COMP Programming
229th ACS National Meeting
San Diego, CA
March 13 - 17, 2005
W. D. Cornell, Program Chair
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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)
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SUNDAY MORNING
Section A
Convention Center -- Room 8John Pople Memorial Symposium
Cosponsored with PHYSH. 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 7BMichael 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 7AGeneral 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 8John Pople Memorial Symposium
Cosponsored with PHYSH. 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. Mó
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 7BMichael 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 7AUnderstanding 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 4Safe Exchange of Chemical Information: Can Relevant Chemical Information be Exchanged Without Disclosing Chemical Structures?
Cosponsored with CINFT. 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 8John Pople Memorial Symposium
Cosponsored with PHYSH. 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 7BMichael 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 7AUnderstanding 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 CINFMONDAY AFTERNOON
Section A
Convention Center -- Room 8John Pople Memorial Symposium
Cosponsored with PHYSH. 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 7BMichael 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 7AUnderstanding 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 2General 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 CINFMONDAY EVENING
Section A
Convention Center -- Sails PavilionSci-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 4John Pople Memorial Symposium
Cosponsored with PHYSH. 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 7BACS 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 7AGeneral 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 TOXITUESDAY AFTERNOON
Section A
Convention Center -- Room 4John Pople Memorial Symposium
Cosponsored with PHYSH. 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 7BACS 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 7AGeneral 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. Grubmüller
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 TOXITUESDAY EVENING
Section A
Convention Center -- Sails PavilionPoster 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. Gutiérrez de Terán, J. Åqvist, 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. Österberg, J. Åqvist
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. Åqvist
175. A structure-based approach to Akt/PKB inhibition. D. Jung, M. Forino, M. Pellecchia
176. Docking of phthalate monoesters to PPAR-ã. 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. Åqvist
186. Accurate predictions of protein-protein binding free energies. M. Almlöf, B. Brandsdal, J. Åqvist
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. Åqvist
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. Davé, 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. López
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 8John Pople Memorial Symposium
Cosponsored with PHYSH. 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. Yáñez
12:00 —252. Network topology of protein structures. S. Vishveshwara, K. V. Brinda
Section B
Convention Center -- Room 7BMichael 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 7AUnderstanding 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 2Applications of Information Theory in Chemistry
Cosponsored with CINFV. 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 TOXIWEDNESDAY AFTERNOON
Section A
Convention Center -- Room 8John Pople Memorial Symposium
Cosponsored with PHYSH. 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 7BMichael 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 7AUnderstanding 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 2General 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. Kállay, 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 CINFTHURSDAY MORNING
Section A
Convention Center -- Room 8John Pople Memorial Symposium
Cosponsored with PHYSL. 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. Quiñonero, M. Elstner, K. Morokuma
10:30 —301. Paradigm shifting energy evaluations. P. V. R. Schleyer
11:00 — Concluding Remarks.
Section B
Convention Center -- Room 7BMichael 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 7AGeneral 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. Claußen
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 2General 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 Schrödinger 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 8Michael 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 7BGeneral 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 7AGeneral 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