Subscribe


The Computers in Chemistry Division
Spring 2000 ACS Meeting Program
San Francisco, CA

Sunday Morning

Application of Effective Core Potentials in HF and DFT Methods

Effective core potential development and applications.
W.J. Stevens

Effective core potentials: How and why they work, or not.
K.G. Dyall

Relativistic pseudopotentials incorporating core/valence polarization and nonlocal effects.
M.M. Marino

Recent developments and applications of model core potentials.
M. Klobukowski

Recent progress in atomic and chemical group effective potentials.
J.C. Barthelat Sr.

The 21st Century: How Far Can COMP Go with the Hardest Problems?

Advancing computational modeling and simulation into the 21st century.
T.H. Dunning

Molecular modeling in biology and materials science: Prospects for the 21st century.
R.A. Friesner

On the role of high-performance computing in simulating complex molecules of biological interest.
P. Kollman

Scaling computational chemistry to peta-FLOP/s computers.
R.J. Harrison

Sunday Afternoon

Application of Effective Core Potentials in HF and DFT Methods

Structures and reaction mechanisms of transition-metal compounds.
G. Frenking

Application of effective core potentials to density functional calculations of inorganic species.
P.J. Hay, R.L. Martin, G. Schreckenbach, N.J. Henson

Energy-consistent ab initio pseudopotentials and their application to f-element systems.
M. Dolg

Modeling spin-orbit effects with ECPs.
W.C. Ermler

Density functional calculations of NMR and EPR parameters for heavy-element compounds.
M. Kaupp, J. Vaara, M. Munzarova, O.L. Malkina, V.G. Malkin

Oxidative addition to (PCP)IrH2 and related transition-metal complexes.
K. Krogh-Jespersen, M. Czerw, A.S Goldman

The 21st Century: How Far Can COMP Go with the Hardest Problems?

Molecular modeling of adsorption in amorphous nanoporous materials.
K.E. Gubbins

Computational challenges in structural and functional genomics.
T. Head-Gordon

Challenge of COTS technology in solving 21st-century scientific computation.
A. Komornicki

W1 and W2 theory: Thermochemistry in the kJ/mol accuracy range.
J.M.L. Martin, G. DeOliveira

Sexy genetic algorithms.
S.N. Burkett, R.D. Clark

Monday Morning

Ab Initio and Semiempirical Studies of Excited-State Studies

CEO/semiempirical calculations of excited electronic states of conjugated molecules.
S. Tretiak, R.L. Martin

Density functional theory based multireference configuration interaction calculations for excited states: Electronic absorption spectra of organic donor-acceptor systems and a series of porphyrin-type molecules including chlorophyll A.
A.B.J. Parusel, S. Grimme

Estimation of physical constants for environmental modeling.
S. Hilal, B.P. Shrestha

Linear-scaling computation of ground state with time-domain localized-density-matrix method.
D. Zhou, S. Yokojima, G. Chen

Vertical electrostatic model 42: Solvatochromic shifts for excitation energies from a generalized Born model.
C.J. Cramer, J. Li, D.G. Truhlar

Application of Effective Core Potentials in HF and DFT Methods

Ab initio determination of the active site of a metalloenzyme.
M. Krauss

Applications of ECP/DFT to the spin states of iron porphyrins.
Y-P. Liu

Density functional, effective core potential study of steric vs. electronic stabilization in (p-R-C6H4-NC)2W(dppe)2.
D.W. Bennett, N.L. Wagner, D.A. Dixon

Effective core potentials and the transactinide ligand field.
C.S. Nash

Theoretical study of the carbonyl substitution reactions of M(CO)5 and M(CO)4(C2H2), where M = Fe, Ru, Os.
S.A. Decker, M. Klobukowski, T.R. Cundari

Co(+2): H2O vs. NH3 ligands.
M.D. Ryan, A.M. Schmiedekamp

Effective core potential applications in transition-metal chemistry.
T.R. Cundari, T.R. Klinckman, W. Fu Jr., T Zhou

Structure-Based Drug Design

Computer simulations for drug lead optimization.
W.L. Jorgensen, J. Tirado-Rives, M.L., Plount, D.J. Price, R.C. Rizzo, D. Wang

Calculation of relative binding free energies: Use for characterizing the AMP binding site of fructose 1,6-bisphosphatase.
M.D. Erion, J. Schanzer, P.D. vanPoelje, M.R. Reddy

Paradigms for rational drug discovery and refinement.
C.L. Brooks, S. Banba, K.V. Damodaran, O. Roche

Evaluation of the linear response method using a continuum solvent model in the prediction of binding affinities.
D.L. Cheney, R. Zhou, R.A. Friesner, J.S Mason

Computational alanine scanning of the 1:1 human growth hormone/receptor complex.
S. Huo, I. Massova, P.A. Kollman

Monday Afternoon

QM/QSAR

Estimation of physical and chemical constants for environmental modeling.
S.H. Hilal, L.A. Carreira, S.W. Karickhoff

Nature and composition of black box topological parameters.
M. Charton, B. Charton

Computational parameters in correlation analysis: Normal boiling points.
R.E. Clark, G.R. Famini, L.Y. Wilson

Electronic descriptors for QSARs of halogenated aliphatic hydrocarbons.
S. Trohalaki, R. Pachter

Atomic index of charge and orbital controlled intermolecular interaction in molecular modeling for QSAR in drug design.
I.B. Bersuker, S. Bahceci, J.E. Boggs

QM/QSAR applications to dental materials.
A.J. Holder, J.A. Morrill, J.D. Eick, C. Chappelow

Structure-Based Drug Design

Recent advances in modeling partial atomic charges, solvation energies, and partition coefficients.
D.G. Truhlar, Y-Y. Chuang, C.J. Cramer, D. Dolney, G.D. Hawkins, J. Li, D.A. Liotard, P. Winget, J. Xidos, T. Zhu

Computer-aided design of bioactive molecules.
H. Carlson, T. Mordasini, J.A. McCammon

Identification of binding sites in a receptor and design and evaluation of ligands at that site.
M. Prabhakaran

Structure-based design of protease inhibitors as therapeutics: Some examples.
S.H. Reich

De novo design of synthetically accessible ligands.
A.P. Johnson, K. Boda, J-F. Marchaland, A. Ting

Monday Evening

Sci-Mix

Applications of ECP/DFT to the spin states of iron porphyrins.
Y-P. Liu

Computational investigations of the B. fragilis metallo-b-lactamase.
F.R. Salsbury, C.L. Brooks

Semiempirical scoring functions for ligand binding based on molecular mechanics and continuum model calculations.
D.L. Cheney, J.S. Mason

Computational study of the structural and energetic properties of calix[4]arene. An investigation of cation-p interactions in the threading reaction path of alkali metal cations.
J.E. Norton, A.T. Macias, J.D. Evanseck

Donor-acceptor-assisted Diels-Alder reactions.
R.A. Wheeler, K.E. Wise

Integration of structure-based and ligand-based approaches to the rational design of HIV-1 protease inhibitors: Binding energy calculations and 3-D-QSAR modeling.
P.R.N. Jayatilleke, A.C. Nair, W.J. Welsh

Computational chemistry comparison and benchmark database.
R.D. Johnson III

Modeling the mammalian nose: Structural motif or mean field olfactory neuron responses?
M. Blanco, W.A. GoddardIII

Tuesday Morning

Computers in Chemistry Award Symposium Honoring Don Truhlar

Energy-transfer-controlled reactions.
S.C. Tucker, S.K. Reese

Quantum reaction dynamics of polyatomic molecules.
D.C. Clary

Organic reactions on-the-fly via QM/MM simulations in solution.
W.L. Jorgensen, J. Chandrasekhar, J. Tirado-Rives, M.P. Repasky

Harpooning studied by transition-state spectroscopy, M..XR+hn®;[M*..XR]ç®;[M+..XR-]ç®;products: Results for M=Li, X=F, R=CH3 or H.
J.B. Giorgi, T.G. Lee, A.J. Hudson, F. Naumkin, H.B. Oh, P. Piecuch, J.C. Polanyi

Quantum transition-state theories: Exact and approximate.
J.C. Light, D.H. Zhang

Structure-Based Drug Design

Molecular mechanics can teach us something about chemistry.
N.L. Allinger

Predicting affinity: The sina qua non of activity.
G.R. Marshall, R. Arimoto, R. Ragno R.D. Head

Binding mode of isatins in caspases, docking, and crystal structure.
M.D. Ryan, M. Head, N.A. Concha, D. Lee

Docking of flexible ligands to RNA targets.
V. Mohan, B.A. Smith, R.H. Griffey, C. McMartin

Database screening by fast flexible docking.
R.D. Clark, S.N. Burkett, T.W Heritage

Tuesday Afternoon

Computers in Chemistry Award Symposium Honoring Don Truhlar

Frequency shifts in the hydrogen-bonded OH stretch in water-halide clusters: The importance of charge transfer.
J.T. Hynes, W.H. Thompson

Water dimer vibration-rotation spectrum: Influence of the monomer's internal motions.
C.J. Leforestier

Nonadiabatic effects in O + H2 and H + OH.
G.C. Schatz

Award Address (ACS Award for Computers in Chemical & Pharmaceutical Research). Recent applications of variational transion-state theory.
D.G. Truhlar

Tuesday Evening

General Posters

On achieving efficient molecular dynamics simulations with the finite difference Poisson-Boltzmann method.
R. Luo, L. David, M.K. Gilson

Comparison of the DHFR wildtype and the Val-121 mutant molecular dynamics simulations.
J.L. Radkiewicz, C.L. Brooks

Computational investigations of the B. fragilis metallo-b-lactamase.
F.R. Salsbury, C.L. Brooks

Water under pressure.
E. Schwegler, G. Galli, F. Gygi

Dynamics of nonspecific interactions between Cro and B-DNA.
C. Fernandes, F. Yang, I. Ouporov, K. Thomasson

Molecular dynamics simulations of alkane crystallization processes: Effect of short-chain branching.
T. Shoji, T. Aoyagi, H. Fukunaga, F. Sawa, J-I. Takimoto, M. Doi, T. Igarashi

Molecular dynamics simulations of the structural and dynamic effects of double bonds in dimyristoyl phosphatidylcholine and its monolayers.
R.L. Wood, A.J. Hopfinger

Molecular dynamics study of HIV-1 reverse transcriptase/DNA/dTTP complex.
S.S. Kerimo, L. Li, L.G. Pedersen, T.A. Darden

Molecular simulations of photodamaged DNA.
O. Wiest, P. Tran

Ab initio studies on the origin of ss-sheet twisting.
I.L. Shamovsky, G.M. Ross, R.J. Riopelle

Computer-based design of monospecific inhibitors of engineered protein kinases.
O.V. Buzko, A.C. Bishop, Y. Liu, K.M. Shokat

DNA repair by photolyase: Theoretical study of docking, dynamics, and electron transfer between photolyase catalytic cofactor FADH- and DNA
pyrimidine dimer.
J. Antony, D.M. Medvedev, A.A. Stuchebrukhov

Docking studies using the low-mode conformational search method.
C. Parish, T. Lyons

Incorporating chemical reactivity in the design of combinatorial libraries.
M. Lindvall, A. Leach, T. Kostka, J. Gasteiger

Ionization properties of oligonucleotides and sequence specific DNA alkylation.
P.R. LeBreton, Q. Zhu

Molecular study of enkephalin-opioid receptor interactions.
C. Parish, R. Gooch

Molecular simulation of racemic mixture adsorption into a chiral zeotype.
L.A. Clark, R.Q. Snurr

New energy partitioning scheme based on the self-consistent charge and configuration method for subsystems: Application to water dimer system.
T. Uchimaru, J. Korchowiec

Semiempirical scoring functions for ligand binding based on molecular mechanics and continuum model calculations.
D.L. Cheney, J.S. Mason

Toward a molecular understanding of enkephalin-opioid receptor interactions.
C. Parish, R. Gooch

Estrogen receptors: Modeling and structural determinants of ligand binding domains.
A. Bhat, R. Abagyan

Atypical exocyclic substituents on nucleobases: Computation of steric indices and their implication for fidelity of DNA replication.
E. Yuriev, J.D. Orbell

Computational study of the structural and energetic properties of calix[4]arene. An investigation of cation-p interactions in the threading reaction path of alkali metal cations.
J.E. Norton, A.T. Macias, J.D. Evanseck

Analysis of the potential energy surfaces of various HIV-1 protease inhibitors.
C. Parish, M. Rappleye

Comparison of quantum chemical approaches to the direct calculation of pKa.
A.T. Pudzianowski, D.L. Cheney

Conformational analysis of tris(nitrohydroximethyl)aminomethane hidrochloride (TNAMH) using semiempirical and density functional methods.
I. Cordova, L. Feliu, D. Bacelo

Manganese-salen catalyzed epoxidation of olefins (Kochi-Jacobsen-Katsuki reaction).
J. El-Bahraoui, O. Wiest, D. Plattner, D. Feichtinger

Computational study of aza-dipeptides and phenprocoumon analogs as HIV-1 protease inhibitors.
P.R.N. Jayatilleke, A.C. Nair, W.J. Welsh

Dynamic conformation changes of furanose ring: A major influence of nucleoside structure on enzyme catalytic activity and inhibition.
L. Mu, M. Nicklaus, S. Sarafianos, H. Ford Jr., H. Mitsuya, V. Marquez

Determining the molecular flexibility of HIV-1 protease inhibitors.
C. Parish, K. Sinclair

Donor-acceptor-assisted Diels-Alder reactions.
R.A. Wheeler, K.E. Wise

Influence of through bond interactions on the rates of ring-opening reactions.
D. Sawicka, K.N. Houk

Molecular origin of aqueous phase catalysis and stereoselectivity of the Diels-Alder reaction.
S. Kong, J.D. Evanseck

Quantum chemical studies of the Ni-Fe hydrogenase active site: A comparative analysis.
H. Harris, Z.X. Barrios, R. Grosely, J. Tilleman

Theoretical study of microscopic solvation of HCl in ammonia clusters: HCl(NH3)n, n=1-3.
D.E. Bacelo

Understanding nonadditive contributions to dispersion forces and short-range exchange effects.
V.M. Audette, D.M. York

Predicting the cleavage reactions of a-substituted nitroalkane radical anions by computational methods.
W.J. Kelly

Studies on the solution conformation and dynamics of maltose, reduced maltotetraose, and he potent glycohydrolase inhibitor acarbose.
H. Mohammed, R.I. Hollingsworth

Synthesis and inclusion complexation studies of a novel molecular receptor for 1,4-disubstituted benzenes and 4,4'-disubstituted
biphenyls.
A.T. Macias, K.A. Kumar, A.P. Marchand, J.D. Evanseck

Toward an accurate quantum mechanical model of phosphate hydrolysis in HIV-1 reverse transcriptase.
J.M. Johnson, D.M. York

Molecular dynamics simulations on the structure and conformational properties of C2'-modified arabinooligonucleotides and their RNA
hybrids.
D. Venkateswarlu, D.M. Ferguson

QSAR on anti-HIV drugs: A comparative study.
R. Garg, C. Hansch

Computational study of opioid analogs: Development of 3-D QSAR models for d, m, and k opioid receptor-binding affinities.
A.C. Nair, S-J. Yu, W.J. Welsh, J. Duchek, N.

Modeling the interaction of agrochemicals with environmental surfaces.

Comparative QSAR study on 5a-reductase inhibitors.
A. Kurup, C. Hansch

CCSDT spectroscopic constants for first-row diatomic hydrides.
J.A. Sordo

Quantum dot cellular automata: Encoding information in molecules.
O.G. Wiest, S. Braun-Sand

Theoretical study of microscopic solvation of SO3 in water clusters: SO3(H2O)n, n = 1-3.
Z. Ocasio, D.E. Bacelo

Theoretical study of potential energy surfaces of the Ne-HCl+ van der Waals complex using finite element methods.
T.J. Dudley, R.R. Pandey, P. Staffin, M.R. Hoffmann

Theoretical study of the boron-nitrogen dative bond in aminomethylphenyl boronates.
F.C. Lightstone, J.H. Satcher, S.M. Lane, M.E. Colvin

Theoretical study of the nucleophilic substitution of sulfides.
S.M. Bachrach, B.D. Gailbreath

Wednesday Morning

Cheminformatics

Ambiguities due to ties in proximity in lead discovery clustering algorithms.
J.D. MacCuish, C.A. Nicolaou, N.E. MacCuish

Similarity-based Shannon-like diversity measure: Theory.
G.M. Maggiora, V. Shanmugasundaram

Similarity-based Shannon-like diversity measure: Application to cell-based chemistry spaces.
V. Shanmugasundaram, G.M. Maggiora

Applying pharmacophoric descriptors in molecular similarity and diversity analysis.
X. Chen

Molecular descriptors and fingerprints to identify molecules with similar biological activity.
J. Bajorath, L. Xue

Pharmacophores in the corporate database: Using 3-D information to select screening sets.
J.P. Holland, T. Mitchell

Structure-Based Drug Design

Analyzing high-throughput screening data by neural networks.
J. Gasteiger, A. Teckentrup, H. Briem

Comparison of CoMFA and QSAR in the study of melatonin receptor ligands for MT1 and MT2 receptors.
J.D. Madura, E. Esposito, P-K. Li

CoMFA and CoMSIA studies on cyclic ureas as HIV-1 protease inhibitors.
X. Wang, W.J. Welsh

Pharmacophore hypothesis generation for antibacterials containing oxazolidinones and its surrogate ring systems.
A. Mehta, S.K. Arora, S. Seth, B. Das, A. Ray

Computational strategies for the rational design of HIV-1 aspartic protease inhibitors: Binding affinity, buried surface area and 3-D-QSAR
approaches.
A.C. Nair, P.R.N. Jayatilleke, R. Zauhar, W.J. Welsh

Integration of structure-based and ligand-based approaches to the rational design of HIV-1 protease inhibitors: Binding energy calculations and 3-D-QSAR modeling.
P.R.N. Jayatilleke, A.C. Nair, W.J. Welsh

Wednesday Afternoon

Cheminformatics

Database access via the data catalog model.
P.M. Smith

Garlic: Database middleware for heterogeneous data sources.
P. Schwarz

MetaSymphony for discovering valuable information in stored data.
L. Jardine, A. Krassavine

Unlocking the value of scientific images.
B. Dunkle

Facilitating global discovery projects with information systems.
F.K. Brown

Materials and Inorganics - PM

Ab initio study of adsorption and decomposition of NH3 on Si(100)-(2x1).
Y. Widjaja, M.M. Mysinger, C.B.

Microstructural insight into the physical and chemical properties of sodium phosphate glasses by molecular dynamics simulation.
J-J. Liang, R.T. Cygan, T.M. Alam

Molecular modeling of adsorption in controlled pore glasses.
L.D. Gelb, K.E. Gubbins

Modeling the relationship between salt load and time in the middle reach of the Rio Grande using "Extend, Imagine That" simulation.
F.M. Howari, P. Goodell, K. Banat

New approach to the interesting structural feature of E(ZXY2)4 compounds.
Z. Xu, Z. Lin

IR absorption cut-offs of molecular nonlinear optical crystals: Ab initio studies on the vibrational spectra of some organic molecules.
K. Wu, J. Li

Theoretical studies on the mechanism of electron transfer at dye-sensitized oxide semiconductor solar cells.
O. Kitao, T. Ogawa, K. Aoki, H. Arakawa

Self-consistent field theory on the polydispersity effects of polymer solutions between polymer-grafted walls.
T. Honda, T. Igarashi, T. Kawakatsu, M. Doi

Structure-Based Drug Design

Similarity-driven flexible ligand docking.
J. Mestres, X. Fradera, R.M.A. Knegtel

Design and development of inhibitors of NAALADase (N-acetylated-a-linked acidic dipeptidase) and prostate-specific membrane antigen.
A.J. Oliver, M.J. Miller, M. Tenniswood,

Differences and similarities in the molecular behavior of various HIV-1 inhibitors.
C. Parish

Molecular modeling of drug resistance.
Y.Z. Chen, X.L. Gu

Computational studies of the resistance patterns of mutant HIV-1 aspartic proteases toward ABT-538 (ritonavir) and design of new derivatives.
A.C. Nair, I. Bonin, A. Tossi, W.J. Welsh, S. Miertus

Thursday Morning

Cheminformatics

Selection and exploratory analysis of compounds tested in 67 assays.
S.S. Young, C. Keefer, H. Chen

Merging bioinformatics and chemoinformatics to map protein interactions.
D. Page, B. Kay

Linking chemical and biological information for safety assessment.
F.P. Stewart

Beyond bioinformatics, R&D for drug discovery.
R. Fallon

General Computational Chemistry, Theory, QM, and Other Topics

Mistakes to avoid in applying and optimizing free-energy perturbation calculations.
D.A. Kofke, N. Lu

Computational chemistry comparison and benchmark database.
R.D. Johnson III

Assessment of the accuracy and efficiency of new density functionals implemented in DGauss.
J.L. Anchell, M.S. Stave

New methods for extracting resonance structures from molecular orbital and DFT calculations.
C.R. Landis, S.H. Feldgus

Mixed quantum-classical method for predicting reactivity in complex systems.
L.A. Clark, R.Q. Snurr, O. Warschkow, D.E. Ellis

Novel approach of calculating the optical spectra of molecules with Duschinsky effects.
K.K. Liang, M. Hayashi, S.H. Lin

Predicting NMR shielding by aldehydes based on ab initio GIAO calculations.
N.H. Martin, N.W. Allen III, L. Vo, J.D. Brown

Thursday Afternoon

General Biological Topics

E-State structure space, molecular similarity, and database searching.
L.H. Hall, L.B. Kier

Prioritization of parallel synthesis by use of 3-D-QSAR with structure-based pharmacophores.
P. Greenidge, J. Deadman

Modeling the mammalian nose: Structural motif or mean field olfactory neuron responses?
M. Blanco, W.A. GoddardIII

Theoretical studies on the mechanism of electron transfer at photosynthetic reaction centers.
K. Aoki, O. Kitao, O. Tesuji

Electron transfer tunneling pathways in bovine heart cytochrome c oxidase.
D.M. Medvedev, A.A. Stuchebrukhov

Simulating protein adsorption using detailed molecular models.
S. Ravichandran, J. Talbot

Computational approaches to elucidate the structure-activity relationship of HIV-1 protease-ligand interactions.
P.R.N. Jayatilleke, A.C. Nair, W.J. Welsh

Ab initio study of guanine-cytosine base pairs in parallel DNA: Twist, wobble, or tautomerize?
D. Barsky, M.E. Colvin

Theoretical studies of S-nitrosothiols.
M.D. Bartberger, K.N. Houk

General Computational Chemistry, Theory, QM, and Other Topics

Ligand effects on the relative stability of rac-meso rotamers of zirconocene catalysts: A DFT study.
J.W. Andzelm, A. Maiti, G. Fitzgerald, N. Tanpipat, J.T. Golab

Theoretical investigation of imidazole, pyrazole, and triazole bases for synthesis of nonnatural nucleoside.
I. Homsek, I. Kolaric, A. Pejcic, B. Kolaric

Intermolecular interactions and lattice energies from experimental charge densities and from periodic Hartree Fock calculations.
Y. Abramov, A. Volkov, P. Coppens

Simulated and experimental spectra of mixtures of water, methanol, acetone, and acetonitrile.
D.S. Venables, C.A. Schmuttenmaer

Statistical model for an electrophilic aromatic substitution reaction.
A.C.R. Fabriani, P.R. Seidl, E.C.A.N. Chrisman

Houdini: A new structure generator for computer-based structure elucidation.
M.E. Munk, A.A. Korytko




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.