COMP Programming
Spring 2003 National Meeting
Washington DC
R. A. Wheeler and W. D. Cornell, Program Chairs
SOCIAL EVENT:
Poster Session/Social Hour, Tue
BUSINESS MEETING: Sat
Sunday Morning
Integrating Diverse Computational Approaches to Complex Problem Solving
Diverse Computational Approaches
Cosponsored with Division of Physical Chemistry, and Women Chemists CommitteeH. F. Schaefer III, Presiding
A. K. Wilson and A. M. Chaka, Organizers
8:00 -- Introductory Remarks.
8:10 --1. Modeling and simulation as a design tool. E. B. Stechel
8:50 --2. Using the common component architecture in chemistry. T. L. Windus, E. R. Jurrus, M. Krishnan, J. Nieplocha, C. L. Janssen, D. E. Bernholdt, L. Curfman McInnes, J. Sarich, S. Benson
9:30 --3. Automatic synthesis of advanced electronic structure programs. M. Nooijen, G. Baumgartner, D. E. Bernholdt, D. Cociorva, R. J. Harrison, S. Hirata, J. Ramanujam, P. Sadayappan, R. M. Pitzer, A. Auer
10:10 -- Intermission.
10:30 --4. Untangling the interactions between Rydberg and valence excited states in the CH2Cl radical. A. I. Krylov, S. V. Levchenko
11:10 --5. Integrated web-based environment for computational science and engineering. T. Cook, T. N. Truong
11:30 --6. Electronic structure of weakly bound covalent complexes: Ab initio calculations of the pi-bonded Al-ethylene complex in its ground and excited states. A. C. Cristian, A. I. Krylov
Section B
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Recent Developments and Applications of Time-Dependent DFT and Related Ab Initio and Semiempirical Methods
Cosponsored with Division of Physical ChemistryJ. McKelvey, Organizer, Presiding
K. Burke, Organizer
8:30 -- Introductory Remarks.
8:35 --7. Recent developments in time-dependent density-functional theory. K. Burke, N. T. Maitra, R. J. Cave, F. Zhang, A. Wasserman
9:20 --8. From wavefunction theory to density-functional theory and back. R. J. Bartlett
10:10 -- Intermission.
10:25 --9. Time-dependent density-functional calculations on the optical spectra of metal-porphyrins and metal-phthalocyanines. E. J. Baerends, A. Rosa, G. Ricciardi, S. J. A. van Gisbergen
11:15 --10. Calculation of accurate exchange-correlation potentials for ground-state, excited-state, and time-dependent DFT. W. Yang, Q. Wu
Section C
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Multiple Length and Time Scales in Molecular Modeling
G. Huber, Organizer
8:30 -- Introductory Remarks.
8:35 --11. Nanomechanics through concurrent multiscale simulation. R. E. Rudd
9:05 --12. Bridging length and time scales in the simulation of biomolecular assemblies. G. A. Voth
9:35 --13. Coarse multiscale computation. D. I. Kopelevich, Y. G. Kevrekidis, A. Z. Panagiotopoulos
10:05 -- Intermission.
10:20 --14. Confined water dynamics at different length scales. K. Leung, A. Luzar, D. Bratko
10:50 --15. Extending the atomistic time scale for the simulation of aerosol formation. A. Violi, H. Xie, M. Cuma
11:20 --16. Hybrid molecular dynamics studies on Cu,Zn superoxide dismutase reveal topologically important residues. S. Khare, F. Ding, N. V. Dokholyan
Section D
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Computational Nanotechnology
Single-Wall Nanotubes and Fullerenes
M. Blanco and W. A. Goddard, Organizers
8:00 --17. Predicting properties of carbon nanotubes: Nanowires with a twist. C. T. White, J. W. Mintmire
8:30 --18. Quantum chemistry studies of carbon nanotubes. G. E. Scuseria
9:00 --19. Nanotubes and nanoribbons in displays, NEMS, and chemical sensors: Recent results from first-principles simulations. A. Maiti
9:30 --20. Energetics of hydrogen chemisorption to cluster models of carbon nanotubes. R. C. Brown
9:50 --21. Mechanism of methane formation for hydrogen storage in single-wall carbon nanotubes. T. N. Truong, F. Mondragn, J. F. Espinal
10:10 --22. Effects of O2 adsorbates on field emission properties in single-wall carbon nanotubes: A density-functional theory study. X. F. Duan, B. Akdim, R. Pachter
10:30 --23. Water-carbon nanotube interactions: Potential energy calibration for molecular dynamics simulations using experiments and quantum system calculations. P. Koumoutsakos, J. Walther, T. Werder, U. Zimmerli, R. Jaffe
11:00 --24. Electron affinities and Jahn-Teller distortions in C60 anions. D. S. Dudis, A. T. Yeates, J. Blaudeau
11:20 --25. Nanobionics and the constructor for nanobionics systems. D. V. Leshchev, S. V. Kozyrev
Section E
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Teaching Medicinal Chemistry and Drug Discovery to Undergraduate Chemistry Majors
J. P. Bowen, Organizer
8:30 --26. Symposium overview: Why teach medicinal chemistry to undergraduate chemistry majors? J. P. Bowen
8:45 --27. Undergraduate medicinal chemistry education at Vanderbilt University. T. P. Lybrand
9:15 --28. A tale of two courses: Medicinal chemistry at two Piedmont colleges. E. E. Gooch, A. G. Glenn
9:45 --29. Molecular Conceptor: The first multimedia drug design courseware. N. C. Cohen, P. Gund, E. Cohen, J. van Gelder, D. Shiftan, R. Sertchook, F. Fischel, O. Fischel, A. Halamish
10:15 --30. SMC Pharmaceuticals: A course company. J. P. Bays
10:45 --31. Genesis and teaching of The Organic Chemistry of Drug Design and Drug Action. R. B. Silverman
Iterative Methods in Quantum Mechanics and Applications to Chemical Problems
Dynamics
Cosponsored with Division of Physical Chemistry
New Electronic Structure Methods: From Molecules to Materials
Large-Scale Methods and Calculations
Cosponsored with Division of Physical ChemistrySUNDAY AFTERNOON
Section A
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Integrating Diverse Computational Approaches to Complex Problem Solving
Toward Higher Accuracy: Development and Applications
Cosponsored with Division of Physical Chemistry, and Women Chemists CommitteeA. K. Wilson, Organizer, Presiding
A. M. Chaka, Organizer
1:30 --32. Calculations on radicals and molecular magnets. E. R. Davidson
2:10 --33. 19F-15N spin-spin coupling constants across F-H-N hydrogen bonds. J. E. Del Bene
2:50 --34. Computational studies of alkanethiol and alkaneselenol interactions with copper, silver, and gold clusters. J. M. Standard, B. W. Gregory, B. K. Clark
3:30 -- Intermission.
3:50 --35. Nanoscale dielectric functions: Nonlocal potential screening. K. L. C. Hunt
4:30 --36. Recent advances in electronic structure theory. H. F. Schaefer III
5:10 --37. Molecular electronic structure and magnetic properties of Y2Ti(µ-X)2TiY2 (X,Y = H,F,Cl,Br) isomers. C. M. Aikens, M. S. Gordon
Section B
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Recent Developments and Applications of Time-Dependent DFT and Related Ab Initio and Semiempirical Methods
Excited-State Geometries from TDDFT: Multireference TDDFT
Cosponsored with Division of Physical ChemistryC. D. Sherrill, Presiding
J. M. McKelvey and K. Burke, Organizers
1:30 --38. Photochemistry and excited-state dynamics with time-dependent density-functional theory. T. J. Martinez
2:20 --39. Large-scale excited-state calculations of polycyclic aromatic hydrocarbons: Unraveling the spectroscopic properties relevant to interstellar chemistry. M. Head-Gordon, J. Weisman, T. Lee
3:10 -- Intermission.
3:25 --40. Time-dependent density-functional treatment of excited-state energetics, structure, and vibrational spectra. F. Furche
4:15 --41. Application of the DFT/MRCI method in theoretical electronic spectroscopy. S. Grimme
Section C
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Multiple Length and Time Scales in Molecular Modeling
G. Huber, Organizer
1:30 --42. Multiscale modeling of polymer-silicate nanocomposites. K. L. Anderson, A. Sinsawa, R. A. Vaia, B. L. Farmer
2:00 --43. Multiscale modeling of xerogels and aerogels. L. D. Gelb, N. Z. Rao
2:30 --44. Multiscale simulation of polyisoprene. R. Faller
3:00 -- Intermission.
3:15 --45. Fast boundary element method for the calculation of forces on macromolecules in an ionic solution. A. Bordner, G. Huber
3:45 --46. Accurate and efficient dynamics simulations with hybrid explicit/implicit solvents. J. Lu, R. Luo
Section D
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Computational Nanotechnology
Electrical/Bio Nanodevices and Methods
M. Blanco and W. A. Goddard, Organizers
1:30 --47. Computational simulation at molecular electronic and molecular electromechanical system. W. Deng, X. Xu, R. Muller, M. Blanco, W. A. Goddard
2:00 --48. Electrical conductance and switching of small molecules and atomic wires. N. D. Lang, P. Avouris
2:30 --49. Multiscale modeling of nanostructured complexity in ferroelectric polymers. A. Strachan, A. Cuitino, W. A. Goddard III
3:00 50. Variations in the geometries and electronic properties of isolated single-walled carbon nanotubes. G. Sun, M. Kertesz, J. Kurti, R. H. Baughman
3:20 --51. Multiscale dynamical potentials with charge transfer. S. R. Atlas, S. M. Valone
3:40 --52. TranSIESTA: A spice for molecular electronics. K. Stokbro, J. Taylor, M. Brandbyge, P. Ordejon
4:10 --53. Molecular dynamics simulations of nanoscale polymers end-capped with biologically active ligands. M. Diallo, B. Baird, G. W. Coates, W. A. Goddard III
4:40 --54. Theoretical studies and modeling of peptide amphiphile nanostructures. S. Tsonchev, G. C. Schatz, M. Ratner
5:10 --55. Development of a QM/MM model for peptide-encapsulated CdS nanocrystals. J. D. Madura, J. Worthington, J. D. Evanseck
Section E
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Teaching Medicinal Chemistry and Drug Discovery to Undergraduate Chemistry Majors
J. P. Bowen, Organizer
1:30 --56. A new special topics course in drug discovery for B.S. chemistry majors at the University of Georgia. J. P. Bowen
2:00 --57. A presentation of the medicinal chemistry course at Furman University. M. Lee
2:30 --58. Computational experiments for teaching structure-based drug design. G. D. Purvis III, N. G. J. Richards
3:00 --59. Designing a medicinal chemistry course for instruction by organic faculty. E. P. Stevens
New Electronic Structure Methods: From Molecules to Materials
Density-Functional Theory
Cosponsored with Division of Physical Chemistry
Iterative Methods in Quantum Mechanics and Applications to Chemical Problems
Electronic Structure
Cosponsored with Division of Physical ChemistryMONDAY MORNING
Section A
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Integrating Diverse Computational Approaches to Complex Problem Solving
Kinetics, Dynamics, and Reactivity
Cosponsored with Division of Physical Chemistry, and Women Chemists CommitteeT. N. Truong, Presiding
A. K. Wilson and A. M. Chaka, Organizers
8:00 --60. Coupling detailed kinetics and transport in solid oxide fuel cell design. A. M. Dean, K. M. Walters, H. Zhu, R. J. Kee
8:40 --61. Hybrid quantum-classical molecular dynamics of hydrogen-transfer reactions in enzymes. S. Hammes-Schiffer
9:20 --62. Chemical kinetics of systems with complex reaction paths: Ensemble-averaged variational transition state theory with multidimensional tunneling. D. G. Truhlar, J. Gao, M. Garcia-Viloca, T. Poulsen, C. Alhambra, J. Corchado, M. L. Sanchez
10:00 -- Intermission.
10:20 --63. Diffusion Monte Carlo approaches for investigating dynamics and spectroscopy of weakly bound complexes. A. B. McCoy, B. M. Auer
11:00 --64. Predicting complex chemical processes: Chemistry, numerics, and software. W. H. Green Jr.
11:40 --65. Automated mechanism generation applied to atmospheric chemistry of volatile organic compounds. S. Khan, Q. Zhang, L. J. Broadbelt
Section B
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Recent Developments and Applications of Time-Dependent DFT and Related Ab Initio and Semiempirical Methods
Evaluation of TDDFT for UV-vis: Computation of NMR Coupling Constants
Cosponsored with Division of Physical ChemistryK. Burke, Organizer, Presiding
J. McKelvey, Organizer
8:30 --66. On the relative accuracy of TDDFT. G. Trucks, M. Frisch, K. B. Wiberg
9:20 --67. Electronically excited states of 3-substituted 1-butenes. K. B. Wiberg, Y. Wang, G. Trucks
10:10 -- Intermission.
10:25 --68. Time-dependent density-functional theory as a foundation for a firmer understanding of sum-over-states density-functional perturbation theory. M. E. Casida, E. Fadda, D. R. Salahub
11:15 --69. NBO analysis of 13C NMR chemical shifts of 2-amino, 2-hydroxyl, and monofluoro derivatives of benzoic acid. R. R. Burnette, F. Weinhold
Section C
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Protein Flexibility
Theory
Cosponsored with Division of Physical ChemistryH. A. Carlson, Organizer
8:30 --70. Achieving extremely high affinity in drug design. E. Freire
9:10 --71. Dynamics of water buried in proteins. C. S. Verma, S. Fischer
9:50 -- Intermission.
10:00 --72. Integrating advanced algorithms to enhance docking and drug design. R. Nussinov
10:40 --73. Flexibility and diffusive motions in proteins. M. F. Thorpe, M. Lei, L. A. Kuhn, M. I. Zavodszky
11:20 --74. Balancing large- and small-scale flexibility in protein/ligand docking. L. A. Kuhn, M. I. Zavodszky, M. F. Thorpe, M. Lei
Section D
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Computational Nanotechnology
Nanodevices: Mechanical
M. Blanco and W. A. Goddard, Organizers
8:00 --75. First-principles simulations of semiconductor nanostructures. G. Galli
8:30 --76. Monte Carlo calculation of the capillary force on a nanoscale AFM tip. J. Jang, G. C. Schatz, M. A. Ratner
9:00 --77. Effect of nanocoating on the behavior of nanofriction and nanowear of some sliding systems. L. Zhang, D. Cheong
9:30 --78. Atomic-scale investigations of friction at amorphous carbon interfaces. J. A. Harrison, G. T. Gao, G. M. Chateauneuf, P. T. Mikulski
10:00 --79. Electronic structure of thiolate self-assembled monolayers on Cu(111) and Au(111) substrates. V. Perebeinos, M. D. Newton
10:30 --80. Normal and multibody modes in structured soft matter systems. B. G. Sumpter, D. W. Noid, B. C. Hathorn, W. A. Goddard III
11:00 --81. Molecular dynamics simulation of the solvation of passivated nanoparticles in supercritical media. M. Lal, M. Plummer, N. J. Richmond, W. Smith
11:30 --82. Scanning calorimetry of isolated larger clusters and related assemblies. R. L. Whetten
Section E
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Biological Applications of Implicit Solvent Models
C. F. Wong, Organizer
8:00 --300. A "second generation" of generalized Born models for protein simulations. D. Case
8:45 --83. SMx models: New developments and comparison to other electrostatic formalisms. C. J. Cramer, F. J. Luque, M. Orozco, M. Ruiz-Lopez, J. D. Thompson, D. G. Truhlar, P. D. Winget
9:30 --84. Dielectric relaxation in proteins with explicit, implicit, and mixed solvent models. T. J. Simonson, G. Archontis, D. A. Case, C. L. Brooks III
10:15 --85. Implicit solvent models in biology: Simulation and pH-dependent properties of proteins. E. L. Mehler, S. A. Hassan
11:00 -- Intermission.
11:15 --86. From implicit solvation to QM: Insights into protein structure. J. Hermans, Y. Vorobjev, H. Hu, G. Butterfoss
12:00 --87. Implicit and explicit electrostatic models for structure function correlation of biomolecules. A. Warshel
Iterative Methods in Quantum Mechanics and Applications to Chemical Problems
Dynamics
Cosponsored with Division of Physical Chemistry
Physical Chemistry of Biomolecular Motors
Rotatory Motors
Cosponsored with Division of Physical Chemistry
New Electronic Structure Methods: From Molecules to Materials
Molecular Problems
Cosponsored with Division of Physical ChemistryMONDAY AFTERNOON
Section A
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Integrating Diverse Computational Approaches to Complex Problem Solving
Biological Applications
Cosponsored with Division of Physical Chemistry, and Women Chemists CommitteeR. A. Wheeler, Presiding
A. K. Wilson and A. M. Chaka, Organizers
1:30 --88. Mixed quantum mechanical/molecular mechanical simulation of biological systems. U. Rothlisberger
2:10 --89. Probing the free-energy landscape of protein folding and peptide aggregation. J. Shea, W. Guo, S. Lampoudi
2:50 --90. Simulations of electron and energy transfer: From macromolecules to arrays. D. Evans
3:30 -- Intermission.
3:50 --91. Topology and energetics in protein folding. C. Clementi
4:30 --92. High-throughput data analysis with SARNavigator. D. C. Young, S. Reiling, S. Burkett, F. Soltanshahi
Section B
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Recent Developments and Applications of Time-Dependent DFT and Related Ab Initio and Semiempirical Methods
TDDFT Spectra of Inorganic Complexes
Cosponsored with Division of Physical ChemistryJ. M. McKelvey, Organizer, Presiding
K. Burke, Organizer
1:30 --93. How to distinguish between enantiomers with density-functional theory: Methodology for optical rotation and circular dichroism, implementation, and benchmark results for organic molecules and transition-metal complexes. J. Autschbach, F. E. Jorge, T. Ziegler
2:20 --94. Application of TD-DFT to CD spectra of transition-metal complexes: Interpretation of the results and assessment of the method. J. Autschbach, F. E. Jorge, T. Ziegler
3:10 -- Intermission.
3:25 --95. Natural transition orbitals. R. L. Martin
4:15 --96. TDDFT studies of the nature of the excited states in d6 transition-metal complexes. P. J. Hay, R. L. Martin, N. L. Gebhart
Section C
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Protein Flexibility
Coupling Motion and Catalysis
Cosponsored with Division of Physical ChemistryH. A. Carlson, Organizer
1:00 --97. Reaction coordinate motion and the ionic state of transition-state analogs in n-ribosyltransferases. V. L. Schramm, A. A. Sauve, S. M. Cahill, H. Deng, C. Grubmeyer, R. Callender
1:40 --98. Contribution of protein conformational energy to enzyme catalysis. J. Gao
2:20 --99. Enzymes in action in the NMR tube: Protein dynamics during catalysis. D. Kern, E. Z. Eisenmesser, D. A. Bosco
3:00 -- Intermission.
3:10 --100. Mapping enzyme dynamics by ultrahigh-resolution crystallography. D. Ringe
3:50 --101. Dynamics coupled to protein catalysis? Factors affecting hydride transfer rates in DHFR. C. L. Brooks III, I. F. Thorpe, T. H. Rod, J. L. Radkiewicz
4:30 --102. Effects of structural fluctuation on acetylcholinesterase catalysis. Y. Zhang, J. Kua, J. A. McCammon
Section D
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Computational Nanotechnology
Nanofabrication
M. Blanco and W. A. Goddard, Organizers
1:00 --103. De novo design of functional nanomaterials and molecular devices. K. S. Kim
1:30 --104. Computational nanomechanics, reactivity, and device applications of carbon nanotubes and fullerenes. D. Srivastava
2:00 --105. Design of a nanomechanical fluid control valve based on functionalized silicon cantilevers: Coupling molecular mechanics and classical engineering design. S. Solares, M. Blanco, W. A. Goddard
2:30 --106. Quantum simulations for computational prototyping of nanofabrication. C. B. Musgrave, J. H. Han, Y. Widjaja, C. Mui, S. F. Bent, J. K. Kang
3:00 --107. The use of fullerenes and endohedrally doped fullerenes as building blocks in nanotechnology. J. A. Larsson, J. C. Greer
3:20 --108. Computational analysis of a switchable rotaxane. L. Frankfort, K. Sohlberg
3:40 --109. The dinitropyridine molecule: A potential molecular switch. P. A. Derosa, S. Guda, J. M. Seminario
4:00 --110. Rigid-body nanomanipulator design criteria for simplified constrained dynamics. A. Jaramillo-Botero
4:20 --111. Elementary and not-so-elementary motions in mechanically interlocked molecules. F. Zerbetto
4:40 --112. Computer-aided design and application of DNA-based nanoinstruments for measuring DNA deformation. A. Hillisch, M. Lorenz, D. Payet, A. A. Travers, F. Stuehmeier, R. M. Clegg, S. Diekmann
5:00 --113. Computational chemistry as the key to developing molecular manufacturing. R. C. Merkle, R. A. Freitas Jr.
Section E
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Biological Applications of Implicit Solvent Models
C. F. Wong, Organizer
1:30 --114. Applications of the PB equation to the analysis and prediction of protein structure and function. B. Honig
2:15 --115. Continuum models of biomolecular activity. J. A. McCammon
3:00 --116. Adding conformational flexibility to continuum electrostatics: Assaying the stability and importance of charges buried in proteins. M. R. Gunner, J. Mao, K. Hauser, J. Kim
3:45 -- Intermission.
4:00 --117. Application of implicit solvent models and density-functional theory to the mechanism of protein tyrosine phosphatase. D. Asthagiri, V. Dillet, R. L. Van Etten, T. Liu, L. Noodleman, D. Bashford
4:45 --118. Use of continuum solvents in protein structure prediction. M. J. Hsieh, E. Wen, R. Luo
New Electronic Structure Methods: From Molecules to Materials
Hybrid Methods and Condensed-Phase Problems
Cosponsored with Division of Physical Chemistry
Iterative Methods in Quantum Mechanics and Applications to Chemical Problems
Mixed
Cosponsored with Division of Physical Chemistry
Physical Chemistry of Biomolecular Motors
Processive Motors
Cosponsored with Division of Physical ChemistryMONDAY EVENING
Section A
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Sci-Mix
R. A. Wheeler, Organizer
8:00 - 10:00
177, 181-183, 186, 188, 190, 192, 196, 199, 202-203, 207-208, 211-212, 215, 219, 223, 225-226, 229, 232, 235, 237-239, 248, 252, 256, 262, 267, 269-271, 276. See subsequent listings.
TUESDAY MORNING
Section A
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Integrating Diverse Computational Approaches to Complex Problem Solving
Biological Applications
Cosponsored with Division of Physical Chemistry, and Women Chemists CommitteeU. Rothlisberger, Presiding
A. K. Wilson and A. M. Chaka, Organizers
8:00 --119. Cool walking: A new Markov chain Monte Carlo sampling method. T. Head-Gordon, S. Brown
8:40 --120. Integrating biology and nanoelectronics: Computational investigations of electron-transfer proteins. F. De Rienzo, R. Di Felice, E. Molinari
9:20 --121. Integrating diverse computational approaches in the design and discovery of crop protection chemicals. D. Kleier
10:00 -- Intermission.
10:20 --122. The importance of computational chemistry in drug design: A CADD approach to nontoxic enediyne anticancer drugs. E. Kraka, D. Cremer
11:00 --123. Identifying a potential conformational gate for ubiquinone-B binding in the bacterial photosynthetic reaction center. S. E. Walden, R. A. Wheeler
11:30 --124. Macromolecular solvation studies using semigrand molecular dynamics. G. C. Lynch, B. M. Pettitt
Section B
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Recent Developments and Applications of Time-Dependent DFT and Related Ab Initio and Semiempirical Methods
Cosponsored with Division of Physical ChemistryK. Burke, Organizer, Presiding
J. McKelvey, Organizer
8:30 --125. A dynamical approach to electron transport in molecular wires. R. Car
9:20 --126. Spectroscopic calculations on transition-metal complexes using TDDFT and ab initio methods: Calibration and application to recent problems in bioinorganic chemistry. F. Neese
10:10 -- Intermission.
10:25 --127. Excited states and nonlinear optical response of conjugated molecules: A TDDFT study. S. Tretiak
11:15 --128. Density-functional excited states through adiabatic connection perturbation theory. M. Levy
Section C
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Protein Flexibility
Inhibitor Discovery Techniques
Cosponsored with Division of Physical ChemistryH. A. Carlson, Organizer
8:30 --348. FlexE: Advancements of docking into flexible sites. H. Clau§en, S. A. Hindle
9:10 --130. Protein flexibility and drug design: How to hit a moving target. H. A. Carlson, K. L. Meagher
9:50 -- Intermission.
10:00 --131. Flexibility of antideath protein Bcl-xL and the significance for designing small-molecule inhibitors. S. Wang, R. Wang, C. Yang, J. Stuckey, Y. Tomita, D. Yang, P. Li, P. P. Roller, H. Sun, K. Ding, G. Wang, G. Tang, J. Chen, M. Zhang, Z. Nikolovska-Coleska, Y. Cao, X. Wu
10:40 --132. Exploring protein flexibility in a model docking site. B. K. Shoichet, B. Wei, A. Ferrari
11:20 --133. Simulating disorder-order transitions in molecular recognition of unstructured proteins: Where folding meets binding. G. M. Verkhivker
Section D
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Computers in Chemistry General Contributions
R. A. Wheeler and W. D. Cornell, Organizers
8:30 --134. Estimation of physiochemical properties of organic compounds by SPARC. S. H. Hilal, L. A. Carreira, S. W. Karickhoff
8:55 --135. Calculation of tautomeric equilibrium network constants using SPARC. S. N. Ayyampalayam, L. A. Carreira
9:20 --136. OptDesign: Extending optimizable K-dissimilarity selection (OptiSim) for use in combinatorial library design. F. Soltanshahi, L. Akella, R. D. Clark
9:45 --137. Predictive toxicology using quantum QSAR descriptors from intermediates. S. Trohalaki, R. Pachter, K. T. Geiss, J. M. Frazier
10:10 --138. 2-D QSAR modeling of NMDA derivatives: A comparative study using GFA and multiple linear regression methods. M. A. Avery, N. Sapre
10:35 --139. 2-D and 3-D QSAR modeling of anti-HIV-1 TIBO derivatives: A comparative study using ANN and multiple linear regression methods. M. A. Avery, N. Sapre
11:00 --140. Web services as applicationsâ integration tool: QikProp case study. W. L. Jorgensen, A. Laoui, V. R. Polyakov
11:25 --141. Data sharing in bioinformatics: Using the MDB's web services. J. M. Castagnetto, S. W. Hennessy, E. D. Getzoff, J. A. Tainer, M. E. Pique
Section E
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Computers in Chemistry General Contributions
Biochemistry
R. A. Wheeler and W. D. Cornell, Organizers
8:30 --142. Ligand binding and conformational changes in DNA gyrase B. R. H. Stote, M. Schechner, A. P. Dejaegere
8:55 --143. Flexibility, energetics, and function in the DNA binding protein Mbp1. A. N. Lane, J. O. Trent
9:20 --144. Atomistic simulation of hybridization and melting of DNA oligomers. M. F. Hagan, A. R. Dinner, D. Chandler, A. K. Chakraborty
9:45 --145. Effect of relative side-chain orientations on the ability of statistical potentials to identify nativelike structures of proteins. N. Buchete, J. E. Straub, D. Thirumalai
10:10 --146. Biorelational mechanics. C. Peng
10:35 --147. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. Y. Duan, S. Chowdhury, C. Wu, G. Xiong, W. Zhang, R. Yang, M. Lee, P. Cieplak, R. Luo, T. Lee, J. Caldwell, J. Wang, P. A. Kollman
11:00 --148. Novel quantum-chemically polarizable force field. N. Anikin, V. Bobrikov, V. Bugaenko, A. Andreyev, V. M. Anisimov
11:25 --149. Evaluation of solvated model chemistries for conformations of amino acid zwitterions. P. Norrby, T. Liljefors, P. Aadal Nielsen
Iterative Methods in Quantum Mechanics and Applications to Chemical Problems
Mixed
Cosponsored with Division of Physical Chemistry
New Electronic Structure Methods: From Molecules to Materials
Many-Body Theory
Cosponsored with Division of Physical Chemistry
Physical Chemistry of Biomolecular Motors
Rotatory Motors
Cosponsored with Division of Physical ChemistryTUESDAY AFTERNOON
Section A
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ACS Award for Computers in Chemical and Pharmaceutical Research
Cosponsored with Accelrys IncW. L. Jorgensen, Organizer
1:00 --150. Theoretical study of secondary structures of peptides. Y. Wu, Y. Zhao
1:40 --151. Theoretical characterization of flexible biomolecules. K. D. Jordan, R. A. Christie, E. Vayner, A. A. DeFusco III
2:20 --152. Computer-aided design and screening of combinatorial drug libraries. W. L. Jorgensen
3:00 --153. The role of conical intersections in the photochemistry of alkenes. S. L. Wilsey
3:40 --154. Remarkable insights from magnetic property computations. P. V. R. Schleyer
4:20 --155. Award Address (ACS Award for Computers in Chemical and Pharmaceutical Research, sponsored by Accelrys, Inc). Discovery through computation. K. N. Houk
Section B
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Computers in Chemistry General Contributions
Materials
R. A. Wheeler and W. D. Cornell, Organizers
1:30 --156. Monte Carlo simulations of the effect of chain flexibility and cross-link functionality on polymer network properties. D. M. Bhawe, F. A. Escobedo, C. Cohen
1:50 --157. A bond-breaking and making lattice model for polymerization. R. Hernandez, M. Vogt
2:10 --158. Multiscale modeling of polyimides. T. C. Clancy, J. A. Hinkley
2:30 --159. The computer-aided design of receptors for tetravalent actinides. J. Uddin, B. P. Hay
2:50 --160. Molecular modeling of the adsorption of anionic and molecular species to zincite surfaces. L. J. Criscenti, R. T. Cygan, J. A. Voigt
3:10 --161. Atomistic molecular dynamics simulation of the catalytically active nano- and bulk a-AlF3 phases using the polarizable ion model. S. Chaudhuri, P. Madden, M. Wilson, C. P. Grey
3:30 --162. Molecular simulations of anhydrous Na6[Al6Si6O24] sodalite. E. C. Moloy, R. T. Cygan, F. Bonhomme, D. M. Teter, A. Navrotsky
3:50 --163. Search for minimum molecular programmable units. J. M. Seminario, L. E. Cordova, P. A. Derosa
4:10 --164. Computational simulation at molecular electronic and molecular electromechanical system. W. Deng, X. Xu, R. P. Muller, M. Blanco, W. A. Goddard
Section C
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Computers in Chemistry General Contributions
Biochemistry
R. A. Wheeler and W. D. Cornell, Organizers
1:30 --165. Calculation of the dielectric permittivity profile for a nonuniform system: Application to a lipid bilayer simulation. H. A. Stern, S. E. Feller
1:55 --166. Mesoscale modeling of drug delivery across biological membranes. S. C. McGrother, A. Maiti, A. A. Gusev, G. Goldbeck-Wood
2:20 --167. Surface charge effects on cancer cell metastasis. M. Sulivan, H. Fynewever, C. Shew
2:45 --168. A new function to distinguish between bound and displaceble water molecules in the binding site of protein-ligand complexes. A. T. Garcia-Sosa, R. L. Mancera
3:10 --169. Solution structural model for human extrinsic blood coagulation complex (TF.VIIa.X): Protein-protein docking and molecular dynamics refinement study. D. Venkateswarlu, R. E. Duke, T. Darden, L. G. Pedersen
3:35 --170. Conformational analysis of the acyl pocket loop in acetylcholinesterase computed by Monte Carlo methods with a generalized Born model of solvation. L. Carlacci, C. Millard, M. Olson
4:00 --171. Quantitative analysis of molecular interactions in liquid chromatography using a computational chemical method. T. Hanai
TUESDAY EVENING
Section A
Unknown Site
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Computers in Chemistry
Poster Session
R. A. Wheeler and W. D. Cornell, Organizers
6:00 - 8:00
172. A DFT study of cysteine adsorption on Au(111). R. Di Felice, F. De Rienzo, A. Selloni, E. Molinari
173. Classification of HIV protease inhibitor toxicity using radial basis function neural networks. S. J. Patankar, P. C. Jurs
Intermission.
174. Conformational energetics of naphthylquinoline derivatives. M. J. Lovell, G. R. Bishop, D. H. Magers
175. Design, synthesis, and biological evaluation of antiangiogenic compounds: Studies of aromatic dienone analogs of curcumin. R. Hubbard IV, T. P. Robinson, T. Ehlers, X. Bai, J. L. Arbiser, D. Goldsmith, J. P. Bowen
176. Design, synthesis, and biological evaluation of antiangiogenic compounds: Studies of aromatic enone analogs of curcumin. T. Ehlers, R. Hubbard IV, T. P. Robinson, X. Bai, J. L. Arbiser, D. Goldsmith, J. P. Bowen
177. Fast binding affinity prediction by incorporating flexible receptor and two-step scoring into molecular docking. S. Yoon, W. J. Welsh
178. Method for the discovery of novel Na, K-ATPase inhibitors for the therapeutic treatment of cardiovascular diseases and conditions. S. M. Keenan, V. Kholodovych, R. K. Delisle, W. J. Ball, W. J. Welsh
179. Molecular modeling and design of subtype selective compounds that target the opioid receptors. Y. Peng, S. Yu, Q. Zhang, W. J. Welsh
180. Preliminary pharmacophore model: Methylphenidate class of dopamine reuptake inhibitor. M. Misra, K. M. Gilbert, R. A. Buono, C. A. Venanzi, M. M. Schweri, Q. Shi, H. M. Deutsch
181. Seeking novel leads through structure-based pharmacophore design. L. S. Fisher, O. F. Gner
182. Comparison of new computational filters for virtual screening of drug candidates for human oral absorption. R. Fraczkiewicz, B. Steere, M. B. Bolger
183. Virtual screening for inhibitors of matrix metalloproteinases combining geometry scoring and quantitative consensus scoring model. X. Hu, W. H. Shelver, F. Pan
184. Protein kinases as targets for virtual ligand screening. C. N. Cavasotto, M. Totrov, R. A. Abagyan
185. Withdrawn.
186. Pattern recognition tools for protein sequence analysis. T. P. Lybrand, Z. Li
187. Ligand recognition in folylpolyglutamate synthetase. M. N. Jagadeesh, H. A. Carlson
188. Comparative modeling of C1 regulatory domains in the protein kinase C isozyme family. M. L. Peach, M. C. Nicklaus, P. M. Blumberg, V. E. Marquez
189. Homology models of the catalytic sites of phosphodiesterase types 5A and 10A and molecular docking of selective apoptotic antineoplastic drugs. A. Wierzbicki, E. A. Salter, G. Sperl, W. J. Thompson
190. Using homology models for ligand docking and scoring: Accounting for protein flexibility. M. K. Gilson, V. Kairys
191. Sequence and ligand similarity relationships: A case study of the nuclear receptors. M. Sud, A. Schafferhans, S. I. OâDonoghue
192. Hydration free energies of hydrophobic and hydrophilic protein cavities. L. R. Olano, S. Rick
193. Free Gibbs energy estimation of cyclobutane pyrimidine dimer in the flipped-in and flipped-out conformation. O. Wiest, P. Tran
194. Mechanistic investigations of the (6-4) photoproduct repair. O. Wiest, C. Harrison
195. Molecular dynamics simulation of a DNA polymerase ternary complex containing a carcinogen-modified DNA template. S. Yan, M. Wu, N. E. Geacintov, S. Broyde
196. Structural studies of an environmental carcinogen within a Y family bypass DNA polymerase. M. Wu, S. Yan, N. E. Geacintov, S. Broyde
197. MD studies of p53-mdm2 and peptidomimetic drug design. H. Zhong, H. A. Carlson
198. Theoretical analysis of interactions in the glutamate receptor binding core. K. G. Speranskiy, M. Kurnikova
199. Use of computational modeling to determine a second stable apo structure of the CopZ copper chaperone. A. R. Hower, J. D. Evanseck, C. T. Dameron
200. MD simulation of resistent effect of HIV-1 RT mutation to NNRTI. Z. Zhou, J. D. Madura, M. Madrid
201. Effects of the K103N mutation on the binding of Sustiva analogs to HIV-1 reverse transcriptase based on Monte Carlo simulations. M. Udier-Blagovic, J. Tirado-Rives, W. L. Jorgensen
202. Comparative molecular dynamics studies on HIV-1 integrase wild type and T66I/M154I: New insights into L-731,988 binding modes and double mutant drug resistance. A. Brigo, K. W. Lee, F. Fogolari, G. I. Mustata, J. M. Briggs
203. Prediction of new HIV-1 integrase lead inhibitors using dynamic pharmacophore models based on MD snapshots. J. Deng, K. W. Lee, J. M. Briggs
204. Pharmacophore development and docking studies for a bacterial alanine racemase. A. J. Barron, G. I. Mustata, J. M. Briggs
205. Molecular dynamics simulation of alanine racemase: A 5ns MD simulation. J. O. Ebalunode, J. M. Briggs
206. Solvation influences the collapse of the flaps in HIV-1 protease: A molecular dynamics investigation. K. L. Meagher, H. A. Carlson
207. Structural prediction and modeling of peptide loops with geometric constraints. S. A. Adcock, J. A. McCammon
208. A unified kinetic and thermodynamic simulation study of the complex folding landscape for an all-atom model peptide in solution. G. Cui, A. E. Roitberg, C. Simmerling
209. Advances in structure prediction techniques. B. A. Strockbine, C. L. Simmerling, A. E. Roitberg
210. Computational approach to detect amyloid fibril-forming sequences. S. Yoon, W. J. Welsh
211. New methods for conformational search and calculation of molecular binding free energies. C. Chang, M. K. Gilson
212. Characterization of crown ether and metal ion interactions by the use of computational chemistry and NMR spectroscopy. L. Xiao, R. R. Burnette
213. A density-functional exploration of copper(II) aqua ion and chiral bis(oxazoline) copper(II) Diels-Alder transition structures. J. DeChancie, O. Acevedo, J. D. Evanseck
214. Quantum chemical studies of the anomeric effect in oxaspirocycles. A. K. Jones, G. S. Tschumper
215. Can aromaticity control the [1,5]-hydrogen shift? A response from DFT computational study. M. Mariappan, I. V. Alabugin
216. Computation of the conventional strain energy in oxaziridine and ethylene oxide. D. H. Magers
217. Conventional ring strain in unsaturated four-membered rings. S. S. Huskey, D. H. Magers
218. Conventional strain energy in the diazetidines and the diphosphetanes. P. L. Honea, A. L. Ringer, D. H. Magers
219. Theoretical characterization of the potential energy surfaces of 2-(3-benzylaminopropanoylamino)benzamide and three derivatives. C. J. Knight, M. C. Milletti
220. Computational characterization of a series of eicosanoids. A. S. A. Gracon, M. C. Milletti
221. Gem dimethyl substituents of cyclopropane and cyclobutane. A. L. Ringer, P. L. Honea, D. H. Magers
222. Reaction of the hydroxyl radical with quinoline: Comparison of DFT calculations to experiment. A. R. Nicolaescu, O. G. Wiest, P. V. Kamat
223. Oxidation of carbon clusters by SO2 and NO2: Theory and experiment. M. G. Arredondo, A. J. Leavitt, R. L. Whetten
224. Ab initio studies of the reaction between peroxynitrite and carbon dioxide. T. P. Hamilton, Z. Chen, W. Hancock, J. S. Beckman
225. Theoretical study of carbon suboxide coordination with transition metals. D. Seghete, P. Pulay
226. Investigation of Ni-catalyzed three-component coupling reactions: A density-functional study. H. P. Hratchian, S. Chowdhury, K. K. D. Amarasinghe, H. B. Schlegel, J. Montgomery
227. Atoms-in-molecules study of the bonding in metallocenes. G. L. Heard, J. D. Meadows, R. Steininger
228. Modified pseudopotentials in quantum mechanical/molecular mechanical calculations for metallocene catalysts. C. J. Cramer, M. E. Varner, C. R. Kinsinger
229. Metallic dicyclopentadienyl superphanes. R. Salcedo, N. Mireles, L. E. Sansores, A. Martinez
230. Binding energies of monovalent and divalent cations with TNT. L. J. Lewis, D. H. Magers
231. Molecular orbital study of tambjamine E and analogs. W. J. Skawinski, T. J. Venanzi, C. A. Venanzi
232. Density-functional theory calculations of biological magnesium complexes. E. A. Mayaan, D. York
233. Competition between £k and non-£k Ag+ binding modes in substituted phenols and indoles: An ab initio molecular orbital study. H. M. Lee, I. N. L. Ma, C. W. Tsang
234. Density-functional studies on the solvation free energy of the proton in methanol. S. Hwang, D. S. Chung
235. Determination of tautomeric preferences and pKa values for oxyluciferin and its constituent heterocycles. E. E. Dahlke, C. J. Cramer
236. Determining pKa values for metallochaperones. J. D. Madura, R. A. El-Rahman, Z. Zhou, C. T. Dameron
237. Computation of titration curves for sodium polyacrylate using a boundary integral/statistical mechanical approach. J. R. Feldkamp
238. Theoretical study of the acidic hydrolysis of adenosine in aqueous solution by density-functional theory. G. Sun, M. C. Nicklaus, V. E. Marquez
239. Carcinogenic activity in estrone and its derivatives: A theoretical study. A. Picazo, R. Salcedo
240. DFT study of the IR and EPR spectra of tyrosinate, tyrosyl radical, and some of their isotopomers. K. Range, I. Ayala, B. A. Barry, D. M. York
241. Artificial intelligence modeling of material properties using SCF-MO/DFT computational parameters. N. C. Mitchell, S. Reddy, J. A. Darsey
242. Utilizing density-functional theory to study nucleophilic substitution reactions: Optimization of an adiabatic connection method and its applications. B. L. Kormos, C. J. Cramer
243. Chemically parameterized fast DFT method. N. Anikin, V. Bugaenko, V. M. Anisimov
244. Density-functional theory calculations with correct long-range potentials. Q. Wu, P. W. Ayers, W. Yang
245. Essential corrections to the NDDO scheme. N. Anikin, V. M. Anisimov
246. Protein decoy screening with AMBER. M. Lee, Y. Duan
247. Polarizable force field calculations based on the principle of chemical potential equalization. T. J. Giese, D. York
248. Linear-scaling implementation of the smooth COSMO method for stable geometry optimization and conformational sampling in solution. J. Khandogin, D. M. York
249. Analytical derivatives for Langevin dipoles solvation model. E. Rosta, A. Warshel
250. Ab initio QM/MM calculations of free energies. M. Strajbl, G. Hong, A. Warshel
251. QM(CDFT)/MM molecular dynamic free-energy studies of enzymatic reactions. G. Hong, M. Strajbl, A. Warshel
252. Principles of chemical reactivity in ionic liquids using quantum and molecular mechanics. O. Acevedo, J. D. Evanseck
253. Quasiharmonic vibrations of water, water clusters, and liquid water from principal component analysis of quantum or QM/MM trajectories. H. Dong, S. E. Boesch, R. A. Wheeler
254. Theoretical study on triple helix of polyglycine as a model for collagen: Origin of hydrogen-bonding stabilization. Y. Zhao, Y. Wu
255. Theoretical study of the microscopic solvation of HCl in ammonia clusters: HCl(NH3)n, n = 1ö4. D. E. Bacelo, S. E. Fioressi
256. Gibbs ensemble Monte Carlo simulations for two benzene models near their triple points. X. S. Zhao, B. Chen, J. I. Siepmann
257. Calculating the heat of formation of hydrocarbons using SPARC. T. S. Whiteside, L. A. Carreira
258. Theoretical estimation of electronic absorption spectra of flavonoids. F. Chau, A. K. T. Yeung, D. K. W. Mok
259. DFT calculation on the tautomeric equilibrium of fluorescein in solution. Y. H. Jang, S. Hwang, D. S. Chung
260. Quantum mechanical/molecular mechanics modeling of the self-catalyzed cyclization reaction in green fluorescent protein. P. N. Day, S. S. Patnaik, K. A. Nguyen, R. Pachter
261. Ab initio calculations and spectral simulations of PO2 SVL emission spectra. D. K. W. Mok, E. P. F. Lee, J. M. Dyke Sr., F. Chau
262. Conformational aspects of fluorophore protonation in green fluorescent protein: A molecular dynamics study. S. S. Patnaik, P. N. Day, R. Pachter
263. DFT calculations of the electronic states of electroluminescent Ir(III) complexes. D. H. Jung, S. Park, D. Shin
264. Time-dependent DFT studies of electroluminescent polymers with symmetry restriction. J. K. Yu, C. Yu
265. A current density-functional approach to electronic conductance in molecular wire junctions. E. Sim, R. J. Magyar, K. Burke
266. Calibrating and qualifying the results of density-functional theory calculations of electronically labile materials with spectroscopic methods. N. L. Gebhart, P. J. Hay, M. L. Kirk
267. Ab initio and DFT modeling of CdS nanoclusters. J. C. Worthington, J. D. Madura
268. Potential surface of the C20 system. K. A. Beran, L. N. King, M. M. Carrillo, J. I. Chavez
269. C28 energetic profiles. K. A. Beran, M. M. Carrillo, J. I. Chavez, L. N. King
270. Isomers of C20: An energy profile III. K. A. Beran, J. I. Chavez, L. N. King, M. M. Carillo
271. Obtaining kinetic information on crystallization from fully crystallized solids. S. L. Weaver, R. V. Amenta
272. Computer simulation of montmorillonite clay with tetrahedral charge: Interlayer uranyl ion. K. F. Enwright, H. R. StellaLevinsohn, J. A. Greathouse, R. T. Pabalan
273. Monte Carlo simulation of aqueous clay minerals: Effect of tetrahedral charge on interfacial structure. H. R. StellaLevinsohn, K. F. Enwright, J. A. Greathouse, R. T. Pabalan
274. Multiscale simulation of a polyelectrolyte membrane for fuel cells. S. Yamamoto, S. Yamakawa, S. Hyodo
275. Modeling calcium oscillations in astrocytes. S. Hemkin, R. B. Harshaw
276. On the F-C-C-F Karplus relationship. S. Kurtkaya, V. Barone, J. E. Peralta, R. H. Contreras, J. P. Snyder
WEDNESDAY MORNING
Section A
Unknown Site
Unknown Room
Integrating Diverse Computational Approaches to Complex Problem Solving
Materials and Diverse Approaches
Cosponsored with Division of Physical Chemistry, and Women Chemists CommitteeA. E. Mattsson, Presiding
A. K. Wilson and A. M. Chaka, Organizers
8:00 --277. On surfaces and nanostructures: Undercoordination controlling the chemistry. T. S. Rahman
8:40 --278. Global optimization and achieving equilibrium in finite temperature simulations. K. D. Jordan
9:20 --279. Methanol chemistry on platinum surfaces: A first-principles analysis. M. Mavrikakis, J. Greeley
10:00 -- Intermission.
10:20 --280. Computational approaches to modeling interactions of Hg with organic compounds. J. A. Steckel, A. V. Cugini
11:00 --281. Confined water dynamics at different length scales. K. Leung, A. Luzar, D. Bratko
11:40 --282. Quantum chemical estimation of effective local dielectric constants in crystal surroundings. W. Sudholt, K. K. Baldridge, J. A. McCammon
Section B
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Unknown Room
Recent Developments and Applications of Time-Dependent DFT and Related Ab Initio and Semiempirical Methods
Cosponsored with Division of Physical ChemistryS. Tretiak, Presiding
K. Burke and J. McKelvey, Organizers
8:30 --283. Excited-state structure of nucleobases and exciton delocalization in DNA. J. M. Jean
9:20 --284. TDDFT calculations on electronically excited states in mono- and binuclear transition-metal complexes containing N, O, or S donor atoms. K. Krogh-Jespersen
10:10 -- Intermission.
10:25 --285. Current density-functional theory for the optical response of solids. N. T. Maitra, K. Burke
11:15 --286. Using all-singles CI and random phase approximations in studies of light absorption of large conjugated systems for PPP and INDO/S methods. J. M. McKelvey, S. Tretiak, S. Grimme
Section C
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Protein Flexibility
Large Systems
Cosponsored with Division of Physical ChemistryH. A. Carlson, Organizer
8:30 --287. Comparing experimental and computational protein backbone dynamics. E. R. P. Zuiderweg, T. Wang, Y. Pang, S. Cai, A. V. Kurochkin
9:10 --288. What can we learn from comparisons of MD simulations and NMR relaxation? D. Case
9:50 -- Intermission.
10:00 --289. Examining complex processes in macromolecular systems. B. R. Brooks, G. Stan, X. Wu, H. L. Woodcock
10:40 --290. Polymerase b mechanisms of DNA fidelity explored by dynamics simulations. T. Schlick
11:20 --291. Using simulation to garner insight into biomolecular flexibility. T. E. Cheatham III
Section D
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Machine Learning in Computational Chemistry
C. M. Breneman, Organizer
8:30 -- Introductory Remarks.
8:40 --292. Application of neural networks and genetic algorithms to learn about metabolism. J. Gasteiger, L. Terfloth, A. Hofmann, A. von Homeyer
9:20 --293. K-PLS for QSAR: A nonlinear SVM-like approach to PLS. M. J. Embrechts, C. M. Breneman, K. P. Bennett
9:40 --294. Building nonlinear PLS models containing discriminating structural features for toxicity prediction. K. P. Cross, P. Blower, G. Myatt, C. Yang
10:00 -- Intermission.
10:10 --295. Predicting the genotoxicity of thiophene derivatives from molecular structure. P. D. Mosier, P. C. Jurs, L. Custer, S. K. Durham, G. M. Pearl
10:30 --296. An automated method for building neural network models for the prediction of molecular properties. B. Steere, R. Fraczkiewicz, M. B. Bolger
10:50 --297. Genetic algorithms that emulate human pattern recognition through machine learning. B. K. Lavine, C. E. Davidson, C. Breneman, W. T. Katt, W. T. Rayens
11:10 --298. Predicting protein-ligand binding affinities using transferable atom equivalent techniques and machine-learning methods. W. Deng, C. M. Breneman, N. Sukumar, M. D. Ryan, J. Feng, A. Tropsha, M. J. Embrechts
11:30 --299. Data-mining applications of neural computing in product formulation. E. A. Colbourn, S. J. Roskilly, R. C. Rowe
Section E
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Biological Applications of Implicit Solvent Models
C. F. Wong, Organizer
8:00 --301. Development and applications of generalized Born theories: >From protein folding to free-energy perturbations. C. L. Brooks III
8:45 --302. Development and testing of continuum solvation models for biomolecular simulation. R. A. Friesner
9:30 -- Intermission.
9:45 --303. Implicit solvent potentials (scoring functions) for protein-ligand binding and folding with thermodynamic constraints. R. Levy, E. Gallicchio, A. Felts, L. Zhang
10:30 --304. Exploring large-scale conformational changes with a modified generalized Born model. A. V. Onufriev, D. Bashford, D. A. Case
Physical Chemistry of Biomolecular Motors
Processive Motors
Cosponsored with Division of Physical ChemistryWEDNESDAY AFTERNOON
Section A
Unknown Site
Unknown Room
Integrating Diverse Computational Approaches to Complex Problem Solving
Materials and Surfaces
Cosponsored with Division of Physical Chemistry, and Women Chemists CommitteeA. M. Chaka, Organizer, Presiding
A. K. Wilson, Organizer
1:30 --305. Coupling chemistry and physics into mechanical engineering models of materials response. R. L. Hayes, B. Zhou, D. Jiang, M. Fago, S. Serebrinsky, M. Ortiz, E. A. Carter
2:10 --306. From first-principles to industrial reactor models: The catalytic hydrogenation of acetylene. M. Neurock, P. A. Sheth, C. M. Smith
2:50 --307. Quantum chemistry of point defects in silica. K. Raghavachari
3:30 -- Intermission.
3:50 --308. Subsystem functionals in density-functional theory. A. E. Mattsson, R. Armiento
4:30 --309. Mesoscopic computer modeling of laser ablation. B. J. Garrison, Y. G. Yingling, L. V. Zhigilei
Section B
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Unknown Room
Recent Developments and Applications of Time-Dependent DFT and Related Ab Initio and Semiempirical Methods
Cosponsored with Division of Physical ChemistryK. Burke, Organizer, Presiding
J. McKelvey, Organizer
1:30 --310. Observation and interpretation of annulated porphyrins: Effects of distortion and conjugation on spectroscopic properties of meso-tetraphenylmetalloporphyrins. K. A. Nguyen, J. E. Rogers, D. C. Hufnagle, D. G. McLean, S. Vinogradov, W. Su, K. M. Gossett, P. N. Day, R. Pachter, P. A. Fleitz
2:20 --311. Extracting scattering information from the Kohn-Sham susceptibility. A. Wasserman, N. T. Maitra, K. Burke
2:45 --312. Double excitations within TDDFT linear response. F. Zhang, N. T. Maitra, R. J. Cave, K. Burke
3:10 -- Intermission.
3:20 --313. Theoretical predictions of two-photon absorption in substituted stilbenes: A time-dependent density-functional theory study. P. N. Day, K. A. Nguyen, R. Pachter
Section C
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Unknown Room
Protein Flexibility
Theory
Cosponsored with Division of Physical ChemistryH. A. Carlson, Organizer
1:00 --314. The role of flexibility in protein function: Insights from simulations. M. Karplus
1:40 --315. Energy landscapes of protein structural change. P. G. Wolynes
2:20 --316. Understanding and exploiting the "glass transition" in protein dynamics. G. A. Petsko, D. Ringe
3:00 -- Intermission.
3:10 --317. Stochastic path to form ensembles and to quantify flexibility in proteins. E. Noy, B. Gorelik, A. Rayan, A. Goldblum
3:50 --318. Side-chain flexibility upon ligand binding: Database analysis and machine learning prediction. R. Najmanovich, M. Edelman, V. Sobolev
4:30 --319. Protein flexibility and interior water molecules. S. Rick, L. R. Olano
Section D
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Unknown Room
Machine Learning in Computational Chemistry
C. M. Breneman, Organizer
1:30 --320. Structure-based drug design using inductive logic programming. D. P. Enot, R. D. King
1:50 --321. Prediction of protein affinity in cation-exchange chromatography using quantitative structure-retention relationship models. A. Ladiwala, K. R. Rege, C. M. Breneman, S. M. Cramer
2:10 --322. Computational estimation of protein-ligand binding affinity utilizing Delaunay tessellation and perceptron learning algorithm. M. Shen, W. Zheng, J. Feng, A. Tropsha
2:30 -- Intermission.
2:40 --323. Mitigating the sensitivity of pharmacophoric fingerprints. J. K. Lanctot, J. Srinivasan, M. L. Lamb, C. Lemmen, J. E. Eksterowicz, S. Putta
3:00 --324. On the proper selection of scoring metrics. H. Wolters, K. Aumond, N. Southall, J. Miller
3:20 --325. Using multidimensional scaling to improve machine learning performance. J. K. Lanctot, J. M. Blaney
3:40 --326. Automated QSAR system for the development of validated models. A. Golbraikh, S. Oloff, M. Shen, Y. Xiao, A. Tropsha
4:00 -- Intermission.
4:10 --327. Data-mining molecular dynamics trajectory data. T. E. Cheatham III
4:30 --328. Hidden Markov models from DNA sequence and molecular dynamics simulations for finding protein binding sites. K. M. Thayer, D. L. Beveridge
4:50 --329. Integrating relational chemical data with machine learning algorithms. D. R. Henry, L. L. Chen, D. L. Grier, J. L. Durant Jr., B. A. Leland
Section E
Unknown Site
Unknown Room
Biological Applications of Implicit Solvent Models
C. F. Wong, Organizer
1:30 --330. Modeling hydrophobic effects. D. Chandler
2:15 --331. A polarization functional approach to the solvation of complex molecules. D. Borgis
3:00 --332. Electrodiffusion models of ion permeation through channel proteins. R. D. Coalson, M. Kurnikova, A. Nitzan, A. Mamonov
3:45 -- Intermission.
4:00 --333. Biomolecule solvation described by the RISM theory. F. Hirata
4:45 --334. Approximate solvation models: Speed, accuracy, and common sense. A. Nicholls, J. A. Grant
Physical Chemistry of Biomolecular Motors
Supermolecular Assemblies
Cosponsored with Division of Physical Chemistry
New Electronic Structure Methods: From Molecules to Materials
Alternative Approaches
Cosponsored with Division of Physical ChemistryTHURSDAY MORNING
Section A
Unknown Site
Unknown Room
Integrating Diverse Computational Approaches to Complex Problem Solving
Materials, Surfaces, and Fluids
Cosponsored with Division of Physical Chemistry, and Women Chemists CommitteeK. D. Jordan, Presiding
A. K. Wilson and A. M. Chaka, Organizers
8:00 --335. Accelerated molecular dynamics methods. A. F. Voter
8:40 --336. Some microscopic aspects of dye-sensitized solar cells. A. Selloni
9:20 --337. Simple models for the interpretation of I-V curves of 2â-amino-4,4â-di(ethynylphenyl)-5â-nitro-1-benzenethiolate. C. A. Gonzlez, Y. Simon-Manso, Y. Aray, V. Mujica
10:00 -- Intermission.
10:20 --338. Simulation approaches to directed assembly of nanoscale systems. S. C. Glotzer
11:00 --339. Quantum simulations of solids, liquids, and nanostructures. G. Galli
Section B
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High-throughput Computational Processes in Drug Discovery
J. Shen, Organizer
8:30 -- Introductory Remarks.
8:35 --340. Industrialization of vHTS: An architecture for generating, storing, and analyzing docking results. M. J. Polley, R. Durvasula, A. Edwards, W. Homer
9:05 --341. A novel integrated computational experimental approach for GPCR drug discovery. S. Shacham, O. M. Becker, Y. Marantz, S. Noiman, M. G. Kauffman
9:35 --342. Application of pharmaceutical Informatics tools in a high-throughput environment. G. M. Banik, D. Kernan, L. Taylor, E. G. Melanson
10:05 -- Intermission.
10:10 --343. Higher-throughput approaches to property and biological profiling, including the use of 3-D pharmacophore fingerprints and applications to virtual screening and target class-focused library design. J. S. Mason, J. E. Mills, C. Barker, J. Loesel, K. Yeap, M. Snarey
10:40 --344. Data mining, virtual screening, and cheminformatics in integrated drug discovery. C. J. Manly
11:10 --345. Molecular modeling in the high-throughput era. J. Shen
Section C
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Protein Flexibility
Inhibitor Discovery Techniques
Cosponsored with Division of Physical ChemistryH. A. Carlson, Organizer
8:30 --346. Current challenges in drug docking: Hitting a moving target. A. J. Olson
9:10 --347. Ensembles of active site conformations allow structure-based redesign and drug design. A. C. Anderson, R. Lilien, V. Popov, B. R. Donald
9:50 -- Intermission.
10:00 --129. Designing enzyme inhibitors in the 21st century: Potential of targeting conformational ensembles. D. H. Rich, M. G. Bursavich
10:40 --349. Analysis and prediction of ligand-induced conformational changes. R. Abagyan
11:20 --350. The importance of concerted motions in defining enzyme specificity. D. A. Agard, C. Fuhrmann, N. Ota
Section D
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Computers in Chemistry General Contributions
Quantum Chemistry
R. A. Wheeler and W. D. Cornell, Organizers
8:30 --351. Mechanistic aspects of addition reactions to metalloaromatic complexes of iridium: A computational investigation. M. A. Iron, M. E. van der Boom, J. M. L. Martin
8:50 --352. Modeling intermolecular binary interactions using quantum mechanics and AIM theory. S. G. Arturo, D. E. Knox
9:10 --353. Raman responses of cis- and trans-polyenes. A. T. Yeates, D. S. Dudis
9:30 --354. Cisoid defects in all-trans polyenes and polyacetylene. D. S. Dudis, J. J. Ryan, A. T. Yeates
9:50 --355. Accurate energetics for in-plane vs out-of-plane phenol, thiophenol, anisole, and thioanisole. R. J. Doerksen, B. Chen, W. F. DeGrado, M. L. Klein
10:10 --356. Relative pKa's from first-principles molecular dynamics: The case of histidine deprotonation. I. Ivanov, M. L. Klein
10:30 --357. Stuctures and energetics of third-row atom cluster: A comparison of ab initio and density-functional theory. S. Yockel, A. K. Wilson
10:50 --358. Thermochemical and structural properties of atmospheric sulfur species. J. J. Seals III, A. K. Wilson
11:10 --359. Analysis of various computational probes of through-space NMR shielding. N. H. Martin, D. M. Loveless, D. C. Wade
Section E
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Biological Applications of Implicit Solvent Models
C. F. Wong, Organizer
8:00 --360. Electrostatic forces at the liquid-solid interface: Biochips. B. M. Pettitt, A. Vainrub
8:45 --361. Accurate electrostatic calculations for transfer energies and conformational sampling. R. Abagyan, A. Bordner, C. N. Cavasotto, M. Totrov
9:30 --362. Computational modeling of phosphoinositide signaling. D. Murray
10:15 -- Intermission.
10:30 --363. Modeling molecular recognition with implicit solvent models. M. K. Gilson
11:15 --364. Solvation effects on protein binding and design. B. Tidor
New Electronic Structure Methods: From Molecules to Materials
Metals, Materials, and Multiscale Modeling
Cosponsored with Division of Physical Chemistry
Physical Chemistry of Biomolecular Motors
Rotatory Motors
Cosponsored with Division of Physical ChemistryTHURSDAY AFTERNOON
Section A
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Integrating Diverse Computational Approaches to Complex Problem Solving
Fluids and Soft Materials
Cosponsored with Division of Physical Chemistry, and Women Chemists CommitteeS. C. Glotzer, Presiding
A. K. Wilson and A. M. Chaka, Organizers
1:00 --365. New simulation approaches for modeling phase transitions in complex fluids. A. Z. Panagiotopoulos
1:40 --366. Molecular simulations of rheological processes. C. McCabe
2:20 --367. Integrated multiscale modeling of industrial processes. J. D. Moore
3:00 -- Intermission.
3:20 --368. Molecular simulation of nucleation phenomena. J. I. Siepmann, B. Chen, M. L. Klein
4:00 --369. Simulation of emulsion systems using dissipative particle dynamics. F. H. Case
Section B
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High-throughput Computational Processes in Drug Discovery
J. Shen, Organizer
1:00 --370. High-throughput computational screening applied to anticarcinoma agents. J. R. Chretien, M. Pintore, N. Piclin, F. Ros
1:25 --371. Efficient screening of a million-compound database for lead identification. L. L. Frye, J. Klicic, T. F. Hendrickson, T. A. Halgren
1:50 --372. 3DPL map technology: Ultrafast, flexible database docking. T. Hurst
2:15 --373. Characterization of protein binding sites using high-throughput solvent mapping. M. Silberstein, K. Clodfelter, T. Kortvelyesi, S. Vajda
2:40 --374. Nearest single neighbor method: Finding families of conformations within large samples. D. Chema, A. Goldblum
3:05 --375. 3-D and 4-D QSAR classification models for virtual HTS qualification. S. B. Bowlus, T. C. Gahman, V. Vvedenskiy, R. Hanecak
3:30 --376. Optimization of molecular properties through structural mutation and virtual screening. W. P. Katt, C. M. Breneman, N. Sukumar, M. J. Embrechts
3:55 --377. Fully flexible pharmacophore multiplet bitmaps as molecular descriptors: Implementation and applications. P. Fox, E. Abrahamian, R. D. Clark, I. T. Christensen, H. Thżgersen
Section C
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Protein Flexibility
Inhibitor Discovery Techniques III
Cosponsored with Division of Physical ChemistryH. A. Carlson, Organizer
1:00 --378. Computational studies of inhibitor resistance in HIV-1 integrase. J. M. Briggs, M. L. Barreca, A. Brigo
1:40 --379. Docking ligands into flexible proteins. G. D. Purvis III, M. A. Thompson
2:20 -- Intermission.
2:30 --380. Protein flexibility: The ultimate limitation to structure-based drug design? D. Rauh, J. Gnther, M. T. Stubbs, G. Klebe
3:10 --381. Rigidity-optimized conformational kinetics to explore protein conformational space. M. Lei, M. F. Thorpe, L. A. Kuhn, M. I. Zavodszky
Section D
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Biological Applications of Implicit Solvent Models
C. F. Wong, Organizer
1:00 --382. Simulations of the pKa's of phosphate groups in model systems and phosphorylated peptides. M. Wojciechowski, T. Grycuk, J. M. Antosiewicz, B. Lesyng
1:45 --383. Free-energy landscape of a beta-hairpin folding in water: Explicit vs implicit solvent. R. Zhou, B. J. Berne
2:30 --384. Association between a negatively charged ligand and the electronegative binding pocket of its receptor. J. M. Briggs, H. Huang
3:15 -- Intermission.
3:30 --385. Insights into protein-protein binding by binding free-energy calculation and free-energy decomposition using a generalized Born model. H. Gohlke, D. A. Case
4:15 --386. New trends in generalized Born implicit solvent methods. M. S. Lee, M. Feig, F. R. Salsbury Jr., C. L. Brooks III