Molecular modeling of zinc paddlewheel molecular complexes and the pores of a flexible metal organic framework

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 Zn(2)(O(2)CR)(4) unit, R = H, CH(3) or CF(3), L = NH(3) or pyridine, and n = 0, 1 or 2. It correctly generates the distorted tetrahedral coordination of the uncapped [Zn(2)(O(2)CR)(4)] species in their ground states as well as giving reasonable structures and energies for the higher symmetry D(4h) 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. [Figure: see text] ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00894-016-2949-5) contains supplementary material, which is available to authorized users.