#
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 Mller

-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. Gonzlez**

**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 Vill**

**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. Cedeo**, 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, B_{12}X _{12}^{n-}, 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 (*r*_{12}-) 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 P_{2}N_{2}: 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 SO_{2} 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/ CO_{2} 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 S_{N}2 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 GABA_{A} receptor. **X. Hong**, M. D. Krasowski, A. J. Hopfinger, N. L. Harrison

**196.** *Ab initio* calculations of atomization energies: The challenging species SO_{3} and SiF_{4}. **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. Vrnai**, 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. Herv 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. Herv du Penhoat

**2:40 — 279.** Conformational Dynamics of Hyaluronan in Solution. **A. Cesro**, 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**

The views and opinions expressed in this page are strictly those of the Division of Computers in Chemistry. The contents of this page have not been reviewed or approved by the American Chemical Society. Please address all comments and other feedback to the the COMP Division.