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Publications

Articles in Refereed Journals

  • Zhang Z., P. Fenter, L. Cheng, N. C. Sturchio, M. J. Bedzyk, M. Předota, A. Bandura, J. D. Kubicki, S. N. Lvov, P. T. Cummings, A. A. Chialvo, M. K. Ridley, P. Bénézeth, L. Anovitz, D. A. Palmer, M. L. Machesky, and D. J. Wesolowski (2004) Ion adsorption at the rutile-water interface: Linking molecular and macroscopic properties. Langmuir, 20, 4954-4969.

  • M. Predota, A. V. Bandura, P. T. Cummings, J. D. Kubicki, D. J Wesolowski, A. A. Chialvo, and M. L. Machesky: "Electric double layer at the rutile (110) surface. 1. Structure of surfaces and interfacial water from molecular dynamics using ab initio potentials", J. Phys. Chem. B 108(32), 12049-12060 (2004).

  • Felipe M. A., Kubicki J. D. and Rye D. M. (2003) Oxygen isotope exchange kinetics between water and dissolved silica from ab initio calculations. Geochimica et Cosmochimica Acta. 68, 949-958.

  • Bandura A. V., Sykes D., Shapovalov V., Truong T. and Kubicki J. D. (2004) Adsorption of water on the TiO2 (rutile) [110] surface: A DFT study. Journal of Physical Chemistry B, 108, 7844-7853.

  • Bandura A. V. and Kubicki J. D. (2003) Derivation of force field parameters for TiO2-H2O systems from ab initio calculations. Journal of Physical Chemistry B. 107: 11072-11081.

  • Fedkin M.V., X.Y. Zhou, J. Kubicki, A.V. Bandura, S.N. Lvov, D.J. Wesolowski, M.L. Machesky (2003) High temperature microelectrophoresis studies of the rutile/aqueous solution interface. Langmuir, 19, 3797-3804.

  • Kubicki J. D. and Heaney P. J. (2003) Modeling interactions of aqueous silica and sorbitol: Complexation, polymerization and association. Geochimica et Cosmochimica Acta, 67, 4113-4121.

  • Clausén M., Öhman L-O., Kubicki J. D. and Persson P. (2002) Characterisation of gallium(III)-acetate complexes in aqueous solution: A potentiometric, EXAFS, IR and molecular orbital modelling study. Journal of the Chemical Society, Dalton Transactions, 2559-2564.

  • Govers H. A. J., Krop H. B., Parsons J. R., Tambach T., Kubicki J. D. (2002) Dissolved organic carbon-contaminant interaction descriptors found by 3D force field calculations. SAR and QSAR in Environmental Research, 13, 271-280.

  • Kubicki J. D. and Toplis M. J. (2002) Molecular orbital calculations on aluminosilicate tricluster molecules. American Mineralogist, 87, 668-678.

  • Felipe M. A., Kubicki J. D. and Rye D. M. (2002) Hydrogen isotope exchange between water and silica from ab initio calculations. Geochimica et Cosmochimica Acta, 67, 1259-1276.

  • Kubicki J. D. (2001) Integral equation formalism polarized continuum model calculations of aqueous Al3+, Fe3+ and Si4+: Correlations of calculated aqueous-phase deprotonation energies with experimental ln(Ka) and pKa values. Journal of Physical Chemistry A, 105, 8756-8762.

  • Hamilton, J. P., Brantley, S. L., Pantano, C. G., Criscenti, L., Kubicki, J. D. (2001) Dissolution of nepheline, jadeite and albite glasses: toward better models for aluminosilicate dissolution. Geochimica Cosmochimica Acta, 65, 3683-3702.

  • Kubicki J. D. (2000) Molecular mechanics and quantum mechanical modeling of hexane soot structure and interactions with pyrene. Geochemical Transactions, 7.

  • Rustad J. R., Dixon D. A., Kubicki J. D., and Felmy A. R. (2000) Gas-phase acidities of tetrahedral oxyacids from ab initio electronic structure theory. Journal of Physical Chemistry A, 104, 4051-4057.

  • Kubicki J. D. and Apitz S. E. (1999) Models of natural organic matter and interactions with organic contaminants. Organic Geochemistry, 30, 911.

  • Kubicki J. D., Sykes D., and Apitz S. E. (1999) Ab initio calculation of aqueous aluminum and aluminum-carboxylate NMR chemical shifts. Journal of Physical Chemistry A, 103, 903-915.

  • Kubicki J. D., Blake G. A., and Apitz S. E. (1999) Molecular models of benzene and selected PAHs in the gas, aqueous, and adsorbed states. Environmental Toxicology and Chemistry, 18, 1656-1662.

  • Kubicki J. D., Itoh M. J., Schroeter L. M., Nguyen B. N., and Apitz S. E. (1999) Attenuated total reflectance Fourier-transform infrared spectroscopy of carboxylic acids adsorbed onto mineral surfaces. Geochimica et Cosmochimica Acta, 63, 2709-2725.

  • Kubicki J. D. and Apitz S. E. (1998) Molecular cluster models of aluminum oxide and aluminum hydroxide surfaces. American Mineralogist, 83, 1054-1066. (Primary author)

  • Kubicki J. D., Blake G. A., and Apitz S. E. (1997) Molecular orbital calculations for modeling acetate-aluminosilicate adsorption and dissolution reactions. Geochimica et Cosmochimica Acta, 61, 1031-1046.

  • Sykes D., Kubicki J. D., and Farrar T. C. (1997) Molecular orbital calculation of 27Al and 29Si NMR parameters in Q3 and Q4 aluminosilicate molecules and implications for the interpretation of hydrous aluminosilicate glass NMR spectra. Journal of Physical Chemistry, 101, 2715-2722.

  • Kubicki J. D., Itoh M. J., Schroeter L. M., and Apitz S. E. (1997) The bonding mechanisms of salicylic acid adsorbed onto illite clay:  An ATR-FTIR and MO study. Environmental Science and Technology, 31, 1151-1156.

  • Kubicki J. D., Blake G. A., and Apitz S. E. (1996) Ab initio calculations on Q3 Si4+ and Al3+ species: Implications for atomic structure of mineral surfaces. American Mineralogist, 81, 789-799.

  • Kubicki J. D., Apitz S. E., and Blake G. A. (1996) Molecular orbital models of aqueous aluminum-acetate complexes. Geochimica et Cosmochimica Acta. 60, 4897-4911.

  • Sykes D. and Kubicki J. D. (1996) Four-membered rings in silica and aluminosilicate glasses. American Mineralogist, 81, 265-272.

  • Kubicki J. D., Blake G. A., and Apitz S. E. (1995) G2 theory calculations on [H3SiO4]-, [H4SiO4], [H3AlO4]2-, [H4AlO4]-, and [H5AlO4]: Basis set and electron correlation effects on molecular structures, atomic charges, infrared spectra, and potential energies. Physics and Chemistry of Minerals, 22, 481-488.

  • Kubicki J. D. and Sykes D. (1995) Molecular orbital calculations on the vibrational spectra of Q3 T-(OH) species and the hydrolysis of a three-membered aluminosilicate ring. Geochimica et Cosmochimica Acta, 59, 4791-4797.

  • Kubicki J. D. and Stolper E. M. (1995) Structural roles of CO2 and [CO3]2- in fully-polymerized sodium aluminosilicate melts and glasses. Geochimica et Cosmochimica Acta, 59, 683-698.

  • Lee W.-J. and Kubicki J. D. (1993) Molecular dynamics simulations of periclase crystallization. Geophysical Research Letters, 20, 2103-2106. (Co-author and supervisor)

  • Kubicki J. D., Sykes D., and Rossman G. R. (1993) Calculated trends of OH infrared stretching vibrations with composition and structure in aluminosilicate molecules. Physics and Chemistry of Minerals, 20, 425-432.

  • Kubicki J. D., Xiao Y., and Lasaga A. C. (1993) Theoretical reaction pathways for the formation of [Si(OH)5]1- and the deprotonation of orthosilicic acid in basic solution. Geochimica et Cosmochimica Acta, 57, 3847-3853.

  • Sykes D. and Kubicki J. D. (1993) A model for H2O solubility mechanisms in albite melts from infrared spectroscopy and molecular orbital calculations. Geochimica et Cosmochimica Acta, 57, 1039-1052.

  • Kubicki J. D. and Sykes D. (1993) Molecular orbital calculations of vibrations in three-membered aluminosilicate rings. Physics and Chemistry of Minerals, 19, 381-391.

  • Kubicki J. D. and Sykes D. (1993) Molecular orbital calculations on H6Si2O7 with a variable Si-O-Si angle: Implications for the high-pressure vibrational spectra of silicate glasses. American Mineralogist, 78, 253-259. 

  • Kubicki J. D. and Lasaga A. C. (1993) Molecular dynamics simulations of interdiffusion in MgSiO3-Mg2SiO4 melts. Physics and Chemistry of Minerals, 20, 255-262. (Primary author)

  • Kubicki J. D., Hemley R. J., and Hofmeister A. M. (1992) Raman and infrared study of pressure-induced structural changes in MgSiO3, CaMgSi2O6, and CaSiO3 glasses. American Mineralogist, 77, 258-269. 

  • Kubicki J. D., Muncill G. E., and Lasaga A. C. (1990) Chemical diffusion in melts on the CaMgSi2O6-CaAl2Si2O8 join under high pressures. Geochimica et Cosmochimica Acta, 54, 2709-2715.

  • Kubicki J. D. and Lasaga A. C. (1991) Ab initio molecular dynamics simulations of melting in forsterite and MgSiO3 perovskite. American Journal of Science, 292, 153-183.

  • Kubicki J. D. and Lasaga A. C. (1991) Molecular dynamics simulations of pressure and temperature effects on MgSiO3 and Mg2SiO4 melts and glasses. Physics and Chemistry of Minerals, 17, 661-673.

  • Hemley R. J. and Kubicki J. D. (1991) Deep mantle melting. Nature, 349, 283-284.

  • Kubicki J. D. and Lasaga A. C. (1988) Molecular dynamics simulations of SiO2 melt and glass. Ionic and covalent models. American Mineralogist, 73, 941-955.

  • Kubicki J. D. and Sykes D. (2004) Ab initio calculation of 17O, 27Al, and 29Si NMR parameters in hydrous silica and Na-aluminosilicate glasses. Geochim. Cosmochim. Acta, Vol 68/19 pp 3909-3918.

 

Books

  • Kubicki J. D. and Bleam W. F. (2003) Molecular Modeling of Clays and Mineral Surfaces, J. D. Kubicki and W. F. Bleam (eds.), CMS Workshop Lectures, Clay Minerals Society, Aurora CO, 229 pp.

  • Cygan R. T. and Kubicki J. D. (2001) Molecular Modeling Theory: Applications in the Geosciences, R. T. Cygan and J. D. Kubicki (eds.), Reviews in Mineralogy and Geochemistry 42, Geochemical Society, Washington DC, 531 pp.

 

Chapters in Books

  • Kubicki J. D. and Trout C. C. (2003) Molecular Modeling of Fulvic Acid: Charging Effects and Interactions with Al3+, Benzene and Pyridine. In Geochemical and Hydrological Reactivity of Heavy Metals in Soils, W. L. Kingery and H. M. Selim (eds). CRC Press, pp. 113-143.

  • Kubicki J. D. and Bleam W. F. (2003) An Introduction to Molecular Modeling. In Molecular Modeling of Clays and Mineral Surfaces, J. D. Kubicki and W. F. Bleam (eds.), CMS Workshop Lectures, pp. 1-21.

  • Kubicki J. D. (2001) Interpretation of Vibrational Spectra using Molecular Orbital Theory Calculations. In Molecular Modeling: Theory: Applications in the Geosciences, Reviews in Mineralogy and Geochemistry 42, R. T. Cygan and J. D. Kubicki (eds.) Geochemical Society, 459-483.

  • Felipe M., Xiao Y. and Kubicki J. D. (2001) Molecular Orbital Modeling and Transition State Theory in the Geosciences. In Molecular Modeling Theory: Applications in the Geosciences, Reviews in Mineralogy and Geochemistry 42, R. T. Cygan and J. D. Kubicki (eds.) Geochemical Society, 485-531.

  • Schott J., Pokrovski G. S. and Kubicki J. D. (1999) Metal speciation in surficial geological fluids. In Geochemistry of the Earth’s Surface, H. Armannsson (ed.), A. A. Balkema, Rotterdam, 417-419.

  • Kubicki J. D. and Lasaga A. C. (1990) Molecular dynamics and diffusion in silicate melts. In Diffusion, Defects, and Mass Transport, J. Ganguly (ed.), Advances in Physical Geochemistry , 8, 1-50. 

 

Manuscripts accepted for publication

  • Kwon K. D. and Kubicki J. D. (2004) Molecular orbital theory study on complexation structures of phosphates to iron hydroxides. Langmuir.

  • Omoike A., Chorover J., Kwon K., and Kubicki J.D. (2004) Adhesion of bacterial exopolymers to alpha-FeOOH: Inner-sphere complexation of phosphodiester groups. Langmuir.

  • Goyne K., Chorover J., Kubicki J. D., Zimmerman A. R., and Brantley S. L. (2004) Sorption of the Antibiotic Ofloxacin to Mesoporous and Non-Porous Alumina and Silica. J. Coll. Interface Sci.

 

 Manuscripts submitted for publication

  • Criscenti L. J., Brantley S. L., Kubicki J. D. (2004) Molecular modeling studies of aluminum coordination changes during aluminosilicate dissolution. Geochimica et Cosmochimica Acta.

  • Lvov, S., J. D. Kubicki, A. V. Bandura, M. Předota, P. T. Cummings and A. A. Chialvo (2003) Zeta potentials of TiO2 in aqueous Solutions from 25 to 250°C: Experimental and molecular dynamics simulation results. Langmuir.

  • Trout C. C., Kubicki J. D. (2003) Correlation of observed and model vibrational frequencies for aqueous organic acids: UV resonance Raman spectra and molecular orbital calculations of benzoic, salicylic, and phthalic acids. Spectrochimica Acta.

·        Trout C. C., Kubicki J.D. (2004) UV resonance Raman spectra and molecular orbital calculations ofsalicylic and phthalic acids complexed to Al3+. J. Phys. Chem. A.

·        Felipe M.A., FreemanK., and Kubicki J.D. (2004) A mechanism for carbon isotope exchange betweenaqueous acetic acid and CO2/ HCO3-:  An ab initio study. OrganicGeochemistry.

 

Recent Talks

  • Kubicki J. D. and Heaney P. J. (2003) Modeling interactions of aqueous silica and sorbitol: Complexation, polymerization and association. Abstr. Pap. Am. Chem. Soc.

  • Kubicki, J. D., Bandura A. V. (2003) Periodic density functional theory calculations of Sr(II) and Zn(II) adsorption onto the (110) face of rutile. Abstr. Pap. Am. Chem. Soc.

  • Kubicki, J. D. (2003) Modeling surface complexes of As(III) and As(V) with Al- and Fe-oxides. Abstr. Pap. Am. Chem. Soc.

  • Campen RK, Kubicki JD, Chorover J (2003) Adsorption of neutral, acidic, basic and amphiphilic polysaccharides on iron oxides and silica particles. ABSTR PAP AM CHEM S 225: 12 Part 1 MAR 2003.

  • Kubicki J. D. (2003) Ab initio calculations of structures of polychlorinated biphenyls for use in predicting partitioning onto soot. SETAC National Meeting, Austin TX.

  • Kubicki J. D. (2003) Interpreting spectra of surface complexes with molecular orbital calculations. Workshop on “The Surface Reactivity of Minerals”, Telluride, CO. INVITED.

  • Kubicki, J. D., Campen, R. K., Kwon K. (2003) Modeling saccharide, amino acid and organophosphate adsorption to silica and Fe-hydroxides. Abs. Am. Geophys. Union.

  • Campen* R. K., Kubicki J. D., Chorover J. (2002) Mechanisms of adsorption of dextrans on hematite and goethite: Batch adsorption experiments and molecular dynamics simulations. Papers of the American Chemical Society, Orlando, FL, April, 123-GEOC.

  • Kubicki J.D. and Trout C. C. (2002) UV Raman spectroscopy and ab initio calculations of carboxylic acids-Al solutions. Abstr. Pap. Am. Chem. Soc. 224: 012-GEOC Part

  • Kubicki J. D., Sykes D. G. (2002) Ab initio modeling and calculations of vibrational frequencies of water dissolved in Na-aluminosilicate glasses. Glass & Optical Materials Division meeting of the American Ceramic Society, Pittsburgh, PA, October. INVITED.

  • *Sykes D. G., Kubicki J. D. (2002) Ab initio calculations of NMR chemical shifts in hydrous Na-aluminosilicate glasses. Glass & Optical Materials Division meeting of the American Ceramic Society, Pittsburgh, PA, October.

  • Kubicki J. D. (2002) Ab initio calculation of NMR chemical shifts in Si-O-C glasses. Glass & Optical Materials Division meeting of the American Ceramic Society, Pittsburgh, PA, October.

  • *Sykes D. G., Kubicki J. D. (2002) Ab initio modeling of vibrational spectra in aluminosilicate glasses. Glass & Optical Materials Division meeting of the American Ceramic Society, Pittsburgh, PA, October.

  • Kubicki J. D. (2002) Ab initio calculations of PAH-soot interaction energies for use in predicting partitioning onto soot. Society for Environmental Toxicology and Chemistry national meeting, Salt Lake City, UT, November. INVITED.

  • *Campen R. K., Kubicki J. D., Chorover J.D., (2002) Mechanisms of adsorption of the neutral polysaccharide dextran on hematite, goethite and amorphous silica. Abstracts of the Am. Geophys. Union, San Francisco, December.

  • *Kwon K., Kubicki J. D. (2002) Short-range interaction energies and forces between glucose and silica. Abstracts of the Am. Geophys. Union, San Francisco, CA, December.

  • Bandura A. V., Kubicki J. D., (2002) Periodic density functional theory calculations of Sr(II) and Zn(II) adsorption onto the (110) face of rutile. Abstracts of the Am. Geophys. Union, San Francisco, CA, December.

  • Heaney P. J., Kubicki J. D. (2002) Structures of Si-carbohydrate aqueous complexes: Comparison of NMR spectra and molecular orbital results. Abstracts of the Am. Geophys. Union, San Francisco, CA, December.

  • Bandura A. V., D. G. Sykes*, J. D. Kubicki (2002) Water speciation on the TiO2 (rutile) [110] surface. Abstracts of Papers of the American Chemical Society, Orlando, FL, April, 073-GEOC.

  • Bandura A. V., D. G. Sykes, J. D. Kubicki (2002) Derivation of force field parameters for TiO2-H2O systems from ab initio calculations. Abstracts of Papers of the American Chemical Society, Orlando, FL, April, 074-GEOC.