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• 2005
• 2004
• 2003
• 2002
• 2001
• 2000
• 1999
• 1998
• before 1997
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PriorPublications
Recent publications

Papers, Thesis, and Invited and Conference Presentations Prior to 2006

Please contact me if you would like to receive a .pdf file of any of my papers or thesis.

    2005
  • • A.H. Xie; P. Sivaprakasam; R.J. Doerksen "CoMFA studies of antimalarial compounds based on 2,5-diaminobenzophenone scaffold." 14th Conference on Current Trends in Computational Chemistry, Jackson, MS, Nov. 2005.
  • • P. Sivaprakasam; P.R. Daga; A.H. Xie; R.J. Doerksen "Probing the physico-chemical and structural requirements among 3-anilino-4-arylmaleimides for GSK-3 inhibitory activity enhancement through 2D and 3D QSAR investigations." 14th Conference on Current Trends in Computational Chemistry, Jackson, MS, Nov. 2005.
  • • R.J. Doerksen "Novel internally hydrogen bonded peptidomimetic antimicrobials: Insights from computational modeling." Department of Chemistry, Mississippi State University, Mississippi, Starkville, MS, October 21, 2005.
  • • H. Tang; R.J. Doerksen; G.N. Tew "Synthesis of urea oligomers and their antibacterial activity," Chemical Communications, 1537-1539 (2005).
  • • R.J. Doerksen "Computational approach to the role of hydrogen bonds in controlling the conformation of antimicrobial oligomers." Division of Physical Chemistry: Poster Session 229th American Chemical Society National Meeting, San Diego, CA, Wednesday, March 16, 2005, 7:00 p.m. and in the Sci-Mix poster session, Monday, March 14, 2005, 8:00 p.m.

    2004
  • • R.J. Doerksen "Computational approach to controlling the conformation of antimicrobial oligomers." 13th Conference on Current Trends in Computational Chemistry, Jackson, MS, November 12, 2004.
  • • R.J. Doerksen "Controlling the conformation of novel arylamide and other nontoxic antimicrobial oligomers." Department of Chemistry and Biochemistry, University of Mississippi, University, MS, October 7, 2004.
  • • R.J. Doerksen; B. Chen; D. Liu; G.N. Tew; W.F. DeGrado; M.L. Klein ""Controlling the conformation of arylamides: Computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers," Chemistry: A European Journal 10, 5008-5016 (2004).
  • • D. Liu; S. Choi; B. Chen; R.J. Doerksen; D.J. Clements; J.D. Winkler; M.L. Klein; W.F. DeGrado "Nontoxic membrane-active antimicrobial arylamide oligomers," Angewandte Chemie International Edition 44, 1158-1162 (2004). Also in Angew. Chemie 116, 1178-1182 (2004). Cover article on February 20, 2004.
  • • R.J. Doerksen; B. Chen; D. Liu; W.F. DeGrado; M.L. Klein "Joint computational-experimental approach to effective and selective antimicrobial oligomers." Division of Computers in Chemistry: Interplay between computer modeling and experiments on complex biological systems, 227th American Chemical Society National Meeting, Anaheim, CA, March 30, 2004, 9:10 a.m.
  • • R.J. Doerksen; B. Chen; J. Yuan; J.D. Winkler; M.L. Klein "Novel conformationally-constrained 8-helical ß-peptides" Division of Organic Chemistry: Proteins, Peptides, Amino Acids, and Nucleotides, 227th American Chemical Society National Meeting, Anaheim, CA, March 30, 2004, 3:00 p.m.
  • • R.J. Doerksen; V.J. Steeves; A.J. Thakkar "Bond orders and polarizabilities as measures of aromaticity: Azines, azoles, oxazoles, and thiazoles," Special Issue on Polarizabilities and Hyperpolarizabilities Journal of Computational Methods in Science and Engineering 4, 427-438 (2004). Also appears in "Computational Aspects of Electric Polarizability Calculations: Atoms, Molecules and Clusters," G Maroulis (Editor) IOS Press, Amsterdam, 2004. ISBN: 158603495
  • • R.J. Doerksen "A composite computational approach for design of nontoxic antimicrobial oligomers." Université de Montréal, Department of Chemistry, Montréal, Canada, Mar. 2, 2004.
  • • R.J. Doerksen "A composite computational approach for design of nontoxic antimicrobial oligomers." University of Missouri, St. Louis, Department of Chemistry & Biochemistry, St. Louis, MO, Feb. 16, 2004.
  • • R.J. Doerksen "A composite computational approach for design of nontoxic antimicrobial oligomers." Yeshiva University, Albert Einstein College of Medicine, Department of Physiology & Biophysics, Bronx, NY, Jan. 29, 2004.
  • • R.J. Doerksen "A composite computational approach for design of nontoxic antimicrobial oligomers." University of Mississippi, Department of Medicinal Chemistry, University, MS, Jan. 26, 2004.
  • • R.J. Doerksen "A composite computational approach for design of nontoxic antimicrobial oligomers." Illinois Institute of Technology, Department of Biological, Chemical, and Physical Sciences, Chicago, IL, Jan. 21, 2004.
  • • R.J. Doerksen "A composite computational approach for design of nontoxic antimicrobial oligomers." University of Cincinnati, Department of Chemistry, Cincinnati, OH, Jan. 13, 2004.

    2003
  • • R.J. Doerksen "A composite computational approach for design of nontoxic antimicrobial oligomers." Virginia Commonwealth University, Department of Chemistry, Richmond, VA, Dec. 15, 2003.
  • • R.J. Doerksen "Computational modeling of antimicrobials." Colgate-Palmolive, Piscataway, NJ, Nov. 20, 2003.
  • • R.J. Doerksen; B. Chen; J. Yuan; J.D. Winkler; M.L. Klein "Novel conformationally-constrained beta-peptides characterized by 1H NMR chemical shifts," Chemical Communications, 2534 (2003).
  • • R.J. Doerksen; B. Chen; M.L. Klein "Intramolecular hydrogen bonds: Ab initio Car-Parrinello simulations of arylamide torsions," Chemical Physics Letters 380, 150 (2003).
  • • R.J. Doerksen; B. Chen; D. Liu; W.F. DeGrado; M.L. Klein "Conformational analysis of the ring-N torsion of De Novo antimicrobial arylamide polymers." 14th Biennial Philadelphia Organic Chemists Club' Day, Philadelphia, PA, May, 2003.
  • • RJ Doerksen; B Chen; WF DeGrado; ML Klein "Methods, systems, and computer program products for computational analysis and design of amphiphilic polymers." U.S. Provisional Application Ser. No. 60/383,884 filed on May 28, 2003. Licensed by biotech start-up company, Polymedix (polymedix.com).
    United States Patent Application 20040107056, Kind Code A1, June 3, 2004
    World Patent Application, 2004
  • • R.J. Doerksen; B. Chen; D. Liu; W.F. DeGrado; M.L. Klein "Designed intramolecular hydrogen bonds stabilizing antimicrobial amphiphilic polymers." Polymer Division: Polymer Design Using Non-covalent Methods 225th American Chemical Society National Meeting, New Orleans, LA, March, 2003. Also in Polymer Preprints 44, 598-599 (2003).
  • • R.J. Doerksen; B. Chen; W.F. DeGrado; M.L. Klein "Accurate energetics for in-plane vs out-of-plane phenol, thiophenol, anisole, and thioanisole." Division of Computers in Chemistry General Contributions: Quantum Chemistry, 225th American Chemical Society National Meeting, New Orleans, LA, March, 2003.
  • • D. Liu; J. Yuan; B. Chen; R.J. Doerksen; Sungwok Choi, M.L. Klein; J.D. Winkler; W.F. DeGrado "De novo design and synthesis of antimicrobial oligo-amino acid-salicylamide." Division of Medicinal Chemistry: General Oral Session, 225th American Chemical Society National Meeting, New Orleans, LA, March, 2003.
  • • D. Liu; B. Chen; R.J. Doerksen; M.L. Klein; W.F. DeGrado "De novo design and synthesis of nonhemolytic biomimetic antimicrobial polymers." Division of Medicinal Chemistry: Poster Session, 225th American Chemical Society National Meeting, New Orleans, LA, March, 2003.

    2002
  • • B. Chen; R.J. Doerksen; M.L. Klein "Computational design of biomimetic materials." Applying Computational Chemistry and Molecular Simulations: Functionalities Session, American Institute of Chemical Engineers 2002 Annual Meeting, Indianapolis, IN, November, 2002.
  • • B. Chen; R.J. Doerksen; M.L. Klein "Computational design of biomimetic materials." Division of Computers in Chemistry General Session, 224th American Chemical Society National Meeting, Boston, MA, August, 2002.
  • • G.N. Tew; D. Liu; B. Chen; R.J. Doerksen; J. Kaplan; P.J. Carroll; M.L. Klein; W.F. DeGrado "De novo design of biomimetic antimicrobial polymers," Proceedings of the National Academy of Sciences of the United States of America 99, 5110 (2002).
  • • R.J. Doerksen "Accurate density-functional theory torsional potentials for de novo amphiphilic antimicrobial peptide design." Taiwan National Health Research Institutes, Division of Biotechnology and Pharmaceutical Research, Taipei, Taiwan, March 20, 2002.
  • • R.J. Doerksen; A.J. Thakkar " Bond orders in heteroaromatic rings ," Per-Oliv Lowdin Memorial Issue International Journal of Quantum Chemistry 90, 534 (2002).

    2001
  • • R.J. Doerksen; M.L. Klein "Accurate torsions and conformations around amide bonds." 14th Canadian Symposium on Theoretical Chemistry , Ottawa, ON, Canada, August 2001.
  • • R.J. Doerksen "Theoretical insight into the reaction of C + C2H2 from ab initio molecular dynamics trajectories and transition state structures." Sandia National Laboratory, Livermore, CA, January 2001.
  • • R.J. Doerksen "Theoretical insight into the reaction of C(3P) + C2H2." Department of Chemistry, University of Arizona, Tucson, AZ, January 2001.

    2000
  • • R.J. Doerksen; R.I. Kaiser; Y.T. Lee; M. Head-Gordon "Theoretical Studies on the Crossed-Beam Reaction of C(3Pj) with acetylene." 16th Annual Symposium on Chemical Physics , University of Waterloo, Waterloo, ON, Canada, November 2000.
  • • R.J. Doerksen; N. El-Bakali Kassimi; V.J. Steeves; A.J. Thakkar "Bond orders and polarizabilities as measures of aromaticity: Azines, azoles, oxazoles, and thiazoles." Conference on Chemical Bonding: State of the art in conceptual quantum chemistry, La Colle-sur-Loup, France, June 2000.
  • • R.J. Doerksen; M. Head-Gordon; R.I. Kaiser; Y.T. Lee "Trajectories on the potential energy surface of C(3Pj) reacting with acetylene." Division of Physical Chemistry session on "Potential Energy Surfaces, From Polyatomics to Macromolecules," 219th American Chemical Society National Meeting, San Francisco, CA, March, 2000.
  • • R.J. Doerksen "Theoretical insight into the reaction of C(3Pj) with acetylene." Department of Chemistry, National Changhua University of Education, Changhua, Taiwan, February 16, 2000.
  • • R.J. Doerksen; M. Head-Gordon; R.I. Kaiser; Y.T. Lee "Theoretical insight into the reaction of C(3Pj) with acetylene: Transition state structures of triplet C3H2, effects of deuteration, and dynamics of the reaction." Pitzer Memorial Symposium on Theoretical Chemistry, Berkeley, CA, January 2000.

    1999
  • • R.J. Doerksen; A.J. Thakkar "Quadrupole and octopole moments of heteroaromatic rings," Journal of Physical Chemistry A 103, 10009 (1999).
  • • R.J. Doerksen; A.J. Thakkar "Structures, vibrational frequencies and polarizabilities of diazaborinines, triazadiborinines, azaboroles, and oxazaboroles," Journal of Physical Chemistry A 103, 2141 (1999).
  • • R.J. Doerksen; A.J. Thakkar; T. Koga; M. Hayashi "Geometries and multipole moments of AlH4-, SiH4, PH3, H2S and HCl," Theochem 488, 217 (1999).

    1998
  • • R.J. Doerksen "Geometries, polarizabilities and aromaticity of ring molecules", Ph.D. Thesis, University of New Brunswick, (1998).
  • • R.J. Doerksen; A.J. Thakkar "Azaborinines: structures, vibrational frequencies and polarizabilities," Journal of Physical Chemistry A 102, 4679 (1998).
  • • R.J. Doerksen; A.J. Thakkar "Novel heteroaromatic boron-nitrogen monocycles: Geometries and stabilities." Division of Physical Chemistry, 216th American Chemical Society National Meeting, Boston, MA, August 1998.
  • • R.J. Doerksen; A.J. Thakkar "Electron-correlated polarizabilities of 87 five- and six-membered-ring azaboracycles." 13th Canadian Symposium on Theoretical Chemistry, Vancouver, BC, Canada, August 1998.

    1997
  • • R.J. Doerksen; N. El-Bakali Kassimi; V.J. Steeves; A.J. Thakkar "Quantitative aromaticity scales derived from accurate polarizabilities and bond orders." 13th Annual Symposium on Chemical Physics, University of Waterloo, Waterloo, ON, Canada, October 1997.

    1996
  • • R.J. Doerksen; A.J. Thakkar "Polarizabilities of heteroaromatic molecules: azines revisited," International Journal of Quantum Chemistry 60, 1633 (1996).
  • • N. El-Bakali Kassimi; R.J. Doerksen; A.J. Thakkar "Polarizabilities of oxazoles: ab initio calculations and simple models," Journal of Physical Chemistry 100, 8752 (1996).
  • • R.J. Doerksen; A.J. Thakkar "Confrontation between theory and experiment for properties of aromatic molecules." 12th Annual Symposium on Chemical Physics, University of Waterloo, Waterloo, ON, Canada, November 1996.
  • • R.J. Doerksen; A.J. Thakkar "Additive models of polarizability for heteroaromatic ring molecules." 36th Sanibel Symposium, St. Augustine, FL, February 1996.

    1995
  • • N. El-Bakali Kassimi; R.J. Doerksen; A.J. Thakkar "Polarizabilities of aromatic five-membered rings: azoles," Journal of Physical Chemistry 99, 12790 (1995).
  • • R.J. Doerksen; N. El-Bakali Kassimi; A.J. Thakkar "Ab initio computations and additive models for the polarizabilities of aromatic five-membered rings: azoles." 12th Canadian Symposium on Theoretical Chemistry, Fredericton, NB, Canada, August 1995.
  • • N. El-Bakali Kassimi; R.J. Doerksen; A.J. Thakkar "Oxazoles: ab initio structures, polarizabilities, and additive models." 12th Canadian Symposium on Theoretical Chemistry, Fredericton, NB, Canada, August 1995.

    1994
  • • R.J. Doerksen; A.J. Thakkar "Uncoupled Hartree-Fock calculations of polarizabilities of heteroaromatic molecules: azines and azoles." Chemcon 94, Fredericton, NB, Canada, July 1994.
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