Subscribe


COMP Programming

227th ACS National Meeting
Anaheim, CA
March 28 - April 1, 2004

R. A. Wheeler and W. D. Cornell, Program Chairs

SUNDAY MORNING

 Section A

Unknown Site -- Unknown Room

Beyond Michael Dewar's Legacy: Modern Semiempirical MO Theory

Cosponsored with PHYS
T. Clark, Organizer, Presiding

8:00 — Introductory Remarks.

8:15 —1. Aggregation effects: Single molecules vs. nanoarrays. M. A. Fox, J. K. Whitesell

9:00 —2. Semiempirical methods with orthogonalization corrections for electronically excited states. W. Thiel

9:45 — Intermission.

10:15 —3. Impact of semiempirical SCF MO theory in biology. K. M. Merz Jr.

11:00 —4. A comparison of computed and observed heats of formation. J. J. P. Stewart

 Section B

Unknown Site -- Unknown Room

Rational Drug Design


M. R. Reddy, Organizer, Presiding

8:30 —5. Free energy calculations in rational drug design. J. A. McCammon

9:05 —6. Rapid identification and synthesis of selective drug leads for Akt-1, GSK3-beta and P38-alpha. C. N. Hodge, K. Williams, I. Popa-Burke, J. Dickson, P. Bernasconi, S. Galasinski, W. P. Janzen

9:40 —7. Computational methods for prediction of the structures and binding afffinities of protein-ligand complexes. R. Friesner

10:15 —8. Chemoinformatic computations relevant to drug bioavailability and ADMET profiles. C. J. Cramer, J. L. Lewin, J. D. Thompson, D. G. Truhlar

10:50 —9. Water's roles in ligand binding to fatty acid binding proteins: Water's hydrophobic nature. T. R. Stouch

11:25 —10. Influence of HIV-RT inhibitors on RT dynamics: Molecular arthritis. J. D. Madura

 Section C

Unknown Site -- Unknown Room

Interplay Between Computer Modeling and Experiments on Complex Biological Systems

Cosponsored with PHYS
R. M. Levy, Organizer
E. Gallicchio, Presiding

8:30 —11. Allosteric flexing of myosin crossbridges at near-atomic resolution. W. R. Wriggers

9:10 —12. Protein motions with an efficient coarse-grained approach. R. L. Jernigan, P. Doruker, I. Bahar, Y. Wang, S. Kundu

9:50 —13. Multi-scale elastic network normal mode analysis enables the annotation of functional motions in biological machines and assemblies from ribosome dynamics to virus swelling. C. L. Brooks III

10:30 — Intermission.

10:40 —14. Thermodynamics and kinetics from nonequilibrium single molecule pulling experiments. G. Hummer, A. Szabo

11:20 —15. Dewetting in nanoscale hydrophobic plates collapse and multi-domain protein folding. R. Zhou, B. J. Berne, X. Huang, C. J. Margulis

 

The Bigger Picture: Linking Bioinformatics to Cheminformatics

Techniques and Databases

Cosponsored with CINF

SUNDAY AFTERNOON

 Section A

Unknown Site -- Unknown Room

Beyond Michael Dewar's Legacy: Modern Semiempirical MO Theory

Organic Chemistry

Cosponsored with PHYS
T. Clark, Organizer
C. J. Cramer, Presiding

1:30 —16. Competing pathways in cycloadditions of thiocarbonyl S-ylides to thioketones. R. Sustmann, W. Sicking, R. Huisgen

2:00 —17. Using AM1 together with DFT in multilayer ONIOM calculations on model peptides. J. J. Dannenberg

2:30 —18. From Dewar's structure for stipitatic acid to mobius aromatics. H. S. Rzepa

3:00 — Intermission.

3:30 —19. Calculation of electron transfer parameters. S. F. Nelsen

4:00 —20. Understanding how ionic liquids impact the Diels-Alder reaction: An ab initio, semiempirical and QM/MM approach. O. Acevedo, J. Plumley, J. D. Evanseck

4:30 —21. Biradicals of four-membered heterocycles contaning boron, silicon, and phosphorus: A challenge to theory. W. W. Schoeller

 Section B

Unknown Site -- Unknown Room

Rational Drug Design


M. R. Reddy, Organizer
V. Mohan, Presiding

1:30 —22. High-throughput structure-based drug design. W. L. Jorgensen, J. Tirado-Rives

2:05 —23. Use of free energy perturbation methodology in drug discovery: Limitations and advantages. M. R. Reddy, M. D. Erion

2:40 —24. Computational binding affinity calculations for enzyme inhibitors, ion channel blockers and protein-protein interactions. J. Aqvist

3:15 —25. Exploring, assessing and improving energy landscapes for protein-ligand binding. C. L. Brooks III

3:50 —26. Directly calculated ligand binding free energies using Folding@Home. M. R. Shirts, C. D. Snow, V. S. Pande

4:25 —27. Thermodynamically based calculations of absolute binding affinities using molecular dynamics simulations in torsion space. P. Carnevali, G. T˜th

 Section C

Unknown Site -- Unknown Room

Interplay Between Computer Modeling and Experiments on Complex Biological Systems

Cosponsored with PHYS
R. M. Levy, Organizer, Presiding

1:30 —28. Applying simulation methods to protein-protein interactions: Lessons from the Ras/Raf complex. D. A. Case

2:10 —29. Studies of the conformational equilibrium of allosteric proteins using advanced sampling algorithms and the AGBNP implicit solvent model. E. Gallicchio, K. P. Ravindranathan, R. M. Levy

2:50 —30. Allosteric transitions in the α7 nicotinic receptor using molecular dynamics simulations. R. Henchman, H. Wang, S. M. Sine, P. W. Taylor, J. A. McCammon

3:30 — Intermission.

3:40 —31. Microscopic mechanism of ion selectivity in the potassium channel. B. Roux

4:20 —32. High resolution protein structure prediction: Comparison of calculated structures with x-ray crystallographic data. R. A. Friesner

 Section D

Unknown Site -- Unknown Room

Computers in Chemistry General Contributions

Quantum Chemical Studies


R. A. Wheeler and W. D. Cornell, Organizers

1:00 —33. An absolute energetic criterion to measure the aromaticity and antiaromaticity. Y. Mo

1:20 —34. First ab initio study on the hetero-Diels-Alder cycloaddition between N-methyl carbonimidic dichloride and 1-methoxy-1,3-butadienes. Z. Wang

1:40 —35. Density functional calculations of the excited states of phenylene-ethynylene-based conducting polymers. R. J. Magyar, S. Tretiak

2:00 —36. Second-order nonlinear optical properties of zwitterionic molecules. P. Ray

2:20 —37. A theoretical study of the spectroscopy of mercury excimers and exciplexes. P. Sinha, M. Omary, P. S. Bagus, A. K. Wilson

2:40 —38. Spin forbidden reactions of heavy transition metals. K. A. Barakat, M. A. Omary, T. R. Cundari, D. C. Rosenfeld, P. T. Wolczanski

3:00 — Intermission.

3:10 —39. Analysis of the chemical shift changes in the 13C NMR of iodoalkynes due to complexation with Lewis bases. N. S. Goroff, W. Moss

3:30 —40. Ab initio study of binding affinity of glycopeptide antibiotics to bacterial cell wall analogs. J. Lee, C. Sagui, T. Darden, C. Roland

3:50 —41. Combined QM/MM studies and free energy simulations on the oxidation of methionine residues in Granulocyte Colony Stimulating Factor. J. Chu, B. R. Brooks, B. Trout

4:10 —42. Hydrolysis and crystal structure of ATP: A density functional study. J. Akola, R. O. Jones

4:30 —43. Distinguishing between electrostatic stabilization and general acid-base mechanisms in Aldehyde Dehydrogenase with MM and QM/MM simulations. T. Wymore, M. J. Field, J. Hempel, H. B. Nicholas Jr., D. W. Deerfield II

 

The Bigger Picture: Linking Bioinformatics to Cheminformatics

Philosophy and Platforms

Cosponsored with CINF

MONDAY MORNING

 Section A

Unknown Site -- Unknown Room

Beyond Michael Dewar's Legacy: Modern Semiempirical MO Theory

New Methods

Cosponsored with PHYS
T. Clark, Organizer
J. J. P. Stewart, Presiding

8:00 —44. Focused semiempiricism. C. J. Cramer

8:45 —45. Improved semiempirical MO methods: PDDG/PM3. W. L. Jorgensen, I. Tubert-Brohman, C. R. W. Guimar‹es

9:30 — Intermission.

10:00 —46. Where good methods go bad: Correcting systematic errors in current semiempirical methods. P. Winget, T. Clark

10:30 —47. Self-consistent polarization NDDO: Application to neutral and ionic water clusters. D. T. Chang, G. K. Schenter, B. C. Garrett

11:00 —48. Uses and application of molecular modelling in undergraduate research. E. F. Healy

11:30 —49. Multicoefficient correlation methods with basis sets balanced for extrapolation. B. J. Lynch, D. G. Truhlar

 Section B

Unknown Site -- Unknown Room

Rational Drug Design


M. R. Reddy, Organizer
V. Mohan, Presiding

8:30 —50. Structure-based discovery of potent inhibitors of human asparagine synthetase. L. Koroniak, J. A. Gutierrez, R. Humkey, N. G. J. Richards

9:00 —51. New developments in protein-ligand scoring functions: LigScore2 and LigScore3. C. M. Venkatachalam, A. Krammer, M. Waldman

9:30 —52. Revisiting free energy calculations: One step closer to rigorous scoring functions and one step beyond MM/PBSA. J. M. J. Swanson, R. Henchman, J. A. McCammon

10:00 —53. Docking flexible ligands to flexible proteins using Monte Carlo simulation with modal moves. G. T˜th, P. Carnevali

10:30 —54. FlexScan: A fast structure-based prescreening tool based on incremental construction. I. Schellhammer, M. Rarey

11:00 —55. Improving docking enrichment: Good and bad ideas. A. Filikov

11:30 —56. Identifying and prioritizing novel inhibitors using LUDI and scoring functions: A validation experiment. J. Srinivasan, M. Lim-Wilby

 Section C

Unknown Site -- Unknown Room

Getting It Right: Variable Selection and Model Validation in (Q)SAR

Variable Selection


R. D. Clark, Organizer

8:30 — Introductory Remarks.

8:35 —57. Insect colonies for feature selection. D. K. Agrafiotis, S. Izrailev, W. Cede–o

9:05 —58. A priori vs. a posteriori: An exhaustive PLS search for biologically-relevant QSAR descriptors. T. I. Oprea, M. Olah, C. G. Bologa

9:35 —59. Variable selection and model validation of 2D and 3D molecular descriptors. A. Nicholls, N. E. MacCuish, J. D. MacCuish

10:05 — Intermission.

10:20 —60. Analysis of multiple QSAR models from genetic function approximation: A basis for experimental design. E. A. Jamois, A. S. Kulkarni, S. Puri

10:50 —61. Comparison of commercially available Genetic Algorithms: GA’s as variable selection tool. S. Schefzick, M. Bradley

11:20 —62. Use of supervised and unsupervised variable selection to specify robust QSAR models from multicollinear data for arylpiperazinyl derivatives with affinity toward α2adrenoceptors. M. G. Ford

 Section D

Unknown Site -- Unknown Room

G-Protein Coupled Receptor Structure, Modeling, and Ligand Design


J. Woolfrey, Organizer
I. Visiers, Organizer, Presiding

8:00 — Introductory Remarks.

8:15 —63. Receptor-mediated cell signaling: Mechanistic insights from computational and experimental probing of structure-function relations. H. Weinstein

8:45 —64. Molecular mechanisms of G protein-coupled receptor activation. L. Pardo

9:15 —65. Ligand-induced conformational changes in the Beta2 adrenoceptor. B. K. Kobilka

9:45 —66. Mapping the binding site for melanocortin 4 receptor agonists: A consistent pharmacophore definition. I. Visiers, K. Hogan, S. Peluso, S. gould, L. Wu, M. D. Ryan

10:15 — Intermission.

10:30 —67. Molecular modeling of purine and pyrimidine G protein-coupled receptors. K. A. Jacobson, S. Kim, S. Costanzi

11:00 —68. Modelling the interactions of CCR2 antagonists with their receptor. F. E. Blaney

11:30 —69. Carboxamide oxygen-K3.28 interaction is responsible for SR141716A inverse agonism at the cannabinoid CB1 receptor. P. H. Reggio, D. P. Hurst, U. Umejiego, H. H. Seltzman, S. D. McAllister, M. E. Abood, D. L. Lewis

MONDAY AFTERNOON

 Section A

Unknown Site -- Unknown Room

Beyond Michael Dewar's Legacy: Modern Semiempirical MO Theory

Transition Metals

Cosponsored with PHYS
T. Clark, Organizer
K. M. Merz Jr., Presiding

1:30 —70. MSINDO: Parametrization and new features. K. Jug

2:15 —71. Use of semi-empirical MO methods to describe transition metal systems. I. H. Hillier, J. P. McNamara, M. Mohr, H. Wang, S. Rajeev, J. Ge, M. Sundararajan

3:00 — Intermission.

3:30 —72. AM1/d method for transition-metal compounds. A. A. Voityuk

4:00 —73. De novo structural prediction of transition metal geometry: A pyramid scheme. T. R. Cundari, C. Buda, A. A. Flores

4:30 —74. De novo prediction of the ground state structure of transition metal complexes using semiempirical and ab initio quantum mechanics. C. Buda, A. A. Flores, T. R. Cundari

 Section B

Unknown Site -- Unknown Room

Rational Drug Design


M. R. Reddy, Organizer, Presiding

1:30 —75. Similarity searching using Atom Environments, information gain based feature selection and the Na•ve Bayesian Classifier. A. Bender, S. Reiling, H. Y. Mussa, R. C. Glen

1:55 —76. Development of novel geometrical chemical descriptors and their application to the prediction of ligand-receptor binding affinity. S. Zhang, A. Golbraikh, A. Tropsha

2:20 —77. Classical electrostatics and drug design: Enumeration and evaluation of isosteric analogs. R. Sayle, G. Skillman, A. Nicholls

2:45 —78. Modeling hERG activity using support vector machine methodology. Y. Han

3:10 —79. QSAR studies of HIV-1 protease inhibitors. R. Garg

3:35 —80. HIV-1 protease molecular dynamics of a wild type and of the V82F/I84V mutant: Possible contributions to drug resistance and a potential new target site for drugs. A. L. Perryman, J. Lin, J. A. McCammon

4:00 —81. Development of 3D-QSAR CoMFA models for Anti-AIDS diarylsulfones. G. T. Mukundan, M. Zanger

4:25 —82. Rational design of a potent inhibitor for unregulated complement activation using molecular dynamics simulations and nuclear magnetic resonance data. B. Mallik, J. D. Lambris, D. Morikis

 Section C

Unknown Site -- Unknown Room

Getting It Right: Variable Selection and Model Validation in (Q)SAR

Data Mining


R. D. Clark, Organizer

1:30 —83. Application of the Support Vector Machine algorithm for the virtual screening of compounds. R. N. Jorissen, M. K. Gilson

2:00 —84. Direct kernel partial least squares (DK-PLS) for QSAR. M. J. Embrechts, K. Bennett, C. Breneman

2:30 —85. The benefits of working in sample space. R. D. Clark, P. Fox

3:00 — Intermission.

3:15 —86. Dimensionality reduction and multiple-instance learning in medicinal chemistry. Y. Bengio, P. L'Heureux, J. Carreau, S. Y. Yue

3:45 —87. Chemical optimization using multiple models. D. Rogers

4:15 —88. Validating ligand-based virtual screening protocols: Enrichments you can count on. A. C. Good, S. J. Cho

 Section D

Unknown Site -- Unknown Room

G-Protein Coupled Receptor Structure, Modeling, and Ligand Design


I. Visiers, Organizer
J. Woolfrey, Organizer, Presiding

1:00 —89. Identification of small molecules targeting Thrombin Receptor /Gq activation. A. Gilchrist

1:30 —90. GBSA/IM: An implicit solvation model for the modeling of membrane proteins. V. Spassov, L. Yan, D. Singh, S. Szalma

2:00 —91. Computational studies of the desensitization process in the bovine Rhodopsin-Arrestin complex. S. K. Gregurick, Y. Ling

2:30 —92. Conformational consensus as a method to distinguish agonists from antagonists. A. H. Katz, G. J. Tawa, K. Mason, S. Gove, J. C. Alvarez

3:00 — Intermission.

3:15 —93. In search of the holy grail: In silico modeling of the human Mu and Kappa opioid receptors. D. Bautista, L. Carpenter

3:45 —94. Modeling and mutagenesis of the mouse S1P4 receptor. T. C. Pham, Y. Inagaki, Y. Igarashi, Y. Fujiwara, G. Tigyi, A. L. Parrill

4:15 —95. Modeling agonist selectivity at the sphingosine-1-phosphate receptors. D. A. Osborne, Y. Fujiwara, S. Cseh, Y. Wang, G. Tigyi, A. L. Parrill

 

Informatics Challenges in Nanotechnology

Cosponsored with CINF

MONDAY EVENING

 Section A

Unknown Site -- Unknown Room

Sci-Mix


R. A. Wheeler and W. D. Cornell, Organizers

6:00 - 8:00

136, 145-147, 149, 152-153, 155, 157-159, 161, 164, 170, 182-184, 187, 194, 198, 201, 205, 212-213, 215, 219, 223-224, 226, 229, 232-233, 237, 241. See subsequent listings.

TUESDAY MORNING

 Section A

Unknown Site -- Unknown Room

Beyond Michael Dewar's Legacy: Modern Semiempirical MO Theory

Biological Systems

Cosponsored with PHYS
T. Clark, Organizer
I. H. Hillier, Presiding

8:30 —96. Quantum chemical and molecular dynamics modeling of charge transfer in DNA. N. Roesch, K. Siriwong, A. A. Voityuk

9:15 —97. Semiempirical methods for biological reactions: New models, QM/MM and linear-scaling applications to RNA catalysis. D. York

10:00 — Intermission.

10:30 —98. Development and troubleshooting of semiempirical QM/MM coupling terms for enzyme simulation applications. J. E. Gready, P. L. Cummins

11:15 —99. QM/MM simulations of biomolecular structures and processes in their electronic ground and excited states using an approximate DFT method. M. Elstner

 Section B

Unknown Site -- Unknown Room

Nucleic Acid Modeling

RNA Motifs and Folding


N. B. Leontis and T. Hermann, Organizers

8:00 — Introductory Remarks.

8:20 —100. Identifying RNA structural motifs with the SCOR database. D. K. Hendrix, P. S. Klosterman, M. Tamura, L. Stefan, S. E. Brenner, S. R. Holbrook

8:50 —101. Structural and cluster analyses of RNA motifs with RMSD distance matrices. H. Huang, U. Nagaswamy, G. E. Fox

9:20 — Intermission.

9:35 —102. Constant time nucleic acid backbone construction. P. Thibault, F. Major

10:05 —103. Progress toward accurate 3D structure prediction of RNA. J. SantaLucia Jr., P. Saro, R. Aduri, V. Matta

10:35 — Discussion.

 Section C

Unknown Site -- Unknown Room

Interplay Between Computer Modeling and Experiments on Complex Biological Systems

Cosponsored with PHYS
R. M. Levy, Organizer
R. Zhou, Presiding

8:30 —104. Microscopic mechanism of antibiotics translocation through a porin. M. Ceccarelli, C. Danelon, A. Laio, M. Parrinello

9:10 —105. Joint computational-experimental approach to effective and selective antimicrobial oligomers. R. J. Doerksen, B. Chen, D. Liu, W. F. DeGrado, M. L. Klein

9:50 —106. Ab initio molecular dynamics study of glycine tautomerization in water. K. Leung, S. B. Rempe

10:30 — Intermission.

10:40 —107. Electrostatics drive C3d-CR2 association. D. Morikis, J. D. Lambris

11:20 —108. Understanding the mechanism of squalene synthase: prediction of ligand binding modes. J. K. Perry

 Section D

Unknown Site -- Unknown Room

G-Protein Coupled Receptor Structure, Modeling, and Ligand Design


J. Woolfrey and I. Visiers, Organizers

8:00 —109. Models, mutagenesis and drug design of G Protein-coupled receptors. S. Krystek Jr.

8:30 —110. Structure based GPCR drug discovery: From the computer to the clinic. O. M. Becker

9:00 —111. First principles structure and function prediction for G protein-coupled receptors. N. Vaidehi, W. B. Floriano, R. J. Trabanino, S. E. Hall, P. L. Freddolino, Y. Kalani, H. Shen, J. Heo, S. Sharma, R. Niemer, W. A. Goddard III

9:30 —112. Pharmacological engineering of multi-receptor drug selectivity and efficacy. J. Ballesteros, D. J. Sieg, T. Bennett, J. Ransom

10:00 — Intermission.

10:15 —113. Hit-finding against GPCR targets: Discovery of potent MCH-1 receptor antagonists by virtual screening. D. E. Clark, C. Higgs, S. P. Wren, H. J. Hunt, M. Wong, D. Norman, P. M. Lockey, A. G. Roach

10:45 —114. Virtual screening of compound and target libraries for identifying novel GPCR ligands. D. Rognan

11:15 —115. A GPCRs groove. A. Pejrolo, I. Visiers

 

Advances in Pharmacophores and 3D Searching

Cosponsored with CINF

TUESDAY AFTERNOON

 Section A

Unknown Site -- Unknown Room

ACS Award for Computers in Chemical and Pharmaceutical Research


W. L. Jorgensen, Organizer

1:30 —116. Integrated computational biology: From the molecule to the cell. J. A. McCammon

2:00 —117. Analyzing protein-DNA recognition. R. Lavery, G. Paillard

2:30 —118. Advances in QM/MM simulations for organic reactions in solution. W. L. Jorgensen, C. R. W. Guimar‹es, O. Acevedo

3:00 —119. A simple and efficient method for improving high-throughput screening and high-throughput docking results. M. Glick

3:30 —120. From diatomics to drugs and distributions. W. G. Richards

 Section B

Unknown Site -- Unknown Room

Nucleic Acid Modeling

Dynamics, Energetics, and Simulation


N. B. Leontis and T. Hermann, Organizers

1:00 — Introductory Remarks.

1:10 —121. Toward a more reliable computational description of nucleic acids: An analysis of intermolecular interactions. S. M. Cybulski

1:40 —122. Mechanism of DNA oxidation. F. L. Gervasio, A. Laio, M. Parrinello

2:10 —123. Malachite Green-RNA aptamer complex: The origin of red-shift, the binding affinity, and the free energy landscape. D. H. Nguyen, W. H. Fink, T. Dieckmann, M. E. Colvin

2:40 — Intermission.

2:55 —124. In silico structural modeling of the ribosome. C. Tung, K. Y. Sanbomatsu

3:35 —125. Ribosome motions modulate electrostatic properties. J. Trylska, R. Konecny, F. Tama, C. L. Brooks III, J. A. McCammon

4:05 —126. Dynamics of RNA kink-turns: Role of water molecules. N. B. Leontis, J. Sponer, F. Razga

4:35 — Discussion.

 Section C

Unknown Site -- Unknown Room

Interplay Between Computer Modeling and Experiments on Complex Biological Systems

Cosponsored with PHYS
R. M. Levy, Organizer
W. R. Wriggers, Presiding

1:30 —127. NMFF: flexible high-resolution annotation of low-resolution experimental data from cryo-EM maps using normal mode analysis. F. Tama, O. Miyashita, C. L. Brooks III

2:10 —128. Conformational variations of fasciculins associated with protein-protein interaction. J. Bui, J. A. McCammon

2:50 — Intermission.

3:00 —129. Reduced-rotamer representations for protein structure modelling with applications to collagen fibrillogenesis. D. J. Anderson, M. C. Goh, I. Graovac, J. K. Rainey

3:40 —130. Comprehensive search method for predicting the packing of parallel transmembrane α-helices. N. Akula, C. Tang, N. Pattabiraman

 Section D

Unknown Site -- Unknown Room

Computational Approaches to Problems in Environmental Chemistry

Molecular Dynamics of Gas Adsorption and Uptake at Liquid and Solid Surfaces


D. J. Tobias, Organizer

1:15 — Introductory Remarks.

1:20 —131. Molecular simulations of gas uptake by liquid water. B. Garrett

2:00 —132. Trapping of hydroxyl radical and ozone at aqueous aerosol surfaces: A molecular dynamics study. M. Roeselov‡, D. J. Tobias, R. B. Gerber, P. Jungwirth

2:40 —133. Application of MD, MC and ab initio results to the interpretation of spectra of bare and adsorbate-coated ice nanocrystals. V. Buch, J. Sadlej, N. Uras-Aytemiz, J. P. Devlin

3:20 — Intermission.

3:35 —134. Energy transfer and chemical reaction in collisions of rare gas and triplet oxygen atoms with hydrocarbon surfaces. W. L. Hase

4:15 —135. Mass accomodation coefficient for water vapor on liquid water from computer simulations. J. S. Vieceli, M. Roeselov‡, D. J. Tobias

 

Advances in Pharmacophores and 3D Searching

Data Mining Applications

Cosponsored with CINF

TUESDAY EVENING

 Section A

Unknown Site -- Unknown Room

Computers in Chemistry Posters


R. A. Wheeler and W. D. Cornell, Organizers

6:00 - 8:00

136. Functional motions of RNA polymerase in transcription. S. Kundu, R. L. Jernigan

137. Atomic force microscopy of programmable, self-assembling tecto-RNAs. A. Y. Koyfman, A. Chworos, E. Oroudjev, S. Magonov, H. G. Hansma, L. Jaeger

138. Thermal stability analysis of self-assembling RNA tecto-squares. I. Severcan, A. Chworos, L. Jaeger

139. Selection and characterization of novel RNA self-assembling building blocks. C. W. Geary, S. C. Baudrey, L. Jaeger

140. Monte Carlo simulation of the RNA organization inside the CCMV capsid. D. Zhang, R. Konecny, J. A. McCammon

141. GNRA and the UNCG type tetraloop folding motifs in larger hairpin loops of ribosomal RNAs. U. Nagaswamy, H. Huang, G. E. Fox

142. Molecular dynamics simulation of flexible RNA motifs. F. Razga, N. B. Leontis, J. Sponer

143. Molecular dynamics simulations of 8-oxoguanine: A mismatch DNA. X. Cheng, C. Simmerling

144. Molecular dynamics simulations of DNA encapsulated in a carbon nanotube. E. Y. Lau, F. C. Lightstone, M. E. Colvin

145. Novel approach to programmable biomaterials based on RNA molecules. A. Chworos, L. Jaeger

146. RNA structural bioinformatics. N. B. Leontis, J. Stombaugh, A. G. Mokdad, C. L. Zirbel

147. Solvent reorganization energy of charge transfer in DNA hairpins. D. LeBard, D. Matyushov, M. Lilichenko, Y. A. Berlin, M. A. Ratner

148. Theoretical study of the conformational equilibrium of the ribose binding protein. K. P. Ravindranathan, E. Gallicchio, R. M. Levy

149. Function of conserved residues of human glutathione synthetase. A. Dinescu, T. R. Cundari, M. E. Anderson, V. Bhansali

150. Identification of disulfide bonds in the enzyme lysyl oxidase. F. Ryvkin, M. Dang, V. L. Stoyneva

151. Modeling studies on inhibitors of Imidazole Glycerol Phosphate Dehydratase¤. E. M. Collantes, P. D. Mosier, B. A. Schweitzer, S. Profeta Jr.

152. Molecular behavior of the calmodulin-edema factor complex in anthrax infection. E. G. Franklin, J. D. Evanseck

153. Molecular dynamics simulations of urease catalysis. G. L. Estiu, K. M. Merz Jr.

154. Molecular modeling of iron ions passing through the three-fold channel of horse spleen ferritin. J. Shao, C. H. Lee, G. D. Watt, S. S. Zimmerman

155. Steered molecular dynamics study of edema factor-calmodulin binding. K. A. Baker, J. D. Evanseck

156. Understanding HIV-1 protease inhibition resistance: A computational study. A. H. C. Horn, F. Wartha, H. Meiselbach, H. Sticht

157. A comparative analysis of the structure and dynamics of wild-type transthyretin and its pathogenic variants: Insights from molecular dynamics simulations. M. Lei, M. Yang, S. Huo

158. Analysis of theoretical ligand/receptor interactions for the alpha 2 (a, b, c) adrenergic receptors. W. D. Penn, L. Rothwell, D. Bautista

159. Binding free energies as a probe of the affinity maturation of an antibody binding site. I. F. Thorpe, C. L. Brooks III

160. Free energy of releasing a localized water molecule from the binding pockets of proteins: Double-decoupling method. D. Hamelberg, J. A. McCammon

161. Energetics of the water conducting channel: Ion excluding mechanism in aquaporin. Y. Ko, J. Huh, W. H. Jo

162. Hydrogen bonding drives the dynamics of a phosphopeptide. S. E. Wong, K. Bernacki, M. P. Jacobson

163. Computational investigation of the structural effects of protein phosphorylation. E. S. Groban, M. P. Jacobson

164. Conformational variations of fasciculins associated with protein-protein interaction. J. Bui, J. A. McCammon

165. Coupled sampling at dual resolution for global optimization. T. W. Lwin, R. Luo

166. Enhanced protein folding simulations in Poisson-Boltzmann molecular dynamics with self-guided forces. E. Wen, M. J. Hsieh, P. A. Kollman, R. Luo

167. Homology modeling of Pfmrk, a new target for antimalaria treatment. Y. Peng, Q. Zhang, S. M. Keenan, W. J. Welsh

168. Hybrid reaction field correction method combining finite difference Poisson-Boltzmann and Kirkwood multipolar expansion for accuracy and scalability. L. Yang, R. Luo, Q. Lu

169. Improvements to the nudged elastic band approach using interpolated surfaces. J. E. Knox, H. B. Schlegel

170. Loop closure and protein loop optimization. C. Seok, E. A. Coutsias, M. P. Jacobson, K. A. Dill

171. Low-resolution modeling: A new tool and its application to protein-nucleic acid interactions. Q. Cui, D. A. Case

172. Molecular dynamics simulations of amyloid-forming peptides: A comparative study. R. D. Hills Jr., C. L. Brooks III

173. Multiple pathways in beta-hairpin folding and unfolding simulations. A. Okur, D. R. Roe, G. Cui, V. Hornak, C. Simmerling

174. Protein NMR structure refinement by replica exchange and implicit solvent. J. Chen, W. Im, C. L. Brooks III

175. Structural role of water in protein folding. Y. M. Rhee, E. J. Sorin, V. S. Pande

176. Theoretical analysis of the mechanism, pathway, and coupling with enzyme dynamics of the cis-trans isomerization reaction of cyclophilin A. C. An, T. H. Rod, C. L. Brooks III

177. Valence topological charge-transfer indices for dipole moments. F. Torrens

178. Protein force field parameterization by free energy calculations. O. Guvench, C. L. Brooks III

179. Development and application of a CHARMM fluctuating charge protein force field. S. Patel, C. L. Brooks

180. An attempt at developing a better implicit water model. I. Chorny, K. A. Dill, M. P. Jacobson, H. Xu

181. Automatic and highly reproducible RESP and ESP charge derivation: Application to the development of programs RED and X RED. A. Pigache, P. Cieplak, F. Dupradeau

182. Carbon-hydrogen and carbon-heteroatom bond activation using iridium(I) complexes. S. Vaddadi, T. R. Cundari

183. Conformational stability of substituted iminium cations. P. Hsueh, H. A. Lindsay, M. C. Milletti

184. Direct ab initio dynamics study of the domcomposition of CH2FO. Q. S. Li, Q. Luo

185. Efficient QM/MM geometry optimization. T. Vreven, M. J. Frisch, K. N. Kudin, K. Morokuma, H. B. Schlegel

186. Principal mode analysis for calculating molecular vibrational spectra. R. A. Wheeler, H. Dong, S. E. Boesch

187. Electronic structure of phosphorescent gold(I) isonitrile complexes. M. W. A. Gonser, O. Elbjeirami, T. R. Cundari, M. A. Omary

188. First principles molecular dynamics simulations of a calcium ion in water. F. C. Lightstone, E. Schwegler, M. Allesch, G. Galli

189. Improved mechanism for the autoxidation of cyclohexane from theoretical and experimental evidence. I. Hermans, T. L. Nguyen, P. A. Jacobs, J. Peeters

190. Improved semiempirical methods: Parameterization of PDDG/PM3 for sulfur. I. Tubert-Brohman, C. R. W. Guimar‹es, W. L. Jorgensen

191. Investigation of the hydride transfer step in investigation of the hydride transfer step in catalysis of dihydrofolate reductase by the ONIOM QM/MM hybrid method. I. V. Rostov, P. L. Cummins, J. E. Gready, T. Vreven, M. Frisch

192. Mechanism of aldehyde inhibitor binding to pi-class Glutathione S-Transferase from MM and QM/MM Simulations. T. Wymore, C. Ramirez-Mondragon, D. W. Deerfield II

193. Models for intermediates in phosphoryl transfer reactions: A theoretical study. D. M. Shaw, A. St-Amant

194. NIST computational chemistry comparison and benchmark database. R. D. Johnson III

195. QM/MM investigations of active site processes in enzymes: Carboxylation of lysine in class D β-lactamase and irreversible inhibition in zinc-dependent proteases. J. Li, J. B. Cross, T. Vreven, S. O. Meroueh, S. Mobashery, H. B. Schlegel

196. Quantitave prediction of electron-transfer rates in metallo-proteins. T. R. Prytkova, I. V. Kurnikov, D. N. Beratan

197. Self-consistent polarization of Molecular Mechanic charges within a QM/MM scheme. J. A. Gascon, V. Batista

198. Substrate binding to Peptide Methionine Sulfoxide Reductase and structure of the sulfurane intermediate by MM and QM/MM simulations. K. D. Messinger, T. Wymore, D. W. Deerfield II

199. Using molecular similarity to construct semiemprical treatments of electron correlation. B. G. Janesko, D. Yaron

200. Ab initio studies of energies, structures and electronic proporties of 5-[bis(2-chloroethyl)amino]-2-methyl-4-nitro(amino)-N-substituted imidazole in vacuo and water. I. Weidlich, S. Sobiak

201. Ab initio study of structural, electronic and optical properties of finite-length (5, 5) carbon nanotubes. Z. Zhou, M. Steigerwald, M. Hybertsen, L. Brus, R. A. Friesner

202. Computation of NMR peptide structures containing spin-1/2 and spin-1 nuclei. K. S. Huang, W. E. Palke, J. T. Gerig

203. Controlling diaza-Cope rearrangement reactions with resonance-assisted hydrogen bonds: Theoretical and experimental investigations. D. Lee, J. Chin, F. Mancin, N. Thavarajah, A. Lough, D. S. Chung

204. Density functional exploration of C=C, N=N and P=P bonds. S. C. Brunello, J. R. Challa, M. C. Simpson

205. Density functional study on the Ziegler-Natta catalyst: The stereospecificity of a model catalyst site for propylene polymerization. J. W. Lee, S. H. Yang, J. Huh, W. H. Jo

206. Exploring the armony between Tteory and computation: Toward a unified electronic structure theory. L. Wei

207. Franck-Condon simulation of the single vibronic level emission spectra of HPCl/DPCl and the chemiluminescence spectrum of HPCl including anharmonicity. D. K. Mok, E. P. F. Lee, F. Chau, J. M. Dyke Sr.

208. Low lying electronic states of HOCl cation: Ab initio calculations. D. K. Mok, A. K. T. Yeung, D. Wang, F. Chau

209. N-heterocyclic carbenes of the transition metals: A computational and structural database study. E. Baba, T. Cundari

210. Optical excitations in some novel dodecadehydrotribenzo [18] annulene-based carbon architectures: A time-dependent density functional study. S. Anand, S. A. Lahankar, J. A. Marsden, M. M. Haley, T. Goodson III, H. B. Schlegel

211. Thermodynamic properties of MALDI matrices. F. H. Yassin, D. S. Marynick

212. Theoretical prediction of fragmentation patterns for polychlorinated biphenyls. L. I. Genes, H. P. Hratchian, C. W. Krapf, M. C. Milletti

213. Theoretical study of structural and electronic characteristics of a series of glycosidase inhibitors. R. D. Anderson, H. A. Lindsay, M. C. Milletti

214. Theoretical study of the competing elimination and substitution reactions in disulfides. S. M. Bachrach, A. Pereverzev

215. Theoretical study of the electronic structure of triangular trigold(I) complexes. L. E. Sansores, R. Salcedo, A. Martinez, N. Mireles

216. Updated numerical performance and throughput benchmark for electronic structure calculations in PC-Linux systems. J. K. Yu, J. Hwang, C. Y. Tang, C. Yu

217. Zinc mediated ligand binding: A quantum mechanics based approach. K. Raha, K. M. Merz Jr.

218. Prediction of retention factors in micellar electrokinetic chromatography using a density functional theory and a semi-empirical method. D. Lee, S. Hwang, D. S. Chung

219. A novel computational approach for lead optimization. J. Zou, D. Joseph-McCarthy, J. C. Alvarez

220. A semi-supervised dimensionality reduction method for QSAR. P. L'Heureux, Y. Bengio, S. Y. Yue

221. Chemically intuitive clustering for better SAR studies. J. Duret, R. D. Brown

222. CATALYST pharmacophores and ESP studies of Lanosterol Synthase inhibitors¤. S. N. Rao, S. Profeta Jr.

223. CoLiBRI: A novel CHEMOMETRIC approach to the analysis of ligand receptor complementarity. S. Oloff, A. Tropsha, J. Feng, W. Deng, C. Breneman

224. Comparative evaluation of five scoring functions for accurate prediction of protein-ligand binding energy. D. Puvanendrampillai, P. M. Marsden, J. B. O. Mitchell, R. C. Glen

225. Comparision of several docking programs in cross docking scenarios utilizing molecular dynamics - generated protein ensembles. D. L. Cheney, D. R. Langley, L. Mueller

226. Effects of green tea polyphenols on human methyltransferase dnmt1. N. Ai, W. J. Welsh, Y. Wang, M. Fang, C. S. Yang

227. α-Lipoic acid-based PPARγ agonists as anti-diabetic agents: Design, synthesis and docking studies. M. A. Avery, A. Patny, A. Chittiboyina, P. V. Desai, M. S. Venkatraman, C. Mizuno, C. Ho, S. C. Benson, T. W. Kurtz, H. A. Pershadsingh

228. Docking study of class I MHC GP2/HLA-A2.1 complexes. H. D. Altman, T. G. Kucukkal, W. S. Meng, J. D. Evanseck

229. Genetic algorithms and self-organizing maps: A powerful combination for modeling complex QSAR and QSPR problems. E. Bayram, P. Santago II, R. Harris, Y. Xiao, A. J. Clauset, J. D. Schmitt

230. JChem AnalogMaker: A computer program for generating targeted novel synthetically available lead molecules. S. Csepregi, G. Pirok, N. Mate, M. Vargyas, F. Csizmadia

231. Novel topological and knowledge-based descriptors in QSAR-based protein-ligand scoring functions. W. Deng, C. M. Breneman, M. J. Embrechts, M. Shen, A. Tropsha

232. Prediction of distribution coefficient using microconstants. J. Szegezdi, F. Csizmadia

233. Prediction of dissociation constant using microconstants. J. Szegezdi, F. Csizmadia

234. Development of Cytochrome P450 3A4 inhibition model. R. Arimoto, E. M. Gifford, M. J. de Groot

235. Prediction of protein affinity in hydrophobic interaction chromatography using quantitative structure-retention relationship (QSRR) models. A. Ladiwala, Q. Luo, J. Chen, F. Xia, D. Zhuang, C. M. Breneman, S. M. Cramer

236. Computer system use for solution of the ''structure -c hromatographic retention - biological activity" problem. S. V. Kurbatova

237. Use of simulated annealing with supervised self-organizing maps for QSAR and QSPR studies. Y. Xiao, E. Bayram, R. Harris, P. Santago II, J. D. Schmitt

238. Investigation of natural gas clathrate hydrate formation and stability through Monte Carlo simulations. L. L. Thomas, T. J. Dick, J. D. Madura

239. Selective partitioning of cations into model cylindrical nanopores. L. Yang, J. S. Dordick, S. Garde

240. An automatic measuring system for the print quality of digital photo paper. J. Tao, G. Chen, M. Zhu, A. Tang, H. Zhang

241. Investigation of the polymorph stability for n-propyl benzene using Gibbs ensemble Monte Carlo simulations. E. E. Dahlke, X. S. Zhao, J. I. Siepmann, H. Y. Ando

242. Importance of micelle asymmetry: Monte Carlo results. G. Mkrtumyan, R. Frisbee, H. Fynewever

WEDNESDAY MORNING

 Section A

Unknown Site -- Unknown Room

Beyond Michael Dewar's Legacy: Modern Semiempirical MO Theory

Biological Systems

Cosponsored with PHYS
T. Clark, Organizer
D. M. York, Presiding

8:30 —243. Theoretical modelling of enzyme catalytic power: Analysis of “cratic” and electrostatic factors in catechol O-methyl transferase. I. H. Williams, M. Roca, S. Mart’, J. AndrŽs, V. Moliner, I. Tu–—n, J. Bertr‡n

9:00 —244. Toward accurate calculations of enzymatic reactions using combined QM/MM models. J. Gao

9:30 —245. Comparison of semiempirical and ab initio quantum mechanical energy components for hydrogen-bonded systems. P. L. Cummins, J. E. Gready, D. Jayatilaka, A. P. Rendell

10:00 — Intermission.

10:30 —246. Mechanism of phosphoryl transfer in kinase catalysis. M. C. Hutter, V. Helms

11:00 —247. Novel techniques for QM modeling of ultra-large bio-molecular systems: Evolution of quantum-mechanical and force field methods. N. A. Anikin, V. M. Anisimov, V. L. Bugaenko, V. V. Bobrikov, A. M. Andreyev

11:30 —248. Modelling nitrogenase with the F8NS9+ cluster: Can DFT calculations make a contribution to understanding the mechanism? M. L. McKee

 Section B

Unknown Site -- Unknown Room

Nucleic Acid Modeling

RNA Tectonics


N. B. Leontis and T. Hermann, Organizers

8:00 — Introductory Remarks.

8:10 —249. Folding dynamics of RNA secondary structures. I. Hofacker

8:50 —250. Design and selection of catalytic RNA. T. Inoue, Y. Ikawa

9:30 — Intermission.

9:45 —251. RNA tectonics and programmable, self-assembling RNA nano-architectures. L. Jaeger, S. Baudrey, A. Chworos, A. Y. Koyfman, I. Severcan, L. Nasalean, N. B. Leontis

10:25 — Discussion.

 Section C

Unknown Site -- Unknown Room

Getting It Right: Variable Selection and Model Validation in (Q)SAR

Model Construction


R. D. Clark, Organizer

8:30 —252. Coupling feature reduction with self-organizing maps for drug discovery. J. D. Schmitt, R. Harris, E. Bayram, Y. Xiao, P. Santago II

9:00 —253. QSPR modeling the aqueous solubility of alcohols by optimization of correlation weights of local graph invariants. P. R. Duchowicz, E. A. Castro, A. A. Toropov, O. M. Nabiev

9:30 —254. QSAR models for metabolic kinetic parameters: Vmax and Km. K. Enslein

10:00 — Intermission.

10:15 —255. Pharmacophore identification based on electronic structure without using arbitrary descriptors and statistical methods. I. Bersuker

10:45 —256. 3D-QSAR illusions. A. M. Doweyko

11:15 —257. Trying to get it right in the first place: PLS, validation and CoMFA. R. Cramer

11:45 — Discussion.

 Section D

Unknown Site -- Unknown Room

Computational Approaches to Problems in Environmental Chemistry

Quantum Chemical Studies of Gas phase Atmospheric Chemistry


D. J. Tobias, Organizer

8:15 —258. (Per)oxy ring-closure in the atmospheric oxidation of isoprene and monoterpenes. L. Vereecken, J. Peeters

8:55 —259. Atmospheric degradation pathways of isoprene. T. S. Dibble

9:35 —260. Computational studies of chemically activated ozonolysis intermediates. K. T. Kuwata, A. S. Hasson, R. V. Dickinson, E. B. Petersen, L. K. Valin

10:15 — Intermission.

10:30 —261. Overtone spectroscopy and overtone-induced processes in HONO, HNO3, HNO4 and HNO3 and HNO3-H2O. R. B. Gerber, Y. Miller, E. Brown

11:10 —262. Theoretical mechanisms and kinetics for the reaction of dimethyl sulfide and ozone in water vapor. F. Tao, A. Shih, C. Ciobanu

WEDNESDAY AFTERNOON

 Section A

Unknown Site -- Unknown Room

Beyond Michael Dewar's Legacy: Modern Semiempirical MO Theory

Biological Systems

Cosponsored with PHYS
T. Clark, Organizer, Presiding

1:30 —263. Machine intelligence in the design of new biologically active chemicals. G. Klopman

2:00 —264. Semiempirical molecular orbital calculations and their application in drug discovery. A. A. Alex, M. J. de Groot

2:30 —265. Quantum mechanical/molecular mechanical (QM/MM) docking: A new protocol and its evaluation for known test systems. A. H. C. Horn, F. Beierlein, H. Lanig, G. Schuerer, T. Clark

3:00 — Intermission.

3:30 —266. The role of post-translational modification in the photoregulation of Fe-type nitrile hydratase. N. G. J. Richards

4:00 —267. Beyond structure: Using linear-scaling quantum calculations to move from protein crystal structures to protein properties. C. H. Reynolds, R. Rajamani, J. Li

4:30 —268. An MD/CI-approach simulating FRET in proteins. F. Beierlein, H. Lanig, O. Othersen, S. Schneider, T. Clark

 Section B

Unknown Site -- Unknown Room

Nucleic Acid Modeling

Designing Drugs that Target Nucleic Acids


N. B. Leontis and T. Hermann, Organizers

1:00 — Introductory Remarks.

1:10 —269. Simulation and visualization of DNA and polyamide complexes. J. D. Evanseck, S. M. Firestine, S. A. Mueller-Stein, A. Loccisano

1:40 —270. Flexible docking of drugs to nucleic acids using molecular modeling. C. Guilbert

2:10 —271. Discovery of a new family of antibacterials targeting the minor groove of DNA. U. Schmitz, J. Botyanszki, N. Dyatkina, M. Gezginci, E. Hanson, J. Keicher, S. Liehr, C. Roberts, D. Shi, A. Kongpachith, C. Hancock, K. Fung, L. Lou, M. Velligan, A. Khorlin, R. Griffith

2:40 — Intermission.

2:55 —272. Challenges for structure-based drug design against RNA targets. F. Aboul-ela, S. D. Morley, B. Davis, R. Klinck, M. Afshar

3:35 —273. Discovery of aminoglycoside mimetics by NMR-based screening of Escherichia coli A-site RNA. L. Yu

4:05 —274. Structure-based ligand design for the ribosomal decoding site RNA. T. Hermann

4:35 — Discussion.

 Section C

Unknown Site -- Unknown Room

Getting It Right: Variable Selection and Model Validation in (Q)SAR

Model Selection


R. D. Clark, Organizer

1:30 —275. How to trust cross-validated R2-values in variable subset regression. K. Baumann, N. Stiefl

2:00 —276. Statistical variation in progressive scrambling. P. Fox, R. D. Clark

2:30 —277. Pareto optimization of QSAR data for model selection and validation. J. H. Kalivas, J. Forrester, H. Seipel

3:00 —278. A multi-objective approach to deriving QSAR models. O. Nicolotti, V. J. Gillet, P. J. Fleming, D. Green

3:30 — Intermission.

3:45 —279. The importance of being earnest: Quality control in predictive QSAR modeling. A. Tropsha, A. Golbraikh

4:15 —280. Appraisal of model robustness and/or validation: Case studies for v-HTS challenges. J. R. Chretien, M. Pintore, N. Piclin, C. Wechman

4:45 —281. Good practice in QSAR model validation. H. Kubinyi

 Section D

Unknown Site -- Unknown Room

Computational Approaches to Problems in Environmental Chemistry

Biodegradation and Toxicology: Mechanism and Modeling


D. J. Tobias, Organizer

1:15 —282. Encoding metabolic logic: Predicting biodegradation. L. B. M. Ellis, B. K. Hou, L. P. Wackett

1:55 —283. A comprehensive approach to model the mode of toxic action. J. Gasteiger, S. Spycher

2:35 —284. Computational investigation of potential targets for haloalkane dehalogenase. B. T. Kawakami, P. V. Roberts

3:15 — Intermission.

3:30 —285. Computational studies of liquid water interfaces. L. X. Dang

4:10 —286. Reactivity of atmospherically relevant clusters via first principle simulations. I. W. Kuo, M. Sharma, C. J. Mundy, R. Car, D. J. Tobias

THURSDAY MORNING

 Section A

Unknown Site -- Unknown Room

Beyond Michael Dewar's Legacy: Modern Semiempirical MO Theory

Photochemistry, Spectroscopy, and Molecular Electronics

Cosponsored with PHYS
T. Clark, Organizer
W. Thiel, Presiding

8:00 —287. Photochemistry in solution with semiempirical CI. T. Clark, S. Schneider

8:45 —288. The advantages of the use of semiempirical methods in Molecular Electronics. J. R. Reimers, G. C. Solomon, N. S. Hush

9:30 — Intermission.

10:00 —289. Spectroscopic study and simulation from recent structural models for Eumelanin. K. Stark, J. Gallas, G. Zajac, M. Eisner, J. T. Golab

10:30 —290. Using INDO/S theory in studying the spectral properties of disordered organic materials. L. A. Liu, L. A. Peteanu, D. Yaron

11:00 —291. Semiempirical methods for modeling of photoexcited dynamics in organic electronic materials. S. Tretiak, A. Saxena, R. L. Martin, A. R. Bishop

11:30 — Concluding Remarks.

 Section B

Unknown Site -- Unknown Room

Computers in Chemistry General Contributions

Molecular Dynamics and Docking Methodologies


R. A. Wheeler and W. D. Cornell, Organizers

8:00 —292. Development and application of PfiScore: A filter function for reducing the false positive rate in docking and structure-based virtual screening. J. B. Cross, M. Jalaie, S. L. Gantt, N. A. Joshi, D. J. Wild, M. E. Snow, L. S. Narasimhan

8:20 —293. Protein ensemble-based lead docking: A comparison of FLO, GLIDE, GOLD and ICM in cross docking scenarios. D. L. Cheney, D. R. Langley, L. Mueller

8:40 —294. Modelling water molecules in protein-ligand docking using GOLD. G. Chessari, M. Verdonk

9:00 —295. Refinement and rescoring of protein-ligand complexes using all atom force fields and implicit solvation. C. Kalyanaraman, K. Bernacki, M. P. Jacobson

9:20 —296. Molecular dynamics simulation of p53. Q. Lu, R. Luo, J. Wang

9:40 —297. Simulations of pyrrole-imidazole polyamide-DNA complexes. A. Loccisano, S. A. Mueller-Stein, S. M. Firestine, J. D. Evanseck

10:00 — Intermission.

10:05 —298. Enhanced sampling methods via nonlinear variable transformations: Model systems, model proteins and all-atom peptides. P. Minary, G. Martyna, M. E. Tuckerman

10:25 —299. Conformational entropy of polypeptides from energy decomposition and WHAM. Y. Z. Ohkubo, I. F. Thorpe, C. L. Brooks III

10:45 —300. Replica-exchange-based free-energy methods. J. W. Essex, C. J. Woods, S. Foucher, M. A. King

11:05 —301. Improved methodologies for extremely precise free energies and their use to test current molecular model force fields. M. R. Shirts, V. S. Pande

11:25 —302. Spherical periodical transform of long-range interactions for molecular simulation. X. Wu, B. R. Brooks

11:45 —303. Application of ReaxFF reactive force fields to transition metal catalyzed nanotube formation. A. C. T. van Duin, K. Nielson, W. Deng, J. Oxgaard, W. A. Goddard III

 Section C

Unknown Site -- Unknown Room

Computational Approaches to Problems in Environmental Chemistry

Nucleation and Vapor Adsorption


D. J. Tobias, Organizer

8:30 —304. Ab initio fully quantum simulations of atmospheric water clusters. N. Goldman, K. R. Glaesemann, L. E. Fried

9:10 —305. Interaction between atmospheric radicals and cloud droplets: A molecular picture of the interface. J. S. Francisco, Q. Shi, S. D. Belair, S. Kais

9:50 — Intermission.

10:05 —306. Prediction of air-water adsorption coefficients. C. J. Cramer, C. P. Kelly, D. G. Truhlar

10:45 —307. Monte Carlo calculations for nucleation phenomena. J. I. Siepmann, B. Chen, M. J. McGrath, C. J. Mundy, M. L. Klein

 

Industrial Applications of Theoretical Chemistry

Cosponsored with PHYS

THURSDAY AFTERNOON

 Section A

Unknown Site -- Unknown Room

Computers in Chemistry General Contributions

Drug Design


R. A. Wheeler and W. D. Cornell, Organizers

1:00 —308. Analysis of albumin-drug interactions by computational chemical calculation using model phases. T. Hanai, R. Miyazaki, Y. Masuda, H. Homma, T. Kinoshita

1:20 —309. QSAR model to predict skin sensitization based on local lymph node assay. A. J. Holder, M. D. Miller, J. D. Eick, C. Chappelow, D. M. Yourtee

1:40 —310. Construction and simulation modeling of Mycobacterium tuberculosis cell walls. X. Hong, S. G. Franzblau, A. J. Hopfinger

2:00 —311. Advancing in silico ADME/Tox prediction via consensus models. M. D'Souza, G. M. Banik, T. Abshear, D. Kernan

2:20 —312. The secret lives of sulfones and sulfonamides. A study of the physiochemical properties and conformational preferences of these functionalities. J. Eksterowicz, R. Weekley, R. Xie, P. Sprengeler

2:40 — Intermission.

2:50 —313. Lead optimization with recursive partitioning. Y. Han

3:10 —314. SiteSorter: A novel approach to computational lead discovery based on the detection of binding site similarities in proteins. D. Debe

3:30 —315. Critical evaluation of methods to incorporate entropic loss due to binding in high-throughput virtual screening. S. Salaniwal, E. S. Manas, R. J. Unwalla, J. C. Alvarez

3:50 —316. AGENT: A program generating tautomers for computer-aided drug design. P. Ballmer, P. Pospisil, G. Folkers, L. Scapozza

4:10 —317. Application of molecular simulation methods to new radiopharmaceutical design: Case study using DNA-binding iodoHoechst ligands. K. Chen, S. J. Adelstein, A. I. Kassis

 Section B

Unknown Site -- Unknown Room

Computational Approaches to Problems in Environmental Chemistry

Interfacial Structure and Reactivity of Atmospheric Aerosols


D. J. Tobias, Organizer

1:00 —318. Sulfate aerosols: Surface properties and reactions. R. Bianco, S. Wang, J. T. Hynes

1:40 —319. Molecular simulations of atmospheric aerosols: Ions at the air/water interface. P. Jungwirth, D. J. Tobias

2:20 — Intermission.

2:35 —320. Determining the reactivity of atmospherically relevant liquid/vapor interfaces via first principles. C. J. Mundy, I. W. Kuo, D. J. Tobias

3:15 —321. Vibrational spectra of several alkali halide-water systems: Predictions from classical molecular dynamics simulations. E. C. Brown, M. Mucha, P. Jungwirth, D. J. Tobias

 Section C

Unknown Site -- Unknown Room

Computers in Chemistry General Contributions


R. A. Wheeler and W. D. Cornell, Organizers

1:00 —322. Iterative band-target entropy minimization (iBTEM): A novel algorithm for recovery of trace spectral components. M. V. Garland, W. Chew

1:20 —323. Application of 2D band-target entropy minimization (BTEM) to 2D nuclear magnetic resonance spectroscopy. M. V. Garland, L. Guo, A. Wiesmath, P. Sprenger

1:40 —324. On the structure and stability of self-assembled zwitterionic peptide amphiphiles. S. Tsonchev, A. Troisi, G. C. Schatz, M. A. Ratner

2:00 —325. Effects of steric congestion by covalent considerations in the minor groove of DNA. S. A. Mueller-Stein, S. M. Firestine, J. D. Evanseck

2:20 —326. A comparison of the interactions of retinoic acid with retinoic acid binding proteins. A. M. Waligorski, J. D. Evanseck

2:40 —327. Molecular dynamic simulation study of the cooperativity in the secondary structure folding of BBA-type proteins. E. Wen, R. Luo

3:00 — Intermission.

3:10 —328. Sequence alignments for high accuracy homology modeling. A. Nayeem, D. Sitkoff, S. Krystek Jr.

3:30 —329. Ultrafast crystallization of polar polymer melts. R. H. Gee, L. E. Fried

3:50 —330. Monte Carlo calculations for phase equilibria using ab initio potentials. M. J. McGrath, J. I. Siepmann, W. I. Kuo, C. J. Mundy

4:10 —331. Path integral thermochemistry. K. R. Glaesemann, L. E. Fried

4:30 —332. Constrained Path integration with projection coordinates. E. Curotto

 

Industrial Applications of Theoretical Chemistry

Cosponsored with PHYS






The views and opinions expressed in this page are strictly those of the Division of Computers in Chemistry. The contents of this page have not been reviewed or approved by the American Chemical Society. Please address all comments and other feedback to the the COMP Division.