COMP Programming
Fall 2000 National Meeting
Washington DC
R. A. Wheeler, Program Chair
SOCIAL EVENT:
Poster Session/Social Hour, Tue
BUSINESS MEETING: Sat
Sunday Morning
Current Status of Molecular Force Fields
Parameterization and validation of the AM1-BCC charge model for organic small molecules.
A. Jakalian, D. Jack, C.I. Bayly
Extending the OPLS-AA force field for ligand functionality.
T.A. Halgren, R.B. Murphy, W.L. Jorgensen, R.A. Friesner
Toward a spectroscopically determined polarizable force field (SDPFF) for proteins.
K. Palmo, B. Mannfors, N.G. Mirkin, W. Qian, S. Krimm
Development of the TraPPE force field for fluid-phase equilibrium calculations.
B. Chen, J.J. Potoff, C.D. Wick, J.M. Stubbs, J.I. Siepmann
Molecular mechanics can teach us something about chemistry.
N.L. Allinger
QSAR In Vivo
Enhancement of binary QSAR analysis by GA-based variable selection method.
H. Gao, M.S. Lajiness, J.H. VanDrie
Wavelet representations of molecular electronic properties: Applications in ADME, QSPR, and QSAR.
C.M. Breneman, N. Sukumar, K.P. Bennett, M.J. Embrechts, M. Sundling, L. Lockwood
Chemically biased scaling of molecular descriptors: A general method for defining druglike libraries.
C.H. Reynolds, R. Druker, L.B. Pfahler
Toward a spectroscopically determined polarizable force field (SDPFF) for proteins.
K. Palmo, B. Mannfors, N.G. Mirkin, W. Qian, S.Krimm
Choosing SAR for QSAR.
A. Tropsha, A. Golbraikh, M. Shen, G. Fels, A. Dietrich
Development of the TraPPE force field for fluid-phase equilibrium calculations.
B. Chen, J.J. Potoff, C.D. Wick, J.M. Stubbs, J.I. Siepmann
Trials and tribulations of developing predictive models for ADME.
M.G. Bures, I. Lico, Y.C. Martin
Molecular mechanics can teach us something about chemistry.
N.L. Allinger
Sunday Afternoon
Current Status of Molecular Force Fields
Comparing available force fields used in molecular dynamics simulations of solvated nucleic acid duplexes.
T.E. Cheatham III
QSAR In Vivo
QSAR: From humans to insects and back again.
C. Hansch
(Q)SAR study on the metabolic stability of steroidal androgens.
R. Bursi, M. deGooyer, A. Grootenhuis
Aquatic toxicity mode-of-action studies applied to QSAR development.
P.K. Schmieder, S.P. Bradbury, C. Russom, S. Broderius
Prediction of tetrahymena acute toxicity for a diverse set of organic compounds from molecular structure.
J.R. Serra, K.L.E. Kaiser, P.C. Jurs
Classification of multidrug resistance reversal agents from molecular structure.
G.A. Bakken, P.C. Jurs
COMPARE: A Web-accessible tool for investigating mechanisms of cell growth inhibition.
D.W. Zaharevitz, S.L. Holbeck, C. Bowerman, P.A. Svetlik
Monday Moring
Computational ADME
Computational approaches for prediction of human in vitro intrinsic clearance.
S. Ekins, R.S. Obach
Review of computational tools for toxicity and metabolism detection.
N. Greene
Computational methods for the prediction of intestinal drug permeability.
P. Stenberg, U. Norinder, K. Luthman, P. Artursson
High-throughput prediction of physicochemical and biochemical processes from structure, using calculated Abraham solvation descriptors.
M.H. Abraham
New approach to the evaluation of bioavailability of drugs.
G. Klopman, L. Stefan, R.D. Saiakhov
Current Status of Molecular Force Fields
CPEFF: A DFT-based many-body force field for molecular simulations.
D.M. York
Development of a polarizable protein force field.
R.A. Friesner
Inter- and intramolecular-interaction energies and nonadditive effects: A parallel ab initio and polarizable molecular mechanics investigation.
N. Gresh
Molecular dynamics simulations with polarizable potential models.
L.X. Dang
Treatment of polarization in large molecular systems.
S.J. Stuart, L. Hu Computational ADME - PM
Monday Afternoon
Computational ADME
Computational modeling of drug solubility.
P.H. Lee, G.M. Maggiora
Simultaneous simulation of diffusion and partitioning of drug in biological systems using the finite element method.
P.J. Missel
Qualitative structure-pharmacokinetic modeling: In silico approaches to protein binding.
S.R. Johnson, E.P. Chen
Novel linear regression model for the prediction of aqueous solubility of drug molecules employing fundamental descriptors.
S.F. Semus
Prediction of ADME properties for drug discovery.
W.J. Egan, K.M. Merz Jr.
Current Status of Molecular Force Fields
Inorganic molecular mechanics and conformational/configurational searching methods.
M. Zimmer
Genetic algorithms for development of transition-metal force fields.
J. Deng, W. Fu Jr., T. Cundari
New bond-dissociating force fields for describing reactions and phase transitions.
W.A. Goddard III, A. Strachan, A.C.T. vanDuin, T. Çagin, J. Che, Y. Qi, D. Chakraborty, S. Dasgupta
Potential energy surface from distortion of Co2+ ligands.
A.M. Schmiedekamp, M.D. Ryan
Ligand field theory in the new millennium: Is there life after DFT?
R.J. Deeth
Valence bond concepts applied to a molecular mechanics description of transition metals with p-bonds.
T.K. Firman, C.R. Landis
Monday Evening
Sci-Mix
Prediction of glycine/NMDA receptor antagonist inhibition from molecular structure.
S.J. Patankar, P.C. Jurs
Prediction of ion mobilities of polypeptides from molecular structure.
P.D. Mosier, P.C. Jurs, A.E. Counterman, D.E.Clemmer
ATTILA: An efficient method for the conformation searching of cyclic molecules.
C-T. Teo, J.M. Goodman
Molecular modeling studies of the interactions between protein kinase C and its ligands.
S-B. Rong, L. Zhao, L. Qiao, S. Wang, A.P. Kozikowski
Convention Center
Computational evidence for two HIV-1 integrase inhibitor interaction sites.
A.L. Parrill, H. Yuan, C. Turner, G.B. Ray
S16F mutant effect on the binding of human SRY protein to DNA from molecular dynamics simulations.
Y. Tang, L. Nilsson
Chorismate mutase reactivity: An ab initio study.
S.E. Worthington, A.E. Roitberg, M. Krauss
Mn-salen catalyzed epoxidation of olefins: Ligand effects.
J. El-Bahraoui, O.G. Wiest, D. Plattner, D. Feichtinger
LHASA, the next step: A paradigm shift from user-directed CAOS to noninteractive generation of optimal retrosynthetic routes using
deterministic search.
C.A. Marby, R. Chen, A.P. Sukharevsky, A.K. Long
Competing [2+2+2] and electrocyclic mechanisms in the ring-opening reactions of cyclohexeno- and benzofused tris(cyclobuteno)cyclohexanes.
D. Sawicka, K.N. Houk, J. Lehmann, K.P.C. Vollhardt
Nontraditional hydrogen bonding in the boron Lewis acid-catalyzed Diels-Alder reaction.
S. Kong, J.D. Evanseck
Atoms in molecules (AIM) studies of nonclassical carbocations.
L.R. Schmitz, T. Dean
Are hydrogen bonds covalent or electrostatic? A molecular orbital comparison of molecules in electric fields and H-bonding environments.
J.J. Dannenberg, A. Masunov, L. Haskamp
Tuesday Morning
Materials Discovery
Charge carriers in polythiophenes.
T. Clark, T. Schindler
Concepts and modeling approaches in conjugated materials.
D.S. Dudis, A.T. Yeates
Polaronic and bipolaronic enhancement of second hyperpolarizabilities in dithienyl polyenes from ab initio quantum methods.
S. Trohalaki, R. Zellmer, R. Pachter
Molecular simulation of gas diffusivity, solubility, and free volume in inorganic polymers.
J.R. Fried, B. Li, N. Hu
Gun tube erosion: Theoretical studies.
M.M. Hurley, C.F. Chabalowski, G.H. Lushington, D. Sorescu
Theoretical studies of the catalytic decomposition of gases on metallic surfaces.
W.J. Welsh, P. Wolohan, R.M. Friedman, J. Ebner
Molecular Connectivity
Development of molecular connectivity and the role of creativity.
L.H. Hall, L.B. Kier
Meaning of molecular connectivity and the dynamic simulation of bond encounters.
L.B. Kier, L.H. Hall
On the variable connectivity index and other variable molecular descriptors.
M. Randic
Trends and possibilities for future developments of topological indices.
A.T. Balaban, S.C. Basak
Tuesday Afternoon
Emerging Technologies
Origin of binding selectivity for celecoxib analogs with COX-1 and COX-2 from combined docking and Monte Carlo simulations.
M.L. PlountPrice, W.L. Jorgensen
Getting 1.4 Å C-a RMSD structure predictions on two small proteins with molecular mechanics.
M.R. Lee, P.A. Kollman
Novel stochastic algorithm for structure predictions in proteins and for biomolecular interactions.
A. Goldblum, M. Glick
Application of the "shape signatures" approach to ligand- and receptor-based drug design.
R.J. Zauhar, W.J. Welsh
Novel approach to improve group contribution predictions based on modern computational chemistry.
S-T. Lin, S.I. Sandler
Design and evaluation of combinatorial libraries using protein crystal structures: Methods and applications to drug discovery.
T.F. Hendrickson, F. Chan, S. Reich, T.O. Johnson
New representations of molecular chirality: Application to the prediction of enantiomeric selectivity in chromatography and chemical reactions.
J.M. Aires-de-Sousa, J. Gasteiger
Materials Discovery
Chemical approaches to hard magnetic nanoparticles and nanocrystal superlattices.
S. Sun, C.B. Murray, D. Weller, L. Folks, A. Moser
Cyanogels: A novel hydrogel system for the sol-gel synthesis of metal oxide solid-state materials.
J.T. Willson, A.B. Bocarsly
Dimensional changes as a function of charge injection for carbon nanotubes.
G. Sun, M. Kertesz, J. Kurti, R.H. Baughman
Fabrication, characterization, and optical properties of ultrathin dendrimer nanocomposite multilayers containing nanosized metallic silver domains in well-structured organic films.
S.M. Redmond, S.C. Rand, H. Tang, D.C. Martin, P. Balogh, L. Balogh
First demonstration of nanoporous palladium superlattices and their novel chemoselectivity.
J. Cheon, H.Y. Lee, H.K. Kang, S.Y. Ryou
New energy-rich molecular systems: From N10 to N60.
M.R. Manaa
Synthesis, characterization photophysics, and organic LED applications of mer-tris ortho-metallated Ir(III) complexes.
S.A. Lamansky, P.I. Djurovich, A. Kershaw, S.A. Balybine, H-E. Lee, M.E. Thompson
Tuesday Evening
Poster Session
Clustering of JP-8 chemicals using structure spaces and property spaces: A computational approach.
D. Mills, S.C. Basak, G.D. Grunwald, B.D. Gute, J. Riviere
Hierarchical clustering of psoralen derivatives using topological invariants: A strategy for molecular design.
D. Mills, S.C. Basak, B.D. Gute, A.T. Balaban, G.D. Grunwald, K. Basak
Retro-regression: A novel variant of multivariate regression analysis.
M. Randic
Selection of molecular similarity methods: A case study examining five structure spaces.
B.D. Gute, G.D. Grunwald, D. Mills, S.C. Basak
Use of variable connectivity indices on biological molecules.
D. Mills, M. Randic, S.C. Basak
High quality of property predictions by Molconn-Z and artificial neural network modeling.
M.E. Parham, L.H. Hall, L.B. Kier
Prediction of surface tension, viscosity, and electrical conductivity of organic solvents from molecular structure.
G.W. Kauffman, P.C. Jurs
Prediction of glycine/NMDA receptor antagonist inhibition from molecular structure.
S.J. Patankar, P.C. Jurs
Prediction of ion mobilities of polypeptides from molecular structure.
P.D. Mosier, P.C. Jurs, A.E. Counterman, D.E. Clemmer
Nonbonded interactions primarily determine molecular geometry.
R.F. See, A.D. Dutoi, K.W. McConnell, R.M. Naylor
Computational study of the rotamers of propylcyclohexane.
F. Freeman, M.L. Kasner, M. Yokota, C. Bray, W.J. Hehre
Computational study of the mechanism of tetrahydro-2H-pyran (THP) ring reversion.
F. Freeman, M.L. Kasner, W.J. Hehre
Further development and application of NAMFIS: NMR analysis of molecular flexibility in solution.
B. Cornett, N. Nevins, D.C. Liotta, J.P. Snyder
Conformational studies of methyl 3-O-methyl-a-D-arabinofuranoside: Toward a method for studying the conformational flexibility of oligofuranosides.
J.B. Houseknecht, P.R. McCarren, T.L. Lowary, C.M. Hadad
Ab initio investigations into the conformational preferences of both methyl 4a-carba-D-arabinofuranosides.
C.S. Callam, T.L. Lowary, C.M. Hadad
ATTILA: An efficient method for the conformation searching of cyclic molecules.
C-T. Teo, J.M. Goodman
Vibrational structure of styrene using a Hessian-biased force field method.
P.M. Hare, H-H. Tsai, M.C. Simpson
Hessian-biased force field study of the vibrational frequencies of cis- and trans-stilbenes.
H-H. Tsai, M.C. Simpson
Hessian-biased force field study of the vibrational structure of Ni-porphine.
M.C. Simpson, H-H. Tsai
Fragment vibrational analysis and its application to selected electron donor-acceptor complexes.
R.A. Wheeler, C. Matthaeus
Optimization of Lennard-Jones parameters for amines and their application in free energy of solvation calculations.
I-J. Chen, A.D. MacKerell Jr.
Benchmarking potential energy models against bulk properties for simulations of bismuth clusters.
D. Coluccio, R.Q. Topper, J.A. Kritzer, A. Deaconescu, J. delaParra Jr., S. Mikhail, K. Demuren
QSAR study and design of melatonin receptor ligands for mt1 and MT2 receptors.
E.X. Esposito, J.D. Madura, P-K. Li
Structure-based, 3-D, quantitative structure-activity relationship between paullones and CDK5/p25.
R. Gussio, C.F. McGrath, D.W. Zaharevitz, G.E. Kellogg, C. Schultz, C. Kunick, M. Leost, L. Meijer, E.A. Sausville
Design and structure: Function relationships of transforming growth factor-b mimicking peptides.
M. Shibata, Y. Chen, A.L. Kazim
Systematic investigations of flexible ligand docking methods.
Z. Zhu, Z. Hu, S. Rong, I.J. Enyedy, S. Wang
Homology model for CDK5/p25.
C.F. McGrath, R. Gussio, D.W. Zaharevitz, E.A. Sausville
Molecular modeling studies of the interactions between protein kinase C and its ligands.
S-B. Rong, L. Zhao, L. Qiao, S. Wang, A.P. Kozikowski
Analysis of CO/O2 binding in hemoglobin through modeling and database studies of the metal-ligand coordination sphere.
R.F. See, M. Goodbread
Molecular dynamics simulation of HIV protease-ligand complex with the finite difference Poisson-Baltzmann method.
R. Luo, W. Wang, P.A. Kollman
Computational evidence for two HIV-1 integrase inhibitor interaction sites.
A.L. Parrill, H. Yuan, C. Turner, G.B. Ray
Dynamic simulation of interaction between HIV-1 RNA loops and PNA-based cyclic molecules.
R. Terreux, S. Antonczak, D. Cabrol-Bass, N. Patino, R.Condom
S16F mutant effect on the binding of human SRY protein to DNA from molecular dynamics simulations.
Y. Tang, L. Nilsson
Computational modeling of antifreeze protein: Ice interactions.
P. Dalal, J.D. Madura, F. Sönnichsen
Quantum mechanical/molecular mechanical study using density functionals and the double link atom method.
D. Das, E.M. Billings, B.R. Brooks
Chorismate mutase reactivity: An ab initio study.
S.E. Worthington, A.E. Roitberg, M. Krauss
Mn-salen catalyzed epoxidation of olefins: Ligand effects.
J. El-Bahraoui, O.G. Wiest, D. Plattner, D. Feichtinger
LHASA, the next step: A paradigm shift from user-directed CAOS to noninteractive generation of optimal retrosynthetic routes using deterministic search.
C.A. Marby, R. Chen, A.P. Sukharevsky, A.K. Long
Competing [2+2+2] and electrocyclic mechanisms in the ring-opening reactions of cyclohexeno- and benzofused tris(cyclobuteno)cyclohexanes.
D. Sawicka, K.N. Houk, J. Lehmann, K.P.C. Vollhardt
Nontraditional hydrogen bonding in the boron Lewis acid-catalyzed Diels-Alder reaction.
S. Kong, J.D. Evanseck
Computational, density-functional (B3LYP) study of singlet- and triplet-state carbene cycloadditions to ethylene: Evidence of a novel mechanism.
L.M. Campos, H.L. Martinez
Accurate NMR chemical shift predictions of fullerenes.
G. Sun, M. Kertesz
Atoms in molecules (AIM) studies of nonclassical carbocations.
L.R. Schmitz, T. Dean
C-H activation by high- and low-valent transition-metal complexes.
T.R. Klinckman, T.R. Cundari, P. Wolczanski, L.M. Slaughter, T.B. Gunnoe
Molecular computing, quantum dot cellular automata might do!
J. El-Bahraoui, S. Braun-Sand, O.G. Wiest
Third-order nonlinear optical response of thiophene homologs.
K. Kiyohara, K. Kamada, K. Ohta
Theoretical study of the photoelectron spectrum of (h5-C5H5)Ni(NO).
T.F. Miller III, M.B. Hall
Are hydrogen bonds covalent or electrostatic? A molecular orbital comparison of molecules in electric fields and H-bonding environments.
J.J. Dannenberg, A. Masunov, L. Haskamp
Theoretical study of structure and stability of HCN-water clusters: HCN(H2O)n, n = 1-3.
D.E. Bacelo
Role of counterpoise correction for BSSE in the geometry optimization of the transition states.
J.J. Dannenberg, N. Kobko
Ab initio studies of the interaction of sulfur trioxide and water.
J.M. Standard, I.K. Buckner, D.H. Pulsifer
Theoretical study of a bisulfate ion adsorbed on a gold cluster.
M.D. Legault, L. Blum, D.E. Bacelo
Nitrile anions: Ab initio modeling.
V.V. Kulkarni, F.F. Fleming, J.D. Madura
Computer simulations of microstructure evolution in diamond CVD.
R.C. Brown
Molecular dynamics modeling of sorption of pesticides onto the surfaces of kaolinite.
L. Yan, G.W. Bailey
Wednesday Morning
Computational ADME
Predictive ADME models from chemical structures.
J.Q. Wu
Use of 2-D, 3-D, TAE, and wavelet coefficient descriptors (WCDs) for generating self-organizing Kohonen maps for QSAR, QSPR, and ADME analyses.
L. Lockwood Jr., C.M. Breneman, M.J. Embrechts, K.P. Bennett, F. Arciniegas
Numerical drug-fitness index.
T. Clark
Prediction of aqueous solubility of a diverse set of compounds using quantitative structure-property relationships.
A. Cheng, K.M. Merz
Molecular Connectivity
Similarity-based estimation of properties: A comparison of structure spaces.
B.D. Gute, G.D. Grunwald, D. Mills, S.C. Basak
Extending molecular connectivity: From bond connectivity to long-range contributions.
E. Estrada
Overall connectivity: A next-generation molecular connectivity.
D. Bonchev
Virtual high-throughput screening of libraries based on classification SAR.
R.D. Brown, T. Stockfish, M. Waldman, M. Hassan
Supercritical Fluid Modelling
Molecular dynamics study of sub- and supercritical water using polarizable potential model and an analysis of hydrogen-bonded clusters.
S. Okazaki
Molecular dynamics study of voids, clusters, and solutes in supercritical fluids.
R.D. Mountain
Local density augmentation in supercritical fluids: Do simulations and experiment agree?
M. Maroncelli, R. Biswas, N. Patel, W. Song
Monte Carlo simulation for solubilities of high boiling compounds in supercritical fluids.
Y. Iwai
Hydrolysis reactions in supercritical water: A computer simulation study.
R.E. Westacott, P.J. Rossky, K.P. Johnston
Wednesday Afternoon
Computational ADME
Modeling of cellular permeability for nonpeptide CCK-A agonists.
H. Wang, W. Andrews, M. Coffin, G. Whitesell, A. Bridgers
Using quantum chemistry to calculate atomic and group descriptors for QSAR and QSPR.
P. Gedeck, B. Martin, T. Schindler, T. Clark
Aqueous solubility prediction of two classes of organic compounds from molecular structure.
N.R. McElroy, P.C. Jurs
Quantum QSPR using diamond properties.
B. Beck
Supercritical Fluid Modeling
Monte Carlo simulations of supercritical fluid extraction systems.
J.I. Siepmann, M.G. Martin, B. Chen, J.M. Stubbs, J.J. Potoff
Polymer adsorption and colloid stability in supercritical fluids: Monte Carlo simulation.
J.C. Meredith, K.P. Johnston
Self-assembly of reverse micelles in supercritical CO2 by molecular dynamics simulation.
H.D. Cochran, S. Salaniwal, S. Cui, P.T. Cummings
Structure and properties of homopolymers and copolymers in near-critical fluid mixtures.
J.J. dePablo, Q. Yan
Theory and simulation of cohesive diffusion in nanopores: Transport in subcritical and supercritical regimes.
S.M. Auerbach
Thursday Morning
General Papers: Biochemical
Ab initio molecular dynamics studies on HIV-1 reverse transcriptase triphosphate binding site: Implications for nucleoside analog drug resistance.
F. Alber, P. Carloni
MD/QM study of the chorismate mutase-catalyzed Claisen rearrangement reaction.
A.E. Roitberg, S.E. Worthington, M. Krauss
Computational study of the role of the ligand flexibility in binuclear nonheme iron enzymes.
M. Torrent, D.G. Musaev, K. Morokuma
Innovative genetic algorithms for chemoinformatics.
B. Lavine, C. Davidson, A. Moores
General Papers: Theoretical
QM/QM methods: Use of composite DFT/semiempirical Hamiltonians in describing the electronic structure of biomolecules.
V. Gogonea, K.M. Merz Jr.
Study interactions between the Sem5 SH3 domain and its ligands using molecular dynamics and continuum solvent model.
W. Wang, J. Wang, R. Luo, J. Wang, A. Jakalian, C. Bayly, W. Lim, P. Kollman
Quantitative description of polymer solvent parameters by the intermolecular force equation.
M. Charton, B. Charton
Computer simulations of Ostwald ripening in a transdermal drug delivery system.
J. Zeng, K.I. Jacob
Quantum chemistry in a molecular polar solvent: The electronic structure and conformation of a betaine dye.
T. Ishida, P.J. Rossky
Thursday Afternoon
General Papers: Biochemical
Binding domain of k-opioid receptor: Peptide mimetic of the second extracellular loop.
L. Zhang, M. Goodman
Defining the ligand specificity of EDG1, 2, and 6 through mutagenesis, docking, and moleculardynamics studies.
A.L. Parrill, D.L. Bautista, D.L. Baker, D-A. Wang, Z. Lörinez, D.J. Fischer, K. Liliom, G. Tigyi, J. VanBrocklyn, S. Spiegel
Molecular modeling studies of the Akt PH domain and its interaction with phosphoinositides.
S-B. Rong, Y. Hu, S. Wang, A.P. Kozikowski
Reversible and competitive binding of b-cyclodextrin to benzyl alcohol in aqueous solution through molecular dynamics simulations.
J. Varady, X. Wu, S. Wang
General Papers: Theoretical
Nanotubes as test tubes: Effect of confinement on hydrocarbon reactions.
S.J. Stuart, B.M. Dickson, D.W. Noid, B.G. Sumpter
Simulations of small biomolecules.
N.C. Braier
Polaron reorganization energies accompanying reduction of methylated poly(benzobisthiazoles).
X.F. Duan, M. Alexander, A.T. Yeates, D.S. Dudis
Comparison of ab initio and AM1 two-photon absorption coefficients of selected organic molecules.
G.P. Das, D.S. Dudis, A.T. Yeates
Theoretical studies on infrared absorption cut-offs of molecular nonlinear optical crystals.
K. Wu
MCSCF ab initio calculations on organic building blocks for magnetic materials: Metal complexes of the dianions of 3,6-dimethylenecyclohexane-1,2,4,5-tetrones.
J.E. Jackson, A.W. Misiolek