Reaction coordinate of incipient methane clathrate hydrate nucleation

Journal of Physical Chemistry B

Volumn 118, Issue 46, 2014, Pages 13236-13243

  Barnes, Brian C ^a   Knott, Brandon C ^b   Beckham, Gregg T ^b   Wu, David T ^a   Sum, Amadeu K ^a  

^a Department of Metallurgical and Materials Engineering   (United States)

^b NATIONAL RENEWABLE ENERGY LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMINERALIZATION; ENERGY RESOURCES; FREE ENERGY; HYDRATION; METHANE; NUCLEATION; SAMPLING;

CLUSTERING MECHANISM; CRITICAL NUCLEUS SIZE; INCLUSION COMPOUNDS; METHANE CLATHRATE HYDRATE; MOLECULAR DESCRIPTORS; MOLECULAR SIMULATIONS; REACTION COORDINATES; SCIENTIFIC DISCIPLINE;

GAS HYDRATES;

METHANE; WATER;

CHEMICAL PHENOMENA; CHEMISTRY; MOLECULAR DYNAMICS; PRESSURE; TEMPERATURE; THERMODYNAMICS;

HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; METHANE; MOLECULAR DYNAMICS SIMULATION; PRESSURE; TEMPERATURE; THERMODYNAMICS; WATER;

EID: 84913529784     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp507959q     Document Type: Article

References (55)

1. Navrotsky, A. Energetic Clues to Pathways in Biomineralization: Precursors, Clusters and Nanoparticles. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 12096-12101.
2. Blagden, N.; Davey, R. J. Polymorph Selection: Challenges for the Future? Cryst. Growth Des. 2003, 3, 873-885.
3. Yamauchi, N.; Reif, R. Polycrystalline Silicon Thin Films Processed with Silicon Ion Implantation and Subsequent Solid-Phase Crystallization: Theory, Experiments, and Thin-Film Transistor Applications. J. Appl. Phys. 1994, 75, 3235-3257.
4. Auer, S.; Frenkel, D. Prediction of Absolute Crystal-Nucleation Rate in Hard-Sphere Colloids. Nature 2001, 409, 1020-1023.
5. Gebauer, D.; Völkel, A.; Cölfen, H. Stable Prenucleation Calcium Carbonate Clusters. Science 2008, 322, 1819-1822.
6. Kashchiev, D.; Cabriolu, R.; Auer, S. Confounding the Paradigm: Peculiarities of Amyloid Fibril Nucleation. J. Am. Chem. Soc. 2013, 135, 1531-1539.
7. Agarwal, V.; Peters, B. In Advances in Chemical Physics, Vol. 135; Rice, S. A., Dinner, A. R., Eds.; John Wiley and Sons, Inc.: Hoboken, New Jersey, 2014; Chapter "Solute precipitate nucleation: a review of theory and simulation advances".
8. Gebauer, D.; Kellermeier, M.; Gale, J. D.; Bergström, L.; Cölfen, H. Pre-Nucleation Clusters As Solute Precursors in Crystallisation. Chem. Soc. Rev. 2014, 43, 2348-2371.
9. Sloan, E. D.; Koh, C. A. Clathrate Hydrates of Natural Gases, 3rd ed.; CRC Press: Boca Raton, FL, 2008; pp 45-111.
10. Koh, C. A.; Sloan, E. D.; Sum, A. K.; Wu, D. T. Fundamental and Applications of Gas Hydrates. Annu. Rev. Chem. Biomol. Eng. 2011, 2, 237-57.
11. Ribero, C. P.; Lage, P. L. C. Modeling of Hydrate Formation Kinetics: State-Of-The-Art and Future Directions. Chem. Eng. Sci. 2008, 63, 2007-2034.
12. Barnes, B. C.; Sum, A. K. Advances in Molecular Simulations of Clathrate Hydrates. Curr. Opin. Chem. Eng. 2013, 2, 184-190.
13. Walsh, M. R.; Koh, C. A.; Sloan, E. D.; Sum, A. K.; Wu, D. T. Microsecond Simulations of Spontaneous Methane Hydrate Nucleation and Growth. Science 2009, 326, 1095-1098.
14. Jacobson, L. C.; Matsumoto, M.; Molinero, V. Order Parameters for the Multistep Crystallization of Clathrate Hydrates. J. Chem. Phys. 2011, 135, 074501.
15. Sarupria, S.; Debenedetti, P. G. Homogeneous Nucleation of Methane Hydrate in Microsecond Molecular Dynamics Simulations. J. Phys. Chem. Lett. 2012, 3, 2942-2947.
16. Liang, S.; Rozmanov, D.; Kusalik, P. G. Crystal Growth Simulations of Methane Hydrates in the Presence of Silica Surfaces. Phys. Chem. Chem. Phys. 2011, 13, 19856-19864.
17. English, N. J.; Phelan, G. M. Molecular Dynamics Study of Thermal-Driven Methane Hydrate Dissociation. J. Chem. Phys. 2009, 131, 074704.
18. Bagherzadeh, S. A.; Englezos, P.; Alavi, S.; Ripmeester, J. A. Molecular Modeling of the Dissociation of Methane Hydrate in Contact with a Silica Surface. J. Phys. Chem. B 2012, 116, 3188-3197.
19. Knott, B.; Molinero, V.; Doherty, M. F.; Peters, B. Homogeneous Nucleation of Methane Hydrates: Unrealistic Under Realistic Conditions. J. Am. Chem. Soc. 2012, 134, 19544-19547.
20. 2 Hydrate Clathrates. J. Chem. Phys. 2002, 117, 1786-1796.
21. Hawtin, R. W.; Quigley, D.; Rodger, P. M. Gas Hydrate Nucleation and Cage Formation at a Water/Methane Interface. Phys. Chem. Chem. Phys. 2008, 10, 4853-4864.
22. Matsumoto, M.; Baba, A.; Ohmine, I. Topological Building Blocks of Hydrogen Bond Network in Water. J. Chem. Phys. 2007, 127, 134504.
23. Chakraborty, S. N.; Grzelak, E. M.; Barnes, B. C.; Wu, D. T.; Sum, A. K. Voronoi Tessellation Analysis of Clathrate Hydrates. J. Phys. Chem. C 2012, 116, 20040-20046.
24. Barnes, B. C.; Beckham, G. T.; Wu, D. T.; Sum, A. K. Two-Component Order Parameter for Quantifying Clathrate Hydrate Nucleation and Growth. J. Chem. Phys. 2014, 140, 164506.
25. Walsh, M. R.; Beckham, G. T.; Koh, C. A.; Sloan, E. D.; Wu, D. T.; Sum, A. K. Methane Hydrate Nucleation Rates from Molecular Dynamics Simulations: Effects of Aqueous Methane Concentration, Interfacial Curvature and System Size. J. Phys. Chem. C 2011, 115, 21241-21248.
26. Radhakrishnan, R.; Schlick, T. Biomolecular Free Energy Profiles by a Shooting/Umbrella Sampling Protocol, "BOLAS". J. Chem. Phys. 2004, 121, 2436-2444.
27. Peters, B.; Zimmermann, N. E. R.; Beckham, G. T.; Tester, J. W.; Trout, B. L. Path Sampling Calculation of Methane Diffusivity in Natural Gas Hydrates from a Water-Vacancy Assisted Mechanism. J. Am. Chem. Soc. 2008, 130, 17342-17350.
28. Abascal, J. L. F.; Sanz, E.; Fernandez, R. G.; Vega, C. A Potential Model for the Study of Ices and Amorphous Water: TIP4P/ice. J. Chem. Phys. 2005, 122, 234511.
29. Jorgensen, W. L.; Madura, J. D.; Swenson, C. J. Optimized Intermolecular Potential Functions for Liquid Hydrocarbons. J. Am. Chem. Soc. 1984, 106, 6638-6646.
30. Hess, B.; Kutznera, C.; van der Spoel, D.; Lindahl, E. Gromacs 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 2008, 4, 435-447.
31. Lynden-Bell, R. M.; van Duijneveldt, J. S.; Frenkel, D. Free Energy Changes on Freezing and Melting Ductile Metals. Mol. Phys. 1993, 80, 801-814.
32. Kashchiev, D.; Firoozabadi, A. Driving Force for Crystallization of Gas Hydrates. J. Cryst. Growth 2002, 241, 220-230.
33. NIST Chemistry WebBook, NIST Standard Reference Database Number 69; Linstrom, P. J., Mallard, W. G., Eds.; National Institute of Standards and Technology: Gaithersburg, MD, 2014; http://webbook.nist.gov (retrieved May 30, 2014).
34. Jensen, L.; Thomsen, K.; von Solms, N.; Wierzchowski, S.; Walsh, M. R.; Koh, C. A.; Sloan, E. D.; Wu, D. T.; Sum, A. K. Calculation of Liquid Water-Hydrate-Methane Vapor Phase Equilibria from Molecular Simulations. J. Phys. Chem. B 2010, 114, 5775-5782.
35. Du, R.; Pande, V. S.; Grosberg, A. Y.; Tanaka, T.; Shakhnovich, E. S. On the Transition Coordinate for Protein Folding. J. Chem. Phys. 1998, 108, 334-350.
36. Geissler, P. L.; Dellago, C.; Chandler, D. Kinetic Pathways of Ion Pair Dissociation in Water. J. Phys. Chem. B 1999, 103, 3706-3710.
37. Bolhuis, P. G.; Dellago, C.; Chandler, D. Reaction Coordinates of Biomolecular Isomerization. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 5877-5882.
38. Peters, B. Using the Histogram Test to Quantify Reaction Coordinate Error. J. Chem. Phys. 2006, 125, 241101.
39. Moroni, D.; ten Wolde, P. R.; Bolhuis, P. G. Interplay Between Structure and Size in a Critical Crystal Nucleus. Phys. Rev. Lett. 2005, 94, 235703.
40. Beckham, G. T.; Peters, B. Optimizing Nucleus Size Metrics for Liquid-Solid Nucleation from Transition Paths of Near-Nanosecond Duration. J. Phys. Chem. Lett. 2011, 2, 1133-1138.
41. Lechner, W.; Dellago, C.; Bolhuis, P. G. Role of the Prestructured Surface Cloud in Crystal Nucleation. Phys. Rev. Lett. 2011, 106, 085701.
42. Mullen, R. G.; Shea, J.-E.; Peters, B. Transmission Coefficients, Committors, and Solvent Coordinates in Ion-Pair Dissociation. J. Chem. Theory Comput. 2014, 10, 659-667.
43. Knott, B.; Momeni, M. H.; Crowley, M. F.; Mackenzie, L. F.; Götz, A. W.; Sandgren, M.; Withers, S. G.; Sta˚hlberg, J.; Beckham, G. T. The Mechanism of Cellulose Hydrolysis by a Two-Step, Retaining Cellobiohydrolase Elucidated by Structural and Transition Path Sampling Studies. J. Am. Chem. Soc. 2014, 136, 321-329.
44. Lechner, W.; Dellago, C.; Bolhuis, P. G. Reaction Coordinates for the Crystal Nucleation of Colloidal Suspensions Extracted from the Reweighted Path Ensemble. J. Chem. Phys. 2011, 135, 154110.
45. Punnathanam, S.; Monson, P. Crystal Nucleation in Binary Hard Sphere Mixtures: A Monte Carlo Simulation Study. J. Chem. Phys. 2006, 125, 024508.
46. Jungblut, S.; Dellago, C. Crystallization of a Binary Lennard-Jones Mixture. J. Chem. Phys. 2011, 134, 104501.
47. Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. TRANSITION PATH SAMPLING: Throwing Ropes over Rough Mountain Passes, in the Dark. Annu. Rev. Phys. Chem. 2002, 53, 291-318.
48. Peters, B. Recent Advances in Transition Path Sampling: Accurate Reaction Coordinates, Likelihood Maximisation and Diffusive Barrier-Crossing Dynamics. Mol. Simul. 2010, 36, 1265-1281.
49. Zahn, D. Atomistic Mechanism of NaCl Nucleation from an Aqueous Solution. Phys. Rev. Lett. 2004, 92, 040801.
50. Bi, Y.; Li, T. Probing Methane Hydrate Nucleation Through Forward Flux Sampling Method. J. Phys. Chem. B [Online early access]. DOI: 10.1021/jp503000u. Published Online: May 21, 2014. http://pubs.acs.org/doi/full/10.1021/jp503000u (accessed May 21, 2014).
51. Devarakonda, S.; Groysman, A.; Myerson, A. S. THF-Water Hydrate Crystallization: An Experimental Investigation. J. Cryst. Growth 1999, 204, 525-538.
52. Abay, H. K.; Svartaas, T. M. Multicomponent Gas Hydrate Nucleation: The Effect of Cooling Rate and Composition. Energy Fuels 2011, 25, 42-51.
53. Kashchiev, D.; Firoozabadi, A. Nucleation of Gas Hydrates. J. Cryst. Growth 2002, 243, 476-489.
54. Filion, L.; Ni, R.; Frenkel, D.; Dijkstra, M. Simulation of Nucleation in Almost Hard-Sphere Colloids: The Discrepancy Between Experiment and Simulation Persists. J. Chem. Phys. 2011, 134, 134901.
55. Ramsteiner, I. B.; Jensen, K. E.; Weitz, D. A.; Spaepen, F. Experimental Observation of the Crystallization of Hard-Sphere Colloidal Particles by Sedimentation onto Flat and Patterned Surfaces. Phys. Rev. E 2009, 79, 011403.