Karl N. Kirschner
Hamilton
College
Clinton, NY 13323
Ph.D. (1999) - University of Georgia, Athens, GA; Physical Chemistry
Dissertation: "Part 1. Theoretical Investigation of Calcium-Ligand Dimers. Part 2. An Electronic Structure Study on N-Acetyl-Duocarmycin SA. Part 3. MM3 Combinatorial Parameterization of Alpha Amino Acid Zwitterions."
B.A. (1995) - Lake Forest College (LFC), Lake Forest, IL; Chemistry
Honors Senior Thesis: "Quantum Mechanical Investigation of Adenosine 3',5'-Cyclic Monophosphate."
Co-Director of the Center for Molecular Design at Hamilton College (2006-present)s
Research Consultant (2005-present)
Visiting Professor at Hamilton College (2004-present)
Postdoctoral Researcher at Complex Carbohydrate Research Center, University of Georgia, Athens (2000-2004)
Teaching Assistant. University of Georgia, Chemistry Department. General Chemistry Laboratory (1995-1998)
Research Assistant. University of Colorado, Biochemistry Department under the direction of Dr. S.C. Schultz and Dr. G.C. Shields. Research involved expressing a methylase/restriction enzyme system. Funded by a National Institute of Health grant (1993)
Research Assistant. Lake Forest College (1992-1995)
A full patent application based on that provisional was filed February 24, 2007. Title: “Alpha-fetoprotein peptides.” T.T. Andersen, J.A. Bennett, H.I. Jacobson, G.C. Shields and K.N. Kirschner
Chemistry 321, Physical Chemistry I: Quantum Mechanics (Fall, 2004: 17 students)
Chemistry 321L, Physical Chemistry I Lab: Introduction to Computational Chemistry - Classical Methodologies (Fall, 2004: 17 students)
Chemistry 322, Physical Chemistry II: Thermodynamics & Kinetics (Spring, 2005: 17 students; Spring 2006: 8 students)
Chemistry 322L, Physical Chemistry I Lab: Introduction to Computational Chemistry - Quantum Methodologies (Spring, 2005: 17 students)
Sophomore Seminar 220, Forever Wild, The Cultural and Natural Histories of the Adirondack Park (Fall, 2004: 13 students)
National Science Foundation-RUI, "Calculating Acid Dissociation constants in Aqueous Solution" ($210,000 for 3 years), co-written with George C. Shields (2005)
National Institutes of Health, "Reactivity and Dynamics of Enediyne Natural Products" ($248,000 for 3 years), co-written with George C. Shields (2005)
Department of Defense, US Army Medical Research and Material Command, from the Department of Defense Breast Cancer Research Program, "Development of a Computational Assay for the Estrogen Receptor" ($113,620 for 1 year), co-written with George C. Shields (2005)
National Institutes of Health Post-Doctoral Fellowship (2001-2004)
Sherer, E.C., Pickard IV, F.C.,* Rein, C.,* Feldgus, S., Kirschner, K.N. and Shields, G.C., “Enediyne Bergman Cyclization of the Chemically Active Region of Esperamicin A1.” will be submitted to the International Journal of Quantum Chemistry.
Kirschner, K.N., Yongye A.B., Tschampel S.M., Daniels C.R. and Woods, R.J., “GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates.” Journal of Physical Chemistry submitted 06/15/07.
Shields, G.C. and Kirschner, K.N., “The Failure of Density Functional Theory to Model Neutral Water Clusters.” submitted to the Journal, Synthesis and Reactivity in Inorganic, Metal-Organic and Nano-Metal Chemistry special edition on water clusters, accepted 05/07.
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, accepted 05/07.
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). [Page 1]
Kirschner, K.N., Harrt, G.M.,* Evans, T.M.,* and Shields, G.C., “In Search of CS2·(H2O)n=1-4 Clusters” Journal of Chemical Physics, 126, 154320 (2007). [Page 1]
Kirschner, K.N., Lexa, K.W.,* Salisburg, A.M.,* Alser, K.A.,* Joseph, L. Andersen, T.T., Bennett, J.A., Jacobson, H.I. and Shields, G.C., “Computational Design and Discovery of an Anti-Estrogenic Peptide Derived from Alpha-Fetoprotein.” Journal of the American Chemistry Society, 129, 6263-6268 (2007). [Page 1]
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). [Page 1]
Pickard F.C.,* Griffith, D.R.,* Ferrara, S.J.,* Liptak M.D.,* Kirschner, K.N. and Shields, G.C., “ CCSD(T), W1, and other Model Chemistry Predictions for Gas-Phase Deprotonation Reactions.” International Journal of Quantum Chemistry, 106, 3122-3128 (2006). [Page 1]
Pickard IV, F.C.,* Shepherd, R.L.,* Gillis,A.E.,* Dunn,M.E.,* Feldgus,S., Kirschner, K.N., Shields, G.C., Manoharan, M. and Alabugin, I.V., “Ortho-Effect in the Bergman Cyclization: Electronic and Steric Effects in Hydrogen Abstraction by 1-Substituted Naphthalene 5,8-Diradicals.” Journal of Physical Chemistry A, 110, 2517-2526 (2006). [Page 1]
Alongi, K.S.,* Dibble, T.S., Shields, G.C. and Kirschner, K.N., “Exploration of the Potential Energy Surfaces, Prediction of Atmospheric Concentrations, and Vibrational Spectra of the HO2∙∙∙(H2O)n (n=1-2) Hydrogen Bonded Complexes.” Journal of Physical Chemistry A, 110, 3686-3691 (2006). [Page 1]
Dunn, M.E.,* Evans, T.M.,* Kirschner, K.N., Shields, G.C., “Prediction of Accurate Anharmonic Experimental Vibrational Frequencies for Water Clusters, (H2O)n, n=2-5.” Journal of Physical Chemistry A, 110, 303-309 (2006). [Page 1]
Gonzalez-Outeirino, J. Kirschner, K.N., Thobhani, S. and Woods, R.J., “Reconciling Solvent Effects on Rotamer Populations in Carbohydrates: a Joint MD and NMR analysis.” Canadian Journal of Chemistry, 84, 569-579 (2006).
Tschampel, S.M., Kirschner, K.N. and Woods, R.J., “Incorporation of Carbohydrates into Macromolecular Force Fields.” A book chapter for NMR Spectroscopy and Modeling of Carbohydrates, Johannes F.G. Vliegenthart and Robert J. Woods Eds.,Washington, DC American Chemical Society Symposium Series 930, (2006). [Page 1]
Day, M.B.,* Kirschner, K.N. and Shields, G.C., “Global Search for Minimum (H2O)n Clusters, n=3-5.” Journal of Physical Chemistry A, 109(30), 6773-6778 (2005). [Page 1]
Day, M.B.,* Kirschner, K.N. and Shields, G.C., “Pople's Gaussian-3 Model Chemistry Applied to an Investigation of (H2O)8 Water Clusters.” International Journal of Quantum Chemistry, 102, 565-572 (2005). [Page 1]
Kirschner, K.N., Lewin, A., Bowen, J.P., "MM3 Parameterization of Alpha Amino Acid Zwitterions." Journal of Computational Chemistry, 24(1), 111-128 (2003). [Page 1]
Kirschner, K.N. and Woods, R.J., "Solvent Interactions Determine Carbohydrate Conformation." Proceedings of the National Academy of Sciences USA, 98, 10541-10545 (2001). [Page 1]
Velasquez III, J., Kirschner, K.N., Reddic, J.E. and Duncan, M.A., "Ca+Ar2 Complex: Linear or Bent?" Chemical Physics Letters, 343, 613-621 (2001). [Page 1]
Kirschner, K.N. and Woods, R.J., "A Quantum Mechanical Study of the Non-Bonded Forces in Water-Methanol Complexes." Journal of Physical Chemistry, 105(16), 4150-4155 (2001). [Page 1]
Kirschner, K.N., "Theoretical Investigation of Ca-RG, Ca+-RG, and Ca2+-RG (RG = Ne and Ar)." Journal of Chemical Physics, 112(23), 10228-10235 (2000). [Page 1]
Kirschner, K.N., Van Dyke, C., Kovacic, P. and Bowen, J.P., "Computational Studies on Electron Transfer by the Iminium Metabolite of Phencyclidine (PCP)." Journal of Molecular Structure (Theochem), 498(1-4), 167-179 (2000). [Page 1]
Kirschner, K.N., Lee, M., Stanley, R.C. and Bowen, J.P., "Density Functional and Ab Initio Studies on N-Acetyl-Duocarmycin SA: Insights into its DNA Interaction Properties." Bioorganic Medicinal Chemistry, 8(2), 329-335 (2000). [Page 1]
Kirschner, K.N., Ma, B., Bowen, J.P. and Duncan, M.A., "Theoretical Investigation of Ca+-N2 and Ca2+-N2 Complexes." Chemical Physics Letters, 295, 204-210 (1998). [Page 1]
Kirschner, K.N., Sherer, E.C. and Shields, G.C., "Use of the Supermolecule Approach to Model the Syn and Anti Conformations of Solvated Cyclic 3', 5'-Adenosine Monophosphate." Journal of Physical Chemistry, 100, 3293-3298 (1996). [Page 1]
Kirschner, K.N. and Shields, G.C., "Quantum-Mechanical Investigation of Cyclic 3', 5'-Adenosine Monophosphate, the Second Hormonal Messenger." Journal of Molecular Structure (Theochem), 362, 297-304 (1996). [Page 1]
Kirschner, K.N. and Shields, G.C., "Quantum-Mechanical Investigation of Large Water Clusters." International Journal of Quantum Chemistry 52, 349-360 (1994). [Page 1]
Jurema, M.W., Kirschner, K.N. and Shields, G.C., "Modeling of Magic Water Clusters (H2O)20 and (H2O)21H+ with the PM3 Quantum-Mechanical Method." Journal of Computational Chemistry, 14(11), 1326-1332 (1993). [Page 1]
* Indicates undergraduate authors.
Kirschner, K.N., chair of session entitled “Case Studies of Computational Methods in Drug Discovery/Design – I.” 47th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, February 2007, St. Simons Island, GA.
Kirschner, K.N., “Gas-phase atmospheric computational chemistry.” 34th Northeast Regional Meeting of the American Chemical Society, Binghamton, NY (October 5, 2006).
Deline, A., Dunn, M. and Kirschner, K.N., “A Dynamics Study on the Diffusion of Water Through Pristine and Molecularly Altered Nanotubes.” Sanibel Symposium, St. Simons, GA (2005).
Kirschner, K.N. and Woods, R.J., "Force Field Development and Molecular Dynamics of Carbohydrate and Proteins." Hamilton College, Clinton, NY (2003).
Kirschner, K.N. and Woods, R.J., "Insights into Rheumatoid Arthritis - the Dynamic Motion of the Glycans Present in IgG Antibodies." Gordon Carbohydrate Conference, Tilton, NH (2003).
Kirschner, K.N. and Woods, R.J., "Solvent Interactions Determine Carbohydrate Conformations." Sanibel Symposium, St. Augustine, GA (2003).
Kirschner, K.N. and Woods, R.J., "Insights into Rheumatoid Arthritis - the Dynamic Motion of the Glycans Present in IgG Antibodies." Glycobiology Conference, San Diego, CA (2003).
Kirschner, K.N. and Woods, R.J., "The Role of Solvent in Determining Carbohydrate Conformation." Vanderbilt Biomolecular Modeling Symposium, Nashville, TN (2002).
Kirschner, K.N. and Woods, R.J., "Calculating Gas-Phase Interaction Energies: the Effects of Basis Set Superposition Error and Fragment Relaxation." Southeast Regional Meeting of ACS, Savannah, GA (2001).
Kirschner, K.N. and Woods, R.J., "Solvent Interactions Determine Carbohydrate Conformations." Southeast Regional Meeting of the ACS, Savannah, GA (2001).
Kirschner, K.N. and Woods, R.J., "Solvent Interactions Determine Carbohydrate Conformations." Eurocarb XI, Lisbon, Portugal (2001).
Kirschner, K.N. and Woods, R.J., "The Gauche Effect in α-Linked Carbohydrates: the Importance of Electronic Structure and Hydrogen Bonding." Michael C. Zerner Memorial Symposium, Gainesville, FL (2000).
Kirschner, K.N., Lee, M., Stanley, R.C. and Bowen, J.P., "Density Functional and Ab Initio Studies on N-Acetyl-Duocarmycin SA: Insights into its DNA Interaction Properties." Genomics: Research and Application, University of Georgia, Athens, GA (2000).
Kirschner, K.N., Lee, M., Stanley, R.C. and Bowen, J.P., "Density Functional and Ab Initio Studies on N-Acetyl-Duocarmycin SA: Insights into its DNA Interaction Properties." Hamilton College, Clinton, NY (1999).
Kirschner, K.N., Lee, M., Stanley, R.C. and Bowen, J.P., "Density Functional and Ab Initio Studies on N-Acetyl Duocarmycin SA: Insights into its DNA Interaction Properties." American Chemical Society Southeastern Regional Meeting, Savannah, GA (1999).
Kirschner, K.N., Lee, M., Stanley, R.C. and Bowen, J.P., "What Do Density Functional and Ab Initio Theories Have to Say About the Duocarmycin Debate?" American Chemical Society National Meeting, New Orleans (1999).
Kirschner, K.N., Lii, J.H., Lewin, A.H. and Bowen, J.P., "Molecular Mechanics Force Field Development for Amino Acid Zwitterions." American Chemical Society National Meeting (1998).
Kirschner, K.N., Van Dyke, C., Kovacic, P. and Bowen, J.P., "Computational Studies on Electron Transfer by the Iminium Metabolite of Phencyclidine (PCP)." American Chemical Society National Meeting (1998).
Kirschner, K.N. and Shields, G.C., "Quantum-Mechanical Investigation of Cyclic 3', 5'-Adenosine Monophosphate, the Second Hormonal Messenger." Sanibel Symposium, St. Augustine, FL (1995).
Kirschner, K.N. and Shields, G.C., "Quantum-Mechanical Investigation of Large Water Clusters." Sanibel Symposium, St. Augustine, FL (1994).
“The Effects of Prereactive Complexes on Gas-Phase Reactions.” Marco A. Allodi,* Karl N. Kirschner and George C. Shields at the 47th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, February 2007, St. Simons Island, GA. Presented by M.A. Allodi, who won the most outstanding undergraduate poster award.
“The Reaction CH4 + OH· → CH3· + H2O, With and Without the Presence of Water; A Kinetic and Quantum Mechanical Approach.” Jovan Livada,* Marco Allodi,* Meghan Dunn,* Karl Kirschner, George Shields at the 47th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, February 2007, St. Simons Island, GA. Presented by J. Livada, who won the most outstanding undergraduate poster award.
“A Case of Computational Drug Design: Creating a Reliable Methodology for Screening Potential Breast Cancer Drugs.” Karilyn Larkin, Rebecca Mackenzie,* Alexa Schwarzman,* Karl Kirschner, and George Shields at the 47th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, February 2007, St. Simons Island, GA. Presented by K. Larkin.
“Honing a Computational Methodology for Breast Cancer Drug Design.” Rebecca Mackenzie,* Alexa Schwarzman,* Karilyn Larkin, Karl Kirschner, and George Shields at the 47th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, February 2007, St. Simons Island, GA. Presented by R. Mackenzie.
“The Development of Accurate pKa Calculations.” James McConnell,* Kristin Alongi,* George C. Shields and Karl N. Kirschner at the 47th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, February 2007, St. Simons Island, GA. Presented by J. McConnell.
“Hydrogen Bond Stabilization in Designing a Pharmacophore.” Amanda Salisburg,* Katrina Lexa, Katherine Alser,* George Shields and Karl Kirschner at the 47th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, February 2007, St. Simons Island, GA. Presented by A. Salisburg.
“Computational Studies of Ternary Aerosol Nucleation: Clusters Containing H2SO4, H2O and NH3.” Charles J. Borton, Kristin S. Alongi, Alexa L. Ashworth, Andrew P. Beyler, Thomas E. Morrell, Karl N. Kirschner and George C. Shields at the 34th Northeast Regional Meeting of the American Chemical Society, October 5th, 2006, Binghamton, NY. Presented by Charles J. Borton.
“An Ab Initio Study of the Kinetics and Thermodynamics of Prereactive Complexes in Gas-Phase Reactions of the OH Radical and Hydrocarbons.” Marco A. Allodi,* Jovan Livada,* Meghan E. Dunn,* Karl N. Kirschner and George C. Shields at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by M. Allodi.
“The Development of Accurate pKa Calculations.” Kristin Alongi,* James McConnell,* Karl N. Kirschner and George C. Shields at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by K. Alongi.
“The Significance of Beta-Turns in Finding a Breast-Cancer Inhibiting, Non-Peptide Mimetic.” Katherine Alser,* Katrina Lexa, Amanda Salisburg,* Karl Kirschner and George C. Shields at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by K. Alser.
“Thermodynamics of the NH3···H2O Dimer.” Alexa Ashworth,* Kristin Alongi,* Charles Borton, Andrew Beyler,* Thomas Morrell,* George C. Shields and Karl N. Kirschner at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by A. Ashworth.
“Thermodynamic Analysis of Small NH3···(H2O)n, n=1-4, Cluster Configurations.” Andrew P. Beyler,* Charles J. Borton, Kristin S. Alongi,* Karl N. Kirschner and George C. Shields at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by A. Beyler.
“Computational Drug Design applied towards the treatment of Human African Trypanosomiasis.” Cecilia Disney,* Karl N. Kirschner and George C. Shields at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by C. Disney.
“Simulation of DNA Cleaved by Enediyne Anti-Cancer Antibiotics.” Sharfi Farhana,* Amber O'Connor,* Katrina Lexa, Karl N. Kirschner and George C. Shields at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by S. Farhana.
“Geometries, Thermodynamics, and Concentrations of Hydrated Carbonyl Sulfide Complexes.”Gregory M. Hartt,* Timothy M. Evans, Karl N. Kirschner and George C. Shields at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by G. Hartt.
“A Deeper Look at Esperamicin A1.” Russell Holz,* Marco Allodi,* Karl Kirschner and George C. Shields at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by R. Holz.
“Dissociation of Molybdenum Chlorides.” Deacon J. Lile,* Jovan Livada,* George Shields and Karl Kirschner at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by D. Lile.
“Kinetics of Bimolecular Decomposition Reactions of Molybdenum-hexachloride.” Jovan Livada,* Deacon Lile,* George Shields and Karl Kirschner at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by J. Livada.
“Developing a Methodology for Computational Drug Design.” Rebecca Mackenzie,* Alexa Schwarzman,* Karilyn Larkin,* Karl Kirschner, and George Shields at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by R. Mackenzie. (She goes by Becky Mackenzie)
“Force Field Development via the Molecular Partition Function.” James H. McConnell,* Karl N. Kirschner and George C. Shields at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by J. McConnell.
“New Thermochemical Predictions for the Formation of Ammonium Water Clusters.” Thomas F. Morrell,* Andrew P. Beyler,* Kristin S. Alongi,* Charles Borton, George C. Shields and Karl N. Kirschner. at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by T. Morrell.
“Simulation of DNA Cleaved by Enediyne Anti-Cancer Antibiotics.” Amber O'Connor,* Sharfi Farhana,* Kat Lexa, Karl Kirschner and George Shields at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by A. O'Connor.
“The Significance of Hydrogen Bonding in Designing a Pharmacophore.” Amanda Salisburg,* Katrina Lexa, Karl Kirschner and George Shields at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by A. Salisburg.
“Analysis of Raloxifene and its Derivatives Binding Affinities to the a Estrogen Rceptor Ligand Binding Domain.” Alexa Schwarzman,* Rebecca Mackenzie,* Karilyn Larkin,* Karl Kirschner and George Shields at the Fifth MERCURY Conference on Computational Chemistry, July 2006, Clinton, NY. Presented by A. Schwarzman.
“Extensive Exploration of the HO2∙∙∙(H2O)n (n=1-2) Potential Energy Surface,” Kristin Alongi,* Theodore S. Dibble, George C. Shields and Karl N. Kirschner at the 231st ACS National Meeting, March 2006, Atlanta, GA. Presented by T. Dibble.
“Analysis of Raloxifene and its Derivative's Binding Affinities to the α-Estrogen Receptor Ligand Binding Domain,” Karilyn Larkin,* Karl Kirschner and George Shields at the 46th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, March 2006, St. Simons Island, GA. Presented by K. Larkin, who won the most outstanding undergraduate poster award.
“Predicting Atmospheric Chemistry Through Quantum Theory: Intermolecular Attractions of OH, O2 and N2 with H2O,” Meghan E. Dunn,* Karl N. Kirschner and George C. Shields at the 46th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, March 2006, St. Simons Island, GA. Presented by M. Dunn, who won the most outstanding undergraduate poster award.
“Methodology Development for the Study of Bergman Cyclization in Enediyne Anticancer Antibiotics,” Frank C. Pickard,* Karl N. Kirschner and George C. Shields at the 46th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, March 2006, St. Simons Island, GA. Presented by F. Pickard, who won the most creative two-minute presentation award.
“Substituent Effects on Enediyne Hydrogen Abstraction from Methanol and Methane,” Tumelano Gopolang,* Frank Pickard IV,* Amber Gillis,* Rebecca Shepherd,* Karl N. Kirschner and George C, Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by T. Gopolang.
“Exotic atmospheres: CO2 clusters in planetary atmospheres,” Pragyan Pradhan,* George C. Shields, Karl N. Kirschner, Meghan Dunn,* Ngoda Nanongi* and James McConnell* at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by P. Pradhan.
“A computational study of the formation of N2(H2O)n clusters in the Atmosphere,” Ngoda P. Nanongi,* Meghan Dunn,* Karl N. Kirschner and George C. Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by N. Manongi.
“Determination of relative and absolute pKa values for histidines in small peptides,” Matroner George,* Katrina Lexa,* George C. Shields and Karl N. Kirschner at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by M. George.
“Modeling anharmonic frequencies of small water clusters to predict absorption and assist spectroscopic detection in the atmosphere,” Meghan E. Dunn,* Timothy M. Evans,* Karl N. Kirschner and George C. Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by M. Dunn.
“Computational Study of the OH Radical Addition to Isoprene,” Marco A. Allodi,* Karl N. Kirschner and George C. Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by M. Allodi.
“Conformational Analysis of Peptides: A Comparison of Methods,” Katrina Lexa,* Amanda Salisburg,* Karl Kirschner and George Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by K. Lexa.
“Analysis of the Affinity of Raloxifene and its derivatives to the α-Estrogen Receptor Ligand Binding Domain,” Karilyn Larkin,* Amy Barrows,* Karl Kirschner and George Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by K. Larkin.
“Extensive Exploration of the HO2(H2O)n (n=1-2) Potential Energy Surface,” Kristin S. Alongi,* Theodore S. Dibble, Karl N. Kirschner, and George C. Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by K. Alongi.
“Conformer Search for HO2(H2O)3 Complexes,” Jared Pienkos,* Kristin S. Alongi,* George C. Shields, and Karl N. Kirschner at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by J. Pienkos.
“Heme Induced Dehalogenation of Halo-phenols,” James McConnell,* Timothy Elgren, Karl N. Kirschner, and George C. Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by J. McConnell.
“High Level Theory Calculations to determine deprotonation energies for simple molecules,” Greg Nizialek,* Dan Griffith,* Christy House,* Skylar Ferrara,* Matt Liptak,* and George C. Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by G. Nizialek.
“Geometries, Energies, and Frequencies of Hydrated Carbon Disulfide Complexes,” Gregory M. Hartt,* Timothy M. Evans,* Karl N. Kirschner, and George C. Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by G. Hartt.
“Methodology Development for the Study of Bergman Cyclization in Enediyne Anticancer Antibiotics,” Frank C. Pickard IV,* Karl N. Kirschner and George C. Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by F. Pickard.
“Methyltrichlorosilane Pyrolysis: A Study of the Bimolecular Decomposition of Methyltrichlorsilane and the Formation of Silicon Carbide,” Evan A. Savage,* Jovan Livada,* Frank Pickard IV,* Karl Kirschner and George Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by E. Savage.
“A Computational Study of the Hydrated Sulfur Complex H2S(H2O)n for n=1-4 waters with the Gaussian-d and Compete Basis Set-QB3 Model Chemistries,” Daniel B. Tomb,* Timothy M. Evans,* Karl N. Kirschner, and George C. Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by D. Tomb.
“A CBS-QB3 Study of the Effects of Water Clusters on Carbon Dioxide,” David S. Hamilton,* Gregg M. Hartt,* Daniel B. Tomb,* Karl N. Kirschner, and George C. Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by D. Hamilton.
“Using Low Energy Conformers to Create Families for Designing a Pharmacophore,” Amanda Salisburg,* Katrina Lexa,* Karl Kirschner, and George C. Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by A. Salisburg.
“Generalized Born Molecular Dynamics and MMPBSA Analysis of the α-Estrogen Receptor bound to Raloxifene, Tamoxifen and Estradiol,” Amy Barrows,* Karilyn Larkin,* Karl Kirschner, and George C. Shields at the Fourth MERCURY Conference in Computational Chemistry, July 2005, Clinton, NY. Presented by A. Barrows.
“Finding Energy Minima for a Breast Cancer Inhibiting Peptide derived from AFP,” Katrina W. Lexa,* Karl N. Kirschner, and George C. Shields at the 45th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, March 2005, St. Simons Island, GA. Presented by K. Lexa, who won the most outstanding undergraduate poster award.
“Structures, Thermodynamics, and Abundances of Neutral and Ionic Clusters in the Atmosphere,” Meghan E. Dunn,* Frank C. Pickard IV,* Karl N. Kirschner, and George C. Shields at the 45th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, March 2005, St. Simons Island, GA. Presented by M. Dunn.
“A Dynamics Study on the Diffusion of Water Through Pristine and Molecularly Altered Nanotubes,” Ashley A. Deline,* Meghan E. Dunn,* and Karl N. Kirschner, at the 45th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, March 2005, St. Simons Island, GA. Presented by K. Kirschner
“Investigation of Atmospherically Relevant Sulfur Species Complexed with Small Water Clusters,” Timothy M. Evans,* Gregory M. Hartt,* Daniel B. Tomb,* Karl N. Kirschner, and George C. Shields at the 45th International Symposium on Atomic, Molecular, Biophysical, and Condensed Matter Theory, March 2005, St. Simons Island, GA. Presented by T. Evans.
“Global Search for Minimum Energy (H2O)n Clusters, n=3-5,” Mary Beth Day,* Karl N. Kirschner, and George C. Shields at the Third MERCURY Conference in Computational Chemistry, July 2004, Clinton, NY. Presented by M. Day.
“Thermodynamics of forming water clusters at various temperatures and pressures using G2, G3, CBS-QB3, & CBS-APNO model chemistries; Implications for Atmospheric Chemistry,” Meghan E. Dunn,* Emma K. Pokon,* Karl N. Kirschner, and George C. Shields at the Third MERCURY Conference in Computational Chemistry, July 2004, Clinton, NY. Presented by M. Dunn.
“Structures of Carbonyl Sulfide(OCS)-Water Cluster Complexes and Water Cluster Catalysis of Atmospheric OCS Reactions,” Timothy M. Evans,* Karl N. Kirschner, and George C. Shields at the Third MERCURY Conference in Computational Chemistry, July 2004, Clinton, NY. Presented by T. Evans.
“CAP-DNA Complex Binding Energies,” Matroner M. George,* Karl N. Kirschner, and George C. Shields at the Third MERCURY Conference in Computational Chemistry, July 2004, Clinton, NY. Presented by M. George.
“Inhibition of biological compounds directed at drug design,” Amber Gillis,* Karl N. Kirschner, and George C. Shields at the Third MERCURY Conference in Computational Chemistry, July 2004, Clinton, NY. Presented by A. Gillis
“Determination of pKa Values with PBE1PBE Density Functional Theory,” Daniel Griffith,* Matthew D. Liptak,* Karl N. Kirschner, and George C. Shields at the Third MERCURY Conference in Computational Chemistry, July 2004, Clinton, NY. Presented by D. Griffith.
“Computational Study of Carbon Disulfide Oxidation with the Hydroxyl Radical and Water Monomer,” Gregory M. Hartt,* Timothy M. Evans,* Karl N. Kirschner, and George C. Shields at the Third MERCURY Conference in Computational Chemistry, July 2004, Clinton, NY. Presented by G. Hartt.
“Mutagenesis of Cocaine Catalytic Antibody 15A10 for Improved Binding to Cocaine Transition State Analog,” Philip J. Hanoian,* Karl N. Kirschner, and George C. Shields at the Third MERCURY Conference in Computational Chemistry, July 2004, Clinton, NY. Presented by P. Hanoian.
“Structural Analysis of Dimethyl Sulfide and (H2O)n for n=1-4,” Philip T. Holdredge,* Timothy M. Evans,* Karl N. Kirschner, and George C. Shields at the Third MERCURY Conference in Computational Chemistry, July 2004, Clinton, NY. Presented by P. Holdredge.
“The Free Energy of Solvation for Ions Calculated by Thermodynamic Cycles,” Chenyan Huang,* Karl N. Kirschner, and George C. Shields at the Third MERCURY Conference in Computational Chemistry, July 2004, Clinton, NY. Presented by C. Huang.
“Finding Energy Minima for a Breast Cancer Inhibiting Peptide derived from AFP,” Katrina Lexa,* Meghan E. Dunn,* Heather Michael,* Damien J. Ellens,* Karl Kirschner and George C. Shields at the Third MERCURY Conference in Computational Chemistry, July 2004, Clinton, NY. Presented by K. Lexa.
“Conformational Analysis of an AFP-derived Cyclic Peptide: cEQC,” Heather Michael,* Meghan Dunn,* Katrina Lexa* and George C. Shields at the Third MERCURY Conference in Computational Chemistry, July 2004, Clinton, NY. Presented by H. Michael.
“A Computational Study of the Thermodynamic and Kinetic Effects of Water Clusters on Hydrogen Sulfide in the Atmosphere,” Daniel B. Tomb,* Timothy M. Evans,* Karl N. Kirschner and George C. Shields at the Third MERCURY Conference in Computational Chemistry, July 2004, Clinton, NY. Presented by D. Tomb.
* Indicates undergraduate author/advisee.
Senior Thesis
Cecilia Disney – Chemistry Thesis: “Computational Drug Design Applied Towards the Treatment of Human African Trypanosomiasis” Hamilton College, expected graduation spring 2007.
James McConnell – Chemistry Thesis: “Force Field Parameterization via the Partition Function” Hamilton College, expected spring graduation 2007.
Meghan Dunn – Chemistry Thesis: “Hydrated N2 and O2 Complexes: Implications of Weakly Bound Species in Atmospheric Chemistry" Hamilton College, 2006. Currently pursuing a Ph.D. in Chemistry, University of Colorado.
Karilyn Larkin – Chemistry Thesis: “Analyses of the Affinity of Raloxifene and its Derivatives to the α-Estrogen Receptor Ligand Binding Domain: A Model for Drug Design" Hamilton College, 2006. Currently pursuing an M.D., Albany Medical School, NY.
Ashley Deline – Chemistry Thesis: “Molecular Dynamic Simulations of a Glycoform and its Constituent Parts Related to Rheumatoid Arthritis“ Hamilton College, 2006. Currently employed by the Fred Hutchinson Cancer Center, Seattle, WA.
Valery Danilack – Biochemistry Thesis: “Testing the Estrogen Receptor Binding Affinity of Pharmacophores of Raloxifene in Search of Anti-Breast Cancer Drugs" Hamilton College, 2006. Currently pursuing an M.S. in Public Health, Yale University.
Tim Evans – Chemistry Thesis: “Hydrated Complexes of Atmospheric Sulfur Species,” Hamilton College, 2005. Currently pursuing an M.S. in Mathematics, New York University.
Scott Huntington – Chemistry Thesis: “Computer Aided Design of Selective Estrogen Receptor Modulators,” Hamilton College, 2005. Currently pursuing an M.D., New York University Medical School.
Katrina Lexa – Chemistry Thesis: “Conformational Analysis of Peptides: Modeling a Breast Cancer Inhibiting Peptide Derived from AFT,” Hamilton College, 2005. Currently pursuing an M.S. in Public Health and Ph.D. in Medicinal Chemistry, University of Michigan.
Frank Pickard – Chemical Physics Thesis: “The Enediyne Anticancer Antibiotics: A Study of the Bergman Cyclization Energy Barriers of Esperamicin A1,” Hamilton College, 2005. Currently pursuing a Ph.D. in Chemistry, University of Georgia.
Research Students
Three Years: Meghan Dunn ('06), Greg Hartt ('08)
Two Years: Kartina Lexa ('05), Frank Pickard ('05), Karilyn Larkin ('06), Matroner George ('07), Dan Tomb ('08), Ngoda Manongi ('08), Marco Allodi ('08), Kristin Alongi ('08), James McConnell ('08), Amanda Salisburg ('08), Jovan Livada ('08), Luke Shields (Clinton Schools)
One Year: Tim Evans ('05) Scott Huntington ('05), Ashley Deline ('06), Amber Gillis ('06), May Beth Day ('07), Sarah Felder ('07), Daniel Griffith ('07), Chenyan Huang ('07), Phil Hanoaian ('07), Philip Holredge ('08), Pragyan Pradhan ('08), Tumelano Gopolang ('08), Evan Savage ('08), Amy Barrows ('08), Greg Nizialek ('08), Katherine Alser ('09), Sharfi Farhana ('09), Alexa Ashworth ('09), Deacon Lile ('09), Amber O'Connor ('09), David Hamilton ('09), Jared Pienkos ('09), Alexa Schwarzman ('09), Rebecca Mackenzie ('09), Andrew Beyler ('10), Russell Holz ('10), Tom Morrell ('10)
Students National Awards
Goldwater Scholars: Marco Allodi ('08) awarded in 2007, Kristin Alongi ('08) awarded in 2008, Daniel R. Griffith ('07) awarded in 2006, Mary Beth Day ('07) awarded in 2005, Meghan Dunn ('06) awarded in 2005
Fulbright Scholar: Daniel R. Griffith ('07) awarded in 2007
American Chemical Society
Sigma Xi, The Scientific Research Society (1994-present)
Richter Apprentice Scholar: Richter Memorial Trust as a Richter Apprentice Scholar (LFC 1991)
Hirsch Scholarship (LFC 1991-1995)
Gardner Brown Scholarship (LFC 1992-1995)
First Stafford Scholar chosen for outstanding research in chemistry (LFC 1994-1995)
Pearl E. Pauker Award for Scientific Excellence (LFC 1994)
Graphical design chosen for the 2004 covers of the Carbohydrate Research journal (UGA 2003) [JPG]
Reviewer for the Journal of Physical Chemistry and Carbohydrate Research.
Assisted in hosting the MERCURY (Molecular Education and Research Consortium in Undergraduate computational chemistRY) Conference at Hamilton College (Summers, 2004-2006)
Mentored and co-supervised a 10 week undergraduate computational research program at Hamilton College (Summers, 2004, 2005 (20 students), & 2006 (22 students))
Mentored National Science Foundation Science Talent Expansion Program students in computational research (Summers, 2004-2006)
George C. Shields, Winslow Professor and Chair, Department of Chemistry, Hamilton College, Clinton, NY.
Peter Albersheim, Co-director, Founder, and Distinguished Research Professor of the Complex Carbohydrate Research Center, University of Georgia, Athens, GA.
Thomas Andersen, Professor and Assistant Dean, Albany Medical College, Albany, NY.
Robert J. Woods, Associate Professor at the Complex Carbohydrate Research Center, University of Georgia, Athens, GA.
Veronica Vaida, Professor and Chair, Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO.
Theodore Dibble, Associate Professor in the Department of Chemistry, SUNY-ESF, Syracuse, NY.
Klaus Jurkschat, Professor, Department of Chemistry, Universität Dortmund, Dortmund, Germany.
Fight the Stigma, Mental Health Benefit Auction, Athens, GA, 30602 - 1 piece donated each year (2000-2001)
Athens Clarke Heritage Foundation Benefit Auction, Athens, GA, 30602 - 1 piece donated (2002)
Complex Carbohydrate Research Center, Athens, GA,60602 - 2 permanent pieces donated (2003)
Juried Show, Kirkland Art Center, Clinton NY 13323 (2005)
Juried Show, Munson William Proctor Art Institute, Side Walk Art Show, Utica, NY 13502 (2005)
Dr. George C. Shields. Department of Chemistry, Hamilton College, Clinton, NY 13323. Department Chair. 315-859-4728 ( gshields@hamilton.edu )
Dr. Robert J. Woods. Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602. 706-542-4454 (rwoods@ccrc.uga.edu )
Dr. J. Phillip Bowen. Department of Chemistry and Biochemistry, University of North Carolina, Greensboro, NC 27402 336-334-4257 (jpbowen@uncg.edu )
Dr. Norman L. Allinger. Department of Chemistry, Computational Center for Molecular Structure and Design, University of Georgia, Athens, GA 30602. Founder and editor of the Journal of Computational Chemistry. 706-542-2043 (allinger@chem.uga.edu )
Dr. Peter Albersheim, Co-director, Founder, and Distinguished Research Professor of the Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602. 706-542-4404 ( palbersh@ccrc.uga.edu )
Karl Kirschner
Chemistry Department
Center
for Molecular Design, Co-Director
Hamilton College
198 College
Hill Road
Clinton, NY 13323 USA
315-859-4742 (office)
315-859-4807 (fax)
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