Molecular modeling of zinc paddlewheel molecular complexes and the pores of a flexible metal organic framework
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- 作者：Khalid A. H. Alzahrani ; Robert J. Deeth
- 关键词：Force field ; Metal organic framework ; Molecular dynamics ; Molecular mechanics ; Transition metal complex
- 刊名：Journal of Molecular Modeling
- 出版年：2016
- 出版时间：April 2016
- 年：2016
- 卷：22
- 期：4
- 全文大小：2,788 KB
- 刊物类别：Chemistry and Materials Science
- 刊物主题：Chemistry
Computer Applications in Chemistry
Biomedicine
Molecular Medicine
Health Informatics and Administration
Life Sciences
Computer Application in Life Sciences - 出版者：Springer Berlin / Heidelberg
- ISSN：0948-5023
文摘
A new all-atom first-principles force field (FF) is constructed for the bimetallic, four-bladed zinc paddlewheel (ZPW) motif. Zinc-ligand interactions are described via Morse functions and the angular geometry at the metal centers is modeled with a pure ligand-ligand repulsion term. The ZPW-FF is principally based on 15 DFT-optimized model systems of general formula ZnPR.nL, where ZnP is the base Zn2(O2CR)4 unit, R = H, CH3 or CF3, L = NH3 or pyridine, and n = 0, 1 or 2. It correctly generates the distorted tetrahedral coordination of the uncapped [Zn2(O2CR)4] species in their ground states as well as giving reasonable structures and energies for the higher symmetry D4h transition state conformations. The zinc-ligand Morse function reference distance, r 0 , is further refined against 30 complexes located in the Cambridge Structural Database and this FF is applied to pore models of the flexible metal-organic framework (MOF) [Zn(bdc)2(dabco)]n (bdc = 1,4-benzendicarboxylate; dabco = 1,4-diazabicyclo(2.2.2)octane). A single pore model reproduces the unit cell of the evacuated MOF system while a 3×3 grid model is necessary to provide good agreement with the observed pronounced structural changes upon adsorption of either dimethylformamide or benzene.