References
- S.A. Adcock and J.A. McCammon, Chem. Rev. 106(5), 1589–1615 (2006). doi:10.1021/cr040426m.
- P.A. Kollman, I. Massova, C. Reyes, B. Kuhn, S. Huo, L. Chong, M. Lee, T. Lee, Y. Duan, W. Wang, O. Donini, P. Cieplak, J. Srinivasan, D.A. Case, and I.T.E. Cheatham, Accounts Chem. Res. 33(12), 889–897 (2000). doi:10.1021/ar000033j.
- N.A. Baker, Methods Enzymol. 383, 94–118 (2004). <http://www.sciencedirect.com/science/article/pii/ S0076687904830052>, Numer. Comput. Methods Part D.
- C.J. Cramer and D.G. Truhlar, Chem. Rev. 99(8), 2161–2200 (1999). doi:10.1021/cr960149m.
- A. Onufriev, D.A. Case, and D. Bashford, J. Comput. Chem. 23(14), 1297–1304 (2002). doi:10.1002/jcc.10126.
- L. Xiao, Q. Cai, X. Ye, J. Wang, and R. Luo, J. Chem. Phys. 139(9), 094106 (2013). doi:10.1063/1.4819471.
- E.L. Ratkova, D.S. Palmer, and M.V. Fedorov, Chem. Rev. 115(13), 6312 (2015). doi:10.1021/cr5000283.
- J.D Weeks, Ann. Rev. Phys. Chem. 53, 533–562 (2002).
- G. Hummer, S. Garde, A.E. Garcia, M.E. Paulaitis, and L.R. Pratt, J. Phys. Chem. B 102(51), 10469–10482 (1998).
- K. Lum, D. Chandler, and J.D. Weeks, J. Phys. Chem. B 103(22), 4570–4577 (1999).
- K. Katsov and J.D. Weeks, J. Phys. Chem. B 105(28), 6738–6744 (2001). doi:10.1021/jp010893x.
- D.M. Huang and D. Chandler, J. Phys. Chem. B 106(8), 2047–2053 (2002).
- Z. Hu and J.D. Weeks, Phys. Rev. Lett. 105(14) (2010).
- D. Chandler and H.C. Andersen, J. Chem. Phys. 57(5), 1930–1937 (1972). doi:10.1063/1.1678513.
- J.C. Rasaiah and H.L. Friedman, J. Chem. Phys. 48(6), 2742–2752 (1968).
- F. Hirata and P.J. Rossky, Chem. Phys. Lett. 83(2), 329–334 (1981).
- F. Hirata, B.M. Pettitt, and P.J. Rossky, J. Chem. Phys. 77(1), 509–520 (1982).
- F. Hirata, P.J. Rossky, and B.M. Pettitt, J. Chem. Phys. 78(6), 4133–4144 (1983).
- J. Perkyns and B.M. Pettitt, J. Chem. Phys. 97(10), 7656–7666 (1992).
- J.E. Mayer, J. Chem. Phys. 18(11), 1426–1436 (1950). doi:10.1063/1.1747506.
- A.R. Allnatt, Mol. Phys. 8(6), 533–539 (1964). doi:10.1080/00268976400100591.
- B.M. Pettitt and P.J. Rossky, J. Chem. Phys. 77(3), 1451–1457 (1982).
- H. Sato and F. Hirata, J. Chem. Phys. 111(18), 8545–8555 (1999).
- A. Kovalenko and F. Hirata, Chem. Phys. Lett. 349(5–6), 496–502 (2001).
- I. Omelyan and A. Kovalenko, J. Chem. Phys. 139(24) (2013).
- S. Gusarov, B.S. Pujari, and A. Kovalenko, J. Comput. Chem. 33(17), 1478–1494 (2012).
- T. Yamazaki and A. Kovalenko, J. Phys. Chem. B 115(2), 310–318 (2011).
- J.P. Hansen and I.R. McDonald, Theory of Simple Liquids (Elsevier, London, 2006).
- F. Hirata, Molecular Theory of Solvation (Kluwer Academic Publishers, Dordrecht 2003).
- J.S. Rowlinson and B. Widom, Molecular Theory of Capillarity (Clarendon Press, Mineola, N. Y., 1989).
- J.D. Weeks, K. Katsov, and K. Vollmayr, Phys. Rev. Lett. 81(20), 4400–4403 (1998).
- R.A. Pierotti, Chem. Rev. 76(6), 717–726 (1976).
- L.R. Pratt and D. Chandler, J. Chem. Phys. 67(8), 3683–3704 (1977). doi:10.1063/1.435308.
- F.H. Stillinger, J. Solution Chem. 2(2), 141–158 (1973). doi:10.1007/BF00651970.
- A. Kovalenko and F. Hirata, Phys. Chem. Chem. Phys. 7(8), 1785–1793 (2005).
- I.P. Omelyan, R. Folk, A. Kovalenko, W. Fenz, and I.M. Mryglod, Phys. Rev. E 79(1) (2009), 1.
- I.P. Omelyan, R. Folk, I.M. Mryglod, and W. Fenz, J. Chem. Phys. 126(12) (2007).
- L. Lue and D. Blankschtein, J. Chem. Phys. 102(10), 4203–4216 (1995).
- L. Lue and D. Blankschtein, J. Chem. Phys. 102(13), 5427–5437 (1995).
- F.O. Raineri and G. Stell, J. Phys. Chem. B 105(47), 11880–11892 (2001).
- G.A. Martynov and G.N. Sarkisov, Mol. Phys. 49(6), 1495–1504 (1983).
- G. Munao, D. Costa, and C. Caccamo, J. Chem. Phys. 130(14) (2009).
- G. Munao, D. Costa, and C. Caccamo, Chem. Phys. Lett. 470(4–6), 240–243 (2009).
- L. Gendre, R. Ramirez, and D. Borgis, Chem. Phys. Lett. 474(4), 366–370 (2009). <http://www.sciencedirect.com/science/article/pii/ S0009261409004175>.
- S. Zhao, R. Ramirez, R. Vuilleumier, and D. Borgis, J. Chem. Phys. 134(19), 194102 (2011). doi:10.1063/1.3589142.
- R. Ishizuka and N. Yoshida, J. Chem. Phys. 136(11), 114106 (2012). doi:10.1063/1.3693623.
- R. Ishizuka and N. Yoshida, J. Chem. Phys. 139(8), 084119 (2013). doi:10.1063/1.4819211.
- D. Beglov and B. Roux, J. Phys. Chem. B 101(39), 7821–7826 (1997). doi:10.1021/jp971083h.
- A.A. Lee, Inverse Ising Inference by Combining Ornstein–Zernike Theory with Deep Learning, ArXiv:1706.08466.
- Y. Dong, X. Feng, N. Zhao, and Z. Hou, J. Chem. Phys. 143(2), 024903 (2015). doi:10.1063/1.4926412.
- B. Larsen, J. Chem. Phys. 68(10), 4511–4523 (1978). doi:10.1063/1.435555.
- T. Imai, R. Hiraoka, A. Kovalenko, and F. Hirata, J. Amer. Chem. Soc. 127(44), 15334–15335 (2005).
- M.C. Stumpe, N. Blinov, D. Wishart, A. Kovalenko, and V.S. Pande, J. Phys. Chem. B 115(2), 319–328 (2011).
- A. Kovalenko, Pure Appl. Chem. 85(1), 159–199 (2013), 32nd International Conference on Solution Chemistry (ICSC) Aug 28–Sep 02, 2011, La Grande Motte, France.
- S.H. Chong and S. Ham, Angew. Chem. Int. Ed. 53(15), 3961–3964 (2014).
- S.H. Chong and S. Ham, Proc. Nat. Acad. Sci. USA 109(20), 7636–7641 (2012).
- L.M. da Costa, S. Hayaki, S.R. Stoyanov, S. Gusarov, X. Tan, M.R. Gray, J.M. Stryker, R. Tykwinski, J.W.d.M. Carneiro, H. Sato, P.R. Seidl, and A. Kovalenko, Phys. Chem. Chem. Phys. 14(11), 3922–3934 (2012).
- Y. Kiyota, R. Hiraoka, N. Yoshida, Y. Maruyama, T. Imai, and F. Hirata, J. Amer. Chem. Soc. 131(11), 3852 (2009).
- S. Genheden, T. Luchko, S. Gusarov, A. Kovalenko, and U. Ryde, J. Phys. Chem. B 114(25), 8505–8516 (2010).
- N. Yoshida, S. Phongphanphanee, Y. Maruyama, T. Imai, and F. Hirata, J. Am. Chem. Soc. 128(37), 12042–12043 (2006).
- D. Nikolic, N. Blinov, D. Wishart, and A. Kovalenko, J. Chem. Theory Comput. 8(9), 3356–3372 (2012).
- E.L. Ratkova and M.V. Fedorov, J. Chem. Phys. 135(24), 244109 (2011). doi:10.1063/1.3672094.
- B.J. Berne, J.D. Weeks, and R. Zhou, Annu. Rev. Phys. Chem. 60, 85–103 (2009).
- D. Chandler, Nature 437(7059), 640–647 (2005).
- X. Huang, C.J. Margulis, and B.J. Berne, Proc. Nat. Acad. Sci. USA 100(21), 11953–11958 (2003).
- M. Mezger, H. Reichert, S. Schoeder, J. Okasinski, H. Schroeder, H. Dosch, D. Palms, J. Ralston, and V. Honkimaki, Proc. Nat. Acad. Sci. USA 103(49), 18401–18404 (2006).
- A. Poynor, L. Hong, I.K. Robinson, S. Granick, Z. Zhang, and P.A. Fenter, Phys. Rev. Lett. 97 26 (2006).
- P. Liu, X.H. Huang, R.H. Zhou, and B.J. Berne, Nature 437(7055), 159–162 (2005).
- X.H. Huang, R.H. Zhou, and B.J. Berne, J. Phys. Chem. B 109(8), 3546–3552 (2005).
- A. Wallqvist and B.J. Berne, J. Phys. Chem. 99(9), 2893–2899 (1995).
- S. Cao, F.K. Sheong, and X. Huang, J. Chem. Phys. 143(5), 054110 (2015). doi:10.1063/1.4928051.
- B. Hess, C. Kutzner, D. van der Spoel, and E. Lindahl, J. Chem. Theory Comput. 4(3), 435–447 (2008).
- A. Kovalenko and F. Hirata, J. Chem. Phys. 110(20), 10095–10112 (1999). doi:10.1063/1.478883.
- S. Woelki and D. Henderson, Condensed Matter Phys. 14(4), 43801 (2011). doi:10.5488/CMP.14.43801.
- I. Omelyan and A. Kovalenko, J. Chem. Theory Comput. 11(4), 1875–1895 (2015).
- J.H. Dymond and R. Malhotra, Int. J. Thermophys. 9(6), 941–951 (1988).
- P.P. Ewald, Ann. Phys. 369(3), 253–287 (1921). doi:10.1002/andp.19213690304.
- T. Darden, D. York, and L. Pedersen, J. Chem. Phys. 98(12), 10089–10092 (1993). doi:10.1063/1.464397.
- T. Luchko, S. Gusarov, D.R. Roe, C. Simmerling, D.A. Case, J. Tuszynski, and A. Kovalenko, J. Chem. Theory Comput. 6(3), 607 (2010).
- P. Pulay, Chem. Phys. Lett. 73(2), 393 (1980).
- D.L. Mobley and J.P. Guthrie, J. Comput.-Aided Mol. Des. 28(7), 711–720 (2014). <https://doi.org/10.1007/s10822-014-9747-x>.
- A. Montellano Lopez, A. Mateo-Alonso, and M. Prato, J. Mater. Chem. 21, 1305–1318 (2011). <http://dx.doi.org/10.1039/C0JM02386H>.
- 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, Jr, 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, Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski, and D.J. Fox, Gaussian 09 Revision D.01 (Gaussian Inc., Wallingford, CT, 2009).
- U.C. Singh and P.A. Kollman, J. Comput. Chem. 5(2), 129–145 (1984). doi:10.1002/jcc.540050204.
- C. Caleman, P.J. van Maaren, M. Hong, J.S. Hub, L.T. Costa, and D. van der Spoel, J. Chem. Theory Comput. 8(1), 61–74 (2012). doi:10.1021/ct200731v.
- N.M. Fischer, P.J. van Maaren, J.C. Ditz, A. Yildirim, and D. van der Spoel, J. Chem. Theory Comput. 11(7), 2938–2944 (2015). doi:10.1021/acs.jctc.5b00190.
- J. Zhang, B. Tuguldur, and D. van der Spoel, J. Chem. Info. Model. 55(6), 1192–1201 (2015). doi:10.1021/acs.jcim.5b00106.
- J. Zhang, B. Tuguldur, and D. van der Spoel, J. Chem. Info. Model. 56(4), 819–820 (2016). doi:10.1021/acs.jcim.6b00081.
- C.I. Bayly, P. Cieplak, W. Cornell, and P.A. Kollman, J. Phys. Chem. 97(40), 10269–10280 (1993). doi:10.1021/j100142a004.