Refining the reaction mechanism of O2 towards its substrate in cofactor-free dioxygenases

Firefly inputs and outputs for the paper "Refining the reaction mechanism of O₂ towards its substrate in cofactor-free dioxygenases", to be submitted to PeerJ on or around 16 Jun 2016.<br>Four files are NOT inputs/outputs of quantum chemical computations:<br>- docking.tar, which contains the results of AutoDock VINA docking computations, as performed by YASARA. The files with .sce or .yob extensions may be viewed with YASARA.<br><br>-HODMe_grid.txt and HODnBu_grid.txt, which contain the data used to generate the 2D potential energy surfaces depicted in Figure 4.In these files, 1st column is C3-C4 distance (in angstrom); 2nd column is O-O distance (alson in angstrom; 3rd column is relative energy (in kcal/mol). <br><br>-BSSE.xls contains the energies for the evaluation of the effect of BSSE on the differences between the energies of radical-pairs at 80 angstrom distance and the values obtained by summing the energies of separate substrates. The gas-phase data clearly show that no BSSE error exists. The difference in solution energies is likewise independent of the SCF energy, and comes about simply due to the way the PCM model treats a system with two separated cavities: the final column ("total interaction") shows that in the radical pair the difference of solvation energy (vs. independent substrates) is almost exactly equal to the difference of total energy. I am still trying to understand why such difference is only apparent in the radical pair system, and not in the HODMe:O2 system. <br>

本数据集为拟于2016年6月16日左右提交至PeerJ期刊的论文《无辅因子加氧酶中O₂与底物的反应机制优化》配套的Firefly量化计算程序输入与输出文件。
以下4个文件不属于量子化学计算的输入/输出文件：
- docking.tar：包含由YASARA调用AutoDock VINA完成的分子对接计算结果。扩展名为.sce或.yob的文件可通过YASARA软件查看。
- HODMe_grid.txt与HODnBu_grid.txt：包含用于生成图4所示二维势能面的数据。该类文件中，第一列为C3-C4键长（单位：埃），第二列为O-O键长（单位：埃），第三列为相对能量（单位：千卡/摩尔）。
- BSSE.xls：包含用于评估基组叠加误差（BSSE）对80埃距离下自由基对能量与独立底物能量之和的差值的影响的相关数据。气相计算数据明确显示不存在基组叠加误差。溶液相中的能量差同样与自洽场（SCF）能量无关，其成因仅为极化连续介质模型（PCM）对双分离空腔体系的处理方式：最后一列（"总相互作用"）显示，自由基对体系中，（与独立底物相比的）溶剂化能量差值几乎完全等于总能量差值。目前笔者仍在探究为何此类差值仅在自由基对体系中显现，而非在HODMe:O₂体系中出现。