skip to main content


Title: 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.  more » « less
Award ID(s):
1555376
NSF-PAR ID:
10175327
Author(s) / Creator(s):
;
Date Published:
Journal Name:
RSC Advances
Volume:
10
Issue:
45
ISSN:
2046-2069
Page Range / eLocation ID:
26944 to 26951
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. A host of important performance properties for metal–organic frameworks (MOFs) and other complex materials can be calculated by modeling statistical ensembles. The principle challenge is to develop accurate and computationally efficient interaction models for these simulations. Two major approaches are (i) ab initio molecular dynamics in which the interaction model is provided by an exchange–correlation theory ( e.g. , DFT + dispersion functional) and (ii) molecular mechanics in which the interaction model is a parameterized classical force field. The first approach requires further development to improve computational speed. The second approach requires further development to automate accurate forcefield parameterization. Because of the extreme chemical diversity across thousands of MOF structures, this problem is still mostly unsolved today. For example, here we show structures in the 2014 CoRE MOF database contain more than 8 thousand different atom types based on first and second neighbors. Our results showed that atom types based on both first and second neighbors adequately capture the chemical environment, but atom types based on only first neighbors do not. For 3056 MOFs, we used density functional theory (DFT) followed by DDEC6 atomic population analysis to extract a host of important forcefield precursors: partial atomic charges; atom-in-material (AIM) C 6 , C 8 , and C 10 dispersion coefficients; AIM dipole and quadrupole moments; various AIM polarizabilities; quantum Drude oscillator parameters; AIM electron cloud parameters; etc. Electrostatic parameters were validated through comparisons to the DFT-computed electrostatic potential. These forcefield precursors should find widespread applications to developing MOF force fields. 
    more » « less
  2. Abstract

    Ammonia is a widely used toxic industrial chemical that can cause severe respiratory ailments. Therefore, understanding and developing materials for its efficient capture and controlled release is necessary. One such class of materials is 3D porous metal‐organic frameworks (MOFs) with exceptional surface areas and robust structures, ideal for gas storage/transport applications. Herein, interactions between ammonia and UiO‐67‐X (X: H, NH2, CH3) zirconium MOFs were studied under cryogenic, ultrahigh vacuum (UHV) conditions using temperature‐programmed desorption mass spectrometry (TPD‐MS) and in‐situ temperature‐programmed infrared (TP‐IR) spectroscopy. Ammonia was observed to interact with μ3−OH groups present on the secondary building unit of UiO‐67‐X MOFs via hydrogen bonding. TP‐IR studies revealed that under cryogenic UHV conditions, UiO‐67‐X MOFs are stable towards ammonia sorption. Interestingly, an increase in the intensity of the C−H stretching mode of the MOF linkers was detected upon ammonia exposure, attributed to NH−π interactions with linkers. These same binding interactions were observed in grand canonical Monte Carlo simulations. Based on TPD‐MS, binding strength of ammonia to three MOFs was determined to be approximately 60 kJ mol−1, suggesting physisorption of ammonia to UiO‐67‐X. In addition, missing linker defect sites, consisting of H2O coordinated to Zr4+sites, were detected through the formation ofnNH3⋅H2O clusters, characterized through in‐situ IR spectroscopy. Structures consistent with these assignments were identified through density functional theory calculations. Tracking these bands through adsorption on thermally activated MOFs gave insight into the dehydroxylation process of UiO‐67 MOFs. This highlights an advantage of using NH3for the structural analysis of MOFs and developing an understanding of interactions between ammonia and UiO‐67‐X zirconium MOFs, while also providing directions for the development of stable materials for efficient toxic gas sorption.

     
    more » « less
  3. Genetic information is encoded in the DNA double helix, which, in its physiological milieu, is characterized by the iconical Watson-Crick nucleo-base pairing. Recent NMR relaxation experiments revealed the transient presence of an alternative, Hoogsteen (HG) base pairing pattern in naked DNA duplexes, and estimated its relative stability and lifetime. In contrast with DNA, such structures were not observed in RNA duplexes. Understanding HG base pairing is important because the underlying "breathing" motion between the two conformations can significantly modulate protein binding. However, a detailed mechanistic insight into the transition pathways and kinetics is still missing. We performed enhanced sampling simulation (with combined metadynamics and adaptive force-bias method) and Markov state modeling to obtain accurate free energy, kinetics, and the intermediates in the transition pathway between Watson-Crick and HG base pairs for both naked B-DNA and A-RNA duplexes. The Markov state model constructed from our unbiased MD simulation data revealed previously unknown complex extrahelical intermediates in the seemingly simple process of base flipping in B-DNA. Extending our calculation to A-RNA, for which HG base pairing is not observed experimentally, resulted in relatively unstable, single-hydrogen-bonded, distorted Hoogsteen-like bases. Unlike B-DNA, the transition pathway primarily involved base paired and intrahelical intermediates with transition timescales much longer than that of B-DNA. The seemingly obvious flip-over reaction coordinate (i.e., the glycosidic torsion angle) is unable to resolve the intermediates. Instead, a multidimensional picture involving backbone dihedral angles and distance between hydrogen bond donor and acceptor atoms is required to gain insight into the molecular mechanism. 
    more » « less
  4. Abstract

    Binuclear alkyne manganese carbonyls of the type (RC≡CR')Mn2(CO)n(R and R'=methyl or dimethylamino;n=8, 7, 6) and their isomers related to the experimentally known (MeC2NEt2)Mn2(CO)n(n=8, 7) structures have been investigated by density functional theory. The alkyne ligand remains intact in the only low energy (Me2N)2C2Mn2(CO)8isomer, which has a central Mn2C2tetrahedrane unit and is otherwise analogous to the well‐known (alkyne)Co2(CO)6derivatives except for one more CO group per metal atom. The low‐energy structures of the unsaturated (Me2N)2C2Mn2(CO)n(n=7, 6) systems include isomers in which the nitrogen atom of one of the dimethylamino groups as well as the C≡C triple bond of the alkyne is coordinated to the central Mn2unit. In other low‐energy (Me2N)2C2Mn2(CO)n(n=7, 6) isomers the alkyne C≡C triple bond has broken completely to form two separate bridging dimethylaminocarbyne Me2NC ligands analogous to the experimentally known iron carbonyl complex (Et2NC)2Fe2(CO)6. The (alkyne)Mn2(CO)n(n=8, 7, 6) systems of the alkynes MeC≡CMe and Me2NC≡CMe with methyl substituents have significantly more complicated potential surfaces. In these systems the lowest energy isomers have bridging ligands derived from the alkyne in which one or two hydrogen atoms have migrated from a methyl group to one or both of the alkyne carbon atoms. These bridging ligands include allene, manganallyl, and vinylcarbene ligands, the first two of which have been realized experimentally in research by Adams and coworkers. Theoretical studies suggest that the mechanism for the conversion of the simple alkyne octacarbonyl (MeC2NMe2)Mn2(CO)8to the dimethylaminomanganaallyl complex Mn2(CO)7[μ‐η4‐C3H3Me2] involves decarbonylation to the heptacarbonyl and the hexacarbonyl complexes. Subsequent hydrogen migrations then occur through intermediates with C−H−Mn agostic interactions to give the final product. Eight transition states for this mechanistic sequence have been identified with activation energies of ∼20 kcal/mol for the first hydrogen migration and ∼14 kcal/mol for the second hydrogen migration.

     
    more » « less
  5. Metal–organic frameworks (MOFs) are a class of nanoporous materials with highly tunable structures in terms of both chemical composition and topology. Due to their tunable nature, high‐throughput computational screening is a particularly appealing method to reduce the time‐to‐discovery of MOFs with desirable physical and chemical properties. In this work, a fully automated, high‐throughput periodic density functional theory (DFT) workflow for screening promising MOF candidates was developed and benchmarked, with a specific focus on applications in catalysis. As a proof‐of‐concept, we use the high‐throughput workflow to screen MOFs containing open metal sites (OMSs) from the Computation‐Ready, Experimental MOF database for the oxidative C—H bond activation of methane. The results from the screening process suggest that, despite the strong C—H bond strength of methane, the main challenge from a screening standpoint is the identification of MOFs with OMSs that can be readily oxidized at moderate reaction conditions. © 2019 Wiley Periodicals, Inc.

     
    more » « less