Molecular simulation of flexible helical metal-organic frameworks
Ouja, Najib (2008) Molecular simulation of flexible helical metal-organic frameworks. PhD thesis, University of Warwick.
WRAP_THESIS_Ouja_2009.pdf - Requires a PDF viewer such as GSview, Xpdf or Adobe Acrobat Reader
Official URL: http://webcat.warwick.ac.uk/record=b2283084~S9
In this work, force fields were developed to model flexible helical metalorganic framework solids (MOFs). Since no suitable force fields to model flexible MOFs had been reported, the study began by benchmarking an existing organic force field, CHARMM22, against Ni3(BTC)2(pyridine)6(4,5octanediol) 3. CHARMM22 force filed did produce a framework that retained its original threedimensional structure for the duration of the simulations, and did so at experimentally relevant temperatures provided a minimum number of 20 solvent molecules per unit cell were included. However, important inadequacies were found between the experimental crystal structure and the simulated one. Therefore a series of refinements of the force field were performed. The three best modified force fields were then used to simulate this MOF and a detailed analysis of its physical properties produced. A key conclusion from the development and testing cycle was that hydrogen bonding between the BTC and the hydroxyl groups of both the solvent and the framework alcohol molecules played a critical role in stabilizing the MOF. The transferability of these forcefields was tested against two new MOFs, for which experimental crystal structures had been reported: Ni3(BTC)2(pyridine)6(2,3butanediol) 3 (called MOF4) and Ni3(BTC)2(pyridine)6(1,2,6hexanetriol) 3 (called MOF6). One forcefield was found to give a good description of MOF4. For MOF6 however, competition for framework bonding between the diol and terminal hydroxyl group on the hexanetriol destabilized the framework with all three force fields. A stable MOF was produced only when the NiOT bond lengths were constrained to the experimental values. It was concluded that polarisation of ligand donor atoms by the Ni2+ needed to be incorporated in any future refinements of the forcefield. Finally, this study showed that the Ni3(BTC)2(pyridine)6(4,5octanediol) 3 MOF can display enantioselective properties. Solvent alcohol molecules of the same enantiomeric form as that incorporated into the framework were found to interact much more strongly with the framework than their enantiomer, and even formed enantiomer specific hydrogen bonds with the framework. Structural differences were also observed in solventBTC, solventNi and solvent pyridine geometries.
|Item Type:||Thesis or Dissertation (PhD)|
|Subjects:||Q Science > QD Chemistry|
|Library of Congress Subject Headings (LCSH):||Nitrogen compounds -- Research, Solvents -- Research, Molecular dynamics, Structural bioinformatics|
|Institution:||University of Warwick|
|Theses Department:||Department of Chemistry|
|Supervisor(s)/Advisor:||Rodger, P. Mark|
|Format of File:||pddf|
|Extent:||142 leaves : col. ill., charts|
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