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COMP Programming

229th ACS National Meeting
San Diego, CA
March 13 - 17, 2005
W. D. Cornell, Program Chair



OTHER SYMPOSIA OF INTEREST:

ADME/tox Informatics (see CINF, Tue, Wed)

Careers in Chemical Information (see CINF, Sun)

Biophysical Aspects of Protein and Peptide Aggregation: Experiment and Theory (see PHYS, Mon, Wed, Thu)

Hydrogen Bonds: Developments in Experiment and Theory (see PHYS, Sun, Mon, Wed, Thu)

Bioinorganic Chemistry and Modeling (see INOR, Tue)

Bioinorganic Modeling (see INOR, Thu)

Bioinorganic Modeling and Other Chemistry (see INOR, Sun)

Computational Chemistry (see INOR, Thu)

Computational Chemistry (see INOR, Tue)



SUNDAY MORNING

 Section A

Convention Center -- Room 8

John Pople Memorial Symposium

Cosponsored with PHYS
H. B. Schlegel, Organizer
L. Radom, Organizer, Presiding

8:50 — Introductory Remarks.

9:05 —1. John Pople: The early years. A. D. Buckingham

9:35 —2. A half-century of a PP friendship. R. G. Parr

10:00 —3. John Pople, the early years: From Carnegie Tech to Carnegie-Mellon. M. S. Gordon

10:30 — Intermission.

11:00 —4. The birth of Gaussian. W. J. Hehre

11:30 —5. The later years: CMU, Stockholm and beyond. P. M. W. Gill

12:00 —6. John in Evanston: Some reminiscences and thoughts. M. A. Ratner

12:25 —7. A friendship late in life. W. Kohn

 Section B

Convention Center -- Room 7B

Michael Klein 65th Birthday Symposium

Advances in Computer Simulation Methods


D. J. Tobias and R. J. Doerksen, Organizers

8:10 — Introductory Remarks.

8:25 —8. Computers as tools of discovery. U. Landman

9:05 —9. Application of non-Hamiltonian molecular dynamics to chemical systems. G. Martyna

9:45 — Intermission.

10:00 —10. Stochastic linear scaling for metals and non metals. M. Parrinello, F. R. Krajewski

10:40 —11. Probing long time-scale events with advanced simulation techniques. B. Chen

 Section C

Convention Center -- Room 7A

General Oral - Molecular Mechanics and Simulation


W. D. Cornell, Organizer

8:10 —12. BioSimGrid: A distributed database for the storage and analysis of biomolecular computer simulations. J. W. Essex, S. E. Murdock, R. J. Gledhill, K. Tai, M. H. Ng, S. Johnston, B. Wu, H. Fangohr, P. Jeffreys, S. Cox, M. Sansom

8:30 —13. Binding energy calculation for FKBP receptor and ligands by generalized BAR method. H. Fujitani, Y. Tanida, M. Ito, M. R. Shirts, C. D. Snow, G. Jayachandran, V. S. Pande

8:50 —14. Coupled reference interaction site model (RISM)/simulation approach for free energy of solvation. H. Freedman, T. N. Truong

9:10 —15. Computational strategy for binding of phenylalanine analogs in phenylalanyl-tRNA synthetase. P. M. Kekenes-Huskey, I. C. Tanrikulu, V. W. T. Kam, N. Vaidehi, W. A. Goddard III

9:30 —16. Computational study of IAG-nucleoside hydrolase: Determination of the preferred ground state conformation and the role of active site residues. D. M. Shivakumar, T. C. Bruice

9:50 —17. Intermolecular potentials of mean force of amino acid side chain interactions in aqueous medium. S. A. Hassan

10:10 —18. Prediction of protein geometry and stability changes for arbitrary single point mutations. A. Bordner, R. Abagyan

10:30 —19. Side-chain conformational changes on ligand binding: An analysis of the PDB. F. Toschi, A. R. Leach, P. Bamborough, J. W. Essex

10:50 —20. Small-system effects in molecular dynamics simulations. R. B. Shirts, S. R. Burt, A. M. Johnson

11:10 —21. Sub-microsecond conformer transitions of protein inhibitor, fasciculin to acetylcholinesterase. J. Bui, J. A. McCammon

11:30 —22. A gating mechanism proposed from a 15 nanosecond simulation of a complete human alpha-7 nicotinic acetylcholine receptor model. R. J. Law, J. A. McCammon, R. Henchman

11:50 —23. A comparison of MacroModel methodologies for ligand conformation generation. J. C. Shelley

SUNDAY AFTERNOON

 Section A

Convention Center -- Room 8

John Pople Memorial Symposium

Cosponsored with PHYS
H. B. Schlegel and L. Radom, Organizers
J. Chandrasekhar, Presiding

2:25 — Introductory Remarks.

2:30 —24. Low-coordination silicon compounds. Interplay and synergism between experiment and theory. Y. Apeloig

3:00 —25. The schizophrenic effect of geminal fluorination on the kinetic stability of molecules containing strained rings. W. T. Borden, D. A. Hrovat, C. Isborn, S. B. Lewis, S. Getty

3:30 —26. Stable carbon(0) compounds: Theoretical analysis of molecules with unusual bonding situations. G. Frenking

4:00 — Intermission.

4:30 —27. What IS the acidity of imidazole? An assessment of theoretical protocols for calculation of pKa values. B. F. Yates, A. M. Magill

5:00 —28. Intramolecular hydrogen bonds versus other weak interactions. O. Mˇ

5:30 —29. On the roles of π-stacking, hydrogen bonding and donor-acceptor interaction in acrolein complexes of chiral oxazaborolidinone catalysts. M. W. Wong

 Section B

Convention Center -- Room 7B

Michael Klein 65th Birthday Symposium

Theory and Modeling of Polymers, Complex Fluids, and Glasses


D. J. Tobias and R. J. Doerksen, Organizers

1:40 —30. Dynamics on the way to forming glass. D. Chandler, J. P. Garrahan

2:20 —31. Structure and interactions in nematic-colloid dispersions. T. G. Sokolovska, R. O. Sokolovskii, G. N. Patey

3:00 —32. Simulation studies of structure and retention in chromatographic systems. J. I. Siepmann, L. Zhang, L. Sun, C. D. Wick, M. R. Schure

3:40 — Intermission.

3:55 —33. Nucleation phenomena in polymer crystallization. R. H. Gee

4:35 —34. Crossover from free Rouse to entangled chain dynamics in polyethylene melts. J -P. Ryckaert

5:15 —35. Simulating polymersomes: A fruitful collaboration in rational coarse graining. D. E. Discher, M. L. Klein

 Section C

Convention Center -- Room 7A

Understanding Protein-Ligand Interactions


K. M. Merz Jr., Organizer
C. H. Reynolds, Organizer, Presiding

1:30 — Introductory Remarks.

1:40 —36. Protein-ligand interactions and computer-aided drug design. W. L. Jorgensen, J. Ruiz-Caro, J. Tirado-Rives

2:10 —37. Free energy calculations in structure-based drug design. J. A. McCammon

2:40 —38. Calculation of binding affinities. M. K. Gilson

3:10 — Intermission.

3:20 —39. Challenges in pKa calculations for internal residues in proteins. B. Garcia-Moreno, D. G. Isom, C. A. Fitch

3:50 —40. Are fragment-protein binding energies sufficient to predict compound affinity? p38 as a case study in structure based design using fragments. F. P. Hollinger, Z. Konteatis, E. L. Michelotti, T. T. Fujimoto, J. L. Ludington, M. Karpusas, M. Bukhtiyarova, M. Saporito, X. Chai, K. Northrop, E. Springman

4:20 —41. Computational studies of protein-solvent and protein-ligand interactions. K. Raha, K. M. Merz Jr

 Section D

Convention Center -- Room 4

Safe Exchange of Chemical Information: Can Relevant Chemical Information be Exchanged Without Disclosing Chemical Structures?

Cosponsored with CINF
T. I. Oprea, Organizer
C. A. Lipinski, Organizer, Presiding

1:20 — Introductory Remarks.

1:30 —42. Can topological indices transmit information on properties but not on structures? A. T. Balaban

2:00 —43. Coding and decoding chemical structure information. J. Gasteiger, D. Hristozov

2:30 —44. Molecular shape and electrostatics in the encoding of relevant chemical information. A. Nicholls, J. A. Grant

3:00 — Intermission.

3:20 —45. Confusing descriptors: Where chemical information gets dizzy. C. G. Bologa, M. Olah, T. I. Oprea

3:50 —46. Anonymous sd (.asd) files. T. Clark

4:20 —47. Similarity-based descriptors (SIBAR) as tool for exchange of chemical information. G. F. Ecker, B. Zdrazil, D. Kaiser

4:50 —48. Encoding and exchange of chemical information using substructural molecular fragments. A. Varnek, D. Fourches, V. P. Solov’ev

MONDAY MORNING

 Section A

Convention Center -- Room 8

John Pople Memorial Symposium

Cosponsored with PHYS
H. B. Schlegel and L. Radom, Organizers
N. Ostlund, Presiding

8:55 — Introductory Remarks.

9:00 —49. One- and two-bond spin-spin coupling constants across X-H-Y hydrogen bonds. J. E. Del Bene

9:30 —50. Theoretical modeling of single molecule magnets. E. R. Davidson

10:00 —51. Donor/acceptor interaction: Electronic structural analysis and associated vibronic features. M. D. Newton

10:30 — Intermission.

11:00 —52. Correlation potential in density functional theory and recollections of Pople's entry into DFT. M. Levy

11:30 —53. Recent progress in the development of exchange-correlation functionals. G. E. Scuseria

12:00 —54. A new hybrid DFT functional: Accurate description of excited states, charge-transfer states, and van der Waals interactions. K. Hirao

 Section B

Convention Center -- Room 7B

Michael Klein 65th Birthday Symposium

Simulation of Biological Ion Channels and Enzyme Reactions


D. J. Tobias and R. J. Doerksen, Organizers

8:10 —55. Molecular dynamics simulations of the open and closed conformations of KirBac3.1.: Structural changes during ion channel gating. C. Domene

8:50 —56. Molecular modeling of ion channels: From ab initio calculations to structural bioinformatics. P. Carloni

9:30 —57. Activation of Shaker B, a voltage-gated potassium channel. M. Tarek, W. Treptow

10:10 — Intermission.

10:25 —58. Mechanism of proteolysis of anthrax lethal factor. An ab initio and hybrid QM/MM molecular dynamics study. A. Magistrato

11:05 —59. Structure and function of vanadium haloperoxidases. S. Raugei

 Section C

Convention Center -- Room 7A

Understanding Protein-Ligand Interactions


C. H. Reynolds, Organizer
K. M. Merz Jr., Organizer, Presiding

8:30 —60. Understanding protein-ligand interactions and binding free energy with an empirical solvation-based model. G. E. Kellogg, M. Fornabaio, P. Cozzini, A. Mozzarelli, F. Spyrakis, D. J. Abraham

9:00 —61. Exploring protein ligand interactions: Binding free energies, docking and scoring. C. L. Brooks III

9:30 —62. Computational modelling of inhibition and catalysis in malaria proteases. J. Aqvist

10:00 — Intermission.

10:10 —63. Modeling protein-ligand interactions via high throughput docking and induced fit methods. R. A. Friesner

10:40 —64. Structure-based modeling of the hERG channel: A two-state linear interaction energy model for ligand binding. B. A. Tounge, R. Rajamani, C. H. Reynolds

11:10 —65. Hierarchical energy functions for the design of protein binding interfaces. D. F. Green, M. D. Altman, B. Tidor

 

Safe Exchange of Chemical Information: Can Relevant Chemical Information be Exchanged Without Disclosing Chemical Structures?

Cosponsored with CINF

MONDAY AFTERNOON

 Section A

Convention Center -- Room 8

John Pople Memorial Symposium

Cosponsored with PHYS
H. B. Schlegel and L. Radom, Organizers
P. Dobosh, Presiding

1:55 — Introductory Remarks.

2:00 —66. Electronic structure studies of materials chemistry using embedded cluster models. K. Raghavachari

2:30 —67. Computation of zero-field splitting in triplet heteroarylnitrenes. Z. Havlas, M. Kyvala, J. Michl

3:00 —68. Calculation of the dispersion energy between large molecules: Graphene plates and the graphene-water system. P. Pulay, A. R. Ford

3:30 — Intermission.

4:00 —69. A complete basis set model chemistry for excited states. G. A. Petersson

4:30 —70. Quantum photochemistry. D. G. Truhlar, A. W. Jasper, S. Nangia, C. Zhu, P. Piecuch, M. J. McGuire

5:00 —71. Advanced computational methods applied to chemistry. T. L. Windus, Y. Alexeev, E. Apra, M. Krishnan, V. Tipparaju, B. J. Palmer, J. Nieplocha

 Section B

Convention Center -- Room 7B

Michael Klein 65th Birthday Symposium

Advances in Computer Simulation Methods


D. J. Tobias and R. J. Doerksen, Organizers

1:40 —72. Practical approaches to condensed phase quantum dynamics based on quantum decoherence. P. J. Rossky

2:20 —73. Linearized path integral approach to calculating non-adiabatic time correlation functions. D. F. Coker, S. Bonella

3:00 —74. Electrochemistry in a very small cell: A computational approach. M. Sprik, J. Blumberger, Y. Tateyama

3:40 — Intermission.

3:55 —75. A coarse grain simulation methodology for structured solutions. J. C. Shelley

4:35 —76. The performance of metadynamics in flexible docking. F. L. Gervasio, A. Laio, M. Parrinello

 Section C

Convention Center -- Room 7A

Understanding Protein-Ligand Interactions


K. M. Merz Jr. and C. H. Reynolds, Organizers
K. Raha, Presiding

1:30 —77. Binding MOAD (Mother of All Databases). H. A. Carlson, M. L. Benson, R. D. Smith, L. Hu

2:00 —78. SAR, binding mode and radioprotective effects of a novel class of Checkpoint2 kinase inhibitors. F. U. Axe, K. L. Arienti, A. Brunmark, K. McClure, A. Lee, J. Blevitt, D. Neff, L. Huang, S. Crawford, C. R. Pandit, L. Karlsson, J. G. Breitenbucher

2:30 —79. Understanding protein-ligand interactions in the field of kinases. I. Morize, D. Kominos, R. Pearlstein

3:00 — Intermission.

3:10 —80. Characterization of protein-ligand interaction sites using computational solvent mapping. S. Vajda, M. Silberstein, K. Clodfelter

3:40 —81. End point free energy calculations: What it takes for success with FK506 Binding Protein. J. M. J. Swanson, J. A. McCammon

4:10 —82. Dynamics of buried water in proteins. C. S. Verma

 Section D

Convention Center -- Room 2

General Oral - Molecular Mechanics and Simulation


W. D. Cornell, Organizer

1:20 —83. A new approach to efficiently explore the free energy surface, trace the reaction pathways and converge the free energy barriers. B. Ensing, A. Laio, M. Parrinello, M. L. Klein

1:40 —84. Application of digital filters to enhance conformational change in protein systems. A. P. Wiley, J. W. Essex

2:00 —85. Atomically detailed simulations of conformational transitions in DNA Polymerases: Implications for DNA synthesis fidelity mechanisms. K. Arora, T. Schlick

2:20 —86. Hybrid molecular dynamics-quantum mechanics simulations of solvation dynamics. M. C. Zwier, C. M. Meeusen, J. M. Shorb, B. P. Krueger

2:40 —87. Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects. X. Li, S. A. Hassan, E. L. Mehler

3:00 —88. Constant pH molecular dynamics in generalized Born implicit solvent. J. T. Mongan, D. A. Case, J. A. McCammon

3:20 —89. Constant-pH molecular dynamics simulations for pKa predictions and conformational dynamics studies of proteins. J. Khandogin, C. L. Brooks III

3:40 —90. Computational studies of chaperonin-mediated protein folding. G. Stan, B. R. Brooks, D. Thirumalai, G. H. Lorimer

4:00 —91. Is Poisson-Boltzmann theory insufficient for protein folding simulations? T. Lwin, J. Lu, R. Zhou, R. Luo

4:20 —92. Protein folding simulations from first principles by a new molecular dynamics method. Z. Huang, Z. Guo, R. A. Wheeler

4:40 —93. Catalytic dynamics of Escherichia coli Thioesterase/Protease I. C -Y. Chou, T -H. Huang, J -H. Lin

5:00 —94. In silico studies of DNA pol X support an induced-fit mechanism. B. A. Sampoli Benitez, K. Arora, T. Schlick

 

Safe Exchange of Chemical Information: Can Relevant Chemical Information be Exchanged Without Disclosing Chemical Structures?

Cosponsored with CINF

MONDAY EVENING

 Section A

Convention Center -- Sails Pavilion

Sci-Mix


W. D. Cornell, Organizer

6:00 - 8:00

142-143, 145, 148, 152-153, 161, 169, 177, 180, 189, 201, 203, 206-207, 214, 220, 223, 239-240. See subsequent listings.

TUESDAY MORNING

 Section A

Convention Center -- Room 4

John Pople Memorial Symposium

Cosponsored with PHYS
H. B. Schlegel and L. Radom, Organizers
S. Topiol, Presiding

8:55 — Introductory Remarks.

9:00 —95. Computational studies on biomolecules and reaction mechanisms. R. J. Boyd

9:30 —96. Alzheimer’s chemistry: Oxidation of methionine by copper(II)? A. Rauk, P. Brunelle, D. Raffa, R. Gomez-Balderas, G. A. Rickard

10:00 —97. Lesions in DNA subunits: Radicals derived from the guanine-cytosine base pair. P. P. Bera, H. F. Schaefer III

10:30 — Intermission.

11:00 —98. New force fields for biomolecular simulations: Better torsions and polarization through QC. C. L. Brooks III

11:30 —99. MD simulations of 136 unique tetranucleotide DNA sequences. D. L. Beveridge

12:00 —100. QM/MM studies of organic and enzymatic reactions. W. L. Jorgensen

 Section B

Convention Center -- Room 7B

ACS Award for Computers in Chemical and Pharmaceutical Research


W. D. Cornell, Organizer

9:00 — Introductory Remarks.

9:05 —101. Scholarly publishing at the crossroads: An overview of the Open Access publishing movement. B. Town

9:40 —102. Twenty five years of progress in cheminformatics. W. A. Warr

10:15 — Intermission.

10:30 —103. Knowledge based screening. J. Delaney

11:05 —104. Multi-objective approaches to screening collection design and analysis of HTS data. S. Pickett

 Section C

Convention Center -- Room 7A

General Oral - Molecular Mechanics and Simulation


W. D. Cornell, Organizer

8:20 —105. Characterization of non-biological antimicrobial polymers in aqueous solution and at water-lipid interfaces from all atom and coarse grained molecular dynamics. I. Ivanov, S. Vemparala, V. Pophristic, K. Kuroda, W. F. DeGrado, M. L. Klein

8:40 —106. Coarse-grain molecular dynamics study of peptide nanotube insertion in lipid bilayers. B. Ensing, S. O. Nielsen, P. B. Moore, M. L. Klein

9:00 —107. Dynamics of the full-length P-glycoprotein in the POPC bilayer. H -H. Tu, J -H. Lin

9:20 —108. Effects of initial radical damage in molecular dynamics simulations of a 1-palmitoyl-2-linoleyl-sn-glycero-3-phosphatidylcholine (PLPC) lipid bilayer. P. Brunelle, G. A. Rickard, A. Rauk

9:40 —109. Implicit modelling of heterogeneous biological environments: Applications to integral membrane proteins. M. Feig

10:00 —110. Molecular dynamics simulations of membrane systems using non-additive force fields. S. Patel, C. L. Brooks III

10:20 —111. Molecular dynamics simulations of phospholamban: Effects of membrane, phosphorylation and aggregation. K. Kuczera, G. S. Jas, Y. Houndonougbo

10:40 —112. Simulations of photofacilitated active transport in doubly illuminated photoactive liquid membranes. T. Longin, T. Fraterman, J. Terhorst, C. Lang

11:00 —113. Self-assembly of peptide nanotubes by molecular dynamics study. E. Khurana, S. O. Nielsen, B. Ensing, M. L. Klein

11:20 —114. First-principles Monte Carlo simulations of liquid water in the isobaric-isothermal ensemble. M. J. McGrath, J. I. Siepmann, W. I -F. Kuo, C. J. Mundy

11:40 —115. Withdrawn.

 

ADME/tox Informatics

Cosponsored with CINF, MEDI, and TOXI

TUESDAY AFTERNOON

 Section A

Convention Center -- Room 4

John Pople Memorial Symposium

Cosponsored with PHYS
H. B. Schlegel and L. Radom, Organizers
J. W. McIver, Presiding

1:55 — Introductory Remarks.

2:00 —116. The Pople years at Northwestern: A dynamicist learns electronic structure theory. G. C. Schatz

2:30 —117. Molecular potential energy surfaces. M. A. Collins, G. E. Moyano, C. R. Evenhuis, V. Deev

3:00 —118. Thermal reaction rates from higher derivatives of the flux-flux autocorrelation function at time zero. W. H. Miller

3:30 — Intermission.

4:00 —119. Nakatsuji theorem, Nooijen conjecture, and constrained coupled-cluster theory. W. Kutzelnigg, D. Mukherjee

4:30 —120. Solving the Schroedinger equation for atoms and molecules. H. Nakatsuji

5:00 —121. Recent developments in geminal model chemistries. V. A. Rassolov

 Section B

Convention Center -- Room 7B

ACS Award for Computers in Chemical and Pharmaceutical Research


W. D. Cornell, Organizer

1:30 — Introductory Remarks.

1:35 —122. Next step in the evolution of molecular alignment tools. R. D. Clark, E. Abrahamian, A. Strizhev, P. R. N. Wolohan, C. Abrams

2:10 —123. Gold and Silver development. J. C. Cole, J. W. M. Nissink, R. Taylor, F. H. Allen

2:45 —124. Contribution of high-throughput docking to the drug discovery process. E. Vangrevelinghe

3:20 — Intermission.

3:35 —125. Award Address (ACS Award for Computers in Chemical and Pharmaceutical Research, sponsored by Accelrys, Inc). Molecular similarity approaches for chemoinformatics. P. Willett

 Section C

Convention Center -- Room 7A

General Oral - Molecular Mechanics and Simulation


W. D. Cornell, Organizer

1:20 —126. A computer-aided molecular design approach for the design of organic molecules (solvents) for crystallization. A. T. Karunanithi, S. Sithambaram, L. E. K. Achenie, S. L. Suib

1:40 —127. CQFF (Consistent Charge Equilibration with general Force Field). O. Kitao, T. Ogawa

2:00 —128. Free energy profile along a discretized reaction path: Computational approach and examples. K. N. Kudin

2:20 —129. Interpreting carcinogen benzo[a]pyrene's effects on transcription initiation-required TATA/TBP binding using molecular dynamics simulations. Q. Zhang, S. Broyde, T. Schlick

2:40 —130. Molecular dynamics simulations of DNA/Polyamide complexes in the crystal environment. A. Loccisano, S. A. Mueller-Stein, S. M. Firestine, J. D. Evanseck

3:00 —131. Molecular dynamics study of slow base flipping in DNA using conformational flooding. B. Bouvier, H. GrubmŘller

3:20 —132. Monte Carlo simulations of polymer-carbon dioxide phase equilibria. C. D. Wick, J. I. Siepmann, D. N. Theodorou

3:40 —133. Relating local energetic roughness and kinetic rates: All-atom accelerated molecular dynamics of cis/trans isomerization of serine-proline motifs. D. Hamelberg, T. Shen, J. A. McCammon

4:00 —134. Semiclassical scattering on conical intersections. A. Piryatinski, M. Stepanov, S. Tretiak, V. Chernyak

4:20 —135. Behavior of a Brownian particle in a nonstationary medium. A. V. Popov, R. Hernandez

4:40 —136. Melting and superheating of FCC metals at high heating rates. X. Liu, C. Meng, C. Liu

 

ADME/tox Informatics

New Methodologies

Cosponsored with CINF, MEDI, and TOXI

TUESDAY EVENING

 Section A

Convention Center -- Sails Pavilion

Poster Session


W. D. Cornell, Organizer

6:00 - 8:00

137. Gaussian-weighted RMSD superposition of proteins. K. L. Damm, H. A. Carlson

138. Binding MOAD (Mother of All Databases). M. L. Benson, L. Hu, R. D. Smith, M. G. Lerner, H. A. Carlson

139. Database mining to characterize protein-ligand binding sites. R. D. Smith, N. Khazanov, H. A. Carlson

140. Creating a smart virtual screening workflow: Application of E. coli DHFR primary HTS data. S. Varma, L. S. Fisher, T. A. Lyons, D. Chen

141. Omega2: Conformer generation redux. M. Stahl, G. Skillman

142. SAESAR: Shape and electrostatics in structure activity relationships. N. E. MacCuish, A. Nicholls, J. D. MacCuish

143. Efficient charges: Optimal ligand charges for binding that might actually work. A. Nicholls, S. Phatak, G. E. Kellogg

144. Shape and electrostatic similarity across a large-scale database of vendor-available compounds. R. Tolbert, A. Nicholls, G. Skillman, M. Tennant

145. Structure-based design, molecular modeling and biophysical studies of conformation adopted by tetrapeptides with inhibitory activity for thrombin. C. Clement, J. Gonzalez, R. Alcantara, M. Philipp

146. Rapid evaluation of compound oral bioavailability using in vitro and in silico ADME properties. S. F. Yan, K. Chen, L. Schaffer, M. Wu, Y. Zhou

147. Role of quantitative structure activity relationship (QSAR) in understanding HIV-1 binding domain and designing protease inhibitors. B. Bhhatarai, R. Garg

148. Three for three: De novo design of multiple novel chemotypes of T-type calcium channel blockers. D. L. Cheney, J. J. Hangeland, T. J. Friends, P. C. Levesque

149. Towards the solution structure of a “mini-insulin”. J. Pecher, G. Le Flem, P. Bogdanowicz, J -P. Pujol, D. A. Case, J. Rochette, F -Y. Dupradeau

150. Towards validation of a model to identify hERG potassium channel blockers. L. C. Van Zant, A. M. van Rhee, N. A. Castle, C. P. Silvia

151. A complete model of human type I collagen monomer. I. Vinogradov, D. J. Anderson, M. C. Goh

152. Ab initio protein loop prediction in internal coordinate space. J. An, M. Totrov, R. Abagyan

153. Characterization of drug and drug carrier interactions by using computational chemistry and X-ray crystallography. L. Xiao, R. R. Burnette, I. A. Guzei

154. Comparative analysis of putative agonist binding modes in the human A1 adenosine receptor. H. GutiÚrrez de Terßn, J. ┼qvist, F. Sanz

155. Comparative QSAR as a cheminformatics tool in the design of HIV-1 protease inhibitors. R. Garg, B. Bhhatarai

156. De novo structure-based design of ion receptors. B. P. Hay, A. A. Oliferenko

157. DNA and estrogen receptor interaction revealed by the fragment molecular orbital calculation. T. Watanabe, Y. Inadomi, S. Tanaka, K. Fukuzawa, T. Nakano, L. Nilsson, U. Nagashima

158. Hierarchical QSAR (HiQSAR) approach to predicting dermal penetration. B. D. Gute, J. Riviere, R. E. Baynes, S. C. Basak

159. Low-resolution modeling of the ribosome assembly of the 30S subunit by molecular dynamics simulations. Q. Cui, D. A. Case

160. Modeling and predicting the structure of G-protein-coupled receptors. M. Michino, W. Im, J. Chen, C. L. Brooks III

161. Modeling human K+ channel and exploring ligand binding using molecular dynamics. F. Ísterberg, J. ┼qvist

162. Modeling peptide association in amyloid-forming peptides. R. D. Hills Jr., C. L. Brooks III

163. Modulation of steric forces in the minor groove of DNA. S. A. Mueller-Stein, A. Loccisano, S. M. Firestine, J. D. Evanseck

164. Molecular dynamics simulations of a RNA-morpholino hybrid. E. Y. Lau, M. E. Colvin

165. Molecular dynamics simulations of human tRNALys,3UUU anticodon stem-loop: Determination of the role of nonstandard bases. N. E. McCrate, M. E. Varner, K. L. Schembri, A. E. Combs, M. C. Nagan

166. Predictor@home: A multiscale, distributed approach for protein structure prediction. C. An, M. Taufer, C. L. Brooks III

167. Accurate prediction of binding sites for diverse protein targets using fragment-based grand canonical Monte Carlo Simulations. S -B. Rong, T. Fujimoto, J. Ludington, B. Alger, I. Shkurko, M. Clark, J. S. S. Wiseman, F. P. Hollinger

168. Incorporating protein flexibility into drug design: HIV-1 protease as a test case. K. L. Meagher, M. G. Lerner, H. A. Carlson

169. Protein ensemble docking: Comparison of fixed charge and polarizable forcefields in scoring. L. Mueller, D. L. Cheney

170. Strategies for efficient ligand-receptor docking: Typical case studies. A. Nayeem, S. Krystek Jr.

171. Virtual screening approach: Application of a hydropathic forcefield to 3D database searches. M. Fornabaio, F. Rastinejad, S. Kharalkar, M. Safo, D. J. Abraham, G. E. Kellogg

172. Docking studies and ligand recognition in folypolyglutamate synthetase. X -J. Tan, H. A. Carlson

173. Docking to large ensembles of homology models reliably explains the substrate binding differences in Cytochrome P450 1As of human and fish species. J. C. Prasad, C. J. Camacho, J. J. Stegeman, S. Vajda

174. Computational prediction of structure, substrate binding mode, mechanism and rate for a malaria protease with a novel type of active site. S. Bjelic, J. ┼qvist

175. A structure-based approach to Akt/PKB inhibition. D. Jung, M. Forino, M. Pellecchia

176. Docking of phthalate monoesters to PPAR-Ń. T. Kaya, S. C. Mohr, D. J. Waxman, S. Vajda

177. Quantitative structure–activity relationship analysis of pyridinone HIV-1 reverse transcriptase inhibitors using the k nearest neighbor method and QSAR-based database mining. J. L. Medina-Franco, A. Golbraikh, R. Castillo, A. Tropsha

178. QSAR study of hemostatic labdane diterpenoids. M. A. Turabekova, U. N. Zainutdinov, S. I. Salikhov

179. 2-Pyrimidinethiol and methyl-2-pyrimidinethiols: A computational study of tautomers and dimers. F. Freeman, H. N. Po

180. A crystal force field: Evaluation of short-range intermolecular interactions for representation of X-ray crystal structures in Cambridge Structure Database. H. Goto, S. Obata, N. Nakayama

181. A theoretical study of active site proton swapping in Subtilisin Carlsberg during catalysis. M. D. Legault

182. A theoretical study of the enantioselectivity of Rhizomucor Miehei lipase during catalysis. B. De Leon Rivera, M. D. Legault, G. L. Barletta

183. A theoretical study on fragmentation pathways and mechanisms of protonated β-alanine. M. K. J. Cheng, O. Y. O. Chan, S. Abirami, N. L. Ma, C. W. Tsang

184. Ab initio genetic algorithm based elucidation of multiply aromatic clusters. A. N. Alexandrova, A. I. Boldyrev, H -J. Zhai, L -S. Wang

185. Absolute and relative entropies from computer simulation with applications to ligand binding. J. Carlsson, J. ┼qvist

186. Accurate predictions of protein-protein binding free energies. M. Alml÷f, B. Brandsdal, J. ┼qvist

187. Automatic clustering of probe molecules to define surface complementarity: Applications to protein-protein interfaces. M. G. Lerner, H. A. Carlson

188. Binding affinity studies of Plasmepsins from Plasmodium falciparum. M. Nervall, J. ┼qvist

189. Binding energy calculation for theophylline-RNA aptamer with generalized BAR method. Y. Tanida, M. Ito, H. Fujitani, M. R. Shirts, C. D. Snow, G. Jayachandran, V. S. Pande

190. Comparison of arbitrary versus tailored similarity spaces in property estimation. B. D. Gute, S. C. Basak, D. Mills, D. M. Hawkins

191. Computation of the absorption spectrum of green fluorescent protein. S. Trohalaki, S. S. Patnaik, R. Pachter

192. Computational approaches to MEK1 and MEK2 structure determination and inhibitor design. H. Chen, J. F. Ohren, C. E. Whitehead, A. Pavlovsky, E. Zhang, P. Kuffa, C. Yan, P. McConnell, A. Delaney, D. T. Dudley, C. Hasemann

193. Computational investigation of structural and electronic characteristics of a series of glycosidase inhibitors and their relationship to experimental activity data. R. D. Anderson, M. C. Milletti

194. Computational modeling study of the C-terminal RING-finger domain of HDM2. Z. Hu, T. Githu, D. Bowen, W. M. Southerland

195. Computational studies of the potential inhibitors of the copper-containing enzyme lysyl oxidase. F. Ryvkin, M. Dang

196. Computational studies of the structure and bonding of sulfur and phosphorous ylides. J. M. Standard, B. A. Copack, R. J. Steidl

197. Conformational interconversion of alanine dipeptide from 100 nanosecond molecular dynamics simulations by implicit and explicit solvation methods. R. A. Newton, J. D. Evanseck

198. Conformational isomerization kinetics of a dipeptide, N-acetyl - tryptophan methyl amide (NATMA): A non-RRKM approach. J. K. Agbo, D. M. Leitner

199. Conformational study of small molecules in crystallographically determined structures. R. G. Karki, M. C. Nicklaus

200. Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DiSCO) algorithm. Q. Zhang, D. A. Beard, T. Schlick

201. Potential ligand design for Dengue virus using high throughput screening, binding affinity evaluation and pharmacophore/scaffold identification. Z. Zhou, C. Post

202. Design and conformational analysis of paclitaxel derivatives of nitroimidazole. I. Weidlich, S. Sobiak

203. Development of a special purpose parallel computer for the first principles DVXƒ┐ calculations. U. Nagashima, T. Sasaki

204. Docking studies and 3D-QSAR analysis for inducible nitric oxide synthase inhibitors. Y. Kyoya, S. Ueda, A. Yano, Y. Tominaga, M. Ido, M. Kawasaki, I. Fujiwara

205. Effect of glycosylation on a model peptide. S. M. Tschampel, R. J. Woods

206. Efficient linear-scaling Ewald method for combined QM/MM calculations: Development and comparison with stochastic boundary and spherical cut-off methods. K. Nam, J. Gao, D. M. York

207. First-principles calculation of the binding free-energy landscape of a trypsin-ligand complex. O. Guvench, C. L. Brooks III

208. Forcefield parameterization of inhalational anesthetics, halothane and isoflurane: An ab initio study. S. Vemparala, I. Ivanov, M. L. Klein

209. Fuzzy relational clustering of molecular conformations using novel features based on DNA base-pair step parameters. M. Misra, D. Pai, R. Woodley, A. Banerjee, R. N. DavÚ, L -Y. Shih, X -J. Lu, A. R. Srinivasan, W. K. Olson, C. A. Venanzi

210. How does autophosphorylation modulate catalysis function and regulation in cAMP-dependent protein kinase? Y. Cheng

211. Investigating targets of antibacterial cysteine protease inhibitors. L. A. Vogt, J. P. Wolbach

212. Kinetic and geometrical isotope effects in hydrogen-atom transfer reaction: Application of multi-component MO method. T. Ishimoto, M. Tachikawa, U. Nagashima

213. Modeling of triclosan analogs for enoyl reductase inhibition. J. G. Longenecker, P. D. Schettler Jr., R. R. Hark, J. P. Wolbach

214. Molecular simulations of model Langmuir monolayers. L. V. Villalobos-Rivera, G. E. Lˇpez

215. Nitrosation of melatonin. J. M. Rintelman, M. S. Gordon, J. E. Rice

216. On the convergence of a hybrid parallel tempering Tsallis statistics Monte Carlo algorithm. H. Liu, K. D. Jordan

217. Pharmacophore identification and antidiabetic activity prediction in the class of guanidino- and aminoguanidinoacetic acid compounds. A. V. Marenich, I. B. Bersuker, J. E. Boggs

218. Q: A novel method to simulate the solvation of hydrophobic surfaces by water and its application to the estimation of protein-ligand binding constants. A. M. Doweyko, S. R. Johnson

219. Rare gases inserted into biological building blocks: A theoretical study of glycine - Rg compounds (Rg=Xe, Kr, Ar). G. M. Chaban

220. Rate constant calculation of ligand binding with solvation force determined by boundary elementary method. B. Z. Lu, D. Zhang, A. J. McCammon

221. Sila-Pummerer rearrangement of cyclic sulfoxides: A computational study of sulfonium ylide intermediates. F. Freeman, S. V. Kirpichenko, B. A. Shainyan

222. Similarity-based chemical clustering techniques. B. D. Gute, S. C. Basak, D. Mills

223. Tautomerization of the HBO base pair model in the DNA major and minor grooves. F -Y. Dupradeau, C. Yu, R. Jimenez, F. E. Romesberg, D. A. Case

224. Theoretical study on glucose polysaccharides. J -S. K. Yu

225. Unbinding study of edema factor-calmodulin complex using steered molecular dynamics. K. A. Baker, J. D. Evanseck, S. M. Firestine

226. Unintended consequences of periodic boundary conditions: Particles of different mass have different effective temperatures. R. B. Shirts, S. R. Burt, A. M. Johnson

227. Predicting chemical shielding in proteins: A QM/MM study combined with MD simulations. S. Moon, D. A. Case

228. Understanding C2-substituent effects of bis(oxazoline) copper(II) catalyzed Diels-Alder reactions by density functional computation. E. G. Franklin, J. DeChancie, J. D. Evanseck

229. Understanding the proficiency of OMP Decarboxylase: An ab initio study. C. L. Stanton, K. N. Houk

230. A computational study of the competing pathways of rearrangement, HF and HCl elimination reactions of CF3CF2CH2Cl and CF3CHClCF3. W. C. Everett, B. E. Holmes, G. L. Heard

231. A QM/QM’ approach to modeling the Zn(II)/Cu(I) core of a protein. M. A. Harrison, L. Ciofini, J. D. Evanseck, C. Adamo, C. T. Dameron

232. Ab-initio fragment orbital theory: Application to the excited states of some organometallic compounds. G. P. Das, J -P. Blaudeau

233. Application of variational reduced-density-matrix theory to organic molecules. G. Gidofalvi, D. A. Mazziotti

234. Bonding or antibonding, an overlap population study. X. Liu, C. Meng, C. Liu

235. Calculating low energy reaction pathways in proteins and RNA: A QM/MM implementation of the Nudged Elastic Band (NEB) method. R. C. Walker, D. H. Mathews, D. Case

236. Computational studies of the phosphorylation reaction in protein kinase A: Ab-initio QM/MM approach. M. Valiev, J. H. Weare

237. Computational study of epoxide ring-opening reactions of 2,3-anhydrosugars. P. Tao, R. B. Sunoj, M. P. DeMatteo, T. L. Lowary, C. M. Hadad

238. Computational study of the reaction mechanism of ethylenimine with DNA. P. M. Todebush

239. Computational study of twisted intramolecular charge transfer (TICT) characteristics of substituted pyrrolyl pyridines. J. L. Menke, E. V. Patterson

240. Determination of the conformation of 2-hydroxy, 2-amino and 2-fluoro benzoic acid dimers in CDCl3 using 13C NMR and DFT/NBO analysis: The central importance of the carboxylic acid carbon. R. R. Burnette, F. Weinhold

241. DFT and ONIOM studies on the oxalate oxidase (Oxo) catalytic mechanism. T. Borowski, A. Bassan, N. G. J. Richards, P. Siegbahn

242. Energetics and barriers of pericyclic reactions involving alkene analogues R2BPR'2 and R2AlNR'2. T. M. Gilbert, J. M. Bailey

243. Large-scale molecular orbitals based on fragment molecular orbital method solved by projection method. Y. Inadomi, H. Umeda, T. Watanabe, T. Sakurai, U. Nagashima

244. ONIOM computations of the water dimer structure and thermodynamics. S. Arnstein, J. D. Evanseck

245. Parallel Fock matrix construction on layered multi-processor system. H. Umeda, Y. Inadomi, H. Honda, U. Nagashima

246. Modeling MAO (methylaluminoxane) formation. L. Negureanu, R. W. Hall, L. G. Butler

WEDNESDAY MORNING

 Section A

Convention Center -- Room 8

John Pople Memorial Symposium

Cosponsored with PHYS
H. B. Schlegel and L. Radom, Organizers
R. F. Stewart, Presiding

8:55 — Introductory Remarks.

9:00 —247. Local electron correlation models. M. Head-Gordon

9:30 —248. Correlation energy extrapolation by intrinsic scaling. K. Ruedenberg, L. Bytautas

10:00 —249. Use of quantum Drude oscillators in describing dispersion interactions between weakly bound electrons and polar molecules. K. D. Jordan, F. Wang

10:30 — Intermission.

11:00 —250. John Pople's interpretive work. R. F. W. Bader

11:30 —251. Some interesting features of gas-phase reactions involving metal dications. M. Yß˝ez

12:00 —252. Network topology of protein structures. S. Vishveshwara, K. V. Brinda

 Section B

Convention Center -- Room 7B

Michael Klein 65th Birthday Symposium

Structure and Dynamics of Clusters, Liquids, and Materials


D. J. Tobias and R. J. Doerksen, Organizers

8:10 —253. Diffusion in liquids: Breakdown of Stokes-Einstein relationship. Y. Subramanian, P. K. Ghorai, S. Sastry

8:50 —254. Assembling phenomena of water-containing clusters and the design of ion selective receptors. K. S. Kim

9:30 —255. Car-Parrinello and classical molecular dynamics simulation studies of supercritical carbon dioxide. B. Sundaram, M. Saharay

10:10 — Intermission.

10:25 —256. Characterization of interfacial n-octanol and 3-octanol with molecular dynamic simulations. P. B. Moore, R. L. Napoleon

11:05 —257. Simulation of fluorinated ionic liquids: From ab initio to classical model. C. Simon, P. Turq, M. Salanne

 Section C

Convention Center -- Room 7A

Understanding Protein-Ligand Interactions


K. M. Merz Jr. and C. H. Reynolds, Organizers
B. A. Tounge, Presiding

8:30 —258. Flexible “Induced Fit” docking of ligands to enzyme active sites. S. N. Rao, R. Farid, H. Beard, T. Day, M. Shelley, J. Perry, S. Krystek Jr., A. Nayeem

9:00 —259. Family 6 glycosyl hydrolases: Automated docking and phylogenetic analysis. B. Mertz, R. S. Kuczenski, R. T. Larsen, A. D. Hill, P. J. Reilly

9:30 —260. Protein-protein docking methods used to study complex protein interactions. D. Haley-Vicente, T. Glennon

10:00 — Intermission.

10:10 —261. Structure-based design of focused drug-like combinatorial libraries. L. L. Frye, R. B. Murphy, T. M. Reboul, P. S. Shenkin, D. T. Mainz, E. W. Chambers, D. Q. McDonald, R. A. Friesner

10:40 —262. Testing compounds for selectivity: Docking helps to find relevant proteins. S. Yoon, A. Smellie, D. S. Hartsough, A. Filikov

11:10 —263. Using physics-based energy functions to estimate the binding free energy of docked complexes. D. Singh, N -J. Deng, C. M. Venkatachalam, M. Lim-Wilby

 Section D

Convention Center -- Room 2

Applications of Information Theory in Chemistry

Cosponsored with CINF
V. Shanmugasundaram, Organizer

8:50 — Introductory Remarks.

9:00 —264. A natural amino acid classification scheme derived from multiple sequence alignments. E. B. Fauman

9:30 —265. Algorithmic complexity of protein structure alignment. G. Dewey, Y. Jia

10:00 —266. Information theory and macromolecular structure. I. D. Kuntz, T. Aynechi

10:30 —267. Shannon entropy as a local surface property. T. Clark

11:00 —268. Group Entropy analysis and hybrid Quantum Mechanical/Molecular Mechanical simulations for elucidation of enzyme function. T. Wymore, H. B. Nicholas, J. Hempel, D. W. Deerfield II

 

ADME/tox Informatics

Applications

Cosponsored with CINF, MEDI, and TOXI

WEDNESDAY AFTERNOON

 Section A

Convention Center -- Room 8

John Pople Memorial Symposium

Cosponsored with PHYS
H. B. Schlegel and L. Radom, Organizers
D. DeFrees, Presiding

1:55 — Introductory Remarks.

2:00 —269. Real-space post-Hartree-Fock correlation models. A. D. Becke

2:30 —270. Addition via subtraction in coupled cluster theory? A reconsideration of the CC and CI interface. R. J. Bartlett, M. Musial

3:00 —271. A generally applicable relativistic methodology based on the regular approximation to the exact relativistic Hamiltonian: Theory and applications utilizing both DFT, many body perturbation and coupled cluster theory. D. Cremer, M. Filatov

3:30 — Intermission.

4:00 —272. Theoretical studies of second row molecules. T. H. Dunning Jr., A. K. Wilson, D. E. Woon

4:30 —273. New assessments of quantum chemical methods using G2 test sets. L. A. Curtiss, K. Raghavachari, P. C. Redfern

5:00 —274. BMK, a novel density functional for thermochemical kinetics. A. D. Boese, J. M. L. Martin

 Section B

Convention Center -- Room 7B

Michael Klein 65th Birthday Symposium

Solids: Bulk and Surface Phenomena


D. J. Tobias and R. J. Doerksen, Organizers

1:40 —275. Electron tunneling through molecular media. Q. Sun, J. Liang, A. Selloni, G. Scoles

2:20 —276. Mechanism underlying the product distribution of 1,3-butadiene absorbed on the Si(100)2x1 surface probed by ab initio molecular dynamics. M. E. Tuckerman

3:00 —277. Multimillion atom simulations of dynamics of oxidation of an aluminum nanoparticle and hypervelocity impact damage in aluminum nitride ceramic. P. Vashishta, R. K. Kalia, A. Nakano

3:40 — Intermission.

3:55 —278. Chemical bonding and properties of high pressure solids. J. S. Tse

4:35 —279. Close-packing and H-bonding in ice and water under extreme conditions. A. M. Saitta

 Section C

Convention Center -- Room 7A

Understanding Protein-Ligand Interactions


K. M. Merz Jr. and C. H. Reynolds, Organizers
F. U. Axe, Presiding

1:30 —280. Modeling allosteric inhibition of LFA-1/ICAM-1 interaction using normal mode analysis. K. Nam

2:00 —281. PRECISE: A database of predicted and consensus interaction sites in enzymes. K. Clodfelter, D. Lancia, M. R. Landon, S. Vajda

2:30 —282. Structural and electronic properties of the oxygen evolving complex in photosystem II: QM/MM study of the complete ligation by protein, water and chloride. E. M. Sproviero, J. A. Gascon, J. P. McEvoy, G. W. Brudvig, V. S. Batista

3:00 — Intermission.

3:10 —283. Interactions of alcohol, anesthetic and aromatic ligands with LUSH, an odorant binding protein using molecular dynamics simulations. S. Vemparala, M. L. Klein

3:40 —284. Mechanism of substrate binding to HIV-1 protease. G. Toth, A. Borics, S. Meshkat

4:10 —285. Computational investigation of specificities of glycoside hydrolase family 1 members. A. D. Hill, P. J. Reilly

4:40 —286. Mechanisms of ammonia activation and ammonium ion inhibition of quinoprotein methanol dehydrogenase: A computational approach. S. Y. Reddy, T. C. Bruice

 Section D

Convention Center -- Room 2

General Oral - Quantum Chemistry


W. D. Cornell, Organizer

1:20 —287. Ab initio Studies of methyl and t-butyl group internal rotation in aromatic molecular crystals. X. Wang, F. B. Mallory, M. M. Francl, P. A. Beckmann

1:40 —288. Importance of post-CCSD(T) correlation effects for molecular properties. A. D. Boese, M. Kßllay, J. Gauss, J. M. L. Martin

2:00 —289. New picture of electron transfer. M. Lundberg, P. Siegbahn

2:20 —290. Scaling the acidic properties of aluminosilicate and aluminophosphate molecular sieves: A PDFT study. M. Elanany, D. P. Vercauteren

2:40 —291. Theoretical confirmation of the experimental Raman spectra of the lower-order diamondoid molecule: Cyclohexamantane (C26H30). S. L. Richardson, T. Baruah, M. J. Mehl, M. R. Pederson

3:00 —292. Theoretical studies on the ethylene forming enzyme 1-aminocyclopropane-1-carboxylic acid oxidase. A. Bassan, T. Borowski, V. Pelmenschikov, C. Schofield, P. Siegbahn

3:20 —293. First principles and tight-binding quantum chemical molecular dynamics approach to vibrationally excited states dynamics of water. E. Broclawik, K. Chiba, Y. Sasaki, A. R. Shaikh, Q. Pei, H. Tsuboi, M. Koyama, M. Kubo, K. Akutsu, M. Hirota, M. Kitada, H. Hirata, A. Miyamoto

3:40 —294. NMR chemical shifts in a DFT QM/MM scheme. D. Sebastiani

4:00 —295. DFT study of the effects of solvent environment on photophysical properties and electronic structure of paracyclophane chromophores. A. Masunov, S. Tretiak, J. W. Hong, G. C. Bazan

4:20 —296. Expanding the scope of DFT calculations: Techniques for calculating the A and C terms of magnetic circular dichroism and the excitation energies of molecules with degenerate ground states. M. Seth, J. Autschbach, T. Ziegler

4:40 —297. GridChem: A computational chemistry grid. S. Pamidighantam

 

Applications of Information Theory in Chemistry

Cosponsored with CINF

THURSDAY MORNING

 Section A

Convention Center -- Room 8

John Pople Memorial Symposium

Cosponsored with PHYS
L. Radom, Organizer
H. B. Schlegel, Organizer, Presiding

9:00 —298. Molecular rearrangements via continuous diradical transition states. K. N. Houk

9:30 —299. Odd-electron bonds and electron transfer in model systems. T. Clark

10:00 —300. Analytical second derivatives, parameterization, and improvement of the DFTB (Density Functional Tight Binding) method. H. A. Witek, G. Zheng, D. G. Musaev, S. Irle, D. Qui˝onero, M. Elstner, K. Morokuma

10:30 —301. Paradigm shifting energy evaluations. P. V. R. Schleyer

11:00 — Concluding Remarks.

 Section B

Convention Center -- Room 7B

Michael Klein 65th Birthday Symposium

Structure and Dynamics of Clusters, Liquids, and Materials


D. J. Tobias and R. J. Doerksen, Organizers

8:10 —302. Influence of temperature and DFT models in ab initio MD simulation of liquid water. J. VandeVondele, F. Mohamed, M. Krack, J. Hutter, M. Sprik, M. Parrinello

8:50 —303. Liquid/vapor interfaces of hydrogen bonding fluids via ab initio molecular dynamics. C. J. Mundy, I. Siepmann, W. I -F. Kuo, M. J. McGrath

9:30 —304. Tractable time correlation function theories of nonlinear spectroscopy. B. Space, R. DeVane, A. Perry, C. Ridley, C. Neipert

10:10 — Intermission.

10:25 —305. Topologies of protonated water clusters: A combined study by vibrational predissociation spectra and Monte Carlo simulations. J -L. Kuo, H -C. Chang, M. L. Klein

11:05 —306. Car-Parrinello molecular dynamics studies of aqueous HCl and HF mixture. K. Laasonen, J. Larrucea

 Section C

Convention Center -- Room 7A

General Oral - Drug Discovery


W. D. Cornell, Organizer
S. F. Yan, Presiding

8:10 —307. Protein ensemble docking: Progress toward an accurate virtual screening protocol. D. L. Cheney, L. Mueller

8:30 —308. Automating inhibitor discovery with multiple protein structures (MPS). H. A. Carlson, M. G. Lerner, K. L. Meagher, K. L. Damm

8:50 —309. Improving the quality of virtual ligand screening against homology models. K. Bernacki, C. Kalyanaraman, I. Chorny, M. P. Jacobson

9:10 —310. Mining docking space. C. Lemmen, M. Gastreich, H. Clau▀en

9:30 —311. Integrating protein sequence and structural information: An in silico method for predicting kinase selectivity. H. Chen, E. B. Fauman

9:50 —312. Uncovering networks within protein structures. B. Albrecht

10:10 —313. Exploration of structure-derived protein sequence alignments. N. Meurice, D. P. Vercauteren, G. M. Maggiora

10:30 —314. De novo design of novel and selective T-type calcium channel blockers. D. L. Cheney, J. J. Hangeland, T. J. Friends, P. C. Levesque

10:50 —315. The application of workflow technology to the creative, computationally intensive and technically challenging area of library design. A. George, J. Sheldon

11:10 —316. Automatic discovery and annotation of organic chemical names in patents. J. W. Cooper, S. Boyer, A. Nevidomsky, A. R. Coden

11:30 —317. Computational design of mutation-resistant HIV-1 protease inhibitor libraries. S. Chellappan, M. K. Gilson

11:50 —318. Modeling of GSK-3’s allosteric pocket and validation by fragment-based grand canonical Monte Carlo simulations and docking. S -B. Rong, F. Guarnieri, J. S. Wiseman, F. P. Hollinger

12:10 —319. Predicted CCR1 structure and binding modes of CCR1 antagonists. S. K. Schlyer, M. Kochanny, G. Phillips, S. Koovakkat, R. Trabanino, R. Horuk, W. B. Floriano, S. E. Hall, N. Vaidehi, W. A. Goddard III

 Section D

Convention Center -- Room 2

General Oral - Quantum Chemistry


W. D. Cornell, Organizer

8:20 —320. BMK: A novel general purpose DFT exchange-correlation functional especially suitable for kinetics and reaction mechanisms. A. D. Boese, J. M. L. Martin

8:40 —321. Duocarmycins binding to DNA explored by molecular simulation. K. Spiegel, U. Rothlisberger, P. Carloni

9:00 —322. A new approximate quantum mechanical method to study biopolymers. X. Chen, Y. Zhang, J. Z. H. Zhang

9:20 —323. Group III atomic wires on Si(100)-(2x1) reconstructed surfaces. D. D. Zorn, M. S. Gordon

9:40 —324. A joint theoretical and experimental study of phenylene-acetylene molecular wires. R. J. Magyar, S. Tretiak

10:00 —325. Ab initio calculations of new polynuclear aromatic subphthalocyanine macrocycles. C. M. McCallum, R. Nohr

10:20 —326. Ab initio studies of aromatic side-chains in solution and in proteins. J. D. Hirst

10:40 —327. Accurately solving the electronic Schr÷dinger equation of small atoms and molecules using the explicitly correlated (r12-) multi-reference averaged coupled-pair functional (MR-ACPF). R. J. Gdanitz

11:00 —328. Calculation of the electronic spectra of molecules in solution and on surfaces. N. A. Besley, J. D. Hirst

11:20 —329. Effect of basis set superposition error on the convergence of intermolecular interaction energies for hydrogen-bonded complexes. M. Masamura

11:40 —330. High precision evaluation of the thermochemistry of some radicals challenged by structural flexibility, strong anharmonic effects, and spin-vibronic coupling. A. V. Marenich, J. E. Boggs

THURSDAY AFTERNOON

 Section A

Convention Center -- Room 8

Michael Klein 65th Birthday Symposium

Biomolecular Interactions: Experiments and Modeling


D. J. Tobias and R. J. Doerksen, Organizers

1:40 —331. Structural aspects of the enzyme attack of phospholipid bilayers. R. K. Thomas, H. P. Vacklin, C. Domene

2:20 —332. Development and applications of an arylamide force field for molecular simulations. V. Pophristic, S. Vemparala, I. Ivanov, M. L. Klein, W. F. DeGrado

3:00 —333. Binding of organoruthenium anticancer drugs to DNA. U. Rothlisberger, C. Gossens, I. Tavernelli

3:40 — Intermission.

3:55 —334. Hydration water dynamics of biological systems and connections to anomalous dynamics of supercooled liquids and glasses. D. Russo, R. K. Murarka, G. L. B. Hura, J. D. Batchelor, T. Head-Gordon

4:35 —335. Correlation between the dynamics of amino acid residues and water molecules in aqueous protein solutions. S. Bandyopadhyay

 Section B

Convention Center -- Room 7B

General Oral - Drug Discovery


W. D. Cornell, Organizer
S. Toba, Presiding

1:00 —336. Crystal structure prediction of diastereomeric salts: A step toward rationalization of racemate resolution. F. J. J. Leusen, C. Liang

1:20 —337. Consensus feature selection for multi-objective SVM modeling of protein ion-exchange displacement chromatography. D. Zhuang, C. M. Breneman, K. P. Bennett, S. M. Cramer

1:40 —338. Developing models for activity using conformation mining. S. Putta, G. A. Landrum, J. E. Penzotti

2:00 —339. Mechanism of action of tirapazamine and its analogs: A computational study. J. Liu, C. M. Hadad, M. S. Platz

2:20 —340. Quantitative analysis of pH effect on the molecular interaction. T. Hanai

2:40 —341. Active learning for compound screening. M. Walker, S. Kasif

3:00 —342. Novel computational quantum chemistry approach in drug screening. R. R. Gupta, I. Stanescu, L. E. K. Achenie

3:20 —343. Structure and binding of glycopeptide antibiotics to bacterial cell wall analogs: Theoretical study. J -G. Lee, C. Sagui, C. Roland

3:40 —344. Virtual exploration of the small molecule chemical universe below 160 daltons. T. Fink, H. Bruggesser, J -L. Reymond

4:00 —345. PEST vs. CoMFA: A comparative study of two 3D-QSAR technologies. C. M. L. Sundling, C. M. Breneman

4:20 —346. The use of exclusion volume in feature based alignment pharmacophore models: Catalyst HipHopRefine. A. J. Maynard, S. Toba, J. Sutter, M. Waldman, J. Li, R. Kuchkuda

4:40 —347. Using pharmacophore models to gain insight into structural binding: An application study. S. Toba, J. Srinivasan

 Section C

Convention Center -- Room 7A

General Oral - Quantum Chemistry


W. D. Cornell, Organizer

1:20 —348. Prediction of absorbtion and emission UV-VIS band shapes using semiempirical methods. J. M. McKelvey, S. Tretiak

1:40 —349. Quantum dynamics of [1,7] hydrogen shift in 1,3,5-heptatrienes. J. D. Thoburn, R. T. Smith

2:00 —350. Tight-binding quantum chemical molecular dynamics approach to the formation dynamics of hydrogen by the chemical reactions of vibrationally excited water on Si surfaces. M. Kubo, Y. Sasaki, K. Chiba, P. Qiang, A. Rajjak, H. Tsuboi, M. Koyama, E. Broclawik, K. Akutsu, M. Hirota, M. Kitada, H. Hirata, A. Miyamoto

2:20 —351. Structure and energetics of thiazolo[5,4-d]thiazole and derivatives: Promising materials for organic electronics. A. T. Yeates, D. S. Dudis, A. V. Fratini, T. E. Reynolds, K. A. Loescher

2:40 —352. Stuctures and energetics of small third-row molecules determined with correlation consistent basis sets. S. Yockel, B. Mintz, A. K. Wilson

3:00 —353. Studies of self-directed growth of ordered organic nanostructures on silicon surfaces. G. A. DiLabio, R. A. Wolkow

3:20 —354. Theoretical study of solvent effects on Kolbe-Schmitt reaction using ab initio calculations and computer aided molecular design. I. Stanescu, L. E. K. Achenie

3:40 —355. Transverse polarizability of carbon nanotubes. E. N. Brothers, K. N. Kudin, G. E. Scuseria, C. Bauschlicher

4:00 —356. Understanding metal-support interaction in bi-functional catalytic Pt/H-ZSM-5 zeolite. P. Treesukol, K. Srisuk, J. Limtrakul, T. N. Truong

4:20 —357. Effects of electric fields on water-mediated proton transport. S. A. Hassan, G. Hummer, Y. Sok-Lee





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