Molecular Simulation of Clay Minerals

Developments in Clay Science

Volumn 5, Issue C, 2013, Pages 405-423

  Greathouse, J A ^a   Cygan, R T ^a  

^a SANDIA NATIONAL LABORATORIES   (United States)

Author keywords

Clay mineral; Layered mineral; Monte Carlo; Simulation molecular dynamics

Indexed keywords

EID: 85023153189     PISSN: 15724352     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-08-098259-5.00016-0     Document Type: Chapter

References (49)

1. R.L. Anderson H.C. Greenwell J.L. Suter P.V. Coveney M.A. Thyveetil Determining materials properties of natural composites using molecular simulation J. Mater. Chem. 19 2009 7251 7262
2. R.L. Anderson I. Ratcliffe H.C. Greenwell P.A. Williams S. Cliffe P.V. Coveney Clay swelling—a challenge in the oilfield Earth-Sci. Rev. 98 2010 201 216
3. G.W. Beall The use of organo-clays in water treatment Appl. Clay Sci. 24 2003 11 20
4. H.J.C. Berendsen J.P.M. Postma W.F. von Gunsteren J. Hermans Interaction models for water in relation to protein hydration B. Pullman Intermolecular Forces 1981 Reidel Dordrecht 331 342
5. E.S. Boek Molecular modeling of clay hydration: a study of hysteresis loops in the swelling curves of sodium montmorillonite Langmuir 11 1995 4629 4631
6. D. Bougeard K.S. Smirnov E. Geidel Vibrational spectra and structure of kaolinite: a computer simulation study J. Phys. Chem. B 104 2000 9210 9217
7. I.C. Bourg G. Sposito Connecting the molecular scale to the continuum scale for diffusion processes in smectite-rich porous media Environ. Sci. Technol. 44 2010 2085 2091
8. 2) solutions J. Colloid Interface Sci. 360 2011 701 715
9. G.E. Brown N.C. Sturchio An overview of synchrotron radiation applications to low temperature geochemistry and environmental science P.A. Fenter M.L. Rivers N.C. Sturchio S.R. Sutton Applications of Synchrotron Radiation in Low-Temperature Geochemistry and Environmental Sciences Reviews in Mineralogy and Geochemistry vol. 49 2002 Mineralogical Society of America Washington, DC 1 115
10. B. Chen J.R.G. Evans H.C. Greenwell P. Boulet P.V. Coveney A.A. Bowden A. Whiting A critical appraisal of polymer-clay nanocomposites Chem. Soc. Rev. 37 2008 568 594
11. S.V. Churakov T. Gimmi Up-scaling of molecular diffusion coefficients in clays: a two-step approach J. Phys. Chem. C 115 2011 6703 6714
12. W.D. Cornell P. Cieplak C.I. Bayly I.R. Gould K.M. Merz D.M. Ferguson D.C. Spellmeyer T. Fox J.W. Caldwell P.A. Kollman A second generation force field for the simulation of proteins, nucleic acids, and organic molecules J. Am. Chem. Soc. 117 1995 5179 5197
13. R.T. Cygan Molecular modeling in mineralogy and geochemistry R.T. Cygan J.D. Kubicki Molecular Modeling Theory: Applications in the Geosciences Reviews in Mineralogy and Geochemistry vol. 42 2001 Mineralogical Society of America Washington, DC 1 35
14. R.T. Cygan J.-J. Liang A.G. Kalinichev Molecular models of hydroxide, oxyhydroxide, and clay phases and the development of a general force field J. Phys. Chem. B 108 2004 1255 1266
15. R.T. Cygan J.A. Greathouse H. Heinz A.G. Kalinichev Molecular models and simulations of layered minerals J. Mater. Chem. 19 2009 2470 2481
16. P. Dauber-Osguthorpe V.A. Roberts D.J. Osguthorpe J. Wolff M. Genest A.T. Hagler Structure and energetics of ligand binding to proteins: Escherichia coli dihydrofolate reductase-trimethoprim, a drug-receptor system Proteins: Struct. Funct. Genet. 4 1988 31 47
17. A. Delville Modeling the clay-water interface Langmuir 7 1991 547 555
18. P. Fenter N.C. Sturchio Mineral-water interfacial structures revealed by synchrotron X-ray scattering Prog. Surf. Sci. 77 2004 171 258
19. D. Frenkel B. Smit Understanding Molecular Simulation: From Algorithms to Applications 2002 Academic Press San Diego
20. M.H. Fu Z.Z. Zhang P.F. Low Changes in the properties of a montmorillonite-water system during the adsorption and desorption of water: hysteresis Clays Clay Miner. 38 1990 485 492
21. J.D. Gale A.L. Rohl The general utility lattice program (GULP) Mol. Simulat. 29 2003 291 341
22. J.A. Greathouse R.T. Cygan Molecular dynamics simulation of uranyl(VI) adsorption equilibria onto an external montmorillonite surface Phys. Chem. Chem. Phys. 7 2005 3580 3586
23. J.A. Greathouse R.T. Cygan Water structure and aqueous uranyl(VI) adsorption equilibria onto external surfaces of beidellite, montmorillonite, and pyrophyllite: results from molecular simulations Environ. Sci. Technol. 40 2006 3865 3871
24. J.A. Greathouse J.S. Durkin J.P. Larentzos R.T. Cygan Implementation of a Morse potential to model hydroxyl behavior in phyllosilicates J. Chem. Phys. 130 2009 134713
25. H.C. Greenwell W. Jones P.V. Coveney S. Stackhouse On the application of computer simulation techniques to anionic and cationic clays: a materials chemistry perspective J. Mater. Chem. 16 2006 708 723
26. H. Heinz H. Koerner K.L. Anderson R.A. Vaia B.L. Farmer Force field for mica-type silicates and dynamics of octadecylammonium chains grafted to montmorillonite Chem. Mater. 17 2005 5658 5669
27. J.-R. Hill J. Sauer Molecular mechanics potential for silica and zeolite catalysts based on ab initio calculations. 2. Aluminosilicates J. Phys. Chem. 99 1995 9536 9550
28. W.L. Jorgensen J. Tiradorives The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin J. Am. Chem. Soc. 110 1988 1657 1666
29. W.L. Jorgensen J. Chandrasekhar J.D. Madura R.W. Impey M.L. Klein Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 79 1983 926 935
30. K. Kawamura Y. Ichikawa M. Nakano K. Kitayama H. Kawamura Swelling properties of smectite up to 90 degrees C: in situ X-ray diffraction experiments and molecular dynamic simulations Eng. Geol. 54 1999 75 79
31. N. Malikova E. Dubois V. Marry B. Rotenberg P. Turq Dynamics in clays—combining neutron scattering and microscopic simulation Z. Phys. Chem. 224 2010 153 181
32. N.W. Ockwig J.A. Greathouse J.S. Durkin R.T. Cygan L.L. Daemen T.M. Nenoff Nanoconfined water in magnesium-rich 2:1 phyllosilicates J. Am. Chem. Soc. 131 2009 8155 8162
33. R.T. Pabalan D.R. Turner F.P. Bertetti J.D. Prikryl Uranium(VI) sorption onto selected mineral surfaces E. Jenne Adsorption of Metals by Geomedia: Variables, Mechanisms, and Model Applications 1998 Academic Press San Diego 99 130
34. B. Rotenberg V. Marry R. Vuilleumier N. Malikova C. Simon P. Turq Water and ions in clays: unraveling the interlayer/micropore exchange using molecular dynamics Geochim. Cosmochim. Acta 71 2007 5089 5101
35. H. Sakuma K. Kawamura Structure and dynamics of water on muscovite mica surfaces Geochim. Cosmochim. Acta 73 2009 4100 4110
36. H. Sato A. Yamagishi K. Kawamura Molecular simulation for flexibility of a single clay layer J. Phys. Chem. B 105 2001 7990 7997
37. G. Scocchi P. Posocco A. Danani S. Pricl M. Fermeglia To the nanoscale, and beyond! Multiscale molecular modeling of polymer-clay nanocomposites Fluid Phase Equilibr. 261 2007 366 374
38. N.T. Skipper K. Refson J.D.C. McConnell Computer simulation of interlayer water in 2:1 clays J. Chem. Phys. 94 1991 7434 7445
39. D.E. Smith Y. Wang A. Chaturvedi H.D. Whitley Molecular simulations of the pressure, temperature, and chemical potential dependencies of clay swelling J. Phys. Chem. B 110 2006 20046 20054
40. J.L. Suter P.V. Coveney Materials properties of clay nanocomposites: onset of negative Poisson ratio in large-scale molecular dynamics simulation Soft Matter. 5 2009 3896 3904
41. J.L. Suter P.V. Coveney H.C. Greenwell M.A. Thyveetil Large-scale molecular dynamics study of montmorillonite clay: emergence of undulatory fluctuations and determination of material properties J. Phys. Chem. C 111 2007 8248 8259
42. J.B. Swadling P.V. Coveney H.C. Greenwell Clay minerals mediate folding and regioselective interactions of RNA: a large-scale atomistic simulation study J. Am. Chem. Soc. 132 2010 13750 13764
43. O. Teleman B. Jonsson S. Engstrom A molecular dynamics simulation of a water model with intramolecular degrees of freedom Mol. Phys. 60 1987 193 203
44. B.J. Teppen K.R. Rasmussen P.M. Bertsch D.M. Miller L. Schafer Molecular dynamics modeling of clay minerals. 1. Gibbsite, kaolinite, pyrophillite, and beidellite J. Phys. Chem. B 101 1997 1579 1587
45. M.A. Thyveetil P.V. Coveney H.C. Greenwell J.L. Suter Computer simulation study of the structural stability and materails properties of DNA-intercalated layered double hydroxides J. Am. Chem. Soc. 130 2008 4742 4756
46. C. Tournassat Y. Chapron P. Leroy M. Bizi F. Boulahya Comparison of molecular dynamics simulations with triple layer and modified Gouy-Chapman models in a 0.1 M NaCl-montmorillonite system J. Colloid Interface Sci. 339 2009 533 541
47. I.F. Vasconcelos B.A. Bunker R.T. Cygan Molecular dynamics modeling of ion adsorption to the basal surfaces of kaolinite J. Phys. Chem. C 111 2007 6753 6762
48. J.W. Wang A.G. Kalinichev R.J. Kirkpatrick R.T. Cygan Structure, energetics, and dynamics of water adsorbed on the muscovite (001) surface: a molecular dynamics simulation J. Phys. Chem. B 109 2005 15893
49. Y. Zheng A. Zaoui I. Shahrour A theoretical study of swelling and shrinking of hydrated Wyoming montmorillonite Appl. Clay Sci. 51 2011 177 181