Identifying misbonded atoms in the 2019 CoRE metal-organic framework database.
Identifying misbonded atoms in the 2019 CoRE metal-organic framework database.
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实验衍生的金属有机框架 (MOF) 晶体结构数据库可用于大规模计算筛选，以确定哪些 MOF 最适合特定应用。然而，必须清洁这些晶体结构以识别和/或纠正各种伪影。最近发布的 2019 CoRE MOF 数据库（Chung 等人，J. Chem. Eng. Data, 2019, 64, 5985–5998）报告了数千个实验衍生的晶体结构，这些结构经过部分清洗以去除溶剂分子，识别数百个无序结构（其中约 30 个被纠正），并手动纠正约 100 个结构（例如，添加缺失的氢原子）。在此，对 2019 CoRE MOF 数据库进行进一步清理，以识别具有错误键合或孤立原子的结构：（i）包含孤立原子的结构，（ii）包含原子太靠近（即重叠原子）的结构，（iii）包含错位氢原子的结构，（iv）包含键合不足碳原子的结构（可能是由缺失氢原子引起的）， (v)含有过度键合碳原子的结构。这项研究不应被视为对该数据库的最终清理，而是朝着有一天实现一套完全清理的实验衍生 MOF 晶体结构的目标前进。我们对所有接受的结构进行了原子分型，以识别那些可以通过之前报道的力场前体进行参数化的结构（Chen 和 Manz, RSC Adv., 2019, 9, 36492–36507）。我们在 2019 年 CoRE MOF 数据库中报告了 5000 多个 MOF 的几种力场前兆（例如，净原子电荷、材料中原子极化率、材料中原子色散系数、电子云参数等）。通过识别包含孤立原子、重叠原子、错位的氢和键合不足/过度的碳的结构，对 2019 年 CoRE MOF 数据库进行了清理。
Databases of experimentally-derived metal–organic framework (MOF) crystal structures are useful for large-scale computational screening to identify which MOFs are best-suited for particular applications. However, these crystal structures must be cleaned to identify and/or correct various artifacts. The recently published 2019 CoRE MOF database (Chung et al., J. Chem. Eng. Data, 2019, 64, 5985–5998) reported thousands of experimentally-derived crystal structures that were partially cleaned to remove solvent molecules, to identify hundreds of disordered structures (approximately thirty of those were corrected), and to manually correct approximately 100 structures (e.g., adding missing hydrogen atoms). Herein, further cleaning of the 2019 CoRE MOF database is performed to identify structures with misbonded or isolated atoms: (i) structures containing an isolated atom, (ii) structures containing atoms too close together (i.e., overlapping atoms), (iii) structures containing a misplaced hydrogen atom, (iv) structures containing an under-bonded carbon atom (which might be caused by missing hydrogen atoms), and (v) structures containing an over-bonded carbon atom. This study should not be viewed as the final cleaning of this database, but rather as progress along the way towards the goal of someday achieving a completely cleaned set of experimentally-derived MOF crystal structures. We performed atom typing for all of the accepted structures to identify those structures that can be parameterized by previously reported forcefield precursors (Chen and Manz, RSC Adv., 2019, 9, 36492–36507). We report several forcefield precursors (e.g., net atomic charges, atom-in-material polarizabilities, atom-in-material dispersion coefficients, electron cloud parameters, etc.) for more than five thousand MOFs in the 2019 CoRE MOF database. The 2019 CoRE MOF database was cleaned by identifying structures containing isolated atoms, overlapping atoms, misplaced hydrogens, and under/over-bonded carbons.
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影响因子：
3.9
作者：
Limas, Nidia Gabaldon;Manz, Thomas A.
通讯作者：
Manz, Thomas A.
影响因子：
3.9
作者：
Chen, Taoyi;Manz, Thomas A.
通讯作者：
Manz, Thomas A.
影响因子：
3.9
作者：
通讯作者：
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影响因子：
8.6
作者：
Chung, Yongchul G.;Camp, Jeffrey;Snurr, Randall Q.
通讯作者：
Snurr, Randall Q.
影响因子：
4.9
作者：
Horton, Joshua T.;Allen, Alice E. A.;Cole, Daniel J.
通讯作者：
Cole, Daniel J.