Fragment Orbital Based Description of Charge Transfer in Peptides Including Backbone Orbitals
Fragment Orbital Based Description of Charge Transfer in Peptides Including Backbone Orbitals
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DOI：
10.1021/jp408907g
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发表时间：
2014-04-24
影响因子：
3.3
通讯作者：
Steinbrecher, Thomas B.
中科院分区：
文献类型：
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作者：
Heck, Alexander;Woiczikowski, P. Benjamin;Steinbrecher, Thomas B.
多肽和蛋白质中的电荷转移可以发生在不同的路径上，这取决于能量景观以及所涉及的轨道之间的耦合。由于机制和途径的细节很难通过实验获得，不同的建模策略在过去被成功地应用于研究这些过程。这些方法可以基于简单的经验路径模型、有效的紧束缚类型的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，允许有效地计算电荷转移参数，是基于将系统分割成功能单元。虽然这对DNA这样的系统很有效，因为在DNA系统中，电荷转移路径自然地被划分为不同的分子片段，但对于沿着多肽和蛋白质骨架进行的电荷转移来说，这就不那么明显了。在这项工作中，我们开发并访问了一种有效的碎片化方法的策略，该方法允许沿着纳秒时间尺度的分子动力学轨迹计算大系统的电子耦合。新的方法被应用于一种溶剂化的多肽，最近已经用经验路径模型研究了它的电荷转移性质。正如可以预期的那样，动力学效应被证明是重要的，这强调了使用有效的量子方法的重要性，这种方法允许足够的采样。然而，计算的速率比实验确定的要小一个数量级，这表明了目前建模方法的缺陷。
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.