Methane hydrate clathrates: effects in the simulation of melting arising from the assumption of simple combining rules in interatomic potentials

References

• Winkler B, Dove MT. Thermodynamic properties of MgSiO3 perovskite derived from large scale molecular dynamics simulations. Phys Chem Miner. 1992;18:407–415. doi:10.1007/bf00200963.
   Web of Science ®Google Scholar
• Smith W, Forester T. DL_POLY_2.0: a general-purpose parallel molecular dynamics simulation package. J Mol Graph. 1996;14:136–141. doi:10.1016/s0263-7855(96)00043-4.
   PubMedGoogle Scholar
• Smith W, Todorov IT. A short description of DL_POLY. Mol Simul. 2006;32:935–943. doi:10.1080/08927020600939830.
   Web of Science ®Google Scholar
• Gambhir M, Dove MT, Heine V. Rigid unit modes and dynamic disorder: SiO2 cristobalite and quartz. Phys Chem Miner. 1999;26:484–495. doi:10.1007/s002690050211.
   Web of Science ®Google Scholar
• Dove MT, Pryde AKA, Keen DA. Phase transitions in tridymite studied using “rigid unit mode” theory, reverse monte carlo methods and molecular dynamics simulations. Mineral Mag. 2000;64:267–283. doi:10.1180/002646100549175.
   Web of Science ®Google Scholar
• Trachenko K, Dove MT. Densification of silica glass under pressure. J Phys Condens Matter. 2002;14:7449–7459. doi:10.1088/0953-8984/14/32/304.
   Web of Science ®Google Scholar
• Trachenko K, Dove MT. Floppy modes in silica glass under pressure. J Phys Condens Matter. 2002;14:1143–1152. doi:10.1088/0953-8984/14/6/303.
   Web of Science ®Google Scholar
• Trachenko K, Dove MT. Compressibility, kinetics, and phase transition in pressurized amorphous silica. Phys Rev B. 2003;67:064107. doi:10.1103/physrevb.67.064107.
   Web of Science ®Google Scholar
• Trachenko K, Dove MT. Intermediate state in pressurized silica glass: reversibility window analogue. Phys Rev B. 2003;67:212203. doi:10.1103/physrevb.67.212203.
   Web of Science ®Google Scholar
• Trachenko K, Dove MT, Brazhkin V, et al. Network rigidity and properties of SiO2 and GeO2 glasses under pressure. Phys Rev Lett. 2004;93:135502. doi:10.1103/physrevlett.93.135502.
   PubMed Web of Science ®Google Scholar
• Trachenko KO, Dove MT, Salje EKH. Atomistic modelling of radiation damage in zircon. J Phys Condens Matter. 2001;13:1947–1959. doi:10.1088/0953-8984/13/9/317.
   Web of Science ®Google Scholar
• Trachenko K, Dove MT, Salje EKH. Large swelling and percolation in irradiated zircon. J Phys Condens Matter. 2002;15:L1–L7. doi:10.1088/0953-8984/15/2/101.
   Web of Science ®Google Scholar
• Trachenko K, Dove MT, Salje EKH. Structural changes in zircon under α-decay irradiation. Phys Rev B. 2002;65:180102. doi:10.1103/physrevb.65.180102.
   Web of Science ®Google Scholar
• Todorov IT, Smith W, Trachenko K, et al. DL_POLY_3: new dimensions in molecular dynamics simulations via massive parallelism. J Mater Chem. 2006;16:1911. doi:10.1039/b517931a.
   Web of Science ®Google Scholar
• Zarkadoula E, Daraszewicz SL, Duffy DM, et al. The nature of high-energy radiation damage in iron. J Phys Condens Matter. 2013;25:125402. doi:10.1088/0953-8984/25/12/125402.
   PubMed Web of Science ®Google Scholar
• Zarkadoula E, Devanathan R, Weber WJ, et al. High-energy radiation damage in zirconia: modeling results. J Appl Phys. 2014;115:083507. doi:10.1063/1.4866989.
   Web of Science ®Google Scholar
• Gao M, Misquitta AJ, Rimmer LHN, et al. Molecular dynamics simulation study of various zeolitic imidazolate framework structures. Dalton Trans. 2016;45:4289–4302. doi:10.1039/c5dt03508b.
   PubMed Web of Science ®Google Scholar
• Gao M, Misquitta AJ, Yang C, et al. Molecular dynamics study of CO2 absorption and desorption in zinc imidazolate frameworks. Mol Syst Des Eng. 2017;2:457–469. doi:10.1039/c7me00034k.
   Web of Science ®Google Scholar
• Yang C, Trachenko K, Hull S, et al. Emergence of microstructure and oxygen diffusion in yttrium-stabilised cubic zirconia. Phys Rev B. 2018; in press.
   Web of Science ®Google Scholar
• Dove MT, Sullivan LA, Walker AM, et al. Molecular dynamics in a grid computing environment: experiences using DL_POLY_3 within the eMinerals escience project. Mol Simul. 2006;32:945–952. doi:10.1080/08927020600883293.
   Web of Science ®Google Scholar
• Walker AM, Sullivan LA, Trachenko K, et al. The origin of the compressibility anomaly in amorphous silica: a molecular dynamics study. J Phys Condens Matter. 2007;19:275210. doi:10.1088/0953-8984/19/27/275210.
   Web of Science ®Google Scholar
• Fang H, Dove MT, Rimmer LHN, et al. Simulation study of pressure and temperature dependence of the negative thermal expansion in Zn(CN)2. Phys Rev B. 2013;88:104306. doi:10.1103/physrevb.88.104306.
   Web of Science ®Google Scholar
• Fang H, Dove MT. Pressure-induced softening as a common feature of framework structures with negative thermal expansion. Phys Rev B. 2013;87:214109. doi:10.1103/physrevb.87.214109.
   Web of Science ®Google Scholar
• Trachenko K, Dove MT, Salje EKH. Reply to comment on “large swelling and percolation in irradiated zircon”. J Phys Condens Matter. 2003;15:6457–6471. doi:10.1088/0953-8984/15/37/n02.
   Web of Science ®Google Scholar
• Chappell HF, Dove MT, Trachenko K, et al. Structural changes in zirconolite under α-decay. J Phys Condens Matter. 2012;25:055401. doi:10.1088/0953-8984/25/5/055401.
   PubMed Web of Science ®Google Scholar
• Gilmore RAJ, Misquitta AJ, Dove MT. Manuscript in preparation. Many-body non-additive polarization energies for water cluster from first principles polarization models.
   Google Scholar
• Jorgensen WL, Madura JD, Swenson CJ. Optimized intermolecular potential functions for liquid hydrocarbons. J Am Chem Soc. 1984;106:6638–6646.
   Web of Science ®Google Scholar
• Verlet L, Weis JJ. Perturbation theory for the thermodynamic properties of simple liquids. Mol Phys. 1972;24:1013–1024.
   Web of Science ®Google Scholar
• Goodbody SJ, Watanabe K, MacGowan D, et al. Molecular simulation of methane and butane in silicalite. J Chem Soc Faraday Trans. 1991;87:1951–1958.
   Google Scholar
• Guillot B, Guissani Y. A computer simulation study of the temperature dependence of the hydrophobic hydration. J Chem Phys. 1993;99:8075–8094.
   Web of Science ®Google Scholar
• Berendsen H, Grigera J, Straatsma T. The missing term in effective pair potentials. J Phys Chem. 1987;91:6269–6271.
   Web of Science ®Google Scholar
• Abascal J, Sanz E, Garcia Fernandez R, et al. A potential model for the study of ices and amorphous water: Tip4p/ice. J Chem Phys. 2005;122:234511.
   PubMed Web of Science ®Google Scholar
• Abascal JL, Vega C. A general purpose model for the condensed phases of water: Tip4p/2005. J Chem Phys. 2005;123:234505.
   PubMed Web of Science ®Google Scholar
• Lorentz HA. Ueber die anwendung des satzes vom virial in der kinetischen theorie der gase. Ann Phys. 1881;248:127–136. doi:10.1002/andp.18812480110.
   Google Scholar
• Berthelot D. Sur le mclange des gaz. C rendus hebdomadaires séances Acad Sci. 1898;126:1703–1855.
   Google Scholar
• Hawtin RW, Quigley D, Rodger PM. Gas hydrate nucleation and cage formation at a water/methane interface. Phys Chem Chem Phys. 2008;10:4853–4864.
   PubMed Web of Science ®Google Scholar
• Walsh MR, Koh CA, Sloan ED, et al. Microsecond simulations of spontaneous methane hydrate nucleation and growth. Science. 2009;326:1095–1098.
   PubMed Web of Science ®Google Scholar
• Walsh MR, Rainey JD, Lafond PG, et al. The cages, dynamics, and structuring of incipient methane clathrate hydrates. Phys Chem Chem Phys. 2011;13:19951–19959.
   PubMed Web of Science ®Google Scholar
• Walsh MR, Beckham GT, Koh CA, et al. 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.
   Web of Science ®Google Scholar
• Bagherzadeh SA, Alavi S, Ripmeester JA, et al. Evolution of methane during gas hydrate dissociation. Fluid Phase Equilib. 2013;358:114–120.
   Web of Science ®Google Scholar
• Das S, Baghel VS, Roy S, et al. A molecular dynamics study of model si clathrate hydrates: the effect of guest size and guest–water interaction on decomposition kinetics. Phys Chem Chem Phys. 2015;17:9509–9518.
   PubMed Web of Science ®Google Scholar
• Bagherzadeh SA, Alavi S, Ripmeester J, et al. Formation of methane nano-bubbles during hydrate decomposition and their effect on hydrate growth. J Chem Phys. 2015;142:214701.
   PubMed Web of Science ®Google Scholar
• Liu Y, Zhao L, Deng S, et al. Evolution of bubbles in decomposition and replacement process of methane hydrate. Mol Simul. 2017;43:1061–1073.
   Web of Science ®Google Scholar
• Misquitta AJ, Szalewicz K. Intermolecular forces from asymptotically corrected density functional description of monomers. Chem Phys Lett. 2002;357:301–306.
   Web of Science ®Google Scholar
• Misquitta AJ, Jeziorski B, Szalewicz K. Dispersion energy from density-functional theory description of monomers. Phys Rev Lett. 2003;91:033201.
   PubMed Web of Science ®Google Scholar
• Misquitta AJ, Szalewicz K. Symmetry-adapted perturbation-theory calculations of intermolecular forces employing density-functional description of monomers. J Chem Phys. 2005;122:214109.
   PubMed Web of Science ®Google Scholar
• Misquitta AJ, Podeszwa R, Jeziorski B, et al. Intermolecular potentials based on symmetry-adapted perturbation theory with dispersion energies from time-dependent density-functional calculations. J Chem Phys. 2005;123:214103.
   PubMed Web of Science ®Google Scholar
• Podeszwa R, Cencek W, Szalewicz K. Efficient calculations of dispersion energies for nanoscale systems from coupled density response functions. J Chem Theory Comput. 2012;8:1963–1969.
   PubMed Web of Science ®Google Scholar
• Camcasp: a program for studying intermolecular interactions and for the calculation of molecular properties in distributed form; 2017. Available from: http://www-stone.ch.cam.ac.uk/programs/camcasp.html.
   Google Scholar
• Orient. 2017. Available from: http://www-stone.ch.cam.ac.uk/programs/orient.html .
   Google Scholar
• Misquitta AJ, Stone AJ. Ab initio atom–atom potentials using camcasp: theory and application to many-body models for the pyridine dimer. J Chem Theory Comput. 2016;12:4184–4208.
   PubMed Web of Science ®Google Scholar
• Millot C, Stone AJ. Towards an accurate intermolecular potential for water. Mol Phys. 1992;77:439–462.
   Web of Science ®Google Scholar
• Fumi FG, Tosi M. Ionic sizes and Born repulsive parameters in the nacl-type alkali halidesi: the Huggins-Mayer and Pauling forms. J Phys Chem Solids. 1964;25:31–43.
   Web of Science ®Google Scholar
• Tosi M, Fumi F. Ionic sizes and Born repulsive parameters in the nacl-type alkali halidesii: The generalized Huggins-Mayer form. J Phys Chem Solids. 1964;25:45–52.
   Web of Science ®Google Scholar
• Mas EM, Bukowski R, Szalewicz K, et al. Water pair potential of near spectroscopic accuracy. i. Analysis of potential surface and virial coefficients. J Chem Phys. 2000;113:6687–6701.
   Web of Science ®Google Scholar
• Misquitta AJ, Stone AJ, Fazeli F. Distributed multipoles from a robust basis-space implementation of the iterated stockholder atoms procedure. J Chem Theory Comput. 2014;10:5405–5418.
   PubMed Web of Science ®Google Scholar
• Ferenczy G, Reynolds C, et al. Mult: a program for calculating electrostatic potential-fitted charges. May be obtained by contacting AJ Stone, email address: [email protected]. 1998.
   Google Scholar
• Valiev M, Bylaska E, Govind N, et al. NWChem: a comprehensive and scalable open-source solution for large scale molecular simulations. Comput Phys Commun. 2010;181:1477–1489. doi:10.1016/j.cpc.2010.04.018.
   Web of Science ®Google Scholar
• Bernal JD, Fowler RH. A theory of water and ionic solution, with particular reference to hydrogen and hydroxyl ions. J Chem Phys. 1933;1:515–548. doi:10.1063/1.1749327.
   Web of Science ®Google Scholar
• Akin-Ojo O, Szalewicz K. Potential energy surface and second virial coefficient of methane-water from ab initio calculations. J Chem Phys. 2005;123:134311.
   PubMed Web of Science ®Google Scholar
• Konrad O, Lankau T. Solubility of methane in water: the significance of the methane- water interaction potential. J Phys Chem B. 2005;109:23596–23604.
   PubMed Web of Science ®Google Scholar
• Docherty H, Galindo A, Vega C, et al. A potential model for methane in water describing correctly the solubility of the gas and the properties of the methane hydrate. J Chem Phys. 2006;125:074510.
   PubMed Web of Science ®Google Scholar
• Jacobson LC, Molinero V. A methane-water model for coarse-grained simulations of solutions and clathrate hydrates. J Phys Chem B. 2010;114:7302–7311.
   PubMed Web of Science ®Google Scholar
• Sloan ED. Gas hydrates: review of physical/chemical properties. Energy Fuel. 1998;12:191–196.
   Web of Science ®Google Scholar
• Fernández DP, Mulev Y, Goodwin A, et al. A database for the static dielectric constant of water and steam. J Phys Chem Ref Data. 1995;24:33–70.
   Web of Science ®Google Scholar
• Tang K, Toennies JP. An improved simple model for the van der Waals potential based on universal damping functions for the dispersion coefficients. J Chem Phys. 1984;80:3726–3741.
   Web of Science ®Google Scholar