Application of the independent molecule model to elucidate the dynamics of structure I methane hydrate

Journal of Molecular Graphics and Modelling

Volumn 25, Issue 6, 2007, Pages 856-869

  Yoshioki, Shuzo ^a  

^a KUMAMOTO NATIONAL COLLEGE OF TECHNOLOGY   (Japan)

Author keywords

Dynamics; Hydrogen bond; Independent molecule model; Methane hydrate; Raman spectrum; Symmetry coordinate; Thermal ellipsoid; Vibrational frequency

Indexed keywords

CRYSTAL SYMMETRY; LATTICE VIBRATIONS; MATHEMATICAL MODELS; METHANE; MOLECULAR DYNAMICS; RAMAN SPECTROSCOPY; STRUCTURAL ANALYSIS;

INDEPENDENT MOLECULE MODEL; METHANE HYDRATE; SYMMETRY COORDINATE; THERMAL ELLIPSOID; VIBRATIONAL FREQUENCY;

GAS HYDRATES;

METHANE; WATER;

ARTICLE; CALCULATION; ENERGY; GAS; HYDROGEN BOND; MATHEMATICAL MODEL; MOLECULAR MODEL; PRIORITY JOURNAL; RAMAN SPECTROMETRY;

HYDROGEN BONDING; METHANE; MODELS, CHEMICAL; MODELS, MOLECULAR; SPECTRUM ANALYSIS, RAMAN; THERMODYNAMICS;

EID: 33846834022     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2006.08.007     Document Type: Article

References (24)

1. Sloan Jr. E.D. Clathrate Hydrates of Natural Gases. 2nd ed. (1998), Marcel Dekker Inc., New York (revised and expanded)
2. McMullan R.K., and Jeffrey G.A. Polyhedral clathrate hydrates. IX. Structure of ethylene oxide hydrate. J. Chem. Phys. 42 (1965) 2725-2732
3. Mak T.C.W., and McMullan R.K. Polyhedral clathrate hydrates. X. structure of the double hydrate of tetrahydrofuran and hydrogen sulfide. J. Chem. Phys. 42 (1965) 2732-2737
4. Chou I.-M., Sharma A., Burruss R.C., Shu J., Mao H., Hemley R.J., Goncharov A.F., Stern L.A., and Kirby S.H. Transformations in methane hydrates. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 13484-13487
5. Sum A.K., Burruss R.C., and Sloan Jr. E.D. Measurement of clathrate hydrates via Raman spectroscopy. J. Phys. Chem. B 101 (1997) 7371-7377
6. Uchida T., Okabe R., Gohara K., Mae S., Seo Y., Lee H., Takeya S., Nagao J., Ebinuma T., and Naria H. Raman spectroscopic observations of methane-hydrate formation and hydrophobic hydration around methane molecules in solution. Can. J. Phys. 81 (2003) 359-366
7. Yoshioki S. Dynamics of a protein and water molecules surrounding the protein: hydrogen-bonding between vibrating water molecules and a fluctuating protein. J. Comput. Chem. 23 (2002) 402-413
8. Yoshioki S. Application of the independent molecule model to the calculation of free energy and rigid-body motions of water hexamers. J. Mol. Graph. Model. 21 (2003) 487-498
9. Yoshioki S. Application of the independent molecule model to the calculation of free energy and rigid-body motions of water heptamers and octamers. J. Mol. Graph. Model. 23 (2004) 111-127
10. Raynes W.T., Lazzeretti P., Zanasi R., Sadlej A.J., and Fowler P.W. Calculations of the force field of the methane molecule. Mol. Phys. 60 (1987) 509-525
11. In: Nishikawa T. (Ed). Physics Dictionary (1984), Baifukan, Tokyo 2362 (in Japanese)
12. Momany F.A., Carruthers L.M., McGuire R.F., and Scheraga H.A. Intermolecular potential from crystal data. III. Determination of empirical potentials and application to the packing configurations and lattice energies in crystals of hydrocarbon, carboxylic acids, amine, and amides. J. Phys. Chem. 78 (1974) 1595-1620
13. Yoshioki S. Formulation of the Hessian matrix for the conformational energy of protein-water systems. J. Phys. Soc. Jpn. 66 (1997) 2927-2935
14. S. Yoshioki, to be prepared.
15. Gill P.E., Murray W., and Wright M.H. Practical Optimization (1981), Academic Press, London p. 105
16. Wilson Jr. E.B. A method of obtaining the expanded secular equation for the vibration frequencies of a molecule. J. Chem. Phys. 7 (1939) 1047-1052
17. Wilson Jr. E.B. Some mathematical methods for the study of molecular vibrations. J. Chem. Phys. 9 (1941) 76-84
18. Wilson Jr. E.B., Decius J.C., and Cross P.C. Molecular Vibrations (1955), McGraw-Hill Book Company Inc., New York p. 117
19. Johnson C.K. ORTEP: A Fortran Thermal Ellipsoid Plot Program, ORNL-3795 (1965), Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
20. Yoshioki S. Motions of water molecules surrounding a rigid protein model. J. Phys. Soc. Jpn. 67 (1998) 1477-1485
21. Greathouse J.A., Cygan R.T., and Simmons B.A. Vibrational spectra of methane clathrates from molecular dynamics simulation. J. Phys. Chem. B 110 (2006) 6428-6431
22. Tse J.S. Vibrations of methane in structure I clathrate hydrate-An ab initio density functional molecular dynamics study. J. Supramol. Chem. 2 (2002) 429-433
23. Itoh H., and Kawamura K. Molecular dynamics simulations of clathrate hydrate. Ann. NY Acad. Sci. 912 (2000) 693-701
24. Gray D.L., and Robiette A.G. The anharmonic force field and equilibrium structure of methane. Mol. Phys. 37 (1979) 1901-1920