Publications

PUBLICATIONS 

Please submit information about publications and presentations that include work done using MERCURY resources to support@mercuryconsortium.org

Acknowledgements

The following acknowledgements are to be used for papers and presentations where MERCURY resources were used:

2001 – 2004

Computational resources were provided in part by the MERCURY consortium (http://mercuryconsortium.org/) under NSF grants CHE-0116435

2005- 2008

Computational resources were provided in part by the MERCURY consortium (http://mercuryconsortium.org/) under NSF grants CHE-0521063

2009 – 2013

Computational resources were provided in part by the MERCURY consortium (http://mercuryconsortium.org/) under NSF grants CHE-0521063 and CHE-0849677.

2013 – 2016

Computational resources were provided in part by the MERCURY consortium (http://mercuryconsortium.org/) under NSF grants CHE-1229354.

2017 –

Computational resources were provided in part by the MERCURY consortium (http://mercuryconsortium.org/) under NSF grants CHE-1229354 and CHE-1662030.

Publications

2017

  • Barnes, G. L., & Podczerwinski, A. (2017). Simulating the Effect of Charge State on Reactive Landing of a Cyclic Tetrapeptide on Chemically Modified Alkylthiolate Self-Assembled Monolayer Surfaces. The Journal of Physical Chemistry C121 (27), pp 14628–14635
  • Taylor, C. A., Miller, B. R., & Parish, C. A. (2017). Design and Computational Verification of a CCR5/CXCR4 Dual Tropic Inhibitor. Journal of Molecular Graphics and Modelling. 75. 71-79. 
  • Rote, J. C., Malkowski, S. N., Cochrane, C. S., Bailey, G. E., Brown, N. S., Cafiero, M., & Peterson, L. W. (2017). Catechol reactivity: Synthesis of dopamine derivatives substituted at the 6-position. Synthetic Communications, 47(5), 435–441. 
  • Phillips, J. A. (2017). Structural and energetic properties of nitrile–BX3 complexes: substituent effects and their impact on condensed-phase sensitivity. Theoretical Chemistry Accounts, 136(1), 16. 
  • Wilson, R. H., Zamfir, S., & Sumner, I. (2017). Molecular dynamics simulations reveal a new role for a conserved active site asparagine in a ubiquitin-conjugating enzyme. Journal of Molecular Graphics and Modelling, 76, 403–411.
  • Gomez, M. A., Kwan, G., Zhu, W., Chelliah, M., Zuo, X., Eshun, A., … Huynh, M. (2017). Ordered yttrium concentration effects on barium zirconate structure, proton binding sites and transition states. Solid State Ionics, 304, 126–134.
  • Taylor, C. A., Miller, B. R., Shah, S. S., & Parish, C. A. (2017). A molecular dynamics study of the binary complexes of APP, JIP1, and the cargo binding domain of KLC. Proteins: Structure, Function, and Bioinformatics, 85(2), 221–234.
  • Kacar, B., Hanson-Smith, V., Adam, Z. R., & Boekelheide, N. (2017). Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree. Geobiology, 15(5), 628–640.
  • Saha, I., Wang, E. B., Parish, C. A., & Ghosh, K. (2017). Triphenylamine-Based Open and Macrocyclic Receptors: A Study Towards Selectivite Recognition of Aliphatic Dicarboxylates. ChemistrySelect, 2(17), 4794–4799.
  • Waller, A. W., Weiss, N. M., Decato, D. A., & Phillips, J. A. (2017). Structural and energetic properties of haloacetonitrile–GeF 4 complexes. Journal of Molecular Structure, 1130, 984–993.
  • Wang, W., Taylor, C. A., Hu, H., Humphries, K. L., Jaini, A., Kitimet, M., … others. (2017). Nanoaggregates of Diverse Asphaltenes by Mass Spectrometry and Molecular Dynamics. Energy & Fuels.
  • Pratihar, S., Ma, X., Homayoon, Z., Barnes, G. L., & Hase, W. L. (2017). Direct chemical dynamics simulations. Journal of the American Chemical Society, 139(10), 3570–3590.
  • Beane, A., Miller, B. R., & Parish, C. A. (2017). Internal abstraction of dynemicin A: An MD approach. Journal of Molecular Graphics and Modelling, 74, 251–264.
  • Wheeler, D. L., Rainwater, L. E., Green, A. R., & Tomlinson, A. L. (2017). Modeling electrochromic poly-dioxythiophene-containing materials through TDDFT. Physical Chemistry Chemical Physics, 19(30), 20251–20258.
  • Temelso, B., Mabey, J. M., Kubota, T., Appiah-Padi, N., & Shields, G. C. (2017). ArbAlign: A Tool for Optimal Alignment of Arbitrarily Ordered Isomers Using the Kuhn–Munkres Algorithm. Journal of Chemical Information and Modeling, 57(5), 1045–1054.
  • Hunter, N. H., Bakula, B. C., & Bruce, C. D. (2017). Molecular Dynamics Simulations of apo and holo forms of Fatty Acid Binding Protein 5 and Cellular Retinoic Acid Binding Protein II Reveal Highly Mobile Protein, Retinoic Acid Ligand, and Water Molecules. Journal of Biomolecular Structure and Dynamics, (just-accepted), 1–48.
  • Pérez, C., Steber, A. L., Rijs, A. M., Temelso, B., Shields, G. C., Lopez, J. C., … Schnell, M. (2017). Corannulene and its complex with water: a tiny cup of water. Phys. Chem. Chem. Phys., 19(22), 14214–14223. http://doi.org/10.1039/C7CP01506B

2016

  • Omorodion, O., Bober, M., & Donald, K. J. (2016). Turn: Weak Interactions and Rotational Barriers in Molecules Insights from Substituted Butynes. The Journal of Physical Chemistry A, 120(44), 8896–8906.
  • Jalife, S., Liu, L., Pan, S., Cabellos, J. L., Osorio, E., Lu, C., … Merino, G. (2016). Dynamical behavior of boron clusters. Nanoscale, 8(40), 17639–17644.
  • Gurunathan, P. K., Acharya, A., Ghosh, D., Kosenkov, D., Kaliman, I., Shao, Y., … Slipchenko, L. V. (2016). Extension of the effective fragment potential method to macromolecules. The Journal of Physical Chemistry B, 120(27), 6562–6574.
  • Chavez III, R., Cai, M., Tlach, B., Wheeler, D. L., Kaudal, R., Tsyrenova, A., … Jeffries-EL, M. (2016). Benzobisoxazole cruciforms: a tunable, cross-conjugated platform for the generation of deep blue OLED materials. Journal of Materials Chemistry C, 4(17), 3765–3773.
  • Kosenkov, D. (2016). PyFREC: Software for Förster electronic coupling evaluation in molecular fragments. Journal of Computational Chemistry, 37(19), 1847–1854.
  • Raccuglia, P., Elbert, K. C., Adler, P. D. F., Falk, C., Wenny, M. B., Mollo, A., … Norquist, A. J. (2016). Machine-learning-assisted materials discovery using failed experiments. Nature, 533(7601), 73–76.
  • Baltrusaitis, J., Patterson, E. V, O’Connor, M., Qu, S., Kolodziej, E. P., & Cwiertny, D. M. (2016). Reversible photohydration of trenbolone acetate metabolites: Mechanistic understanding of product-to-parent reversion through complementary experimental and theoretical approaches. Environmental Science & Technology, 50(13), 6753–6761.
  • Nourmahnad, A., Wenny, M. B., Zeller, M., Schrier, J., & Norquist, A. J. (2016). The role of inorganic acidity on templated vanadate composition and dimensionality. Journal of Solid State Chemistry, 236, 215–221.
  • Borgatta, J., Paskavitz, A., Kim, D., & Navea, J. G. (2016). Comparative evaluation of iron leach from different sources of fly ash under atmospherically relevant conditions. Environmental Chemistry, 13(5), 902–912.
  • Kosenkov, D., Shaw, J., Zuczek, J., & Kholod, Y. (2016). Transient-Absorption Spectroscopy of Cis–Trans Isomerization of N, N-Dimethyl-4, 4′-azodianiline with 3D-Printed Temperature-Controlled Sample Holder. Journal of Chemical Education, 93(7), 1299–1304.
  • Pratihar, S., Barnes, G. L., Laskin, J., & Hase, W. L. (2016). Dynamics of protonated peptide ion collisions with organic surfaces: consonance of simulation and experiment. The Journal of Physical Chemistry Letters, 7(16), 3142–3150.
  • Pratihar, S., Barnes, G. L., & Hase, W. L. (2016). Chemical dynamics simulations of energy transfer, surface-induced dissociation, soft-landing, and reactive-landing in collisions of protonated peptide ions with organic surfaces. Chemical Society Reviews, 45(13), 3595–3608.
  • Weiss, N. M., Waller, A. W., & Phillips, J. A. (2016). Infrared spectrum of CH 3 CN–HCl in solid neon, and modeling matrix effects in CH 3 CN–HCl and H 3 N–HCl. Journal of Molecular Structure, 1105, 341–349.
  • Hatstat, A. K., Morris, M., Peterson, L. W., & Cafiero, M. (2016). Ab initio study of electronic interaction energies and desolvation energies for dopaminergic ligands in the catechol-O-methyltransferase active site. Computational and Theoretical Chemistry, 1078, 146–162.
  • Du Pont, K. E., McKenzie, A. M., Kokhan, O., Sumner, I., & Berndsen, C. E. (2016). The Disulfide Bonds within BST-2 Enhance Tensile Strength during Viral Tethering. Biochemistry, 55(6), 940–947.
  • Homayoon, Z., Pratihar, S., Dratz, E., Snider, R., Spezia, R., Barnes, G. L., … Hase, W. L. (2016). Model Simulations of the Thermal Dissociation of the TIK (H+) 2 Tripeptide: Mechanisms and Kinetic Parameters. The Journal of Physical Chemistry A, 120(42), 8211–8227.
  • Adler, P. D. F., Xu, R., Olshansky, J. H., Smith, M. D., Elbert, K. C., Yang, Y., … Norquist, A. J. (2016). Probing structural adaptability in templated vanadium selenites. Polyhedron, 114, 184–193.
  • Richardson, J. O., Perez, C., Lobsiger, S., Reid, A. A., Temelso, B., Shields, G. C., … Althorpe, S. C. (2016). Concerted hydrogen-bond breaking by quantum tunneling in the water hexamer prism. Science, 351(6279), 1310–1313. http://doi.org/10.1126/science.aae0012

2015

  • Bresnahan, C. G.; Reinhardt, C. R.; Bartholow, T. G.; Rumpel, J. P.; North, M.; Bhattacharyya, S., Effect of Stacking Interactions on the Thermodynamics and Kinetics of Lumiflavin: A Study with Improved Density Functionals and Density Functional Tight-Binding Protocol. J. Phys. Chem. A 2015, 119 (1), 172-182.
  • Miller, B. R., III; Parish, C. A.; Wu, E. Y., Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I. Plos Computational Biology 2014, 10 (12). 216. Miller, B. R., III; Beese, L. S.; Parish, C. A.; Wu, E. Y., The Closing Mechanism of DNA Polymerase I at Atomic Resolution. Structure 2015, 23 (9), 1609-1620.
  • Muya, J. T.; Ceulemans, A.; Gopakumar, G.; Parish, C. A., Jahn-Teller Distortion in Polyoligomeric Silsesquioxane (POSS) Cations. J. Phys. Chem. A 2015, 119 (18), 4237-4243.
  • Swan, J. S.; Findeis, P. M.; Hilton, S.; Lebold, K. M.; Temelso, B.; Shields, G. C., Formation of deprotonated 2-imidazoline-4(5)-one product ions in the collision-induced dissociation of some serine-containing dipeptides. International Journal of Mass Spectrometry 2015, 381, 25-32.
  • Wu, E. Y.; Walsh, A. R.; Materne, E. C.; Hiltner, E. P.; Zielinski, B.; Miller, B. R., III; Mawby, L.; Modeste, E.; Parish, C. A.; Barnes, W. M.; Kermekchiev, M. B., A Conservative lsoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase. Biochemistry 2015, 54 (3), 881-889.
  • Temelso, B.; Renner, C. R.; Shields, G. C., Importance and Reliability of Small Basis Set CCSD(T) Corrections to MP2 Binding and Relative Energies of Water Clusters. J. Chem. Theory Comput. 2015, 11 (4), 1439-1448.
  • Seybold, P. G.; Shields, G. C., Computational estimation of pK(a) values. Wiley Interdisciplinary Reviews-Computational Molecular Science 2015, 5 (3), 290-297.
  • Bigler, D. J.; Peterson, L. W.; Cafiero, M., DFT and MP2 study of the effects of mutations on the binding of ligands within the SULT1A3 active site. Comput. Theor. Chem. 2015, 1068, 63-71.
  • Bigler, D. J.; Peterson, L. W.; Cafiero, M., Effects of implicit solvent and relaxed amino acid side chains on the MP2 and DFT calculations of ligand-protein structure and electronic interaction energies of dopaminergic ligands in the SULT1A3 enzyme active site. Comput. Theor. Chem. 2015, 1051, 79-92.
  • Krueger, R. A.*; Haibach, F. G.; Fry, D. L.*; Gomez, M. A., Centrality measures highlight proton traps and access points to proton highways in kinetic Monte Carlo trajectories. J. Chem. Phys. 2015, 142 (15).
  • Donald, K. J.; Tawfik, M.; Buncher, B., Weak Interactions as Diagnostic Tools for Inductive Effects. J. Phys. Chem. A 2015, 119 (16), 3780-3788.
  • Donald, K. J.; Kretz, W. J.; Omorodion, O., The HgF2 Ionic Switch: A Triumph of Electrostatics against Relativistic Odds. Chem.-Eur. J. 2015, 21 (47), 16848-16858. 230.
  • Donald, K. J.; Stewart, J.; Guarino, M., Structure, bonding, relativistic effects, and dispersion in the group 12 dihalide (MX2)(3) clusters, with lessons from the extended solids. Structural Chemistry 2015, 26 (5-6), 1179-1195.
  • Nguyen, A. H.; Koc, M. A.; Shepherd, T. D.; Molinero, V., Structure of the Ice- Clathrate Interface. Journal of Physical Chemistry C 2015, 119 (8), 4104-4117.

2014

  • Bartholow, T. G., Sanford, B. L., Cao, B., Schmit, H. L., Johnson, J. M., Meitzner, J., et al. (2014). Strictly Conserved Lysine of Prolyl-tRNA Synthetase Editing Domain Facilitates Binding and Positioning of Misacylated tRNA(Pro). Biochemistry, 53(6), 1059–1068.
  • Temelso, B.; Alser, K. A.; Gauthier, A.; Palmer, A. K.; Shields, G. C., Structural Analysis of alpha-Fetoprotein (AFP)-like Peptides with Anti-Breast-Cancer Properties. J. Phys. Chem. B 2014, 118 (17), 4514-4526.
  • Bustos, D. J.; Temelso, B.; Shields, G. C., Hydration of the Sulfuric Acid- Methylamine Complex and Implications for Aerosol Formation. J. Phys. Chem. A 2014, 118 (35), 7430-7441.
  • Wenzel, S.; Nemec, H.; Anderson, K. E.; Siepmann, J. I., Monte Carlo Simulations of Thin Hydrocarbon Films: Composition Heterogeneity and Structure at the Solid-Liquid and Liquid-Vapor Interfaces. Langmuir 2014, 30 (11), 3086-3094.
  • Pérez, C.; Zaleski, D. P.; Seifert, N. A.; Temelso, B.; Shields, G. C.; Kisiel, Z.; Pate, B. H., Hydrogen Bond Cooperativity and the Three-Dimensional Structures of Water Nonamers and Decamers. Angew Chem Int Ed Engl 2014, 53 (52), 14368-14372. 198.
  • Nguyen, P. H.; West, H.; Feske, B. D.; Padgett, C. W., Enantioselectivity and Enzyme-Substrate Docking Studies of a Ketoreductase from Sporobolomyces salmonicolor (SSCR) and Saccharomyces cerevisiae (YOL151w). International Scholarly Research Notices 2014, 12428.
  • Whiteside, T. S.; Priest, M. A.; Padgett, C. W., Modeling the interfacial thermal resistance of diamond nanorod composites and related materials. International Journal of Computational Materials Science and Engineering 2014, 3 (3), 1450014-1.
  • Strom, A. M.; Fehling, S. C.; Bhattacharyya, S.; Hati, S., Probing the global and local dynamics of aminoacyl-tRNA synthetases using all-atom and coarse-grained simulations. Journal of Molecular Modeling 2014, 20 (5).
  • Gao, D.; Lang, D.; Robinson, T., Computational study of the thermodynamic stabilities of hydrogen-bonded complexes in solution. Theoretical Chemistry Accounts 2014, 133 (11).
  • Tlach, B. C.; Tomlinson, A. L.; Morgan, K. D.; Collins, C. R.; Zenner, M. D.; Jeffries-El, M., Effect of Extended Conjugation on the Optoelectronic Properties of Benzo 1,2-d:4,5-d’ bisoxazole Polymers. Australian Journal of Chemistry 2014, 67 (5), 711-721.
  • Cervantes-Navarro, F.; Martinez-Guajardo, G.; Osorio, E.; Moreno, D.; Tiznado, W.; Islas, R.; Donald, K. J.; Merino, G., Stop rotating! One substitution halts the B-19(-) motor. Chemical Communications 2014, 50 (73), 10680-10682.
  • Kanters, R. P. F.; Donald, K. J., CLUSTER: Searching for Unique Low Energy Minima of Structures Using a Novel Implementation of a Genetic Algorithm. J. Chem. Theory Comput. 2014, 10 (12), 5729-5737.
  • Tawfik, M.; Donald, K. J., Halogen Bonding: Unifying Perspectives on Organic and Inorganic Cases. J. Phys. Chem. A 2014, 118 (43), 10090-10100.
  • Helminiak, H. M.; Knauf, R. R.; Danforth, S. J.; Phillips, J. A., Structural and Energetic Properties of Acetonitrile-Group IV (A & B) Halide Complexes. J. Phys. Chem. A 2014, 118 (24), 4266-4277.
  • Murdachaew, G.; Varner, M. E.; van der Veer, W. E.; Gerber, R. B.; Phillips, L. F., Raman spectroscopy of solutions and interfaces containing nitrogen dioxide, water, and 1,4 dioxane: Evidence for repulsion of surface water by NO2 gas. J. Chem. Phys. 2014, 140 (18).
  • Wrass, J. P.; Sadowsky, D.; Bloomgren, K. M.; Cramer, C. J.; Phillips, J. A., Quantum chemical and matrix-IR characterization of CH3CN-BCl3: a complex with two distinct minima along the B-N bond potential. Phys. Chem. Chem. Phys. 2014, 16 (31), 16480-16491.
  • Zimmer, M. H.; Li, B.; Shahid, R.; Peshkepija, P.; Zimmer, M., Structural consequences of chromophore formation and exploration of conserved lid residues amongst naturally occurring fluorescent proteins. Chemical Physics 2014, 429, 5-11. 214.
  • Kohrt, D.; Crary, J.; Zimmer, M.; Patrick, A. N.; Ford, H. L.; Hinds, P. W.; Grossel, M. J., CDK6 binds and promotes the degradation of the EYA2 protein. Cell Cycle 2014, 13 (1), 62-71.
  • Eggimann, B. L.; Sunnarborg, A. J.; Stern, H. D.; Bliss, A. P.; Siepmann, J. I., An online parameter and property database for the TraPPE force field. Molecular Simulation 2014, 40 (1-3), 101-105.
  • O’Grady, C.E.*, P. Talpey*, T. E. Elgren, and A. W. Van Wynsberghe, 2014. The development and implementation of a bio-molecular docking exercise for the general chemistry laboratory. In Annual Reports in Computational Chemistry, Vol. 10. Ralph Wheeler, editor. Elsevier, United Kingdom, pp. 167-187.
  • Miller, B. R., III; Parish, C. A.; Wu, E. Y., Molecular Dynamics Study of the Opening Mechanism for DNA Polymerase I. Plos Computational Biology 2014, 10 (12). 216. Miller, B. R., III; Beese, L. S.; Parish, C. A.; Wu, E. Y., The Closing Mechanism of DNA Polymerase I at Atomic Resolution. Structure 2015, 23 (9), 1609-1620.
  • Wu, E. Y.; Walsh, A. R.; Materne, E. C.; Hiltner, E. P.; Zielinski, B.; Miller, B. R., III; Mawby, L.; Modeste, E.; Parish, C. A.; Barnes, W. M.; Kermekchiev, M. B., A Conservative lsoleucine to Leucine Mutation Causes Major Rearrangements and Cold Sensitivity in KlenTaq1 DNA Polymerase. Biochemistry 2015, 54 (3), 881-889.
  • Muya, J. T.; Ceulemans, A.; Gopakumar, G.; Parish, C. A., Jahn-Teller Distortion in Polyoligomeric Silsesquioxane (POSS) Cations. J. Phys. Chem. A 2015, 119 (18), 4237-4243.

2013

  • Baltrusaitis, J., de Graaf, C., Broer, R., & Patterson, E. V. (2013). H2S-Mediated Thermal and Photochemical Methane Activation. Chemphyschem, 14(17), 3960–3970.
  • Buchberger, A. R., Danforth, S. J., Bloomgren, K. M., Rohde, J. A., Smith, E. L., Gardener, C. C. A., et al. (2013). Condensed-Phase Effects on the Structural Properties of FCH2CN-BF3 and ClCH2CN-BF3: A Matrix-Isolation and Computational Study. Journal Of Physical Chemistry B, 117(39), 11687–11696.
  • Copeland, K. L., Pellock, S. J., Cox, J. R., Cafiero, M. L., & Tschumper, G. S. (2013). Examination of Tyrosine/Adenine Stacking Interactions in Protein Complexes. Journal Of Physical Chemistry B, 117(45), 14001–14008.
  • DiGiovanni, K. M., Hatstat, A. K., Rote, J., & Cafiero, M. (2013). MP2//DFT calculations of interaction energies between acetaminophen and acetaminophen analogues and the aryl sulfotransferase active site. Computational And Theoretical Chemistry, 1007, 41–47.
  • Donald, K. J., & Kovac, J. (2013). The Scientist’s Education and a Civic Conscience. Science And Engineering Ethics, 19(3), 1229–1240.
  • Donald, K. J., & Tawfik, M. (2013). The Weak Helps the Strong: Sigma-Holes and the Stability of MF4 center dot Base Complexes. Journal Of Physical Chemistry A, 117(51), 14176–14183.
  • Eggimann, B. L., Vostrikov, V. V., Veglia, G., & Siepmann, J. I. (2013). Modeling helical proteins using residual dipolar couplings, sparse long-range distance constraints and a simple residue-based force field. Theoretical Chemistry Accounts, 132(10).
  • Gomez, M. A., & Liu, F. – J. (2013). Protons in Al doped BaZrO3 escape dopant traps to access long range proton conduction highways. Solid State Ionics, 252, 40–47.
  • Johnson, J. M., Sanford, B. L., Strom, A. M., Tadayon, S. N., Lehman, B. P., Zirbes, A. M., et al. (2013). Multiple Pathways Promote Dynamical Coupling between Catalytic Domains in Escherichia coli Prolyl-tRNA Synthetase. Biochemistry, 52(25), 4399–4412.
  • Lindsey, R. K., Rafferty, J. L., Eggimann, B. L., Siepmann, J. I., & Schure, M. R. (2013). Molecular simulation studies of reversed-phase liquid chromatography. Journal Of Chromatography A, 1287, 60–82.
  • Perez, C., Lobsiger, S., Seifert, N. A., Zaleski, D. P., Temelso, B., Shields, G. C., et al. (2013). Broadband Fourier transform rotational spectroscopy for structure determination: The water heptamer. Chemical Physics Letters, 571, 1–15.
  • Qu, S., Kolodziej, E. P., Long, S. A., Gloer, J. B., Patterson, E. V., Baltrusaitis, J., et al. (2013). Product-to-Parent Reversion of Trenbolone: Unrecognized Risks for Endocrine Disruption. Science, 342(6156), 347–351.
  • Temelso, B., Koeddermann, T., Kirschner, K. N., Klein, K., & Shields, G. C. (2013). Structure and thermodynamics of H3O+(H2O)(8) clusters: A combined molecular dynamics and quantum mechanics approach. Computational And Theoretical Chemistry, 1021, 240–248.
  • Witts, R. N., Hopson, E. C., Koballa, D. E., Van Boening, T. A., Hopkins, N. H., Patterson, E. V., et al. (2013). Backbone-Base Interactions Critical to Quantum Stabilization of Transfer RNA Anticodon Structure. Journal Of Physical Chemistry B, 117(25), 7489–7497.

2012

    • Baltrusaitis, J., Patterson, E. V., & Hatch, C. (2012). Computational Studies of CO2 Activation via Photochemical Reactions with Reduced Sulfur Compounds. Journal Of Physical Chemistry A, 116(37), 9331–9339.
    • Crigger, C., Wittmaack, B. K., Tawfik, M., Merino, G., & Donald, K. J. (2012). Plane and simple: planar tetracoordinate carbon centers in small molecules. Physical Chemistry Chemical Physics, 14(43), 14775–14783.
    • Fisher, S. Q., Weck, M., Landers, J. E., Emrich, J., Middleton, S. A., Cox, J., et al. (2012). Evidence that the kinesin light chain domain contains tetratricopeptide repeat units. Journal Of Structural Biology, 177(3), 602–612.
    • Gomez, M. A., Shepardson, D., Nguyen, L. T., & Kehinde, T. (2012). Periodic long range proton conduction pathways in pseudo-cubic and orthorhombic perovskites. Solid State Ionics, 213, 8–13.
    • Husar, D. E., Temelso, B., Ashworth, A. L., & Shields, G. C. (2012). Hydration of the Bisulfate Ion: Atmospheric Implications. Journal Of Physical Chemistry A, 116(21), 5151–5163.
    • Klimavicz, J. S., Mike, J. F., Bhuwalka, A., Tomlinson, A. L., & Jeffries-EL, M. (2012). Synthesis of benzobisoxazole-based D-pi-A-pi-D organic chromophores with variable optical and electronic properties. Pure And Applied Chemistry, 84(4), 991–1004.
    • Knauf, R. R., Helminiak, H. M., Wrass, J. P., Gallert, T. M., & Phillips, J. A. (2012). Structural and energetic properties of alkylfluoride-BF3 complexes in the gas phase and condensed-phase media: computations and matrix infrared spectroscopy. Journal Of Physical Organic Chemistry, 25(6), 493–501.
    • Kobilka, B. M., Dubrovskiy, A. V., Ewan, M. D., Tomlinson, A. L., Larock, R. C., Chaudhary, S., et al. (2012). Synthesis of 3,7-diiodo-2,6-di(thiophen-2-yl)benzo[1,2-b:4,5-b ‘]difurans: functional building blocks for the design of new conjugated polymers. Chemical Communications, 48(71), 8919–8921.
    • Li, B., Shahid, R., Peshkepija, P., & Zimmer, M. (2012). Water diffusion in and out of the beta-barrel of GFP and the fast maturing fluorescent protein, TurboGFP. Chemical Physics, 392(1), 143–148.
    • Parker, A. J., Stewart, J., Donald, K. J., & Parish, C. A. (2012). Halogen Bonding in DNA Base Pairs. Journal Of The American Chemical Society, 134(11), 5165–5172.
    • Perez, C., Muckle, M. T., Zaleski, D. P., Seifert, N. A., Temelso, B., Shields, G. C., et al. (2012). Structures of Cage, Prism, and Book Isomers of Water Hexamer from Broadband Rotational Spectroscopy. Science, 336(6083), 897–901.
    • Sanford, B., Cao, B., Johnson, J. M., Zimmerman, K., Strom, A. M., Mueller, R. M., et al. (2012). Role of Coupled Dynamics in the Catalytic Activity of Prokaryotic-like Prolyl-tRNA Synthetases. Biochemistry, 51(10), 2146–2156.
    • Shepherd, T. D., Koc, M. A., & Molinero, V. (2012). The Quasi-Liquid Layer of Ice under Conditions of Methane Clathrate Formation. Journal Of Physical Chemistry C, 116(22), 12172–12180.
    • Song, X., Fanelli, M. G., Cook, J. M., Bai, F., & Parish, C. A. (2012). Mechanisms for the Reaction of Thiophene and Methylthiophene with Singlet and Triplet Molecular Oxygen. Journal Of Physical Chemistry A, 116(20), 4934–4946.
    • Temelso, B., Morrell, T. E., Shields, R. M., Allodi, M. A., Wood, E. K., Kirschner, K. N., et al. (2012). Quantum Mechanical Study of Sulfuric Acid Hydration: Atmospheric Implications. Journal Of Physical Chemistry A, 116(9), 2209–2224.
    • Temelso, B., Thuong Ngoc Phan, & Shields, G. C. (2012). Computational Study of the Hydration of Sulfuric Acid Dimers: Implications for Acid Dissociation and Aerosol Formation. Journal Of Physical Chemistry A, 116(39), 9745–9758.
    • Zimmer, M. (2012). What does it take to improve existing fluorescent proteins for in vivo imaging applications? Methods in molecular biology (Clifton, 872, 235–41.

2011

  • Perez-Peralta, N; Contreras, M; Tiznado, W; Stewart, J; Donald, KJ; Merino, G, “Stabilizing carbon-lithium stars”, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, p. 12975, vol. 13, (2011). Published, 10.1039/c1cp21061
  • Wittmaack, BK; Crigger, C; Guarino, M; Donald, KJ, “Charge Saturation and Neutral Substitutions in Halomethanes and Their Group 14 Analogues”, JOURNAL OF PHYSICAL CHEMISTRY A, p. 8743, vol. 115, (2011). Published, 10.1021/jp204316
  • Martinez-Guajardo, G; Donald, KJ; Wittmaack, BK; Vazquez, MA; Merino, G, “Shorter Still: Compressing C-C Single Bonds. (vol 12, pg 4058, 2010)”, ORGANIC LETTERS, p. 172, vol. 13, (2011). Published, 10.1021/ol102654
  • Donald, KJ; Bober, M, “Predicting the Relative Stability of Simple versus ansa-Sandwich Systems Across Groups: Structure, Bonding, and (In)Stability in Tris(sandwich)benzene Complexes”, CHEMISTRY-A EUROPEAN JOURNAL, p. 1936, vol. 17, (2011). Published, 10.1002/chem.20100138
  • Ghosh, K; Sen, T; Patra, A; Mancini, JS; Cook, JM; Parish, CA, “(rac)-1,1 ‘-Binaphthyl-Based Simple Receptors Designed for Fluorometric Discrimination of Maleic and Fumaric Acids”, JOURNAL OF PHYSICAL CHEMISTRY B, p. 8597, vol. 115, (2011). Published, 10.1021/jp202304
  • Song, XL; Parish, CA, “Pyrolysis Mechanisms of Thiophene and Methylthiophene in Asphaltenes”, JOURNAL OF PHYSICAL CHEMISTRY A, p. 2882, vol. 115, (2011). Published, 10.1021/jp111845
  • Gentile, L.*; Caudhill, L.; Fetea, M.; Hill, A.; Hoke, K.; Lawson, B.; Lipan, O.; Kerckhove, M.; Parish, C.; Stenger, K.; Szajda, D., “Challenging Disciplinary Boundaries in the First-Year: A New Introductory Integrated Science Course for STEM Majors”, Journal of College Science Teaching, p. in press, vol. 41, (2011). Accepted,
  • Maria A. Gomez, Dylan Shepardson, Luong T. Nguyena, Tolu Kehinde, “Periodic long range proton conduction pathways in pseudo-cubic and orthorhombic perovskites”, Solid State Ionics, p. , vol. in pres, (2011). Published, doi:10.1016/j.ssi.2011.08.001
  • Temelso, B; Archer, KA; Shields, GC, “Benchmark Structures and Binding Energies of Small Water Clusters with Anharmonicity Corrections”, JOURNAL OF PHYSICAL CHEMISTRY A, p. 12034, vol. 115, (2011). Published, 10.1021/jp206948
  • Temelso, B; Shields, GC, “The Role of Anharmonicity in Hydrogen-Bonded Systems: The Case of Water Clusters”, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, p. 2804, vol. 7, (2011). Published, 10.1021/ct200330
  • Tsutakawa, SE; Van Wynsberghe, AW; Freudenthal, BD; Weinacht, CP; Gakhar, L; Washington, MT; Zhuang, ZH; Tainer, JA; Ivanov, I, “Solution X-ray scattering combined with computational modeling reveals multiple conformations of covalently bound ubiquitin on PCNA”, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, p. 17672, vol. 108, (2011). Published, 10.1073/pnas.111048010
  • Sinko, W; de Oliveira, C; Williams, S; Van Wynsberghe, A; Durrant, JD; Cao, R; Oldfield, E; McCammon, JA, “Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand-bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target”, CHEMICAL BIOLOGY & DRUG DESIGN, p. 412, vol. 77, (2011). Published, 10.1111/j.1747-0285.2011.01101.
  • Utkov, HE; Price, AM; Cafiero, M, “MP2, density functional theory, and semi-empirical calculations of the interaction energies between a series of statin-drug-like molecules and the HMG-CoA reductase active site”, COMPUTATIONAL AND THEORETICAL CHEMISTRY, p. 171, vol. 967, (2011). Published, 10.1016/j.comptc.2011.04.01
  • Durham, CR; Chase, JM; Nivens, DA; Baird, WH; Padgett, CW, “Chemical Environment Effects on K beta/K alpha Intensity Ratio: An X-ray Fluorescence Experiment on Periodic Trends”, JOURNAL OF CHEMICAL EDUCATION, p. 819, vol. 88, (2011). Published, 10.1021/ed100695
  • Priest, MA; Padgett, LW; Padgett, CW, “Demonstrating the Temperature Dependence of Density via Construction of a Galilean Thermometer”, JOURNAL OF CHEMICAL EDUCATION, p. 983, vol. 88, (2011). Published, 10.1021/ed100854

2010

  • Morrell, TE; Shields, GC, “Atmospheric Implications for Formation of Clusters of Ammonium and 1-10 Water Molecules”, JOURNAL OF PHYSICAL CHEMISTRY A, p. 4266, vol. 114, (2010). Published, 10.1021/jp911493
  • Crill, JW; Ji, X; Irving, DL; Brenner, DW; Padgett, CW, “Atomic and multi-scale modeling of non-equilibrium dynamics at metal-metal contacts”, MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING, p. , vol. 18, (2010). Published, 10.1088/0965-0393/18/3/03400
  •  Hunter Utkov, Maura Livengood, Mauricio Cafiero, “Using Density Functional Theory methods for modeling induction and dispersion interactions in ligand-protein complexes”, Annual Reports in Computational Chemistry, p. 97, vol. 6, (2010). Published,
  •  Van Sickle, K; Shroyer, MC; Cafiero, M, “Relative stability of complexes of six-carbon-rings with variable numbers of double bonds: DFT and ab initio results”, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, p. 78, vol. 941, (2010). Published, 10.1016/j.theochem.2009.11.00
  •  Kristin S. Alongi and George C. Shields, “Theoretical Calculations of Acid Dissociation Constants: A Review Article”, Annual Reports in Computational Chemistry, p. 113, vol. 6, (2010). Published,
  • Gomez, MA; Chunduru, M; Chigweshe, L; Fletcher, KM, “The effect of dopant at the Zr site on the proton conduction pathways of SrZrO3: An orthorhombic perovskite”, JOURNAL OF CHEMICAL PHYSICS, p. , vol. 133, (2010). Published, 10.1063/1.347179
  • Gomez, MA; Chunduru, M; Chigweshe, L; Foster, L; Fensin, SJ; Fletcher, KM; Fernandez, LE, “The effect of yttrium dopant on the proton conduction pathways of BaZrO3, a cubic perovskite”, JOURNAL OF CHEMICAL PHYSICS, p. , vol. 132, (2010). Published, 10.1063/1.344737
  • Sung, JC; Van Wynsberghe, AW; Amaro, RE; Li, WW; McCammon, JA, “Role of Secondary Sialic Acid Binding Sites in Influenza N1 Neuraminidase”, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, p. 2883, vol. 132, (2010). Published, 10.1021/ja907367
  • Van Wynsberghe, AW; Cui, Q, “Conservation and Variation of Structural Flexibility in Protein Families”, STRUCTURE, p. 281, vol. 18, (2010). Published, 10.1016/j.str.2010.02.00
  • Hamm, ML; Parker, AJ; Steele, TWE; Carman, JL; Parish, CA, “Oligonucleotide Incorporation and Base Pair Stability of 9-Deaza-2 ‘-deoxyguanosine, an Analogue of 8-Oxo-2 ‘-deoxyguanosine”, JOURNAL OF ORGANIC CHEMISTRY, p. 5661, vol. 75, (2010). Published, 10.1021/jo101076
  • Wang, EB; Parish, CA, “Conformational Analysis of a Model for the trans-Fused FGH Ether Rings in Brevetoxin A”, JOURNAL OF ORGANIC CHEMISTRY, p. 1582, vol. 75, (2010). Published, 10.1021/jo902558
  • Ghosh, K; Saha, I; Masanta, G; Wang, EB; Parish, CA, “Triphenylamine-based receptor for selective recognition of dicarboxylates”, TETRAHEDRON LETTERS, p. 343, vol. 51, (2010). Published, 10.1016/j.tetlet.2009.11.02
  • Nivens, DA; Padgett, CW; Chase, JM; Verges, KJ; Jamieson, DS, “Art, Meet Chemistry; Chemistry, Meet Art: Case Studies, Current Literature, and Instrumental Methods Combined To Create a Hands-On Experience for Nonmajors and Instrumental Analysis Students”, JOURNAL OF CHEMICAL EDUCATION, p. 1089, vol. 87, (2010). Published, 10.1021/ed100352
  • Donald, KJ; Wittmaack, BK; Crigger, C, “Tuning sigma-Holes: Charge Redistribution in the Heavy (Group 14) Analogues of Simple and Mixed Halomethanes Can Impose Strong Propensities for Halogen Bonding”, JOURNAL OF PHYSICAL CHEMISTRY A, p. 7213, vol. 114, (2010). Published, 10.1021/jp102856
  • Martinez-Guajardo, G; Donald, KJ; Wittmaack, BK; Vazquez, MA; Merino, G, “Shorter Still: Compressing C-C Single Bonds”, ORGANIC LETTERS, p. 4058, vol. 12, (2010). Published, 10.1021/ol101671
  • Tvedte, LM; Smith, KL; Patterson, EV; Baughman, RG, “2-Amino-5-(3,4-dimethoxybenzylidene)-1-methylimidazol-4(5H)-one N,N-dimethylformamide monosolvate”, ACTA CRYSTALLOGRAPHICA SECTION C-CRYSTAL STRUCTURE COMMUNICATIONS, p. O101, vol. 66, (2010). Published, 10.1107/S01082701100001
  •  Menke, JL; Patterson, EV; McMahon, RJ, “Effects of Cyano Substituents on Cyclobutadiene and Its Isomers”, JOURNAL OF PHYSICAL CHEMISTRY A, p. 6431, vol. 114, (2010). Published, 10.1021/jp101063
  • Shields, RM; Temelso, B; Archer, KA; Morrell, TE; Shields, GC, “Accurate Predictions of Water Cluster Formation, (H2O)(n=2-10)”, JOURNAL OF PHYSICAL CHEMISTRY A, p. 11725, vol. 114, (2010). Published, 10.1021/jp104865
  • Whiteside, TS; Priest, MA; Padgett, CW, “Enthalpies of formation of methyl substituted naphthalenes”, THERMOCHIMICA ACTA, p. 17, vol. 510, (2010). Published, 10.1016/j.tca.2010.06.01

2009

  • Joseph, LC; Bennett, JA; Kirschner, KN; Shields, GC; Hughes, J; Lostritto, N; Jacobson, HI; Andersen, TT, “Antiestrogenic and anticancer activities of peptides derived from the active site of alpha-fetoprotein”, JOURNAL OF PEPTIDE SCIENCE, p. 319, vol. 15, (2009). Published, 10.1002/psc.111
  • Salisburg, AM; Deline, AL; Lexa, KW; Shields, GC; Kirschner, KN, “Ramachandran-Type Plots for Glycosidic Linkages: Examples from Molecular Dynamic Simulations Using the Glycam06 Force Field”, JOURNAL OF COMPUTATIONAL CHEMISTRY, p. 910, vol. 30, (2009). Published, 10.1002/jcc.2109
  • Megley, CM; Dickson, LA; Maddalo, SL; Chandler, GJ; Zimmer, M, “Photophysics and Dihedral Freedom of the Chromophore in Yellow, Blue, and Green Fluorescent Protein”, JOURNAL OF PHYSICAL CHEMISTRY B, p. 302, vol. 113, (2009). Published, 10.1021/jp806285
  • Zimmer, M, “Are classical molecular mechanics calculations still useful in bioinorganic simulations?”, COORDINATION CHEMISTRY REVIEWS, p. 817, vol. 253, (2009). Published, 10.1016/j.ccr.2008.04.00
  • Remmert, S; Hollis, H; Parish, CA, “Conformational analysis of trimeric maleimide substituted 1,5,9-triazacyclododecane HIV fusion scaffolds”, BIOORGANIC & MEDICINAL CHEMISTRY, p. 1251, vol. 17, (2009). Published, 10.1016/j.bmc.2008.12.02
  • Remmert, S; Parish, C, “Energetic Analyses of Chair and Boat Conformations of Maleimide Substituted Cyclohexane Derivatives”, JOURNAL OF COMPUTATIONAL CHEMISTRY, p. 992, vol. 30, (2009). Published, 10.1002/jcc.2112
  • Seburg, RA; Patterson, EV; McMahon, RJ, “Structure of Triplet Propynylidene (HCCCH) as Probed by IR, UV/vis, and EPR Spectroscopy of Isotopomers”, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, p. 9442, vol. 131, (2009). Published, 10.1021/ja901606
  • Irving, DL; Padgett, CW; Brenner, DW, “Coupled molecular dynamics/continuum simulations of Joule heating and melting of isolated copper-aluminum asperity contacts”, MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING, p. , vol. 17, (2009). Published, 10.1088/0965-0393/17/1/01500
  • Doug L. Irving, Clifford W. Padgett, Y. Gou, John W. Mintmire, Donald W. Brenner, “Multi-Scale Modeling of Metal-Metal Contact Dynamics under High Electromagnetic Stress: Timescales and Mechanisms for Joule Melting Of Al-Cu Asperitites”, IEEE Transactions on Magnetics, p. 331, vol. 45, (2009). Published,
  • Craciun, S; Donald, KJ, “Radical Bonding: Structure and Stability of Bis(Phenalenyl) Complexes of Divalent Metals from across the Periodic Table”, INORGANIC CHEMISTRY, p. 5810, vol. 48, (2009). Published, 10.1021/ic900058
  • Cerpa, E; Krapp, A; Flores-Moreno, R; Donald, KJ; Merino, G, “Influence of Endohedral Confinement on the Electronic Interaction between He atoms: A He-2@C20H20 Case Study”, CHEMISTRY-A EUROPEAN JOURNAL, p. 1985, vol. 15, (2009). Published, 10.1002/chem.20080139
  • Donald, KJ; Hargittai, M; Hoffmann, R, “Group 12 Dihalides: Structural Predilections from Gases to Solids”, CHEMISTRY-A EUROPEAN JOURNAL, p. 158, vol. 15, (2009). Published, 10.1002/chem.20080103
  • Shields, GC, “Computational approaches for the design of peptides with anti-breast cancer properties”, FUTURE MEDICINAL CHEMISTRY, p. 201, vol. 1, (2009). Published, 10.4155/FMC.09.1
  • Padgett, CW; Gutt, KJ; Whiteside, TS, “Computational studies on the mechanical properties of diamond nanotoroids”, COMPUTATIONAL MATERIALS SCIENCE, p. 491, vol. 46, (2009). Published, 10.1016/j.commatsci.2009.03.03
  • Crill, JW; Ji, X; Irving, DL; Brenner, DW; Padgett, CW, “Atomic and multi-scale modeling of non-equilibrium dynamics at metal-metal contacts”, MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING, p. , vol. 18, (2010). Published, 10.1088/0965-0393/18/3/0340
  • C.W. Padgett, A. Saad, “Genetic Algorithms in Chemistry: Success or Failure is in the Genes”, Applications of Soft Computing: From Theory to Praxis, p. 181, vol. AISC 58, (2009). Published,
  • Kee, EA; Livengood, MC; Carter, EE; McKenna, M; Cafiero, M, “Aromatic Interactions in the Binding of Ligands to HMGCoA Reductase”, JOURNAL OF PHYSICAL CHEMISTRY B, p. 14810, vol. 113, (2009). Published, 10.1021/jp904508
  • Hofto, LR; Lee, CE; Cafiero, M, “The Importance of Aromatic-Type Interactions in Serotonin Synthesis: Protein-Ligand Interactions in Tryptophan Hydroxylase and Aromatic Amino Acid Decarboxylase”, JOURNAL OF COMPUTATIONAL CHEMISTRY, p. 1111, vol. 30, (2009). Published, 10.1002/jcc.2113
  • Zimmer, M, “GFP: from jellyfish to the Nobel prize and beyond”, CHEMICAL SOCIETY REVIEWS, p. 2823, vol. 38, (2009). Published, 10.1039/b904023 Michael, LA; Chenault, JA; Miller, BR; Knolhoff, AM; Nagan, MC, “Water, Shape Recognition, Salt Bridges, and Cation-Pi Interactions Differentiate Peptide Recognition of the HIV Rev-Responsive Element”, JOURNAL OF MOLECULAR BIOLOGY, p. 774, vol. 392, (2009). Published, 10.1016/j.jmb.2009.07.04
  • Maki, BE; Patterson, EV; Cramer, CJ; Scheidt, KA, “Impact of Solvent Polarity on N-Heterocyclic Carbene-Catalyzed beta-Protonations of Homoenolate Equivalents”, ORGANIC LETTERS, p. 3942, vol. 11, (2009). Published, 10.1021/ol901545

    2008:

  • Carol Parish, Matthew M. Lauer, James W. Leslie, Ashley Mynar, Shelly A. Stamper, Anthony D. Martinez, Adrian J. Bray, Senai Negassi, Kevin McDonald, Eric Ferraris, Aaron Muzny, Shawn McAvoy, Keith Walters, Keith C. Russell, Evan Wang and Betsy Nuez, “Synthesis, Spectroscopy and Theoretical Calculations for a Series of Push-Pull [14]-pyridoannulenes”, Journal of Organic Chemistry, 2008, 73, 474-484.
    Shields, G.C. and Kirschner, K.N., “The Limitations of Certain Density Functional Theory in Modeling Neutral Water Clusters.” Journal, Synthesis and Reactivity in Inorganic, Metal-Organic and Nano-Metal Chemistry special edition on water clusters, 38, 1-8 (2008).
  • Sherer, EC; Kirschner, KN; Pickard, FC; Rein, C; Feldgus, S; Shields, GC, “Efficient and Accurate Characterization of the Bergman Cyclization for Several Enediynes Including an Expanded Substructure of Esperamicin A(1)”, JOURNAL OF PHYSICAL CHEMISTRY B, p. 16917, vol. 112, (2008). Published, 10.1021/jp807341
  • Hartt, GM; Shields, GC; Kirschner, KN, “Hydration of OCS with one to four water molecules in atmospheric and laboratory conditions”, JOURNAL OF PHYSICAL CHEMISTRY A, p. 4490, vol. 112, (2008). Published, 10.1021/jp800229
  • Allodi, M.A. Kirschner, K.N. and Shields, G.C., “The Thermodynamics of the Hydroxyl Radical with Isoprene.” Submitted to the Journal of Physical Chemistry A accepted 04/24/08
  • Salisburg, A.M.; Deline, A.L.; Lexa, K.W.; Shields, G.C.; Kirschner, K.N., “Ramachandran-type Plots for Glycosidic Linkages: Examples from Molecular Dynamics Simulations using the Glycam06 Force Field”, Journal of Computational Chemistry, p. , vol. , (2008). Published, 10.1002/jcc.21099
  • Dunn, M. E.; Shields, G. C.; Takahashi, K.; Skodje, R. T.; Vaida, V., “Experimental and theoretical study of the OH vibrational spectra and overtone chemistry of gas-phase vinylacetic acid”, Journal of Physical Chemistry A, p. 10226, vol. 112, (2008). Published, 10.1021/jp805746t
  • Remmert, S.; Parish, C., “Energetic Analysis of Chair and Boat Conformations of Maleimide Substituted Cyclohexane Derivatives”, Journal of Computational Chemistry, p. , vol. , (2008). Accepted
  • Wang, EB; Parish, CA; Lischka, H, “An extended multireference study of the electronic states of para-benzyne”, JOURNAL OF CHEMICAL PHYSICS, p. , vol. 129, (2008). Published, 10.1063/1.295574
  • Lemay, NP; Morgan, AL; Archer, EJ; Dickson, LA; Megley, CM; Zimmer, M, “The role of the tight-turn, broken hydrogen bonding, Glu222 and Arg96 in the post-translational green fluorescent protein chromophore formation”, CHEMICAL PHYSICS, p. 152, vol. 348, (2008). Published, 10.1016/j.chemphys.2008.02.05
  • Lauer, MG; Leslie, JW; Mynar, A; Stamper, SA; Martinez, AD; Bray, AJ; Negassi, S; McDonald, K; Ferraris, E; Muzny, A; McAvoy, S; Miller, CP; Walters, KA; Russell, KC; Wang, E; Nuez, B; Parish, C, “Synthesis, spectroscopy, and theoretical calculations for a series of push-pull [14]-pyridoannulenes”, JOURNAL OF ORGANIC CHEMISTRY, p. 474, vol. 73, (2008). Published, 10.1021/jo701972
  • Daniel, KA; Kopff, LA; Patterson, EV, “Computational studies on the solvolysis of the chemical warfare agent VX”, JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, p. 321, vol. 21, (2008). Published, 10.1002/poc.133
  • Cerpa, E; Tenorio, FJ; Contreras, M; Villanueva, M; Beltran, HI; Heine, T; Donald, KJ; Merino, G, “Pentadienyl complexes of alkali metals: Structure and bonding”, ORGANOMETALLICS, p. 827, vol. 27, (2008). Published, 10.1021/om070244
  • Donald, K.J.; Hargittai, M.; Hoffmann, R., “Group 12 Dihalides: Structural Predilections from Gases to Solids”, Chemistry – A European Journal, p. , vol. , (2008). Accepted
  • Jambor, R; Kasna, B; Kirschner, KN; Schuermann, M; Jurkschat, K, “[{2,6-(Me2NCH2)(2)C6H3}Sn](2): An intramolecularly coordinated diorganodistannyne”, ANGEWANDTE CHEMIE-INTERNATIONAL EDITION, p. 1650, vol. 47, (2008). Published, 10.1002/anie.20070463
  • Kirschner, KN; Yongye, AB; Tschampel, SM; Gonzalez-Outeirino, J; Daniels, CR; Foley, BL; Woods, RJ, “GLYCAM06: A generalizable Biomolecular force field. Carbohydrates”, JOURNAL OF COMPUTATIONAL CHEMISTRY, p. 622, vol. 29, (2008). Published, 10.1002/jcc.2082
  • Zhong, H; Kirschner, KN; Lee, M; Bowen, JP, “Binding free energy calculation for duocarmycin/DNA complex based on the QPLD-derived partial charge model”, BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, p. 542, vol. 18, (2008). Published, 10.1016/j.bmcl.2007.11.09

2007

  • Karl N. Kirschner, Katrina W. Lexa, Amanda M. Salisburg, Katherine A. Alser, Leroy Joseph, Thomas T. Andersen, James A. Bennett, Herbert I. Jacobsen, and George C. Shields,”Computational Design and Experimental Discovery of an Anti-estrogenic Peptide Derived from Alpha-Fetoprotein”  J. Am. Chem. Soc. 129 (2007) 6263-6258. Download from ACS
  • Karl N. Kirschner, Gregory M. Hartt, Timothy M. Evans and George C. Shields, “In Search of CS2(H2O)n=1-4 Clusters”  J. Chem. Phys. 126 (2007) 154320. Download from AIP
  • Kirschner, K.N. Sorensen, J.B. and Bowen, J.P., “Calculating Interaction Energies Using First Principle Theories – Consideration of Basis Set Superposition Error and Fragment Relaxation.” Journal of Chemical Education, 84 (7) 1225-1229 (2007).
  • Lexa, K.W., Alser, K.A.,Salisburg, A.M., Ellens, D., Hernandez, L., Bono, S.J., Derby, J., Skiba, J.G., Feldgus,S., Kirschner, K.N. and Shields, G.C., “The Search for Low Energy Conformational Families of Small Peptides.: Searching for Active Conformations of Small Peptides in the Absence of a Known Receptor.” International Journal of Quantum Chemistry, 107 (2007) 3001-3012.
  • Carol Parish, A. Szczepanska, J. L. Espartero, A. J. Moreno-Vargas, A. T. Carmona, I. Robina and Sarah Remmert and , “Synthesis and Conformational Analysis of Novel Trimeric Maleimide Cross-Linking Reagents”, Journal of Organic Chemistry, 2007 72, 6776-6785.
  • Carol Parish, Edyta M. Brzostowska and Roald Hoffmann, “Tuning the Bergman Cyclization by Introduction of Metal Fragments at Various Positions of the Enediyne.  MetallaBergman Cyclizations”, Journal of the American Chemical Society, 2007 129, 4401-4409.
  • M. A. Gomez, S. Jindal, K. M. Fletcher, L. S. Foster, N. D. A. Addo, D. Valentin, C. Ghenoiu, A. Hamilton, “A comparison of proton conduction in KTaO3 and SrZrO3”, Journal of Chemical Physics, p. 194701, vol. 126, (2007). Published
  • F. G. Haibach, M. A. Gomez, E Fitzgerald, K. E. Paczkowski, “NIR imaging of paintings: Looking for deeper meaning”, Chemical Educator, p. 349, vol. 12, (2007). Published
  • M. A. Gomez, L. R. Pratt, J. D. Kress, and D. Ashthagiri, “Water adsorption and dissociation on BeO (001) and (100) surfaces”, Surface Science, p. 1608, vol. 601, (2007). Published
  • Branchini, BR; Ablamsky, DM; Rosenman, JM; Uzasci, L; Southworth, TL; Zimmer, M, “Synergistic mutations produce blue-shifted bioluminescence in firefly luciferase”, BIOCHEMISTRY, p. 13847, vol. 46, (2007). Published, 10.1021/bi701505
  • Cafiero, M; Adamowicz, L, “Non-born-oppenheimer calculations of the ground state of H-3”, INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, p. 2679, vol. 107, (2007). Published, 10.1002/qua.2141
  • Hofto, L; Hofto, M; Cross, J; Cafiero, M, “Using simple molecular orbital calculations to predict disease: fast DFT methods applied to enzymes implicated in PKU, Parkinson’s disease and Obsessive Compulsive Disorder”, CompLife 2007: 3rd International Symposium on Computational Life Science, p. 127, vol. 940, (2007). Published
  • Hofto, ME; Cross, JN; Cafiero, M, “Interaction energies between tetrahydrobiopterin analogues and aromatic residues in tyrosine hydroxylase and phenylalanine hydroxylase”, JOURNAL OF PHYSICAL CHEMISTRY B, p. 9651, vol. 111, (2007). Published, 10.1021/jp072518
  • Hofto, ME; Godfrey-Kittle, A; Cafiero, M, “Substrate-protein interaction energy in the enzyme phenylalanine hydroxylase: DFT and ab initio results”, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, p. 125, vol. 809, (2007). Published, 10.1016/j.theochem.2007.01.02
  • Van Sickle, K; Culberson, LM; Holzmacher, JL; Cafiero, M, “Evaluation of density functional theory methods for the electronic interactions between indole and substituted benzene: Applications to horseradish peroxidase”, INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, p. 1523, vol. 107, (2007). Published, 10.1002/qua.2128

2006:

  • Marco A. Allodi, Meghan E. Dunn, Jovan Livada, Karl N. Kirschner and George C. Shields, “Do Hydroxyl Radical-Water Clusters, OH(H2O)n, n=1-5, Exist in the Atmosphere?”  J. Phys. Chem. A 110 (2006) 13283-13289. Download from ACS
  • Frank C. Pickard IV, Daniel R. Griffith, Skylar J. Ferrara, Matthew D. Liptak, Karl N. Kirschner and George C. Shields “Comparison of CCSD(T), W1, and other Model Chemistry Predictions for Gas Phase Deprotonation Reactions”  Int. J. Quantum Chem. (2006) 3122-3128
  • Kristin S. Alongi, Theodore S. Dibble, George C. Shields and Karl N. Kirschner, “Exploration of the Potential Energy Surfaces, Prediction of Atmospheric Concentrations, and Vibrational Spectra of the HO2•••(H2O)n (n=1-2) Hydrogen Bonded Complexes”  J. Phys. Chem. A 110 (2006) 3686-3691. Download from ACS
  • Frank C. Pickard IV, Rebecca L. Shepherd, Amber E. Gillis, Meghan E. Dunn, Steven Feldgus, Karl N. Kirschner, George C. Shields, Mariappan Manoharan, and Igor V. Alabugin “Ortho-Effect in the Bergman Cyclization: Electronic and Steric Effects in Hydrogen Abstraction by 1-Substituted Naphthalene 5,8-Diradicals” J. Phys. Chem. A 110 (2006) 2517-2526. Dowload from ACS
  • Meghan E. Dunn, Timothy M. Evans, Karl N. Kirschner and George C. Shields, “Prediction of Accurate Anharmonic Experimental Vibrational Frequencies for Water Clusters, (H2O)n, n=2-5”  J. Phys. Chem. A 110 (2006) 303-309. Download from ACS
  • Nina E. McCrate; Mychel E. Varner; Kenny I. Kim and Maria C. Nagan, “Molecular Dynamics Simulations of Human tRNALys,3UUU: The Role of Modified Bases in mRNA Recognition”  Nucleic Acids Res. 34 (2006) 5361-5368. Download from NAR
  • Sanchita Hati, Brigitte Ziervogel, Julius SternJohn, Fai-Chu Wong, Maria C. Nagan, Abbey E. Rosen, Paul G. Siliciano, Joseph W. Chihade, and Karin Musier-Forsyth, “Pre-transfer Editing by Class II Prolyl-tRNA Synthetase: Role of Aminoacylation Active Site in ?Selective Release? of Noncognate Amino Acids”, Journal of Biological Chemistry, p. 27862, vol. 281, (2006). Published
  • Allodi, M.A., Dunn, M.E., Livada, J., Kirschner, K.N. and Shields, G.C., “Do Hydroxyl Radical-Water Clusters, OH(H2O)n, n=1-5, Exists in the Atmosphere?” Journal of Physical Chemistry A, 110 (49), 13283-13289 (2006).
  • S.L. Maddalo and M. Zimmer, “The Role of the Protein Matrix in GFP Fluorescence”, Photochemistry and Photobiology, p. 367, vol. 82, (2006). Published

2005:

  • Frank C. Pickard IV, Emma K. Pokon, Matthew D. Liptak, and George C. Shields, “Comparison of complete basis set-QB3, complete basis set-APNO, Gaussian-2, and Gaussian-3 thermochemical predictions with experiment for formation of ionic clusters of hydronium and hydroxide ions complexed with water”, Journal of Chemical Physics, p. 024302, vol. 122, (2005). Download from AIP
  • Mary Beth Day, Karl N. Kirschner, and George C. Shields, “Pople’s Gaussian-3 model chemistry applied to an investigation of (H2O)8 water clusters”, International Journal of Quantum Chemistry, p. 565, vol. 102, (2005).
  • Carol Parish, Sean Hillson, Emelyn Smith and Martel Zeldin, “Cages, Baskets, Ladders and Tubes; Conformational Studies of Polyoligomeric Silsesquioxanes”, Journal of Physical Chemistry A, 2005 109, 8371-8378.
  • Chang-Guo Zhan, Shi-Xian Deng, Jaime G. Skiba, Beth A. Hayes, Sarah M. Tschampel, George C. Shields and Donald W. Landry, “First-principle studies of intermolecular and intramolecular catalysis of protonated cocaine”, Journal of Computational Chemistry, p. 980, vol. 26, (2005). Published
  • Frank C. Pickard IV, Meghan E. Dunn and George C. Shields, “Comparison of Model Chemistry and Density Functional Theory Thermochemical Predictions with Experiment for Formation of Ionic Clusters of the Ammonium Cation Complexed with Water and Ammonia; Atmospheric Implications”, Journal of Physical Chemistry A, p. 4905, vol. 109, (2005). Published
  • Mary Beth Day, Karl N. Kirschner and George C. Shields, “Global Search for Minimum Energy (H2O)n Clusters, n=3-5”, Journal of Physical Chemistry A, p. 6773, vol. 109, (2005). Published
  • Matthew D. Liptak and George C. Shields, “Comparison of Density Functional Theory Predictions of Gas Phase Deprotonation”, International Journal of Quantum Chemistry, p. 580, vol. 105, (2005). Published
  • N.-Y. Baffour-Awuah, F. Fedeles, M. Zimmer, “Structural features responsible for GFPuv and S147P-GFP?s improved fluorescence”, Chemical Physics, p. 25, vol. 310, (2005). Published
  • B.R. Branchini, T.L. Southworth, M.H. Murtiashaw, S.R. Wilkinson, N.F. Khattak, J.C. Rosenberg, and M. Zimmer, “Mutagenesis Evidence that the Partial Reactions of Firefly Bioluminescence Are Catalyzed by Different Conformations of the Luciferase C-Terminal Domain”, Biochemistry, p. 1385, vol. 44, (2005). Published

2004:

  • Carol Parish, Matthew Yarger, Kent Sinclair, Alla Goldberg and Myrianne Dure, “Molecular Modeling Studies of Cyclic Urea HIV-1 Protease Inhibitors”, Journal of Medicinal Chemistry, p. 4838, vol. 47, (2004). Download from ACS
  • Carol Parish, Hilda Castillo, Matthew Yarger and Melissa Rappleye, “A Comparison of the AMBER*, OPLSAA and HF Potential Energy Surfaces for a Series of Diastereomeric Cyclic Urea HIV–1 Inhibitors”,  Journal of Molecular Structure (THEOCHEM), 2004 710, 73-76.
  • Owen F. Speer, Brian C. Wengerter, and Ramona S. Taylor, “Molecular Dynamics Simulations of Simple Liquids”, Journal of Chemical Education, p. 1330, vol. 81, (2004).
  • Carol Parish, Roald Hoffman and Larry Scott, “A Theoretical Study of Dicyclobuta[de,ij]naphthalene and Dicyclopenta[cd,gh]pentalene”, Journal of Organic Chemistry, p. 8093, vol. 69, (2004).
  • D. Asthagiri, L.R. Pratt, J.D. Kress, and M.A. Gomez, “Hydration and mobility of HO-(aq)”, Proceedings of the National Academy of Sciences (USA), p. 7229, vol. 101, (2004).
  • L.V. Desai and M. Zimmer, “Substrate Selectivity and Conformational Space Available to Bromoxynil and Acrylonitrile in Iron Nitrile Hydratase”, Dalton Transactions, p. 872, (2004).
  • H. Debari and M. Zimmer, “Structural Analysis of the Conformational Flexibility of Tris(pyrazolyl)borate Ligands and Their Analogues”, Inorganic Chemistry, p. 3344, vol. 43, (2004).
  • N.-Y. Baffour and M. Zimmer, “Hula-Twisting in Green Fluorescent Protein”, Chemical Physics, p. 7, vol. 303, (2004).
  • Meghan E. Dunn, Emma K. Pokon, and George C. Shields , “Thermodynamics of Forming Water Clusters at Various Temperatures and Pressures by Gaussian-2, Gaussian-3, Complete Basis Set-QB3, and Complete Basis Set-APNO Model Chemistries; Implications for Atmospheric Chemistry”, Journal of the American Chemical Society, p.2647, vol. 126, (2004).
  • Matthew W. Palascak and George C. Shields, “Accurate Experimental Values for the Free Energies of Hydration of H+, OH-, and H3O+”, Journal of Physical Chemistry A, p. 3692, vol. 108, (2004).
  • Meghan E. Dunn, Emma K. Pokon, and George C. Shields, “The ability of the Gaussian-2, Gaussian-3, Complete Basis Set-QB3, and Complete Basis Set-APNO model chemistries to model the geometries of small water clusters”, International Journal of Quantum Chemistry, p.1065, vol. 100, (2004).
  • M.D. Griffin, K.D. Rule, V. Cooper, and M.A. Gomez, “Proton binding sites and transition states in perovskite oxides”, Journal of Physical Chemistry, p. , vol. , ( ). in preparation

2003:

  • O.F. Zaidan, J.A. Greathouse, and R.T. Pabalan, “Monte Carlo and Molecular Dynamics Simulation of Uranyl Adsorption on Montmorillonite Clay”, Clays and Clay Minerals, p. 372, vol. 51, (2003). Published
  • Carol Parish, Martel Zeldin, Jennifer Pratt and Sean Hilson, “Conformational Analysis of Siloxane-Based Enzyme-Mimic Precursors”, Macromolecular Symposia, p. 327, vol. 196, (2003). Published
  • Ramona S. Taylor and Roseanne L. Shields, “Molecular Dynamics Simulations of the Ethanol Liquid/Vapor Interface”, Journal of Chemical Physics, p. 12569, vol. 119, (2003). Published
  • D. Asthagiri, L.R. Pratt, J.D. Kress, and M.A. Gomez, “The hydration state of HO-“, Chemical Physics Letters, p. 530, vol. 380, (2003). Published
  • M.S. Zaveer and M. Zimmer, “Structural Analysis of the Immature Form of the GFP Analog DsRed”, Bioorganic & Medicinal Chemistry Letters, p. 3919, vol. 13, (2003). Published

2002:

  • Parish, Carol; Zeldin, Martel; Pratt, Jennifer, “Conformational Analysis and Modeling Studies of Synthetic 4-Dialkylaminopyridine-Siloxane Oligomers with Selective Esterase Activity”,Journal of Inorganic and Organometallic Polymers, p. 31, vol. 12, (2002). Published
  • Parish, Carol; Rappleye, Melissa; Dure, Myrianne, “A Comparison of the Low Mode and Monte Carlo Conformational Search Methods”,
    Journal of Molecular Graphics and Modeling, p. 129, vol. 21, (2002). Published
  • T.V. Davis, M.S. Zaveer, and M. Zimmer, “Using the Cambridge Structural Database to Introduce Important Inorganic Concepts”, Journal of Chemical Education, p. 1278, vol. 79, (2002). Published
  • L.N. Todd and M. Zimmer, “The Moderating Influence of Proteins on Non-Planar Tetrapyrrole Deformations. Coenzyme F430 in Methyl Coenzyme-M Reductase”, Inorganic Chemistry, p. 6831, vol. 41, (2002). Published
  • P. Grabowski, D. Riccardi, M.A. Gomez, D. Asthagiri, and L.R. Pratt, “Quasi-chemical theory and the standard free energy of H+(aq)”, Journal of Physical Chemistry A, p. 9145, vol. 106, (2002). Published
  • M. Zimmer, “Green Fluorescent Protein (GFP): Applications, Structure and Related Photophysical Behavior”, Chemical Reviews, p. 759, vol. 102, (2002). Published
  • T.V. Davis, M.S. Zaveer, and M. Zimmer, “Using the Cambridge Structural Database to Introduce Important Inorganic Concepts”, Journal of Chemical Education, p. 1278, vol. 79, (2002). Published
  • L.N. Todd and M. Zimmer, “The Moderating Influence of Proteins on Non-Planar Tetrapyrrole Deformations. Coenzyme F430 In Methyl Coenzyme-M Reductase”, Inorganic Chemistry, p. 6831, vol. 41, (2002). Published
  • Matthew D. Liptak, Kevin C. Gross, Paul G. Seybold, Steven Feldgus, and George C. Shields, “Absolute pKa Determinations for Substituted Phenols”, Journal of the American Chemical Society, p. 6421, vol. 124, (2002). Published
  • Jeffery A. Greathouse and Erik W. Storm, “Calcium hydration on montmorillonite clay surfaces studied by Monte Carlo simulation”, Molecular Simulation, p. 633, vol. 28, (2002). Published
  • Jeffery A. Greathouse, Robert J. O’Brien, Gregory Bemis, and Robert T. Pabalan, “Molecular Dynamics Study of Aqueous Uranyl Interactionswith Quartz (010)”, Journal of Physical Chemistry B, p. 1646, vol. 106, (2002). Published