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COMP Programming

Fall 2004 National Meeting
W. D. Cornell, Program Chair

OTHER SYMPOSIA OF INTEREST:

Academic Employment Initiative (see AEI, Mon)

Advances in Virtual High-Throughput Screening (see CINF, Wed, Thu)

Emerging Technologies in Chemical Information (see CINF, Sun)

Forging Leadership Pathways for Women in Science (see CINF, Sun)

Graduate Education in Chemical Informatics: Needs and Opportunities (see CINF, Mon)

Diversity and Chemogenomics (see MEDI, Mon)

Molecular Modeling on an Undergraduate Budget - A Symposium in Memory of Prof. Wayne P. Anderson (see CHED, Wed)

State of the Art - Rational Drug Design, Applications to Teaching (see CHED, Sun)

Teaching Bioinformatics in the Undergraduate Curriculum (see CHED, Sun)

Molecular Modeling in Environmental Chemistry (see ENVR, Sun)

Computational Chemistry (see INOR, Wed)

Computational Chemistry (see INOR, Sun)

NSF Sponsored Center for Workshops in the Chemical Sciences and the Impact of the Workshops on Curriculum Development (see CHED, Wed)

Integration of Analytical and Experimental Data into Enterprise-Wide Systems (see CINF, Mon)

BUSINESS MEETING: Sat

SUNDAY MORNING

 Section A

Pennsylvania Convention Center -- 109B

Docking and Scoring

Docking Programs

Cosponsored with CINF
G. L. Warren and N. Nevins, Organizers
G. McGaughey, Organizer, Presiding

9:00 — Introductory Remarks.

9:05 —1. Docking with water and post-docking analysis: New developments to the GOLD docking program. J. C. Cole

9:35 —2. Identification of novel p38 MAP kinase inhibitors using new Glide docking and scoring algorithms. T. A. Halgren, L. L. Frye, J. R. Greenwood, R. B. Murphy, R. A. Friesner

10:05 —3. Docking and scoring: Improvements in screening enrichment and docking accuracy. A. Jain

10:35 — Intermission.

10:45 —4. Modeling correlated protein main-chain and side-chain motions in ligand docking and screening. L. A. Kuhn, M. I. Zavodszky, S. Arora, M. Lei, M. F. Thorpe

11:15 —5. Docking conformationally flexible molecules with MVP. M. H. Lambert

11:45 —6. Scoring functions: What works and what doesn't. M. McGann

12:15 — Concluding Remarks.

 Section B

Pennsylvania Convention Center -- 104A&B

Computers in Chemistry General

W. D. Cornell, Organizer

8:20 —7. Biased torsional mutations and their role in conformational GA. A. Strizhev, R. D. Clark, E. Abrahamian, P. R. N. Wolohan

8:40 —8. Application of QM-QSAR method to predict mutagenicity of dental monomer. A. J. Holder, L. Ye, E. Kostoryze, C. Chappelow, J. D. Eick

9:00 —9. On the role of fluorine in intermolecular interactions. S. Mecozzi

9:20 —10. Possible regions of fullerene self-assembly in laser-produced plasma. P. M. Mitrasinovic

9:40 —11. Halide ions in a "methyl pocket": Competition between hydrogen bonding and ion-dipole interactions. Q. K. Timerghazin, T. N. Nguyen, G. Peslherbe

10:00 —12. From philosophy of computational quantum chemistry to philosophy of computational biology. B. Ma

10:20 —13. Integrated web-based grid-computing environment for research and collaboration in computational science and engineering. T. N. Truong

10:40 —14. Theoretical study of atmospherically important complexes of Criegee intermediate with water clusters and its reactions. A. Ryzhkov, P. Ariya

11:00 —15. Family 18 chitolectins: Comparison of MGP40 and GP39. P. Dalal, J. D. Madura, N. N. Aronson Jr.

11:20 —16. Chiral recognition by silver: A Q2MM study. E. Kieken, O. Wiest, P. Helquist, P. O. Norrby

11:40 —17. Nanoscale manipulation of hydrogen storage in NaAlH4: Exploring catalytic surfaces using density functional theory. S. Chaudhuri, P. Liu, J. T. Muckerman

12:00 —18. DFT study of the interactions of antiwear additives with iron and iron oxide. H. Wen, S. M. Opalka, C. V. Cooper

 

Molecular Modeling in Environmental Chemistry

Cosponsored with GEOC

SUNDAY AFTERNOON

 Section A

Pennsylvania Convention Center -- 109B

Docking and Scoring

Scoring Functions

Cosponsored with CINF
G. McGaughey and N. Nevins, Organizers
G. Warren, Organizer, Presiding

1:30 — Introductory Remarks.

1:35 —19. Methods of consensus scoring for in silico screening. K. M. Branson, B. J. Smith

2:05 —20. Can we learn from active ligands to improve the efficiency of virtual screening? The BHB scoring function. M. Feher, E. Deretey, S. Roy

2:35 —21. Native atom types for knowledge-based potentials: Application to binding energy prediction. B. N. Dominy, E. Shakhnovich

3:05 —22. SAR-directed docking. G. Skillman, S. Wlodek, M. Stahl, A. Nicholls

3:35 — Intermission.

3:45 —23. Modeling the active site of β-secretase: Application to drug discovery. R. Rajamani, C. H. Reynolds

4:15 —24. Evaluating scoring functions for docking and designing β-secretase inhibitors. M. K. Holloway, J. C. Culberson, J. Shpungin, S. Munshi, C. A. Coburn, S. J. Stachel, K. G. Jones, E. Loutzenhiser, A. R. Gregro, M. T. Lai, M. C. Crouthamel, B. L. Pietrak

4:45 —25. Improving docking enrichments by picking "the right pose". H. E. Purkey, E. Evensen, K. E. Lind, E. K. Bradley

5:15 — Concluding Remarks.

 Section B

Pennsylvania Convention Center -- 104A&B

Computers in Chemistry General

Quantum Chemistry


W. D. Cornell, Organizer

1:30 —26. Scalable second-order Moller-Plesset linear R12 method with non-exact HF orbitals. E. F. Valeev, C. L. Janssen

1:50 —27. Self-consistent relativistic density functional calculations including scalar and spin-orbit effects. J. E. Peralta, G. E. Scuseria

2:10 —28. Systematic improvement of approximate density functionals. V. N. Staroverov, G. E. Scuseria, J. P. Perdew, J. Tao, E. R. Davidson

2:30 —29. Transition metal chemistry: A step toward high accuracy description of structural and energetic properties. A. K. Wilson, P. Sinha, M. A. Omary, P. S. Bagus

2:50 —30. Nth-order derivatives of nuclear attraction integrals (NAIs) and electron repulsion integrals (ERIs). F. W. Aquino, J. H. Rodriguez

3:10 —31. On emerging fields of quantum chemistry at finite temperature. L. Wei

3:30 —32. Hybrid density functional studies of bulk actinide oxides. I. D. Prodan, K. N. Kudin, R. L. Martin, G. E. Scuseria

3:50 —33. Computational study of the C-H bond dissociation enthalpies and radical reactions with substituted ethylenes and benzenes. J. K. Merle, C. M. Hadad

4:10 —34. Correlation energy extrapolation by intrinsic scaling. L. Bytautas, K. Ruedenberg

4:30 —35. Computational estimates of the gas-phase basicities and proton affinities of the six isomers of dihydroxybenzoic acid. F. H. Yassin, D. S. Marynick

4:50 —36. Activation of the alpha carbon of an alpha,beta-unsaturated carbonyl compound toward nucleophilic attack: An experimental and theoretical study. D. C. Chatfield, E. Lewandowska, A. Gairola, C. D'Cunha, C. Alvarez

5:10 —37. Ab initio studies of methyl and t-butyl group motions in aromatic molecular solids. X. Wang, P. A. Beckmann, F. B. Mallory, M. M. Francl

 Section C

Pennsylvania Convention Center -- 106A&B

Emerging Technologies in Computational Chemistry


C. Breneman, Organizer

1:30 — Introductory Remarks.

1:40 —38. Near-neighbor net MD: A perturbation method for non-additive Hamiltonians. L. V. Woodcock

2:05 —39. Calculation of the binding affinities for Stromelysin-1 (MMP-3) inhibitors using a linear scaling semi-empirical quantum chemistry method. J. Li, C. H. Reynolds

2:30 —40. A new hybrid explicit/implicit solvent method for biomolecular simulations. M. S. Lee, M. Olson

2:55 — Intermission.

3:10 —41. ALL-QSAR: A novel automated lazy aearning QSAR Approach and its application to experimental datasets. S. Zhang, A. Golbraikh, A. Tropsha

3:35 —42. Automated Bayesian neural network modeling for chemists: Creating local models. N. R. McElroy, P. Bruneau

4:00 —43. Discovering cause-and-effect models in small formulation data sets using neurofuzzy logic. E. A. Colbourn, S. J. Roskilly, R. C. Rowe

4:25 — Awards Presentation.

 

State of the Art - Rational Drug Design, Applications to Teaching

Cosponsored with CHED

MONDAY MORNING

 Section A

Pennsylvania Convention Center -- 109A

Docking and Scoring

Docking Programs

Cosponsored with CINF
G. McGaughey and G. Warren, Organizers
N. Nevins, Organizer, Presiding

9:00 — Introductory Remarks.

9:05 —44. FlexX-Docking: Past, present and planned technological advancements. C. Lemmen, S. A. Hindle, M. Gastreich, I. Dramburg, H. Claußen

9:35 —45. Importance of accurate docking for potency prediction. C. McMartin

10:05 —46. Recent advances in AutoDock: Search, representation and scoring. G. M. Morris, R. Huey, W. Lindstrom, C. Li, Y. Zhao, W. E. Hart, R. Belew, M. F. Sanner, D. S. Goodsell, A. J. Olson

10:35 — Intermission.

10:45 —47. Model systems for docking. B. Shoichet

11:15 —48. Enhanced ligand docking and scoring with LigandFit. C. M. Venkatachalam, J. Jiang, A. Krammer, M. Waldman

11:45 —49. Ehits: Exhaustive flexible ligand docking with customizable scoring function tailored to protein families. Z. Zsoldos

12:15 — Concluding Remarks.

 Section B

Pennsylvania Convention Center -- 104A&B

Symposium in Honor of Henry F. Schaefer's 60th Birthday

Cosponsored with PHYS
P. V. R. Schleyer, E. R. Davidson, W. T. Borden, L. Radom, and P. R. Schreiner, Organizers

9:00 — Introductory Remarks.

9:30 —50. Bonding ideas out of calculations. R. Hoffmann

10:00 —51. MO crossings in cycloaromatization reactions. I. V. Alabugin

10:30 —52. In pursuit of subchemical accuracy in computational thermochemistry. W. D. Allen, M. Schuurman, S. Wheeler, J. P. Kenny, H. F. Schaefer III

11:00 —53. Two-component approach to molecular parity violation. R. Berger, C. van Wüllen

11:30 —54. Investigations of the properties of functionalized single-walled carbon nanotubes. H. F. Bettinger

12:00 —55. Interallylic bonding in the transition structures for degenerate Cope rearrangements: Modification by substituents and by strain, and the effects of changes in interallylic bonding on the calculated barrier heights. W. T. Borden

MONDAY AFTERNOON

 Section A

Pennsylvania Convention Center -- 109B

Docking and Scoring

De novo Design/Lead Progression

Cosponsored with CINF
G. McGaughey and N. Nevins, Organizers
G. Warren, Organizer, Presiding

1:30 — Introductory Remarks.

1:35 —56. Limitations of interactive drug design: Can de novo programs fill the gap? R. S. Bohacek

2:05 —57. Interactive rapid ligand prototyping: The MindRocket. C. M. W. Ho

2:35 —58. Improved methods for the de novo design of synthetically accessible ligands. A. P. Johnson, K. Boda, T. Lengyel, S. Weaver

3:05 — Intermission.

3:15 —59. Automated de novo design with LUDI, minimizer, QSAR, and scoring functions: Development and validation of AutoLudi. M. Lim-Wilby, J. Srinivasan, J. Koska, A. Krammer, C. M. Venkatachalam, M. Waldman

3:45 —60. Combinatorial computational ligand optimization. B. Tidor

4:15 — Concluding Remarks.

 Section B

Pennsylvania Convention Center -- 104A&B

Symposium in Honor of Henry F. Schaefer's 60th Birthday

Cosponsored with PHYS
P. V. R. Schleyer, E. R. Davidson, W. T. Borden, L. Radom, and P. R. Schreiner, Organizers

1:30 —113. Using decompositions in electronic structure methods to obtain reduced scaling. H. Koch, T. B. Pedersen, A. Sánchez de Merás

2:00 —62. Aromaticity beyond the organic chemistry domain. Z. Chen

2:30 —63. Diverting diradicals: From methylene to metal-dioxygen complexes. C. J. Cramer

3:00 —64. Coupled cluster calculations of optical rotation. T. D. Crawford

3:30 —65. Modeling mechanisms of hydron transfer in the condensed phase. N. A. Burton, R. Sharma, S. Nunez, G. Tresadern, I. H. Hillier

4:00 —66. Insights into mesoscale and electronic events during keV particle bombardment of solids. B. J. Garrison

4:30 —67. High-accuracy first-principles rovibrational spectroscopy. A. G. Császár

 

Integration of Analytical and Experimental Data into Enterprise-Wide Systems

Cosponsored with CINF

MONDAY EVENING

 Section A

Pennsylvania Convention Center -- 202B

Sci-Mix


W. D. Cornell, Presiding

8:00 - 10:00 68. Withdrawn.

69. Linking chemical and biological data using ChemCart and SRS Gateway for Oracle. M. Sud, A. Schafferhans, D. León, Y. Shimshock

70. Mechanistic insight from computer models of tyrosine kinase mutations that cause ligand-independent activation of the receptor. M. Torrent, K. Rickert, B. Sheng-Pan, L. Sepp-Lorenzino

71. Computational identification of proteins for selectivity assays. S. Yoon, A. Smellie, D. S. Hartsough, A. Filikov

72. Physical basis for conformational energies in substituted ethanes. R. F. See

73. De novo computational method to increase ligand-receptor binding selectivity. D. L. Chen, G. E. Kellogg

74. Analysis of changes of protein fluctuation upon ligand binding and incorporation of protein fluctuation into scoring function development for structural-based drug design. C. Y. Yang, R. Wang, S. Wang

75. Calculations of hydration force. L. Tian, R. Zauhar

76. Can a QSAR model reliably predict a query compound’s activity? L. He, P. C. Jurs

77. Characterization of the ice/water interface with TIP4P-Ew water. T. J. Dick, J. D. Madura, P. Dalal

78. Redesigning interaction specificity of short peptide oligomerization domains. C. M. Taylor, M. H. Ali, B. Imperiali, A. E. Keating

79. Trajectory and energy perturbed multiple microcanonical ensemble simulations for mapping potential energy landscapes and conformations of polypeptides. Z. Huang, R. A. Wheeler

80. Improved workflow and results in the NMR lab: Integrated processing, prediction, searching, and data management. V. Rafalovsky, M. Scandone, D. Kernan

81. Modeling outer-sphere disorder in the symmetry breaking of PPV. L. A. Liu, D. Yaron

82. Structure and stability of lower fullerenes C38-C50 and nitrogen-substituted heterofullerenes. G. Sun

128. See subsequent listings.

TUESDAY MORNING

 Section A

Pennsylvania Convention Center -- 109B

Docking and Scoring

Docking Evaluations

Cosponsored with CINF
N. Nevins and G. Warren, Organizers
G. McGaughey, Organizer, Presiding

9:00 — Introductory Remarks.

9:05 —83. BOMB for growing and scoring protein-ligand complexes. W. L. Jorgensen, J. Tirado-Rives

9:35 —84. CAPRI: Assessing protein docking algorithms in the blind structure prediction of protein-protein complexes. J. Janin

10:05 —85. Interdependence of docking performance and scoring accuracy in virtual screening. M. Kontoyianni, L. McClellan, G. Sokol

10:35 — Intermission.

10:45 —86. Virtual ligand screening by combined use of two grid-based docking methods, FLOG and ICM. V. N. Maiorov, R. P. Sheridan

11:15 —87. Critical assessment of docking programs and scoring functions. G. L. Warren, W. Andrews III, A. M. Capelli, B. P. Clarke, J. M. LaLonde, M. H. Lambert, M. Lindvall, N. Nevins, C. E. Peishoff, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, M. S. Head

11:45 —88. Improving the enrichment of high-throughput docking results using machine learning. A. E. Klon, M. Glick, J. W. Davies

12:15 — Concluding Remarks.

 Section B

Pennsylvania Convention Center -- 104A&B

Symposium in Honor of Henry F. Schaefer's 60th Birthday

Cosponsored with PHYS
P. V. R. Schleyer, E. R. Davidson, W. T. Borden, L. Radom, and P. R. Schreiner, Organizers

9:00 —89. Computational main group thermochemistry. D. A. Dixon, W. A. deJong, K. A. Peterson

9:30 —90. Remarkable structures and interaction potentials of clusters of molecular hydrogen and acetylenes. C. E. Dykstra

10:00 —91. Adventures in the land of triple bonds: The bonding situation in heavy-atom homologues of acetylene. G. Frenking

10:30 —92. Theoretical prediction of spectra. M. Frisch

11:00 —93. Reactions of ozone with acetylene: Density functional theory for concerted and stepwise mechanisms. J. D. Goddard, C. Weng, W. T. Chan

11:30 —94. Computational study of the mechanism and reactivity for the alkaline hydrolysis of N-phenylacetamides. B. Galabov, S. Ilieva, D. Cheshmedzhieva

 Section C

Pennsylvania Convention Center -- 106A&B

3-D Visualization Technology for Teaching Chemistry

Cosponsored with CHED, and CINF
S. A. Fleming, Organizer

9:00 — Introductory Remarks.

9:10 —95. Animations of intrinsic reaction coordinates for pericyclic and pseudopericyclic reactions, including valley-ridge inflection points. D. M. Birney, C. Zhou, S. V. Addepalli

9:40 —96. Conquer without dividing: Volume rendering of intact molecular charge densities effectively illustrates key concepts in bonding and reactivity. P. J. MacDougall, C. E. Henze

10:10 —97. Modeling, simulations and visualization in materials chemistry. T. Cagin

10:40 — Intermission.

11:00 —98. SymApps: A 3-D point group calculation and visualization tool. V. Rafalovsky, K. Nedwed, M. Scandone, G. M. Banik, D. Kernan

11:30 —99. Mol4D: Visualization and interactivity. J. H. Borkent

12:00 —100. VRML in the undergraduate curriculum. C. P. Calloway

TUESDAY AFTERNOON

 Section A

Pennsylvania Convention Center -- 109B

Docking and Scoring

Scoring Functions

Cosponsored with CINF
G. McGaughey and G. Warren, Organizers
N. Nevins, Organizer, Presiding

1:30 — Introductory Remarks.

1:35 —101. PMF scoring revisited. I. A. Muegge

2:05 —102. Application of HINT interaction scores and Hydropathic Intermolecular Field Analysis (HIFA) to the prediction of ligand binding affinity. S. F. Semus, G. E. Kellogg

2:35 —103. How well can we score now and where do we go from here: Comprehensive evaluation of 13 scoring functions on 800 protein-ligand complexes and development of new scoring functions. S. Wang, R. Wang, X. Fang, C. Y. Yang, Y. Lu

3:05 — Intermission.

3:15 —104. Improving accuracy in protein-ligand affinity calculations. M. K. Gilson, C. E. Chang, W. Chen

3:45 —105. Potential functions for virtual screening and ligand binding calculations: Some theoretical considerations. K. A. Sharp

4:15 —106. End-point free energy calculations: Synergy from continuum solvent and molecular dynamics methods. J. M. J. Swanson, J. A. McCammon

4:45 — Concluding Remarks.

 Section B

Pennsylvania Convention Center -- 104A&B

Symposium in Honor of Henry F. Schaefer's 60th Birthday

Cosponsored with PHYS
P. V. R. Schleyer, E. R. Davidson, W. T. Borden, L. Radom, and P. R. Schreiner, Organizers

1:30 —107. First principles predictions of the tertiary structures for membrane proteins. W. A. Goddard III

2:00 —108. Time-dependent density functional theory applied to carotenoids, chlorophylls and porphyrins. M. P. Head-Gordon

2:30 —109. Multireference spin-adapted variant of density functional theory. M. R. Hoffmann, Y. G. Khait

3:00 —110. Future prospects for Brillouin-Wigner-based quantum chemical methods. I. Hubac, S. Wilson, J. Pittner, P. Carsky

3:30 —111. Polarization consistent basis sets. F. Jensen

4:00 —112. Sigma bonds prevent short pi bonds. E. D. Jemmis, B. Pathak, H. F. Schaefer III, R. B. King

4:30 —61. Insights from momentum space. E. R. Davidson

 Section C

Pennsylvania Convention Center -- 106A&B

3-D Visualization Technology for Teaching Chemistry

Cosponsored with CHED, and CINF
S. A. Fleming, Organizer

1:30 — Introductory Remarks.

1:40 —114. Adding the third dimension to the chemistry lecture hall. J. J. Grabowski

2:10 —115. A novel mass spectrometry internet teaching tool. M. E. Bier, C. G. Yang, J. J. Grabowski

2:40 —116. VS-C: Cross-linked studies in chemistry. G. Fels

3:10 — Intermission.

3:30 —117. Web term papers: Learning structural biology through the creation of website content. W. H. Gallagher

4:00 —118. Animations of bio-organic reactions. P. B. Savage, S. A. Fleming

TUESDAY EVENING

 Section A

Pennsylvania Convention Center -- Hall D

General Poster Session


W. D. Cornell, Organizer

6:00 - 8:00

119. AEI: Knowledge-based potentials in drug design. B. N. Dominy

120. CoLiBRI: A novel method for the prediction of complementary ligands based on receptor information and its application to database screening. S. Oloff, S. Zhang, A. Tropsha

121. Parallel simulations of four-atom wavepacket dynamics. D. M. Medvedev, S. K. Gray, E. M. Goldfield

122. Computational design of protein complex with non-biological cofactor. W. Wang, F. Cochran, V. Nanda, S. Wu, M. J. Therien, W. F. DeGrado, J. G. Saven

123. Molecular dynamics simulation of E-coli dihydrofolate reductase and its circular permuted variants: Relative stabilities in experiment and simulations. Z. Hu, B. Ma, R. Nussinov, W. M. Southerland

124. Computational evaluation of stereoelectronic effects in fluorinated amines. J. J. Urban

125. Computational modeling studies of multi-targeted antifolates. A. J. Jackson, Z. Hu, W. M. Southerland

126. New algorithms for computational chemistry: Partial charges, resonance forms, symmetry, and conformational search. M. K. Gilson, M. J. Potter, W. Chen, H. S. R. Gilson, J. Huang

127. Computational studies of MALDI matrices interacting with tripeptides as a model of MALDI matrix-analyte interactions. F. H. Yassin, D. S. Marynick

128. Computational study of hyperthermophilic indole glycerol phosphate synthase: Structural alterations at the active site with temperature. D. Mazumder, T. C. Bruice

129. Computational study of the structure of di-lithium Phthalocyanine/Pyrite interface. Y. Zhang, L. G. Scanlon, P. B. Balbuena

130. Computational study on the role of bridging water molecules in the energetics of protein-ligand binding. M. Fornabaio, P. Cozzini, F. Spyrakis, A. Mozzarelli, D. J. Abraham, G. E. Kellogg

131. Computer simulation of acetone with a polarizable potential model. T. M. Chang, T. Lerro

132. Free energy calculations from non-equilibrium pulling simulations on a single peptide molecule. H. Xiong, H. P. Cheng, A. Roitberg

133. Computing the intrinsic conformational preferences of substituted cyclohexanes and tetrahydropyrans: Some surprises and new insights. A. K. Jones, G. S. Tschumper

134. Conformational analysis of piperazine and piperidine analogs of GBR12909: Effect of force field and solvent. D. Pandit, W. Roosma, M. Misra, K. M. Gilbert, D. Matecka, T. Prisinzano, K. C. Rice, C. A. Venanzi

135. Conformational study of polypeptides implicated in Alzheimer’s disease. T. H. Click, Z. Huang, R. A. Wheeler

136. Cytosine radicals and their respective anions: Molecular structure and electron affinities. D. J. Zhang

137. Defining privileged reagents using sub-similarity comparison: A method for reagent ranking. B. A. Tounge, C. H. Reynolds

138. Designing a combinatorial library of mutation-resistant HIV protease inhibitors. S. Chellappan, M. X. Fernandes, M. K. Gilson

139. Determination of cysteine pKas in a copper chaperone. R. R. Abd El-Rahman, J. D. Madura, C. T. Dameron

140. Determining partial atomic charges for fragments used in de novo drug design. J. L. Ludington, T. T. Fujimoto, F. P. Hollinger

141. Development of an effective strategy for lead docking. D. Cheney, L. Mueller, D. R. Langley

142. DFT, molecular dynamics, and free energy calculations on the multi-coordinate Cu(I)-binding protein Hah1. K. M. Merz Jr., B. T. Op't Holt

143. Effects of grid sizes on the calculation of solvation free energy in a quantum continuum solvation model. K. M. Merz Jr., N. Liao

144. Estimation of conformational entropy loss in protein-ligand binding process using 2-D and 3-D graph indices. X. Fang, R. Wang, S. Wang

145. Evaluation of semi-empirical methods for protein minimization and decoy discrimination. A. M. Wollacott, K. M. Merz Jr.

146. Human intestinal absorption (HIA) model using simple molecular descriptors. M. D'Souza, G. M. Banik

147. Fuzzy clustering as a means of classifying conformations of a flexible dopamine reuptake inhibitor. M. Misra, A. Banerjee, R. N. Davé, C. A. Venanzi

148. Homology modeling studies of Yersinia Kinase YpkA: Implications for structure-based drug design. X. Hu, G. Prehna, C. E. Stebbins

149. Ligand-based design of pyridinone derivatives with potential activity against mutant strains of HIV-1 reverse transcriptase. J. L. Medina-Franco, S. Rodríguez-Morales, A. Hernandez, C. Juárez-Gordiano, J. Jimenez-Barbero, R. Castillo

150. MD/NMR characterization of internal motions of peptide toxins. D. C. Chatfield, C. D'Cunha, A. Gairola, A. Augsten

151. Computational combinatorial protein design: Sequence search and statistical design. X. Yang, J. G. Saven

152. Filling the gap between conventional and “mean-field” molecular dynamics: Implementing the EXACT approximation. C. A. Hixson, J. Chen, Z. Huang, R. Wheeler

153. Fragmentation analysis of vibrational circular dichroism of polypeptides. J. H. Choi, M. Cho

154. Full quantum mechanical ab initio computation of protein-ligand interaction energy and QM map for protein-ligand binding. A. Gao, J. Z. H. Zhang

155. Important roles of crystallographic water molecules in protein-ligand interaction: A comprehensive analysis of water molecules observed in the X-ray crystal structures of protein-ligand complex. Y. Lu, R. Wang, C. Y. Yang, S. Wang

156. In silico screening for the hERG K+ ion channel affinity. M. Song, J. Bi, C. M. Breneman

157. Investigation of salt bridge strength in the Generalized Born water solvation model. R. Geney, C. L. Simmerling

158. Investigation of selenium-aromatic ring interaction in proteins. I. Hartman, R. Zauhar

159. MD simulation study of NMA-methanol system: Calculations of linear and nonlinear vibrational spectra. K. Kwac, M. Cho

160. Method for computing protein binding affinity. C. F. F. Karney, J. E. Ferrara, S. Brunner

161. Minimizing Lennard-Jones-dipole-dipole clusters: Improvements on the basin hopping strategy for parameter space searches. E. Curotto, C. Oppenheimer

162. Molecular dynamics simulations of the Glutamate Receptor GluR2 tetramer structure. K. Speranskiy, M. Kurnikova

163. Mutational studies of the Trp-cage mini-protein. M. M. Layten, B. A. Strockbine, N. H. Andersen, C. L. Simmerling

164. New scoring functions for discovery of lead peptides inhibitors for thrombin. C. Clement, M. Philipp

165. Non-Hamiltonian hybrid Monte Carlo algorithms for biophysical systems. M. Eleftheriou, G. Martyna

166. Novel conformational searching technique for low degree polymers. A. B. Silver, K. Sohlberg

167. Prediction of ligand binding modes and binding affinities of SAH/MTA nucleosidase inhibitors. J. K. Perry, V. A. Feher

168. Pyrolysis of styrene. J. Rienstra-Kiracofe, T. Pham, M. C. Lin

169. QSAR and molecular modeling studies of small molecule inhibitors of Plasminogen Activator Inhibitor-1. K. Y. Fan, H. Elokdah, D. L. Crandall, A. Aulabaugh, A. H. Katz

170. Quantum mechanical and docking studies of acetylcholinesterase inhibitors of the N-arylmaleimide type. J. L. Medina-Franco, R. T. Lino Joel, S. Rodríguez-Morales, R. Castillo, P. Melchor-Macias, J. Trujillo-Ferrara

171. 3D-QSAR comparative molecular field analysis on opioid receptor antagonists: Pooling data from different studies. Y. Peng, S. M. Keenan, Q. Zhang, V. Kholodovych, W. J. Welsh

172. Ab initio predictions of the heats of formation of nitroprismanes. T. P. Hamilton, O. Olubajo

173. Ab initio studies of the structure and bonding of sulfur and sulfoxonium ylides. J. M. Standard, B. A. Copack, T. K. Johnson, D. E. Przybyla, K. J. McDonald, R. J. Steidl, B. N. Ida

174. Ab initio studies on the structure and stability of the anion trimers of hydrogen fluoride, water and ammonia. X. Bai, P. Yang, R. E. Brown

175. Accurate calculation of aqueous host-guest binding affinities. W. Chen, C. E. Chang, M. K. Gilson

176. Analysis of protein-oligosaccharide docking interactions using principal component analysis. J. Leiss, P. Dalal, J. D. Madura

177. Characterization of unbound conformations of gp120 core domain. Y. Pan, B. Ma, R. Nussinov

178. Clustering analysis of flexible GBR 12909 dialkyl piperazine and piperidine analogs. K. M. Gilbert, D. Matecka, T. Prisinzano, K. C. Rice, C. A. Venanzi

179. Collection of binding affinities for protein-ligand complexes with known 3-D structures: The PDBbind database. R. Wang, X. Fang, Y. Lu, C. Y. Yang, S. Wang

180. Component-based integration of chemistry and optimization software. J. P. Kenny, S. J. Benson, Y. Alexeev, J. Sarich, C. L. Janssen, L. Curfman McInnes, M. Krishnan, J. Nieplocha, E. R. Jurrus, C. A. Fahlstrom, T. L. Windus, D. E. Bernholdt

181. Computational approach to find selective Cox-2 inhibitors. M. Kumar, R. J. Zauhar

182. Intramolecular proton migration in fully deprotonated myo-inositol 2-monophosphate and the formation of four-center hydrogen bonds. P. Yang, X. Bai, R. E. Brown

183. Quantum chemical approach to understand the contribution of ligand functional groups to estrogen receptor-a/b selectivity. R. J. Unwalla, E. S. Manas

184. Refinement of ligand structure from a comparison of experimental and calculated chemical shift perturbations. B. Wang, K. Raha, K. M. Merz Jr

185. Selectivity between alkali-metal ions to 12-Crown-4 in MeOH: A Monte Carlo simulations study. H. S. Kim

186. Shape signatures and receptor based drug design. L. Tian, R. J. Zauhar

187. Simulation studies of helical m-phenylene ethynylene foldamers. O. S. Lee, J. G. Saven

188. The computational study of the deprotonation of cyclohexene oxide catalyzed by isopinocampheyl based chiral lithium amides. Y. Xiao, D. Jung, T. Gund, S. V. Malhotra

189. Theoretical study of the electron density distributions in a dipeptide molecule. K. M. Merz Jr., N. Yu

190. Towards novel therapeutics against HIV infection and drug resistance. Y. Che, G. R. Marshall, B. R. Brooks

191. Using similarity and classification methods to determine applicability of QSAR models to query set compounds. R. Guha, P. C. Jurs

192. Using walkers to find transition states from reactant and product minima. H. P. Hratchian, H. B. Schlegel

193. "Reverse-docking" as a computational tool for the study of asymmetric organocatalysis. D. J. Harriman, G. Deslongchamps

WEDNESDAY MORNING

 Section A

Pennsylvania Convention Center -- 104A&B

Symposium in Honor of Henry F. Schaefer's 60th Birthday

Cosponsored with PHYS
P. V. R. Schleyer, E. R. Davidson, W. T. Borden, L. Radom, and P. R. Schreiner, Organizers

9:00 —194. Theoretical studies of atmospheric chemistry and developments in coupled-cluster theory. T. J. Lee

9:30 —195. Computational studies of molecular frame photoelectron angular distributions. R. R. Lucchese

10:00 —196. Modeling molecular interactions in MALDI mass spectrometry. D. S. Marynick

10:30 —197. Two face-to-face benzenes and o,o'-dibenzene: Electronic states and photochemical interconversion. J. Tonne, M. Schottelius, J. Chalupsky, Z. Havlas, H. Prinzbach, J. Michl

11:00 —198. Theoretical design of ion selective receptors. K. S. Kim

11:30 —199. Computational studies of the O-O bond activation and olefin epoxidation catalyzed by Mn-Salen complexes. K. Morokuma, I. V. Khavrutskii, R. R. Rahim, D. G. Musaev

 Section B

Pennsylvania Convention Center -- 109B

Computers in Chemistry General

Molecular Mechanics and Simulation


W. D. Cornell, Organizer

8:30 —200. Development of an improved four-site water model for bio-molecular simulations: TIP4P-Ew. H. W. Horn, W. Swope, J. Pitera, J. D. Madura, T. J. Dick, G. L. B. Hura, T. Head-Gordon

8:50 —201. Studies of brine using TIP4P-Ew and DYNAMO. P. E. Krouskop, J. D. Madura

9:10 —202. Molecular level studies of water-mediated interactions between ions and their relevance to biomolecular interactions. S. Rajamani, T. Ghosh, S. Garde

9:30 —203. Reaction mechanism, free energy profiles and structural changes along the reaction path of catalysis in the wild type and two active site mutants of medium chain acyl-CoA dehydrogenase. S. Bhattacharyay, M. T. Stankovich, J. Gao

9:50 —204. Novel "linear" Monte Carlo approach to free energy calculations. M. Clark, I. Shkurko, Q. Wang

10:10 —205. A structure and thermodynamic model of the binding of botulinum neurotoxin Type A inhibitors computed by Monte Carlo methods of docking and thermodynamic evaluation. L. Carlacci, M. Olson

10:30 —206. Liquid-liquid phase transitions in phosphorus: Insight from simulations. R. O. Jones, P. Ballone

10:50 —207. Systematic method for identifying reaction coordinates in complex systems. A. Ma, A. R. Dinner

11:10 —208. Directly calculated ligand binding free energies using Folding@Home. M. R. Shirts, G. Jayachandran, C. D. Snow, V. S. Pande

11:30 —209. Validation of a complete polarizable force field for proteins by computing geometric and energetic properties of isolated and solvated systems. G. A. Kaminski

11:50 —210. Ab initio and empirical model simulation studies of "neat" liquid water and of a solvated peptidic fragment in aqueous solution. Y. A. Mantz, B. Chen, H. Gerard, R. Iftimie, G. J. Martyna

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WEDNESDAY AFTERNOON

 Section A

Pennsylvania Convention Center -- 109B

High Performance Computing in Computational Chemistry


W. D. Cornell and V. S. Pande, Organizers

1:30 —211. High performance computing in the Blue Gene project at IBM Research. W. Swope

2:05 —212. Folding@Home: Can a grid of 100,000 CPUs tackle fundamental barriers in molecular simulation? V. S. Pande

2:40 —213. Asymptotic improvement in the parallel evaluation of pairwise particle interactions. D. E. Shaw

3:15 — Intermission.

3:25 —214. Turbo-charged applications on ClearSpeed's streaming processors. S. McIntosh-Smith

4:00 —215. Evolution of the Locus "Titan" computing cluster. K. Milligan, M. Clark

4:35 —216. High performance computing at Novartis Institutes for Biomedical Research. D. Mikhailov

 Section B

Pennsylvania Convention Center -- 104A&B

Symposium in Honor of Henry F. Schaefer's 60th Birthday

Cosponsored with PHYS
P. V. R. Schleyer, E. R. Davidson, W. T. Borden, L. Radom, and P. R. Schreiner, Organizers

1:30 —217. Semiclassical correction to quantum energy levels. W. H. Miller, A. L. Kaledin, C. W. McCurdy

2:00 —218. Linear-scaling methods for large molecules: Development and application. C. Ochsenfeld

2:30 —219. Fritz Schaefer and the periodic table. R. M. Pitzer

3:00 —220. Thermochemistry of calcium-containing molecules: An examination of the performance of high-level theoretical procedures. L. Radom, M. B. Sullivan, N. L. Haworth, A. K. Wilson, L. A. Curtiss, J. M. Martin

3:30 —221. Resonant electron scattering by soft box CCSD(T) calculations. W. Meyer, D. Spelsberg

4:00 —222. Electroweak quantum chemical kinetics and molecular parity violation. M. Quack

4:30 —223. The ages of quantum chemistry. W. G. Richards

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THURSDAY MORNING

 Section A

Pennsylvania Convention Center -- 109A

Symbolic Calculation in Chemistry


M. P. Barnett, Organizer

8:30 — Introductory Remarks.

8:35 —224. Kinematic view of loop closure. E. A. Coutsias, C. Seok

9:05 —250. Some uses of computer algebra in enzyme kinetics. N. Yildirim

9:35 —226. Enzyme kinetics using manifold theory. S. J. Fraser

10:05 — Intermission.

10:25 —228. Symbolic calculations in the theory of atoms. J. Javanainen

10:55 —225. Symbolic generation of perturbation equations for the vibrational-rotational analysis of potential energy surfaces. W. C. Ermler

11:25 —247. Symbolic computation in the determination of hyperspherical harmonics. A. Kuppermann

 Section B

Pennsylvania Convention Center -- 104A&B

Symposium in Honor of Henry F. Schaefer's 60th Birthday

Cosponsored with PHYS
P. V. R. Schleyer, E. R. Davidson, W. T. Borden, L. Radom, and P. R. Schreiner, Organizers

9:00 —229. Towards a universal potential for water. R. J. Saykally

9:30 —230. Towards an understanding of 3-D aromaticity. P. V. R. Schleyer, Z. Chen, R. B. King

10:00 —231. How to "Cope" with biradicals from enediynes and the like. P. R. Schreiner

10:30 —232. Recent progress in the development of exchange-correlation functionals. G. E. Scuseria

11:00 —233. Potential energies of weakly and strongly interacting systems: From pi-stacking to bond-breaking. C. D. Sherrill

11:30 —234. Thermodynamic and kinetic simulations of protein folding at IBM Research. W. Swope

 Section C

Pennsylvania Convention Center -- 103C

Computers in Chemistry General

Drug Design


W. D. Cornell, Organizer

8:20 —235. Quantum mechanical studies of HIV-1 protease inhibitors and drug design based on full ab initio MFCC computation. D. Zhang, J. Z. H. Zhang

8:40 —236. PREDICT modeling and in silico screening for GPCR: From amino acid sequence to the clinic. S. Shacham, Y. Marantz, S. Noiman, O. M. Becker, M. G. Kauffman

9:00 —237. QMQSAR: A semi-empirical (PM3) field-based QSAR program. S. Dixon, K. M. Merz Jr., G. Lauri, J. Ianni, M. C. Kozlowski

9:20 —238. Computational investigations on novel catalytic antibodies: Aldolase and anti-cocaine. Y. Hu, A. Olson

9:40 —239. Importance of electric charges in molecular docking: QM/MM approach. A. E. Cho, V. Guallar, B. J. Berne, R. A. Friesner

10:00 —240. Computer-aided design of novel natural-product-based matrix metalloproteinase-3 inhibitors. E. A. Amin, W. J. Welsh

10:20 —241. High quality homology models for structure-based drug design: A comparative study. A. Nayeem, D. Sitkoff, S. Krystek Jr.

10:40 —242. GQSAR: A new ab intio/DFT 3-D-QSAR program. J. Ianni, M. Kozlowski

11:00 —243. Graph isomorphisms for computer-aided drug discovery. N. T. Southall, T. Nguyen, D. Ajay

11:20 —244. Conformational consensus as a method to distinguish agonists from antagonists II: Identification of selective conformations. G. J. Tawa, A. H. Katz, J. C. Alvarez

11:40 —245. Lead docking protocol featuring improved sampling and scoring. L. Mueller, D. R. Langley, D. L. Cheney

246. Withdrawn.

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THURSDAY AFTERNOON

 Section A

Pennsylvania Convention Center -- 109B

Symbolic Calculation in Chemistry


M. P. Barnett, Organizer

248. Withdrawn.

1:15 —249. Symbolic computation in coupled cluster theory. P. Piecuch

1:45 —227. Conventional and unconventional symbolic computation in chemistry. F. E. Harris

2:15 — Intermission.

2:35 — Panel Discussion.

4:35 — Concluding Remarks.

 Section B

Pennsylvania Convention Center -- 104A&B

Symposium in Honor of Henry F. Schaefer's 60th Birthday

Cosponsored with PHYS
P. V. R. Schleyer, E. R. Davidson, W. T. Borden, L. Radom, and P. R. Schreiner, Organizers

1:30 —251. Computational strategies for high-accuracy computations of hydrogen bonding and π - π stacking prototypes. G. S. Tschumper

2:00 —252. Conical intersections are generalized lines not isolated points. D. R. Yarkony

2:30 —253. High accuracy theoretical pKa calculations. B. F. Yates, A. M. Magill

3:00 —254. Three- vs. four-coordinate phosphorus: More reasons for tight d functions. S. S. Wesolowski

3:30 —255. Ab initio vibration-rotation spectroscopy. W. Thiel

4:00 —256. Modeling of the CVD of 13-15 composites: From donor-acceptor complexes to rings and clusters. A. Y. Timoshkin

4:30 — Concluding Remarks. Henry F. Schaefer III.

 

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Pharmacophore-Based Approaches

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