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The Computers in Chemistry Division
Spring 2001 ACS Meeting Program

SOCIAL EVENT:
Poster Session/Social Hour, Tue

BUSINESS MEETING: Sat

SUNDAY MORNING

Energy Landscapes of Proteins, Glasses, and Clusters: Dynamics, Folding, Function, and Prediction

Cosponsored with Division of Physical Chemistry

J. N. Onuchic, C. L. Brooks III, D. J. Wales, R. M. Stratt, Organizers

8:30—Introductory Remarks.

8:50—1. Award Address (ACS Award for Computers in Chemical & Pharmaceutical Research) Protein folding: Simple insights into a complex reaction. M. Karplus

9:30—Intermission.

9:50—2. Experimental landscapes for protein folding and misfolding. C. M. Dobson

10:30—3. Strip mining the energy landscape for physical insights. F. H. Stillinger

11:10—4. Wandering home in many dimensions: Trails of crumbs? R. S. Berry

Artificial Intelligence in Computational Chemistry

C. M. Breneman, Organizer

9:00—Introductory Remarks.

9:10—5. Self-organizing neural networks in drug design. J. Gasteiger

9:30—6. Comparison of 3-D physicochemical properties of ligands for the thromboxane A2 receptor using the Kohonen self-organizing maps technique. J. Petit, D. P. Vercauteren, J-M. Dogne, F. Durant

9:50—7. QSARs for binding affinity of inhibitors of human type 1 5a-reductase using structure-based descriptors. G. A. Bakken, P. C. Jurs

10:10—Intermission.

10:25—8. Boosting support vector machines for VHTS, ADME, and QSAR. C. M. Breneman, K. P. Bennett, M. J. Embrechts, J. Bi, A. Demiriz, L. Lockwood Jr., M. Momma, N. Sukumar

10:45—9. Text-influenced molecular indexing. S. B. Singh, R. D. Hull, E. M. Fluder

11:05—10. Quantitative structure-activity relationship models for the prediction of selective cyclooxygenase-2 inhibition. G. W. Kauffman, P. C. Jurs

11:25—11. Genetic algorithms for chemoinformatics. B. K. Lavine, C. Davidson

Computational Studies of Reaction Mechanisms and Enzyme Modes of Action

T. Clark, Organizer

8:30—Introductory Remarks.

8:40—12. DNA alkylation and photoionization patterns in the interior of guanine runs. P. R. LeBreton, Q. Zhu

9:10—13. Withdrawn.

9:40—14. Theoretical studies of DNA deamination: Pyrimidine ring opening and recyclizations in the nitrosative deaminations of guanine, cytosine, and adenine. R. Glaser, S. Rayat, M. Lewis, T. Carl, B. Hodgen

10:10—Intermission.

10:40—15. Conservation of electrostatic properties within enzyme families and superfamilies. D. R. Livesay, S. Subramaniam

11:00—16. Development and application of a new computational approach for studying enzyme reactions. Y. Zhang, H. Liu, W. Yang

11:20—17. Form, function, and dynamics of tetrapyrroles in proteins. J. A. Shelnutt

11:40—18. Novel insights into reaction mechanisms from computer-aided chemistry. D. Gallagher

SUNDAY AFTERNOON

Energy Landscapes of Proteins, Glasses, and Clusters: Dynamics, Folding, Function, and Prediction

Cosponsored with Division of Physical Chemistry

J. N. Onuchic, C. L. Brooks III, D. J. Wales, R. M. Stratt, Organizers

2:00—19. Energy landscapes and beyond. P. G. Wolynes

2:40—20. Structural properties and mechanistic role of early intermediates in protein folding. H. Roder, M. C. R. Shastry, H. Cheng

3:20—21. Dynamics of the primary processes of protein folding: Helix nucleation. J. H. Werner, R. M. Fesinmeyer, N. H. Andersen, R. B. Dyer

3:50—Intermission.

4:00—22. Exploring the energy landscape of peptides in explicit solvent. A. E. Garcia, K. Y. Sanbonmatsu

4:40—23. FOLD-X: An algorithm to predict and engineer folding pathways. L. Serrano, R. Guerois

Artificial Intelligence in Computational Chemistry

C. M. Breneman, Organizer

1:30—24. Improving activity classification of high-throughput screening data. A. Calvet, K. Johnson, G. Cowan

1:50—25. Overview of evolutionary algorithm applications in computer-aided molecular design. D. E. Clark

2:10—26. Comparisons of genetic algorithm-based descriptor selection methods for QSAR. M. J. Embrechts, C. M. Breneman, K. P. Bennett

2:30—Intermission.

2:45—27. Pattern recognition techniques in drug discovery. W. G. Richards, D. D. Robinson

3:05—28. Empirical intelligence in physical-property prediction. R. S. DeWitte, E. Kolovanov

3:25—29. Investigation of the performance and optimal composition of a genetic algorithm for the parametrization of the MM3 force field. T. Strassner, M. Busold, W. A. Herrmann

3:45—Concluding Remarks.

Computational Studies of Reaction Mechanisms and Enzyme Modes of Action

T. Clark, Organizer

1:30—30. Effect of surface phosphorus on the oxidative dehydrogenation of ethane: A first-principles investigation. A. Maiti, P. Kung, D. King-Smith, J. E. Miller, C. Zhang, G. Whitwell

2:00—31. Computational mechanistic studies to rationalize unusual stereo- and regiochemical outcomes of of extrusion/insertion reactions of iodine(III) and palladium(0) reagents. H. S. Rzepa, S. Martin-Santamaria, D. A. Widdowson, M. Carroll, V. Pike

2:30—32. Recent applications of density functional theory to complex reaction mechanisms. J. Weber, P. Boulet, F. Gilardoni, A. Goursot, M. J. Mayor-Lopez, H. Sidorenkova, T. A. Wesolowski

3:00—Intermission.

3:30—33. Nucleophilic or electrophilic phosphinidene complexes LnM=PH: What makes the difference? K. Lammertsma

4:00—34. Catalytic formation of three-membered rings: Comparing epoxidation, aziridination, and cyclopropanation. P-O. Norrby, T. Rasmussen, P. Brandt, C. Linde

4:30—35. Monte Carlo simulations of bimolecular electron transfer between myoglobin and cytochrome b5. I. V. Kurnikov, Z-X. Liang, J. M. Nocek, B. M. Hoffman, D. N. Beratan

MONDAY MORNING

Energy Landscapes of Proteins, Glasses, and Clusters: Dynamics, Folding, Function, and Prediction

Cosponsored with Division of Physical Chemistry
J. N. Onuchic, C. L. Brooks III, D. J. Wales, R. M. Stratt, Organizers

8:30—36. Energy landscapes: From clusters to biomolecules. D. J. Wales

9:10—37. Constrained simulations to test Adam and Gibbs theory. R. J. Speedy

9:50—38. Energy landscapes and dynamical anomalies in supercooled liquids. M. Dzugutov

10:10—Intermission.

10:30—39. Equilibrium and dynamical inherent structures: A cluster perspective. J. D. Doll

11:10—40. Potential energy landscapes and melting behavior of (H2O)n and (H2O)nH+ clusters. K. D. Jordan

11:50—41. Exploring energy landscapes using "ion chromatography." M. F. Jarrold

Methods for Addressing Time- and Length-Scale Problems in Molecular Simulations

Cosponsored with Division of Physical Chemistry

M. Challacombe, Organizer

8:00—Introductory Remarks.

8:05—42. Locality principle of chemistry and its reflection in O(N) algorithms. S. Goedecker

9:00—43. Linear-scaling methods for DFT calculations on very large systems with plane-wave accuracy. M. J. Gillan, D. R. Bowler

9:55—Intermission.

10:10—44. Linear-scaling DFT calculations with numerical atomic orbitals. P. Ordejón, J. M. Soler, E. Artacho, J. Javier, D. Sanchez-Portal, G. Alberto, J. Gale

11:05—45. Local methods for dynamical and nondynamical electron correlation. M. P. Head-Gordon

Computational Studies of Reaction Mechanisms and Enzyme Modes of Action

T. Clark, Organizer

8:00—46. Computational modeling of electron transfer in AhpF: Sequence, structure, function, and mechanism. A. Nayeem, L. Poole

8:20—47. Possible electron-transfer pathway(s) in nitrogenase: Application of a new semiempirical technique. T. Herz, N. Richards, J. R. Sabin

8:40—48. Role of quantum mechanical tunneling in enzyme catalysis explored by QM/MM calculations. I. H. Hillier, N. A. Burton, P. Faulder, L. Jitariu, R. M. Nicoll

9:10—49. Using computer simulations to elucidate the origin of enzyme catalysis. A. Warshel, J. Villà, M. Strajbl, J. Florián

9:40—Intermission.

10:10—50. DFT investigations of transition-metal-dependent enzymes. N. Richards, A. J. Boone, C. Chang, T. Herz

10:40—51. Hydrolysis of cyclic phosphodiester in ribonuclease A: An ab initio molecular dynamics study. F. Alber, P. Carloni

11:10—52. Theoretical characterization of the reaction intermediates in models of the nickel-iron and Fe-only hydrogenases. M. B. Hall

Designing Focused Libraries for Drug Discovery: Hit to Lead to Drug

C. H. Reynolds, A. Tropsha, Organizers, Presiding

8:45—Introductory Remarks.

9:00—53. Some nontrivial aspects of "similarity" in the contexts of focused library design and near-neighbor searching. R. S. Pearlman, K. M. Smith

9:30—54. Combinatorial library design using both properties and 3-D pharmacophore fingerprints. B. R. Beno, J. S. Mason

10:00—Intermission.

10:15—55. Combinatorial library design for maximum information. J. E. Eksterowicz, E. R. Evensen, C. H. Lemmen, G. P. Brady Jr., P. D. J. Grootenhuis, J. M. Blaney, D. C. Spellmeyer

10:45—56. Methods for compound selection focused on hits and application in drug discovery. F. Lebreton Stahura, L. Xue, J. Bajorath

11:15—57. Virtual high-throughput screening of large datasets using TAE/RECON descriptors. N. Sukumar, C. M. Breneman, W. P. Katt

MONDAY AFTERNOON

Energy Landscapes of Proteins, Glasses, and Clusters: Dynamics, Folding, Function, and Prediction

Cosponsored with Division of Physical Chemistry

J. N. Onuchic, C. L. Brooks III, D. J. Wales, R. M. Stratt, Organizers

2:00—58. Prediction of protein structure and function on a genomic scale. J. Skolnick, A. Kolinski, P. Rotkiewicz, B. Ilkowski

2:40—59. Prediction of folding mechanism for circular-permuted proteins. C. Clementi, P. A. Jennings, J. N. Onuchic

3:00—60. Ab initio prediction of the structures of clusters, crystals, peptides, and proteins. H. A. Scheraga, A. Liwo, J. Pillardy, J. Lee, C. Czaplewski, D. R. Ripoll, R. Wawak, Y. A. Arnautova, W. J. Wedemeyer, J. A. Saunders, K. D. Gibson

3:40—Intermission.

3:50—61. Evolutionary perspectives on protein folding. R. A. Goldstein

4:30—62. Associative memory Hamiltonians for structure prediction without homology. C. Hardin, M. Eastwood, Z. Luthey-Schulten, P. G. Wolynes

Methods for Addressing Time- and Length-Scale Problems in Molecular Simulations

Cosponsored with Division of Physical Chemistry

M. Challacombe, Organizer

1:00—63. Targeting specific eigenvectors with an arbitrary selection criteria. A. R. Tackett

1:55—64. Efficient computation of Hartree-Fock exchange matrices. E. Schwegler

2:50—Intermission.

3:10—65. Combining linear scaling and parallelization techniques in the Amsterdam Density Functional program. S. J. A. van Gisbergen, C. Fonseca Guerra, E. J. Baerends

4:05—66. Linear-scaling Gaussian orbital methods for the ab initio simulation of periodic systems. C. J. Tymczak, M. Challacombe

Computational Studies of Reaction Mechanisms and Enzyme Modes of Action

T. Clark, Organizer

1:30—67. Reaction mechanisms driven by the Jahn-Teller effect. I. B. Bersuker

2:00—68. QM/MM studies on reactions involving organic substrates and enzyme models. J. Chandrasekhar, W. L. Jorgensen

2:30—69. How do substrates enter and products exit the buried active sites of cytochrome P450 enzymes? An investigation by molecular dynamics simulation. R. C. Wade, P. Winn, S. K. Luedemann, R. Gauges, V. X. H. Lounnas

3:00—Intermission.

3:30—70. Mode of action of zinc-b-lactamases. K. M. Merz Jr.

4:00—71. b-Lactamase: A semiempirical study and novel mechanism. W. A. King, T. Clark

4:20—72. Reaction mechanism of protein kinases studied by semiempirical calculations. V. Helms, M. C. Hutter

4:40—73. Study of the reaction mechanism of bovine lens leucine aminopeptidase using semiempirical methods. G. Schuerer, T. Clark

Designing Focused Libraries for Drug Discovery: Hit to Lead to Drug

C. H. Reynolds, A. Tropsha, Organizers, Presiding

1:30—74. Methods for library design and comparison. R. P. Sheridan

2:00—75. Multiobjective approach to combinatorial library design. V. J. Gillet, W. Khatib, P. Willett, P. J. Fleming, D. V. S. Green

2:30—76. Computational design of libraries. D. S. Hartsough

3:00—Intermission.

3:15—77. On the similarity of chemistry spaces. G. M. Maggiora, V. Shanmugasundaram

3:45—78. Library design using deterministic inverse imaging. J-L. Faulon, M. D. Rintoul, D. P. Visco Jr.

4:15—79. Using topomer shape similarity to design "lead-hopping" libraries. R. D. Cramer

MONDAY EVENING

Sci-Mix

R. A. Wheeler, Organizer

8:00–10:00

136. See subsequent listing.

134. See subsequent listing.

135. See subsequent listing.

125. See subsequent listing.

123. See subsequent listing.

132. See subsequent listing.

133. See subsequent listing.

141. See subsequent listing.

140. See subsequent listing.

143. See subsequent listing.

139. See subsequent listing.

180. See subsequent listing.

218. See subsequent listing.

172. See subsequent listing.

171. See subsequent listing.

149. See subsequent listing.

168. See subsequent listing.

160. See subsequent listing.

159. See subsequent listing.

157. See subsequent listing.

148. See subsequent listing.

156. See subsequent listing.

181. See subsequent listing.

182. See subsequent listing.

TUESDAY MORNING

Energy Landscapes of Proteins, Glasses, and Clusters: Dynamics, Folding, Function, and Prediction

Cosponsored with Division of Physical Chemistry

J. N. Onuchic, C. L. Brooks III, D. J. Wales, R. M. Stratt, Organizers

8:30—80. Glass formation and liquid fragility interpreted in the landscape paradigm. C. A. Angell

9:10—81. Thermodynamics and aging of supercooled liquids: The energy landscape approach. F. Sciortino

9:30—82. How far do protein structures dictate the pathway of folding? The "fold approach." J. Clarke, E. Cota, S. B. Fowler, S. J. Hamill, A. Steward, C. Chothia

10:10—Intermission.

10:30—83. New methods for distributed dynamics: Folding proteins in all-atom detail with thousands of PCs. V. S. Pande

11:10—84. Multiple deep folding funnels and the winding index. C. R. Locker, R. Hernandez

11:30—85. IBM's Blue Gene Project to study protein folding: Early status report. W. Swope

Methods for Addressing Time- and Length-Scale Problems in Molecular Simulations

Cosponsored with Division of Physical Chemistry

M. Challacombe, Organizer

8:00—86. Efficient algorithms for density-matrix calculations and for geometry optimization. K. Németh, G. E. Scuseria, O. Coulaud, G. Monard, J. G. Ángyán

8:55—87. On complexity reduction for density-matrix computations. G. Beylkin, M. J. Mohlenkamp

9:50—Intermission.

10:10—88. Multiresolution density-matrix scheme for electronic structure calculations. A. M. N. Niklasson, C. J. Tymczak, H. Roder

11:05—89. Multiscale methods for solution of the Kohn-Sham equations. T. L. Beck

Computational Studies of Molecular Electronic Devices

O. G. Wiest, Organizer

9:00—Introductory Remarks.

9:05—90. Molecular bridges, molecular wires, and molecular interconnects: Mechanisms. M. Ratner, A. Nitzan, V. Mujica

9:50—91. Conductance in molecular films. A. M. Bratkovsky, P. E. Kornilovich

10:35—Intermission.

10:45—92. Field-induced geometrical relaxation effects in molecular rectifiers by ab initio quantum chemical calculations. B. Champagne

11:10—93. Influence of correlation and electron reduction on electronic transport properties of a molecular device. Y. Luo, C-K. Wang, Y. Fu

11:35—94. Computational studies of mixed-valence molecules for use in molecular electronics. O. Wiest, S. Braun-Sand

Designing Focused Libraries for Drug Discovery: Hit to Lead to Drug

A. Tropsha, C. H. Reynolds, Organizers, Presiding

9:00—95. In silico library design tools. K. M. Merz Jr.

9:30—96. Subcellular pharmacokinetics in library focusing. S. Balaz, V. Lukacova

10:00—Intermission.

10:15—97. Computer simulations for drug-lead development. W. L. Jorgensen, J. Tirado-Rives, R. C. Rizzo, M. L. Plount-Price, D. Wang, A. C. Pierce

10:45—98. Lead generation demonstrated by the use of a novel shape-based descriptor. R. V. Stanton, J. Srinivasan, E. K. Bradley, J. E. Eksterowicz, P. D. J. Grootenhuis

11:15—99. High-throughput lead discovery using predictive substructural analysis. D. Domine, J. Colinge, D. Church

11:45—Concluding Remarks.

Advances in 3-D Searching and Pharmacophores cosponsored with Division of Chemical Information (see page xx)

TUESDAY AFTERNOON

Energy Landscapes of Proteins, Glasses, and Clusters: Dynamics, Folding, Function, and Prediction

Cosponsored with Division of Physical Chemistry

J. N. Onuchic, C. L. Brooks III, D. J. Wales, R. M. Stratt, Organizers

2:00—100. Statistical mechanics of proteins: Perspective from analytical theory and simulations. E. Shakhnovich, J. Shimada, E. Kussell, N. Dokholyan

2:40—101. Molecular dynamics study of the mechanism and thermodynamics of folding of the src-SH3 protein. J-E. Shea, J. N. Onuchic, C. L. Brooks III

3:20—102. Evolutionary landscape of functional model proteins. J. D. Hirst

3:40—Intermission.

3:50—103. Protein structure prediction using distance information. J-L. Faulon, M. D. Rintoul

4:10—104. Understanding the folding of b-sheet proteins: Connection between theory and experiment. P. A. Jennings

4:50—105. Exploring conformational space in a de novo b-hairpin. H. Nymeyer, A. García, J. Onuchic

Methods for Addressing Time- and Length-Scale Problems in Molecular Simulations

Cosponsored with Division of Physical Chemistry

M. Challacombe, Organizer

1:00—106. Linear-scaling gradients of density functional theory. M. R. Salazar, M. Challacombe

1:55—107. Linear-scaling quantum chemistry calculation for excited states. G. Chen

2:50—Intermission.

3:10—108. Density-matrix minimization techniques for linear-scaling DFT calculations using nonorthogonal localized basis sets. P. D. Haynes, C. K. Gan, M. C. Payne

4:05—109. Efficient Chebyshev expansion method for density functional theory calculations with Gaussian orbitals. C. Saravanan, R. Baer, M. Head-Gordon, P. N. Ross

Computational Studies of Molecular Electronic Devices

O. G. Wiest, Organizer

1:30—110. Long-range electronic coupling of donor/acceptor sites in organic and organometallic systems: Theory and computation. M. D. Newton

2:15—111. Electronic transport in molecular devices. M. Di Ventra

3:00—Intermission.

3:10—112. Time-dependent density functional evolution for studying molecular wires. R. Baer

3:35—113. Photoexcitations in poly(p-phenylenevinylene) thin films. G. Chen

4:00—114. Energy landscapes for exciton motion in disordered organic semiconductors. D. Yaron, M. Pasquinelli

4:25—Concluding Remarks.

New Computer Architectures in Chemistry: Challenges and Benefits

A. C. Pineda, Organizer, Presiding

1:00—Introductory Remarks.

1:10—115. Advances in scalable cluster computing. M. S. Gordon, B. M. Bode, R. A. Kendall, D. Halstead

1:45—116. Performance of computational chemistry and materials codes on Linux superclusters. S. R. Atlas, A. C. Pineda, B. T. Smith, F. L. Gilfeather, A. A. Mammoli, M. Mahmoodi, J. Chen, M. Enlow

2:20—117. Multithreaded shared memory parallel implementation of the electronic structure code GAMESS. K. K. Baldridge, B. Bolding

2:55—118. New and emerging technologies destined to influence the practice of computational chemistry. T. M. Jackman

3:30—Intermission.

3:50—119. Scalability matters: High-performance architectures for computational chemistry. J. Landman, D. Zirl, R. Gomperts

4:25—120. Computational symbiosis: Coupling simulation and visualization on SMP machines. G. Johnson, A. Snavely

5:00—121. Mapping of parallel Monte Carlo and fast multipole algorithms on parallel machines. A. Majumdar

Advances in 3-D Searching and Pharmacophores cosponsored with Division of Chemical Information (see page xx)

TUESDAY EVENING

Convention Center
Sails Pavilion

General Posters

R. A. Wheeler, Organizer

7:00–10:00

122. Electron delocalization and the shell structure in atomic and molecular systems. P. M. Mitrasinovic

123. Following reaction pathways using a damped classical trajectory algorithm. H. P. Hratchian, H. B. Schlegel

124. Chemical graph theory approach for automated mechanism generation. A. T. Ratkiewicz, T. N. Truong

125. Cost-effective computation strategy for modeling mechanism of carbon gasification. A. Montoya, F. Modragón, T. N. Truong

126. Effects of hydrogen on the epitaxial growth of Ni. K. Haug

127. Hydrogenation of carbon monoxide on cobalt and rhodium. E. D. Glendening

128. Photocatalytic decomposition of NO on copper-exchanged ZSM-5: An embedded cluster approach. P. Treesukol, J. Limtrakul, T. N. Truong

129. A first-principles molecular dynamics simulation of magnesium ion in water. F. C. Lightstone, E. Schwegler, R. Q. Hood, F. Gygi, G. Galli

130. Time-dependent density functional theory study of the absorption spectra of substituted peroxy radicals. J. Weisman, M. Head-Gordon

131. Finite-field Lanczos method for calculation of hyperpolarizabilities. M. J. Ondrechen, L. F. Murga

132. On the prediction of nonlinear absorption for two-photon and reverse saturable absorption dyes using time-dependent density functional theory. K. A. Nguyen, P. N. Day, J. Kennel, R. Pachter

133. Ground and excited states of zinc complexes of porphyrin, tetraazaporphyrin, tetrabenzoporphyrin, and phthalocyanine: A density functional theory study. K. A. Nguyen, R. Pachter

134. Butadiene radical cations: Exploring the limits of DFT. J. Oxgaard, O. Wiest

135. Computational reevaluation of benzene-chlorine atom complexation. W. J. Kelly

136. Permanganate: A DFT study on the oxidation mechanism. T. Strassner, M. Busold

137. Theoretical study of transition-metal pyranyl complexes. J. E. Eilers, M. A. Cooper, M. J. Shaw

138. Regiochemistry of aryl nitrenium ion adduct formation with guanine. G. P. Ford, J. M. Parks

139. Computational study on the reaction mechanism of histone deacetylases. D-F. Wang, P. Helquist, N. L. Wiech, O. G. Wiest, A. J. Oliver

140. Catalytic mechanism of haloalkane dehalogenase: A combined QM/MM study of the initial reaction step. L. S. D. Kesavan, J. Gao

141. Opsin shift of bacteriorhodopsin in a DPPC bilayer: A combined molecular dynamics/configuration interaction study. R. Rajamani, J. Gao

142. Computational study of the catalytic properties of dihydrofolate reductase. T. H. Rod, C. L. Brooks III

143. Computational studies of a metallo-b-lactamase. F. R. Salsbury, C. L. Brooks III

144. Viral capsid chemistry: Understanding cleavage maturation in flock house virus. R. Morton, C. L. Brooks III, J. E. Johnson

145. Theoretical studies of RNA-metal binding. V. Tsui, D. A. Case

146. Entropy loss of hydroxyl groups of balanol upon binding to protein kinase A. J. A. McCammon, C. F. Wong, G. Gidofalvi

147. Predictive toxicology using quantum QSAR descriptors from excited states. S. Trohalaki, R. Pachter

148. Structure-activity relationships analysis using ab initio calculations and artificial neural networks. X. Tu, E. Geesaman, K. Wang, J. T. Arnason, C. M. Compadre, J. A. Darsey

149. Pharmacophore elucidation and comparison on ileal Na+/bile acid transporter inhibitors. X. Wang, W. J. Welsh, S. J. Tremont

150. Classification and regression tree model for prediction of potential estrogenic endocrine disruptors. H. Hong

151. Possible allosteric effects in anticancer compounds: A QSAR study. R. Garg, A. Kurup, C. Hansch

152. Comparative QSAR and toxicology of the aromatic nitro group. S. B. Mekapati, A. Kurup, R. Garg, C. Hansch

153. Comparative QSAR studies on topoisomerase-I inhibitors: Bi- and terbenzimidazoles. S. B. Mekapati, A. Kurup, R. Garg, C. Hansch

154. QSAR study on some tyrosine kinase inhibitors. A. Kurup, R. Garg, C. Hansch

155. Quantitative structure-permeability relationship analysis of diverse drug molecules through MDCK cell monolayers. S. Ren, S. S. C. Huang, E. J. Lien

156. Using theoretical descriptors in linear free-energy relationships: pKa. I. Chambi, M. Payne, L. Wilson, G. Famini

157. Structure-activity relationships of artemisinin analogs by comparative molecular similarity indices analysis. M. Alvim-Gaston, Y. A. Sabnis, M. A. Avery

158. CoMFA analysis of methylphenidate analogs with phenyl-ring substituents. C. A. Venanzi, R. A. Buono, M. Misra, O. Emenaka, Q. Shi, H. M. Deutsch, M. M. Schweri

159. Multiple conformer protocol: 3-D QSAR of flexible ligands. A. M. Doweyko

160. Profile-based recursive clustering algorithm. O. Buzko, K. M. Shokat

161. Protein family clustering as an aid to drug design. D. F. Sitkoff, S. R. Krystek, D. A. Bassolino, D. L. Cheney, M. E. Davis, D. Loughney, J. S. Mason

162. Prediction of ferredoxin-like selenoprotein in Japanese encephalitis virus. H. Zhong, E. W. Taylor

163. Theoretical investigations of the d-9 desaturase structure-function relationship. E. Vivas, C. Parish

164. Preparation of 3-D coordinates of small molecules from chemical structural formula. K. Nakamura, A. Itai

165. Molecular modeling studies of the Mosher configurational model. R. Lombardi, C. Parish

166. Comparing the conformational behavior of a series of enantiomeric cyclic urea HIV inhibitors using the low-mode and Monte Carlo conformational search methods. K. Sinclair, C. Parish

167. Molecular dynamics simulations and spectroscopic studies of amorphous tetraglyme [CH3O(CH2CH2O)4CH3] and tetraglyme:LiCF3SO3 structures. R. A. Wheeler, J-K. Hyun, H. Dong, C. P. Rhodes, R. Frech

168. Protocols for prediction of protein loop structure. D. L. Cheney, D. A. Bassolino, M. E. Davis, S. R. Krystek, D. R. Langley, T. R. Stouch

169. Conformational analysis of the nonplanar deformations of cobalt porphyrin complexes in the Cambridge structural database. L. Desai, M. Zimmer

170. Conformational/configurational analysis of all the binding geometries of cobalt(III) bleomycin. F. Fedeles, M. Zimmer

171. Computation of DNA conformational transitions: Base slippage in d(CTG)n triplet repeat DNA. E. J. Chambers, E. A. Price, M. Bayramyan, I. S. Haworth

172. Procedure for selecting starting conformations for energy minimization of nucleosides and nucleotides. D. G. Harris, J. Shao, J. M. Anderson, D. P. Marx, S. S. Zimmerman

173. Theoretical study of microscopic molecular structure of helicene/bisquinone aggregates. H. S. Choi, K. S. Kim

174. Molecular modeling of full-length HIV-1 integrase and its complexes with viral and human DNAs. Y. Tang, M. C. Nicklaus

175. Computational studies of a new library of HIV-1 integrase inhibitors. H. Ni, C. Sotriffer, A. J. McCammon

176. Identification of potential inhibitors against HIV-1 integrase via computer-aided drug design methods. I-J. Chen, N. Neamati, A. D. MacKerell Jr.

177. Docking and dynamics studies of ligands bound to HIV integrase. D. K. Chalmers, I. T. Crosby, J. Wielens

178. Comparative docking studies of the binding of polycyclic aromatic hydrocarbons to the estrogen receptor. K. W. Brown, S. B. Little, J. R. Rabinowitz

179. Docking and molecular dynamic studies of diacylglycerols binding to protein kinase C. S. Yan, D. M. Sigano, Y. Tang, J. H. Voigt, M. C. Nicklaus, V. E. Marquez

180. Comparative protein structure modeling and validation of falcipain2, a principal trophozoite cysteine protease of Plasmodium falciparum. Y. A. Sabnis, P. J. Rosenthal, M. A. Avery

181. Rapid and accurate recognition of pattern changes in 2-D NMR spectra. C. Peng, S. Szalma

182. MM3 parametrization of rhenium compounds using a genetic algorithm. T. Strassner, M. Busold, W. A. Herrmann

183. Pseudo-atomic models of swollen CCMV from cryo-electron microscopy. H. Liu, C. Qu, J. E. Johnson, D. A. Case

WEDNESDAY MORNING

Energy Landscapes of Proteins, Glasses, and Clusters: Dynamics, Folding, Function, and Prediction

Cosponsored with Division of Physical Chemistry

J. N. Onuchic, C. L. Brooks III, D. J. Wales, R. M. Stratt, Organizers

8:30—184. Kinetic partitioning mechanism in protein folding. D. Thirumalai

9:10—185. Structural and energetic heterogeneity in protein folding. S. S. Plotkin

9:50—186. Mesoscopic simulation of protein aggregation as a competitive process to refolding at finite protein concentration. D. Bratko, H. W. Blanch

10:10—Intermission.

10:30—187. How a b-sheet folds. M. Gruebele

11:10—188. Studying the landscape of an a-helix using 2-D IR spectroscopy. M. T. Zanni, J. Stenger, S. M. Decatur, R. M. Hochstrasser

11:30—189. Electron- and energy-transfer probes of protein folding. J. C. Lee, J. Lyubovitsky, I-J. Chang, H. B. Gray, J. R. Winkler

Methods for Addressing Time- and Length-Scale Problems in Molecular Simulations

Cosponsored with Division of Physical Chemistry

M. Challacombe, Organizer

8:00—190. Multiscale quantum models for biological macromolecules. D. M. York

8:55—191. Toward all-electron modeling of biomolecular systems. K. M. Merz Jr.

9:50—Intermission.

10:10—192. Meeting the challenge of length scales in materials modeling. E. A. Carter

11:05—193. Use and accuracy of O(N) DFT-based, Green's function electronic structure calculations for atomic- and continuum-scale materials science problems. D. D. Johnson, A. V. Smirnov

Visualizing Chemistry: Using Animations, Graphics, and Modeling To Teach Chemistry

R. S. Cole, Organizer, Presiding

8:30—Introductory Remarks.

8:35—194. Using computer animations to help students acquire models and to help students visualize chemistry at the particulate nature of matter level of representation. T. J. Greenbowe

9:20—195. Using digitized video, virtual reality, and molecular modeling in general chemistry. J. W. Moore, J. L. Holmes

10:05—196. Modeling matter: New ChemCom strategies to develop student understanding in high school chemistry. L. Langdon, A. Powers, R. Milne, H. Heikkinen

10:25—197. Designing media for learning chemistry. M. Tinnesand, R. Tasker

10:45—198. Making animations work for you: Sacrificing accuracy for understanding. J. L. March

11:05—199. Developing interactive educational animations using Macromedia Flash. S. M. Halpine

11:25—200. To visualize or not to visualize: That is the question. E. R. Scerri

11:45—Discussion.

Structure-Based Data Mining cosponsored with Division of Chemical Information (see page xx)
Computational Chemistry and Molecular Modeling Instruction cosponsored with Division of Chemical Education (see page xx)
Physical Organic Chemistry: Calculations, Mechanisms, and High-Energy Species cosponsored with Division of Organic Chemistry (see page xx)

WEDNESDAY AFTERNOON

Energy Landscapes of Proteins, Glasses, and Clusters: Dynamics, Folding, Function, and Prediction

Cosponsored with Division of Physical Chemistry

J. N. Onuchic, C. L. Brooks III, D. J. Wales, R. M. Stratt, Organizers

2:00—201. Statistical theory for protein combinatorial libraries. J. G. Saven

2:40—202. New model for solvation effect in protein folding. M. S. Cheung, J. N. Onuchic

3:00—203. Mapping protein unfolding/folding at atomic resolution. V. Daggett

3:40—Intermission.

3:50—204. Dynamics of contact formation in polypeptides. L. J. Lapidus, W. A. Eaton, J. Hofrichter

4:30—205. Prediction and design of protein structures and folding mechanisms. D. Baker

5:10—Concluding Remarks.

Methods for Addressing Time- and Length-Scale Problems in Molecular Simulations

Cosponsored with Division of Physical Chemistry

M. Challacombe, Organizer

1:00—206. Building large-scale polymeric systems. J-L. Faulon

1:55—207. First-principles molecular dynamics simulations: Successes and open problems. G. Galli

2:50—Intermission.

3:10—208. Concurrent multiscale simulation and coarse-grained molecular dynamics. R. E. Rudd

4:05—209. Multiscale modeling of a protein-DNA complex. A. Balaeff, K. Schulten

Visualizing Chemistry: Using Animations, Graphics, and Modeling To Teach Chemistry

R. S. Cole, Organizer
J. L. March, Presiding

1:30—Introductory Remarks.

1:35—210. Comparison of virtual models and hands-on models for teaching crystallography. I. L. Kelly, W. R. Robinson

2:20—211. Dynamic visualization in chemistry: Using multimedia to enhance learning. J. P. Birk, D. E. Leedy, R. Morgan

3:05—212. Graphics augmentation of HyperChem using TCL scripts. R. Starkey, W. Shay

3:25—213. Using molecular origami to explore molecular structure and bonding. R. M. Hanson

3:45—214. Teaching structure-function relationships in proteins with RasMol and Mage. S. W. Weiner

4:05—215. Molecular modeling program for teaching biochemistry. J. C. Dabrowiak, P. J. Hatala, M. P. McPike

4:25—216. Synthesis, IR spectroscopy, and vibrational analysis of benzenetricarbonylchromium(0): An inorganic experiment incorporating molecular modeling. E. J. Voss, I. A. Parlatore, D. S. Baker

4:45—Discussion.

Structure-Based Data Mining cosponsored with Division of Chemical Information (see page xx)
Computational Chemistry and Molecular Modeling Instruction cosponsored with Division of Chemical Education (see page xx)

WEDNESDAY EVENING

Convention Center
Sails Pavilion

Poster Session

Energy Landscapes of Proteins, Glasses, and Clusters

Cosponsored with Division of Physical Chemistry

J. N. Onuchic, R. A. Wheeler, Organizers

7:00–10:00

217. ProMatch: A program for distantly related protein homology modeling. H. Zhong, E. T. Kraemer, E. W. Taylor

218. Structure and dynamics of zymogenic form of blood coagulation factor X: Molecular dynamics investigation. D. Venkateswarlu, L. Perera, T. Darden, L. G. Pedersen

219. Computation of geometry necessary for nucleation: Self-assembly of diverse peptides. P. V. Narutis

220. Computer prediction of the water-mediated binding of peptides to class I MHC molecules. H-H. Bui, I. S. Haworth

221. Direct measurement of low-frequency dynamics of hydrated protein films using femtosecond Raman spectroscopy. C. J. Fecko, A. L. Stevens, J. D. Eaves, A. Tokmakoff

THURSDAY MORNING

Computers in Chemistry: General Theoretical

C. F. Wong, Presiding

8:30—222. Modeling macroscopic transport through ordered nanoporous membranes from atomistic principles. D. S. Sholl, A. Skoulidas

8:55—223. Withdrawn.

8:55—224. Cooperative dynamics in glassy systems: Energy landscape model. U. Mohanty

9:20—225. Origin of the heat capacity peak in a glass-forming mixture. H. Fynewever, F. Padilla, P. Harrowell

9:45—226. Fast numerical integrator for nonstationary stochastic dynamics. E. Hershkovitz, R. Hernandez

10:10—227. Multiple Taylor series expansions in geometry optimization of stereoregular polymers. B. Champagne, D. Jacquemin

10:35—228. Geometry optimization of solids using delocalized internal coordinates. J. W. Andzelm, R. D. King-Smith, G. Fitzgerald

11:00—229. Comparing the efficiency and accuracy of the projector augmented wave DFT method against Gaussian-based DFT methods. E. J. Bylaska, M. Valiev, J. H. Weare

Methods for Addressing Time- and Length-Scale Problems in Molecular Simulations

Cosponsored with Division of Physical Chemistry

M. Challacombe, Organizer

8:00—230. Withdrawn.

8:55—231. Multigrid methods for classical molecular dynamics. R. D. Skeel

9:50—Intermission.

10:10—232. Thermodynamical anomalies and optimization techniques. C. Tsallis

11:05—233. Quantum thermal annealing and sampling of systems with rough energy landscapes. B. J. Berne, Y-H. Lee

Computers in Chemistry: General Biochemical

W. D. Cornell, Organizer

8:30—234. "Four-phase" approach for priority setting of xenoestrogens. H. Fang, W. Tong

9:00—235. Carbohydrate-protein recognition in aqueous solution: Theoretical analysis of oligosaccharide binding to concanavalin A. R. A. Bryce

9:30—236. Withdrawn.

10:00—237. Conformation substates and transitions in carbon monoxymyoglobin by conformational flooding simulations. J. D. Evanseck, B. G. Schulze, H. Grubmuller

10:30—238. Design and development of new inhibitors of prostate-specific membrane antigen. A. J. Oliver, O. G. Wiest, M. J. Miller, M. Tenniswood

11:00—239. Development of CB1 receptor-based molecular superposition model for cannabimimetics. J-Y. Shim, W. J. Welsh, A. C. Howlett

THURSDAY AFTERNOON

Computers in Chemistry: General Theoretical

C. F. Wong, Presiding

1:00—240. Parallel adaptive solution of the Poisson-Boltzmann equation for large biomolecules. N. A. Baker, D. Sept, M. J. Holst, J. A. McCammon

1:30—241. Desolvation-cavity-induced microscopic cooperativity in b-sheet formation. C-L. Guo, H. Levine

2:00—242. Comparison of high-throughput property prediction methods. C. J. Blankley, E. M. Gifford

2:30—243. Application of nonparametric regression to QSAR. J. D. Hirst

3:00—244. Advances in electronic property-encoded molecular shape descriptors. C. M. Sundling, C. M. Breneman

3:30—245. Benzene quadrupolarity and arene-arene interactions. R. Glaser, Z. Wu

4:00—246. Quantitative characterization of the P–C bonds in ylides of phosphorus. P. M. Mitrasinovic, R. L. Fulton

4:30—247. Temperature and energy dependence of the HF stretch red shift in Arn-HF clusters. E. Curotto

Methods for Addressing Time- and Length-Scale Problems in Molecular Simulations

Cosponsored with Division of Physical Chemistry

M. Challacombe, Organizer

1:00—248. Long-timescale simulations of surface processes within harmonic transition-state theory. H. Jonsson, G. Henkelman

1:55—249. Extending atomistic simulation time scales. A. F. Voter

2:50—Intermission.

3:10—250. Protracted colored-noise dynamics: A novel method for the efficient relaxation of vitreous systems. J. W. Jenkins, P. J. Ludovice

4:05—251. Aggregation-volume-bias Monte Carlo: A novel Monte Carlo algorithm for simulating strongly associating fluids. B. Chen, J. M. Stubbs, J. I. Siepmann

Computers in Chemistry: General Biochemical

W. D. Cornell, Organizer

1:00—252. Finding putative protein targets of a small molecule by a computer approach. Y. Z. Chen

1:30—253. Modeling the deamidation of asparagine residues via succinimide intermediates in solution. V. Aviyente, A. Sungur Konuklar, G. Monard, M. Ruiz-Lopez

2:00—254. Pyridoxal phosphate in different protein environments: How does structure influence catalytic function? M. J. Ondrechen

2:30—255. Voltage-dependent interactions between the antimicrobial peptide alamethicin and model membranes. D. P. Tieleman, M. S. P. Sansom




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