Data for: Photoinduced charge separation and DNA self-repair depend on sequence directionality and stacking pattern

This directory contains the key computational data generated for the research generated for the research article entitled 'Photoinduced charge separation and DNA self-repair depend on sequence directionality and stacking pattern' by Kufner, C.L.*, Crucilla, S., Ding, D., Stadlbauer, P., Sponer, J., Szostak J.W., Sasselov D.D., Szabla, R.*. The article was resubmitted to the journal Chemical Science in December 2023, after revisions. The directories included here are listed below together with a brief description:- QMMM-pdb-files: final PDB files containing the minimum-energy geometries of the key points on excited-state and ground-state potential energy surfaces as discussed in the main article. The names of the files should be self-explanatory and correspond to the naming used in the main article. GS - ground state, S1 - first excited state, CI - conical intersection.- QMMM-results: directories containing raw data from the key QM/MM calculations.- clustering-based-on-MD: two sub-directories containing PDB files with the structures of clusters generated after processing of the molecular-dynamics (MD) trajectories, and .dat files containing information about cluster populations.- xyz-files: final xyz files containing only the structures of nucleobases or the whole tetranucleotide resulting from the QM/MM geometry optimizations. These structures are equivalent to the PDB files, albeit containing smaller fragments of the whole system (no MM part).<br>

本目录包含为Kufner, C.L.*、Crucilla, S.、Ding, D.、Stadlbauer, P.、Sponer, J.、Szostak J.W.、Sasselov D.D.、Szabla, R.*所撰写的研究论文《光诱导电荷分离与DNA自修复依赖于序列方向性与堆叠模式》生成的核心计算数据。该论文经修订后于2023年12月重新提交至《Chemical Science》期刊。
本次收录的目录及其简要说明如下：
- QMMM-pdb-files：包含本文正文讨论的激发态与基态势能面上关键节点的最低能量几何结构的最终PDB（Protein Data Bank）文件。文件名直观易懂，与正文中使用的命名规则一致。其中GS代表基态（ground state），S1代表第一激发态，CI代表锥形交叉点（conical intersection）。
- QMMM-results：包含核心量子力学/分子力学（QM/MM, Quantum Mechanics/Molecular Mechanics）计算原始数据的目录。
- clustering-based-on-MD：包含两个子目录，其一存放经分子动力学（molecular dynamics, MD）轨迹处理后生成的簇结构PDB文件，其二存放包含簇群分布占比信息的.dat数据文件。
- xyz-files：包含仅由QM/MM几何优化得到的核碱基结构或完整四核苷酸结构的最终xyz文件。此类结构与PDB文件等效，但仅包含整个系统的较小片段（不含分子力学部分）。