner Marcus, Steinbrecher Thomas B
Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Kaiserstrasse 12, Karlsruhe Institute of Technology , 76131 Karlsruhe, Germany.
J Phys Chem B. 2014 Apr 24;118(16):4261-72. doi: 10.1021/jp408907g. Epub 2014 Apr 11.
Charge transfer in peptides and proteins can occur on different pathways, depending on the energetic landscape as well as the coupling between the involved orbitals. Since details of the mechanism and pathways are difficult to access experimentally, different modeling strategies have been successfully applied to study these processes in the past. These can be based on a simple empirical pathway model, efficient tight binding type atomic orbital Hamiltonians or ab initio and density functional calculations. An interesting strategy, which allows an efficient calculations of charge transfer parameters, is based on a fragmentation of the system into functional units. While this works well for systems like DNA, where the charge transfer pathway is naturally divided into distinct molecular fragments, this is less obvious for charge transfer along peptide and protein backbones. In this work, we develop and access a strategy for an effective fragmentation approach, which allows one to compute electronic couplings for large systems along nanosecond time scale molecular dynamics trajectories. The new methodology is applied to a solvated peptide, for which charge transfer properties have been studied recently using an empirical pathway model. As could be expected, dynamical effects turn out to be important, which emphasizes the importance of using effective quantum approaches which allow for sufficient sampling. However, the computed rates are orders of magnitude smaller than experimentally determined, which indicates the shortcomings of present modeling approaches.
肽和蛋白质中的电荷转移可以通过不同途径发生，这取决于能量格局以及相关轨道之间的耦合。由于实验上难以获取该机制和途径的细节，过去已成功应用不同的建模策略来研究这些过程。这些策略可以基于简单的经验途径模型、高效的紧束缚型原子轨道哈密顿量或从头算和密度泛函计算。一种有趣的策略基于将系统分解为功能单元，它能有效地计算电荷转移参数。虽然这对于像DNA这样的系统效果很好，其电荷转移途径自然地分为不同的分子片段，但对于沿着肽和蛋白质主链的电荷转移来说就不那么明显了。在这项工作中，我们开发并采用了一种有效的分解方法策略，该策略能让人们沿着纳秒时间尺度的分子动力学轨迹计算大型系统的电子耦合。这种新方法应用于一个溶剂化肽，最近使用经验途径模型对其电荷转移性质进行了研究。正如预期的那样，动力学效应被证明很重要，这强调了使用能够进行充分采样的有效量子方法的重要性。然而，计算得到的速率比实验测定值小几个数量级，这表明当前建模方法存在不足。
