Andrew Pohorille Publications
Home Up

Publications 1978-1999 Andrew Pohorille

  1. ``Molecular orbital studies on the conformations of 8-amino- and 8-dimethylamino- adenosine 5'-monophosphate", A. Pohorille, D. Perahia, and B. Pullman, Biochim. Biophys. Acta 517 (1978), 511-516.
  2. ``Atomic dipole approximation and energies of interactions between purine and pyrimidine bases. I. Electrostatic inter- actions of adenine with uracil, thymine, thiouracils, dihydrouracil and fluorouracil", M. Geller, A. Jaworski, and A. Pohorille, Int. J. Quantum Chem. 15 (1979) 369-377.
  3. ``Tautomerism of pyrimidine bases - uracil, cytosine, and isocytosine: theoretical study with complete optimization of geometry", R. Czerminski, B. Lesyng, and A. Pohorille, Int. J. Quantum Chem. 16 (1979) 605-613.
  4. ``Tautomerism of oxopyridines and oxopyrimidines: theoretical study with complete optimization of geometry", R. Czerminski, B. Lesyng, and A. Pohorille, Int. J. Quantum Chem. 16 (1979) 1141-1148.
  5. ``Interactions batween nucleic acid bases and molecules of polar and nonpolar solvents", P. Cieplak, M. Geller and A. Pohorille, Proc. of the IV Congress of Polish Biophys. Soc., D. Tyrawska-Spychalowa and T. Wilczok Eds., Siedlce, Poland 1980, pp 7-22.
  6. ``Energy of planar autoassociation of xantine and spatial structure of poly(riboxantylic acid)", M. Geller, B. Lesyng and A. Pohorille, Int. J. Quantum Chem. 17 (1980), 293-298.
  7. ``Comparison of theoretical and experimental approaches to determination of conformation of nucleosides about the glycosidic bond", R. Stolarski, A. Pohorille, L. Dudycz and D. Shugar, Biochim. Biophys. Acta 610 (1980), 1-20.
  8. ``Protein backbone interaction with nucleic acid base pairs. A theoretical investigation", R.V. Hosur and A. Pohorille, Int. J. Quantum Chem. 20 (1981), 33-40.
  9. ``Interaction of the mutagenic base analogs O6-methylguanine and N4-hydroxycytosine with potentially complementary bases", A. Psoda, B. Kierdaszuk, A. Pohorille, M. Geller, J.T. Kusmierek and D. Shugar, Int. J. Quantum Chem. 20 (1981), 543-554.
  10. ``The influence of water on the stability of DNA base pairs", A. Pohorille, S. K. Burt, and R. D. MacElroy, Proc. of the First Symposium on Chemical Evolution and the Origin and Evolution of Life, D. L. DeVincenzi and L. G. Pleasant Eds., NASA 2276, Washington, 1982, p 67.
  11. ``Monte Carlo simulation of the influence of solvent on nucleic acid base associations", A. Pohorille, S. K. Burt, and R. D. MacElroy, J. Am. Chem. Soc., 106 (1984), 402-409.
  12. ``Solution influence on biomolecular equilibria: nucleic acid base associations", A. Pohorille, L. R. Pratt, S. K. Burt, and R. D. MacElroy, J. of Biomolecular Struct. and Dynamics, 1 (1984), 1257-1280.
  13. ``Base-pairing properties of O-methylated bases of nucleic acids; energetic and steric considerations", A. Pohorille and G. H. Loew, Biophys. Chem. 22 (1985), 37-51.
  14. ``Molecular dynamics test of the Brownian description of Na+ motion in water", M. A. Wilson, A. Pohorille, and L. R. Pratt, J. Chem. Phys. 83 (1985), 5832-5836.
  15. ``Molecular microenvironment: solvent interactions with nucleic acid bases and ions'', R. D. MacElroy and A. Pohorille, Proc. of the Second Symposium on Chemical Evolution and the Origin and Evolution of Life, D. L. DeVincenzi and P. A. Dufour Eds., NASA 2425, Washington, 1986, p 70.
  16. ``Theoretical methods for obtaining free energies of bio- molecular equilibria in aqueous solutions", A. Pohorille and L. R. Pratt in Methods of Enzymology vol 127 (1986), 64-78.
  17. "Molecular dynamics of ion motion is solution and near solution interfaces", M. A. Wilson, A. Pohorille and L. R. Pratt, Biophys. J. 49, p 1a. (1986).
  18. ``Properties of ionophore assisted ion transport across membranes'', B. Owenson, R. D. MacElroy, and A. Pohorille, Proceedings of the Symposium Three Decades of Life Science Research in Space, Washington, 1987, pp 266-268.
  19. ``Molecular dynamics of the water liquid-vapor interface", M. A. Wilson, A. Pohorille, and L. R. Pratt, J. Phys. Chem., 91, 4873-4878 (1987).
  20. ``Comparison of the structure of harmonic aqueous glasses and liquid water", A. Pohorille, L. R. Pratt, R. A. LaViolette, M. A. Wilson, and R. D. MacElroy, J. Chem. Phys., 87, 6070-6077 (1987).
  21. ``Effect of environment on organization and recognition in prebiotic systems'', A. Pohorille and R. D. MacElroy, Origins of Life 16, 504-505 (1987).
  22. ``Surface potential of the water liquid-vapor interface'', M. A. Wilson, A Pohorille, and L. R. Pratt, J. Chem. Phys. 88, 3281-3285, (1988).
  23. ``A molecular dynamics study of chloride binding by the cryptand SC24'', B. Owenson, R. D. MacElroy, and A. Pohorille, J. Mol. Struct., THEOCHEM, 179, 467-484, (1988).
  24. ``Molecular dynamics study of ion capture from water by a model ionophore, tetraprotonated cryptand SC24'', B. Owenson, R. D. MacElroy, and A. Pohorille, J. Am. Chem. Soc., 110 6992-7000, (1988)
  25. ``Interaction of a sodium ion with the water liquid-vapor interface'',M. A. Wilson, A. Pohorille, and L. R. Pratt, Chem. Phys., 129 209-212, (1989).
  26. ``Comment on study of the liquid-vapor interface of water'' ,M. A. Wilson, A. Pohorille, and L. R. Pratt, J. Chem. Phys., 90 5211-5213 (1989).
  27. ``Ions in aqueous solutions and at water interfaces - supercomputer simulation tests of basic theories'', A. Pohorille and R. D. MacElroy, Proceedings of the Fourth International Conference on Supercomputing, (L. Kartashev and S. Kartashev, eds.) International Supercomputing Institute, St. Petersburg Fla., 1989, 49-56.
  28. ``Cavities in molecular liquids and the theory of hydrophobic solubilities'', A. Pohorille and R. L.  Pratt, J. Am. Chem. Soc., 112 5066-5074 (1990).
  29. ``DNA dynamics in aqueous solution: opening the double helix'', A. Pohorille, W. S. Ross and I. Tinoco Int. J. of Supercomputer Applications, 4 81-96 (1990).
  30. ``Molecular dynamics of phenol at the liquid-vapor interface of water'', A. Pohorille and I. Benjamin, J. Chem. Phys., 94 5599-5605 (1991).
  31. ``Interaction of monovalent ions with the liquid-vapor interface of water: a molecular dynamics study'', M. Wilson and A. Pohorille, J. Chem. Phys., 95 6005-6013 (1991).
  32. ``Theory of hydrophobicity: transient cavities in molecular liquids'', L. R. Pratt and A. Pohorille Proc. Natl. Acad. Sci., 89 2995-2999 (1992).
  33. ``Computer folding of RNA molecules: a Monte Carlo method'', A. Pohorille, T. K. Nguyen and A. Waleh, in Biomedical Modeling and Simulation, J. Eisenfeld, M. Witten and D. S. Levine, eds., North Holland, Amsterdam, 1992, pp. 257-264.
  34. ``Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular dynamics study'', I. Benjamin and A. Pohorille, J. Chem. Phys. 98 236-242 (1993).
  35. ``Structure and energetics of model amphiphilic molecules at the Water liquid-vapor interface. A molecular dynamic study'', A. Pohorille and I. Benjamin, J. Phys. Chem., 97 2664-2670 (1993).
  36. ``Molecular structure of aqueous interfaces'', A. Pohorille and M. A. Wilson, J. Mol. Struct. (THEOCHEM), 284 271-298 (1993).
  37. ``Hydrophobic effect from cavity statistics'', L. R. Pratt and A. Pohorille, in Proceedings of the EBSA International Workshop on Water-Biomolecule Interactions, M. U. Palma, M. B. Palma-Vittorelli and F. Parak, eds., SIF, Bologna, 1993, pp 261-268.
  38. ``Structure of bilayer-water and monolayer-water interfaces: a molecular dynamics study'', A. Pohorille and M. A. Wilson, in Proceedings of the EBSA International Workshop on Water-Biomolecule Interactions, M. U. Palma, M. B. Palma-Vittorelli and F. Parak, eds., SIF, Bologna, 1993, pp 227-230.
  39. ``Isomerization reactions at aqueous interfaces'', A. Pohorille and M. A. Wilson, in Proceedings on the 26 Jerusalem Symposium on Quantum Chemistry and Biochemistry, Reaction Dynamics in Clusters and Condensed Phases, B. Pullman and R. Levine, eds., Kluwer, Dordrecht, 1994, pp 207-226.
  40. ``Molecular dynamics of a water - lipid bilayer interface'' M. A. Wilson and A. Pohorille, J. Am. Chem. Soc. 116, 1490-1501, (1994).
  41. ``Probing the structure of prebiotic ice'', M. A. Wilson, A. Pohorille, P. Jenniskens and D. Blake, Origins of Life and Evolution of Biosphere, 25, 3-19 (1995).
  42. ``Molecular dynamics studies of simple membrane-water interfaces: structure and functions in the beginnings of cellular life'', A. Pohorille and M. A. Wilson, Origins of Life and Evolution of Biosphere 25, 21-46 (1995).
  43. ``Scattering of Ne from the liquid-vapor interface of glycerol: a molecular dynamics study'', I. Benjamin, M. A. Wilson and A. Pohorille, J. Chem. Phys. 100, 6500-6507 (1994).
  44. ``Interaction of a model peptide with a water-bilayer system'', A. Pohorille and M. A. Wilson, in Aqueous Solutions - Structure, Energetics and Reactivity, ACS Symposium Series, C. Cramer and D. Truhlar, eds., ACS Books, Boca Raton, 1994, pp. 395-408.
  45. ``Scattering of water from the glycerol liquid-vapor interface'', I. Benjamin, M. A. Wilson, A. Pohorille and G. M. Nathanson, Chem. Phys. Lett. 243, 222-228 (1995).
  46. ``High-density amorphous ice, the frost on interstellar grains'', P. Jenniskens, D. F. Blake, M. A. Wilson and A. Pohorille, Astrophys. J. 455, 389-401 (1995).
  47. `` Molecular modeling of protocellular functions'', A. Pohorille, C. Chipot, M. H. New and M. A. Wilson in Pacific Symposium on Biocomputing, L. Hunter and T. E. Klein, eds., World Scientific, Singapore, 1996, pp. 550-569.
  48. `` Interactions of anesthetics with the membrane-water interface'', A. Pohorille, P. Cieplak and M. A. Wilson, Chem. Phys. 204, 337-345 (1996).
  49. ``Excess chemical potential of small solutes across water-membrane and water-hexane interfaces'', A. Pohorille and M. A. Wilson, J. Chem. Phys. 104, 3760-3773 (1996).
  50. ``Mechanism of unassisted ion transport across membrane bilayers'', M. A. Wilson and A. Pohorille, J. Am. Chem. Soc., 118, 6580-6587 (1996).
  51. ``An information theory model of hydrophobic interactions'', G. Hummer, S. Garde, A. E. Garcia, A. Pohorille and L. R. Pratt, Proc. Natl. Acad. Sci. USA, 93, 8951-8955 (1996).
  52. ``Interactions of anesthetics with the water-hexane interface. A molecular dynamics study'', C. Chipot, M. A. Wilson and A. Pohorille, J. Phys. Chem., 101, 782-791 (1997).
  53. ``Hypothesis: Inhaled anesthetics produce immobility and amnesia by different mechanisms at different sites'', E. I. Eger, D. D. Koblin, A. Harris, J. J. Kendig, A. Pohorille, M. J. Halsey and J. Trudell, Anesthesia and Analgesia, 84, 915-918 (1997)
  54. ``Adsorption and solvation of ethanol at the water liquid-vapor interface: A molecular dynamics study'', M. A. Wilson and A. Pohorille,  J. Phys. Chem.,  101, 3130-3135 (1997).
  55. ``Interaction of Alcohols and Anesthetics with the Water--Hexane Interface: a Molecular Dynamics Study'', A. Pohorille, M. A. Wilson and C. Chipot,  Prog. Colloid Polym. Sci.,  103 29-40 (1997).
  56. ``Structure and Dynamics of Small Peptides at Aqueous Interfaces.  A Multi-nanosecond Molecular Dynamics Study'', C. Chipot and A. Pohorille,  J. Mol. Struct. (THEOCHEM),  398 529-535 (1997).
  57. ``Conformational equilibria of terminally blocked single amino acids at the water-hexane interface. A molecular dynamcs study'' C. Chipot and A. Pohorille,  J. Phys. Chem.,  102 281-290 (1997).
  58. ``Transient cavities in liquids and the nature of the hydrophobic effect'', A. Pohorille,  Polish J. Chem.,  72 1680-1690 (1998)
  59. ``The development/application of a ``minimalist'' organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data'', P. Kollman, R. Dixon, W. Cornell, T. Fox, C. Chipot and A. Pohorille, in  Computer simulation of biomolecular systems: Theoretical and experimental applications (Van Gunsteren, W. F. and Weiner, P. K., eds.), Escom, The Netherlands, 1997, pp 83-96.
  60. ``Concentrations of anesthetics across the water-membrane interface; the Meyer-Overton hypothesis revisited'', Pohorille, A; Wilson, MA; New, MH; Chipot, C.,  Toxicology Lett.  101 421-430 (1998).
  61. ``Phenomena at aqueous interfaces'', A. Pohorille,  The Encyclopedia of Computational Chemistry, Schleyer, P. v. R.; Allinger, N. L., Clark, T.; Gasteiger, J.; Kollman, P. A.; Schaefer III, H. F.; Schreiner, P. R. (Eds.); John Wiley & Sons: Chichester, 1998, pp. 30-44.
  62. ``Folding and translocation of the undecamer of poly--L--leucine across the water--hexane interface'', C. Chipot and A. Pohorille,  J. Am. Chem.Soc., 120 11912-11924 (1998).
  63. ``Minimum Aleolar Anesthetic Concentration of Fluorinated Alkanols in Rats: Relevance to Theories of Narcosis'', E. I. Eger, P. Ionescu, M. J. Laster, D. Gong, T. Hudlicky, J. J. Kendig, R. A. Harris, J. R. Trudell and A. Pohorille,  Anesth. Analg  88 867-76 (1999).
  64. ``Insights from Computer Simulations into the Interaction of Small Molecules with Lipid Bilayers'', A. Pohorille, M. H. New, K. Schweighofer and M. A. Wilson,  Curr. Topics in Membranes  48, 49-76 (1999).
  65. ``Interactions of Small Molecules and Peptides in Membranes'', A. Pohorille, M. A. Wilson, C. Chipot, M. H. New and K. Schweighofer, in  Computational Molecular Biology, (J. Leszczynski, Ed.), Elsevier, Amsterdam, 1999.
  66. ``Early Events in the Folding of an Amphiphatic Peptide: A Multi-nanosecond Molecular Dynamics Study'', C. Chipot, B. Maigret and A. Pohorille,  Proteins: Structure, Function, Genetics, in press.
  67. ``An Inherited Efficiencies Model of Non-genomic Evolution'', M. H. New and A. Pohorille,  Simulation Theory and Practice, submitted.
  68. ``Computer Simulation of Ion Channel gating: the M$_2$ Channel of Influenza-A Virus in a Lipid Bilayer'',  Biophys. J., submitted.