Energy and Climate
Energy and ClimateClimate/EnvironmentCarbon ManagementMolecular Geochemistry

Molecular Geochemistry

Research

Geochemistry, mineralogy, and materials science specializing in application of chemical kinetics, mineral equilibria, molecular spectroscopy, and molecular simulation to complex multicomponent and multiphase systems; particular emphasis on the use of molecular simulation and various spectroscopies to understand material behavior.

Capabilities

Atomistic simulation with applications to geochemistry, materials science, and related areas.

  • Ion-ion and ion-surface potential of mean force calculations
  • Molecular dynamics (classical and ab initio)
  • Grand canonical Monte Carlo
  • Quantum chemistry (density functional theory)
  • Upscaling from atomistic to continuum-scale models
  • Aqueous speciation, solubility and reactive transport modeling
  • Adsorption and surface complexation modeling
  • Validation with spectroscopy (nuclear magnetic resonance, inelastic neutron scattering, infrared/Raman)

Molecular Geochemistry Facilities

Red Sky is a 217-teraflop supercomputer at Sandia National Laboratories, comprised of SUN X6275 blades with 18,544 computing cores.


Geochemistry group computer clusters; 28 node AMD and Intel clusters with 192 processors.

Geochemistry Molecular Modeling Publications

Layered Minerals

  • R.T. Cygan, J.E. Post, P.J. Heaney, and J.D. Kubicki (2012) Molecular models of birnessite and related hydrated layered minerals. American Mineralogist, 97(8-9), 1505-1514. http://dx.doi.org/10.2138/am.2012.3957
  • R.T. Cygan, V.N. Romanov, and E.M. Myshakin (2012) Molecular simulation of carbon dioxide capture by montmorillonite using an accurate and flexible force field. Journal of Physical Chemistry C, 116(24), 13079-13091. http://dx.doi.org/10.1021/jp3007574
  • J.A. Greathouse and R.T. Cygan. (2012) Molecular Simulations of Clay Minerals. in Handbook of Clay Science, F. Bergaya and B.K.G. Theng, Eds., Elsevier, in press.
  • J.A. Greathouse, D.B. Hart, M.E. Ochs (2012) Alcohol and Thiol Adsorption on (Oxy)hydroxide and Carbon Surfaces: Molecular Dynamics Simulation and Desorption Experiments. Journal of Physical Chemistry C, 116, 26756-26764. http://dx.doi.org/10.1021/jp305275q
  • S.L. Teich-McGoldrick, J.A. Greathouse, R.T. Cygan. (2012) Molecular Dynamics Simulations of Structural and Mechanical Properties of Muscovite: Pressure and Temperature Effects. Journal of Physical Chemistry C, 116, 15099-15107. http://dx.doi.org/ 10.1021/jp303143s
  • T.R. Zeitler, J.A. Greathouse, and R.T. Cygan, (2012) Effects of Thermodynamic Ensembles and Mineral Surfaces on Interfacial Water Structure. Physical Chemistry Chemical Physics, 14(5), 1728-1734. http://dx.doi.org/10.1039/C2CP22593J
  • G. Zhang, Z. Wei, R.E. Ferrell, S.J. Guggenheim, R.T. Cygan, and J. Luo (2010) Evaluation of the elasticity normal to the basal plane of non-expandable 2:1 phyllosilicates by nanoindentation. American Mineralogist, 95(5-6), 863-869. http://dx.doi.org/10.2138/am.2010.3398
  • R.T. Cygan, J.A. Greathouse, H. Heinz, A.G. Kalinichev (2009) Molecular models and simulations of layered materials. Journal of Materials Chemistry, 19(17), 2470-2481. http://dx.doi.org/10.1039/b819076c
  • J.A. Greathouse, J.S. Durkin, J.P. Larentzos, R.T. Cygan (2009) Implementation of a Morse potential to model hydroxyl behavior in phyllosilicates. Journal of Chemical Physics, 130(13), 134713. http://dx.doi.org/10.1063/1.3103886
  • N.W. Ockwig, J.A. Greathouse, J.S. Durkin, R.T. Cygan, L.L. Daemen, and T.M. Nenoff (2009) Nanoconfined water in magnesium-rich 2:1 phyllosilicates. Journal of the American Chemical Society, 131(23), 8155-8162. http://dx.doi.org/10.1021/ja900812m
  • J.P. Larentzos, J.A. Greathouse, and R.T. Cygan (2007) An ab initio and classical molecular dynamics investigation of the structural and vibrational properties of talc and pyrophyllite. Journal of Physical Chemistry C, 111(34), 12752-12759. http://dx.doi.org/10.1021/jp072959f
  • I.F. Vasconcelos, B.A. Bunker, and R.T. Cygan (2007) Molecular dynamics modeling of ion adsorption to the basal surfaces of kaolinite. Journal of Physical Chemistry C, 111(18), 6753-6762. http://dx.doi.org/10.1021/jp065687
  • P.S. Braterman and R.T. Cygan (2006) Vibrational spectroscopy of brucite: A molecular simulation investigation. American Mineralogist, 91(7), 1188-1196. http://dx.doi.org/10.2138/am.2006.2094
  • J.A. Greathouse and R.T. Cygan (2006) Water structure and aqueous uranyl (VI) adsorption equilibria onto external surfaces of beidellite, montmorillonite, and pyrophyllite: Results from molecular simulations. Environmental Science & Technology, 40(12), 3865-3871. http://dx.doi.org/10.1021/es052522q
  • J.A. Greathouse and R.T. Cygan (2005) Molecular dynamics simulation of uranyl(VI) sorption equilibria onto an external montmorillonite surface. Physical Chemistry Chemical Physics, 7(20), 3580-3586. http://dx.doi.org/10.1039/b509307d
  • J. Wang, A.G. Kalinichev, R.J. Kirkpatrick, and R.T. Cygan (2005) Structure, energetics, and dynamics of water adsorbed on the muscovite (001) surface: A molecular dynamics simulation. Journal of Physical Chemistry B, 109(33), 15893-15905. http://dx.doi.org/10.1021/jp045299c

 

Ion Pairing, Surface Speciation, and Thermodynamics

  • L.J. Criscenti and R.T. Cygan (2012) Molecular simulations of carbon dioxide and water: Cation solvation. Environmental Science & Technology, 116, in press.  http://dx.doi.org/10.1021/es301608c
  • Katz, L.E., Criscenti, L.J., Chen, C.C., Larentzos, J.P., and Liljestrand, H.M. (2012) Temperature effects on alkaline earth metal ions adsorption on gibbsite:  Approaches from macroscopic sorption experiments and molecular dynamics simulations.  Journal of Colloid and Interface Science, http://dx.doi.org/10.1016/j.jcis.2012.05.011
  • Leung, K. and Criscenti, L.J. (2012) Predicting the pKa of a goethite hydroxyl group from first principles.  Journal of Physics:  Condensed Matter, invited, http://dx.doi.org/10.1088/0953-8984/24/12/124105
  • Leung, K., Nielsen, I. M. B., and Criscenti, L. J. (2009) Elucidating the bimodal acid-base behavior of the water-silica interface from first principles. Journal of American Chemical Society, 131, 18358-18365. http://dx.doi.org/10.1021/ja906190t  
  • Carroll, S., S. Roberts, L.J. Criscenti, and P.A. O’Day (2008) Surface Complexation Model for Strontium Sorption to Amorphous Silica and Goethite. Geochemical Transactions, 9, article 2. http://dx.doi.org/10.1186/1467-4866-9-2
  • Goldberg, S. and L.J. Criscenti (2008) Modeling adsorption of heavy metals and metalloids by soil components.In: Biophysico-chemical processes of heavy metals and metalloids in soil environments. A. Violante, P. M. Huang, and G. Gadd (eds.), John Wiley and Sons, Chichester, England.
  • Larentzos, J. P. and Criscenti, L. J. (2008) A molecular dynamics study of alkaline earth metal-chloride complexation in aqueous solution.  Journal of Physical Chemistry B, 112(45), 14243-14250.
  • Xu, M., J. P. Larentzos, M. Roshdy, L.J. Criscenti, and H. C. Allen (2008) Aqueous divalent metal-nitrate interactions: hydration versus ion pairing. Physical Chemistry Chemical Physics, 10, 4793-4801.
  • Goldberg, S., L.J. Criscenti, D.R. Turner, J. A. Davis, and K. J. Cantrell (2007) Adsorption-desorption processes in subsurface reactive transport modeling. Vadose Zone Journal, 6, 407-435.
  • Criscenti, L.J., J.D. Kubicki, and S.L. Brantley (2006) Silicate glass and mineral dissolution:  calculated reaction paths and activation energies for hydrolysis of a Q3 Si by H3O+ using ab initio methods. Journal of Physical Chemistry A, 110, 198-206. http://dx.doi.org/10.1021/jp044360a
  • Criscenti, L. J., S. L. Brantley, K. T. Mueller, N. Tsomaia, and J. D. Kubicki (2005) Theoretical and 27Al CPMAS NMR Investigation of Aluminum Coordination Changes During Aluminosilicate Dissolution. Geochimica et Cosmochimica Acta, 69, 2205-2220. http://dx.doi.org/10.1016/j.gca.2004.10.020
  • L.J. Criscenti, R.T. Cygan, A.S. Kooser, and H.K. Moffat (2008) Water and halide adsorption to corrosion surfaces:  Molecular simulations of atmospheric interactions with aluminum oxyhydroxide and gold.  Chemistry of Materials, 20(14), 4682-4693.  http://dx.doi.org/10.1021%2Fcm702781r
  • R.T. Cygan, C.T. Stevens, R.W. Puls, S.B. Yabusaki, R.D. Wauchope, C.J. McGrath, C.J., G.P. Curtis, M.D. Siegel, L.A. Veblen, and D.R. Turner (2007) Research activities at U.S. government agencies in subsurface reactive transport modeling.  Vadose Zone Journal, 6(4), 805-822.  http://dx.doi.org/10.2136/vzj2006.0091
  • T.D. Perry, R.T. Cygan, and R. Mitchell (2007) Molecular models of a hydrated calcite mineral surface.  Geochimica et Cosmochimica Acta, 71(24), 5876-5887.  http://dx.doi.org/10.1016/j.gca.2007.08.030
  • K.J. Johnson, R.T. Cygan, and J.B. Fein (2006) Molecular simulations of metal adsorption to bacterial surfaces.  Geochimica et Cosmochimica Acta, 70(20), 5075-5088.  http://dx.doi.org/10.1016/j.gca.2006.07.028
  • T.D. Perry, R.T. Cygan, and R. Mitchell (2006) Molecular models of alginic acid:  Interactions with calcium ions and calcite surfaces.  Geochimica et Cosmochimica Acta, 70(14), 3508-3532.  http://dx.doi.org/10.1016/j.gca.2007.08.030
  • S.J. Altman, M.L. Rivers, M. Reno, R.T. Cygan, and A.A. McLain (2005) Characterization of sorption sites on aggregate soil samples using synchrotron X-ray computerized microtomography.  Environmental Science & Technology, 39(8), 2679-2685.  http://dx.doi.org/10.1021/es049103y

 

Gas Hydrates

  • J.S. Clawson, R.T. Cygan, T.M. Alam, K. Leung, and S.B. Rempe (2010) Ab initio study of hydrogen storage in water clathrates.  Journal of Computational and Theoretical Nanoscience, 7(12), 2602-2606.  http://dx.doi.org/10.1166/jctn.2010.1648
  • J.A. Greathouse, R.T. Cygan, R.A. Bradshaw, E.H. Majzoub, and B.A. Simmons (2007) Computational and spectroscopic studies of dichlorofluroethane hydrate structure and stability.  Journal of Physical Chemistry C, 111(45), 16787-16795.  http://dx.doi.org/10.1021/jp072968o
  • J.A. Greathouse, R.T. Cygan, and B.A. Simmons (2006) Vibrational spectra of methane clathrate hydrates from molecular dynamics simulation.  Journal of Physical Chemistry B, 110(13), 6428-6431.  http://dx.doi.org/10.1021/jp060471t

 

Nanoporous Materials

  • Hou, Y., Fang, X., Kwon, K., Criscenti, L.J., Davis, D., Lambert, T. and Nyman, M. (accepted) Computational and Experimental Characterization and Corroboration of a Cagelike Fe15 Polycation. European Journal of Inorganic Chemistry, Special Issue for Mike Pope’s 80th birthday.
  • Zeitler, T. and Criscenti, L.J. (accepted) Classical Potentials for Nuclear Materials. Chapter for OECD/NEA Volume on Multi-scale Materials Modeling. Invited by V. Tikare, Chair of OECD NEA Expert Group on Multi-scale Materials Modeling.
  • S.T. Meek, S.L. Teich-McGoldrick, J.J. Perry, J.A. Greathouse, and M.D. Allendorf.  (2012) Effects of Polarizability on the Adsorption of Noble Gases at Low Pressures in Monohalogenated Isoreticular Metal-Organic Frameworks. Journal of Physical Chemistry C, 116, 19765-19772. http://dx.doi.org/10.1021/jp303274m
  • A.L. Robinson, V. Stavila, T.R. Zeitler, M.I. White, S.M. Thornberg, J.A. Greathouse, M.D. Allendorf. (2012) Ultrasensitive Humidity Detection Using Metal–Organic Framework-Coated Microsensors. Analytical Chemistry, 84, 7043-7051. http://dx.doi.org/10.1021/ac301183w
  • T. Van Heest, S.L. Teich-McGoldrick, J.A. Greathouse, M.D. Allendorf, D.S. Sholl. (2012) Identification of metal-organic framework materials for adsorption separation of rare gases: Applicability of IAST and effects of inaccessible framework regions. Journal of Physical Chemistry C, 116, 13183-13195. http://dx.doi.org/ 10.1021/jp302808j
  • T.R. Zeitler, M.D. Allendorf, J.A. Greathouse (2012) Grand Canonical Monte Carlo Simulation of Low-pressure Methane Adsorption in Nanoporous Framework Materials for Sensing Applications.  Journal of Physical Chemistry C, in press.  http://dx.doi.org/10.1021/jp208596e
  • D.F. Sava, M.A. Rodriguez, K.W. Chapman, P.J. Chupas, J.A. Greathouse, P.S. Crozier, and T.M. Nenoff, (2011) Capture of Volatile Iodine, a Gaseous Fission Product, by Zeolitic Imidazolate Framework-8. Journal of the American Chemical Society, 133(32), 12398-12401.  http://dx.doi.org/10.1021/ja204757x
  • S.T. Meek, J.J. Perry, S. Teich-McGoldrick, J.A. Greathouse, and M.D. Allendorf (2011) Complete Series of Mono-Halogenated Isoreticular Metal-Organic Frameworks: Synthesis and the Importance of Activation Method.  Crystal Growth & Design, 23, 249-267.  http://dx.doi.org/10.1021/cg201136k
  • S.T. Meek, J.A. Greathouse, and M.D. Allendorf (2011) Metal-Organic Frameworks: A Rapidly Growing Class of Versatile Nanoporous Materials.  Advanced Materials, 23, 249-267.  http://dx.doi.org/10.1002/adma.201002854
  • J.A. Greathouse, N.W. Ockwig, L.J. Criscenti, T.R. Guilinger, P. Pohl, and M.D. Allendorf (2010) Computational screening of metal-organic frameworks for large-molecule chemical Sensing.  Physical Chemistry Chemical Physics,12(39), 12621-12629.   http://dx.doi.org/10.1039/C0CP00092B
  • R.K. Raghunandan, J.L. Herberg, B. Jacobs, A. Highley, R. Behrens, N.W. Ockwig, J.A. Greathouse, and M.D. Allendorf (2009) Metal-organic frameworks as templates for nanoscale NaAlH4.  Journal of the American Chemical Society, 131(37), 13198-13199.  http://dx.doi.org/10.1021/ja904431x
  • J.A. Greathouse and M.D. Allendorf (2009) Adsorption and separation of noble gases by IRMOF-1:  Grand canonical Monte Carlo simulations.  Industrial & Engineering Chemistry Research.  48(7), 3425-3431.  http://dx.doi.org/10.1021/ie801294n
  • J.A. Greathouse and M.D. Allendorf (2008) Force field validation for molecular dynamics simulations of IRMOF-1 and other isoreticular zinc carboxylate coordination polymers.  Journal of Physical Chemistry C, 112, 5795-5802.  http://dx.doi.org/10.1021/jp076853w
  • N.W. Ockwig, R.T. Cygan, L.J. Criscenti, and T.M. Nenoff (2008) Molecular dynamics studies of nanoconfined water in clinoptilolite and heulandite zeolites.  Physical Chemistry Chemical Physics, 10(6), 800-807.  http://dx.doi.org/10.1039/b711949f
  • N.W. Ockwig, R.T. Cygan, M.A. Hartl, L.L. Daemen, and T.M. Nenoff (2008) Incoherent inelastic neutron scattering studies of nanoconfined water in clinoptilolite and heulandite zeolites.  Journal of Physical Chemistry C, 112(35), 13629-13634.  http://dx.doi.org/10.1021%2Fjp803770v
  • T.M. Nenoff, N.W. Ockwig, R.T. Cygan, T.M. Alam, K. Leung, J.D. Pless, H. Xu, M.A. Hartl, and L.L. Daemen (2007) Role of water in selectivity of niobate-based octahedral molecular sieves.  Journal of Physical Chemistry C, 111(35), 13212-13221.  http://dx.doi.org/10.1021/jp073969j
  • J.A. Greathouse and M.D. Allendorf (2006) The interaction of water with MOF-5 simulated by molecular dynamics.  Journal of the American Chemical Society, 128, 10678-10679.  http://dx.doi.org/10.1021/ja063506b

 

Waste Forms and Nuclear Materials

  • Zeitler, T. and Criscenti, L.J. (accepted) Classical Potentials for Nuclear Materials. Chapter for OECD/NEA Volume on Multi-scale Materials Modeling. Invited by V. Tikare, Chair of OECD NEA Expert Group on Multi-scale Materials Modeling.
  • A.E. Ismail, J.A. Greathouse, P.S. Crozier, and S.M. Foiles (2010) Electron-ion coupling effects on simulations of radiation damage in pyrochlore waste forms.  Journal of Physics:  Condensed Matter, 22(22), 225405.  http://dx.doi.org/10.1088/0953-8984/22/22/225405

 

Water Treatment

 

Technical Reports

Contact Us

Comments are closed.