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