Accurate calculation of solvation free energies in supercritical fluids by fully atomistic simulations: Probing the theory of solutions in energy representation

Journal of Chemical Theory and Computation

Volumn 11, Issue 5, 2015, Pages 2245-2256

  Frolov, Andrey I ^a  

^a INSTITUTE OF SOLUTION CHEMISTRY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84929179452     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/acs.jctc.5b00172     Document Type: Article

References (59)

1. Ben-Naim, A. Molecular Theory of Solutions; Oxford University Press, 2006.
2. Klamt, A.; Eckert, F.; Arlt, W. COSMO-RS: An Alternative to Simulation for Calculating Thermodynamic Properties of Liquid Mixtures Annu. Rev. Chem. Biomol. Eng. 2010, 1, 101-122
3. Guthrie, J. P. A. Blind Challenge for Computational Solvation Free Energies: Introduction and Overview J. Phys. Chem. B 2009, 113, 4501-4507
4. Sander, R. Compilation of Henry's law constants, version 3.99 Atmos. Chem. Phys. Discuss. 2014, 14, 29615-30521
5. Reinisch, J.; Klamt, A. Prediction of free energies of hydration with COSMO-RS on the SAMPL4 data set J. Comput.-Aided Mol. Des. 2014, 28, 169-173
6. Klamt, A.; Mennucci, B.; Tomasi, J.; Barone, V.; Curutchet, C.; Orozco, M.; Luque, F. J. On the Performance of Continuum Solvation Methods. A Comment on Universal Approaches to Solvation Modeling Acc. Chem. Res. 2009, 42, 489-492
7. Ratkova, E. L.; Chuev, G. N.; Sergiievskyi, V. P.; Fedorov, M. V. An Accurate Prediction of Hydration Free Energies by Combination of Molecular Integral Equations Theory with Structural Descriptors J. Phys. Chem. B 2010, 114, 12068-12079
8. Palmer, D. S.; Frolov, A. I.; Ratkova, E. L.; Fedorov, M. V. Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction J. Phys.: Condens. Matter 2010, 22, 492101
9. Frolov, A. I.; Ratkova, E. L.; Palmer, D. S.; Fedorov, M. V. Hydration Thermodynamics Using the Reference Interaction Site Model: Speed or Accuracy? J. Phys. Chem. B 2011, 115, 6011-6022
10. Ratkova, E. L.; Fedorov, M. V. Combination of RISM and Cheminformatics for Efficient Predictions of Hydration Free Energy of Polyfragment Molecules: Application to a Set of Organic Pollutants J. Chem. Theory Comput. 2011, 7, 1450-1457
11. Palmer, D. S.; Frolov, A. I.; Ratkova, E. L.; Fedorov, M. V. Toward a Universal Model To Calculate the Solvation Thermodynamics of Druglike Molecules: The Importance of New Experimental Databases Mol. Pharmaceutics 2011, 8, 1423-1429
12. Geballe, M. T.; Skillman, A. G.; Nicholls, A.; Guthrie, J. P.; Taylor, P. J. The SAMPL2 blind prediction challenge: introduction and overview J. Comput.-Aided Mol. Des. 2010, 24, 259-279
13. Lamoureux, G.; Roux, B. Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm J. Chem. Phys. 2003, 119, 3025-3039
14. 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, 5740-5761
15. Mobley, D. L.; Liu, S.; Cerutti, D. S.; Swope, W. C.; Rice, J. E. Alchemical prediction of hydration free energies for SAMPL J. Comput.-Aided Mol. Des. 2011, 26, 551-562
16. Pasquali, I.; Bettini, R.; Giordano, F. Supercritical fluid technologies: An innovative approach for manipulating the solid-state of pharmaceuticals Adv. Drug Delivery Rev. 2008, 60, 399-410
17. Jung, J.; Perrut, M. Particle design using supercritical fluids: Literature and patent survey J. Supercrit. Fluids 2001, 20, 179-219
18. Herrero, M.; Mendiola, J. A.; Cifuentes, A.; Ibáñez, E. Supercritical fluid extraction: Recent advances and applications J. Chromatogr. A 2010, 1217, 2495-2511
19. Dobbs, J. M.; Wong, J. M.; Johnston, K. P. Nonpolar co-solvents for solubility enhancement in supercritical fluid carbon dioxide J. Chem. Eng. Data 1986, 31, 303-308
20. Oparin, R. D.; Idrissi, A.; Fedorov, M. V.; Kiselev, M. G. Dynamic and Static Characteristics of Drug Dissolution in Supercritical CO2 by Infrared Spectroscopy: Measurements of Acetaminophen Solubility in a Wide Range of State Parameters J. Chem. Eng. Data 2014, 59, 3517-3523
21. Su, Z.; Maroncelli, M. Simulations of solvation free energies and solubilities in supercritical solvents J. Chem. Phys. 2006, 124, 164506-164506-15
22. Anderson, K. E.; Siepmann, J. I. Solubility in Supercritical Carbon Dioxide: Importance of the Poynting Correction and Entrainer Effects J. Phys. Chem. B 2008, 112, 11374-11380
23. Frolov, A. I.; Kiselev, M. G. Prediction of Cosolvent Effect on Solvation Free Energies and Solubilities of Organic Compounds in Supercritical Carbon Dioxide Based on Fully Atomistic Molecular Simulations J. Phys. Chem. B 2014, 118, 11769-11780
24. Matubayasi, N.; Nakahara, M. Theory of solutions in the energetic representation. I. Formulation J. Chem. Phys. 2000, 113, 6070-6081
25. Matubayasi, N.; Nakahara, M. Theory of solutions in the energy representation. II. Functional for the chemical potential J. Chem. Phys. 2002, 117, 3605-3616
26. Matubayasi, N.; Nakahara, M. Theory of solutions in the energy representation. III. Treatment of the molecular flexibility J. Chem. Phys. 2003, 119, 9686-9702
27. Matubayasi, N. Free-energy analysis of solvation with the method of energy representation Front. Biosci., Landmark Ed. 2009, 14, 3536-3549
28. Dobbs, J. M.; Wong, J. M.; Lahiere, R. J.; Johnston, K. P. Modification of supercritical fluid phase behavior using polar cosolvents Ind. Eng. Chem. Res. 1987, 26, 56-65
29. Frolov, A. I. Theory of Solutions in Energy Representation in NPT-ensemble: Derivation Details. arXiv:1502.04355. arXiv.org e-Print archive. http://arxiv.org/abs/1502.04355 (accessed February 20, 2015).
30. Bennett, C. H. Efficient estimation of free energy differences from Monte Carlo data J. Comput. Phys. 1976, 22, 245-268
31. 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, 134508-134508-13
32. Shirts, M. R.; Pande, V. S. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration J. Chem. Phys. 2005, 122, 144107
33. Matubayasi, N. Lecture notes of Prof. N. Matubayasi on the theory of solutions in energy representation. http://sourceforge.net/projects/ermod/files/ (accessed February 7, 2013).
34. Hansen, J. P.; McDonald, I. R. Theory of Simple Liquids, 3 rd ed.; Academic Press: London, 1991.
35. Sakuraba, S.; Matubayasi, N. ERmod: Fast and versatile computation software for solvation free energy with approximate theory of solutions J. Comput. Chem. 2014, 35, 1592-1608
36. White, J. A.; Velasco, S. The Ornstein-Zernike equation in the canonical ensemble Europhys. Lett. 2001, 54, 475
37. Hernando, J. A. Density functional theory in the canonical ensemble: I. General formalism J. Phys.: Condens. Matter 2002, 14, 303
38. Percus, J. K. Approximation Methods in Classical Statistical Mechanics Phys. Rev. Lett. 1962, 8, 462-463
39. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447
40. van der Spoel, D.; Lindahl, E.; Hess, B. GROMACS User Manual version 4.6.4; 2013; available at www.gromacs.org.
41. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A Smooth Particle Mesh Ewald Method J. Chem. Phys. 1995, 103, 8577-8593
42. Zhang, L.; Siepmann, J. I. Pressure Dependence of the Vapor-Liquid-Liquid Phase Behavior in Ternary Mixtures Consisting of n-Alkanes, n-Perfluoroalkanes, and Carbon Dioxide J. Phys. Chem. B 2005, 109, 2911-2919
43. 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, 11225-11236
44. Maestro, version 9.3; Schrödinger, LLC: New York, NY, 2012.
45. Martinez, L.; Andrade, R.; Birgin, E. G.; Martínez, J. M. PACKMOL: A package for building initial configurations for molecular dynamics simulations J. Comput. Chem. 2009, 30, 2157-2164
46. Weeks, J. D.; Chandler, D.; Andersen, H. C. Role of Repulsive Forces in Determining the Equilibrium Structure of Simple Liquids J. Chem. Phys. 1971, 54, 5237-5247
47. Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Shirts, M. R.; Dill, K. A. Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations J. Chem. Theory Comput. 2009, 5, 350-358
48. Wu, D.; Kofke, D. A. Phase-space overlap measures. I. Fail-safe bias detection in free energies calculated by molecular simulation J. Chem. Phys. 2005, 123, 054103
49. de Jong, D. H.; Schäfer, L. V.; de Vries, A. H.; Marrink, S. J.; Berendsen, H. J. C.; Grubmüller, H. Determining equilibrium constants for dimerization reactions from molecular dynamics simulations J. Comput. Chem. 2011, 32, 1919-1928
50. Roux, B. The calculation of the potential of mean force using computer simulations Comput. Phys. Commun. 1995, 91, 275-282
51. Matubayasi, N.; Liang, K. K.; Nakahara, M. Free-energy analysis of solubilization in micelle J. Chem. Phys. 2006, 124, 154908
52. Takahashi, H.; Matubayasi, N.; Nakahara, M.; Nitta, T. A quantum chemical approach to the free energy calculations in condensed systems: the QM/MM method combined with the theory of energy representation J. Chem. Phys. 2004, 121, 3989-3999
53. Takahashi, H.; Ohno, H.; Kishi, R.; Nakano, M.; Matubayasi, N. Computation of the reduction free energy of coenzyme in aqueous solution by the QM/MM-ER method Chem. Phys. Lett. 2008, 456, 176-180
54. Takahashi, H.; Ohno, H.; Yamauchi, T.; Kishi, R.; Furukawa, S.-I.; Nakano, M.; Matubayasi, N. Investigation of the dominant hydration structures among the ionic species in aqueous solution: novel quantum mechanics/molecular mechanics simulations combined with the theory of energy representation J. Chem. Phys. 2008, 128, 064507
55. Matubayasi, N.; Takahashi, H. Free-energy analysis of the electron-density fluctuation in the quantum-mechanical/molecular-mechanical simulation combined with the theory of energy representation J. Chem. Phys. 2012, 136, 044505
56. Saito, H.; Matubayasi, N.; Nishikawa, K.; Nagao, H. Hydration property of globular proteins: An analysis of solvation free energy by energy representation method Chem. Phys. Lett. 2010, 497, 218-222
57. Kawakami, T.; Shigemoto, I.; Matubayasi, N. Free-energy analysis of water affinity in polymer studied by atomistic molecular simulation combined with the theory of solutions in the energy representation J. Chem. Phys. 2012, 137, 234903
58. Kawakami, T.; Shigemoto, I.; Matubayasi, N. Erratum: Free-energy analysis of water affinity in polymer studied by atomistic molecular simulation combined with the theory of solutions in the energy representation J. Chem. Phys. 2014, 140, 169903
59. Karino, Y.; Fedorov, M. V.; Matubayasi, N. End-point calculation of solvation free energy of amino-acid analogs by molecular theories of solution Chem. Phys. Lett. 2010, 496, 351-355