1-Octanol/water partition coefficients of n-Alkanes from molecular simulations of absolute solvation free energies

Journal of Chemical Theory and Computation

Volumn 5, Issue 9, 2009, Pages 2436-2446

  Garrido, Nuno M ^a,b   Queimada, António J ^a   Jorge, Miguel ^a   Macedo, Eugénia A ^a   Economou, Ioannis G ^b  

^a UNIVERSITY OF PORTO   (Portugal)

^b INSTITUTE OF NANOSCIENCE AND NANOTECHNOLOGY   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84961979135     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct900214y     Document Type: Article

References (88)

1. Leo, A.; Hansch, C.; Elkins, D. Partition Coefficients and Their Uses. Chem. Rev. 1971, 71 (6), 525-616.
2. Hansch, C.; Leo, A.; Hoekman, D. Exploring QSAR:Hydrophobic, Electronic and Steric Constants. American Chemical Society:Washington, DC, 1995.
3. Sangster, J. Octanol-Water Partitioning Coefficients:Fundamentals and Physical Chemistry. John Willey & Sons:Chichester, U.K., 1997.
4. Perlovich, G.L.; Kurkov, S.V.; Kinchin, A.N.; Bauer-Brandl, A. Solvation and Hydration Characteristics of Ibuprofen and Acetylsalicylic Acid. AAPS PharmSciTech 2004, 6 (1), 1-9.
5. Hansch, C.; Leo, A.; Hoekman, D. Exploring QSAR:Fundamentals and Applications in Chemistry and Biology. American Chemical Society:Washington DC, 1995.
6. Betageri, G.V.; Rogers, J.A. Correlation of Partitioning of Nitroimidazoles in the Normal Octanol Saline and Liposome Systems with Pharmacokinetc Parameters and Quantitative Structure Activity Relationships (QSAR). Pharmaceut. Res. 1989, 6 (5), 399-403.
7. Yalkowsky, S.H. Solubility and Solubilization in Aqueous Media. Oxford University:Oxford, U.K., 1999.
8. Pinho, S.P.; Macedo, E.A. Solubility in Food, Pharmaceuticals, and Cosmetic Industries. In Developments and Applications in Solubility, Letcher, T.M., Ed. Royal Society of Chemistry:Cambridge, U.K., 2003; pp 309-326.
9. Hansch, C.; Fujita, T. ρ-π-σ analysis. A Method for the Correlation of Biological Activity and Chemical Structure. J. Am. Chem. Soc. 1964, 86 (8), 1616-1626.
10. Leo, A.J. Calculating log P(Oct) from Structures. Chem. Rev. 1993, 93 (4), 1281-1306.
11. Viswanadhan, V.N.; Ghose, A.K.; Singh, U.C.; Wendoloski, J.J. Prediction of Solvation Free energies of Small organic Molecules:Additive-constitutive models based on molecular fingerprints and atomic constants. J. Chem. Inf. Comput. Sci. 1999, 39 (2), 405-412.
12. Bodor, N.; Buchwald, P. Molecular Size Based Approach to Estimate Partition Properties for Organic Solutes. J. Phys. Chem. B 1997, 101 (17), 3404-3412.
13. Kamlet, M.J.; Doherty, R.M.; Abraham, M.H.; Marcus, Y.; Taft, R.W. Linear Solvation Energy Relationships 46:An Improved Equation for Correlation and Prediction of Octanol Water Partition Coefficients of Organic Nonelectrolytes (Including Strong Hydrogen-Bond Donor Solutes). J. Phys. Chem. 1988, 92 (18), 5244-5255.
14. Karelson, M. Molecular Descriptors in QSAR/QSPR. Wiley Interscience:New York, 2000.
15. Best, S.A.; Merz, K.M.; Reynolds, C.H. Free Energy Perturbation Study of Octanol/Water Partition Coefficients:Comparison with Continuum GB/SA Calculations. J. Phys. Chem. B 1999, 103 (4), 714-726.
16. Curutchet, C.; Orozco, M.; Luque, F.J. Solvation in Octanol:Parametrization of the Continuum MST Model. J. Comput. Chem. 2001, 22 (11), 1180-1193.
17. Westergren, J.; Lindfors, L.; Hoglund, T.; Luder, K.; Nordholm, S.; Kjellander, R. In Silico Prediction of Drug Solubility:1. Free Energy of Hydration. J. Phys. Chem. B 2007, 111 (7), 1872-1882.
18. Duffy, E.M.; Jorgensen, W.L. Prediction of Properties from Simulations:Free Energies of Solvation in Hexadecane, Octanol, and Water. J. Am. Chem. Soc. 2000, 122 (12), 2878-2888.
19. Orozco, M.; Luque, F.J. Theoretical Methods for the Description of the Solvent Effect in Biomolecular Systems. Chem. Rev. 2000, 100 (11), 4187-4225.
20. Bergstrom, C.A.S.; Norinder, U.; Luthman, K.; Artursson, P. Experimental and Computational Screening Models for Prediction of Aqueous Drug Solubility. Pharmaceut. Res. 2002, 19 (2), 182-188.
21. Glomme, A.; Marz, J.; Dressman, J.B. Comparison of a Miniaturized Shake-Flask Solubility Method with Automated Potentiometric Acid/Base Titrations and Calculated Solubilities. J. Pharm. Sci. 2005, 94 (1), 1-16.
22. Loftsson, T.; Hreinsdottir, D. Determination of Aqueous Solubility by Heating and Equilibration:A technical Note. AAPS PharmSciTech 2006, 7 (1), E1-E4.
23. Chen, X.Q.; Venkatesh, S. Miniature Device for Aqueous and Non-aqueous Solubility Measurements during Drug Discovery. Pharmaceut. Res. 2004, 21 (10), 1758-1761.
24. Jorgensen, W.; Briggs, J.; Contreras, M. Relative Partition Coefficients for Organic Solutes from Fluid Simulations. J. Phys. Chem. 1990, 94, 1683-1686.
25. Essex, J.W.; Reynolds, C.A.; Richards, W.G. Relative Partition Coefficients from Partition Functions:A Theoretical Approach to Drug Transport. Chem. Commun. 1989, (16), 1152-1154.
26. Jorgensen, W. Free Energy Calculations:A Breaktrough for Modeling Organic Chemistry in Solution. Acc. Chem. Res. 1989, 22, 184-189.
27. Shirts, M.R.; Pitera, J.W.; Swope, W.C.; Pande, V.S. Extremely Precise Free Energy Calculations of Amino Acid Side Chain Analogs:Comparison of Common Molecular Mechanics Force Fields for Proteins. J. Chem. Phys. 2003, 119 (11), 5740-5761.
28. Hess, B.; van der Vegt, N.F.A. Hydration Thermodynamic Properties of Amino Acid Analogues:A Systematic Comparison of Biomolecular Force Fields and Water Models. J. Phys. Chem. B 2006, 110 (35), 17616-17626.
29. Oostenbrink, C.; Villa, A.; Mark, A.E.; Van Gunsteren, W.F. A Biomolecular Force Field Based on the Free Enthalpy of Hydration and Solvation:The GROMOS ForceField Parameter sets 53A5 and 53A6. J. Comput. Chem. 2004, 25 (13), 1656-1676.
30. Shivakumar, D.; Deng, Y.; Roux, B. Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model. J. Chem. Theory Comput. 2009, 5 (4), 919-930.
31. Tomasi, J.; Persico, M. Molecular Interactions in Solution - an Overview of Methods Based on Continuous Distributions of the Solvent. Chem. Rev. 1994, 94 (7), 2027-2094.
32. Tieleman, D.P.; Marrink, S.J.; Berendsen, H.J.C. A Computer Perspective of Membranes:Molecular Dynamics Studies of Lipid Bilayer Systems. Biochim. Biophys. Acta, Rev. Biomembr. 1997, 1331 (3), 235-270.
33. Debolt, S.E.; Kollman, P.A. Investigation of Structure, Dynamics and Solvation in 1-Octanol and its Water-Saturated Solution:Molecular Dynamics and Free-Energy Perturbation Studies. J. Am. Chem. Soc. 1995, 117 (19), 5316-5340.
34. Shih, P.; Pedersen, L.G.; Gibbs, P.R.; Wolfenden, R. Hydrophobicities of the Nucleic Acid Bases:Distribution Coefficients from Water to Cyclohexane. J. Mol. Biol. 1998, 280 (3), 421-430.
35. Chen, B.; Siepmann, J.I. Microscopic Structure and Solvation in Dry and Wet Octanol. J. Phys. Chem. B 2006, 110 (8), 3555-3563.
36. MacCallum, J.L.; Tieleman, D.P. Structures of Neat and Hydrated 1-Octanol from Computer Simulations. J. Am. Chem. Soc. 2002, 124 (50), 15085-15093.
37. Chen, B.; Siepmann, J.I. Partitioning of Alkane and Alcohol Solutes between Water and (Dry or Wet) 1-Octanol. J. Am. Chem. Soc. 2000, 122 (27), 6464-6467.
38. Kollman, P. Free Energy Calculations -Applications to Chemical and Biochemical Phenomena. Chem. Rev. 1993, 93 (7), 2395-2417.
39. Kollman, P.A. Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules. Acc. Chem. Res. 1996, 29 (10), 461-469.
40. Jorgensen, W.L. The Many Roles of Computation in Drug Discovery. Science 2004, 303 (5665), 1813-1818.
41. Palmer, D.S.; Llinas, A.; Morao, I.; Day, G.M.; Goodman, J.M.; Glen, R.C.; Mitchell, J.B.O. Predicting Intrinsic Aqueous Solubility by a Thermodynamic Cycle. Mol. Pharmaceut. 2008, 5 (2), 266-279.
42. Ashbaugh, H.S.; Kaler, E.W.; Paulaitis, M.E. Hydration and Conformational Equilibria of Simple Hydrophobic and Amphiphilic Solutes. Biophys. J. 1998, 75 (2), 755-768.
43. Kaminski, G.; Duffy, E.M.; Matsui, T.; Jorgensen, W.L. Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom Model. J. Phys. Chem. 1994, 98, 13077-13082.
44. Mobley, D.L.; Dumont, E.; Chodera, J.D.; Dill, K.A. Comparison of Charge Models for Fixed-Charge Force Fields:Small-molecule Hydration Free Energies in Explicit Solvent. J. Phys. Chem. B 2007, 111 (9), 2242-2254.
45. Shirts, M.R.; Pande, V.S. Solvation Free Energies of Amino Acid Side Chain Analogs for Common Molecular Mechanics Water Models. J. Chem. Phys. 2005, 122 (13), 134508.
46. Slusher, J.T. Accurate Estimates of Infinite-dilution Chemical Potentials of Small Hydrocarbons in Water via Molecular Dynamics Simulation. J. Phys. Chem. B 1999, 103 (29), 6075-6079.
47. Wescott, J.T.; Fisher, L.R.; Hanna, S. Use of Thermodynamic Integration to Calculate the Hydration Free Energies of n-alkanes. J. Chem. Phys. 2002, 116 (6), 2361-2369.
48. Christophe Chipot; Pohorille, A. Free Energy Calculations -Theory and Applications in Chemistry and Biology. Springer:Berlin, Germany, 2007.
49. Wolfenden, R.; Andersson, L.; Cullis, P.M.; Southgate, C.C.B. Affinities of Amino Acid Side Chains for Solvent Water. Biochemistry 1981, 20 (4), 849-855.
50. Ben-Naim, A.; Marcus, Y. Solvation Thermodynamics of Nonionic Solutes. J. Chem. Phys. 1984, 81 (4), 2016-2027.
51. Leach, A., Molecular Modeling:Principles and Applications. Prentice-Hall:2001.
52. Kirkwood, J.G. Statistical Mechanics of Pure Fluids. J. Chem. Phys. 1935, 3, 300-313.
53. Van der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A.E.; Berendsen, H.J.C. GROMACS:Fast, Flexible, and Free. J. Comput. Chem. 2005, 26 (16), 1701-1718.
54. Spoel, D.L., E.; Hess, B.; Buuren, A.; Apol, E.; Meuulenhof, P.; Tieleman, D.; Sijbers, A.; Feenstra, K.; Drunen, R.; Berendsen, H. Gromacs User Manual -Version 3.3. The Netherlands, 2006.
55. van Gunsteren, W.F.; Berendsen, H.J.C. A Leap-frog Algorithm for Stochastic Dynamics. Molec Sim. 1988, 1 (3), 173-185.
56. Berendsen, H.J.C.; Postma, J.P.M.; Vangunsteren, W.F.; Dinola, A.; Haak, J.R. Molecular Dynamics with Coupling to an External Bath. J. Chem. Phys. 1984, 81 (8), 3684-3690.
57. Liu, D.C.; Nocedal, J. On the Limited Memory BFGS Method for Large Scale Optimization. Math. Program. 1989, 45 (3), 503-528.
58. Chapra, S.; Canale, R. Numerical Methods for Engineers, 5th ed.; McGraw-Hill:New York, USA, 2006.
59. Beuler, T., M. R.; van Schaik, R.C.; Gerber, P.R.; van Gunsteren, W.F. Avoiding Singularities and Numerical Instabilities in Free Energy Calculations based on Molecular Simulations. Chem. Phys. Lett. 1994, 222, 529-539.
60. Pitera, J.W.; Van Gunsteren, W.F. A Comparison of Nonbonded Scaling Approaches for Free Energy Calculations. Mol. Simul. 2002, 28 (1-2), 45-65.
61. van Gunsteren, W.F.; Billeter, S.R.; Eising, A.A.; Hünenberger, P. H.; Krüger, P.; Mark, A.E.; Scott, W.R.P.; Tironi, I.G. Biomolecular Simulation:GROMOS96 Manual and User Guide;. Vdf Hochschulverlag AG an der ETH Zürich: Zürich, Switzerland, 1996.
62. Jorgensen, W.L. Optimized Intermolecular Potential Functions for Liquid Alcohols. J. Phys. Chem. 1986, 90 (7), 1276-1284.
63. Jorgensen, W.L.; Madura, J.D.; Swenson, C.J. Optimized Intermolecular Potential Functions for Liquid Hydrocarbons. J. Am. Chem. Soc. 1984, 106 (22), 6638-6646.
64. Jorgensen, W.L.; Maxwell, D.S.; Tirado-Rives, J. Development and Testing of the OPLS All-atom Force Field on Conformational Energetics and Properties of Organic Liquids. J. Am. Chem. Soc. 1996, 118 (45), 11225-11236.
65. Chen, B.; Potoff, J.J.; Siepmann, J.I. Monte Carlo Calculations for Alcohols and their Mixtures with Alkanes. Transferable Potentials for Phase Equilibria. 5. United-atom description of Primary, Secondary, and Tertiary Alcohols. J. Phys. Chem. B 2001, 105 (15), 3093-3104.
66. Martin, M.G.; Siepmann, J.I. Transferable Potentials for Phase Equilibria. 1. United-atom description of n-Alkanes. J. Phys. Chem. B 1998, 102 (14), 2569-2577.
67. Martin, M.G.; Siepmann, J.I. Novel Configurational-bias Monte Carlo Method for Branched Molecules. Transferable Potentials for Phase Equilibria. 2. United-atom description of Branched Alkanes. J. Phys. Chem. B 1999, 103 (21), 4508-4517.
68. Brooks, B.R.; Bruccoleri, R.E.; Olafson, D.J.; States, D.J.; Swaminathan, S.; Karplus, M. CHARMM:A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comput. Chem. 1983, 4, 187-217.
69. Hess, B.; Bekker, H.; Berendsen, H.J.C.; Fraaije, J. LINCS:A Linear Constraint Solver for Molecular Simulations. J. Comput. Chem. 1997, 18 (12), 1463-1472.
70. Boulougouris, G.C.; Economou, I.G.; Theodorou, D.N. Engineering a Molecular Model for Water Phase Equilibrium over a Wide Temperature Range. J. Phys. Chem. B 1998, 102 (6), 1029-1035.
71. Lee, F.S.; Warshel, A. A Local Reaction Field Method for Fast Evaluation of Long-range Electrostatic Interactions in Molecular Simulations. J. Chem. Phys. 1992, 97 (5), 3100-3107.
72. Lide, D.R. CRC Handbook of Chemistry and Physics, 85 ed.; CRC Press:Boca Raton, FL, 2005.
73. Schaftenaar, G.; Noordik, J.H. Molden:a Pre and Post-processing Program for Molecular and Electronic Structures. J. Comput.-Aided Mol. Des. 2000, 14 (2), 123-134.
74. Schuettelkopf, A.W.; Aalten, D.M.F. v., PRODRG -a Tool for High-throughput Crystallography of Protein-ligand Complexes. Acta Cryst. D 2004, 60, 1355-1363.
75. Stubbs, J.M.; Potoff, J.J.; Siepmann, J.I. Transferable Potentials for Phase Equilibria. 6. United-atom description for Ethers, Glycols, Ketones, and Aldehydes. J. Phys. Chem. B 2004, 108 (45), 17596-17605.
76. Wick, C.D.; Martin, M.G.; Siepmann, J.I. Transferable Potentials for Phase Equilibria. 4. United-atom description of Linear and Branched Alkenes and Alkylbenzenes. J. Phys. Chem. B 2000, 104 (33), 8008-8016.
77. Wick, C.D.; Stubbs, J.M.; Rai, N.; Siepmann, J.I. Transferable Potentials for Phase Equilibria. 7. Primary, Secondary, and Tertiary Amines, Nitroalkanes and Nitrobenzene, Nitriles, Amides, Pyridine, and Pyrimidine. J. Phys. Chem. B 2005, 109 (40), 18974-18982.
78. Bernazzani, L.; Cabani, S.; Conti, G.; Mollica, V. Thermodynamic Study of the Partitioning of Organic Compounds between Water and Octan-1-ol. J. Chem. Soc., Faraday Trans. 1995, 91 (4), 649-655.
79. Berti, P.; Cabani, S.; Conti, G.; Mollica, V. Thermodynamic Study of Organic Compunds in Octan-1-ol:Processes of Transfer from Gas to and from Dilute Aqueous Solution. J. Chem. Soc., Faraday Trans. 1 1986, 82, 2547-2556.
80. Dallas, A.J.; Carr, P.W. A Thermodynamic and Solvatochromic Investigation of the Effect of Water on the Phase Transfer Properties of Ocatn-1-ol. J. Chem. Soc., Perkin Trans. 2 1992, (12), 2155-2161.
81. Michielan, L.; Bacilieri, M.; Kaseda, C.; Moro, S. Prediction of the Aqueous Solvation Free Energy of Organic Compounds by Using Autocorrelation of Molecular Electrostatic Potential Surface Properties Combined with Response Surface Analysis. Bioorg. Med. Chem. 2008, 16 (10), 5733-5742.
82. Miertus, S.; Scrocco, E.; Tomasi, J. Electrostatic Interaction of a Solute with a Continuum:a Direct Utilization of Abinitio Molecular Potentials for the Prevision of Solvent Effects. Chem. Phys. 1981, 55 (1), 117-129.
83. Bordner, A.J.; Cavasotto, C.N.; Abagyan, R.A. Accurate transferable model for water, n-octanol, and n-hexadecane solvation free energies. J. Phys. Chem. B 2002, 106 (42), 11009-11015.
84. Daubert, T.; Danner, R. Physical and Thermodynamic Properties of Pure Chemicals:Data Compilation, Version 4.1.1; Hemisphere:New York, 2003.
85. Hales, J.L.; Ellender, J.H. Liquid Densities from 293 to 490 K of 9 Aliphatics Alcohols. J. Chem. Thermodyn. 1976, 8 (12), 1177-1184.
86. Smith, B.D.; Srivastava, R. Thermodynamic Data for Pure Compounds. Part B. Halogenated Hydrocarbons and Alcohols. Elsevier:Amsterdam, The Netherlands, 1986.
87. Cabani, S.; Gianni, P.; Mollica, V.; Lepori, L. Group Contributions to the Thermodynamic Properties of Non-Ionic Organic Solutes in Dilute Aqueous Solution. J. Solut. Chem. 1981, 10 (8), 563-595.
88. Rytting, E.; Lentz, K.A.; Chen, X.Q.; Qian, F.; Venkatesh, S. Aqueous and cosolvent solubility data for drug-like organic compounds. AAPS J. 2005, 7 (1), E78-E105.