Publications
PUBLICATIONS AND PRESENTATIONS
Please submit information about publications and presentations that include work done using MERCURY resources to:
Acknowledgements
The following acknowledgements are to be used for papers and presentations where MERCURY resources were used:
Computational resources were provided in part by the MERCURY supercomputer consortium (http://mercury.chem.hamilton.edu) under NSF grant's CHE-0116435, CHE-0521063, and CHE-0849677.
This project was supported in part by NSF grant CHE-0116435 as part of the MERCURY supercomputer consortium (http://mercury.chem.hamilton.edu)
Journal Publications:
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.
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
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
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
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
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).
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.
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).
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
Georges, Christophre, "Bounded Memory, Overparameterized Forecast Rules, and Instability", Economics Letters, p. , vol. , (2007). Accepted
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
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
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).
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.
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).
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
Georges, Christophre, "Bounded Memory, Overparameterized Forecast Rules, and Instability", Economics Letters, p. , vol. , (2007). Accepted
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
S.L. Maddalo and M. Zimmer, "The Role of the Protein Matrix in GFP Fluorescence", Photochemistry and Photobiology, p. 367, vol. 82, (2006). Published
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
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
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
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).
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
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
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
2001:
L.R. Pratt, R.A. LaViolett, M.A. Gomez, and M.E. Gentile, "Quasi-chemical Theory for the Statistical Thermodynamics of the Hard Sphere Fluid", Journal of Physical Chemistry B, p. 11662, vol. 105, (2001). Published
M. Zimmer, "Molecular Mechanics, Data and Conformational Analysis of First-Row Transition Metal Complexes in the Cambridge Structural Database", Coord. Chem. Rev., p. 133, vol. 212, (2001). Published
A. Warren and M. Zimmer, "Computational Analysis of Thr203 in Green Fluorescent Protein", J. Mol. Graphics & Modelling, p. 297, vol. 19, (2001). Published
P.E.M. Siegbahn, M. Wirstam, and M. Zimmer, "A Theoretical Study of the Mechanism of Peptide Ring Formation in Green Fluorescent Protein", International Journal of Quantum Chemistry, p. 1557, vol. 81, (2001). Published
F. Fedeles and M. Zimmer, "Conformational/Configurational Analysis of All the Binding Geometries of Cobalt(III) Bleomycin", Inorganic Chemistry, p. 1557, vol. 40, (2001). Published
D.L. Cullen, L.V. Desai, M. Zimmer, and J.A. Shelnutt, "Conformational Analysis of the Non-Planar Deformations of Cobalt Porphyrin Complexes in the Cambridge Structural Database", Structural Chemistry, p. 237, vol. 12, (2001). Published
M. Donnelly, F. Fedeles, M. Wirstam, P.E.M. Siegbahn,and M. Zimmer, "Computational Analysis of the Autocatalytic Posttranslational Cyclization Observed in Histidine Ammonia-Lyase. A Comparison with Green Fluorescent Protein", Journal of the American Chemical Society, p. 4679, vol. 123, (2001). Published
M.C. Chen, C.R. Lambert, J.D. Lambert, and M. Zimmer, "Photoisomerization of Green Fluorescent Protein and the Dimensions of the Chromophore Cavity", Chemical Physics, p. 157, vol. 120, (2001). Published
Ann Marie Toth, Matthew D. Liptak, Danielle Phillips and George C. Shields, "Accurate relative pKa calculations for carboxylic acids using complete basis set and Gaussian-n models combined with continuum solvations methods", Journal of Chemical Physics, p. 4595, vol. 114, (2001). Published
Matthew D. Liptak and George C. Shields, "Accurate pKa Calculations for Carboxylic Acids Using Complete Basis Set and Gaussian-n Models Combined with CPCM Continuum Solvation Methods", Journal of the American Chemical Society, p. 7314, vol. 123, (2001). Published
Edward C. Sherer, Sam J. Bono, and George C. Shields, "Further Quantum Mechanical Evidence that Difluorotoluene does not Hydrogen Bond", Journal of Physical Chemistry B, p. 8445, vol. 105, (2001). Published
Matthew D. Liptak and George C. Shields, "Experimentation with different thermodynamic cycles used for pKa calculations on carboxylic acids using Complete Basis Set and Gaussian-n Models combined with CPCM Continuum Solvation Methods", International Journal of Quantum Chemistry, p. 727, vol. 85, (2001). Published
Steven Feldgus and George C. Shields, "An ONIOM Study of the Bergman Reaction: A Computationally Efficient and Accurate Method for Modeling the Enediyne Anticancer Antibiotics", Chemical Physics Letters, p. 505, vol. 347, (2001). Published
Emma K. Pokon, Matthew D. Liptak, Steven Feldgus, and George C. Shields, "Comparison of CBS-QB3, CBS-APNO, and G3 predictions of gas phase deprotonation data", Journal of Physical Chemistry A, p. 10483, vol. 105, (2001). Published
J.A. Greathouse, G. Bemis, and R.T. Palaban, "Molecular dynamics simulation of the uranyl ion near quartz surfaces", Proceedings of the International Symposium on Water-Rock Interaction, p. 173, vol. 1, (2001). Published
M. Zimmer, "Molecular Mechanics, Data and Conformational Analysis of First-Row Transition Metal Complexes in the Cambridge Structural Database", Coord. Chem. Rev., p. 133, vol. 212, (2001). Published
A. Warren and M. Zimmer, "Computational Analysis of Thr203 in Green Fluorescent Protein", J. Mol. Graphics & Modelling, p. 297, vol. 19, (2001). Published
P.E.M. Siegbahn, M. Wirstam, and M. Zimmer, "A Theoretical Study of the Mechanism of Peptide Ring Formation in Green Fluorescent Protein", International Journal of Quantum Chemistry, p. 1557, vol. 81, (2001). Published
F. Fedeles and M. Zimmer, "Conformational/Configurational Analysis of All the Binding Geometries of Cobalt(III) Bleomycin", Inorganic Chemistry, p. 1557, vol. 40, (2001). Published
D.L. Cullen, L.V. Desai, M. Zimmer, and J.A. Shelnutt, "Conformational Analysis of the Non-Planar Deformations of Cobalt Porphyrin Complexes in the Cambridge Structural Database", Structural Chemistry, p. 237, vol. 12, (2001). Published
M. Donnelly, F. Fedeles, M. Wirstam, P.E.M. Siegbahn,and M. Zimmer, "Computational Analysis of the Autocatalytic Posttranslational Cyclization Observed in Histidine Ammonia-Lyase. A Comparison with Green Fluorescent Protein", Journal of the American Chemical Society, p. 4679, vol. 123, (2001). Published
M.C. Chen, C.R. Lambert, J.D. Lambert, and M. Zimmer, "Photoisomerization of Green Fluorescent Protein and the Dimensions of the Chromophore Cavity", Chemical Physics, p. 157, vol. 120, (2001). Published
Ann Marie Toth, Matthew D. Liptak, Danielle Phillips and George C. Shields, "Accurate relative pKa calculations for carboxylic acids using complete basis set and Gaussian-n models combined with continuum solvations methods", Journal of Chemical Physics, p. 4595, vol. 114, (2001). Published
Matthew D. Liptak and George C. Shields, "Accurate pKa Calculations for Carboxylic Acids Using Complete Basis Set and Gaussian-n Models Combined with CPCM Continuum Solvation Methods", Journal of the American Chemical Society, p. 7314, vol. 123, (2001). Published
Edward C. Sherer, Sam J. Bono, and George C. Shields, "Further Quantum Mechanical Evidence that Difluorotoluene does not Hydrogen Bond", Journal of Physical Chemistry B, p. 8445, vol. 105, (2001). Published
Matthew D. Liptak and George C. Shields, "Experimentation with different thermodynamic cycles used for pKa calculations on carboxylic acids using Complete Basis Set and Gaussian-n Models combined with CPCM Continuum Solvation Methods", International Journal of Quantum Chemistry, p. 727, vol. 85, (2001). Published
Steven Feldgus and George C. Shields, "An ONIOM Study of the Bergman Reaction: A Computationally Efficient and Accurate Method for Modeling the Enediyne Anticancer Antibiotics", Chemical Physics Letters, p. 505, vol. 347, (2001). Published
Emma K. Pokon, Matthew D. Liptak, Steven Feldgus, and George C. Shields, "Comparison of CBS-QB3, CBS-APNO, and G3 predictions of gas phase deprotonation data", Journal of Physical Chemistry A, p. 10483, vol. 105, (2001). Published
J.A. Greathouse, G. Bemis, and R.T. Palaban, "Molecular dynamics simulation of the uranyl ion near quartz surfaces", Proceedings of the International Symposium on Water-Rock Interaction, p. 173, vol. 1, (2001). Published
