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The Computers in Chemistry Division
Spring 1999 ACS Meeting Program

Sunday Morning

Computational Intelligence and Data Mining in High-Throughput Screening: Dirty QSAR

4-D-QSAR analysis for virtual high-throughput screening, docking alignments, and hypothesis generation.
A.J. Hopfinger, P. Venkatarangan, S.Wang, A. Reaka, J. Duca

Applying ligand-docking technology to large datasets.
T.W. Heritage, S.N. Burkett, A. Nayeem R.D. Clark

In silico screening applied to the rational design of novel immunosuppressive compounds.
R. Lahana, A. Yasri, G. Grassy, B. Calas, M. Kaczorek, R. Buelow

Structure-based design of combinatorial libraries.
R.D. Brown, J. Jiang, P.D. Kirchoff, C.M. Venkatachalam

Conformational Analysis: Stepping Up to the New Challenges

Combinatorial libraries and structure-based design.
A.G. Skillman, I.D. Kuntz

Confort: A rational conformation analysis tool.
R. Balducci, R.S. Pearlman

Skizmo: A new program for rapid conformational analysis and structure-based design of combinatorial libraries.
W.P. Walters, M.T. Stahl, J.J. Corkery, M.A. Murcko

Conformational analysis: Finding the global minimum.
J.M. Leonard, A. Nayeem

Recent advances in rule-based conformational analysis.
K. Davies, M. Baird

Conformational analysis by intersection: Ring conformations.
A. Smellie, S.L. Teig

Using Computers to Facilitate Learning

Facilitating chemical education with computers: World Wide Web-based interactive materials and organizational tools for learning exercises.
A.L. Parrill, J. Ellsworth

Do World Wide Web-based practice quizzes improve student performance on exams?
J.H. Reeves, S. Broadway, C.R. Ward

Research methods in chemistry.
J.M. LoBue, J. Orvis

World Wide Web-based exercises for chemistry students using "live" molecular models.
H.G. Ungar, L. Calciano, A.E. Baucom, J.S. Lipscomb, J.N. Camara

TutOrg—an intelligent tutoring system: Application to bonding, resonance, and isomerism.
W.T. Wipke, J. Shoop, P. Madrid, J. Junker

Sunday Afternoon

Applications of Computational Chemistry to Toxicology and the Development of Agricultural Chemicals

Current trends in toxicology.
H. Salem

Computational investigations on the reaction of oximes with organophosphorus compounds.
J.B. Wright, W.P. Ashman, W.E. White

Theoretical study of the SNV reaction of trichloroethylene + CH3S- as a model for glutathione conjugation of TCE.
J-Y. Shim, P.F. Boon, A.M. Richard

Theoretical studies of DNA base deamination: The structure of "guanine diazonium ion" in its aggregate with cytosine.
R. Glaser, M. Lewis, S. Rayat

Regiochemistry of nucleic acid adduct formation via aryl nitrenium ion intermediates.
G.P. Ford

Computational Intelligence and Data Mining in High-Throughput Screening: Dirty QSAR

Designing large "smart" combinatorial libraries: Activity-based validations of diversity hypotheses.
D. Schnur

De novo design using HTS data.
K. Davies

Search techniques used in identifying actives in a large HTS dataset.
R.W. Spencer

Analyzing large datasets with decision trees: Discriminating between potential drugs and nondrugs.
M. Wagener, V. vanGeerestein

Conformational Analysis: Stepping Up to the New Challenges

Rapid conformation search applied to ligand discovery.
M.T. Stahl, A. Nicholls, R.A. Sayle, J.A. Grant

Implementation of fast conformational search strategi

Filtering techniques for 3-D database searching with catalyst pharmacophores.
R. Griffith, P.A. Keller, S. Leach

Alignment of 3-D structures by the method of 2-D projections.
P.D. Lyne, D.D. Robinson, W.G. Richards

Prediction of the bioactive conformation of arachidonyl ethanolamide using distance-constrained systematic search.
J-Y. Shim, W.J. Welsh, B. Berglund, A.C. Howlett, P.F. Fleming, K.C. Rice

Investigations into polysaccharide conformations via potential of mean force calculations.
K.J. Naidoo, M. Kuttel

Why dynamic simulations are necessar

Regular patterns followed by distributions of oligopeptide sequences among structural motifs.
S.G. Jacchieri

Using Computers to Facilitate Learning

Chemsite for nonmajors chemistry.
D.D. Shillady

Conservation laws and kinetic simulations.
S.L. Cooke

Interactive computer-based pedagogical tools.
M.A. McBrien, A.J. Williams

Learning biochemistry with highly interactive multimedia.
D. Mackay, J. Fetrow, A. Hagler

New approach to laboratory reporting.
B. Jacob, A. Fraiman

C-MoR chemistry project: Development of tools for visualizing chemical entities and chemical concepts.
R.N. Dominey, W.H. Myers, E.W. Goldman, R.P.F. Kanters

Monday Morning

Applications of Computational Chemistry to Toxicology and the Development of Agricultural Chemicals

Quantitative structure-activity relationship models useful for risk assessment in predicting suspected endocrine-disrupting compounds.
W.J. Welsh, S-J. Yu, Y. Chen, W. Tong, R. Perkins, D. Sheehan

Relationship of reactivity of organophosphorus compounds to toxicity.
W.E. White

Prediction of acute fathead minnow toxicity of organic compounds from molecular structure.
P.C. Jurs, D.V. Eldred, C.L. Weikel

Combined application of QSAR and database mining in search of environmental estrogens.
A. Tropsha, W. Zheng, J.D. McKinney

Prediction of rice blast activity using the electron-conformational method of identification of the pharmacophore and antipharmacophore shielding.
I.B. Bersuker, R.S. Pearlman, S. Bahceci, J.E. Boggs

Bridging the Gap Between Chemical Modeling and Engineering

From atomistic simulations to engineering models.
W.A. Goddard III, M. Blanco, T. Cagin, J. Sefcik, S. Hwang, Y. Jang, Y. Zhou

Computational chemistry and its use for process design.
D.A. Dixon

Quantum mechanics as a valuable partner in pilot-plant process development.
A.M. Chaka

interface of electronic structure theory and dynamics for the calculation of chemical reaction rate constants.
D.G. Truhlar, Y-Y. Chuang, J.C. Corchado, P. Fast, M.L. Radhakrishnan, J.M. Rodgers, M.L. Sanchez, J. Villa, B. Lynch, C.J. Cramer

Between chemistry and chemical engineering: Theoretical chemistry methods lead to reactor simulations.
H. Sellers, J. Gislason

From first-principles quantum chemistry to catalytic kinetics.
M. Neurock, P.S. Venkataraman, E.W. Hansen

Opportunities for quantum chemistry in chemical engineering.
J. Ruiz

Insights into NOx reduction catalysis from molecular modeling.
W.F. Schneider, K.C. Hass, B.R. Goodman, D. Sengupta, J.B. Adams

Acyl transfer mechanisms revisited: Computational mechanistics of anhydride alcoholysis.
P.M. Margl, B.E. Wilson

Computational Intelligence and Data Mining in High-Throughput Screening: Dirty QSAR

Dirty CoMFA, dirty docking, and a clean method for inverse QSAR-based drug design.
R.S. Pearlman, R. Balducci, K.M. Smith, M-Y. Brusniak

SPD: The generation of spacially resolved property descriptors.
C.E. Whitehead, C. Breneman

Parallel QSAR.
D.K. Agrafiotis, V.S. Lobanov, D.N.Rassokhin

Rapid generation of polarization-corrected electrostatic fields using the TAE/RECON method.
C.E. Whitehead, C. Breneman, D. Ryan

Monday Afternoon

Applications of Computational Chemistry to Toxicology and the Development of Agricultural Chemicals

Modeling interaction potentials as tools for understanding ligand-binding processes in chemical toxicity.
J. Rabinowitz, S.B. Little

Molecular dynamics simulations of tetracoordinate phosphonyl and carbonyl adducts of acetylcholinesterase.
I.M. Kovach, I.J. Enyedy

Ab initio structures of metalloenzyme active sites: Application to metalloglutathione transferase.
M. Krauss

Modeling dynamic chemical systems using cellular automata.
P.G. Seybold, L.B. Kier, C.K. Cheng

Application of computer modeling to toxicology.
R.S.H. Yang

Bridging the Gap Between Chemical Modeling and Engineering

Causes, consequences, and correctives for the gap in modeling between chemistry and chemical engineering.
S.W. Churchill

Chemical engineering applications of molecular simulation and computational chemistry.
P.T. Cummings

Computational materials design to address real world challenges.
A.M. Rappe

Physical property modeling: Some whys, whats, hows, and what-ifs.
J.P. O'Connell

Prediction of chemical properties of organic compounds using GA-CNN modeling of calculated structural descriptors.
P.C. Jurs, S.R. Johnson, H.L. Engelhardt, D.V. Eldred, G.A. Bakken, E.S. Goll

Reaction engineering of flame suppression: Integrating ab initio computations to flow/chemistry modeling.
M.R. Zachariah, D. Burgess, W. Tsang, P.R. Westmoreland

Molecular modeling applied to industrial chemical systems.
L.M. Bormann-Rochotte, J.T. Golab

Using molecular dynamics to design an effective corrosion barrier for a high-temperature superconductor.
C.A. Wells, J.E. Ritchie, J.T. McDevitt, D.R. Kanis

Structure-activity modeling methods in materials chemistry, materials formulations, and materials combinatorial chemistry.
M.J. Doyle

Computational Intelligence and Data Mining in High-Throughput Screening: Dirty QSAR

Binary QSAR: A new method for the determination of quantitative structure-activity relationships.
P. Labute

Combined recursive partitioning and fast conformation-generation methods for identifying pharmacophores from large chemical datasets.
X. Chen, A. Rusinko III, A. Tropsha, S.S. Young

Application of binary-QSAR to large combinatorial libraries.
D.L. Lynch, G. Lauri

Pharmacophore model generation from high-throughput screening datasets.
J.W. Elling, S.I. Bassett, R.F. Nutt

Monday Evening

Sci-Mix - EVE

Lateral validation of Hansch's models for Salmonella typhimurium determined by mutagenicity of nitroaromatics using Comfa.
R.L. Compadre, M. Fan, C. Byrd, C.M. Compadre

Toxic-substituted phenols in mainstream cigarette smoke condensate.
C.J. Smith, C. Hansch

NMR solution structure of the cons

Theoretical studies on the mechanism of electron transfer at the photosynthetic reaction center.
N. Miura, O. Kitao

Scampi: Statistical classification of activities of molecules for pharmacophore identification.
X. Chen, A. Rusinko III, A. Tropsha, S.S. Young

Structure of liquid clusters of Lennard-Jones atoms.
B.G. Moore, A.A. Al-Quraishi

Methodology for the optimization of chemical processes through statistical modeling with application on the nitration of bromobenzene.
A.C.R. Fabriani, E.A.N. Chrisman

Molecular modeling of polymer melts and blends.
J.D. Weinhold, J.G. Curro

Tuesday Morning

Bridging the Gap Between Chemical Modeling and Engineering

Molecular modeling of adsorption in amorphous nanoporous materials.
K.E. Gubbins, L.D. Gelb

Modeling the separation mechanism of oxygen-containing a

Molecular modeling and characterization of zeolites for sorptive separations.
B.K. Peterson

Atomistic simulations of boundry lubricant-bonding interactions with metal oxide surfaces.
S.M. Opalka, L.G. Hector Jr.

Modeling medium effects in condensed phases.
C.J. Cramer, J. Li, P.D. Winget, T. Zhu, D.G. Truhlar, D.A. Liotard

Functional mesoscopic dynamics of phase separation in complex copolymer liquids.
J.G.E. Fraaije, A.V. Zvelindovsky, G.J.A. Sevink, N.M. Maurits

Theoretical investigations of solute transport in liquid membranes containing photoactive carriers.
T.L. Longin

Modeling solvent effects on optical-limiting materials.
P.N. Day, K.A. Nguyen, R. Pachter

Multiscale modeling of structured materials.
D.B. Nicolaides, P. Kung

Computational Intelligence and Data Mining in High-Throughput Screening: Dirty QSAR

SACCS: Statistical analysis of combinatorial chemical sequences.
P. Shenkin

SAR information from screening data: Better than you would think.
G. Lauri

Some expectations of HTS.
J.J. Morris

Supervised GA-based regression clustering for data mining of molecular properties.
M. Embrechts, C. Breneman

High-throughput and combinatorial QSAR.
R.D. Clark

Corwin Hansch Award Symposium

QSAR, 3-D QSAR, and beyond.
H. Kubinyi, J. Sadowski

Have we made progress in predicting biological activity?
Y.C. Martin

Award Address (ACS Award for Computers in Chemical & Pharmaceutical Research). Demonstration of the use of a QSAR database to illustrate the development of a model for estrogenic toxicity.
C. Hansch

QSAR model for drug human oral bioavailability.
J.G. Topliss, F. Yoshida

Tuesday Afternoon

Bridging the Gap Between Chemical Modeling and Engineering

Chemistry to engineering: A bridge over troubled waters? Nah!
C.K. Hall

Infrastructure for quantum chemistry applications.
K.K. Irikura, R.D. Johnson III, C.A.Gonzalez, T.C. Allison, W.J. Stevens, C.B. Kellogg, U. Richter

Polymer modeling at Los Alamos: Atoms to continuum.
E.M. Kober

Force-field technology suitable for calculating thermodynamic parameters
of condensed phases.
J.M. Newsam, H. Sun, D. Rigby, B.E. Eichinger, A. Bick, C.M. Freeman, A.M. Gorman

Tales from the trail: Modeling polymerization catalysis.
A.K. Rappe

Critical issues in the steps to connect quantum calculations to bulk properties of glassy polymers.
P.J. Ludovice, S. Ahmed, J.V. Order, J. Jenkins

Developing polyhydroxamide as a low-flammability polymer: An interplay among computational chemistry, polymer synthesis and kinetics data.
P.R. Westmoreland, K. Rotem, T. Inguilizian, C. Gao, S.W. Kantor, R.E. Lyon

DMOL/COSMO-RS: A bridge between chemistry and chemical engineering.
N. Tanpipat, A. Klamt, I. Clausen, J. Andzelm

Calculation of acidities and basicities of silanols for reaction engineering of alkoxysilane
polycondensation.
J. Sefcik, W.A. Goddard III

Computational Intelligence and Data Mining in High-Throughput Screening: Dirty QSAR

Quick and dirty? No, fast and accurate: The K nearest-neighbor QSAR method.
A. Tropsha, W. Zheng, G. Ethiraj

Molecular descriptors for compound clustering.
H. Gao, J. Godden, J. Bajorath Convention

Development of a fingerprint to select training sets for predicting log P values.
S-Y. Yue, N. Tokinson, E. Roberts

Corwin Hansch Award Symposium

Calculating log P octanol: No missing fragments.
A.J. Leo

Structure-activity relationships for ligand-protein interactions: What can molecular dynamics simulations tell us?
P.A. Kollman

Recent success stories of classical QSAR procedure leading to (potentially) commercializable bioactive
compounds.
T. Fujita

Development of structure-activity relationships for assessing ecological risks.
S.P. Bradbury, G.D. Veith

Signposts along the road from classical QSAR to 3-D-QSAR to ??.
R.D. Cramer

Tuesday Evening

Poster Session

Comparative QSAR studies on anti-HIV HEPT derivatives.
R. Garg, C. Hansch

Utility of electron affinity as a QSAR descriptor in predictive toxicology.
S. Trohalaki, R. Pachter

Synthesis and structure-activity relationship of a series of 4-X-thiophenols. R.P. Verma, C.D. Selassie, S. Kapur, O.
Barberena, C. Hansch

Lateral validation of Hansch's models for Salmonella typhimurium determined by mutagenicity of nitroaromatics using Comfa.
R.L. Compadre, M. Fan, C. Byrd, C.M. Compadre

Measurements and prediction of log P values for highly lipophilic bioactive compounds.
C. Yamagami, T. Fujita

Use of computational techniques for predicting biodegradability of halogenated compounds by haloalkane dehalogenase.
B.T. Kawakami, P.V. Roberts

Comparative molecular field analysis of bisaromatic , -unsaturated ketone inhibitor of farnesyl protein transferase.
S-J. Yu, W.J. Welsh, N-D. Sung, M. Akamatsu, B-M. Kwon

Quantitative structure-activity relationship models for predicting the estrogenic activity of xenoestrogens.
S-J. Yu, W.J. Welsh, Y. Chen, W. Tong, R.
Perkins, D.M. Sheehan

Toxic-substituted phenols in mainstream cigarette smoke condensate.
C.J. Smith, C. Hansch

Amiloride binds to the more flexible sites on -DNA.
D.A. Bondarev, C.A. Venanzi

Influence of ligand binding on the dynamics of the M20 loop of DHFR and the implications for catalysis.
J.L. Radkiewicz, C.L. Brooks III

Normal-mode analysis of heme within myoglobin and related small molecules.
S.F. Sontum, I.I. Beraha, J.W. Dimmig, V.C.
Sundar

Standard force fields are not able to accurately model the energetics of very polar
compounds.
J.J. Harr, R.B. Shirts

Structural model for tubulin polymerization inhibition by colchicine site agents: A 3-D quantitative structure-activity relationship study.
Y. Fan, S-J. Zhang, S. Holden, J.B. Partridge,
N-S. Shen, T-N. Huang

NMR solution structure of the conserved 790 loop of 16S RRNA.
S. Varma, S. SantaLucia Jr.

Molecular modeling of the inhibition of mitochondrial malate dehydrogenase by cyclic AMP.
D.G. Harris, S. ScottZimmerman

Theoretical studies on the mechanism of electron transfer at the photosynthetic reaction center.
N. Miura, O. Kitao

Novel class of molecular shape descriptors and a method for validation of chemical diversity.
J. Liang

Optimizing small combinatorial libraries using a genetic algorithm.
D.J. Gordon, E.M. Bellott, B. Tenenbaum

Nonparametric analysis and design
of heteropolymer libraries. P. Constans, J.D. Hirst

Generation of isomers of organic molecules using genetic algorithms.
Q. Hui, W. Cai, M. Zhang

TheRate: A web-based tool for modeling kinetics of gas-phase reactions.
T.N. Truong, W.T. Duncan

Cerius2-SDK: A foundation for rapid local simulation software development.
M.A. VanDaelen, M.G. Peeler, S.D. Kahn

Scampi: Statistical classification of activities of molecules for pharmacophore identification.
X. Chen, A. Rusinko III, A. Tropsha, S.S. Young

Quantitative structure-activity relationships of RGD mimetics as fibrinogen-receptor antagonists.
M. Akamatsu, M. Miyashita, Y. Nakagawa, Y. Hayashi, Y. Sato, T. Fujita, T. Ueno

3-D-QSAR studies of taxoids and analogs.
M.A. Avery, J.B. Bhonsle, J.R. Woolfrey, J.K. Buolamwini, T. Mineno

Comparative molecular-field analysis 3-D-QSAR study of conformationally restricted cinnamyl HIV integrase inhibitors.
J.K. Buolamwini

Hologram QSAR of artemisinin analogs.
J.R. Woolfrey, C.R. Rodriges, M.Alvim-Gaston, E.J. Barreiro, F.E. Cohen, M.A.
Avery

3-D QSAR of peroxidic antimalarials based on artemisinin.
M.A. Avery, M. Alvim-Gaston, J.R. Woolfrey

3-D pharmacophore models of antimalarial drugs.
O.O. Clement, S.M. Efange

3-D QSAR of cyclic urea derivative as HIV-1 protease inhibitors.
A.K. Debnath

3-D QSAR of D4 antagonists based on full conformational searches and quantum
mechanically derived descriptors. M. Hennemann, T. Clark, H. Lanig

Quantum mechanical estimation of pK(HB).
M. Hennemann, T. Clark

Quantum mechanical and molecular mechanical modeling of enzyme-substrate interactions in alanine racemase.
M.J. Ondrechen, J.M. Briggs

Computational study of anomeric effects, stereoelectroni effects, and conformational energies of 2-substituted tetrahydro-2H-pyrans.
M.L. Kasner, F. Freeman, W.J. Hehre

Quantum chemical analysis of para-substitution effects on the electronic structure of phenylnitrenium ions in the gas phase and aqueous solution.
M.B. Sullivan, K. Brown, C.J. Cramer, D.G. Truhlar

Predicting NMR shielding by alkenes based on ab initio GIAO calculations.
N.H. Martin, N.W. Allen III, S.T. Ingrassia, E.K. Minga, J.D. Brown

Molecular mechanics (MM3) force-field development for tetravalent boron-containing compounds.
T.A. Holme, L.S. Fisher

Use of hexahydropyridobenzodioxins to examine the ability of molecular orbital methods to model hydrogen bonding.
W.H. Shelver, W.L. Shelver, K. Gholami

Low-barrier hydrogen bonds: Substituent effects on strength and geometry.
G.A. Kumar, M.A. McAllister

Solvation effect on stability of E/Z conformers of methyl acetate and its enolate anion: Ab initio combined QM/MM simulations.
K. Byun, J. Gao

Calibration of model core potentials: Application to the group 4 transition-metal halogen complexes.
S.A. Decker, M. Klobukowski, Y. Sakai, E. Miyoshi

Structure of liquid clusters of Lennard-Jones atoms.
B.G. Moore, A.A. Al-Quraishi

Computational methods for conformational analysis of unsymmetrical 1,3-diamines: 3-Aminotropanes.
J.B. Sorensen, A.H. Lewin, J.A. Dustman, J.P. Bowen

Computational study of organotellurium compounds.
H.N. Po, F. Freeman, W.J. Hehre

Paper 155: Reaction-class dynamical approach for modeling kinetics of gas-phase reactions.
D.K. Maity, T.N. Truong

Model potential of methane based on CCSD(T) calculations of methane dimers.
S. Tsuzuki, T. Uchimaru, M. Mikami, K. Tanabe

New tool for comparing vibrations of similar molecules and its application to models for the cysteine-linked tyrosyl radical from galactose oxidase.
R.A. Wheeler, K.E. Wise

Ab initio optimized geometric parameters for the 1,2-dinucleotide adducts of cisplatin.
F.H. Hausheer, P. Seetharamulu, S. Yao, J.D. Saxe, D. Reddy, K. Haridas, D. Murali, M. Zhao, P.N.V. Petluru

Recent developments in modeling nonlinear optical properties of inorganic complexes.
T. Zhou, T.R. Cundari, H.A. Kurtz

Applying ab initio methods toward improved protein circular dichroism calculations.
J.D. Hirst, N.A. Besley

Paper 161: Structure and energetics of Gd(III) interactions with water and ammonia.
E.D. Glendening, P.A. Petillo

Paper 162: Theoretical study of microscopic solvation of LiCl in water clusters: LiCl(H2O)n,
n=1–4.
D.E. Bacelo

Interaction of methanol with zeolitic petrochemical catalysts: A new ab initio embedded cluster study.
P. Treesukol, J. Vollmer, T.N. Truong, T. Limtrakul

Methodology for the optimization of chemical processes through statistical modeling with application on the nitration of bromobenzene.
A.C.R. Fabriani, E.A.N. Chrisman

Binding of divalent ligand to polyelectrolyte: A novel method to calculate the binding free energy and the salt dependence of free energy.
H. Ni, C. Anderson, M.T. Record, C.F. Charles

Parameterization and application of a generalized born model for proteins and nucleic acids.
B.N. Dominy, C.L. Brooks III

Modeling intermediate Q in the catalytic cycle of methane monooxygenase (MNO).
L.M. Thomson, M.B. Hall

Electronic structure and spectra of the ground and excited states of potential optical-limiting materials.
K.A. Nguyen, P.N. Day, R. Pachter

O(3P) reactions with alkanes (n=2–5), C2H5F, C2F6, C2F5Cl, and PHC2H5: A computational study of reaction mechanisms.
A. Gindulyte

Improved heats of formation from DFT calculations and an empirical group increment scheme.
L.R. Schmitz, N.L. Allinger, M. Chen, J. Labanowski

Molecular modeling of polymer melts and blends.
J.D. Weinhold, J.G. Curro

Wednesday Morning

Bridging the Gap Between Chemical Modeling and Engineering

Predicting thermophysical properties of multicomponent mixtures from
molecular simulations.
J.I. Siepmann, M.G. Martin, B. Chen, N.D. Zhuravlev, C. Wick

General approach for molecular simulation of phase equilibria in complex mixtures.
F.A. Escobedo

Molecular simulation of phase equilibria of 1-olefin systems.
I.G. Economou, T. Spyriouni, D.N. Theodorou

Methodologies for predicting thermal rate constants of gas-phase reactions.
T.N. Truong, W.T. Duncan

Improved calculation of bond dissociation energies of organic compounds based on the concept of stabilization energy.
E.A. Castro, M. Firpo, L. Gavernet

Hydrogen peroxide dissociation in supercritical water.
N. Akiya, P.E. Savage

New concept for the application of linear free-energy relationships in catalysis.
M.M. Ramírez-Corredores, I. Machín, M.E. Grillo

Using computational approaches to model hematite surfaces.
I. Lado-Touriño, F. Tsobnang, P. Ngoepe

Combinatorial Chemistry

Comparing methods of diversity selection for combinatorial chemistry and screening selection.
J.P. Holland, T.J. Mitchell

Paper 181: Rational selections from virtual libraries.
V.S. Lobanov, D.K. Agrafiotis, D.N. Rassokhin

Recent applications of ChemSpace shape similarity searching.
R.D. Cramer, M.A. Poss, M.A. Hermsmeier, T. Caulfield, M. Kowala

Leveraging HTS results to improve compound selection strategies.
M.G. Bures, Y.C. Martin

Paper 184: Diversity sampling: Selection, space coverage, and
visualization.
A. Tropsha, W. Zheng, G. Ethiraj, C.H. Reynolds, R. Druker, L.B. Pfahler, S.J. Chakravorty, T. Schlick, D. Xie

Evaluation of reagent-based and product-based strategies in the design of combinatorial libraries.
E.A. Jamois

Physical, Chemical, and Biological Property Prediction

Property prediction by combined simulation and QSAR/QSPR analysis.
A.J. Hopfinger, A. Kulkami, J.S. Duca

Density functional theory of spin-coupled diiron centers: -oxo-bis(-acetato) and -hydroxo-bis(-acetato) bridged models for diiron-oxo proteins.
J.K. McCusker, J.H. Rodriguez

Mathematical programming approach to DHFR inhibitor drug design.
A.K. Karalapakkam, L.E.K. Achenie

Prediction of physicochemical properties using a structure-fragment approach.
E.A. Kolovanov

Rapid calculation of polar molecular surface area and its application to the prediction of transport phenomena.
D.E. Clark

Wednesday Afternoon

Combinatorial Chemistry

Novel algorithms for the design of diverse and focused combinatorial libraries.
R.S. Pearlman, K.M. Smith

Sensitivity analysis and other tools for combinatorial library design.
E.J. Martin, A.K. Wong, J.M. Blaney, J.M. Hoeffel, J.M. Jansen

New developments in molecular diversity, similarity, and library design using both ligand and protein target-based information.
D.L. Cheney, J.S. Mason, B.R. Beno

Design of maximum information libraries as a highly efficient tool for lead generation: Theory and methods.
P. Beroza, R. Feinstein, J. Greene, B. Goldman, J.A. Mount, A. Smellie

Design of maximum information libraries as a highly efficient tool for lead generation: Application of the method.
E.K. Bradley, P. Beroza, J. Eksterowicz, H. Genin, P. Grootenhuis, D. Miller, J. Miller, J. Penzotti, W. Shirley, D. Spellmeyer, J. Srinivasan, R. Stanton

Search techniques used in identifying actives in a large HTS dataset.
P. Labute

Ligand Design and Biological Problems

Ligand docking for structure-based drug design.
X. Jiang, C.M. Venkatachalam, T. Oldfield, M. Waldman

Comparison of various docking strategies.
D. Joseph-McCarthy, B. Thomas, J.C. Alvarez

Design and synthesis of PDGFR-selective inhibitors.
C. Liang, C. Sun, G. McMahon, C. Tang

Computational approaches to ligand design against polymorphic targets.
R.J. Zauhar, G. Moyna, W.J. Welsh

Insights into -hairpin formation and stability from molecular dynamics simulation of short peptide folding.
H. Wang, S.S. Sung

Spontaneous base flipping in DNA.
Y-C. Chen, V. Mohan, R.H. Griffey

Physical, Chemical, and Biological Property Prediction

Estimation of gas-liquid critical properties.
A.N. Burgess, M.H. Barley, D. McCaughy

Prediction of liquid-crystal clearing temperatures from molecular structure.
P.C. Jurs, S.R. Johnson

3-D information-rich databases derived from quantum-mechanical calculations.
B. Beck, T. Clark, A. Horn, J. Carpenter

Molecular structure description: The electrotopological state.
L.H. Hall, L.B. Kier

Electrotopological state: Use in similarity and database management.
L.B. Kier, L.H. Hall

Thursday Morning

Combinatorial Chemistry

Structure-based library design: Application of new systematic protein-active site pharmacophore analysis.
I. Morize

Structure-based discovery and in-parallel optimization of novel competitive inhibitors of thymidylate synthase.
B. Shoichet, D. Tondi, U. Slomczynska, S. Ghelli, M. PaolaCosti, D.M. Watterson

Use of de novo structure-based design methods to focus combinatorial libraries.
E. Evensen, D. Joseph-McCarthy, G.A. Weiss, S.L. Schreiber, M. Karplus

Discovery of novel serine protease inhibitors by structure-based computational screening of virtual combinatorial libraries.
J.W. Liebeschuetz

Structure-based approaches to the design of combinatorial libraries.
J.H. VanDrie

Structure-based selection of combinatorial library subsets.
P. Johnson, A. Leach, J-F. Marchaland, Z. Szabo, M. Vargyas

General

Ab initio optimized geometric parameters for the DNA-base adducts of cisplatin.
P.N.V. Petluru, P. Seetharamulu, S. Yao, D. Reddy, K. Haridas, D. Murali, M. Zhao, F.H. Hausheer, J.D. Saxe

Effecient development of molecular mechanics parameters for transition metals.
W. Fu, T.R. Cundari

Classical conformational analysis to the max: Energy surfaces for disaccharides.
A.D. French, G.P. Johnson, M.K. Dowd, A-M. Kelterer

Canonical and Gibbs ensemble Monte Carlo simulations for systems with adiabatic separation of nuclear and electronic degrees of freedom.
B. Chen, J.I. Siepmann

IR and Raman spectra of bicyclic molecules using scaled correlated and noncorrelated force fields.
W.B. Collier, I. Magdo, T.D. Klots

Limitations of coupled cluster theory in predicting atomization energies.
D.F. Feller, K.A. Peterson

Physical, Chemical, and Biological Property Prediction

Using molecular hologram to predict n-octanol/water partition coefficient.
S-Y. Yue, N. Tomkinson, E. Roberts

Modeling partitioning phenomena with CM2-charge-based models for medium effects.
C.J. Cramer, J. Li, P.D. Winget, T. Zhu, D.G. Truhlar

Accurate prediction of solvation free energy and lipophilicity of organic molecules using atomic constants and fingerprints.
V.N. Viswanadhan, A.K. Ghose, U.C. Singh, J.J. Wendolowski

Modeling molecular interactions.
L.Y. Wilson, G.R. Famini

Use of quantum mechanics for QSPR and QSAR models with error estimation.
T. Clark, B. Beck, M. Breindl, M. Hennemann

Using the TLSER to investigate Henry's law constant and related properties.
G.R. Famini, D. Benyamin, C. Kim, R. Veerawat, L.Y. Wilson

Thursday Afternoon

Combinatorial Chemistry

Knowledge-based approach in designing combinatorial and medicinal chemistry libraries for drug discovery: 1.Qualitative and quantitative definitions of a druglike molecule.
A.K. Ghose, V.N. Viswanadhan, J.J. Wendolowski

Knowledge-based approach in designing combinatorial and medicinal chemistry libraries for drug discovery: 2. The design of a druglike library.
V.N. Viswanadhan, A.K. Ghose, A. Kiselyov, L. Smith, G. Rishton, J.J. Wendolowski

Chemsymphony: Java tools for handling diverse data in combinatorial chemistry.
P. Tebbutt, A. Krassavine, A. Hodgkin

NMR prediction software and tubeless NMR: An analytical tool for screening of combinatorial libraries.
A. Williams

General

Application of calibration transforming matrix method in simultaneous determination of tetradic mixtures of aromatic compounds using ultraspectrophotometry.
Q. Hui, W. Cai, M. Zhang

Adsorption of oxygen on reduced copper chromite catalyst.
R.A. Stowe, D.A. Hucul, R.K. Helling

Road to ammonium nitrate.
K.A. Mort, R.A. Jackson, P.J. Wilde

Physical, Chemical, and Biological Property Prediction

Using progressive scrambling to validate regression models.
R.D. Clark, J.M. Leonard

Prediction of molecular properties from momentum-space wavefunctions.
M.J. Sykes, E.F. McCoy

Empirically corrected ab initio thermochemistry.
K.K. Irikura, X. Wang

Linear-scaling
localized-density-matrix method and its applications.
G. Chen, S. Yokojima, W. Liang, D. Zhou, X. Wang




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