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The Computers in Chemistry Division
Spring 2002 ACS Meeting Program

223rd ACS Meeting
Orlando FL
April 7-11, 2002

Final Program:

SUNDAY MORNING

Recent Advances in Electron Correlation Methodology
Coupled Cluster and Configuration Interaction Methods

Cosponsored with Division of Physical Chemistry
A. K. Wilson, Organizer

8:20 — Introductory Remarks.
8:40 — 1. Internally contracted multireference coupled cluster theory. Computer aided implementation of advanced electronic structure methods M. A. Nooijen
9:20 — 2. A locally correlated equation-of-motion coupled cluster approach for excited states of large molecules. T. D. Crawford, R. A. King
10:00 — Intermission.
10:15 — 3. New single- and multi-reference coupled-cluster methods for molecular potential energy surfaces and excited states. P. Piecuch, K. Kowalski, I. S. O. Pimienta
10:55 — 4. Simulation of electronic spectra using coupled-cluster methods. J. F. Stanton
11:35 — 5. Local Pseudospectral Multi-Reference Singles and Doubles Configuration Interaction. D. Walter, E. A. Carter

Rational Drug Design
M. R. Reddy, Organizer, Presiding

8:30 — 6. Solvation modeling for rational drug design. D. G. Truhlar, C. J. Cramer, J. D. Thompson, P. D. Winget, J. D. Xidos
9:05 — 7. Design, synthesis, and biological evaluation of novel angiogenesis inhibitors J. P. Bowen, S. Furness, T. P. Robinson, T. Ehlers, J. L. Arbiser, D. Goldsmith
9:40 — 8. Flexible ligand docking with GLIDE: evaluation of structure prediction performance and utility for virtual ligand screening. R. Friesner, T. A. Halgren, P. Shenkin, R. B. Murphy, J. Banks, H. Beard, J. Klicic, D. Mainz, J. Perry, T. F. Hendrickson
10:15 — 9. Changing the HTS process to increase the information content. F. K. Brown
10:50 — 10. Docking Study of Non-nucleoside Inhibitors of HIV-1 Reverse Transcriptase. Z. Zhou, M. Madrid, J. Madura
11:25 — 11. Rational discovery of asparagine synthetase inhibitors using computational methods. Y. Ding, N. G. J. Richards

Modeling Nucleic Acids
Integrating Structural and Sequence Data
N. Leontis, Organizer

8:40 — Introductory Remarks.
8:50 — 12. Use of isostericity matrices in the reverse folding of RNA. E. Westhof, B. Masquida
9:30 — 13. Isostericity matrices: A tool for comparative sequence analysis. N. Leontis, E. Westhof, J. Stombaugh
10:00 — 14. Integrated system for RNA analysis and visualization. H. M. Berman, J. D. Westbrook, H. Yang, E. Westhof, F. Jossinet, N. Leontis
10:30 — Intermission.
10:45 — 15. Statistically derived base pair stacking free energies for RNA folding. M. Zuker
11:15 — 16. Genetic determination of ribosomal RNA structure. P. R. Cunningham, H. D. Cho, K. Lee, M. Waddington, K. A. Baker, A. Sarayia, E. Laios

Enhanced Sampling Techniques in Molecular Dynamics and Monte Carlo Simulations
C. Simmerling and A. Roitberg, Organizer

8:40 — Introductory Remarks.
8:55 — 17. The generalized-ensemble approach for protein folding studies. U. H. E. Hansmann
9:35 — 18. Enhanced sampling of protein dynamics by conformational flooding simulations. J. D. Evanseck
10:00 — Intermission.
10:15 — 19. Generalized-ensemble algorithms: Enhanced sampling techniques for molecular simulations. Y. Okamoto
10:55 — 20. Enhancing sampling of biomolecules using novel variable transformations. G. J. Martyna, M. E. Tuckerman, Z. Zhu, K. Pihakari, S. Samuelson
11:35 — 21. Digital signal processing methods to analyze and enhance conformational change. J. W. Essex, S. C. Phillips, R. J. Gledhill, C. M. Edge

SUNDAY AFTERNOON

Recent Advances in Electron Correlation Methodology

Advanced Ab Initio Methodology

Cosponsored with Division of Physical Chemistry
A. K. Wilson, Organizer

1:30 — 22. Coupled cluster methods for high accuracy and bond-breaking. M. Head-Gordon
2:10 — 23. Describing multi-reference situations within a single-reference formalism: The Equation-of-Motion Spin-Flip model and its applications to diradicals. A. I. Krylov
2:50 — Intermission.
3:05 — 24. A model for electron correlation using Wigner intracules. P. M. W. Gill, N. A. Besley, D. P. O'Neill
3:45 — 25. Calculation of second-order Mšller

-Plesset energies for large molecules. P. Pulay, J. Baker, S. Saebo, K. Wolinski
4:25 — 26. Compact description of correlation using localized orbitals. L. Bytautas, J. Ivanic, K. Ruedenberg

Rational Drug Design

M. R. Reddy, Organizer

M. D. Erion, Presiding

1:30 — 27. Automated Design of High-Affinity, Drug-like Protein Inhibitors W. L. Jorgensen, J. Tirado-Rives
2:05 — 28. Computer Aided Drug Design Methods for Drug Discovery: Limitations and Advantages. M. R. Reddy, M. D. Erion
2:40 — 29. Ligand binding affinities from MD simulations. J. qvist
3:15 — 30. Ligand-binding landscapes: Conditions of necessity and sufficiency in the design of docking and scoring methods. C. L. Brooks III
3:50 — 31. Applications of sensitivity analysis and comparative sequence/structure analysis to designing specific protein kinase inhibitors. C. F. Wong, J. A. McCammon
4:25 — 32. De novo Design and Modeling of Selective Inhibitors of Pneumocystis carinii Dihydrofolate Reductase. W. T. Wipke, R. McClellan

Modeling Nucleic Acids - Thermodynamics and Modeling

N. Leontis, Organizer

1:30 — 33. Prediction of RNA secondary structure. D. H. Turner, S. J. Schroeder, M. E. Burkard, D. H. Mathews
2:10 — 34. DNA thermodynamic database and new algorithms for probe design. J. SantaLucia Jr.
2:40 — 35. Computer models of DNA four-way junctions. W. K. Olson, A. R. Srinivasan
3:10 — 36. Studies on the mechanism of migration of intrinsically curved DNA (A-TRACTS) through gels. U. mohanty, A. Spasic, J. F. Mohanty
3:40 — 37. Structure-based ligand design for RNA targets. T. Hermann

Enhanced Sampling Techniques in Molecular Dynamics and Monte Carlo Simulations

C. L. Simmerling and A. Roitberg, Organizer

1:30 — 38. Multiple Copy and Random Expulsion Molecular Dynamics as tools for exploring protein-ligand binding and unbinding. R. C. Wade, S. Luedemann, L. Ehrlich, P. Winn, B. Das
2:10 — 39. Protein structure refinement with molecular dynamics on a smoothed energy surface. C. L. Simmerling, V. Hornak
2:35 — 40. Rigorous classical-mechanical derivation of a multiple-copy algorithm for sampling statistical mechanical ensembles. R. A. Wheeler, C. A. Hixson
3:00 — Intermission.
3:15 — 41. Enhanced sampling and global optimization techniques for complex systems. J. E. Straub, T. Whitfield, I. Andricioaei
3:55 — 42. LES shows less restrictive fluorescent probes dynamics inside protein cavities. W. Nowak
4:20 — 43. Accelerated conformational sampling by combining Poisson-Boltzmann continuum solvent and self-guided forces: Application to folding of small protein domains. R. Luo

ADME/Tox Informatics

Theory

Cosponsored with Division of Chemical Information

MONDAY MORNING

Recent Advances in Electron Correlation Methodology
Density Functional Theory

Cosponsored with Division of Physical Chemistry
A. K. Wilson, Organizer

8:20 — 44. Electronic energy as a functional of the charge density and the nonlocal charge-density susceptibility. K. L. C. Hunt
9:00 — 45. Nondynamical correlation in Density-Functional Theory. A. D. Becke
9:40 — Intermission.
9:55 — 46. Energy density in density functional theory. K. Burke, F. Zahariev, J. Larkin, C. Bock
10:35 — 47. On the transferability of hybrid density functional. C. A. Gonzˆlez
11:05 — 48. Constructing the Kohn-Sham potential for orbital dependent functionals. S. V. Kuemmel

Symposium in Remembrance of Peter A. Kollman

W. L. Jorgensen and D. C. Spellmeyer,

Organizers

8:45 — 49. Introduction and Tribute. - Abstract Text not Available I. D. Kuntz
9:00 — 50. Growing-Up with Peter from Water Dimer to Biomolecular Simulations. W. L. Jorgensen
9:45 — 51. Radical Anions of DNA Base Pairs: A Tribute to Peter Kollman. - Abstract Text not Available H. F. Schaefer III
10:30 — Intermission.
10:40 — 52. Towards all-electron modeling of biological systems. K. M. Merz Jr.
11:25 — 53. Theory and modeling of protein-catalyzed decarboxylations. K. N. Houk

Tools for Exploring Potential Energy Surfaces for Chemical Reactions

H. B. Schlegel, Organizer

8:45 — 54. Using force field methods for locating transition structures. F. Jensen, P. T. Olsen
9:15 — 55. Isopotential searching for discovering chemical reactions. K. K. Irikura, R. D. Johnson III
9:45 — 56. Efficient and reliable geometry optimization for QM/MM methods. M. Frisch, T. Vreven, H. B. Schlegel, K. Morokuma
10:15 — 57. Examining complex processes and reactions: the Replica/Path method. B. R. Brooks, H. L. Woodcock, T. E. Cheatham III, X. Wu
10:45 — 58. Efficient algorithms to study chemical reactions with DFT. J. Andzelm, G. Fitzgerald, N. Govind, P. Sykes
11:15 — 59. Expanding quantum chemistry: density functional calculations with Gaussian orbitals and periodic boundary conditions. K. N. Kudin

Computers in Chemistry: General Contributions

L. M. Balbes, Presiding

8:30 — 60. Web-Enabled Innovation. D. Anthony
8:50 — 61. Computational investigation of chemical warfare agents to enhance modeling and simulation based test and evaluation of chemical defense commodities. T. J. Evans
9:10 — 62. Structural insights by molecular dynamics simulations on differential repair efficiency for ethano-dA vs. etheno-dA adducts by the human alkyladenine DNA glycosylase (AAG) A. B. Guliaev, B. Hang, B. Singer
9:30 — 63. A computational procedure to determine binding modes of adenine derivatives with cyclin dependent kinase 2. J. Shen, D. Borcherding
9:50 — 64. Atmospheric chemistry of a- and b-pinene. T. S. Dibble
10:10 — Intermission.
10:20 — 65. Biological Datamining with ALOFT. B. Wythoff, B. Alexander
10:40 — 66. Data pipelining for dynamic data integration in cheminformatics. M. Hahn
11:00 — 67. Development of database for head and neck cancer employing bioinformatics for drug development. B. K. Malik, M. Malik
11:20 — 68. Development of database for tuberculosis using bioinformatics for drug discovery. B. K. Malik, T. Kaur
11:40 — 69. Influence of point mutations on the structural stability of KIF investigated by MD simulation. B. Nick, I. N. Kastanja, J. Schweizer, F. Wortmann

ADME/Tox Informatics

Applications

Cosponsored with Division of Chemical Information

MONDAY AFTERNOON

Recent Advances in Electron Correlation Methodology

Density Functional Theory

Cosponsored with Division of Physical Chemistry
A. K. Wilson, Organizer

1:30 — 70. Construction of density functionals beyond the generalized gradient approximation. J. P. Perdew
2:10 — 71. DFT for transition metals, transition states and hydrogen bonds D. R. Salahub
2:50 — 72. Microscopic study of exchange-correlation functionals in DFT by using Green's function perturbation techniques. K. Peirs, D. Van Neck, M. Waroquier
3:20 — Intermission.
3:35 — 73. Understanding electron correlation. N. Handy
4:15 — 74. Accuracy of DFT calculations? K. Glassford, K. Stark, J. Andzelm, G. Fitzgerald
4:55 — 75. DFT based Effective Fragment Potential Method. I. Adamovic, M. S. Gordon

ACS COMP Division Symposium in Remembrance of Peter A. Kollman

W. L. Jorgensen and D. C. Spellmeyer, Organizer

1:30 — 76. Remembrance and New Advances. - Abstract Text not Available L. C. Allen
1:45 — 77. Pattern recognition and massively distributed computing. G. Richards
2:30 — 78. Computer modelling of ion extraction: from host-guest complexes to liquid-liquid interfaces and microemulsions. G. Wipff
3:15 — Intermission.
3:25 — 79. Sequence-dependent structure and flexibility of TATA elements. X. Qian, D. Strahs, T. Schlick
4:10 — 80. Amber and its associated force fields: an update. D. A. Case

Tools for Exploring Potential Energy Surfaces for Chemical Reactions

H. B. Schlegel, Organizer
G. E. Scuseria, Presiding

1:30 — 81. Geometry optimization and molecular dynamics in internal coordinates. P. Pulay, J. Baker, B. Paizs
2:00 — 82. From potential energy surfaces to chemical dynamics through reaction path Hamiltonian. J. M. Bofill Villˆ
2:30 — 83. Gradient fields and gradient extremals on potential energy surfaces. K. Ruedenberg, J. Sun, G. J. Atchity, S. S. Xantheas
3:00 — 84. Principal component analysis and related decomposition methods for the analysis of biomolecular dynamics trajectories. D. Strahs, D. Barash, X. Qian, T. Schlick
3:30 — 85. Long time scale simulations of transitions in and on the surface of solids. G. Henkelman, H. Jonsson

ADME/Tox Informatics

Predictive Models

Cosponsored with Division of Chemical Information

MONDAY EVENING

Sci Mix - COMP posters

R. A. Wheeler, Organizer

8:00 - 10:00

120, 127, 130, 144-147, 150, 152, 155-156, 160, 162, 167, 187, 195. See subsequent listings.

TUESDAY MORNING

Recent Advances in Electron Correlation Methodology

Basis Sets and CBS Limits

Cosponsored with Division of Physical Chemistry
A. K. Wilson, Organizer

8:20 — 86. Importance of subvalence correlation in Group I and II compounds --- a benchmark study. M. B. Sullivan, L. Radom, M. A. Iron, J. M. L. Martin
9:00 — 87. Almost linear extrapolations to the CCSD(T)/CBS limit. G. A. Petersson
9:40 — 88. Accurate basis sets with pseudopotentials: Correlation consistent basis sets for heavy elements and transition metals. K. A. Peterson
10:10 — Intermission.
10:25 — 89. Complete basis set estimates for benzene dimer and other weakly bound systems. C. D. Sherrill, M. O. Sinnokrot, E. F. Valeev
11:05 — 90. A multi-resolution approach to quantum chemistry. R. J. Harrison, G. I. Fann
11:45 — 91. A Comparison of Algorithms to Construct Sequences of Gaussian Basis Sets. S. Zhong, G. A. Petersson

Near-neighbor searching for lead follow-up: algorithms and descriptors

(first of two sessions)

R. S. Pearlman, Organizer

9:00 — Introductory Remarks.
9:05 — 92. Pharmacophoric 3D mill hashed fingerprints: Add another dimension to your similarity searching. A. Pozzan, A. Feriani, G. Tedesco, A. M. Capelli
9:35 — 93. Biological descriptors as alternatives to chemical descriptors. P. Beroza
10:05 — 94. Comparing fingerprint-based and distance matrix-based BCUT methods in lead identification and lead hopping: A case study. M. R. Lee, C. R. Sage
10:35 — Intermission.
10:50 — 95. The use of RECON/PEST software and electron density-derived descriptors for virtual high throughput database screening and refinement. N. Sukumar, C. M. Breneman, D. Zhuang, W. P. Katt, M. J. Embrechts, K. Bennett
11:20 — 96. Nearest neighbor and kernel regression using particle swarms. W. Cede–o, D. Agrafiotis

Carbohydrate Modeling

Cosponsored with Division of Carbohydrate Chemistry
S. Perez, Presiding

8:30 — Introductory Remarks.
8:35 — 97. MM4 force field for carbohydrates. N. L. Allinger
9:10 — 98. Density functional/ab initio study of mono- and pentahydrates of a- and b-D-glucopyranose. F. A. Momany, G. Strati, J. L. Willett
9:45 — 99. Increasing the accuaracy of normal mode analysis: The SPASIBA spectroscopic force field introduced into the CHARMM program and the modeling of the structure and dynamics of carbohydrates. G. Vergoten
10:20 — Intermission.
10:35 — 100. Ab Initio quantum mechanics studies of trehalose. A. D. French, A. Kelterer, G. P. Johnson, E. D. Stevens, C. J. Cramer
11:10 — 101. Molecular modeling of catalytic mechanism of inverting and retaining glycosyltransferases. I. Tvaroska, I. Andre, J. P. Carver
11:45 — 102. Calculation of solvation energies and enzyme dynamics for carbohydrates. D. G. Truhlar, C. J. Cramer, J. D. Thompson, P. D. Winget, J. D. Xidos, J. Gao, M. Garcia-Viloca

TUESDAY AFTERNOON

ACS Award for Computers in Chemical and Pharmaceutical Research

P. Gund, Presiding

1:30 — Introductory Remarks.
1:45 — 103. Secondary structural propensities versus tertiary contact-assisted secondary structure formation in the folding of proteins. V. Daggett
2:25 — 104. Simple model of water, the hydrophobic effect, and ion solvation K. A. Dill, N. Southall, T. Truskett, B. Hribar, K. Silverstein, A. Haymet, V. Vlachy
3:05 — 105. Peptoids: a new class of abiological folded molecules. F. E. Cohen
3:45 — Intermission.
3:55 — 106. Structure-based inhibitor design and discovery against Beta-Lactamase. B. Shoichet
4:35 — 107. Punch cards and how they grew. I. D. Kuntz

Computers in Chemistry: General Contributions

J. D. Evanseck, Presiding

1:30 — 108. Automatic force field parameterization. H. Sun
1:50 — 109. Computational studies of channel function in glutamine-dependent amidotransferases. X. Wang, A. E. Roitberg, N. G. J. Richards
2:10 — 110. DFT studies of Fe(III) and Mn(II)-containing complexes. T. Herz, S. N. Greene, N. G. J. Richards
2:30 — 111. Hydrogen on and in Ni(111): potential energy surfaces and acetylene hydrogenation. M. Mavrikakis, J. Greeley
2:50 — 112. Theoretical calculations of dissociative adsorption of methane on metal surfaces. G. Henkelman, H. Jonsson
3:10 — Intermission.
3:20 — 113. When force field parameters are not transferable. J. Goto, F. Sato, S. Hojo, H. Sun
3:40 — 114. Computational analysis of the origin of the disorder in a highly dipole parallel-aligned molecular crystal. R. Glaser, Z. Wu, M. Lewis
4:00 — 115. DFT study of anionic and neutral per-substituted twelve-vertex boron cage systems, B12X 12n-, n=2, 1, 0 M. L. McKee
4:20 — 116. Error analysis in density functional theory: Atomization energies. X. Wang, A. K. Wilson
4:40 — 117. Accurately solving the electronic Schrödinger equation of small atoms and molecules using the explicitly correlated (r12-) multi-reference averaged coupled-pair functional (MR-ACPF). R. J. Gdanitz

TUESDAY EVENING

Computers in Chemistry General Poster Session

R. A. Wheeler, Organizer

7:00 - 10:00

118. Web-Enabled Innovation. D. Anthony
119. Simulation Study of Instantaneous Heat Trace in Bubbling Fluidized Beds. K. R. Sharma PE
120. Simulation Study of Sputtering Process. K. R. Sharma PE
121. Nucleation, Particulation in Fluidized Bed Degasifier K. R. Sharma PE
122. Optimization of Heat Sink in SLSI. K. R. Sharma PE
123. Simulation Study of Gas Convection Effects and Eddy Movement of Packets for Intermediate Size Particles. K. R. Sharma PE
124. Bounded Expression for Particle Conduction using Hyperbolic Heat Wave Propagative Equation. K. R. Sharma PE
125. Test of the LANL2DZpd basis set using molecular electron affinities. C. E. Check, T. M. Gilbert, L. S. Sunderlin, K. C. Lobring
126. The split Monte Carlo method: Efficient sampling by separating long-range and short-range potential interactions. K. Bernacki, B. Hetenyi, B. J. Berne
127. On the Physical Origin of Blue-Shifted Hydrogen Bonds. X. Li, L. Liu, H. B. Schlegel
128. Theoretical assessment of catalytic and stereoselective influence of bis(oxazoline)-Cu(II) complexes upon Diels-Alder reactions. J. DeChancie, O. Acevedo, J. D. Evanseck
129. Predicting the genotoxicity of secondary and aromatic amines from molecular strucure. G. W. Kauffman, P. C. Jurs
130. RNA tectonics: Modular design and directional assembly of one-dimensional supramolecular arrays. B. Yard, N. B. Leontis, L. Nasalean, L. Jaeger
131. Simple molecular solids: New studies on di-t-butylbenzene and hexamethylbenzene. C. E. Nettles, D. H. Magers, E. J. Valente
132. Theoretical calculations of structures and energetics of P2N2: Potential high energy species. O. Kwon, P. M. Almond, Y. Kwon, M. L. McKee
133. Structures and binding energies of methyl tert-butyl ether-water complexes. P. Sawunyama, G. W. Bailey
134. Born Atomic Radii for Continuum Electrostatics Calculations of Nucleic Acids. N. K. Banavali, B. Roux
135. Computational study of hydrogen bonding in model cellobiose analogs at the B3LYP/6-311++G** level. G. L. Strati, J. L. Willett, F. A. Momany
136. Computer modeling of absorption kinetics of J-aggregates. J. Lopez, I. Struganova
137. Compounds selection and prioritization during lead identification: Which compounds to screen and in what order? M. Sud, M. Lee, J. Deckman, K. Holme, C. Sage
138. Library Design: R-Group ranking for favorable ADME characteristics. M. Sud, N. Hebert, C. Sage
139. Delivering drug discovery solutions to chemists at the desktop. M. Sud, K. Holme, C. Sage
140. Dipole moment derivatives for SO2 using density functional theory and wavefunction-based methods. P. J. Stimac, R. J. Hinde
141. Diverse library screening: The virtual becomes reality. K. O'Malley, J. Davies, D. France, W. D. Cornell
142. Virtual deconvolution of high throughput screening results on mixtures using docking and pharmacophore screening. K. Nam, R. Schweitzer, N. Tart-Risher, C. Schumacher, P. Marshall, W. D. Cornell
143. Homology Modeling and Discovery of Ligands via Virtual Screening with Protein Kinase Cz. S. Yan, M. C. Nicklaus, P. M. Blumberg, V. E. Marquez
144. Docking study of HDAC: Implication to inhibitor design. D. Wang, O. G. Wiest, P. Helquist
145. Protein conformational gate controlling binding site and migration for ubiquinone-B in the Rhodobacter sphaeroides photosynthetic reaction center. R. A. Wheeler, S. E. Walden
146. Classification of protein tyrosine phosphate 1B inhibitors and prediction of their antihyperglycemic activity from molecular structure. S. J. Patankar, P. C. Jurs
147. Feature selection and QSPR modeling: Non-linear PLS vs SVM. C. M. Breneman, F. Arciniegas, M. J. Embrechts, K. Bennett
148. Finding transition states using trajectories: Burning the wick from both ends. H. P. Hratchian, H. B. Schlegel
149. Hydrogen abstraction and oxygen addition in derivatives of 2-pyrrolidinone. M. L. Bagwell, D. H. Magers, C. W. Miller
150. Insights from theoretical simulations of the association of ion channel toxins with the potassium ion channel. S. Yang, K. S. Kim
151. Interaction between potassium cation (K+) with glycylglycine (glygly). C. H. S. Wong, I. N. L. Ma, C. W. Tsang
152. Molecular details of how ionic liquids influence chemical reactivity and stereoselectivity. O. Acevedo, J. D. Evanseck
153. Molecular dynamics of diffusion in water. G. L. Dempsey, J. L. Gainer
154. Molecular Dynamics Simulations of RNA motifs. K. Csaszar, N. Spackova, J. Sponer, N. B. Leontis
155. Molecular dynamics studies of interaction between crystals of calcium pyrophosphate dihydrate and phospholipid membranes. P. Dalal, A. Wierzbicki, J. D. Madura, H. S. Cheung
156. Potentials of mean force between charged aminoacid sidechains in aqueous solution. A. Masunov, T. Lazaridis
157. Recent advances of PC-Linux systems for electronic structure theories by the optimized compilers and numerical libraries. J. K. Yu, C. Yu
158. Folding kinetics of the hairpin ribozyme. M. M. Rhodes, N. G. Walter
159. H/D exchange in polypeptides: An ab initio direct dynamics study. J. E. Knox, H. B. Schlegel
160. Identification of a Putative MTP (Microsomal Triglyceride Transfer Protein) Ligand Binding Site Using Structural, Photo-Affinity and Computational Approaches A. M. Doweyko, J. K. Dickson, H. Jamil, C. Chu
161. Conformational analysis of (S,S)-dimethyldiketopyridino-18-crown-6 ether O. Lee Sr., D. Lee, D. S. Chung
162. Ligand distortions in chiral catalysts: Can molecular deformations enhance a catalyst's chirality content? S. Schefzick, K. B. Lipkowitz
163. Methanol adsorption on faujasitic petrochemical catalysts: an electronic embedded cluster study. S. Nokbin, T. N. Truong, J. Limtrakul
164. Model of a-helix electron channel in photosynthetic reaction center. Y. Song
165. Computational modeling of Brine/ CO2 sequestration. T. J. Dick, P. Dalal, J. D. Madura
166. Computer-simulated model of the copper-binding site of lysyl oxidase using extended systematic force field (ESFF) calculations. F. Ryvkin, F. T. Greenaway
167. From Biological Molecular Recognition to Subnanowires: A Theoretical Exploration of the Cation-p Interaction. E. C. Lee, J. C. Kim, Y. Kim, D. Kim, K. S. Kim
168. Extended Electron Correlations applied to self-consistent field semi-empirical calculations. E. C. M. Chen, E. S. Chen
169. Molecular dynamics and the Effective Fragment Potential method. H. M. Netzloff, M. S. Gordon, J. Sorenson
170. Computation of ring strain in azetidine, phosphetane, oxaphosphetane, and oxadiphosphetane K. E. Hand, D. H. Magers
171. Computational analysis of calcium coordination sites in cadherin adhesion molecules. N. C. Vosnidou, D. L. Worcester
172. Computational evidence for chlorine atom complexation in "noncomplexing " solvents. W. J. Kelly
173. Computational investigation of a metal-promoted SN2 reaction in the active site of the zinc-dependent protease carboxypeptidase A and its implication for the catalytic mechanism of the enzyme. J. B. Cross, S. Mobashery, H. B. Schlegel
174. Computational investigation of the solution-phase mechanism of nucleophilic substitution at sulfur. J. M. Hayes, S. M. Bachrach
175. Computational investigation of the stereochemistry of the addition of water to enoyl-CoA hydratase. D. Smith, S. Su
176. Extrapolating finite basis electronic structure calculations to the complete basis set limit: Does it work for potential energy curves? T. C. Lillestolen, R. J. Hinde
177. Fate of alkoxy radicals from oxygenated organics. T. S. Dibble, M. A. Ferenac, A. J. Davis, A. S. Holloway
178. Protein-ligand interaction scoring using TAE knowledge-based potentials. W. Deng, C. M. Breneman, A. Tropsha, J. Feng, M. D. Ryan
179. QSAR/QSPR analysis of large data sets using a fast variable selection approach based on k-nearest neighbor principle. Y. Xiao, M. Shen, A. Tropsha
180. QSPR analysis of human S9 metabolic turnover dataset using k-nearest neighbor method. M. Shen, Y. Xiao, A. Golbraikh, V. Gombar, A. Tropsha
181. QSPR studies using probabilistic neural networks and generalized regression neural networks. P. D. Mosier, P. C. Jurs
182. Theoretical Investigations of Self-Assembly in Organic Nanotubes. J. C. Kim, Y. Kim, E. C. Lee, K. S. Kim
183. Timings of SCF, DFT, and MP2 calculations on a Beowulf cluster M. B. Moore, D. H. Magers, M. Wiggins
184. Topology and force field parameters for retinoid p-conjugation. A. M. Waligorski, A. A. Nelson, I. Thorpe, J. D. Evanseck
185. Computer-aided prediction of activity spectra for substances (PASS). D. A. Filimonov, Y. V. Borodina, V. V. Poroikov
186. Ab initio Study of potential energy surface of five-member rings. J. Feng, M. H. Lambert, S. S. Young
187. Theoretical and experimental studies of mixed-valence complexes: Implications for molecular electronics. O. Wiest, S. B. Braun-Sand
188. FFGenerAtor 2.0 T. Strassner, M. Busold, H. Radrich
189. Effects of functional and basis set choice in the calculation of atomization energies of second-row compounds. X. Wang, A. K. Wilson
190. Anharmonic Franck-Condon Factor analysis and simulation of the Cl2O He I photoelectron spectrum. D. K. W. Mok, F. Chau, E. P. F. Lee, J. M. Dyke
191. A density functional theory study of the adsorption of bisulfate on small gold clusters. D. Bacelo, M. D. Legault
192. Accurate semiempirical functional: A new quantum era of computational biochemistry. V. M. Anisimov, N. Anikine, V. Bugaenko, V. Bobrikov, A. Andreyev
193. An embedded density functional study of Beckmann rearrangement mechanism on H-ZSM-5 catalyst. S. Jungsuttiwong, P. Khongpracha, J. Sirijaraensre, T. N. Truong, J. Limtrakul
194. 3D Structure generation based on distance geometry algorithm. K. Nakamura, N. Tomioka, A. Itai
195. 4D-QSAR analysis of a set of propofol analogs: Mapping binding sites for an anesthetic phenol on the GABAA receptor. X. Hong, M. D. Krasowski, A. J. Hopfinger, N. L. Harrison
196. Ab initio calculations of atomization energies: The challenging species SO3 and SiF4. J. J. Seals III, A. K. Wilson

WEDNESDAY MORNING

Tools for Exploring Potential Energy Surfaces for Chemical Reactions

H. B. Schlegel, Organizer

8:45 — 197. Simulating Reactive Dynamics on Ab Initio PESs Without a Global Fit. M. R. Salazar
9:15 — 198. Exploring potential energy surfaces using interpolation and classical dynamics. M. A. Collins
9:45 — 199. Direct Dynamics Calculations. M. S. Gordon, H. Netzloff, P. N. Day, P. Bandyopadhyay, D. Fedorov
10:15 — 200. Sampling initial conditions for direct dynamics classical trajectory simulations. W. L. Hase, K. Song, L. Sun, O. Meroueh, C. Doubleday
10:45 — 201. Ab Initio Molecular Dynamics: Propagating the Density Matrix with Gaussian Orbitals. S. Iyengar
11:15 — 202. Multiconfigurational nuclear-electronic molecular orbital approach. S. Hammes-Schiffer, S. Webb, T. Iordanov

Rational Drug Design

M. R. Reddy, Organizer
T. Hendrickson, Presiding

8:30 — 203. Definition and characterization of topologically biased atom pair fingerprints. R. D. Clark, R. Dorfman, T. W. Heritage
9:00 — 204. Massive acceleration of virtual screening using distributed computing. D. W. Goddette
9:30 — 205. Informatic Approaches to Parallel Drug Discovery. M. Hansen, K. Richard, H. Villar
10:00 — 206. Enrichment: a new estimator of classification accuracy of QSAR models. A. Golbraikh, M. Shen, A. Tropsha
10:30 — 207. Pharmacophore Generation, Development, and Use in Drug Design - Accelerated Drug Discovery through prediction of Chemical reactivities A. Mehta, R. H. Dodd
11:00 — 208. Implementation of multiple binding modes in CoMFA. V. Lukacova, S. Balaz
11:30 — 209. Realistic receptor-site models. P. Baricic, M. Mackov, S. Balaz

Modeling Nucleic Acid - Force Fields and Electrostatics

N. Leontis, Organizer

9:00 — 210. Using polarizable force fields and implicit solvent models for DNA and RNA. D. A. Case
9:40 — 211. Recent developments in the CHARMM All-Atom Force Field for Nucleic Acids. N. K. Banavali, A. D. MacKerell
10:10 — 212. Molecular interactions of nucleic acid bases. From ab initio calculations to molecular dynamics simulations J. Sponer
10:40 — 213. Electrostatic modeling of the DNA double helix with counterion condensation theory. G. S. Manning, J. Ray

Carbohydrate Modeling - II

Cosponsored with Division of Carbohydrate Chemistry
I. Tvaroska, Presiding

8:40 — 214. Molecular dynamics simulations of carbohydrate solvation. J. W. Brady
9:15 — 215. Carbohydrate structure and reactivity from free energy surfaces. K. J. Naidoo
9:50 — 216. The anomeric equilibrium of carbohydrates: insights into molecular mechanics parameter transferability and solvation effects. C. L. Simmerling, P. A. Kollman
10:25 — Intermission.
10:40 — 217. Oligosaccharide binding site of b1,4-galactosyltransferases (Gal-Ts) defined by docking various glycan substrates in the binding site P. K. Qasba, B. Ramakrishnan, P. V. Balaji
11:15 — 218. Flexible docking of carbohydrates to proteins: Development and application of specific empirical free energy models. A. Laederach, P. M. Coutinho, P. J. Reilly

WEDNESDAY AFTERNOON

Tools for Exploring Potential Energy Surfaces for Chemical Reactions

H. B. Schlegel, Organizer
M. S. Gordon, Presiding

1:30 — 219. MP2 for Periodic Systems: Theory and Applications. G. E. Scuseria
2:00 — 220. Conical intersections and the spin-orbit interaction:A new dimension in conical intersections. D. R. Yarkony
2:30 — 221. First-principle Molecular Dynamic studies on the reaction pathways at T = 0 K and at finite-temperatures. A. Michalak, T. Ziegler
3:00 — 222. Photodissociation pathways of vinoxy radical: the usefulness of qualitative electronic structure analysis. K. Morokuma, D. V. Khoroshun
3:30 — 223. Exploring potential energy surfaces. H. B. Schlegel

Rational Drug Design

M. R. Reddy, Organizer
S. B. Singh, Presiding

1:30 — 224. Anti-HIV drug design based on a model of HIV-1 integrase complexed with viral DNA. Y. Tang, M. C. Nicklaus
2:00 — 225. Knowledge-Based 2D Structure Queries for Searching Protease Inhibitors. J. Shen, J. Hong, I. Morize
2:30 — 226. Structure-based design and discovery of novel inhibitors of protein tyrosine phosphatases. P. Huang, J. Ramphal, C. Liang, J. Wei, G. McMahon, C. Tang
3:00 — 227. Structure-assisted discovery of potent, orally effective antithrombotics active against factor Xa J. W. Liebeschuetz, L. Brady, S. Burkitt, N. P. Camp, A. P. A. Crew, J. Hargreaves, S. D. Jones, H. Martin, J. Mahler, A. Lyons, P. Morgan, C. W. Murray, S. Richards, B. Wazskowycz, K. Wilkinson, W. A. Wylie
3:30 — 228. Optimization of zinc parmaters for AUTODOCK studies of MMP inhibitors. X. Hu, W. H. Shelver
4:00 — 229. Structural model for Mycobacterium tuberculosis GFAT: Evidence for an ammonia channel and implications for drug discovery. T. C. Cordova de Sintjago, N. G. J. Richards
4:30 — 230. Shape-based denovo Drug Design. W. T. Wipke, Z. Wang

Modeling Nucleic Acid - Molecular Dynamics and Related Methods

N. Leontis, Organizer

1:30 — 231. Structural genomics based on molecular dynamics simulations of DNA bending and flexibility. D. L. Beveridge, K. M. Thayer
2:00 — 232. Structure and dynamics of nucleic acid solvation shells viewed by molecular dynamics simulations. P. Auffinger, E. Westhof
2:30 — 233. Monte Carlo simulations of DNA helix-coil transitions. J. I. Siepmann, J. Lee
3:00 — 234. Base flipping in DNA double helix. P. V‡rnai, E. Giudice, R. Lavery

Enhanced Sampling Techniques in Molecular Dynamics and Monte Carlo Simulations

C. L. Simmerling and A. Roitberg, Organizer

1:40 — 235. Counting Sequences that Fit. R. Elber
2:20 — 236. Mixing Monte Carlo moves more efficiently with an evolutionary algorithm. B. Leblanc, H. Toulhoat, E. Lutton, B. Braunnschweig
2:45 — 237. A novel stochastic search method finds global minima and low-energy populations. A. Goldblum, M. Glick, A. Rayan, B. Gorelik, G. Brinker
3:10 — Intermission.
3:25 — 238. Accelerated molecular dynamics methods. A. F. Voter, F. Montalenti, T. C. Germann, B. P. Uberuaga, J. A. Sprague
4:05 — 239. Monte Carlo studies of cystine-knot peptide structures. M. W. Deem

THURSDAY MORNING

Recent Advances in Electron Correlation Methodology

High Accuracy Approaches

Cosponsored with Division of Physical Chemistry
A. K. Wilson, Organizer

8:30 — 240. Quantifying quantum chemistry. T. H. Dunning Jr.
9:10 — 241. Explicitly correlated basis functions for large molecules. W. Klopper, C. C. M. Samson
9:50 — 242. Quantum chemical models for accurate thermochemistry: Recent advances. K. Raghavachari
10:30 — Intermission.
10:45 — 243. The determination of accurate equilibrium geometries. P. Jorgensen
11:25 — 244. Advances in the treatment of electron correlation in molecules: coupled-cluster theory and ab initio DFT. R. J. Bartlett

Near-neighbor searching for lead follow-up: algorithms and descriptors
(second of two sessions)

R. S. Pearlman, Organizer

8:45 — Introductory Remarks.
8:50 — 245. Comparing performance of descriptors and methods for combinatorial library design. E. Evensen, E. K. Bradley, C. Oshiro, R. V. Stanton, J. E. Eksterowicz, P. D. J. Grootenhuis
9:20 — 246. Focused-diverse library design: A novel algorithm based on receptor-relevant distances. R. S. Pearlman, K. M. Smith
9:50 — 247. Nearest neighbor approaches to classify drug-like compounds. K. P. Cross, P. E. Blower Jr., M. Fligner, J. Verducci
10:20 — Intermission.
10:35 — 248. Introduction of bias into K-optimizable dissimilarity selection. R. D. Clark, J. Kar, F. Soltanshahi
11:05 — 249. A novel similarity searching system based on the fusion of 2D fragments of different sizes. X. Chen, L. Alquier, C. H. Reynolds
11:35 — 250. Application of multiple-Y recursive partitioning methods to mining large databases. D. M. Roush, L. Zhang, T. P. Stockfisch, S. N. Rao

Carbohydrate Modeling - III

Cosponsored with Division of Carbohydrate Chemistry
D. A. Brant, Presiding

8:40 — 251. Theoretical calculations of NMR parameters in oligosaccharides using density functional theory: J-Couplings across flexible bonds. A. S. Serianni, I. Carmichael
9:15 — 252. Interpretation of NMR relaxation of oligosaccharides: Don't leave your theoretical toolbox at home. R. W. Pastor, R. M. Venable
9:50 — 253. Interplay between molecular simulations and NMR spectroscopy in the analysis of carbohydrate conformation and dynamics. G. Widmalm
10:25 — Intermission.
10:40 — 254. The combination of molecular modeling with residual dipolar coupling in NMR spectroscopy for conformations of complex oligosaccharides. C. A. Bush
11:15 — 255. Conformation of a nucleotide-sugar in solution and in an enzyme binding site. A. Imberty, P. Petrova, C. HervŽ du Penhoat, J. Koca
11:50 — 256. Conformational investigations of arabinofuranosides from mycobacteria. J. B. Houseknecht, C. S. Callam, P. R. McCarren, C. M. Hadad, T. L. Lowary

Computers in Chemistry: General Contributions

R. A. Wheeler, Organizer

8:50 — 257. Improved implicit solvation model for nonaqueous solvents. I. Park, Y. H. Jang, S. Hwang, D. S. Chung
9:10 — 258. Nitrosative adenine deamination: A theoretical study of the decomposition pathways of adeninediazonium ion. R. Glaser, B. Hodgen, S. Rayat
9:30 — 259. Novel measures of variability in multiple alignments as a basis for modeling 3D structures of G-protein coupled receptors. S. Cherno-Schwartz, A. Rayan, A. Goldblum
9:50 — 260. Novel software for evaluating multi-technique chemical information. E. G. Melanson, G. M. Banik
10:10 — 261. Semi-empirical calculations for the components of DNA, RNA and proteins E. S. Chen, E. C. M. Chen
10:30 — Intermission.
10:40 — 262. Software for physical property estimation with corresponding states group contribution method. C. Sun
11:00 — 263. The auxiliary field Monte Carlo method for ab initio electronic structure of molecules. R. Baer
11:20 — 264. Theoretical Investigation of the Bonding in the Ylides of Phosphorus. P. M. Mitrasinovic, R. L. Fulton
11:40 — 265. Theoretical study of phenylboronic acids as a source of phenyl anions. R. Glaser, N. Knotts

THURSDAY AFTERNOON

Recent Advances in Electron Correlation Methodology

Electronic Structure Advances and the Future

Cosponsored with Division of Physical Chemistry
A. K. Wilson, Organizer

1:30 — 266. Development and applications of the ONIOM method for accurate correlation calculations for large molecules. K. Morokuma, T. Vreven
2:10 — 267. New methods of including electron correlation in chemical reaction modeling. D. G. Truhlar, B. J. Lynch
2:50 — Intermission.
3:05 — 268. New Advances in Scalable Electronic Structure Methods. M. S. Gordon, Y. Alexeev, Z. Gan, M. W. Schmidt, R. A. Kendall, J. Ivanic, K. Ruedenberg
3:45 — 269. Current and future needs for improvement in electron correlation methodology: The industrial perspective. A. M. Chaka, R. D. Johnson III
4:25 — 270. Quantum chemistry in the twenty-first century. H. F. Schaefer III

Enhanced Sampling Techniques in Molecular Dynamics and Monte Carlo Simulations

C. L. Simmerling and A. Roitberg, Organizer

1:30 — 271. Replica exchange methods for simulating proteins. M. Feig, J. Karanicolas, Y. Z. Ohkubo, C. L. Brooks III
2:10 — 272. Atomic simulations of structural transformations in large peptides. A. E. Garcia, K. Y. Sanbonmatsu, T. Ghosh, S. Garde
2:50 — 273. Aggregation-volume-bias Monte Carlo simulations of nucleation phenomena. B. Chen, J. I. Siepmann, K. J. Oh, M. L. Klein
3:15 — Intermission.
3:30 — 274. Exploring free energy landscape of a beta-hairpin folding in water with Replica Exchange Method. R. Zhou, R. Germain, B. J. Berne
4:10 — 275. Modeling of diffusion in tight-fitting zeolite host-guest systems by Normal Mode Monte Carlo. S. C. Turaga, S. M. Auerbach
4:35 — 276. Computer simulations of molecular recognition using generalized-ensemble Monte Carlo methods. G. Verkhivker

Carbohydrate Modeling - IV

Cosponsored with Division of Carbohydrate Chemistry
A. Bush, Presiding

1:30 — 277. Modeling of Carbohydrate Macromolecules. D. A. Brant, D. J. Tobias, S. Jaud
2:05 — 278. Deciphering the molecular structures and interactions of pectic polysaccharides. S. Perez, M. Rodriguez-Carvajal, K. Mazeau, C. HervŽ du Penhoat
2:40 — 279. Conformational Dynamics of Hyaluronan in Solution. A. Cesˆro, S. Letardi, G. La Penna, A. Perico, E. Chiessi
3:15 — Intermission.
3:30 — 280. Hyaluronan - a dynamic perspective. A. Almond
4:05 — 281. Computational carbohydrate chemistry: Strengths, weaknesses and future Prospects R. J. Woods




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