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.
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 Edition44, 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 Engineering4, 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; 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 Letters380, 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 Preprints44, 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 America99, 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
Chemistry90, 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 A103, 10009 (1999).
R.J. Doerksen; A.J. Thakkar "Structures, vibrational frequencies
and polarizabilities of
diazaborinines, triazadiborinines, azaboroles, and oxazaboroles,"
Journal of Physical Chemistry A103,
2141 (1999).
R.J. Doerksen; A.J. Thakkar; T. Koga; M. Hayashi "Geometries and
multipole moments of AlH4-,
SiH4, PH3, H2S and HCl,"
Theochem488, 217 (1999).
R.J. Doerksen; A.J. Thakkar "Azaborinines: structures,
vibrational frequencies and
polarizabilities,"
Journal of Physical Chemistry A102,
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 Chemistry60,
1633 (1996).
N. El-Bakali Kassimi; R.J. Doerksen; A.J. Thakkar
"Polarizabilities of oxazoles: ab initio
calculations and simple models,"
Journal of Physical Chemistry100, 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 Chemistry99, 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.
