Statistical–mechanical, 3D-RISM-KH molecular theory of solvation (3D reference interaction site model with the Kovalenko–Hirata closure) is promising as an essential part of multiscale methodology for chemical and biomolecular nanosystems in solution. 3D-RISM-KH explains the molecular mechanisms of self-assembly and conformational stability of synthetic organic rosette nanotubes (RNTs), aggregation of prion proteins and β-sheet amyloid oligomers, protein-ligand binding, and function-related solvation properties of complexes as large as the Gloeobacter violaceus pentameric ligand-gated ion channel (GLIC) and GroEL/ES chaperone. Molecular mechanics/Poisson–Boltzmann (generalized Born) surface area [MM/PB(GB)SA] post-processing of molecular dynamics (MD) trajectories involving SA empirical nonpolar terms is replaced with MM/3D-RISM-KH statistical–mechanical evaluation of the solvation thermodynamics. 3D-RISM-KH has been coupled with multiple time-step (MTS) MD of the solute biomolecule driven by effective solvation forces, which are obtained analytically by converging the 3D-RISM-KH integral equations at outer time-steps and are calculated in between by using solvation force coordinate extrapolation (SFCE) in the subspace of previous solutions to 3D-RISM-KH. The procedure is stabilized by the optimized isokinetic Nosé–Hoover (OIN) chain thermostatting, which enables gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties. The multiscale OIN/SFCE/3D-RISM-KH algorithm is implemented in the Amber package and illustrated on a fully flexible model of alanine dipeptide in aqueous solution, exhibiting the computational rate of solvent sampling 20 times faster than standard MD with explicit solvent. Further substantial acceleration can be achieved with 3D-RISM-KH efficiently sampling essential events with rare statistics such as exchange and localization of solvent, ions, and ligands at binding sites and pockets of the biomolecule. 3D-RISM-KH was coupled with ab initio complete active space self-consistent field (CASSCF) and orbital-free embedding (OFE) Kohn–Sham (KS) density functional theory (DFT) quantum chemistry methods in an SCF description of electronic structure, optimized geometry, and chemical reactions in solution. The (OFE)KS-DFT/3D-RISM-KH multi-scale method is implemented in the Amsterdam Density Functional (ADF) package and extensively validated against experiment for solvation thermochemistry, photochemistry, conformational equilibria, and activation barriers of various nanosystems in solvents and ionic liquids (ILs). Finally, the replica RISM-KH-VM molecular theory for the solvation structure, thermodynamics, and electrochemistry of electrolyte solutions sorbed in nanoporous materials reveals the molecular mechanisms of sorption and supercapacitance in nanoporous carbon electrodes, which is drastically different from a planar electrical double layer.
Conference
International Conference on Solution Chemistry (ICSC-32), International Conference on Solution Chemistry, ICSC, Solution Chemistry, 32nd, La Grande Motte, France, 2011-08-28–2011-09-02
References
1 J.-P. Hansen, I. McDonald. Theory of Simple Liquids, 3rd ed., Elsevier, Amsterdam (2006).Search in Google Scholar
2 F. Hirata (Ed.). Molecular Theory of Solvation, Series: Understanding Chemical Reactivity, P. G. Mezey (Ed.), Vol. 24, p. 360, Kluwer Academic, Dordrecht (2003).10.1007/1-4020-2590-4Search in Google Scholar
3 10.1063/1.451510, D. Chandler, J. McCoy, S. Singer. J. Chem. Phys.85, 5971 (1986).Search in Google Scholar
4 10.1063/1.451511, D. Chandler, J. McCoy, S. Singer. J. Chem. Phys.85, 5977 (1986).Search in Google Scholar
5 10.1063/1.469602, D. Beglov, B. Roux. J. Chem. Phys.103, 360 (1995).Search in Google Scholar
6 10.1021/jp971083h, D. Beglov, B. Roux. J. Phys. Chem. B101, 7821 (1997).Search in Google Scholar
7 10.1016/S0009-2614(98)00471-0, A. Kovalenko, F. Hirata. Chem. Phys. Lett.290, 237 (1998).Search in Google Scholar
8 10.1063/1.478883, A. Kovalenko, F. Hirata. J. Chem. Phys.110, 10095 (1999).Search in Google Scholar
9 10.1063/1.481676, A. Kovalenko, F. Hirata. J. Chem. Phys.112, 10391 (2000).Search in Google Scholar
10 10.1063/1.481677, A. Kovalenko, F. Hirata. J. Chem. Phys.112, 10403 (2000).Search in Google Scholar
11 A. Kovalenko. “Three-dimensional RISM theory for molecular liquids and solid-liquid inter-faces”, in Molecular Theory of Solvation, F. Hirata (Ed.), Series: Understanding Chemical Reactivity, Vol. 24, pp. 169–275, Kluwer, Dordrecht (2003).10.1007/1-4020-2590-4_4Search in Google Scholar
12 10.1063/1.481564, H. Sato, A. Kovalenko, F. Hirata. J. Chem. Phys.112, 9463 (2000).Search in Google Scholar
13 10.1021/jp054344t, S. Gusarov, T. Ziegler, A. Kovalenko. J. Phys. Chem. A110, 6083 (2006).Search in Google Scholar
14 10.1021/ct6001785, D. Casanova, S. Gusarov, A. Kovalenko, T. Ziegler. J. Chem. Theory Comput.3, 458 (2007).Search in Google Scholar
15 10.1021/jp100158h, J. W. Kaminski, S. Gusarov, T. A. Wesolowski, A. Kovalenko. J. Phys. Chem. A114, 6082 (2010).Search in Google Scholar
16 10.1021/jp810887z, M. Malvaldi, S. Bruzzone, C. Chiappe, S. Gusarov, A. Kovalenko. J. Phys. Chem. B113, 3536 (2009).Search in Google Scholar
17 10.1016/S0009-2614(01)01241-6, A. Kovalenko, F. Hirata. Chem. Phys. Lett.349, 496 (2001).Search in Google Scholar
18 10.1142/S0219633602000282, A. Kovalenko, F. Hirata. J. Theor. Comput. Chem.1, 381 (2002).Search in Google Scholar
19 10.1021/ja051496t, J. G. Moralez, J. Raez, T. Yamazaki, R. K. Motkuri, A. Kovalenko, H. Fenniri. J. Am. Chem. Soc.127, 8307 (2005).Search in Google Scholar PubMed
20 10.1021/ja0706192, R. S. Johnson, T. Yamazaki, A. Kovalenko, H. Fenniri. J. Am. Chem. Soc.129, 5735 (2007).Search in Google Scholar PubMed
21 10.1021/la8001114, G. Tikhomirov, T. Yamazaki, A. Kovalenko, H. Fenniri. Langmuir24, 4447 (2007).Search in Google Scholar PubMed
22 10.1002/cphc.200900324, T. Yamazaki, H. Fenniri, A. Kovalenko. ChemPhysChem11, 361 (2010).Search in Google Scholar PubMed
23 10.1021/ja908775g, R. Chhabra, J. Moralez, J. Raez, T. Yamazaki, J.-Y. Cho, A. Myles, A. Kovalenko, H. Fenniri. J. Am. Chem. Soc. Commun.132, 32 (2010).Search in Google Scholar PubMed PubMed Central
24 10.1021/ja054434b, T. Imai, R. Hiraoka, A. Kovalenko, F. Hirata. J. Am. Chem. Soc. Commun.127, 15334 (2005).Search in Google Scholar PubMed
25 10.1021/jp807068k, N. Yoshida, T. Imai, S. Phongphanphanee, A. Kovalenko, F. Hirata. J. Phys. Chem. B (Feature Article) 113, 873 (2009).Search in Google Scholar PubMed
26 10.1021/jp2015758, T. Imai, N. Miyashita, Y. Sugita, A. Kovalenko, F. Hirata, A. Kidera. J. Phys. Chem. B115, 8288 (2011).Search in Google Scholar PubMed
27 10.1529/biophysj.107.123000, T. Yamazaki, N. Blinov, D. Wishart, A. Kovalenko. Biophys. J.95, 4540 (2008).Search in Google Scholar PubMed PubMed Central
28 10.1016/j.bpj.2009.09.062, N. Blinov, L. Dorosh, D. Wishart, A. Kovalenko. Biophys. J.98, 282 (2010).Search in Google Scholar PubMed PubMed Central
29 10.1080/08927022.2010.544306, N. Blinov, L. Dorosh, D. Wishart, A. Kovalenko. Mol. Simul.37, 718 (2011).Search in Google Scholar
30 10.1016/j.molliq.2011.09.011, A. Kovalenko, N. Blinov. J. Mol. Liq.164, 101 (2011).Search in Google Scholar
31 10.1021/ct300257v, D. Nikolic, N. Blinov, D. Wishart, A. Kovalenko. J. Chem. Theory Comput.8, 3356 (2012).Search in Google Scholar PubMed
32 10.1021/jp102587q, M. C. Stumpe, N. Blinov, D. Wishart, A. Kovalenko, V. S. Pande. J. Phys. Chem. B115, 205 (2011).Search in Google Scholar
33 10.1039/c1sm06542d, A. Kovalenko, A. E. Kobryn, S. Gusarov, O. Lyubimova, X. Liu, N. Blinov, M. Yoshida. Soft Matter8, 1508 (2012).Search in Google Scholar
34 10.1021/jp013400x, K. Yoshida, T. Yamaguchi, A. Kovalenko, F. Hirata. J. Phys. Chem. B106, 5042 (2002).Search in Google Scholar
35 10.1142/S0219633603000501, I. Omelyan, A. Kovalenko, F. Hirata. J. Theor. Comput. Chem.2, 193 (2003).Search in Google Scholar
36 10.1039/b416615a, A. Kovalenko, F. Hirata. Phys. Chem. Chem. Phys.7, 1785 (2005).Search in Google Scholar
37 A. Kovalenko, F. Hirata. “A molecular theory of solutions at liquid interfaces”, in Interfacial Nanochemistry: Molecular Science and Engineering at Liquid-Liquid Interfaces, H. Watarai (Ed.), Series: Nanostructure Science and Technology, D. J. Lockwood (Ed.), pp. 97–125, Springer (2005).10.1007/0-387-27541-X_5Search in Google Scholar
38 10.1063/1.463485, J. S. Perkyns, B. M. Pettitt. J. Chem. Phys.97, 7656 (1992).Search in Google Scholar
39 10.1007/BF01438859, B. Kvamme. Int. J. Thermophys.16, 743 (1995).Search in Google Scholar
40 10.1063/1.1748352, J. G. Kirkwood, F. P. Buff. J. Chem. Phys.19, 774 (1951).Search in Google Scholar
41 10.1063/1.1369138, Y. Harano, T. Imai, A. Kovalenko, M. Kinoshita, F. Hirata. J. Chem. Phys.114, 9506 (2001).Search in Google Scholar
42 10.1002/1097-0282(200112)59:7<512::AID-BIP1056>3.0.CO;2-C, T. Imai, Y. Harano, A. Kovalenko, F. Hirata. Biopolymers59, 512 (2001).Search in Google Scholar
43 10.1021/ct9000729, T. Yamazaki, A. Kovalenko. J. Chem. Theory Comput.5, 1723 (2009).Search in Google Scholar
44 10.1021/jp1082938, T. Yamazaki, A. Kovalenko. J. Phys. Chem. B115, 310 (2011).Search in Google Scholar
45 10.1021/ja905029t, T. Imai, K. Oda, A. Kovalenko, F. Hirata, A. Kidera. J. Am. Chem. Soc.131, 12430 (2009).Search in Google Scholar
46 10.1002/jcc.22974, S. Gusarov, B. S. Pujari, A. Kovalenko. J. Comput. Chem.33, 1478 (2012).Search in Google Scholar
47 10.1002/(SICI)1096-987X(19990715)20:9<928::AID-JCC4>3.0.CO;2-X, A. Kovalenko, S. Ten-no, F. Hirata. J. Comput. Chem.20, 928 (1999).Search in Google Scholar
48 10.1016/0009-2614(80)80396-4, P. Pulay. Chem. Phys. Lett.73, 393 (1980).Search in Google Scholar
49 10.1137/0907058, Y. Saad, M. H. Schultz. J. Sci. Stat. Comput.7, 856 (1986).Search in Google Scholar
50 10.1021/ct8002817, J. J. Howard, J. S. Perkyns, N. Choudhury, B. M. Pettitt. J. Chem. Theory Comput.4, 1928 (2008).Search in Google Scholar
51 10.1063/1.2431809, N. Minezawa, S. Kato. J. Chem. Phys.126, 054511 (2007).Search in Google Scholar
52 10.1073/pnas.0600118103, J. A. Wagoner, N. A. Baker. Proc. Natl. Acad. Sci. USA103, 8331 (2006).Search in Google Scholar
53 10.1021/ja029833a, R. M. Levy, L. Y. Zhang, A. K. Felts. J. Am. Chem. Soc.125, 9523 (2003).Search in Google Scholar
54 10.1002/jcc.10379, H. Gohlke, D. A. Case. J. Comput. Chem.25, 238 (2004).Search in Google Scholar
55 10.1021/jp984327m, K. Lum, D. Chandler, J. Weeks. J. Phys. Chem. B103, 4570 (1999).Search in Google Scholar
56 10.1016/0301-0104(73)80059-X, E. J. Baerends, P. Ros, D. E. Ellis. Chem. Phys.2, 41 (1973).Search in Google Scholar
57 10.1002/jcc.1056, G. te Velde, F. Bickelhaupt, S. van Gisbergen, C. Guerra, E. Baerends, J. Snijders, T. Ziegler. J. Comput. Chem.22, 931 (2001).Search in Google Scholar
58 C. F. Guerra, J. Snijders, G. te Velde, E. Baerends. Theor. Chem. Acc.99, 391 (1998).10.1007/s002140050021Search in Google Scholar
59 10.1021/j100132a040, T. A. Wesolowski, A. Warshel. J. Phys. Chem.97, 8050 (1993).Search in Google Scholar
60 10.1063/1.454603, L. Versluis, T. Ziegler. J. Chem. Phys.88, 322 (1988).Search in Google Scholar
61 10.1002/jcc.20844, T. Miyata, F. Hirata. J. Comput. Chem.29, 871 (2008).Search in Google Scholar PubMed
62 10.1063/1.3637035, I. P. Omelyan, A. Kovalenko. J. Chem. Phys.135, 114110 (2011).Search in Google Scholar PubMed
63 10.1063/1.476736, E. Barth, T. Schlick. J. Chem. Phys.109, 1617 (1998).Search in Google Scholar
64 10.1063/1.1332996, J. A. Izaguirre, D. P. Catarello, J. M. Wozniak, R. D. Skeel. J. Chem. Phys.114, 2090 (2001).Search in Google Scholar
65 10.1080/0026897021000018321, R. D. Skeel, J. A. Izaguirre. Mol. Phys.100, 3885 (2002).Search in Google Scholar
66 10.1137/S1540345903423567, Q. Ma, J. A. Izaguirre. Multiscale Model. Simul.2, 1 (2003).Search in Google Scholar
67 10.1063/1.2753496, S. Melchionna. J. Chem. Phys.127, 044108 (2007).Search in Google Scholar
68 10.1080/00268979600100761, G. J. Martyna, M. E. Tuckerman, D. J. Tobias, M. L. Klein. Mol. Phys.87, 1117 (1996).Search in Google Scholar
69 10.1021/jp990231w, A. Cheng, K. M. Merz Jr. J. Phys. Chem. B103, 5396 (1999).Search in Google Scholar
70 10.1016/S0166-1280(99)00314-0, J. Komeiji. Mol. Struct.: THEOCHEM530, 237 (2000).Search in Google Scholar
71 10.1002/jcc.10249, W. Shinoda, M. Mikami. J. Comput. Chem.24, 920 (2003).Search in Google Scholar PubMed
72 10.1063/1.3669385, I. P. Omelyan, A. Kovalenko. J. Chem. Phys.135, 234107 (2011).Search in Google Scholar PubMed
73 10.1063/1.1534582, P. Minary, G. J. Martyna, M. E. Tuckerman. J. Chem. Phys.118, 2510 (2003).Search in Google Scholar
74 10.1103/PhysRevLett.93.150201, P. Minary, M. E. Tuckerman, G. J. Martyna. Phys. Rev. Lett.93, 150201 (2004).Search in Google Scholar PubMed
75 J. B. Abrams, M. E. Tuckerman, G. J. Martyna. Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology, Vol. 1, Springer, Berlin (2006) [Lecture Notes in Physics703, 139 (2006)].Search in Google Scholar
76 10.1021/ct900460m, T. Luchko, S. Gusarov, D. R. Roe, C. Simmerling, D. A. Case, J. Tuszynski, A. Kovalenko. J. Chem. Theory Comput.6, 607 (2010).Search in Google Scholar PubMed PubMed Central
77 10.1080/08927022.2012.700486, I. P. Omelyan, A. Kovalenko. Mol. Simul. (2012).Search in Google Scholar
78 10.1038/nature07462, N. Bocquet, H. Nury, M. Baaden, C. Le Poupon, J.-P. Changeux, M. Delarue, P.-J. Corringer. Nature457, 111 (2009).Search in Google Scholar PubMed
79 10.1213/ANE.0b013e3181c4bc69, Y. Weng, L. Yang, P.-J. Corringer, J. M. Sonner. Anesthesia Analgesia110, 59 (2010).Search in Google Scholar PubMed PubMed Central
80 10.1529/biophysj.107.105478, D. Boda, W. Nonner, M. Valiskó, D. Henderson, B. Eisenberg, D. Gillespie. Biophys. J.93, 1960 (2007).Search in Google Scholar PubMed PubMed Central
81 10.1063/1.2212423, D. Boda, M. Valiskó, B. Eisenberg,W. Nonner, D. Henderson, D. Gillespie. J. Chem. Phys.125, 034901 (2006).Search in Google Scholar PubMed
82 10.1103/PhysRevLett.98.168102, D. Boda, M. Valiskó, B. Eisenberg, W. Nonner, D. Henderson, D. Gillespie. Phys. Rev. Lett.98, 168102 (2007).Search in Google Scholar PubMed
83 10.1021/j100188a054, D. J. Tobias, C. L. Brooks III. J. Phys. Chem.96, 3864 (1992).Search in Google Scholar
84 10.1021/jp048540w, D. S. Chekmarev, T. Ishida, R. M. Levy. J. Phys. Chem. B108, 19487 (2004).Search in Google Scholar
85 10.1063/1.1409954, A. Kovalenko, F. Hirata. J. Chem. Phys.115, 8620 (2001).Search in Google Scholar
86 A. Kovalenko, F. Hirata. Condensed Matter Phys.4, 643 (2001).10.5488/CMP.4.4.643Search in Google Scholar
87 10.1016/S0009-2614(03)01336-8, A. Tanimura, A. Kovalenko, F. Hirata. Chem. Phys. Lett.378, 638 (2003).Search in Google Scholar
88 10.1166/jctn.2004.038, A. Kovalenko. J. Comput. Theor. Nanosci.1, 398 (2004).Search in Google Scholar
89 10.1021/la061617i, A. Tanimura, A. Kovalenko, F. Hirata. Langmuir23, 1507 (2007).Search in Google Scholar
90 10.1103/PhysRevA.45.816, J. Given. Phys. Rev. A45, 816 (1992).Search in Google Scholar
91 10.1063/1.463883, J. Given, G. Stell. J. Chem. Phys.97, 4573 (1992).Search in Google Scholar
92 10.1016/0378-4371(94)90200-3, J. Given, G. Stell. Physica A209, 495 (1994).Search in Google Scholar
93 J. Given, G. Stell. In Condensed Matter Theories, Vol. 8, L. Blum, F. B. Malik (Eds.), pp. 395–410, Plenum, New York (1993).10.1007/978-1-4615-2934-7_35Search in Google Scholar
94 10.1063/1.463379, L. L. Lee. J. Chem. Phys.97, 8606 (1992).Search in Google Scholar
95 M. Endo, T. Takeda, Y. J. Kim, K. Koshiba, K. Ishii. Carbon Sci.1, 117 (2001).10.7209/tanso.2001.14Search in Google Scholar
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