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Dureckova H, Woo TK, Alavi S, Ripmeester JA. Molecular dynamics simulation of halogen bonding in Cl2, BrCl, and mixed Cl2/Br2 clathrate hydrates. CAN J CHEM 2015. [DOI: 10.1139/cjc-2014-0593] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Clathrate hydrate phases of dihalogen molecules have properties that differ from those of other guest molecules of similar size. The water oxygen–chlorine distances in the structure I (sI) Cl2 hydrate are smaller than the sum of the van der Waals radii of oxygen and chlorine. Bromine hydrate forms a unique clathrate hydrate structure that is not seen in other guest substances. In mixed Cl2/Br2 structure I hydrate, the water oxygen–bromine distances are also smaller than the sum of the oxygen and bromine van der Waals radii. We previously studied the structure of three dihalogen clathrate hydrates using single crystal X-ray diffraction and described these structural features in terms of halogen bonding between the dihalogen and water molecules. In this work, we perform molecular dynamics simulations of cubic sI Cl2, mixed Cl2/Br2, and BrCl clathrate hydrate phases. We perform quantum chemical computations on the dihalogen molecules to determine the nature of σ-hole near the halogen atoms. We fit the electrostatic potential of the molecules to point charge models including dummy atoms that represent σ-holes adjacent to the halogen molecules. Molecular dynamics simulations are used to determine the lattice constants, radial distribution functions, and guest dynamics in these phases. We determine the effect of guest size and difference in halogen bonding on the properties of the clathrate hydrate phase. Simulations for the Cl2, BrCl, and mixed Cl2/Br2 hydrates are performed with small cages of the sI clathrate hydrate phases completely full or filled with experimental occupancies with Cl2 guests.
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Affiliation(s)
- Hana Dureckova
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Tom K. Woo
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Saman Alavi
- Department of Chemistry, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
| | - John A. Ripmeester
- National Research Council Canada, 100 Sussex Drive, Ottawa, ON K1A 0R6, Canada
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Moudrakovski IL, Udachin KA, Alavi S, Ratcliffe CI, Ripmeester JA. Facilitating guest transport in clathrate hydrates by tuning guest-host interactions. J Chem Phys 2015; 142:074705. [DOI: 10.1063/1.4907720] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Igor L. Moudrakovski
- National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A 0R6, Canada
| | - Konstantin A. Udachin
- National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A 0R6, Canada
| | - Saman Alavi
- National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A 0R6, Canada
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | | | - John A. Ripmeester
- National Research Council of Canada, 100 Sussex Dr., Ottawa, Ontario K1A 0R6, Canada
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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Torres Trueba A, Kroon MC, Peters CJ, Moudrakovski IL, Ratcliffe CI, Alavi S, Ripmeester JA. Inter-cage dynamics in structure I, II, and H fluoromethane hydrates as studied by NMR and molecular dynamics simulations. J Chem Phys 2014; 140:214703. [PMID: 24908031 DOI: 10.1063/1.4874636] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Prospective industrial applications of clathrate hydrates as materials for gas separation require further knowledge of cavity distortion, cavity selectivity, and defects induction by guest-host interactions. The results presented in this contribution show that under certain temperature conditions the guest combination of CH3F and a large polar molecule induces defects on the clathrate hydrate framework that allow intercage guest dynamics. (13)C NMR chemical shifts of a CH3F/CH4/TBME sH hydrate and a temperature analysis of the (2)H NMR powder lineshapes of a CD3F/THF sII and CD3F/TBME sH hydrate, displayed evidence that the populations of CH4 and CH3F in the D and D' cages were in a state of rapid exchange. A hydrogen bonding analysis using molecular dynamics simulations on the TBME/CH3F and TBME/CH4 sH hydrates showed that the presence of CH3F enhances the hydrogen bonding probability of the TBME molecule with the water molecules of the cavity. Similar results were obtained for THF/CH3F and THF/CH4 sII hydrates. The enhanced hydrogen bond formation leads to the formation of defects in the water hydrogen bonding lattice and this can enhance the migration of CH3F molecules between adjacent small cages.
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Affiliation(s)
- Alondra Torres Trueba
- Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, Ontario, K1A 0R6, Canada
| | - Maaike C Kroon
- Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, Separation Technology Group, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Cor J Peters
- Eindhoven University of Technology, Department of Chemical Engineering and Chemistry, Separation Technology Group, Den Dolech 2, 5612 AZ Eindhoven, The Netherlands
| | - Igor L Moudrakovski
- Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, Ontario, K1A 0R6, Canada
| | - Christopher I Ratcliffe
- Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, Ontario, K1A 0R6, Canada
| | - Saman Alavi
- Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, Ontario, K1A 0R6, Canada
| | - John A Ripmeester
- Steacie Institute for Molecular Sciences, National Research Council Canada, Ottawa, Ontario, K1A 0R6, Canada
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Hiratsuka M, Ohmura R, Sum AK, Yasuoka K. Vibrational modes of methane in the structure H clathrate hydrate from ab initio molecular dynamics simulation. J Chem Phys 2013; 137:144306. [PMID: 23061847 DOI: 10.1063/1.4757914] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Vibrational spectra of guest molecules in clathrate hydrates are frequently measured to determine the characteristic signatures of the molecular environment and dynamical properties of guest-host interactions. Here, we present results of our study on the vibrational frequencies of methane molecules in structure H clathrate hydrates, namely, in the 5(12) and 4(3)5(6)6(3) cages, as the frequencies of stretching vibrational modes in these environments are still unclear. The vibrational spectra of methane molecules in structure H clathrate hydrate were obtained from ab initio molecular dynamics simulation and computed from Fourier transform of autocorrelation functions for each distinct vibrational mode. The calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules were found to be lower in the 4(3)5(6)6(3) cages than in the 5(12) cages (3.8 cm(-1) for symmetric stretching and 6.0 cm(-1) for asymmetric stretching). The C-H bond length and average distance between methane molecules and host-water molecules in 4(3)5(6)6(3) cages were slightly longer than those in the 5(12) cages.
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Affiliation(s)
- Masaki Hiratsuka
- Department of Mechanical Engineering, Keio University, Yokohama, Kanagawa 223-8522, Japan
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