Publications (continued)

[1] Raymond J. Abraham, Paul E. Smith, Colette Deleuze, and Vincent Lo Gatto. Conformational analysis part 8: A lanthanide-induced shift nmr investigation of the conformation of amiodarone derivatives.
Mag. Res. Chem., 25:147-153, 1987.
 
[2] Raymond J. Abraham and Paul E. Smith.
Charge calculations in molecular mechanics 4: A general method for conjugated systems.
J. Comp. Chem., 9:288-297, 1987.
 
[3] Raymond J. Abraham and Paul E. Smith.
Charge calculations in molecular mechanics 6: The calculation of partial atomic charges in nucleic acid bases and the electrostatic contribution to DNA base pairing.
Nucleic Acids Res., 16:2639-2657, 1988.
 
[4] Raymond J. Abraham, Derek J. Chadwick, Paul E. Smith, and Fernando Sancassan.
Conformational analysis part 14: A lanthanide-induced shift nmr analysis of indan-1-one and norcamphor.
J. Chem. Soc. Perkin Trans. II, 1377-1384, 1989.
 
[5] Raymond J. Abraham and Paul E. Smith.
Charge calculations in molecular mechanics 7: Applications to polar pi systems incorporating nitro, cyano, amino, C=S and thio substituents.
J. Computer-Aided Mol. Des., 3:175-187, 1989.
 
[6] Raymond J. Abraham, Craig J. Medforth, and Paul E. Smith.
Conformational analysis 16: Conformational free energies in substituted piperidines and piperidinium salts.
J. Computer-Aided Mol. Des., 5:205-212, 1991.
 
[7] Raymond J. Abraham, Guy H. Grant, Ian S. Haworth, and Paul E. Smith.
Charge calculations in molecular mechanics 8: Partial atomic charges from classical calculations.
J. Computer-Aided Mol. Des., 5:2139, 1991.
 
[8] Paul E. Smith, Liem X. Dang, and B. Montgomery Pettitt.
Simulation of the structure and dynamics of the bis(penicillamine) enkephalin zwitterion.
J. Am. Chem. Soc., 113:67-73, 1991.
 
[9] Paul E. Smith, Fahad Al-Obeidi, and B. Montgomery Pettitt.
Aspects of the design of conformationally constrained peptides.
Meth. Enzymol., 202:411-436, 1991.
 
[10] Paul E. Smith and B. Montgomery Pettitt.
Effects of salt on the structure and dynamics of the bis(penicillamine) enkephalin zwitterion: A simulation study.
J. Am. Chem. Soc., 113:6029-6037, 1991.
 
[11] Paul E. Smith and B. Montgomery Pettitt.
Peptides in ionic solutions: A comparison of the Ewald and switching function techniques.
J. Chem. Phys., 95:8430-8441, 1991.
 
[12] Stephen D. O'Connor, Paul E. Smith, Fahad Al-Obeidi, and B. Montgomery Pettitt.
Quenched molecular dynamics simulations of tuftsin and proposed cyclic analogues.
J. Med. Chem., 35:2870-2881, 1992.
 
[13] Paul E. Smith and B. Montgomery Pettitt.
Amino acid side chain populations in aqueous and saline solution: Bis-penicillamine enkephalin.
Biopolymers, 32:1623-1629, 1992.
 
[14] Paul E. Smith, Roger M. Brunne, Alan E. Mark, and Wilfred F. van Gunsteren.
Dielectric properties of trypsin inhibitor and lysozyme from molecular dynamics simulations.
J. Phys. Chem., 97:2009-2014, 1993.
 
[15] Paul E. Smith, B. Montgomery Pettitt, and Martin Karplus.
Stochastic dynamics simulations of the alanine dipeptide using a solvent modified potential energy surface.
J. Phys. Chem., 97:6907-6913, 1993.
 
[16] John J. Tanner, Paul E. Smith, and Kurt L. Krause.
Molecular dynamics simulations and rigid body (TLS) analysis of aspartate carbamoyltransferase: Evidence for an uncoupled R state.
Protein Sci., 2:927-935, 1993.
 
[17] Paul E. Smith, Gail E. Marlow, and B. Montgomery Pettitt.
Peptides in ionic solutions: A simulation study of Bis-penicillamine enkephalin in sodium acetate solution.
J. Am. Chem. Soc., 115:7493-7498, 1993.
 
[18] V. Mohan, Paul E. Smith, and B. Montgomery Pettitt.
Evidence for a new spine of hydration: Solvation of DNA triple helices.
J. Am. Chem. Soc., 115:9297-9298, 1993.
 
[19] Paul E. Smith and Wilfred F. van Gunsteren.
The viscosity of SPC and SPC/E water at 277K and 300K.
Chem. Phys. Letts., 215:315-318, 1993.
 
[20] V. Mohan, Paul E. Smith, and B. Montgomery Pettitt.
Molecular dynamics simulation of ions and water around triplex DNA.
J. Phys. Chem., 97:12984-12990, 1993.
 
[21] Paul E. Smith and Wilfred F. van Gunsteren.
Methods for the evaluation of long range forces in computer simulations of molecular systems.
In W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, editors, Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Volume 2, pages 182-212. ESCOM, Leiden, 1993.
 
[22] Wilfred F. van Gunsteren, Thomas C. Beutler, Franca Fraternali, Paul M. King, Alan E. Mark, and Paul E. Smith.
Computation of free energy in practice: Choice of approximations and accuracy limiting factors.
In W. F. van Gunsteren, P. K. Weiner, and A. J. Wilkinson, editors, Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Volume 2, pages 315-348. ESCOM, Leiden, 1993.
 
[23] Paul E. Smith and Wilfred F. van Gunsteren.
Predictions of free energy differences from a single simulation of the initial state.
J. Chem. Phys., 100:577-585, 1994.
 
[24] Paul E. Smith and Wilfred F. van Gunsteren.
Consistent dielectric properties of the simple point charge and extended point charge water models at 277 and 300K.
J. Chem. Phys., 100:3169-3174, 1994.
 
[25] Paul E. Smith and Wilfred F. van Gunsteren.
Translational and rotational diffusion of proteins.
J. Mol. Biol., 236:629-636, 1994.
 
[26] Alan E. Mark, Steven P. van Helden, Paul E. Smith, Lambert H. M. Janssen, and Wilfred F. van Gunsteren.
Convergence properties of free energy calculations: a-cyclodextrin complexes as a case study.
J. Am. Chem. Soc., 116:6293-6302, 1994.
 
[27] Paul E. Smith and B. Montgomery Pettitt.
Modelling solvent in biomolecular systems.
J. Phys. Chem., 98:9700-9711, 1994.
 
[28] Paul E. Smith and Wilfred F. van Gunsteren.
When are free energy components meaningful?
J. Phys. Chem., 98:13735-13740, 1994.
 
[29] Paul E. Smith, Rene van Schaik, Thomas Szyperski, Kurt Wuethrich, and Wilfred F. van Gunsteren.
Internal mobility of the basic pancreatic trypsin inhibitor in solution: A comparison of nmr spin relaxation measurements and molecular dynamics simulations.
J. Mol. Biol., 246:356-365, 1995.
 
[30] Samantha Weerasinghe, Paul E. Smith, V. Mohan, Yuen-Kit Cheng, and B. Montgomery Pettitt.
Nanosecond dynamics and structure of a model DNA triple helix in salt water solution.
J. Am. Chem. Soc., 117:2147-2158, 1995.
 
[31] Ilario Tironi, Rene Sperb, Paul E. Smith, and Wilfred F. van Gunsteren.
A generalized reaction field method for molecular dynamics simulations.
J. Chem. Phys., 102:5451-5459,1995.
 
[32] Liqiu Yang, Samantha Weerasinghe, Paul E. Smith, and B. Montgomery Pettitt.
Dielectric response of triplex DNA in ionic solution from simulations.
Biophysical J., 69:1519-1527, 1995.
 
[33] Wilfred F. van Gunsteren, Phillippe H. Huenenberger, Alan E. Mark, Paul E. Smith, and Ilario G. Tironi.
Computer simulation of protein motion.
Comput. Phys. Comm., 91:305-319, 1995.
 
[34] Paul E. Smith and B. Montgomery Pettitt.
Efficient Ewald electrostatic calculations for large systems.
Comput. Phys. Comm., 91:339-344, 1995.
 
[35] Paul E. Smith and Wilfred F. van Gunsteren.
Reaction field effects on the simulated properties of liquid water.
Mol. Simulation, 15:233-245, 1995.
 
[36] Samantha Weerasinghe, Paul E. Smith, and B. Montgomery Pettitt.
Structure and stability of a model py.pu.pu DNA triple helix with a GC-T mismatch by simulation.
Biochemistry, 34:16269-16278, 1995.
 
[37] Paul E. Smith and B. Montgomery Pettitt.
Ewald artifacts in liquid state molecular dynamics simulations.
J. Chem. Phys., 105:4289-4293, 1996.
 
[38] Paul E. Smith, Herb D. Blatt, and B. Montgomery Pettitt.
A simple two dimensional representation for the common secondary structural elements of polypeptides and proteins.
Proteins: Structure, Function, and Genetics, 27:227-234, 1997.
 
[39] Paul E. Smith, Herb D. Blatt, and B. Montgomery Pettitt.
On the presence of rotational Ewald artifacts in the equilibrium and dynamical properties of a zwitterionic tetrapeptide in aqueous solution.
J. Phys. Chem. B, 101:3886-3890, 1997.
 
[40] Paul E. Smith, Herb D. Blatt, and B. Montgomery Pettitt.
Environmentally dependent conformational preferences of peptides
 J. Am. Chem. Soc., 119:8714-8715, 1997.
 
[41] Herb D. Blatt, Paul E. Smith, and B. Montgomery Pettitt.
Protonation effects on the equilibrium and dynamical properties of the alanine tetrapeptide.
J. Phys. Chem. B, 101:7628-7634, 1997.
 
[42] Liskin Swint-Kruse, Kathleen S. Mathews, Paul E. Smith, and B. Montgomery Pettitt.
Comparison of simulated and experimentally determined dynamics for a variant of the Lacl DNA-binding domain, NLac-P.
Biophysical J., 74:413-421, 1998.
 
[43] Paul E. Smith.
Review of "Statistical Mechanics for Chemists" by Jerry Goodisman.
J. Am. Chem. Soc., 120:4055-4056, 1998.
 
[44] Paul E. Smith.
Computer simulation of cosolvent effects on hydrophobic hydration.
J. Phys. Chem. B, 103:525-534, 1999.
 
[45] Ninad V. Prabhu, John S. Perkyns, Herb D. Blatt, Paul E. Smith, and B. Montgomery Pettitt. Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation.
Biophys. Chem., 78:113-126, 1999.
 
[46] Paul E. Smith.
The alanine dipeptide free energy surface in solution.
J. Chem. Phys., 111:5568-5579, 1999.
 
[47] Paul E. Smith and John J. Tanner.
Molecular dynamics simulations of nicotinamide adenine dinucleotide (NAD+).
J. Am. Chem. Soc., 121:8637-8644, 1999.
 
[48] Paul E. Smith and John J. Tanner.
Conformations of nicotinamide adenine dinucleotide (NAD+) in various environments.
J. Mol. Recognition, 13:27-34, 2000.
 
[49] Rajappa Chitra and Paul E. Smith.
Molecular dynamics simulations of the properties of cosolvent solutions.
J. Phys. Chem. B, 104:5854-5864, 2000.
 
[50] Vladimir A. Makarov, B. Kim Andrews, Paul E. Smith, and B. Montgomery Pettitt.
Residence times of water molecules in the hydration sites of myoglobin.
Biophysical  J., 79:2966-2974, 2000.
 
[51] Rajappa Chitra and Paul E. Smith.
Properties of 2,2,2-trifluoroethanol and water mixtures.
J. Chem. Phys., 114:426-435, 2001.
 
[52] Rajappa Chitra and Paul E. Smith.
A comparison of the properties of 2,2,2-trifluoroethanol and 2,2,2-trifluoroethanol/water mixtures using different force fields.
J. Chem. Phys., 115: 5521-5530, 2001.
 
[53] Rajappa Chitra and Paul E. Smith.
Preferential interactions of cosolvents with hydrophobic solutes.
J. Phys. Chem. B, 105:11513-11522, 2001.
 
[54] Rajappa Chitra and Paul E. Smith.
Molecular associations in solution: A Kirkwood-Buff analysis of sodium chloride, ammonium sulfate, guanidinium chloride, urea and 2,2,2-trifluoroethanol in water.
J. Phys. Chem. B, 106:1491-1500, 2002.
 
[55] Mahalaxmi Aburi and Paul E. Smith.
A conformational analysis of leucine enkephalin as a function of pH.
Biopolymers, 64:177-188, 2002.
 
[56] Christopher A. Bottoms, Paul E. Smith, and John J. Tanner.
A Structurally conserved water molecule in Rossmann dinucleotide-binding domains.
Protein Sci., 11:2125-2137, 2002.
 
[57] Hongxing Lei and Paul E. Smith.
Structure and dynamics of chymotrypsin inhibitor 2 by computer simulation.
J. Phys. Chem. B, 107:1396-1402, 2003.
 
[58] Samantha Weerasinghe and Paul E. Smith.
Cavity formation and preferential interactions in urea solutions: Dependence on urea aggregation.
J. Chem. Phys., 118:5901-5910, 2003.
 
[59] Samantha Weerasinghe and Paul E. Smith.
A Kirkwood-Buff derived force field for mixtures of urea and water.
J. Phys. Chem. B, 107:3891-3898, 2003.
 
[60] Samantha Weerasinghe and Paul E. Smith.
A Kirkwood-Buff derived force field for mixtures of acetone and water.
J. Chem. Phys., 118:10663-10670, 2003.
 
[61] Hongxing Lei and Paul E. Smith.
The role of the unfolded state in hairpin stability. Biophysical J., in press.
 
Hongxing Lei and Paul E. Smith.
Fast folding of a 3:5 b-hairpin by simulation in explicit solvent.
Eur. Biophys. J., submitted.
 
Samantha Weerasinghe and Paul E. Smith.
A Kirkwood-Buff derived force field for sodium chloride in water.
J. Chem. Phys., submitted.
 
Mahalaxmi Aburi and Paul E. Smith.
The effects of salt on the conformational preferences of leucine enkephalin in solution: A combined simulation and Kirkwood-Buff approach.
J. Phys. Chem. B, submitted.