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COMP Programming

Spring 2006 National Meeting
Washington DC

W. D. Cornell and J. D. Madura, Program Chairs

SUNDAY MORNING

 Section A

Georgia World Congress Center -- B304

Frontier Applications and Developments of Density Functional Theory: A Symposium in Honor of Robert G. Parr's 85th Birthday

Cosponsored with PHYS
W. Yang and P. W. Ayers, Organizers
R. Pariser, Presiding

8:40 — Introductory Remarks. Weitao Yang.

8:50 —1. Van der Waals theory in the spirit of Maxwell. W. Kohn

9:20 —2. Van der Waals interactions from the exchange hole dipole moment. A. D. Becke, E. R. Johnson

9:50 —3. Applications of van der Waals density functional (vdW-DF). D. C. Langreth

10:20 — Intermission.

10:30 —4. Improvements in density functionals theory and applications to nanoelectronics. W. A. Goddard III

11:00 —5. Hydrogen bonds and other weak interactions in DFT. D. R. Salahub

11:30 —113. Discontinuity of the chemical potential in reduced-density-matrix-functional theory. E. Gross, N. Helbig, N. Lathiotakis

 Section B

Georgia World Congress Center -- B305

Protein Kinases: Computer Modeling and Experiment

Cosponsored with MEDI
C. F. Wong, Organizer

8:30 —7. Profiling protein kinase substrate specificity using peptide arrays. B. E. Turk

9:10 —8. Regulation of protein motions in MAP kinases. N. Ahn

9:50 —9. Surrogate approaches to AGC-kinase inhibition. D. Bossemeyer, M. Gassel, S. Bonn, C. B. Breitenlechner, R. A. Engh

10:30 — Intermission.

10:40 —10. Processing conformation of MAP kinases. E. J. Goldsmith, T. Zhou

11:20 —11. A structural view of the protein kinase family and family-based drug discovery. S -H. Kim, J. Hou, C. Zhang

12:00 —12. A switched electrostatic network guides Src conformational activation. E. Ozkirimli, C. Post

 Section C

Georgia World Congress Center -- B306

General Oral - Molecular Mechanics and Simulation


J. D. Madura, Organizer, Presiding

8:40 —13. Analytical electrostatics: Beyond the generalized Born model. A. Onufiev

9:05 —14. Calculating free energies with fast implicit solvent models. J. Michel, R. D. Taylor, M. L. Verdonk, J. W. Essex

9:30 —15. Modeling polarization in MD. D. M. Elking

9:55 —16. Metadynamics study of the free energy surfaces of the alanine dipeptide in vacuum and in water: How do molecular mechanics force fields affect backbone conformational transition of proteins and peptides? Z. Liu, P. B. Moore, B. Ensing

10:20 — Intermission.

10:35 —17. Implementation of SCC-DFTB in AMBER. G. D. M. Seabra, R. C. Walker, A. E. Roitberg

11:00 —18. Molecular dynamics integration and molecular vibrational theory. D. Janezic

11:25 —19. Computational methods for the enhanced calculation of time-correlation functions. I. Andricioaei

11:50 —20. Multi-mode molecular dynamics and QM/MM methods for binding affinity estimation of metalloprotein ligands. A. Khandelwal, S. Balaz

SUNDAY AFTERNOON

 Section A

Georgia World Congress Center -- B304

Frontier Applications and Developments of Density Functional Theory: A Symposium in Honor of Robert G. Parr's 85th Birthday

Cosponsored with PHYS
W. Yang and P. W. Ayers, Organizers
J. Z. Zhou, Presiding

1:30 —21. Exact exchange as a component of density functional approximations. J. Perdew, V. Staroverov, G. Scuseria, J. Tao

2:00 —22. New density functionals applied to old problems. G. E. Scuseria

2:30 —23. Use of the adiabatic connection for constructing exchange-correlation functionals in density functional theory. P. Mori-Sánchez, A. J. Cohen, W. Yang

3:00 —24. Spin-current density-functional methods. A. Goerling

3:30 — Intermission.

3:40 —25. Advances in orbital-free density functional theory and its applications. E. A. Carter

4:10 —26. Orbital-corrected orbital-free density functional theory. B. Zhou, Y. A. Wang

4:40 —27. Recent developments in conceptual density functional theory. P. Geerlings, F. De Proft

 Section B

Georgia World Congress Center -- B305

Protein Kinases: Computer Modeling and Experiment

Cosponsored with MEDI
C. F. Wong, Organizer

1:30 —28. Processive phosphorylation of splicing factors. J. A. Adams

2:10 —29. Conformational energy landscape of Src kinase activation processes. B. Roux, N. K. Banavali

2:50 — Intermission.

3:00 —30. Conformational changes in protein loops and helices induced by post-translational phosphorylation. M. P. Jacobson, E. S. Groban, A. Narayanan

3:40 —31. Simple models for protein kinases and their interactions with small molecule inhibitors. A. H. Elcock

4:20 —32. Classification of the human kinome based on active site features and small molecule interaction profile. K. Nam, R. P. Sheridan, V. N. Maiorov

 Section C

Georgia World Congress Center -- B306

General Oral - Quantum Chemistry


J. D. Madura, Organizer
Y. Qin, Presiding

1:00 —33. Electron and proton affinities of the 3d-block transition metals using quantum Monte Carlo methods. A. A. Gibson, F. Fayton Jr., J. A. Harkless

1:25 —34. Ab initio determination of chiroptical properties. M. L. Abrams, T. D. Crawford

1:50 —35. Analysis and development of basis sets for optimal ab initio and density functional performance. A. K. Wilson, B. P. Prascher, B. Mintz, X. Wang

2:15 —36. Efficient treatment of electronic structure in highly-correlated molecular systems. G. J. Beran, M. P. Head-Gordon

2:40 —37. A first-principles method for open systems. G. Chen, X. Zheng, F. Wan

3:05 — Intermission.

3:20 —38. Analytic energy derivatives for the locally projected methods: Theory and applications. R. Z. Khaliullin, A. T. Bell, M. Head-Gordon

3:45 —39. Effective computational cost reduction via basis set truncation: Extended systems. B. Mintz, A. Shah, A. K. Wilson

4:10 —40. Scaling of GAMESS quantum chemistry calculations on a small COTS cluster. S. J. Kirkby

4:35 —41. The correlation-consistent Composite Approach (ccCA). N. DeYonker, T. R. Cundari, A. K. Wilson

5:00 —42. Calculation of acid dissociation constants by the SM6 quantum mechanical implicit solvation model. C. P. Kelly, C. J. Cramer, D. G. Truhlar

MONDAY MORNING

 Section A

Georgia World Congress Center -- B304

Frontier Applications and Developments of Density Functional Theory: A Symposium in Honor of Robert G. Parr's 85th Birthday

Cosponsored with PHYS
W. Yang and P. W. Ayers, Organizers
S. Liu, Presiding

8:20 —43. Ab initio density functional theory: The seamless connection with wavefunction theory. R. J. Bartlett, I. Schweigert, V. Lotrich, D. Bokhan

8:50 —44. New density functionals for electronic structure and dynamics. R. Baer, Y. Kurzweil, D. Neuhauser

9:20 —45. Some progress in DFT: Efficiency, accuracy and open system. G. Chen

9:50 —46. Subsystem functionals: A path to improved functionals. A. E. Mattsson, R. Armiento

10:20 — Intermission.

10:30 —47. Exchange-correlation functional for organometallic, inorganometallic, and nonmetallic bonding, noncovalent interactions, and reaction barriers. D. G. Truhlar, Y. Zhao, N. E. Schultz

11:00 —48. Mixed relativistic and non-relativistic DFT calculations for large systems containing heavy elements. L -M. Li, X -Q. Hu, F. Wang

11:30 —49. Density functional methods and vibronic interactions: Lessons from computational studies of DMX-. A. I. Krylov

 Section B

Georgia World Congress Center -- B306

Protein Kinases: Computer Modeling and Experiment

Cosponsored with MEDI
C. F. Wong, Organizer

8:30 —50. Structure based optimization of cyclin dependant kinase inhibitors. C. McInnes

9:10 —51. Docking studies to advance the discovery and optimization of kinase inhibitors. M. L. Lamb

9:50 — Intermission.

10:00 —52. Design of selective protein inhibitors using PASSA and PAS-Dock. K. Tondel, E. Anderssen, F. Drablos

10:40 —53. Regulatory subunit RI-alpha and PKA: Allostery and dynamic binding. J. Gullingsrud, C. Kim, S. S. Taylor, J. A. McCammon

11:20 —54. Biasing for favored substituents in kinase library design. F. Soltanshahi, Q. Liu, R. D. Clark

 Section C

Georgia World Congress Center -- B305

Virtual Screening Using Structure-based and Ligand-based Methods for Lead Identification

Cosponsored with MEDI
L. A. Kuhn, L. Narasimhan, and W. Lau, Organizers

8:15 —55. Understanding hits and decoys in molecular docking. B. Shoichet, R. Brenk, S. Boyce

8:45 —56. Finding inhibitors of protein association by ICM docking into induced surface pockets. R. Abagyan, S. Saldanha, M. Totrov, M. Mallya, R. L. Phillips, D. Lomas

9:15 —57. Use of negative data in the refinement of scoring functions for virtual screening. A. N. Jain, T. A. Pham

9:45 — Intermission.

10:00 —58. Accurate prediction of ligand-receptor binding energies. B. W. Sherman, R. Farid, M. P. Repasky

10:30 —59. Validation of quantum-mechanical docking and scoring procedures. V. M. Anisimov

11:00 —60. Better knowledge – better scoring: Tailoring DrugScore to a particular protein yields improved pose and affinity predictions and allows to incorporate conformational variability. H. Gohlke, S. Radestock, B. Breu

11:30 — Panel Discussion.

 Section D

Georgia World Congress Center -- B307

General Oral - Molecular Mechanics and Simulation


J. D. Madura, Organizer
J. M. Moix, Presiding

8:20 —61. Assembling the small ribosomal subunit in silico: A novel approach to determine binding interdependencies. K. Hamacher, J. Trylska, J. A. McCammon

8:45 —62. Exploring the assembly of the 30S ribosomal subunit. J. Trylska, J. A. McCammon, C. L. Brooks III

9:10 —63. Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates protonation of the substrate dihydrofolate. I. V. Khavrutskii, D. J. Price, J. Lee, C. L. Brooks III

9:35 —64. Deprotonation of solvated formic acid from Car Parrinello molecular dynamics plus the novel metadynamics method. J -G. Lee, E. K. Asciutto, V. Babin, C. Sagui, T. Darden, C. Roland

10:00 — Intermission.

10:15 —65. Understanding the decarboxylation mechanism of N-carboxy-2-imidazolidinone, a Car-Parrinello molecular dynamics investigation. M. E. McKenzie, B. Chen

10:40 —66. QM/MM model of the O2-evolving complex of photosystem II. E. M. Sproviero, J. A. Gascon, J. P. McEvoy, G. W. Brudvig, V. S. Batista

11:05 —67. Modeling the key recognition event at the heart of the immune response. S. Wan, P. V. Coveney, D. R. Flower

11:30 —68. Multi-configuration molecular mechanics based on combined quantum mechanical and molecular mechanical calculations. H. Lin, Y. Zhao, D. G. Truhlar

11:55 —144. Solvent polarization and kinetic isotope effects in nitroethane deprotonation and implications to the nitroalkane oxidase reaction. D. T. Major, D. M. York, J. Gao

MONDAY AFTERNOON

 Section A

Georgia World Congress Center -- B304

Frontier Applications and Developments of Density Functional Theory: A Symposium in Honor of Robert G. Parr's 85th Birthday

Cosponsored with PHYS
W. Yang and P. W. Ayers, Organizers
M. L. Berkowitz, Presiding

1:30 —69. Early days of DFT with RGP, and a general theory of hybrids. M. Levy, A. Cohen, P. Mori-Sanchez, W. Yang

2:00 —70. Importance of the exchange-correlation potential in Kohn-Sham theory. D. J. Tozer

2:30 —71. Kohn-Sham calculations without density functionals. P. Gori-Giorgi, A. Savin

3:00 —72. Assessment of exchange-correlation functionals from the adiabatic connection. A. J. Cohen, P. Mori-Sánchez, W. Yang

3:30 — Intermission.

3:40 —73. A new hybrid DFT functional: Accurate description of response properties and van der Waals interactions. K. Hirao

4:10 —74. Density scaling and a generalized Kohn-Sham scheme. A. Nagy

4:40 —75. Time-dependent density functionals derived from variational functionals of the Green function. R. van Leeuwen

 Section B

Georgia World Congress Center -- B305

Virtual Screening Using Structure-based and Ligand-based Methods for Lead Identification

Cosponsored with MEDI
L. Narasimhan, L. A. Kuhn, and W. Lau, Organizers

1:30 —76. Progress in Computer-Aided Drug Design. W. L. Jorgensen

2:00 —77. BACE: Accounting for flexibility in a scoring Function. G. McGaughey, B. Feuston, S. Graham, M. K. Holloway, S. Lindsley, P. Nantermet, H. Rajapakse, S. Stauffer

2:30 —78. Pharmacophore-based virtual screening. J. Van Drie

3:00 — Intermission.

3:15 —79. A comparison of structure-based and shape-based tools for virtual screening. P. C. D. Hawkins

3:45 —80. PubChem: An information resource linking chemistry and biology. S. Bryant

4:15 —81. Beyond PEST descriptors: Binding site and ligand shape/property fingerprints. C. M. Breneman, C. M. Sundling, N. Sukumar, K. P. Bennett, M. J. Embrechts, S. Cramer

4:45 — Panel Discussion.

 Section C

Georgia World Congress Center -- B306

General Oral - Quantum Chemistry


J. D. Madura, Organizer
A. Roitberg, Presiding

1:00 —82. Wave-packets and density matrices: Using DFT for ab initio dynamics. S. S. Iyengar

1:25 —83. Dopant effects on excited states of a novel photocatalyst: A QM/MM study of ETS-10. A. M. Zimmerman, M. Nash, D. J. Doren, R. F. Lobo

1:50 —84. Models and mechanisms of the DNA (6-4) photoproduct repair by (6-4) photolyase. C. Harrison, O. Wiest

2:15 —85. Unconventional Catalytic Mechanism for histone deacetylase suggested by a DFT-QM/MM study. C. Corminboeuf, P. Hu, M. E. Tuckerman, Y. Zhang

2:40 —86. Theoretical studies on farnesyl cation cyclization: pathways to pentalenene and diversions to other natural products. P. Gutta, D. J. Tantillo

3:05 — Intermission.

3:20 —87. Theoretical studies of intramolecular hydrogen bonding in malonamide derivatives. J. N. Woodford

3:45 —88. The molecular properties of electronically excited states. C. E. Smith, T. D. Crawford

4:10 —89. Time-dependent density functional theory calculations of the electronic excited states of tryptophan in proteins. J. D. Hirst

90. Withdrawn.

4:35 —91. Computing physical properties of simple aromatics. M. H. Kassaee, D. Keffer, W. V. Steele

MONDAY EVENING

 Section A

Georgia World Congress Center -- Ex. Hall B4

Sci-Mix


W. D. Cornell, Presiding

8:00 - 10:00

150, 156, 158, 161, 163, 166, 171-172, 180-183, 186, 190-191, 202, 208-210, 212, 214, 220-222, 224, 228, 239, 252. See subsequent listings.

TUESDAY MORNING

 Section A

Georgia World Congress Center -- B304

Frontier Applications and Developments of Density Functional Theory: A Symposium in Honor of Robert G. Parr's 85th Birthday

Cosponsored with PHYS
W. Yang and P. W. Ayers, Organizers
Z -Z. Yang, Presiding

8:20 —92. Kinetic approach to electron transport in nanoscale devices. R. Car

8:50 —93. Advances in formal and practical time-dependent density-functional theory. S. Hirata

9:20 —94. Excited-state spin-contamination in time-dependent density-functional theory for molecules with open-shell ground states. M. E. Casida, A. Ipatov

9:50 —95. Nonperturbative treatment of atomic and molecular multiphoton processes in intense laser fields: Self-interaction-free TDDFT approaches. S -I. Chu

10:20 — Intermission.

10:30 —96. The application of TDDFT to systems with a spin or space degenerate ground state. T. Ziegler, M. Seth, F. Wang

11:00 —97. Time-dependent relativistic density functional theory and applications. W. Liu

11:30 —98. Quantum defect and time-dependent density functional theory. K. Burke, M. van Faassen, A. Wasserman

 Section B

Georgia World Congress Center -- B305

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

Cosponsored with MEDI
J. Woolfrey and I. Visiers, Organizers

8:30 —99. Exploration of GPCRs: Structure and function. K. Palczewski

9:00 —100. Crystal structures of rhodopsin. J. Ballesteros, K. Palczewski

9:30 —101. High throughput membrane protein structure determination by electron crystallography. H. Stahlberg, Z. Y. Zhang, B. Gipson, R. Hill, H -T. Chou, P -L. Chiu, L. Renault, X. Zeng

10:00 — Intermission.

10:15 —102. Protein interactions in GPCR signaling: A very moving story. H. Weinstein

10:45 —103. G Protein coupled receptors: Structure, ligand recognition, and receptor activation. L. Pardo

11:15 —104. Modeling ligand interactions at adenosine and P2Y nucleotide recptors: Influence of ribose conformation. K. A. Jacobson, S -K. Kim, A. A. Ivanov, S. Costanzi

 Section C

Georgia World Congress Center -- B306

General Oral - Molecular Mechanics and Simulation


J. D. Madura, Organizer
A. Tucker, Presiding

8:30 —105. Novel methods for modeling aluminum nanoclusters. M. Iron

8:55 —106. Computational design of an enzyme mutant for anti-cocaine medication. D. Gao, W. Yang, Y. Yang, H -H. Tai, C -G. Zhan

9:20 —107. Effects of tautomerism and hydration on the speciation of molecules: A study using SPARC. S. N. Ayyampalayam, L. Carreira

9:45 —108. Interaction of Protegrin-1 (PG-1) with lipid bilayers: Membrane thinning effect. H. Jang, B. Ma, T. B. Woolf, R. Nussinov

10:10 — Intermission.

10:25 —109. A minimal model for stabilization of biomolecules by hydrocarbon cross-linking. K. Hamacher, A. Hübsch, J. A. McCammon

10:50 —110. Metadynamics molecular simulations with accurate quantum chemistry calculation for the study of the anions forms of Malonic Acid. E. K. Asciutto, C. Sagui

11:15 —111. Replica exchange molecular dynamics study on aralyamide and heparin in water: Sampling effects and analysis of the detailed binding mode. Z. Liu, V. Pophristic

11:40 —112. Replica-exchange molecular dynamics simulations of protein adsorption on a hydrophobic surface. Y. Sun, R. A. Latour

 

Advances in Pharmacophores and 3-D Screening

New Approaches

Sponsored by CINF, Cosponsored with COMP, and MEDI

TUESDAY AFTERNOON

 Section A

Georgia World Congress Center -- B304

Frontier Applications and Developments of Density Functional Theory: A Symposium in Honor of Robert G. Parr's 85th Birthday

Cosponsored with PHYS
W. Yang and P. W. Ayers, Organizers
R. C. Morrison, Presiding

1:30 —6. Density functional theory for non-equilibrium systems. M. Ernzerhof

2:00 —114. A canonical transformation theory for multireference problems. G. K. Chan, T. Yanai

2:30 —115. Quantum phase space and the local virial theorem. L. Cohen

3:00 —116. Stress tensor in the standard model of elementary particles and the origin of the electronic spindle structure of chemical bond. A. Tachibana

3:30 — Intermission.

3:40 —117. Designing molecules by optimizing potentials. D. N. Beratan

4:10 —118. New computational strategies for density functional calculations. R. J. Harrison, A. Beste

4:40 —119. Using Density functional theory, new algorithms and computer simulation to probe biophysical, materials and chemical systems. G. Martyna

 Section B

Georgia World Congress Center -- B305

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

Cosponsored with MEDI
J. Woolfrey and I. Visiers, Organizers

1:30 —120. How bilayers cope with transmembrane helices: Insights from translocon-assisted helix insertion. S. H. White

2:00 —121. Ab initio modeling of the loops in G-protein coupled receptors. E. L. Mehler

2:30 —122. Studying the photochemistry of retinal proteins with quantum chemical methods. M. Elstner

3:00 — Intermission.

3:15 —123. Models for the GPCR proton sensors OGR1, GPR4, and TDAG8. R. M. Wolf, M -G. Ludwig, K. Seuwen

3:45 —124. Binding site sxpansion and induced fit docking for GPCR ligand binding mode prediction: Application to the b-adrenergic and chemokine receptors. A. Tebben, S. R. Kimura, P. H. Carter, Q. Zhao, S. R. Krystek Jr.

4:15 —125. The molecular basis of antagonist binding to CCR1: Molecular modeling and experiment. S. K. Schlyer, R. Horuk, S. Koovakkat, M. J. Kochanny, R. Trabanino, W. A. Goddard III, R. Abrol, W. B. Floriano, J. Pease, J. Fox, F. Lopez de Mendoca, S. Sharma, V. Nagarajan

 Section C

Georgia World Congress Center -- B306

Thomas Kuhn Paradigm Shift Award Competition


A. Nicholls and G. Skillman, Organizers

1:30 — Introductory Remarks.

1:40 —126. Toward a force field based on density fitting. G. A. Cisneros, J -P. Piquemal, N. Gresh, T. A. Darden

2:20 —127. Assigning the protonation states of the key aspartates in β-secretase using QM/MM X-ray structure refinement. N. Yu, K. M. Merz Jr.

3:00 — Intermission.

3:20 —128. Virtual screening: The king (quite often) has no clothes. R. C. Glen, A. Bender

4:00 —129. Iterative focussed screening using Random Forest: A comparison with HTS/random screening for two extreme cases. C. I. Bayly, C. Brideau, A. Liaw, V. Svetnick

4:40 — Award Announcement.

 Section D

Georgia World Congress Center -- B307

General Oral - Quantum Chemistry


J. D. Madura, Organizer
G. D. M. Seabra, Presiding

1:20 —130. Solvation studies by DFT of Carbohydrates: a/b-anomeric ratios of epimers of glucose using a continuum-solvation model (COSMO). U. Schnupf, J. L. Willett, F. A. Momany

1:45 —131. Molecular modeling insights into the catalytic mechanism of a family 38 glycosyl hydrolase, Golgi α-mannosidase II. S. P. Kawatkar, G -J. Boons, R. J. Woods

2:10 —132. Modeling of complex hydrides: Lattice anomaly in NaAlH4. J. Ojwang', G. J. Kramer

2:35 —133. Solvation of bihalide anions with water. D. D. Kemp, M. S. Gordon

3:00 — Intermission.

3:15 —134. Theoretical study of solvation of NaOH. P. Arora, M. S. Gordon

3:40 —135. Cyanogen and diacetylene dimer potential energy surfaces: New π--π prototypes. B. W. Hopkins, G. S. Tschumper

4:05 —136. Structural and vibrational properties of boron nitride (BN) analogs of diamondoids. S. L. Richardson, K. Park, T. Baruah, M. R. Pederson

4:30 —137. Silica-supported silver salt for paraffin/olefin separation: A DFT study. D. E. Jiang, B. G. Sumpter, S. Dai

4:55 —138. Importance of basis set construction in density functional theory. B. P. Prascher, A. K. Wilson

 

Advances in Pharmacophores and 3-D Screening

Applications

Sponsored by CINF, Cosponsored with COMP, and MEDI

TUESDAY EVENING

 Section A

Georgia World Congress Center -- Ex. Hall B4

Poster Session


W. D. Cornell, Organizer

6:00 - 8:00

139. Conformational study of small molecules in the protein environment. I. Weidlich, M. C. Nicklaus

140. Flexible docking of the inhibitors into Tyrosyl-DNA Phosphodiesterase (Tdp1) active sites. I. Weidlich, M. C. Nicklaus

141. Computational modeling of kinases. D. J. Smith, W. Duan, C. S. Verma

142. Novel empirical free energy function for use in the protein-protein docking problem. J. Audie

143. Withdrawn.

145. A line integral reaction path approximation for large systems via nonlinear constrained optimization: Application to alanine dipeptide and β-hairpin of protein G. I. V. Khavrutskii, R. Byrd, C. L. Brooks III

146. Absence of aromaticity at residue 6.44 contributes to cannabinoid CB2 receptor constitutive activity. R. C. Serbanescu, J. Barnett-Norris, R. Zhang, T -K. Kim, Z -H. Song, P. H. Reggio

147. Absolute binding free energy calculation for theophylline and its analogs to RNA aptamer using BAR method with GAFF. Y. Tanida, M. Ito, H. Sato, A. Matsuura, H. Fujitani

148. Analyzing force field and charge conditions to enhance biological activity predictions of Cathepsin D inhibitors. H. N. Biles, M. W. Ellis, C. J. Collar, L. Fabry-Asztalos

149. Atomistic simulations of carbon dioxide diffusion within zeolites. D. Kohen, D. S. Davis

150. Better than RMSD: Faster methods for conformer comparison. J. J. Yang

151. Biomolecular electrostatic potential: An analytical approach. A. T. Fenley, J. C. Gordon, A. V. Onufriev

152. Computational analysis of conformational diversity of FLPs neuropeptides. G. Leonis, A. E. Roitberg

153. Computational methods for the analysis of small angle scattering spectra. J. E. Curtis, W. Ratcliff II, S. Krueger

154. Computational studies into the mechanism of human tyrosyl-DNA phosphodiesterase. B. E. Richardson, A. C. Goren

155. Computational studies of asymmetric organocatalysis. D. J. Harriman, G. Deslongchamps

156. Computational tools for LIPID metabolite and pathways strategy. M. Sud, E. Fahy, R. Byrnes, D. Cotter, A. Maer, Y. Zhao, S. Subramaniam

157. Computer simulations of glycolytic enzyme/enzyme association and implications for substrate binding. V. F. Waingeh, I. V. Ouporov, K. A. Thomasson

158. Computer-aided molecular design of Histone Deacetylase Class I inhibitors. E. X. Esposito, G. R. Cook

159. Conformational analysis of a GBR 12909 analog. C. A. Venanzi, D. Pandit, J. Naik, S. Abraham

160. Conformational sampling and folding in polyalanine peptides. S. Kim, A. E. Roitberg

161. Contributions of conformational flexibility to Brugia malayi asparaginyl-tRNA synthetase specificity for inhibitors identified by structure-based screening. S. C. K. Sukuru, T. Crepin, J. C. Morris, M. Grotli, F. Danel, M. G. P. Page, M. Haertlein, S. Cusack, M. A. Kron, L. A. Kuhn

162. Crystal-GA: A program for crystal structure determination via X-ray powder diffraction data. H. Arman, C. W. Padgett, W. T. Pennington

163. Cyclopentane: Forcefield and molecular dynamics analysis. A. T. Swann, P. J. Ludovice

164. De novo structure-based design of tris-urea tripodal and macrocyclic anion receptors. V. Bryantsev, B. P. Hay

165. Design of novel enzyme catalysts: Combining the benefits of quantum mechanics, rational design and directed evolution. X. Zhang, T. M. Handel, A. Chowdry

166. Detection of hidden sequence propensity for amyloid fibril formation using support vector machine. Q. Zhang, W. J. Welsh

167. Development of quantitative structure-activity relationship models of Sodium/Potassium ATPase inhibition by cardiac glycosides. D. Rothgeb, S. Paula

168. Differential DNA-binding by some Rel/NF-κB proteins: Molecular dynamics of a κB DNA element. C. Mura, J. A. McCammon

169. Distance dependence of flurbiprofen and dapsone in the CYP 2C9 active site as studied by molecular dynamics. J. S. Aguilar, Z. R. Hartman, A. G. Niehaus, P. M. Gannett

170. Docking and molecular dynamics studies of copper containing enzyme diamine oxidase. M. R. Flaherty, S. Aditya, F. Ryvkin

171. Dramatically different structural strategies to achieve the same metabolic goal: Molecular modeling comparison of CYP6B8v1 and CYP321A1. T -L. Chiu, Z. Wen, M. A. Schuler

172. Effects of the L100I and L100I+K103N mutations on the binding of etravirine analogs to HIV-1 reverse transcriptase based on Monte Carlo simulations. T. M. Lyons, J. Tirado-Rives, W. L. Jorgensen

173. Errors in gel acrylamide electrophoresis due to effect of charge. K. R. Sharma

174. Evaluation of loop prediction protocols. C. A. Weigelt, K. A. Rossi, S. R. Krystek Jr., A. Nayeem

175. Exploring the mechanism of Trypanosoma cruzi trans-sialidase. Ö. Demir, A. Roitberg

176. Feed-forward neural network models of potential sulfonamide-substituted cycloalkylpyranone HIV protease inhibitors. C. R. Bernier, B. Bhhatarai, S. Kumar, R. Garg

177. First principles molecular dynamics simulations of benzene in water. F. C. Lightstone, E. R. Schwegler, M. Allesch, G. Galli

178. Free energy calculation from non-equilibrium simulations. H. Xiong, H -P. Cheng, A. E. Roitberg

179. Free energy profiles of DNA unzipping under tension and torque. E. C. Brunk, I. Andricioaei

180. Guiding chemical reaction path searches with graph theory. B. W. Hopkins, G. S. Tschumper

181. Hydrophobic-aided replica exchange: An efficient algorithm for sampling biological systems in explicit solvent. X. Huang, P. Liu, R. Zhou, B. Berne

182. Improved efficiency of replica exchange simulations through use of a hybrid explicit/implicit solvation model. A. Okur, L. Wickstrom, M. M. Layten, K. Song, V. Hornak, C. Simmerling

183. Improvements in predictive ADMET modeling stemming from atomic partial charges obtained by a new empirical method. R. Fraczkiewicz, G. Fraczkiewicz, M. B. Bolger, W. S. Woltosz

184. Influence of structural characteristics over the cytotoxic and hepatoprotective activities of cucurbitacin analogs. J. Bartalis, F. T. Halaweish

185. Investigation of HIV protease cyclic urea inhibitors using computational approach. D. Patel, B. Bhhatarai, R. Garg

186. Ligand-based approach for the identification of novel inhibitors: Application to Salvinorin A, a selective kappa opioid receptor (KOP) agonist. N. Singh, G. Chevé, S. Narayanan, C. R. McCurdy

187. Ligand-docking-based homology model of the melanin-concentrating hormone 1 receptor. A. J. Orry, C. N. Cavasotto

188. Limitations in the modeling of physical properties using the Hosoya Index. K. J. Dawson, K. McLaughlin

189. Lipid properties on nano-disc particles of Apo A-I. M. P. Aliste, S. C. Harvey

190. Modeling of human blood:air and tissue:air partition coefficients using structural descriptors. M. Kuanar

191. Modeling of peptidic inhibitors of Immunoglobulin-G degrading enzyme of Streptococcus pyogenes. J. G. Longenecker, J. P. Wolbach

192. Molecular Dynamics analysis of the interaction of Lys237 with the H-cluster of Fe-only hydrogenase. D. Dogaru, S. Motiu, V. Gogonea

193. Molecular dynamics and stochastic simulations of surface diffusion. J. M. Moix, R. Hernandez

194. Molecular dynamics simulation of conformational changes in nicotinic acetylcholine receptor triggered by agonist binding. X. Cheng, J. A. McCammon

195. Molecular dynamics study of hydrogen bonding interactions of dapsone and flurbiprofen within the CYP 2C9 active site. Z. R. Hartman, J. L. Fry, B. L. Gardner, J. S. Aguilar, P. M. Gannett

196. Molecular modeling of phase behavior and microstructure of acetone-chlorforom-methanol binary mixtures. G. K. Kamath, J. J. Potoff

197. Molecular modeling, circular dichroism and FTIR studies of conformation adopted by tetrapeptides with inhibitory activity for thrombin. C. Clement, C. Matthaeus, M. Philipp

198. Molecular modeling studies of novel cyclic urea HIV protease inhibitors. D. Patel, R. Garg

199. On the derivation of a damped wave transport equation from Spring-Dashpot viscoelastic model. K. R. Sharma

200. On the second law violation in Fourier heat conduction. K. R. Sharma

201. On the use of cutrices in restriction mapping of three enzymes. K. R. Sharma

202. Principal mode analysis for calculating vibrational frequencies and modes of models for the peptide bond. R. A. Wheeler, K. Brorsen, S. E. Boesch

203. Probabilistic neural networks: Predicting good HIV protease inhibitors. C. R. Bernier, B. Bhhatarai, S. Kumar, R. Garg

204. Proteomics and dimensional separation. K. R. Sharma

205. Quantum Monte Carlo simulations in high-dimensional configuration spaces: A comparison of second- and fourth-order propagators. B. Magnusson, R. J. Hinde

206. Rotational disorder in conjugated oligomers: A nonlinear one-dimensional configuration-coordinate model. L. Liu, M. A. Berg, D. Yaron

207. Side-chain mobility and binding selectivity of naphthylquinoline derivatives. A. Sood, M. J. Lovell, G. R. Bishop, D. H. Magers

208. Site-of-metabolism prediction: A computational model based on reactivity and P450-substrate complementarity. M. Wu, M. R. Wester, Y -A. He, D. Dalvie, B. Holwerda, R. Love, H. Parge, C. Lee, B. Burke

209. Strategies for building fullerenes and nanotubes on Spartan. J. Mann, K. Jones, T. Manning, I. Barton

210. Structural determinants of binding of small molecules to extracellular matrix: Multi-species, multi-mode 3-D-QSAR analysis. Y. Zhang, V. Lukacova, V. Bartus, S. Balaz

211. Structure-based design of reversible peptides inhibitors for Factor VIIa. C. Clement, L. Gingold, M. Philipp

212. Understanding agonism in the NMDA receptor: Comparing NR2A and NR2D using MD. M. T. Geballe, K. Erreger, S. F. Traynelis, J. P. Snyder

213. Using QSAR techniques: Analysis of estradiolic ligand binding to the estrogen receptor. L. C. Streeter, R. Garg

214. Vibrational mode mixing analysis of a HIV-1 protease-inhibitor complex. H. Goto, T. Kmakura

215. Web-based entropic scoring functions: Advances in protein structure validation. J. Foley IV, S. Zhong, G. Ozer, R. Hernandez

216. Withdrawn.

217. Molecular dynamics simulation of the human P2Y14 receptor and study of ligand-receptor interactions. A. A. Ivanov, K. A. Jacobson

218. Systematic active site refinement of GPCR models through molecular dynamics simulation. S. R. Kimura, S. Krystek Jr., A. Tebben, D. R. Langley

219. Quantum chemical treatment of the Ene reaction activation parameters. M. Rectenwald, J. D. Evanseck

220. Quantum dynamics of [1,5] hydrogen shift in 1,3-pentadiene: implications for kinetic isotope effects and Swain-Schaad exponents. J. D. Thoburn, D. N. Peles

221. Quantum mechanical analysis of cadmium sulfide/selenium quantum dots. J. M. Bair, J. D. Madura

222. Prediction of excited states for carbon, nitrogen and oxygen systems using quantum Monte Carlo. F. Fayton Jr., A. A. Gibson, J. A. Harkless

223. Semiempirical and QM calculations of absorbance wavelengths of environmentally sensitive near-IR dyes for biosensor applications. D. B. Sherman, K. J. Thomas, A. Ambroise, J. B. Pitner

224. Theoretical study of the isomerization mechanism of azobenzene and symmetrically disubstituted azobenzene Derivatives. C. R. Crecca, A. Roitberg

225. Ab initio study of meta-substituted diphenyl ureas. S. Dehghan, V. M. Wurster, C. A. Capacci, R. Hiremath, J. A. Swift

226. Ab initio studies of diboracarbonyl molecules. J. L. Meeks

227. A computational study of 1,2-HBr elimination and 1,2-ClBr interchange in hydrobromocarbons and bromochlorocarbons. G. L. Heard, C. M. Olson, L. W. Friederich, B. E. Holmes

228. Stability of H2 clathrates vs. cavity occupancy. V. N. McCarthy, K. D. Jordan

229. A computational study of the barrier height of the 1,2-FCl exchange reaction of substituted ethanes. W. C. Everett, B. E. Holmes, G. L. Heard

230. The effect of chromophore conformation in green fluorescent protein on its absorption spectrum: A QM/MM and TDDFT study. S. Trohalaki, S. S. Patnaik, R. Pachter

231. Accuracy of FMO-MO for Large Scale Molecule. Y. Inadomi, H. Umeda, T. Watanabe, U. Nagashima, T. Ishimoto

232. Theoretical studies of dissociation of perfluorohydroxylamine. H. Sayin, M. L. McKee

233. Accurate proton affinity and gas-phase basicity values of molecules important in biocatalysis. K. Range, A. Moser, D. M. York

234. Theoretical studies on adduct formations of Pt (IV) and Pd (IV) complexes with an engineered oligonucleotide. M. Jeudy, B. Cardelino

235. Activation of the C-X bond by palladium: Ab initio benchmarks and evaluation of DFT. G. T. de Jong, F. M. Bickelhaupt

236. Theoretical studies on iron-substituted barium titanate perovoskite clusters. C. F. Bryant, B. Cardelino

237. Alternate mechanisms for the formation of volatile selenium species. T. R. I. Takatani, J. M. Galbraith

238. Theoretical study of the magnetic properties of quinoidal oligothiophenes. L. R. Waller, T. Waller

239. Anomeric control of high energy bonds. E. A. Ruben, M. S. Chapman, J. D. Evanseck

240. Application of FMO-MO fior Large-Scale Molecule: Effect of solvent molecules. T. Watanabe, Y. Inadomi, H. Umeda, T. Ishimoto, U. Nagashima

241. Benchmark quantum mechanical computations on the acid-catalyzed Diels-Alder reaction between butadiene and methyl acrylate. R. A. Newton, J. A. Plumley, J. D. Evanseck

242. Calculation of nuclear spin-spin coupling constants of molecules with first and second row atoms in study of basis-set dependence. W. Deng, J. R. Cheeseman, M. Frisch

243. Computational studies of gas and condensed phase properties of donor-acceptor complexes of sulfur trioxide. J. M. Standard, P. S. Fudacz, B. N. Ida

244. Computational study of Cadmium Sulfide with amino acids as organic capping agents. D. J. Bunk

245. Conventional ring strain in unsaturated four-membered rings. Q. Cheng, S. S. Huskey, D. H. Magers

246. Conventional strain energy and sigma delocalization in small heterocycles of carbon and germanium. L. A. Taylor, C. B. Coghlan, D. H. Magers

247. Conventional strain energy and sigma delocalization in small heterocycles of carbon and silicon. H. McAlexander, B. Magers, C. B. Coghlan, D. H. Magers

248. Conventional strain energy in boracycloproane, diboracyclopropane, boracyclobutane, and diboracyclobutane. B. Magers, H. McAlexander, D. H. Magers

249. Core-valence correlation consistent basis sets revisited for the second-row atoms (Al-Ar). S. Yockel, A. K. Wilson

250. Counter-ion effects of bis(oxazoline) copper(II) catalyzed Diels-Alder reactions. E. G. Franklin, J. DeChancie, J. D. Evanseck

251. Coupled cluster calculations of the H-/H2 potential energy and dipole moment function. P. K. Moehlen, R. J. Hinde

252. Density functional theory study on the mechanism of the ribosome. H. Liu

253. Development of protonic and deuteronic basis functions using Gaussian-type functions. T. Ishimoto, M. Tachikawa, Y. Inadomi, H. Umeda, T. Watanabe, U. Nagashima

254. Direct Born-Oppenheimer dynamics of the Bauld-plateau rearrangements. C. Harrison, C. Doubleday, O. Wiest

255. Disconnection of maximum stereoelectronic effects from the transition structure. J. A. Plumley, J. D. Evanseck, O. Acevedo

256. Enthalpies of formation for thio ethers by homodesmotic reactions. R. Fortenberry, D. H. Magers

257. Generalization of planar hexacoordinate carbon. K. Ito, Z. Chen, C. S. Wannere, P. V. R. Schleyer

258. Hydrogen abstraction reactions using hybrid density functional theory with specific reaction parameters. N. De Silva, S. Swaminathan, T. V. Albu

259. Investigation of metal dependent behavior of HIV-1 integrase inhibitors: DFT calculations. N. Nunthaboot

260. Investigation of the inhibition of Fe-only and Ru-modified H-cluster by molecular oxygen: A density functional theory study. S. Motiu, D. Dogaru, V. Gogonea

261. Modeling of d10 coinage-metal complex excited states. T. V. Grimes, T. R. Cundari, M. A. Omary

262. Parallel Fock matrix construction on the Grid. H. Umeda, Y. Inadomi, T. Watanabe, T. Ishimoto, U. Nagashima

263. DFTB Energy decomposition analysis of interactions in Fullerene@SWNT nanopeapods. Z. Wang, S. Irle, G. Zheng, K. Morokuma, R. Kitaura, H. Shinohara

264. Enthalpies of formation of TNT derivatives by homodesmotic reactions. A. Sood, P. L. Honea, D. H. Magers

265. Theoretical study of the electronic and geometrical structures of organic semiconductors. M. M. Bader, G. P. Gutshall, A. Scotto Di Marco, H. Lin

266. Thermodynamic studies on the effect of metal complexes, similar to those used as anticancer drugs, on an oligonucleotide. J. Stoudmire, A. R. Siler, B. Cardelino

267. N1s and C1s core electron binding energies for 2-, 3-, and 4-substituted pyridines calculated by density functional theory (DFT): Correlations with Hammett substitutent constants. Y. Takahata

268. Philicity concept revisited. P. K. Chattaraj, U. Sarkar, D. R. Roy, R. Parthasarathi, J. Padmanabhan, V. Subramanian

269. Spin-Potential functional formalism for current-carrying noncollinear magnetic systems. T. Heaton-Burgess, P. W. Ayers, W. Yang

270. Confined atoms and molecules: Some new results. K. D. Sen

271. Control and monitoring of physical objects in biomolecular systems: Some novel experimental tools and theoretical models. K. Rupnik

272. Correlation energy density functionals for two-electron systems. J. Katriel, S. Roy, M. Springborg

273. EEM and Spectrophores. W. Langenaeker, H. De Winter, G. Thijs, J. Taminau

274. From coordinate space density to momentum-space density sans wave functions. R. K. Pathak

275. Fundamental importance of the Coulomb hole sum rule to understanding of the Colle-Salvetti wave function. X -Y. Pan, V. Sahni, L. Massa

276. Molecular dynamics simulations with the ABEEM force field based on density functional theory. Z -Z. Yang

WEDNESDAY MORNING

 Section A

Georgia World Congress Center -- B304

Frontier Applications and Developments of Density Functional Theory: A Symposium in Honor of Robert G. Parr's 85th Birthday

Cosponsored with PHYS
W. Yang and P. W. Ayers, Organizers
P. K. Chattaraj, Presiding

8:20 —277. An "atoms" in "molecules" based chemical reactivity theory. M. H. Cohen, A. Wasserman

8:50 —278. Fractional charge in diatomics-in-molecules hamiltonians. S. M. Valone, S. R. Atlas

279. Withdrawn.

9:20 —280. Chemical reactivity indexes and the auxiliary density. A. Vela

9:50 — Intermission.

10:00 —281. Link between reaction force and DFT reactivity descriptors. S. Gutiérrez-Oliva, B. Herrera, A. Toro-Labbé

10:30 —282. Role of the density response function in the interaction of a hard and a soft species. A. Cedillo

11:00 —283. Why does the Hard-Soft Acid-Base Principle work? Insights obtained by considering acid (or base) exchange reactions. P. W. Ayers

 Section B

Georgia World Congress Center -- B305

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

Cosponsored with MEDI
J. Woolfrey and I. Visiers, Organizers

8:30 —284. Beyond keeping it together: Extracellular loops in the cannabinoid receptor and rhodopsin play a key role in receptor stability and ligand binding. D. L. Farrens, J. F. Fay

9:00 —285. Molecular dynamics simulations of cannabinoid CB1 receptor/endogenous ligand recognition via the membrane bilayer. P. H. Reggio, D. L. Lynch

9:30 —286. Molecular dynamics simulations of the structural stability of the cannabinoid-CB1 receptor inactive state model in a POPC bilayer. D. L. Lynch, J. Barnett-Norris, D. P. Hurst, P. H. Reggio

10:00 — Intermission.

10:15 —287. Computational studies of G-protein coupled receptor oligomers. M. Filizola

10:45 —288. Defining the ligand binding site on the human C5a receptor. P. N. Monk, A. Higginbottom, P. K. Madala, J. D. A. Tyndall, M. Stoermer, D. P. Fairlie

11:15 —289. Inactive and active states and supramolecular organization of GPCRs: Insights from computational modeling. F. Fanelli, P. G. De Benedetti

 Section C

Georgia World Congress Center -- B306

General Oral - Molecular Mechanics and Simulation


J. D. Madura, Organizer
G. Ozer, Presiding

8:20 —290. Computer simulation of nano tin melting behavior: Effect of particle size and temperature ramping up rate. H. Dong, K -S. Moon, H. Jiang, C. Wong, M. I. Baskes, F. Hua

291. Withdrawn.

8:45 —292. Hydration and dewetting near fluorinated superhydrophobic plates. X. Li, J. Li, M. E. Eleftheriou, R. Zhou

9:10 —293. Mass transport of O2 and N2 in nanoporous carbon (C168 Schwarzite) using quantum mechanical force field and molecular dynamics simulations. G. Arora, S. I. Sandler

9:35 — Intermission.

9:50 —294. Nucleation, growth and domain formation in solid-solid phase transitions. S. Leoni, D. Zahn

10:15 —295. Nucleation and growth in the fluorite to PbCl2-type pressure-induced phase transition in CaF2. S. E. Boulfelfel, D. Zahn, O. Hochrein, Y. Grin, S. Leoni

10:40 —296. Quantitative chiral recognition in silico, from chromatography to proteins. T. Hanai

11:05 —297. The Brownian dynamics in suspension of swelling/shrinking colloids. A. Popov, R. Hernandez

WEDNESDAY AFTERNOON

 Section A

Georgia World Congress Center -- B304

Frontier Applications and Developments of Density Functional Theory: A Symposium in Honor of Robert G. Parr's 85th Birthday

Cosponsored with PHYS
W. Yang and P. W. Ayers, Organizers
H. Weinstein, Presiding

1:30 —298. Density functional studies of orgnometallic systems. H. F. Schaefer III

2:00 —299. Using hybrid DFT methods to understand the structure and reactivity of transition metal-dependent enzymes. N. G. J. Richards

2:30 —300. DFT and approximate SCC-DFTB methods applied to biological systems: Successes and problems. M. Elstner

3:00 —301. A DFT and QM/MM study of the active site of human DNA Polymerase Beta. L. G. Pedersen, P. Lin

3:30 — Intermission.

3:40 —302. Clusters: Structures and properties. M. S. Gordon, R. M. Olson, S. A. Varganov

4:10 —303. Development and application of density functional theory QM/MM approach to studying metalloenzymes. Y. Zhang

4:40 —304. Modeling biological reactions with density-functional theory: Multi-scale. D. York

 Section B

Georgia World Congress Center -- B305

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

Cosponsored with MEDI
J. Woolfrey and I. Visiers, Organizers

1:30 —305. Structure-based design of opioid ligands. D. M. Ferguson

2:00 —306. Predicting and understanding GPCR-ligand binding using feature-map vectors. J. E. Penzotti, G. A. Landrum

2:30 —307. Homology modeling of angiotensin II type 1 (AT1) receptor and in silico screening in search of unique AT1 antagonists with selective PPAR-ă modulating activity. A. Patny, P. V. Desai, M. Avery

3:00 — Intermission.

3:15 —308. Optimizing diverse combinatorial libraries around known targets. T. E. Mansley, F. Soltanshahi, R. D. Clark

3:45 —309. Large-scale ligand-based modeling for predictive drug design. A. N. Jain, A. E. Cleves

 Section C

Georgia World Congress Center -- B306

General Oral - Quantum Chemistry


J. D. Madura, Organizer
G. Leonis, Presiding

1:20 —310. A computational study on the stability of new krypton-bonded molecules. S. Yockel, E. Gawlik, A. K. Wilson

1:45 —311. Activation of the C-X bond by palladium: Direct oxidative insertion vs. SN2 and the importance of relativistic and solvent effects. G. T. de Jong, F. M. Bickelhaupt

2:10 —312. Adsorption of H2S on carbon nantube. Y. Wang

2:35 —313. Combined ab initio and ab initio molecular dynamics studies on the oxygen reduction reaction on Pt surface. Y. Wang

3:00 — Intermission.

3:15 —314. Investigation of H2 adsorption sites in MOFs using ab initio methods. C. Buda, B. D. Dunietz

3:40 —315. Quantum chemical molecular dynamics study of single-walled carbon nanotube (SWCNT) nucleation on metal catalyst nanoparticles Fe38/Co38/Ni38. G. Zheng, S. Irle, M. Elstner, K. Morokuma

4:05 —316. Electronic structure of oxo-Mn(salen). J. S. Sears, C. D. Sherrill

4:30 —317. Ab initio insight on the interaction of Urate with Li+, Na+, K+, Be2+, Mg 2+ and Ca2+ Metal Cations. R. N. Allen, M. K. Shukla, J. Leszczynski

4:55 —318. MFCC-DM with pairwise interaction correction for quantum chemical study of protein. X. Chen, Y. Zhang, J. Z. Zhang

THURSDAY MORNING

 Section A

Georgia World Congress Center -- B304

Frontier Applications and Developments of Density Functional Theory: A Symposium in Honor of Robert G. Parr's 85th Birthday

Cosponsored with PHYS
P. W. Ayers, Organizer
W. Yang, Organizer, Presiding

8:20 —319. Questionable spin parameters from DFT. E. R. Davidson

8:50 —320. Further development and applications of the DFTB (Density Functional Tight Binding) method. K. Morokuma

9:20 —321. Hydrogen-bonded clusters. A. J. Thakkar

9:50 —322. Density functional theory of materials modeling at different length scales. S. K. Ghosh

10:20 — Intermission.

10:30 —323. Chemical accuracy along reaction paths: Full ab-initio calculation of the full vibrational spectrum of the fluorine molecule to wavenumber accuracy. K. Ruedenberg, L. Bytautas, T. Nagata, N. Matsunaga, M. S. Gordon

11:00 —324. Solving the Schrödinger and Dirac-Coulomb Equations and developing the Giant SAC/SAC-CI Method. H. Nakatsuji

11:30 — Concluding Remarks. Robert G. Parr.

 Section B

Georgia World Congress Center -- B305

Structure Determination Using NMR and Computational Methods


J. P. Bowen, Organizer

8:20 — Introductory Remarks.

8:25 —325. A DFT study of the action of Vitamin K Carboxylase. L. G. Pedersen, C. H. Davis

8:55 —326. Did amyloid seed the origins of life? D. Lynn, A. Mehta, K. Lu, J. Dong, Y. Liang, P. Liu, R. Ni, W. S. Childers, J. Simmons, S. Dublin

9:25 —327. Development of diffusion ordered NMR spectroscopy: Promise and pitfalls. C. S. Johnson Jr.

9:55 —328. Molecular modeling of the oxidized form of nuclear factor κB suggests a mechanism for redox regulation of DNA binding and transcriptional activation. E. W. Taylor, V. Chandrasekaran

10:25 —329. Molecular Skeleton Analysis (MoSA) and its application for NMDA/glycine/kynurenic binding complex. G. Liang, S. Li, Y. Gu, A. Lewin, J. P. Bowen

10:55 —330. QSAR studies of high potency sweeteners and novel sweetener discovery. L. L. D'Angelo, G. A. Iacobucci

11:25 —331. Selective isotopic labeling in macromolecular NMR studies. R. E. London, S. A. Gabel, T. W. Kirby, B. Bose-Basu, E. F. DeRose, G. Gao, G. A. Mueller, W. A. Beard, S. H. Wilson

 Section C

Georgia World Congress Center -- B306

General Oral - Drug Discovery


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

8:00 —332. Successful structure-based design of novel protein tyrosine phosphatase inhibitors. M. J. Bower, A. P. Combs, E. W. Yue, P. J. Ala, B. Wayland, B. Douty, A. Takvorian, P. Polam, Z. Wasserman, W. Zhu, M. Crawley, J. Pruitt, R. Sparks, B. Glass, D. Modi, E. McLaughlin, L. Bostrom, M. Li, L. Galya, K. Blom, M. Hillman, L. Gonneville, B. G. Reid, M. Wei, M. Becker-Pasha, R. Klabe, R. Huber, Y. Li, G. Hollis, T. C. Burn, R. Wynn, P. Liu, B. Metcalf

8:25 —333. Hierarchical representation of protein conformation: Application in flexible receptor docking. Y. Zhao, D. Stoffler, M. F. Sanner, A. Olson

8:50 —334. Homology modeling: Evaluation of loop modeling protocols. K. A. Rossi, C. A. Weigelt, S. R. Krystek Jr., A. Nayeem

9:15 —335. D2Score: A fully automated web server for the dihedral angle based analysis of protein structures. G. Ozer, J. Foley IV, S. Zhong, R. Hernandez

9:40 —336. Assessment of protein structures at the residue level using an entropic score of dihedral-angle correlation. S. Zhong, S. Quirk, R. Hernandez

10:05 — Intermission.

10:15 —337. Hinge-bending motion in S-adenosyl-L-homocysteine hydrolase: Mutagenesis, fluorescence and modeling. K. Kuczera, R. T. Borchardt, R. L. Schowen, C. K. Johnson, M. Wang, C. Hu

10:40 —338. Molecular modeling of the C-terminal end of human intestinal mucin (MUC2) predicts a cysteine-knot tertiary structure. V. D. Sadasivan, D. E. Budil, A. Sacco Jr, R. L. Carrier

11:05 —339. Prediction of Human DP Receptor Structure and Binding mode for prostanoid compounds. Y. Li, F. Zhu, N. Vaidehi, W. A. Goddard III

11:30 —340. Structural model of CCR5 for the discovery of entry inhibitors for the therapeutic intervention of HIV-1 infection. D. Das, K. Maeda, K. Tsuchiya, H. Mitsuya

 Section D

Georgia World Congress Center -- B307

General Oral - Molecular Mechanics and Simulation


J. D. Madura, Organizer
J. L. Gohres, Presiding

8:30 —341. Improved docking method for organics adsorbed in zeolite catalysts. S. S. Jirapongphan, J. Warzywoda, D. E. Budil, A. Sacco Jr.

8:55 —342. Integration of in-silico filters and computational quantum chemistry for structure based COX-II specific drug design and screening. R. R. Gupta, L. E. K. Achenie

9:20 —343. Modeling fragmentation reactions of gas-phase peptide-ions. C. R. Kinsinger, K. K. Irikura

9:45 —344. Molecular modeling of chemical warfare agents. G. K. Kamath, J. J. Potoff

10:10 — Intermission.

10:25 —345. Rapid and accurate evaluation of the electromagnetic response properties of noble metal nanoparticles. R. J. Hinde

10:50 —346. Reactive molecular dynamic approach to thermal decomposition of kerogen. E. Salmon, F. Lorant, F. Behar, P. Metzger, C. Largeau, A. C. van Duin, W. A. Goddard III

11:15 —347. Structural characterization of n-octanol and 3-octanol interfaces using molecular dynamic simulations. P. B. Moore, N. Z. Rao, R. L. Napoleon

11:40 —348. Optimization of ROMP poly(norbornene) as a catalyst support using molecular simulations. A. T. Swann, P. J. Ludovice

THURSDAY AFTERNOON

 Section A

Georgia World Congress Center -- B304

Structure Determination Using NMR and Computational Methods


J. P. Bowen, Organizer

1:30 —349. Computational chemistry with "MULTIMODE" and new strategies for ab initio potential energy surface . J. M. Bowman, B. Braams, S. Carter, X. Huang, Z. Jin, Z. Xie

2:00 —350. Structural features of hairpin triloops in rRNA in light of global conformational changes upon ligand binding. P. M. Mitrasinovic

2:30 —351. Molecular docking and analysis of interactions between vascular endothelial growth factor (VEGF) and SPARC protein. V. Chandrasekaran, E. W. Taylor, J. Ambati

3:00 —352. New NMR approaches to the structure of carbohydrates bound to proteins. J. H. Prestegard

3:30 —353. Recent developments and applications of the ONIOM Method. K. Morokuma

4:00 —354. Tautomerization states of pteridine analogs: Quantum mechanics calculations and 13C NMR studies. J. P. Bowen, H. Zhong

 Section B

Georgia World Congress Center -- B305

General Oral - Drug Discovery


W. D. Cornell, Organizer
P. C. D. Hawkins, Presiding

1:15 —355. Using shape, chemistry and electrostatics to identify bioisosteric fragments. A. G. Skillman, R. Tolbert, A. Nicholls

1:40 —356. A new way to find the needles in a haystack: Identify promising HTS hits in SAR-bearing clusters. S. F. Yan, H. Asatryan, J. Li, Y. Zhou

2:05 —357. QSAR Data cleansing with independent component analysis. C. M. Breneman, M. J. Embrechts, L. Han

2:30 —358. Reverse fingerprinting, multiple seed similarity searching and fingerprint bit importance. C. Williams

2:55 — Intermission.

3:05 —359. Computational target validation based on 3-D QSAR for antiparasitic leads. P. Athri, R. R. Tidwell, W. D. Wilson

3:30 —360. Spectrophore technology for fast and reliable virtual screening. W. Langenaeker, H. De Winter, G. Thijs, J. Taminau

3:55 —361. Structure and binding of glycopeptide antibiotics to bacterial cell wall analogs: Solvent and dimerization effects. J -G. Lee, C. Sagui, C. Roland

362. Withdrawn.

4:20 —363. STIMD: A grid-based method for accelerating the calculation of differences in binding free energies and its application to the binding of peptides to Src SH2 protein domains. P. W. Fowler, S. Jha, P. V. Coveney

 Section C

Georgia World Congress Center -- B306

General Oral - Quantum Chemistry


J. D. Madura, Organizer
C. L. Shukla, Presiding

1:30 —364. An application of QM-QSAR to predict and rationalize the refractive index of a wide variety of simple organic/organosilicon molecules. A. Holder, L. Ye, J. D. Eick, C. Chappelow

1:55 —365. Quantum mechanical structure-activity relationship to predict volume shrinkage. M. D. Miller, A. Holder, K. Kilway, C. Chappelow, J. D. Eick

2:20 —366. Effect of electron donating and withdrawing substituents on the ring stability of cyclobutadiene. M. W. Zakaria, S. J. Kirkby

2:45 —367. On the delocalization of electrons in donor-acceptor molecules. P. M. Mitrasinovic

3:10 — Intermission.

3:25 —368. Potential energy surface of cation-pi interaction: Quantum chemical studies. S. Dakshanamurthy

3:50 —369. On the accuracy of density functional theory for iron-sulfur clusters. R. K. Szilagyi, M. A. Winslow

4:15 —370. Quantum Monte Carlo studies of S4 conformer energetics. J. A. Harkless, J. S. Francisco

4:40 —371. To achieve stable spherical clusters: General principles and experimental confirmations. Z. Chen, S. Neukermans, X. Wang, E. Janssens, S. Roger E, R. B. King, P. V. R. Schleyer, P. Lievens

5:05 —372. Role of oxygen vacancies on growth of 1B (Au, Ag and Cu) particles on TiO2(110). D. Pillay, G. S. Hwang




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