My research primarily concerns itself with the structure and dynamics of polar and ionic liquid systems. The laboratory interests are broad and range from the basic physics governing polar molecules in the liquid state to work that is aimed at elucidating the fundamental aspects of biomolecular conformational structure and dynamics in solution. Most of the work uses the tools of classical statistical mechanics where possible and quantum mechanics elsewhere.

One interest is in the area of the thermodynamics and structure of ionic solutions. We have recently consider the structural basis for the solubilities of various salts. We found that the nonlinear trends with respect to cation and anion size can be explained by the structure induced in the solvent by the ions at finite concentration. This work has been extended to the common ion effect and the solvation of conformationally flexible zwitterions.

The basic advances in theory and understanding of the liquid systems mentioned above have provided new insights into the microscopic mechanisms of conformational changes in small biologically interesting molecules. This is an exciting area of theoretical chemistry for which new approaches are being developed in this laboratory. We have analyzed the conformations of neurotransmitters and antiviral drug molecules in saline solution. New methods are being developed in the group to examine the free energy consequences of changing both functional sidechains and conformations near a substrate to study the elementary physical processes involved in binding and recognition. This work in molecular design provides several collaborating experimental groups with several new candidates for synthesis.

"Molecular Dynamics at a Constant pH," Supercomputer Applications and High Performance Computing 8 47-53 (1994); John Mertz and B.M. Pettitt.

"Peptide Conformations Are Restricted by Solution Stability", J. Phys. Chem, 99 1-2 (1995); John Perkyns and B.M. Pettitt.

" Salting in Peptides: Conformationally dependent solubilities and phase behavior of a tripeptide zwitterion in electrolyte solution," J. Am. Chem. Soc. 118, 1164-1172 (1996); John Perkyns, Y. Wang and B.M. Pettitt.

"The dependence of hydration free energy on solute size," J. Phys. Chem. 100, 1323-1329 (1996); John S. Perkyns and B.M. Pettitt.

"Salt effects on peptide conformers: A dielectric study of tuftsin," Biophysical J. 71 3022-3029 (1996); L. Yang, C.V. Valdeavella, H.D. Blatt and B. M. Pettitt.

"Ewald Artifacts in Liquid State Molecular Dynamics Simulations," by J. Chem. Phys. 105 4289-4293 (1996); Paul E. Smith and B. M. Pettitt.

"On the Presence of Rotational Ewald Artifacts in the Equilibrium and Dynamical Properties of a Zwitterionic Tetrapeptide in Solution," J. Phys. Chem. 101 3886-3890 (1997); Paul Smith, Herb Blatt and B. M. Pettitt.

"Environmentally Dependent Conformational Preferences of Peptides," J. Am. Chem. Soc. 119 8714-8715 (1997); Paul Smith, Herb Blatt and B. M. Pettitt.

"Computationally useful bridge diagram series for the structure and thermodynamics of Lennard-Jones fluids," Theo. Chem. Accounts 96 61-70 (1997); John Perkyns, and B. M. Pettitt.

"Experiment vs. Force Fields: DNA conformation from Molecular Dynamics Simulation," J. Phys. Chem. 101 7361-7363 (1997); Michael Feig and B. M. Pettitt.

"Protonation effects on the Equilibrium and Dynamical Properties of the Alanine Tetrapeptide," J. Phys. Chem. 101 7628-7634 (1997); Herb Blatt, Paul Smith, and B. M. Pettitt.

"Grand Canonical Ensemble Molecular Dynamics Simulations: Reformulation of Extended System Dyanmcis Approaches," J. Chem. Phys. 107 8594-8610 (1997); G. Lynch and B. M. Pettitt.

"Crystallographic Water Sites from a Theoretical Perspective" Structure, 6 1351-1354 (1998); M. Feig and B. M. Pettitt.

"Diffusion of Solvent around Biomolecular Solutes: a Molecular Dynamics SImulation Study," Biophysical J. 75 1-9 (1998); Vladimir Makarov, M. Feig, K.A. Andrews, and B. M. Pettitt.

"Characterizing Global Substates of Myoglobin" Structure 6 587-594 (1998); B. Kim Andrews, Tod Romo, James B. Clarage, B. M. Pettitt and George N. Phillips Jr.

"A Reexamination of the Virial Coefficients of the Lennard-Jones Fluid," T. Chem. Acc. 105 244-251 (2001); Kippi Dyer, J.S. Perkyns and B. M. Pettitt.

"Comparison of the Potentials of Mean Force for Alanine Tetrapeptide between Integral Equation Theory and Simulation" Biophysical Chemistry 78 113-126 (1999); N. Prabhu, J. Perkyns, H. Blatt, P. Smith and B.M. Pettitt.

) "Structure and Dynamics of alpha-MSH using DRISM Integral Equation theory and Stochastic Dynamics" Biopolymers, 50, 255-272 (1999); N.V. Prabhu, J.S. Perkyns and B. M. Pettitt.

"Modeling of alpha-MSH conformations with implicit solvent" Journal of Peptide Research, 54 394-407 (1999); N.V. Prabhu, J.S. Perkyns and B.M. Pettitt.

"Kirkwood-Buff Thermodynamics Derived from Grand Canonical Molecular Dyannmics and DRISM Calculations" Journal of Computational Physics, 151 , 135-145 (1999); G. Lynch, J.S. Perkyns and B.M. Pettitt.

"Crystallographic Water Sites from a Theoretical Perspective" Structure, 6 1351-1354 (1998); M. Feig and B. M. Pettitt.

"Sodium and Chlorine Ions as Part of the DNA Solvation Shell " Biophysical J. 77 1769-1781 (1999); Michael Feig, B. M. Pettitt.

"A perspective on `Volume and Heat of Hydration of Ions', Born M (1920) Z Phys 1:45", Theo. Chem. Accounts, 103 171-172 (2000); B. M. Pettitt.

"Residence times of water molecules in the hydration sites of myoglobin" Biophysical J. 79 2966-2974 (2000); V. Makarov, K. Andrews, P. Smith, and B. M. Pettitt .

"A comparison between simulation and Poisson-Boltzmann fields" Simulation and Theory of Electrostatic Interactions in Solution Eds. L.R. Pratt and G. Hummer, AIP Press, 411-416 (1999); B. M. Pettitt and C.V. Valdeavella.

"A Molecular Simulation Picture of DNA Hydration around A- and B-DNA" Biopolymers 48 199-209 1998:(2000); Michael Feig and B. M. Pettitt.

"Conformations of an Adenine Bulge in a DNA Octamer and its Influence on DNA Structure from a Molecular Dynamics Simulation", Biophys. J. 81 352 - 370 (2001); Michael Feig, Martin Zacharias and B. M. Pettitt.

"Thermodynamics of Association to a Molecule Immobilized in an Electric Double Layer" Chem. Phys. Let. 323 160- 166 (2000); Arnold Vainrub and B.M. Pettitt.

"A New Boundary Condition for Computer Simulations of Interfacial Systems" Chem. Phys. Let. 326 193 - 198 (2000); Ka-Yiu Wong and B.M. Pettitt.

"Semi grand canonical ensemble molecular dynamics simulation of BPTI" Chem. Phys. 258 405-413 (2000); G. Lynch and B.M. Pettitt.

"Spontaneous Formation of Structures on the Surface of DNA microarrays by an All-atom Molecular Dyanmics Simulation" Theo. Chem. Accounts (2001); Ka-Yiu Wong and B.M. Pettitt.

"Simulations of the Bis-Penicillamine Enkephalin in Sodium Chloride Solution: A Parameter Study" Biopolyymers 60 134-152 (2001); Gail Marlow and B. M. Pettitt

"Fine tuning function: Correlation of hinge domain interactions with functional dis- tinctions between LacI and PurR " Protein Science 11 778-794 (2002); Liskin Swint- Kruse, C. Larson, B. M. Pettitt and K.S. Matthews.

"Computationally useful bridge diagram series II. Diagrams in h-bonds," J. Chem. Phys. 116 9404-9413 (2002); John Perkyns, Kippi Dyer and B. M. Pettitt.

"Computationally useful bridge diagram series III. Lennard-Jones mixtures," J. Chem. Phys. 116 9413-9422 (2002); Kippi Dyer, John Perkyns, and B. M. Pettitt.

"Solvation and Hydration of Proteins and Nucleic acids: a Theoretical View of Simu- lation and Experiment" Accounts of Chemical Res. 35 376- 384 (2002); V. Makarov, B.M. Pettitt and M. Feig.

"Surface Electrostatic Effects in Oligonucleotide Microarrays: Control and Optimiza- tion of Binding Thermodynamics" Biopolymers (2003); A. Vainrub and B.M. Pet- titt.

"Coulomb Blockage of Hybridization in Two-Dimensional DNA Arrays" Phys. Rev. E 66, 41905 (2002); A. Vainrub and B.M. Pettitt.

"Simulation of the Bis-Penicillamine Enkephalin in Ammonium Chloride Solution:a comparison with Sodium Chloride" Biopolymers (2003); Gail E. Marlow and B. M. Pettitt.

Theoretical Considerations for the E±cient Design of DNA Arrays", in Biomedical Technology and Devices Handbook, Eds. James E. Moore Jr. and George Zouri- dakis CRC Press,14:1-12, 2003; Arnold Vainrub, Tong Bin Li, Yuriy Fofanov and B. M. Pettitt.

"A non-Watson-Crick Motif of Base-pairing On Surfaces for Untethered Oligonu- cleotides", Molecular Simulation 30, 121-129 (2004); Ka-Yiu Wong, Arnold Vainrub, Tom Powdrill, Michael Hogan, and B. M. Pettitt.

"Microscopic DNA Fluctuations are in accord with macroscopic DNA stretching elas- ticity without strong dependence on force field choice" NATO ASI Series: Metal Ligand Interactions Kluwer Academic Press, ed. N. Russo 193-204 (2003); John Marko, Michael Feig and B. M. Pettitt.

"Sensitive Quantitative Nucleic Acid Detection Using Oligonucleotide Microarrays", J. Am. Chem. Soc., 125, 7798-7799 (2003); Arnold Vainrub and B. M. Pettitt.

"Orientation of DNA on a surface from simulation", Biopolymers, 73, 570-578 (2004); Ka-Yiu Wong and B. M. Pettitt.

"Theoretical aspects of genomic variation screening using DNA microarrays", Biopoly- mers 73, 614-620 (2004); Arnold Vainrub and B. M. Pettitt.

"A fast solver for the Ornstein-Zernike Equations", J. Comp. Phys. 197/2 491-501 (2004); C.T. Kelly and B.M. Pettitt.

"A Statistical Thermodynamic Approach to the Chemical Activities in Two- Component Solutions", J. Phys. Chem. B 108, 2048-2055(2004); Joerg Roesgen, B. Montgomery Pettitt, John Perkyns, and David Wayne Bolen.

"Uncovering the basis of non-ideal behavior of biological molecules", Biochemistry 43(45), 14472-14484 (2004); Joerg Roesgen, B. M. Pettitt, David Wayne Bolen.

"On the Mechanism of association of nanoscopic solutes" J. Am. Chem. Soc. 127, 3556-3567 (2005); Niharendu Choudhury and B.M. Pettitt.

"Combined hopping-super exchange model of a hole transfer in DNA" Chem. Phys. Lett. 400(1-3), 47-53 (2004); V. D. Lakhno, V. B. Sultanas, B.M. Pettitt.

"DNA Saline Solutions Near Surfaces: Design Parameters of DNA Arrays" NATO Sci- ence Series Kluwer Academic Press, ed. D Henderson, M. Holovko and A. Trokhymchuk 206, 381-393 (2005); B.M. Pettitt, Arnold Vainrub, and Ka-Yiu Wong.

"Dynamics of water trapped between hydrophobic solutes" J. Phys. Chem. B 109, 6422-6429 (2005); Niharendu Choudhury and B.M. Pettitt.

"Local Density Profiles are Coupled to Solute Size and Attractive Potential for Nanoscopic Hydrophobic Solutes" Molecular Simulations 31, 457-463 (2005); Ni- harendu Choudhury, B.M. Pettitt.

"Simple Bond Length Dependence: A Correspondence Between Reactive Fluid The- ories" J. Chem. Phys. 122 (23) 236101/1-236101/2 (2005); Kippi M. Dyer, John S. Perkyns and B.M. Pettitt.

"Protein Folding, Stability and Solvation Structure in Osmolal Solutions" Biophys. J. 89, 29882997 (2005); Joerg Roesgen, B. M. Pettitt, David Wayne Bolen.

"Effective Density Terms in Proper Integral Equations" J. Chem. Phys. 123(20), 204512/1-204512/11 (2005); Kippi M. Dyer, John S. Perkyns and B.M. Pettitt.

The role of attractive forces on the dewetting of large hydrophobic solutes", Modelling Molecular Structure and Reactivity in Biological Systems Ed: Naidoo, K.J. Royal Society of Chemistry, Cambridge, UK, 49-57 (2006); Niharendu Choudhury and B.M. Pettitt.

"Electrostatics of DNA-DNA juxtapositions: Consequences for type II topoisomerase function" J. Phys. Cond. Matter, 18(14), S173-S185 (2006); Graham L. Randall, B. M. Pettitt, Gregory R. Buck, E. Lynn Zechiedrich.

"Enthalpy-Entropy contributions to the potential of mean force of nanoscopic hy- drophobic solutes" J. Phys. Chem. B, 110(16), 8459-8463(2006); Niharendu Choudhury and B.M. Pettitt.

"Force Field Comparisons of the Heat Capacity of Carbon Nanotubes", Mol. Simulation 32 839-848 (2006); Cliff Y. Guo, B.M. Pettitt, Lewis T. Wheeler.

" A Systematic Investigation of Theories of Transport in the Lennard-Jones Fluid", J. Chem. Phys. 126, 034502-1:10 (2007); Kippi Dyer, B. M. Pettitt, George Stell.

"An Analysis of the Molecular Origin of Osmolyte-dependent Protein Stability" Prot. Sci. 16, 733-743 (2007); Joerg Roesgen, B. M. Pettitt, David Wayne Bolen.

" An optimized theory for simple and molecular fluids", J. Chem. Phys. 126 124107- 1:9 (2007); M. Marucho and B. M. Pettitt.

"The Dewetting transition and the Hydrophobic Effect" Journal of the American Chemical Society, 129(15), 4848-4852 (2007); Niharendu Choudhury and B.M. Pettitt.

"Preferential Solvation in Urea Solutions at Different Concentrations: Properties from Simulation Studies" J. Phys. Chem. 111(19), 5233-5242 (2007); H. Kokubo and B. M. Pettitt.

"A Site-Renormalized Molecular Fluid Theory" J. Chem. Phys. 127(19), 194506/1- 194506/14(2007); Kippi M. Dyer, John S. Perkyns and B.M. Pettitt.

"An Angle Dependent Site-Renormalized Theory for the Conformations of n-butane in a simple °uid"Cond. Mat. Phys. 10 331-342 (2007); Kippi M. Dyer, John S. Perkyns, B.M. Pettitt and George Stell.

"Molecular basis of the near ideality of urea solutions"Biophysical J. 93, 3392-3407 (2007); H. Kokubo, Joerg Roesgen, David Wayne Bolen and B.M. Pettitt.

"Free Energy Calculations for DNA near surfaces using an Ellipsoidal Geometry", Comm. Phys. Comm. 3, 1117-1131 (2008); J. Ambia-Garrido, and B.M. Pettitt