Publications
Works relevant to chemistry computation published by our chemistry department faculty. Please note: if you feel something was left out, please contact us.
2006
As of June 2006:
Ellison, P.A. and Cavagnero, S. (2006). Role of unfolded state heterogeneity and en-route ruggedness in protein folding kinetics. Protein Science, 15(3), 564-582.
Iung C, Ribeiro F, Sibert EL. (2006). Comparison of perturbative and variational treatments of molecular vibrations: Application to the vibrational spectrum of HFCO up to 8000 cm(-1). Journal of Physical Chemistry A. 110, 16, 5420-5429.
Jin, S. and Wen, X. (2006). Hamiltonian-preserving schemes for the Liouville equation of geometrical optics with discontinuous local wave speeds. Journal of Computational Physics, 214, 2, 672-697.
Jungbauer, L.M., Bakke, C.K., and Cavagnero, S. (2006). Experimental and computational analysis of translation products in apomyoglobin expression [Review]. Journal of Molecular Biology, 357(4), 1121-1143.
Muenter, A.H., DeZwaan, J.L. and Nathanson, G.M. (2006). Collisions of DCl with pure and salty glycerol: Enhancement of interfacial D -> H exchange by dissolved NaI. Journal of Physical Chemistry B, 110 (10), 4881-4891.
Nelsen, S.F., Weaver, M.N., Luo, Y., Lockard, J.V., Zink, J.I. (2006). Use of the neighboring orbital model for analysis of electronic coupling in Class III intervalence compounds. Chemical Physics, 324, 1, 195-201.
Stich, T.A., Seravalli, J., Venkateshrao, S., Spiro, T.G., Ragsdale, S.W. and Brunold, T.C. (2006). Spectroscopic studies of the corrinoid/iron-sulfur protein from Moorella thermoacetica, Journal of the American Chemical Society, 128, (15), 5010-5020.
Weinhold, F. (2006). Resonance character of hydrogen-bonding interactions in water and other H-bonded species [Review]. Ed. Baldwin, R.L., and Baker, D. PEPTIDE SOLVATION AND H-BONDS. p. 121-+.
2005
Brooks, A.J., Fox, C.C., Marsh, E.N.G., Vlasie, M. Banerjee, R., and Brunold, T.C. (2005). Electronic structure studies of the adenosylcobalamin cofactor in glutamate mutase. Biochemistry, 44(46), 15167-15181.
Fiedler, A.T. and Brunold, T.C. (2005). Combined spectroscopic/computational study of binuclear Fe(I)-Fe(I) complexes: Implications for the fully-reduced active-site cluster of Fe-only hydrogenases. Inorganic Chemistry, 44(6), 1794-1809.
Fiedler, A.T., Bryngelson, P.A., Maroney, M.J., Brunold, T.C. (2005). Spectroscopic and computational studies of Ni superoxide dismutase: Electronic structure contributions to enzymatic function. Journal of the American Chemical Society, 127(15), 5449-5462.
Jin, S., Liu, H.L., Osher, S., and Tsai, Y.H.R. (2005). Computing multivalued physical observables for the semiclassical limit of the Schrodinger equation. Journal of Computational Physics, 205(1), 222-241.
Jin, S., Liu, H.L., Osher, S., and Tsai, R. (2005). Computing multi-valued physical observables for the high frequency limit of symmetric hyperbolic systems. Journal of Computational Physics, 210(2), 497-518.
Jin, S. and Wen, X. (2005). Two interface-type numerical methods for computing hyperbolic systems with geometrical source terms having concentrations. SIAM Journal on Scientific Computing, 26(6), 2079-2101.
Riccardi, D., Schaefer, P., and Cui, Q. (2005). pK(a) calculations in solution and proteins with QM/MM free energy perturbation simulations: A quantitative test of QM/MM protocols [Review]. Journal of Physical Chemistry B, 109(37), 17715-17733.
Scarborough, C.C., Popp, B.V., Guzei, I.A., and Stahl, S.S. (2005). Development of 7-membered N-heterocyclic carbene ligands for transition metals. Journal of Organometallic Chemistry, 690(24-25), 6143-6155.
Schenker, R., Kieber-Emmons, M.T., Riordan, C.G., and Brunold, T.C. (2005). Spectroscopic and computational studies on the trans-mu-1,2-peroxo-bridged dinickel(II) species [{Ni(tMC)}2(02)](OTf)2: Nature of end-on peroxo-nickel(II) bonding and comparison with peroxo-copper(II) bonding. Inorganic Chemistry, 44(6), 1752-1762.
Schenker, R., Mock, M.T., Kleber-Emmons, M.T., Riordan, C.G., and Brunold, T.C. (2005). Spectroscopic and computational studies on [Ni(tmc)CH3]OTf: Implications for Ni-methyl bonding in the A cluster of acetyl-CoA synthase. Inorganic Chemistry, 44(10), 3605-3617.
Stich, T.A., Buan, N.R., Escalante-Semerena, J.C., and Brunold, T.C. (2005). Spectroscopic and computational studies of the ATP : Corrinoid adenosyltransferase (CobA) from Salmonella enterica: Insights into the mechanism of adenosylcobalamin biosynthesis. Journal of the American Chemical Society, 127(24), 8710-8719.
Tulpan, D., Andronescu, M., Chang, S.B., Shortreed, M.R., Condon, A., Hoos, H.H., and Smith, L.M. (2005). Thermodynamically based DNA strand design. Nucleic Acids Research, 33(15), 4951-4964.
Van Wynsberghe, A.W. and Cui, Q. (2005). Comparison of mode analyses at different resolutions applied to nucleic acid systems. Biophysical Journal, 89(5), 2939-2949.
Yoon, S., Holiday, R.J. and Crim, F.F. (2005). Vibrationally controlled chemistry: Mode- and bond-selected reaction of CH3D with CI. Journal of Physical Chemistry B., 109(17), 8388-8392.
2004
Alabugin, I. V., Manoharan, M., & Weinhold, F. A. (2004). Blue-shifted and red-shifted hydrogen bonds in hypervalent rare-gas FRg-H center dot center dot center dot Y sandwiches. Journal of Physical Chemistry A Molecules, 108(21), 4720-4730.
Brooks, A. J., Vlasie, M., Banerjee, R., & Brunold, T. C. (2004). Spectroscopic and computational studies on the adenosylcobalamin-dependent methylmalonyl-CoA mutase: Evaluation of enzymatic contributions to co-C bond activation in the Co3+ ground state. Journal of the American Chemical Society, 126(26), 8167-8180.
Brunold, T. C. (2004). Combined spectroscopic/computational studies of metal centers in proteins and cofactors: Application to coenzyme B-12. Chimia, 58(4), 186-193.
Brunold, T. C. (2004). Spectroscopic and computational insights into the geometric and electronic properties of the A-cluster of acetyl-coenzyme A synthase. Journal of Biological Inorganic Chemistry, 9(5), 533-541.
Corcelli, S. A., Lawrence, C. P., & Skinner, J. L. (2004). Combined electronic structure/molecular dynamics approach for ultrafast infrared spectroscopy of dilute HOD in liquid H2O and D2O [review]. Journal of Chemical Physics, 120(17), 8107-8117.
Craft, J. L., Horng, Y. C., Ragsdale, S. W., & Brunold, T. C. (2004). Spectroscopic and computational characterization of the nickel-containing F-430 cofactor of methyl-coenzyme M reductase. Journal of Biological Inorganic Chemistry, 9(1), 77-89.
Dhiman, A., Muller, T., West, R., & Beeker, J.Y. (2004). Electrochemistry and computations of stable silylenes and germylenes. Organometallics. 23(24), 5689-5693.
Fox, D. C., Fiedler, A. T., Halfen, H. L., Brunold, T. C., & Halfen, J. A. (2004). Electronic structure control of the nucleophilicity of transition metal-thiolate complexes: An experimental and theoretical study. Journal of the American Chemical Society, 126(24), 7627-7638.
Fujita, K., Schenker, R., Gu, W. W., Brunold, T. C., Cramer, S. P., & Riordan, C. G. (2004). A monomeric nickel-dioxygen adduct derived from a nickel(I) complex, and O-2. Inorganic Chemistry, 43(11), 3324-3326.
Hutchison, J. M., Holiday, R. J., Bach, A., Hsieh, S., & Crim, F. F. (2004). Action spectroscopy and photodissociation of vibrationally excited methanol. Journal of Physical Chemistry A Molecules, 108(39), 8115-8118.
Jackson, T. A., & Brunold, T. C. (2004). Combined spectroscopic/computational studies on fe- and mn-dependent superoxide dismutases: Insights into second-sphere tuning of active site properties [review]. Accounts of Chemical Research, 37(7), 461-470.
Jackson, T. A., Karapetian, A., Miller, A. F., & Brunold, T. C. (2004). Spectroscopic and computational studies of the azide-adduct of manganese superoxide dismutase: Definitive assignment of the ligand responsible for the low-temperature thermochromism. Journal of the American Chemical Society, 126(39), 12477-12491.
Li, G. H., & Cui, Q. (2004). Mechanochemical coupling in myosin: A theoretical analysis with molecular dynamics and combined QM/MM reaction path calculations. Journal of Physical Chemistry B, 108(10), 3342-3357.
Popp, B.V., Thorman, J.L., Morales, C.M., Landis, C.R., & Stahl, S.S. (2004). Inverse-electron-demand" ligand substitution: Experimental and computational insights into olefin exchange at palladium(0). Journal of the American Chemical Society. 126(45), 14832-14842.
Riccardi, D., Li, G. H., & Cui, Q. (2004). Importance of van der waals interactions in QM/MM simulations. Journal of Physical Chemistry B, 108(20), 6467-6478.
Schmidt, J. R., Corcelli, S. A., & Skinner, J. L. (2004). Ultrafast vibrational spectroscopy of water and aqueous N-methylacetamide: Comparison of different electronic structure/molecular dynamics approaches. Journal of Chemical Physics, 121(18), 8887-8896.
Stich, T. A., Buan, N. R., & Brunold, T. C. (2004). Spectroscopic and computational studies of Co2+ corrinoids: Spectral and electronic properties of the biologically relevant base-on and base-off forms of Co2+ cobalamin. Journal of the American Chemical Society, 126(31), 9735-9749.
Su, X. P., & Smith, L. M. (2004). Demonstration of a universal surface DNA computer. Nucleic Acids Research, 32(10), 3115-3123
Zhou, S., Kile, A., Bechner, M., Place, M., Kvikstad, E., & Deng, W. et al. (2004). Single-molecule approach to bacterial genomic comparisons via optical mapping. Journal of Bacteriology, 186(22), 7773-7782.
2003
Ardavan, A., Austwick, M., Benjamin, S. C., Briggs, G. A. D., Dennis, T. J. S., & Ferguson, A. et al. (2003). Nanoscale solid-state quantum computing. Philosophical Transactions of the Royal Society of London Series A-Mathematical Physical & Engineering Sciences, 361(1808), 1473-1485.
Cao, X. P., & Hamers, R. J. (2003). Molecular and dissociative bonding of amines with the si(111)-(7 x 7) surface. Surface Science, 523(3), 241-251.
Craft, J. L., Mandimutsira, B. S., Flujita, K., Riordan, C. G., & Brunold, T. C. (2003). Spectroscopic and computational studies of a ni+-CO model complex: Implications for the acetyl-CoA synthase catalytic mechanism. Inorganic Chemistry, 42(3), 859-867.
Florio, G. M., Zwier, T. S., Myshakin, E. M., Jordan, K. D., & Sibert, E. L. (2003). Theoretical modeling of the OH stretch infrared spectrum of carboxylic acid dimers based on first-principles anharmonic couplings. Journal of Chemical Physics, 118(4), 1735-1746.
Hansen, M. J., Wendt, M. A., & Weinhold, F. (2003). Tests of quantum cluster equilibrium (QCE)-based computational methods for describing formic acid clustering. Molecular Physics, 101(8), 1147-1153.
Jackson, T. A., Yikilmaz, E., Miller, A. F., & Brunold, T. C. (2003). Spectroscopic and computational study of a non-heme iron {fe-NO}(7) system: Exploring the geometric and electronic structures of the nitrosyl adduct of iron superoxide dismutase [review]. Journal of the American Chemical Society, 125(27), 8348-8363.
Jendrejack, R. M., Schwartz, D. C., Graham, M. D., & de Pablo, J. J. (2003). Effect of confinement on DNA dynamics in microfluidic devices. Journal of Chemical Physics, 119(2), 1165-1173.
Li, G. H., Zhang, X. D., & Cui, Q. (2003). Free energy perturbation calculations with combined QM/MM potentials complications, simplifications, and applications to redox potential calculations. Journal of Physical Chemistry B, 107(33), 8643-8653.
Schenker, R. P., & Brunold, T. C. (2003). Computational studies on the A cluster of acetyl-coenzyme A synthase: Geometric and electronic properties of the NiFeC species and mechanistic implications. Journal of the American Chemical Society, 125(46), 13962-13963.
Stich, T. A., Brooks, A. J., Buan, N. R., & Brunold, T. C. (2003). Spectroscopic and computational studies of Co3+-corrinoids: Spectral and electronic properties of the B-12 cofactors and biologically relevant precursors. Journal of the American Chemical Society, 125(19), 5897-5914.
Weise, C. F., & Weisshaar, J. C. (2003). Conformational analysis of alanine dipeptide from dipolar couplings in a water-based liquid crystal. Journal of Physical Chemistry B, 107(14), 3265-3277.
Winokur, M. J., & West, R. (2003). X-ray diffraction and molecular modeling studies of poly(di-n-alkylsilanes): The near planar type phases of poly(di-n-butylsilane) and poly(di-n-hexylsilane). Macromolecules, 36(19), 7338-7347.
Wright, J. C., Condon, N. J., Murdoch, K. M., Besemann, D. M., & Meyer, K. A. (2003). Quantitative modeling of nonlinear processes in coherent two-dimensional vibrational spectroscopy. Journal of Physical Chemistry A Molecules, 107(40), 8166-8176.
Yoon, S., Holiday, R. J., Sibert, E. L., & Crim, F. F. (2003). The relative reactivity of CH3D molecules with excited symmetric and antisymmetric stretching vibrations. Journal of Chemical Physics, 119(18), 9568-9575.
Zimmerman, H. E., & Nesterov, E. E. (2003). An experimental and theoretical study of the type C enone rearrangement: Mechanistic and exploratory organic photochemistry. Journal of the American Chemical Society, 125(18), 5422-5430.
Zimmerman, H. E., & Sereda, G. A. (2003). Solution and crystal lattice effects on the photochemistry of 6-substituted cyclohexenones. Journal of Organic Chemistry, 68(2), 283-292.
Zimmerman, H. E., & Wang, P. F. (2003). An unusual abnormal wolff rearrangement. Canadian Journal of Chemistry, 81(6), 517-524.