State Key Laboratory of Molecular Reaction Dynamics, Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China.
Nat Protoc. 2015 Apr;10(4):632-42. doi: 10.1038/nprot.2015.038. Epub 2015 Mar 26.
This protocol is intended to provide chemists and physicists with a tool for predicting the charge carrier mobilities of π-stacked systems such as organic semiconductors and the DNA double helix. An experimentally determined crystal structure is required as a starting point. The simulation involves the following operations: (i) searching the crystal structure; (ii) selecting molecular monomers and dimers from the crystal structure; (iii) using density function theory (DFT) calculations to determine electronic coupling for dimers; (iv) using DFT calculations to determine self-reorganization energy of monomers; and (v) using a numerical calculation to determine the charge carrier mobility. For a single crystal structure consisting of medium-sized molecules, this protocol can be completed in ∼4 h. We have selected two case studies (a rubrene crystal and a DNA segment) as examples of how this procedure can be used.
本方案旨在为化学家与物理学家提供一种预测π堆积体系（如有机半导体和 DNA 双螺旋）载流子迁移率的工具。该方案需要以实验确定的晶体结构作为起点。模拟涉及以下操作：（i）搜索晶体结构；（ii）从晶体结构中选择分子单体和二聚体；（iii）使用密度泛函理论（DFT）计算确定二聚体的电子耦合；（iv）使用 DFT 计算确定单体的自重组能；以及（v）使用数值计算确定载流子迁移率。对于由中等大小分子组成的单晶结构，本方案大约需要 4 小时即可完成。我们选择了两个案例研究（芘晶体和 DNA 片段），作为说明此程序如何使用的示例。
