Supporting Information for the Journal Article "High-throughput ab initio reaction mechanism exploration in the cloud with automated multi-reference treatment"
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This dataset contains the supporting information for the journal article "High-throughput ab initio reaction mechanism exploration in the cloud with automated multi-reference treatment". It consists of two files: "structures.json", containing 3335 unique structures found in the exploration, and "energies.json", containing 2227 elementary steps and its energies found in the exploration In the file "structures.json", the following keys are used to characterize a structure: _id: the ID of the structure nAtoms: the total number of atoms in the structure atoms: the XYZ coordinates of the atoms in atomic units charge: the total charge of the structure multiplicity: the spin multiplicity 2S+1 of the structure label: the position of the structure on the minimum energy pathway In the file "energies.json", there are two major fields: structures and reactions. In the field "structures", the keys are: id: the ID of structure (can be linked to XYZ coordinates in "structures.json") label: the position of the structure on the minimum energy pathway energy_dft: PBE-D3BJ/def2-SVP total energy in atomic units energy_hf: HF/cc-pVDZ total energy in atomic units energy_ccsd: CCSD/cc-pVDZ total energy in atomic units energy_ccsd_t: CCSD(T)/cc-pVDZ total energy in atomic units energy_gibbs_correction: PBE-D3BJ/def2-SVP Gibbs free energy correction in atomic units In the field "reactions", the keys are: id: the ID of the elementary step lhs: the structure IDs on the left-hand side of the reaction rhs: the structure IDs on the right-hand side of the reaction type: regular or barrierless barrierless: binary key to indicate whether the elementary step has a barrier ts: ID of the transition state structure reaction: the ID of the reaction to which the elementary step belongs Due to the nature of exploration, certain structures can be explored from multiple elementary steps. Therefore, duplicated structures are common in the reaction exploration. In "structures.json", we de-duplicated the structures and only list the unique ones. The coordinates (in bohr) and global attributes like spin multiplicity and charge are provided. In "energies.json", each "step" represents an elementary step. 1260 of the steps are barrierless, while 967 of the steps have a barrier. The structures keys cited in "lhs", "rhs", and "ts" are before de-duplication. The "id" in each structure key points to the unique, de-duplicated structure in "structures.json". The main catalytical pathways (figure 9) can be found in the dataset with the following elementary_step IDs: 62066d2fb8e290f3afb607e2 6206704db8e290f3afb607e3 62067db7b8e290f3afb607e4 620a6d49b8e290f3afb607e5 620a6dbeb8e290f3afb607e6 620a6e2fb8e290f3afb607e7 620a6e78b8e290f3afb607e8 620a7f01b8e290f3afb607e9 620a7f54b8e290f3afb607ea
本数据集为期刊论文《基于自动化多参考处理的云端高通量从头算（ab initio）反应机理探索》的配套支撑信息。本数据集包含两个文件："structures.json"与"energies.json"。其中，"structures.json"收录了本次探索中得到的3335个独特结构；"energies.json"则包含本次探索发现的2227个基元反应步骤及其对应能量。 在"structures.json"文件中，每个结构通过以下关键字段表征： _id：结构的唯一标识符； nAtoms：结构内原子总数量； atoms：以原子单位（atomic units，a.u.）给出的原子XYZ坐标； charge：结构的总电荷； multiplicity：结构的自旋多重度2S+1（spin multiplicity）； label：该结构在最小能量路径上的位置。 "energies.json"包含两个核心字段：structures与reactions。 在structures字段中，其关键字段包括： id：结构标识符（可关联至"structures.json"中的原子坐标信息）； label：该结构在最小能量路径上的位置； energy_dft：以原子单位表示的PBE-D3BJ/def2-SVP总能量； energy_hf：以原子单位表示的HF/cc-pVDZ总能量； energy_ccsd：以原子单位表示的CCSD/cc-pVDZ总能量； energy_ccsd_t：以原子单位表示的CCSD(T)/cc-pVDZ总能量； energy_gibbs_correction：以原子单位表示的PBE-D3BJ/def2-SVP吉布斯自由能校正值。 在reactions字段中，其关键字段包括： id：基元反应步骤的唯一标识符； lhs：反应左侧（反应物侧）的结构标识符； rhs：反应右侧（产物侧）的结构标识符； type：反应类型，分为常规反应与无势垒反应； barrierless：二元标记字段，用于指示该基元反应步骤是否存在势垒； ts：过渡态结构的标识符； reaction：该基元反应所属的总反应标识符。 由于反应探索的特性，部分结构可通过多个基元反应步骤得到，因此探索过程中会出现大量重复结构。本数据集已对"structures.json"中的结构进行去重处理，仅保留独特结构，并提供了以玻尔（bohr）为单位的原子坐标，以及自旋多重度、总电荷等全局属性。 在"energies.json"中，每个"step"字段均对应一个基元反应步骤：其中1260个步骤为无势垒反应，967个步骤存在势垒。字段"lhs"、"rhs"与"ts"中引用的结构标识符为去重前的编号，而每个结构字段中的"id"则指向"structures.json"中已完成去重的唯一结构。 本数据集包含核心催化循环路径（图9）对应的基元反应步骤标识符如下： 62066d2fb8e290f3afb607e2、6206704db8e290f3afb607e3、62067db7b8e290f3afb607e4、620a6d49b8e290f3afb607e5、620a6dbeb8e290f3afb607e6、620a6e2fb8e290f3afb607e7、620a6e78b8e290f3afb607e8、620a7f01b8e290f3afb607e9、620a7f54b8e290f3afb607ea
