COMP

DIVISION OF COMPUTERS IN CHEMISTRY Times, days, and paper numbers may not be final.

SOCIAL EVENT: Poster Session: Tue BUSINESS MEETING: Sat

SUNDAY MORNING Section A

Integrating Diverse Computational Approaches to Complex Problem Solving

Diverse Computational Approaches

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

Recent Developments and Applications of Time-Dependent DFT and Related Ab Initio and Semiempirical Methods

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

Multiple Length and Time Scales in Molecular Modeling

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

Computational Nanotechnology

Single-Wall Nanotubes and Fullerenes

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. Mondrag—n, 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

Teaching Medicinal Chemistry and Drug Discovery to Undergraduate Chemistry Majors

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

New Electronic Structure Methods: From Molecules to Materials

Large-Scale Methods and Calculations

SUNDAY AFTERNOON

 Section A

Integrating Diverse Computational Approaches to Complex Problem Solving

Toward Higher Accuracy: Development and Applications

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

Recent Developments and Applications of Time-Dependent DFT and Related Ab Initio and Semiempirical Methods

Excited-State Geometries from TDDFT: Multireference TDDFT

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

Multiple Length and Time Scales in Molecular Modeling

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

Computational Nanotechnology

Electrical/Bio Nanodevices and Methods

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

Teaching Medicinal Chemistry and Drug Discovery to Undergraduate Chemistry Majors

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

Iterative Methods in Quantum Mechanics and Applications to Chemical Problems

Electronic Structure

MONDAY MORNING

 Section A

Integrating Diverse Computational Approaches to Complex Problem Solving

Kinetics, Dynamics, and Reactivity

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

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

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

Protein Flexibility

Theory

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

Computational Nanotechnology

Nanodevices: Mechanical

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

Biological Applications of Implicit Solvent Models

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

Physical Chemistry of Biomolecular Motors

Rotatory Motors

New Electronic Structure Methods: From Molecules to Materials

Molecular Problems

MONDAY AFTERNOON

 Section A

Integrating Diverse Computational Approaches to Complex Problem Solving

Biological Applications

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

Recent Developments and Applications of Time-Dependent DFT and Related Ab Initio and Semiempirical Methods

TDDFT Spectra of Inorganic Complexes

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

Protein Flexibility

Coupling Motion and Catalysis

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

Computational Nanotechnology

Nanofabrication

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

Biological Applications of Implicit Solvent Models

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

Iterative Methods in Quantum Mechanics and Applications to Chemical Problems

Mixed

Physical Chemistry of Biomolecular Motors

Processive Motors

MONDAY EVENING

 Section A

Sci-Mix

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

Integrating Diverse Computational Approaches to Complex Problem Solving

Biological Applications

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

Recent Developments and Applications of Time-Dependent DFT and Related Ab Initio and Semiempirical Methods

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

Protein Flexibility

Inhibitor Discovery Techniques

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

Computers in Chemistry General Contributions

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

Computers in Chemistry General Contributions

Biochemistry

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

New Electronic Structure Methods: From Molecules to Materials

Many-Body Theory

Physical Chemistry of Biomolecular Motors

Rotatory Motors

TUESDAY AFTERNOON

 Section A

ACS Award for Computers in Chemical and Pharmaceutical Research

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

Computers in Chemistry General Contributions

Materials

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

Computers in Chemistry General Contributions

Biochemistry

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

Computers in Chemistry

Poster Session

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. GŸner

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 pK_a values for oxyluciferin and its constituent heterocycles. E. E. Dahlke, C. J. Cramer

236. Determining pK_a 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

Integrating Diverse Computational Approaches to Complex Problem Solving

Materials and Diverse Approaches

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

Recent Developments and Applications of Time-Dependent DFT and Related Ab Initio and Semiempirical Methods

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

Protein Flexibility

Large Systems

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

Machine Learning in Computational Chemistry

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

Biological Applications of Implicit Solvent Models

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

WEDNESDAY AFTERNOON

 Section A

Integrating Diverse Computational Approaches to Complex Problem Solving

Materials and Surfaces

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

Recent Developments and Applications of Time-Dependent DFT and Related Ab Initio and Semiempirical Methods

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

Protein Flexibility

Theory

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

Machine Learning in Computational Chemistry

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

Biological Applications of Implicit Solvent Models

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

New Electronic Structure Methods: From Molecules to Materials

Alternative Approaches

THURSDAY MORNING

 Section A

Integrating Diverse Computational Approaches to Complex Problem Solving

Materials, Surfaces, and Fluids

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. Gonzˆlez, 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

High-throughput Computational Processes in Drug Discovery

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

Protein Flexibility

Inhibitor Discovery Techniques

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

Computers in Chemistry General Contributions

Quantum Chemistry

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 pK_a'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

Biological Applications of Implicit Solvent Models

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

Physical Chemistry of Biomolecular Motors

Rotatory Motors

THURSDAY AFTERNOON

 Section A

Integrating Diverse Computational Approaches to Complex Problem Solving

Fluids and Soft Materials

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

High-throughput Computational Processes in Drug Discovery

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. Th¿gersen

 Section C

Protein Flexibility

Inhibitor Discovery Techniques III

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. GŸnther, 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

Biological Applications of Implicit Solvent Models

1:00 ÷382. Simulations of the pK_a'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

Physical Chemistry of Biomolecular Motors

Processive Motors III