Dataset Information

Torsional flexibility in zinc-benzenedicarboxylate metal-organic frameworks.

ABSTRACT: We explore the role and nature of torsional flexibility of carboxylate-benzene links in the structural chemistry of metal-organic frameworks (MOFs) based on Zn and benzenedicarboxlyate (bdc) linkers. A particular motivation is to understand the extent to which such flexibility is important in stabilising the unusual topologically aperiodic phase known as TRUMOF-1. We compare the torsion angle distributions of TRUMOF-1 models with those for crystalline Zn/1,3-bdc MOFs, including a number of new materials whose structures we report here. We find that both periodic and aperiodic Zn/1,3-bdc MOFs sample a similar range of torsion angles, and hence the formation of TRUMOF-1 does not require any additional flexibility beyond that already evident in chemically-related crystalline phases. Comparison with Zn/1,4-bdc MOFs does show, however, that the lower symmetry of the 1,3-bdc linker allows access to a broader range of torsion angles, reflecting a greater flexibility of this linker.

SUBMITTER: Meekel EG

PROVIDER: S-EPMC10823780 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature

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Torsional flexibility in zinc-benzenedicarboxylate metal-organic frameworks.

Meekel Emily G EG Nicholas Thomas C TC Slater Ben B Goodwin Andrew L AL

CrystEngComm 20231229 5

We explore the role and nature of torsional flexibility of carboxylate-benzene links in the structural chemistry of metal-organic frameworks (MOFs) based on Zn and benzenedicarboxlyate (bdc) linkers. A particular motivation is to understand the extent to which such flexibility is important in stabilising the unusual topologically aperiodic phase known as TRUMOF-1. We compare the torsion angle distributions of TRUMOF-1 models with those for crystalline Zn/1,3-bdc MOFs, including a number of new m ...[more]

PMID: 38293003

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Project description:In this work, forcefield flexibility parameters were constructed and validated for more than 100 metal-organic frameworks (MOFs). We used atom typing to identify bond types, angle types, and dihedral types associated with bond stretches, angle bends, dihedral torsions, and other flexibility interactions. Our work used Manz's angle-bending and dihedral-torsion model potentials. For a crystal structure containing N atoms in its unit cell, the number of independent flexibility interactions is 3(N atoms - 1). Because the number of bonds, angles, and dihedrals is normally much larger than 3(N atoms - 1), these internal coordinates are redundant. To reduce (but not eliminate) this redundancy, our protocol prunes dihedral types in a way that preserves symmetry equivalency. Next, each dihedral type is classified as non-rotatable, hindered, rotatable, or linear. We introduce a smart selection method that identifies which particular torsion modes are important for each rotatable dihedral type. Then, we computed the force constants for all flexibility interactions together via LASSO regression (i.e., regularized linear least-squares fitting) of the training dataset. LASSO automatically identifies and removes unimportant forcefield interactions. For each MOF, the reference dataset was quantum-mechanically-computed in VASP via DFT with dispersion and included: (i) finite-displacement calculations along every independent atom translation mode, (ii) geometries randomly sampled via ab initio molecular dynamics (AIMD), (iii) the optimized ground-state geometry using experimental lattice parameters, and (iv) rigid torsion scans for each rotatable dihedral type. After training, the flexibility model was validated across geometries that were not part of the training dataset. For each MOF, we computed the goodness of fit (R-squared value) and the root-mean-squared error (RMSE) separately for the training and validation datasets. We compared flexibility models with and without bond-bond cross terms. Even without cross terms, the model yielded R-squared values of 0.910 (avg across all MOFs) ± 0.018 (st. dev.) for atom-in-material forces in the validation datasets. Our SAVESTEPS protocol should find widespread applications to parameterize flexible forcefields for material datasets. We performed molecular dynamics simulations using these flexibility parameters to compute heat capacities and thermal expansion coefficients for two MOFs.

Dataset Information

Torsional flexibility in zinc-benzenedicarboxylate metal-organic frameworks.

Publications

Torsional flexibility in zinc-benzenedicarboxylate metal-organic frameworks.

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