Publications (continued)

 

[1] Conformational analysis part 8: A lanthanide-induced shift nmr investigation of the conformation of amiodarone derivatives.
Raymond J. Abraham, Paul E. Smith, Colette Deleuze, and Vincent Lo Gatto.
Mag. Res. Chem., 25:147-153, 1987.

[2] Charge calculations in molecular mechanics 4: A general method for conjugated systems.
Raymond J. Abraham and Paul E. Smith.
J. Comp. Chem., 9:288-297, 1987.

[3] Charge calculations in molecular mechanics 6: The calculation of partial atomic charges in nucleic acid bases and the electrostatic contribution to DNA base pairing.
Raymond J. Abraham and Paul E. Smith.
Nucleic Acids Res., 16:2639-2657, 1988.

[4] Conformational analysis part 14: A lanthanide-induced shift nmr analysis of indan-1-one and norcamphor.
Raymond J. Abraham, Derek J. Chadwick, Paul E. Smith, and Fernando Sancassan.
J. Chem. Soc. Perkin Trans. II, 1377-1384, 1989.

[5] Charge calculations in molecular mechanics 7: Applications to polar pi systems incorporating nitro, cyano, amino, C=S and thio substituents.
Raymond J. Abraham and Paul E. Smith.
J. Computer-Aided Mol. Des., 3:175-187, 1989.

[6] Conformational analysis 16: Conformational free energies in substituted piperidines and piperidinium salts.
Raymond J. Abraham, Craig J. Medforth, and Paul E. Smith.
J. Computer-Aided Mol. Des., 5:205-212, 1991.

[7] Charge calculations in molecular mechanics 8: Partial atomic charges from classical calculations.
Raymond J. Abraham, Guy H. Grant, Ian S. Haworth, and Paul E. Smith.
J. Computer-Aided Mol. Des., 5:2139, 1991.

[8] Simulation of the structure and dynamics of the bis(penicillamine) enkephalin zwitterion.
Paul E. Smith, Liem X. Dang, and B. Montgomery Pettitt.
J. Am. Chem. Soc., 113:67-73, 1991.

[9] Aspects of the design of conformationally constrained peptides.
Paul E. Smith, Fahad Al-Obeidi, and B. Montgomery Pettitt.
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] Molecular dynamics simulation of ions and water around triplex DNA.
V. Mohan, Paul E. Smith, and B. Montgomery Pettitt.
J. Phys. Chem., 97:12984-12990, 1993.

[21] Methods for the evaluation of long range forces in computer simulations of molecular systems.
Paul E. Smith and Wilfred F. van Gunsteren.
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] Computation of free energy in practice: Choice of approximations and accuracy limiting factors.
Wilfred F. van Gunsteren, Thomas C. Beutler, Franca Fraternali, Paul M. King, Alan E. Mark, and Paul E. Smith.
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] Predictions of free energy differences from a single simulation of the initial state.
Paul E. Smith and Wilfred F. van Gunsteren.
J. Chem. Phys., 100:577-585, 1994.

[24] Consistent dielectric properties of the simple point charge and extended point charge water models at 277 and 300K.
Paul E. Smith and Wilfred F. van Gunsteren.
J. Chem. Phys., 100:3169-3174, 1994.

[25] Translational and rotational diffusion of proteins.
>Paul E. Smith and Wilfred F. van Gunsteren.
J. Mol. Biol., 236:629-636, 1994.

[26] Convergence properties of free energy calculations: a-cyclodextrin complexes as a case study.
Alan E. Mark, Steven P. van Helden, Paul E. Smith, Lambert H. M. Janssen, and Wilfred F. van Gunsteren.
J. Am. Chem. Soc., 116:6293-6302, 1994.

[27] Modelling solvent in biomolecular systems.
Paul E. Smith and B. Montgomery Pettitt.
J. Phys. Chem., 98:9700-9711, 1994.

[28] When are free energy components meaningful?
Paul E. Smith and Wilfred F. van Gunsteren.
J. Phys. Chem., 98:13735-13740, 1994.

[29] Internal mobility of the basic pancreatic trypsin inhibitor in solution: A comparison of nmr spin relaxation measurements and molecular dynamics simulations.
>Paul E. Smith, Rene van Schaik, Thomas Szyperski, Kurt Wuethrich, and Wilfred F. van Gunsteren.
J. Mol. Biol., 246:356-365, 1995.

[30] Nanosecond dynamics and structure of a model DNA triple helix in salt water solution.
Samantha Weerasinghe, Paul E. Smith, V. Mohan, Yuen-Kit Cheng, and B. Montgomery Pettitt.
J. Am. Chem. Soc., 117:2147-2158, 1995.

[31] A generalized reaction field method for molecular dynamics simulations.
Ilario Tironi, Rene Sperb, Paul E. Smith, and Wilfred F. van Gunsteren.
J. Chem. Phys., 102:5451-5459,1995.

[32] Dielectric response of triplex DNA in ionic solution from simulations.
Liqiu Yang, Samantha Weerasinghe, Paul E. Smith, and B. Montgomery Pettitt.
Biophysical J., 69:1519-1527, 1995.

[33] Computer simulation of protein motion.
Wilfred F. van Gunsteren, Phillippe H. Huenenberger, Alan E. Mark, Paul E. Smith, and Ilario G. Tironi.
Comput. Phys. Comm., 91:305-319, 1995.

[34] Efficient Ewald electrostatic calculations for large systems.
>Paul E. Smith and B. Montgomery Pettitt.
Comput. Phys. Comm., 91:339-344, 1995.

[35] Reaction field effects on the simulated properties of liquid water.
Paul E. Smith and Wilfred F. van Gunsteren.
Mol. Simulation, 15:233-245, 1995.

[36] Structure and stability of a model py.pu.pu DNA triple helix with a GC-T mismatch by simulation.
Samantha Weerasinghe, Paul E. Smith, and B. Montgomery Pettitt.
Biochemistry, 34:16269-16278, 1995.

[37] Ewald artifacts in liquid state molecular dynamics simulations.
Paul E. Smith and B. Montgomery Pettitt.
J. Chem. Phys., 105:4289-4293, 1996.

[38] A simple two dimensional representation for the common secondary structural elements of polypeptides and proteins.
Paul E. Smith, Herb D. Blatt, and B. Montgomery Pettitt.
Proteins: Structure, Function, and Genetics, 27:227-234, 1997.

[39] On the presence of rotational Ewald artifacts in the equilibrium and dynamical properties of a zwitterionic tetrapeptide in aqueous solution.
Paul E. Smith, Herb D. Blatt, and B. Montgomery Pettitt.
J. Phys. Chem. B, 101:3886-3890, 1997.

[40] Environmentally dependent conformational preferences of peptides
Paul E. Smith, Herb D. Blatt, and B. Montgomery Pettitt.
 J. Am. Chem. Soc., 119:8714-8715, 1997.

[41] Protonation effects on the equilibrium and dynamical properties of the alanine tetrapeptide.
Herb D. Blatt, Paul E. Smith, and B. Montgomery Pettitt.
J. Phys. Chem. B, 101:7628-7634, 1997.

[42] Comparison of simulated and experimentally determined dynamics for a variant of the Lacl DNA-binding domain, NLac-P.
Liskin Swint-Kruse, Kathleen S. Mathews, Paul E. Smith, and B. Montgomery Pettitt.
Biophysical J., 74:413-421, 1998.

[43] Review of "Statistical Mechanics for Chemists" by Jerry Goodisman.
Paul E. Smith.
J. Am. Chem. Soc., 120:4055-4056, 1998.

[44] Computer simulation of cosolvent effects on hydrophobic hydration.
Paul E. Smith.
J. Phys. Chem. B, 103:525-534, 1999.

[45] Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation.
Ninad V. Prabhu, John S. Perkyns, Herb D. Blatt, Paul E. Smith, and B. Montgomery Pettitt.
Biophys. Chem., 78:113-126, 1999.

[46] The alanine dipeptide free energy surface in solution.
Paul E. Smith.
J. Chem. Phys., 111:5568-5579, 1999.

[47] Molecular dynamics simulations of nicotinamide adenine dinucleotide (NAD+).
Paul E. Smith and John J. Tanner.
J. Am. Chem. Soc., 121:8637-8644, 1999.

[48] Conformations of nicotinamide adenine dinucleotide (NAD+) in various environments.
Paul E. Smith and John J. Tanner.
J. Mol. Recognition, 13:27-34, 2000.

[49] Molecular dynamics simulations of the properties of cosolvent solutions.
Rajappa Chitra and Paul E. Smith.
J. Phys. Chem. B, 104:5854-5864, 2000.

[50] Residence times of water molecules in the hydration sites of myoglobin.
Vladimir A. Makarov, B. Kim Andrews, Paul E. Smith, and B. Montgomery Pettitt.
Biophysical  J., 79:2966-2974, 2000.

[51] Properties of 2,2,2-trifluoroethanol and water mixtures.
Rajappa Chitra and Paul E. Smith.
J. Chem. Phys., 114:426-435, 2001.

[52] A comparison of the properties of 2,2,2-trifluoroethanol and 2,2,2-trifluoroethanol/water mixtures using different force fields.
Rajappa Chitra and Paul E. Smith.
J. Chem. Phys., 115: 5521-5530, 2001.

[53] Preferential interactions of cosolvents with hydrophobic solutes.
Rajappa Chitra and Paul E. Smith.
J. Phys. Chem. B, 105:11513-11522, 2001.

[54] Molecular associations in solution: A Kirkwood-Buff analysis of sodium chloride, ammonium sulfate, guanidinium chloride, urea and 2,2,2-trifluoroethanol in water.
Rajappa Chitra and Paul E. Smith.
J. Phys. Chem. B, 106:1491-1500, 2002.

[55] A conformational analysis of leucine enkephalin as a function of pH.
Mahalaxmi Aburi and Paul E. Smith.
Biopolymers, 64:177-188, 2002.

[56] A Structurally conserved water molecule in Rossmann dinucleotide-binding domains.
Christopher A. Bottoms, Paul E. Smith, and John J. Tanner.
Protein Sci., 11:2125-2137, 2002.

[57] The effects of internal water molecules on the structure and dynamics of chymotrypsin inhibitor 2.
Hongxing Lei and Paul E. Smith.
J. Phys. Chem. B, 107:1396-1402, 2003.

[58] Cavity formation and preferential interactions in urea solutions: Dependence on urea aggregation.
Samantha Weerasinghe and Paul E. Smith.
J. Chem. Phys., 118:5901-5910, 2003.

[59] A Kirkwood-Buff derived force field for mixtures of urea and water.
Samantha Weerasinghe and Paul E. Smith.
J. Phys. Chem. B, 107:3891-3898, 2003.

[60] A Kirkwood-Buff derived force field for mixtures of acetone and water.
Samantha Weerasinghe and Paul E. Smith.
J. Chem. Phys., 118:10663-10670, 2003.

[61] A Kirkwood-Buff derived force field for sodium chloride in water.
Samantha Weerasinghe and Paul E. Smith.
J. Chem. Phys., 119:11342-11349, 2003.

[62] The role of the unfolded state in hairpin stability.
Hongxing Lei and Paul E. Smith.
Biophysical J., 85:3513-3520, 2003.

[63] A combined simulation and Kirkwood-Buff approach to quantify cosolvent effects on the conformational preferences of peptides in solution.
Mahalaxmi Aburi and Paul E. Smith.
J. Phys. Chem. B, 108:7382-7388, 2004.

[64] A Kirkwood-Buff derived force field for the simulation of aqueous guanidinium chloride solutions.
Samantha Weerasinghe and Paul E. Smith.
J. Chem. Phys., 121:2180-2186, 2004.

[65] Modeling and simulation of the Human Delta Opioid Receptor.
Mahalaxmi Aburi and Paul E. Smith.
Protein Science, 13:1997-2008, 2004.

[66] Local chemical potential equalization model for cosolvent effects on biomolecular equilibria.
Paul E. Smith.
J. Phys. Chem. B, 108:16271-16278, 2004.

[67] Cosolvent interactions with biomolecules: Relating computer simulation data to experimental thermodynamic data.
Paul E. Smith.
J. Phys. Chem. B, 108:18716-18724, 2004.

[68] Protein volume changes on cosolvent denaturation.
Paul E. Smith.
Biophys. Chem., 113:299-302, 2005.

[69] A Kirkwood-Buff derived force field for methanol and aqueous methanol solutions.
Samantha Weerasinghe and Paul E. Smith.
J. Phys. Chem. B, 109:15080-15086, 2005.

[70] NMR structure and dynamic studies of an anion binding, channel-forming heptapeptide.
Gabriel A. Cook, Robert Pajewski, Mahalaxmi Aburi, Paul E. Smith, Om Prakash, John M. Tomich and George W. Gokel.
J. Am. Chem. Soc., 128:1633-1638, 2006.

[71] Equilibrium dialysis data and the relationships between preferential interaction parameters in biological systems in terms of Kirkwood-Buff integrals.
Paul E. Smith.
J. Phys. Chem. B, 110:2862-2868, 2006.

[72] A Kirkwood-Buff derived force field for amides.
Myungshim Kang and Paul E. Smith.
J. Comput. Chem., 27:1477-1485, 2006.

[73] Chemical potential derivatives and preferential interaction parameters in biological systems from Kirkwood-Buff theory.<
Paul E. Smith.
Biophysical J., 91:849-856, 2006.

[74] Preferential interaction parameters in biological systems from Kirkwood-Buff theory and computer simulation.
Myungshim Kang and Paul E. Smith.
Fluid Phase Eq., 256:14-19, 2007.

[75] Simulated surface tensions of common water models.
Feng Chen and Paul E. Smith.
J. Chem. Phys., 126:221101, 2007.

[76] Recent applications of Kirkwood-Buff theory to biological systems.
Veronica Pierce, Myungshim Kang, Mahalaxmi Aburi, Samantha Weerasinghe and Paul E. Smith.
Cell Biochem. Biophys., 50:1-22, 2008.

[77] MspA Porin-Gold Nanoparticle Assemblies: Enhanced Binding through a Controlled Cysteine Mutation.
Raj Kumar Dani, Myungshim Kang, Mausam Kalita, Paul E. Smith, Stefan H. Bossmann and Viktor Chikan.
Nano Letts., 8:1229-1236, 2008.

[78] Theory and computer simulation of solute effects on the surface tension of liquids.
Feng Chen and Paul E. Smith.
J. Phys. Chem. B, 2008, in press.

[79] On the Theory of Solute Solubility in Mixed Solvents.
Paul E. Smith and Robert M. Mazo.
J. Phys. Chem. B, 112:7875-7884, 2008.

 [80] Kirkwood-Buff Theory of Four and Higher Component Mixtures.
Myungshim Kang and Paul E. Smith.
J. Chem. Phys., 128: 244511, 2008.