Issue 45, 2020

Identifying misbonded atoms in the 2019 CoRE metal–organic framework database


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.

Graphical abstract: Identifying misbonded atoms in the 2019 CoRE metal–organic framework database

Supplementary files

Article information

Article type
18 Mar 2020
10 Jul 2020
First published
20 Jul 2020
This article is Open Access
Creative Commons BY license

RSC Adv., 2020,10, 26944-26951

Identifying misbonded atoms in the 2019 CoRE metal–organic framework database

T. Chen and T. A. Manz, RSC Adv., 2020, 10, 26944 DOI: 10.1039/D0RA02498H

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