Subscribe


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




The views and opinions expressed in this page are strictly those of the Division of Computers in Chemistry. The contents of this page have not been reviewed or approved by the American Chemical Society. Please address all comments and other feedback to the the COMP Division.