104. Patel, S., Brooks, C.L.: CHARMM fluctuating charge force field for proteins: I – Parameterization and application to bulk organic liquid simulations. J. Comput. Chem. 25(1), 1–15
(2004)
105. Patel, S., MacKerell, A.D., Brooks, C.L.: CHARMM fluctuating charge force field for
proteins: II – Protein/solvent properties from molecular dynamics simulations using a
nonadditive electrostatic model. J. Comput. Chem. 25(12), 1504–1514 (2004)
106. Kaminski, G.A., Stern, H.A., Berne, B.J., Friesner, R.A.: Development of an accurate and
robust polarizable molecular mechanics force field from ab initio quantum chemistry. J. Phys.
Chem. A 108(4), 621–627 (2004)
107. Kaminski, G.A., Stern, H.A., Berne, B.J., Friesner, R.A., Cao, Y.X.X., Murphy, R.B., Zhou,
R.H., Halgren, T.A.: Development of a polarizable force field for proteins via ab initio
quantum chemistry: first generation model and gas phase tests. J. Comput. Chem. 23(16),
1515–1531 (2002)
108. Gresh, N., Claverie, P., Pullman, A.: Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies.
Comparison with ab initio scf computations. Theor. Chim. Acta 66(1), 1–20 (1984)
109. Guo, H., Gresh, N., Roques, B.P., Salahub, D.R.: Many-body effects in systems of peptide
hydrogen-bonded networks and their contributions to ligand binding: a comparison of the
performances of DFT and polarizable molecular mechanics. J. Phys. Chem. B 104(41),
9746–9754 (2000)
110. Adcock, S.A., McCammon, J.A.: Molecular dynamics: survey of methods for simulating the
activity of proteins. Chem. Rev. 106(5), 1589–1615 (2006)
111. Wende, T., Wanko, M., Jiang, L., Meijer, G., Asmis, K.R., Rubio, A.: Spectroscopic
characterization of solvent-mediated folding in dicarboxylate dianions. Angew. Chem. Int.
Ed. 50, 3807–3810 (2011)
112. Laio, A., Parrinello, M.: Escaping free-energy minima. PNAS 99(20), 12562–12566 (2002)
113. Brancato, G., Barone, V., Rega, N.: Theoretical modeling of spectroscopic properties of
molecules in solution: toward an effective dynamical discrete/continuum approach. Theor.
Chem. Acc. 117(5–6), 1001–1015 (2007)
114. Brancato, G., Rega, N., Barone, V.: A quantum mechanical/molecular dynamics/mean field
study of acrolein in aqueous solution: analysis of h bonding and bulk effects on spectroscopic
properties. J. Chem. Phys. 125(16), 164,515 (2006)
115. Georg, H.C., Coutinho, K., Canuto, S.: A sequential monte carlo quantum mechanics study of
the hydrogen-bond interaction and the solvatochromic shift of the n-pi(*) transition of
acrolein in water. J. Chem. Phys. 123, 124307 (2005)
116. Hoffmann, M., Wanko, M., Strodel, P., Ko ¨nig, P., Frauenheim, T., Schulten, K., Thiel, W.,
Tajkhorshid, E., Elstner, M.: Color tuning in rhodopsins: the mechanism for the spectral shift
between bacteriorhodopsin and sensory rhodopsin II. J. Am. Chem. Soc. 128, 10808–10818
(2006)
117. Rajamani, R., Gao, J.: Combined QM/MM study of the opsin shift in bacteriorhodopsin.
J. Comput. Chem. 23(1), 96–105 (2002)
118. Warshel, A., Chu, Z.T.: Nature of the surface crossing process in bacteriorhodopsin: computer simulations of the quantum dynamics of the primary photochemical event. J. Phys.
Chem. B 105, 9857–9871 (2001)
119. Ro ¨hrig, U.F., Sebastiani, D.: Nmr chemical shifts of the rhodopsin chromophore in the dark
state and in bathorhodopsin: a hybrid qm/mm molecular dynamics study. J. Phys. Chem. B
112, 1267–1274 (2008)
120. Yang, X., Fu, Y.J., Wang, X.B., Slavicek, P., Mucha, M., Jungwirth, P., Wang, L.S.: Solventmediated folding of a doubly charged anion. J. Am. Chem. Soc. 126(3), 876–883 (2004)
121. Plasser, F., Barbatti, M., Aquino, A., Lischka, H.: Electronically excited states and
photodynamics: a continuing challenge. Theor. Chem. Acc. 131(1), 1–14 (2012)
122. Tully, J.C.: Perspective: Nonadiabatic dynamics theory. J. Chem. Phys. 137(22), 22A301
(2012)
64
M. Wanko and A. Rubio
(2004)
105. Patel, S., MacKerell, A.D., Brooks, C.L.: CHARMM fluctuating charge force field for
proteins: II – Protein/solvent properties from molecular dynamics simulations using a
nonadditive electrostatic model. J. Comput. Chem. 25(12), 1504–1514 (2004)
106. Kaminski, G.A., Stern, H.A., Berne, B.J., Friesner, R.A.: Development of an accurate and
robust polarizable molecular mechanics force field from ab initio quantum chemistry. J. Phys.
Chem. A 108(4), 621–627 (2004)
107. Kaminski, G.A., Stern, H.A., Berne, B.J., Friesner, R.A., Cao, Y.X.X., Murphy, R.B., Zhou,
R.H., Halgren, T.A.: Development of a polarizable force field for proteins via ab initio
quantum chemistry: first generation model and gas phase tests. J. Comput. Chem. 23(16),
1515–1531 (2002)
108. Gresh, N., Claverie, P., Pullman, A.: Theoretical studies of molecular conformation. Derivation of an additive procedure for the computation of intramolecular interaction energies.
Comparison with ab initio scf computations. Theor. Chim. Acta 66(1), 1–20 (1984)
109. Guo, H., Gresh, N., Roques, B.P., Salahub, D.R.: Many-body effects in systems of peptide
hydrogen-bonded networks and their contributions to ligand binding: a comparison of the
performances of DFT and polarizable molecular mechanics. J. Phys. Chem. B 104(41),
9746–9754 (2000)
110. Adcock, S.A., McCammon, J.A.: Molecular dynamics: survey of methods for simulating the
activity of proteins. Chem. Rev. 106(5), 1589–1615 (2006)
111. Wende, T., Wanko, M., Jiang, L., Meijer, G., Asmis, K.R., Rubio, A.: Spectroscopic
characterization of solvent-mediated folding in dicarboxylate dianions. Angew. Chem. Int.
Ed. 50, 3807–3810 (2011)
112. Laio, A., Parrinello, M.: Escaping free-energy minima. PNAS 99(20), 12562–12566 (2002)
113. Brancato, G., Barone, V., Rega, N.: Theoretical modeling of spectroscopic properties of
molecules in solution: toward an effective dynamical discrete/continuum approach. Theor.
Chem. Acc. 117(5–6), 1001–1015 (2007)
114. Brancato, G., Rega, N., Barone, V.: A quantum mechanical/molecular dynamics/mean field
study of acrolein in aqueous solution: analysis of h bonding and bulk effects on spectroscopic
properties. J. Chem. Phys. 125(16), 164,515 (2006)
115. Georg, H.C., Coutinho, K., Canuto, S.: A sequential monte carlo quantum mechanics study of
the hydrogen-bond interaction and the solvatochromic shift of the n-pi(*) transition of
acrolein in water. J. Chem. Phys. 123, 124307 (2005)
116. Hoffmann, M., Wanko, M., Strodel, P., Ko ¨nig, P., Frauenheim, T., Schulten, K., Thiel, W.,
Tajkhorshid, E., Elstner, M.: Color tuning in rhodopsins: the mechanism for the spectral shift
between bacteriorhodopsin and sensory rhodopsin II. J. Am. Chem. Soc. 128, 10808–10818
(2006)
117. Rajamani, R., Gao, J.: Combined QM/MM study of the opsin shift in bacteriorhodopsin.
J. Comput. Chem. 23(1), 96–105 (2002)
118. Warshel, A., Chu, Z.T.: Nature of the surface crossing process in bacteriorhodopsin: computer simulations of the quantum dynamics of the primary photochemical event. J. Phys.
Chem. B 105, 9857–9871 (2001)
119. Ro ¨hrig, U.F., Sebastiani, D.: Nmr chemical shifts of the rhodopsin chromophore in the dark
state and in bathorhodopsin: a hybrid qm/mm molecular dynamics study. J. Phys. Chem. B
112, 1267–1274 (2008)
120. Yang, X., Fu, Y.J., Wang, X.B., Slavicek, P., Mucha, M., Jungwirth, P., Wang, L.S.: Solventmediated folding of a doubly charged anion. J. Am. Chem. Soc. 126(3), 876–883 (2004)
121. Plasser, F., Barbatti, M., Aquino, A., Lischka, H.: Electronically excited states and
photodynamics: a continuing challenge. Theor. Chem. Acc. 131(1), 1–14 (2012)
122. Tully, J.C.: Perspective: Nonadiabatic dynamics theory. J. Chem. Phys. 137(22), 22A301
(2012)
64
M. Wanko and A. Rubio