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Crossley-Lewis J, Dunn J, Buda C, Sunley GJ, Elena AM, Todorov IT, Yong CW, Glowacki DR, Mulholland AJ, Allan NL. Interactive molecular dynamics in virtual reality for modelling materials and catalysts. J Mol Graph Model 2023; 125:108606. [PMID: 37660615 PMCID: PMC7616772 DOI: 10.1016/j.jmgm.2023.108606] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/05/2023]
Abstract
Interactive molecular dynamics simulation in virtual reality (iMD-VR) is emerging as a promising technique in molecular science. Here, we demonstrate its use in a range of fifteen applications in materials science and heterogeneous catalysis. In this work, the iMD-VR package Narupa is used with the MD package, DL_POLY [1]. We show how iMD-VR can be used to: (i) investigate the mechanism of lithium fast ion conduction by directing the formation of defects showing that vacancy transport is favoured over interstitialcy mechanisms, and (ii) guide a molecule through a zeolite pore to explore diffusion within zeolites, examining in detail the motion of methyl n-hexanoate in H-ZSM-5 zeolite and identifying bottlenecks restricting diffusion. iMD-VR allows users to manipulate these systems intuitively, to drive changes in them and observe the resulting changes in structure and dynamics. We make these simulations available, as a resource for both teaching and research. All simulation files, with videos, can be found online (https://doi.org/10.5281/zenodo.8252314) and are provided as open-source material.
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Affiliation(s)
- Joe Crossley-Lewis
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Josh Dunn
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Corneliu Buda
- Applied Sciences, bp Innovation and Engineering, BP plc, 150 West Warrenville Road, Naperville, IL, 60563, USA
| | - Glenn J Sunley
- Applied Sciences, bp Innovation and Engineering, BP plc, Saltend, Hull, HU12 8DS, UK
| | - Alin M Elena
- Scientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK
| | - Ilian T Todorov
- Scientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK
| | - Chin W Yong
- Scientific Computing Department, STFC Daresbury Laboratory, Daresbury, UK
| | - David R Glowacki
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Neil L Allan
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
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Zabihpour A, Ahmadpour J, Yaripour F. Strategies to control reversible and irreversible deactivation of ZSM-5 zeolite during the conversion of methanol to propylene (MTP): a review. Chem Eng Sci 2023. [DOI: 10.1016/j.ces.2023.118639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
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Zhou Z, Jiang R, Chen X, Wang X, Hou H. One-step synthesis of hierarchical lamellar H-ZSM-5 zeolite and catalytic performance of methanol to olefin. J SOLID STATE CHEM 2021. [DOI: 10.1016/j.jssc.2021.122132] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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