DL-POLY-2 adaptations for solvation studies

Molecular Simulation

Volumn 37, Issue 1, 2011, Pages 43-52

  Cazade, P A ^a   Bordat, P ^a   Baraille, I ^a   Brown, R ^a   Smith, W ^b   Todorov, I T ^b  

^a UNIVERSITÉ DE PAU ET DES PAYS DE L'ADOUR   (France)

^b DARESBURY LABORATORY   (United Kingdom)

Author keywords

free energy; molecular dynamics; solvation; spectroscopy

Indexed keywords

DIMETHYL SULPHOXIDES; EXCESS FREE ENERGY; HOST MATRICES; MICROPOROUS SILICA; RELATIVE IMPORTANCE; SHIFT-AND; SILICALITE; SOLVATION DYNAMICS; SPECTRAL SHIFT; STOKES SHIFT; SUPPLEMENTARY INFORMATION; THERMODYNAMIC INTEGRATION; TOTAL ENERGY; WATER MOLECULE; WEIGHTING FUNCTIONS;

ADSORPTION; CHEMICAL ANALYSIS; DYNAMICS; FREE ENERGY; HAMILTONIANS; METHANOL; MOLECULES; SILICA; SOLVATION;

MOLECULAR DYNAMICS;

EID: 79551505863     PISSN: 08927022     EISSN: 10290435     Source Type: Journal    
DOI: 10.1080/08927022.2010.517531     Document Type: Article

References (30)

1. W. Smith, C.W. Yong, and P.M. Rodger, DL-POLY: Applications to molecular simulation, Mol. Simul. 28 (2002), pp. 385-471.
2. W. Smith, Special issue: DL-POLY: Applications to molecular simulation II, Mol. Simul. 32 (2006), pp. 933-1121.
3. B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation, J. Chem. Theory Comput. 4 (2008), pp. 435-447.
4. J.C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R.D. Skeel, L. Kale, and K. Schulten, Scalable molecular dynamics with NAMD, J. Comput. Chem. 26 (2005), pp. 1781-1802.
5. B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M.J. Karplus, CHARMM: A program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem. 4 (1983), pp. 187-217.
6. U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen, A smooth particle mesh Ewald method, J. Chem. Phys. 103 (1995), pp. 8577-8593.
7. J. Tersoff, Modelling solid state chemistry: Interaction potentials for multicomponent systems, Phys. Rev. B 39 (1989), pp. 5566-5568.
8. M.W. Finnis and J.E. Sinclair, A simple empirical N body potential for transition metals, Philos. Mag. A 50 (1984), pp. 45-55.
9. M.S. Daw and M.I. Baskes, Embedded-atom method: Derivation and application to impurities, surfaces, and other defects in metals, Phys. Rev. B 29 (1984), pp. 6443-6453.
10. V. Georgieva, I.T. Todorov, and A. Bogaerts, Molecular dynamics simulation of oxide thin film growth: Importance of the inter-atomic interaction potential, Chem. Phys. Lett. 485 (2010), pp. 315-319.
11. I.T. Todorov, J.A. Purton, N.L. Allan, and M.T. Dove, Simulation of radiation damage in gadolinium pyrochlores, J. Phys. Condens. Matter 18 (2006), pp. 2217-2234.
12. M.E. Lee and N.F.A. van der Vegt, Molecular thermodynamics of methane solvation in tert-butanol-water mixtures, J. Chem. Theory Comput. 3 (2007), pp. 194-200.
13. J. Chowdhary and B.M. Ladanyi, Hydrogen bond dynamics at the water/hydrocarbon interface, J. Phys. Chem. B 113 (2009), pp. 4045-4053.
14. P. Bordat, P.A. Cazade, I. Baraille, and R. Brown, Host and adsorbate dynamics in silicates with flexible frameworks: Empirical force field simulation of water in silicalite, J. Chem. Phys. 132 (2010), pp. 94501/1-94501/8.
15. P.W. Atkins, Molecular Quantum Mechanics, Clarendon Press, Oxford, 1990.
16. P. Guionneau, M. Marchivie, G. Bravic, J.F. Létard, and D. Chasseau, Structural aspects of spin crossover. Example of the [Fe II Ln (NCS) 2] complexes, Top. Curr. Chem. 234 (2004), pp. 97-128.
17. E.A. Carter and J.T. Hynes, Solvation dynamics for an ion pair in a polar solvent: Time-dependent fluorescence and photochemical charge transfer, J. Chem. Phys. 94 (1991), pp. 5961-5979.
18. H. Jin, X. Li, and M. Maroncelli, Heterogeneous solute dynamics in room temperature ionic liquids, J. Phys. Chem. B 111 (2007), pp. 13473-13478.
19. P.A. Cazade, Interactions chromophore-substrat dans des matériaux hybrides, Université de Pau et des pays de l'Adour, 64053 Pau Cedex, France (2008)
20. C. Cantau, S. Larribau, T. Pigot, M. Simon, M. Maurette, and S. Lacombe, Oxidation of nauseous sulphur compounds by photocatalysis or photosensitization, Catal. Today 122 (2007), pp. 27-38.
21. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. DiNola, and J.R. Haak, Molecular dynamics with coupling to an external bath, J. Chem. Phys. 81 (1984), pp. 3684-3690.
22. W.L. Jorgensen, D.S. Maxwell, and J. Tirado-Rives, Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids, J. Am. Chem. Soc. 118 (1996), pp. 11225-11236.
23. R.J. Babbitt and M.R. Topp, Jet spectroscopy of anthracene-alkane complexes, Chem. Phys. Lett. 135 (1987), pp. 182-188.
24. E.U. Wallenborn, R. Brown, and U.P. Wild, Analysis of the optical spectra of aromatic-alkane clusters, J. Chem. Phys. 107 (1997), pp. 8338-8348.
25. M.P. Allen and D.J. Tildesley, Computer Simulation of Liquids, Clarendon Press, Oxford, 1989.
26. D. Frenkel and B. Smit, Understanding Molecular Simulation, Elsevier/Academic Press, New York, 2002.
27. T.C. Beutler, A.E. Mark, R.C. van Schaik, P.R. Gerber, and W.F. van Gunsteren, Avoiding singularities and numerical instabilities in free energy calculations based on molecular simulations, Chem. Phys. Lett. 222 (1994), pp. 529-539.
28. P. Bordat, J. Sacristan, D. Reith, S. Girard, A. Glättli, and F. Müller- Plathe, An improved dimethyl sulfoxide force field for molecular dynamics simulations, Chem. Phys. Lett. 374 (2003), pp. 201-205.
29. J.A. Riddick, W.B. Bunger, and T.K. Sakand, Organic Solvents Physical Properties and Methods of Purification, New York, Wiley, 1986.
30. F. Müller-Plathe, YASP: A molecular simulation package, Comput. Phys. Commun. 78 (1993), pp. 77-94