References
- L.C. Marr, T.W. Kirchstetter, R.A. Harley, A.H. Miguel, S.V. Hering, and S.K. Hammond, Environ. Sci. Technol. 33, 3091–3099 (1999).
- L.S. Lee, M. Hagwell, J.J. Delfino, and P.S.C. Rao, Environ. Sci. Technol. 26, 2104–2110 (1992).
- H.I. Abdel-Shafy and M.S.M. Mansour, Egypt J. Pet. 25, 107–123 (2016).
- Diesel Fuel Standards. https://www.epa.gov/diesel-fuel-standards.
- C.D. Wilfred, C.F. Kiat, Z. Man, M.A. Bustam, M.I.M. Mutalib, and C.Z. Phak, Fuel Process. Technol. 93, 85–89 (2012).
- J.M. Prausnitz, R.N. Lichtenthaler, and E.G. de Azevedo, Molecular Thermodynamics of Fluid-phase Equilibria, 3rd ed. (Prentice-Hall, Inc., Upper Saddle River, NJ, 1999).
- J.H. Hildebrand, J.M. Prausnitz, and R.L. Scott, Regular and Related Solutions (Van Nostrand Reinhold Company, New York, 1970).
- S.M. Walas, Phase Equilibria in Chemical Engineering (Butterworth Publishers, Stoneham, MA, 1985).
- F.L. Nordström and A.C. Rasmuson, J. Chem. Thermodyn. 40, 1684–1692 (2008).
- F.L. Nordström and A.C. Rasmuson, Eur. J. Pharm. Sci. 36, 330–344 (2009).
- H. Yang, J. Thati, and A.C. Rasmuson, J. Chem. Thermodyn. 48, 150–159 (2012).
- A.S. Hukkerikar, B. Sarup, A.T. Kate, J. Abildskov, G. Sin, and R. Gani, Fluid Phase Equilib. 321, 25–43 (2012).
- D.M. Eike and E.J. Maginn, J. Chem. Phys. 124, 164503 (2006).
- S. Jayaraman and E.J. Maginn, J. Chem. Phys. 127, 214504 (2007).
- A.S. Paluch, S. Jayaraman, J.K. Shah, and E.J. Maginn, J. Chem. Phys. 133, 124504 (2010).
- Recall that .
- B.E. Poling, J.M. Prausnitz, and J.P. O’Connell, The Properties of Gases and Liquids, 5th ed. (McGraw-Hill, New York, 2001).
- J. Gmehling, J. Chem. Thermodyn. 41, 731–747 (2009).
- J.P. O’Connell, R. Gani, P.M. Mathias, G. Maurer, J.D. Olson, and P.A. Crafts, Ind. Eng. Chem. Res. 48, 4619–4637 (2009).
- S. Gracin, T. Brinck, and A.C. Rasmuson, Ind. Eng. Chem. Res. 41, 5114–5124 (2002).
- H. Hojjati and S. Rohani, Org. Process Res. Dev. 10, 1110–1118 (2006).
- Group Assignment: Online Group Assignment for UNIFAC and PSRK. http://www.ddbst.com/unifacga.html.
- C. Chen and P.A. Crafts, Ind. Eng. Chem. Res. 45, 4816–4824 (2006).
- M.J. Lazzaroni, D. Bush, C.A. Eckert, T.C. Frank, S. Gupta, and J.D. Olson, Ind. Eng. Chem. Res. 44, 4075–4083 (2005).
- L.C. Draucker, M. Janakat, M.J. Lazzaroni, D. Bush, C.A. Eckert, T.C. Frank, and J.D. Olson, Ind. Eng. Chem. Res. 46, 2198–2204 (2007).
- G.B. Fuerst, R.T. Ley, and A.S. Paluch, Ind. Eng. Chem. Res. 54, 9027–9037 (2015).
- R.T. Ley, G.B. Fuerst, B.N. Redeker, and A.S. Paluch, Ind. Eng. Chem. Res. 55, 5415–5430 (2016).
- J.R. Phifer, K.J. Solomon, K.L. Young, and A.S. Paluch, AIChE J. 63, 781–791 (2017).
- S. Diaz-Rodriguez, S.M. Bozada, J.R. Phifer, and A.S. Paluch, J. Comput. Aided Mol. Des. 30, 1007–1017 (2016).
- C.E. Cox, J.R. Phifer, L.F. da Silva, G.G. Nogueira, R.T. Ley, E.J. O’Loughlin, A.K.P. Barbosa, B.T. Rygelski, and A.S. Paluch, J. Comput. Aided Mol. Des. (2017). doi:10.1007/s10822-016-0001-6
- R.F. Blanks and J.M. Prausnits, Ind. Eng. Chem. Fundam. 3, 1–8 (1964).
- C.M. Hansen, Ind. Eng. Chem. Prod. Res. Dev. 8, 2–11 (1969).
- E.R. Thomas and C.A. Eckert, Ind. Eng. Chem. Proc. Des. Dev. 23, 194–209 (1984).
- It is useful to put the calculation of the solvation free energy using SMD/SM8 in the context/language of a conventional molecular simulation free energy calculation. The free energy of solvation is computed as the change in free energy of coupling/decoupling a single solute molecule to solution. When coupling/decoupling a single solute molecule when performing a molecular simulation free energy calculation, the SMD/SM8 calculation assumes that the simulation box is approximately the same size when the solute is fully coupled and fully decoupled. This may equivalently be expressed as the change in free energy of taking a single solute molecule from an ideal gas phase (or vacuum) to solution at the same concentration. Note that in the Supporting Information accompanying the electronic version of ref. [27], we prove the equivalence of the residual chemical potential of the solute at infinite dilution and the solvation free energy.
- A.S. Paluch and E.J. Maginn, AIChE J. 59, 2647–2661 (2013).
- A.V. Marenich, C.J. Cramer, and D.G. Truhlar, J. Phys. Chem. B 113, 6378–6396 (2009).
- A.V. Marenich, R.M. Olson, C.P. Kelly, C.J. Cramer, and D.G. Truhlar, J. Chem. Theory. Comput. 3, 2011–2033 (2007).
- P. Winget, G.D. Hawkins, C.J. Cramer, and D.G. Truhlar, J. Phys. Chem. B 104, 4726–4734 (2000).
- J.P. O ’Connell and J.M. Haile, Thermodynamics: Fundamentals for Applications (Cambridge University Press, New York, 2005).
- T.C. Frank, J.J. Anderson, J.D. Olson, and C.A. Eckert, Ind. Eng. Chem. Res. 46, 4621–4625 (2007).
- J. Marrero and J. Abildskov, editors, Solubility and Related Properties of Large Complex Chemicals Part 1: Organic Solutes Ranging from C4 to C40 (DECHEMA, Frankfurt am Main, Germany, 2003).
- N. Rai and J.I. Siepmann, J. Phys. Chem. B 111, 10790–10799 (2007).
- N. Rai and J.I. Siepmann, J. Phys. Chem. B 117, 273–288 (2013).
- M.G. Martin and J.I. Siepmann, J. Phys. Chem. B 102, 2569–2577 (1998).
- M.G. Martin and J.I. Siepmann, J. Phys. Chem. B 103, 4508–4517 (1999).
- B. Chen, J.J. Potoff, and J.I. Siepmann, J. Phys. Chem. B 105, 3093–3104 (2001).
- J.M. Stubbs, J.J. Potoff, and J.I. Siepmann, J. Phys. Chem. B 108, 17596–17605 (2004).
- J. Wang, R.M. Wolf, J.W. Caldwell, P.A. Kollman, and D.A. Case, J. Comput. Chem. 25, 1157–1174 (2004).
- J. Wang, W. Wang, P.A. Kollman, and D.A. Case, J. Mol. Graph. Model. 25, 247–260 (2006).
- W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein, J. Chem. Phys. 79, 926 (1983).
- B. Chen and J.I. Siepmann, J. Phys. Chem. B 110, 3555–3563 (2006).
- J.L. Rafferty, L. Sun, J.I. Siepmann, and M.R. Schure, Fluid Phase Equilib. 290, 25–35 (2010).
- N. Rai, D. Bhatt, J.I. Siepmann, and L.E. Fried, J. Chem. Phys. 129, 194510 (2008).
- Y. Zhao and D.G. Truhlar, Theor. Chem. Account. 120, 215–241 (2008).
- C.J. Cramer, Essentials of Computational Chemistry (John Wiley & Sons Ltd., Chichester, West Sussex, 2002).
- C.P. Kelly, C.J. Cramer, and D.G. Truhlar, J. Chem. Theory. Comput. 1, 1133–1152 (2005).
- R.M. Olson, A.V. Marenich, C.J. Cramer, and D.G. Truhlar, J. Chem. Theory Comput. 3, 2046–2054 (2007).
- Y. Shao, Z. Gan, and E. Epifanovsky, Mol. Phys. 113, 184–215 (2015).
- B. Hess, C. Kutzner, D. van der Spoel, and E. Lindal, J. Chem. Theory Comput. 4, 435–447 (2008).
- S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M.R. Shirts, J.C. Smith, P.M. Kasson, D. van der Spoel, B. Hess, and E. Lindahl, Bioinformatics 29, 845–854 (2013).
- GROMACS: Fast, Flexible, Free. <http://www.gromacs.org/ >.
- K.S. Shing and S.T. Chung, J. Phys. Chem. 91, 1674–1681 (1987).
- D.A. Kofke and P.T. Cummings, Mol. Phys. 92, 973–996 (1997).
- M.R. Shirts, J.W. Pitera, W.C. Swope, and V.S. Pande, J. Chem. Phys. 119, 5740–5761 (2003).
- D.A. Kofke and P.T. Cummings, Fluid Phase Equilib. 150–151, 41–49 (1998).
- C. Chipot and A. Pohorille, editors, Free Energy Calculations: Theory and Applications in Chemistry and Biology, Springer Series in Chemical Physics, Vol. 86 (Springer, New York, 2007).
- C.H. Bennett, J. Comp. Phys. 22, 245–268 (1976).
- M.R. Shirts, E. Bair, G. Hooker, and V.S. Pande, Phys. Rev. Lett. 91, 140601 (2003).
- N. Lu, J.K. Singh, and D.A. Kofke, J. Chem. Phys. 118, 2977–2984 (2003).
- M.R. Shirts and J.D. Chodera, J. Chem. Phys. 129, 124105 (2008).
- T.C. Beutler, A.E. Mark, R.C. van Schaik, P.R. Gerber, and W.F. van Gunsteren, Chem. Phys. Lett. 222, 529–539 (1994).
- M.R. Shirts and V.S. Pande, J. Chem. Phys. 122, 134508 (2005).
- T. Steinbrecher, D.L. Mobley, and D.A. Case, J. Chem. Phys. 127, 214108 (2007).
- PyMBAR: Python implementation of the Multistate Bennett Acceptance Ratio (MBAR). <https://github.com/choderalab/pymbar >.
- J.D. Chodera, W.C. Swope, J.W. Pitera, C. Seok, and K.A. Dill, J. Chem. Theory Comput. 3, 26–41 (2007).
- P.V. Klimovich, M.R. Shirts, and D.L. Mobley, J. Comput. Aided Mol. Des. 29, 397–411 (2015).
- M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J.A. Montgomery, J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M. Cossi, N. Rega, J.M. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, Ö. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, and D.J. Fox, Gaussian 09, Revision C.01 2009.
- A.V. Marenich, C.J. Cramer, and D.G. Truhlar, J. Chem. Theory. Comput. 9, 609–620 (2013).
- Minnesota Solvation Models and Solvation Software. <http://comp.chem.umn.edu/solvation/ >
- The exception to this is the value for water which MOSCED doubles (v = 36 cm3/mol) to obtain better agreement with experiment when predicting infinite dilution activity coefficients. We use the value of v = 18 cm3/mol when computing reference solvent normalised activity coefficients using our SMD and SM8 solvation free energies.
- B. Efron, The Jackknife, the Bootstrap and Other Resampling Plans (Society for Industrial and Applied Mathematics, Philadelphia, PA, 1982).
- We compute 11 values of ln γ∞2, 1 using molecular simulation. These 11 values make up our sample set. From this sample set, we next generate 20,000 bootstrap samples (or training) sets. Each bootstrap sample is composed of 11 values of ln γ∞2, 1 selected at random and with replacement from the sample set. In practice, we index the values of ln γ∞2, 1 computed using molecular simulation from 1 to 11. To construct a bootstrap sample, we generate 11 random integers between 1 and 11, and use these to select the corresponding value of ln γ∞2, 1 from the sample set. This is performed 20,000 times to generate 20,000 bootstrap samples. Using each bootstrap sample, we regress a unique set of MOSCED parameters by minimising the objective function. Our final MOSCED values are then taken as the average over all 20,000 values, and the uncertainty is taken to be the 95% confidence interval.
- R. Storn and K. Price, J. Global. Optim. 11, 341–359 (1997).
- J.W. Eaton, D. Bateman, and S. Hauberg, GNU Octave Version 3.0.1 Manual: A High-Level Interactive Language for Numerical Computations (2009) (CreateSpace Independent Publishing Platform, 2009). ISBN 1441413006.
- The uncertainty is taken as the 95% confidence interval computed following [92] as , where n is the number of bootstrap samples (or observations; 20,000), s is the sample standard deviation (of the 20,000 bootstrap samples), and t is the value of student's t computed at the 95% confidence interval with n − 1 degrees of freedom.
- J.M. Smith, H.C. Van Ness, and M.M. Abbott, Introduction to Chemical Engineering Thermodynamics, 7th ed. (McGraw-Hill, New York, 2005).
- C.L. Yaws, P.K. Narasimhan, and C. Gabbula, Yaws’ Handbook of Antoine Coefficients for Vapor Pressure, 2nd electronic ed. (Knovel, 2009). <http://app.knovel.com/hotlink/toc/id: kpYHACVPEH/yaws-handbook-antoine/yaws-handbook-antoine >.
- J.J. Potoff and A. Bernard-Brunel, J. Phys. Chem. B 113, 14725–14731 (2009).
- C. Vega, J.L.F. Abascal, and I. Nezbeda, J. Chem. Phys. 125, 034503 (2006).
- J. Abildskov, editor, Solubility and Related Properties of Large Complex Chemicals Part 2: Organic Solutes ranging from C2 to C41 (DECHEMA, Frankfurt am Main, 2005).
- W.E. Acree, Jr and M.H. Abraham, Can. J. Chem. 79, 1466–1476 (2001).
- D.C. Harris, Quantitative Chemical Analysis, 6th ed. (W. H. Freeman and Company, New York, 2003).