62. Lin, H., Truhlar, D.G.: Redistributed charge and dipole schemes for combined quantum
mechanical and molecular mechanical calculations. J. Phys. Chem. A 109(17), 3991–4004
(2005)
63. Reuter, N., Dejaegere, A., Maigret, B., Karplus, M.: Frontier bonds in QM/MM methods: a
comparison of different approaches. J. Phys. Chem. A 104(8), 1720–1735 (2000)
64. Riccardi, D., Schaefer, P., Cui, Q.: pK(a) calculations in solution and proteins with QM/MM
free energy perturbation simulations: a quantitative test of QM/MM protocols. J. Phys. Chem.
B 109(37), 17715–17733 (2005)
65. Ferre, N., Assfeld, X., Rivail, J.L.: Specific force field parameters determination for the
hybrid ab initio QM/MM LSCF method. J. Comput. Chem. 23(6), 610–624 (2002)
66. Thery, V., Rinaldi, D., Rivail, J.L., Maigret, B., Ferenczy, G.G.: Quantum-mechanical
computations on very large molecular-systems - the local self-consistent-field method.
J. Comput. Chem. 15(3), 269–282 (1994)
67. Gao, J., Amara, P., Alhambra, C., Field, M.J.: A generalized hybrid orbital (GHO) method for
the treatment of boundary atoms in combined QM/MM calculations. J. Phys. Chem. A 102
(24), 4714–4721 (1998)
68. Rodriguez, A., Oliva, C., Gonzalez, M., van der Kamp, M., Mulholland, A.J.: Comparison of
different quantum mechanical/molecular mechanics boundary treatments in the reaction of
the hepatitis C virus NS3 protease with the NS5A/5B substrate. J. Phys. Chem. B 111(44),
12909–12915 (2007)
69. Philipp, D.M., Friesner, R.A.: Mixed ab initio QM/MM modeling using frozen orbitals and
tests with alanine dipeptide and tetrapeptide. J. Comput. Chem. 20, 1468–1494 (1999)
70. Fornili, A., Loos, P.F., Sironi, M., Assfeld, X.: Frozen core orbitals as an alternative to
specific frontier bond potential in hybrid quantum mechanics/molecular mechanics methods.
Chem. Phys. Lett. 427(1–3), 236–240 (2006)
71. Zhang, Y.K.: Pseudobond ab initio QM/MM approach and its applications to enzyme
reactions. Theor. Chem. Acc. 116(1–3), 43–50 (2006)
72. Zhang, Y.K., Lee, T.S., Yang, W.T.: A pseudobond approach to combining quantum
mechanical and molecular mechanical methods. J. Chem. Phys. 110(1), 46–54 (1999)
73. DiLabio, G.A., Hurley, M.M., Christiansen, P.A.: Simple one-electron quantum capping
potentials for use in hybrid QM/MM studies of biological molecules. J. Chem. Phys. 116,
9578–9584 (2002)
74. Bessac, F., Alary, F., Carissan, Y., Heully, J.L., Daudey, J.P., Poteau, R.: Effective group
potentials: a powerful tool for hybrid QM/MM methods? THEOCHEM 632, 43–59 (2003)
75. Poteau, R., Ortega, I., Alary, F., Solis, A.R., Barthelat, J.C., Daudey, J.P.: Effective group
potentials. I. Method. J. Phys. Chem. A 105(1), 198–205 (2001)
76. Yasuda, K., Yamaki, D.: Simple minimum principle to derive a quantum-mechanical/
molecular-mechanical method. J. Chem. Phys. 121(9), 3964–3972 (2004)
77. Antes, I., Thiel, W.: Adjusted connection atoms for combined quantum mechanical and
molecular mechanical methods. J. Phys. Chem. A 103, 9290–9295 (1999)
78. Lin, H., Truhlar, D.G.: QM/MM: what have we learned, where are we, and where do we go
from here? Theor. Chem. Acc. 117(2), 185–199 (2007)
79. Senn, H.M., Thiel, W.: QM/MM methods for biological systems. Top. Curr. Chem. 268,
173290 (2007)
80. Hayashi, S., Ohmine, I.: Proton transfer in bacteriorhodopsin: structure, excitation, IR
spectra, and potential energy surface analyses by an ab initio QM/MM method. J. Phys.
Chem. B 104, 10678–10691 (2000)
81. Schreiber, M., Buß, V., Sugihara, M.: Exploring the opsin shift with ab initio methods:
geometry and counterion effects on the electronic spectrum of retinal. J. Chem. Phys. 119
(23), 12045–12048 (2003)
82. Reed, A.E., Weinstock, R.B., Weinhold, F.: Natural population analysis. J. Chem. Phys. 83
(2), 735–746 (1985)
62
M. Wanko and A. Rubio
mechanical and molecular mechanical calculations. J. Phys. Chem. A 109(17), 3991–4004
(2005)
63. Reuter, N., Dejaegere, A., Maigret, B., Karplus, M.: Frontier bonds in QM/MM methods: a
comparison of different approaches. J. Phys. Chem. A 104(8), 1720–1735 (2000)
64. Riccardi, D., Schaefer, P., Cui, Q.: pK(a) calculations in solution and proteins with QM/MM
free energy perturbation simulations: a quantitative test of QM/MM protocols. J. Phys. Chem.
B 109(37), 17715–17733 (2005)
65. Ferre, N., Assfeld, X., Rivail, J.L.: Specific force field parameters determination for the
hybrid ab initio QM/MM LSCF method. J. Comput. Chem. 23(6), 610–624 (2002)
66. Thery, V., Rinaldi, D., Rivail, J.L., Maigret, B., Ferenczy, G.G.: Quantum-mechanical
computations on very large molecular-systems - the local self-consistent-field method.
J. Comput. Chem. 15(3), 269–282 (1994)
67. Gao, J., Amara, P., Alhambra, C., Field, M.J.: A generalized hybrid orbital (GHO) method for
the treatment of boundary atoms in combined QM/MM calculations. J. Phys. Chem. A 102
(24), 4714–4721 (1998)
68. Rodriguez, A., Oliva, C., Gonzalez, M., van der Kamp, M., Mulholland, A.J.: Comparison of
different quantum mechanical/molecular mechanics boundary treatments in the reaction of
the hepatitis C virus NS3 protease with the NS5A/5B substrate. J. Phys. Chem. B 111(44),
12909–12915 (2007)
69. Philipp, D.M., Friesner, R.A.: Mixed ab initio QM/MM modeling using frozen orbitals and
tests with alanine dipeptide and tetrapeptide. J. Comput. Chem. 20, 1468–1494 (1999)
70. Fornili, A., Loos, P.F., Sironi, M., Assfeld, X.: Frozen core orbitals as an alternative to
specific frontier bond potential in hybrid quantum mechanics/molecular mechanics methods.
Chem. Phys. Lett. 427(1–3), 236–240 (2006)
71. Zhang, Y.K.: Pseudobond ab initio QM/MM approach and its applications to enzyme
reactions. Theor. Chem. Acc. 116(1–3), 43–50 (2006)
72. Zhang, Y.K., Lee, T.S., Yang, W.T.: A pseudobond approach to combining quantum
mechanical and molecular mechanical methods. J. Chem. Phys. 110(1), 46–54 (1999)
73. DiLabio, G.A., Hurley, M.M., Christiansen, P.A.: Simple one-electron quantum capping
potentials for use in hybrid QM/MM studies of biological molecules. J. Chem. Phys. 116,
9578–9584 (2002)
74. Bessac, F., Alary, F., Carissan, Y., Heully, J.L., Daudey, J.P., Poteau, R.: Effective group
potentials: a powerful tool for hybrid QM/MM methods? THEOCHEM 632, 43–59 (2003)
75. Poteau, R., Ortega, I., Alary, F., Solis, A.R., Barthelat, J.C., Daudey, J.P.: Effective group
potentials. I. Method. J. Phys. Chem. A 105(1), 198–205 (2001)
76. Yasuda, K., Yamaki, D.: Simple minimum principle to derive a quantum-mechanical/
molecular-mechanical method. J. Chem. Phys. 121(9), 3964–3972 (2004)
77. Antes, I., Thiel, W.: Adjusted connection atoms for combined quantum mechanical and
molecular mechanical methods. J. Phys. Chem. A 103, 9290–9295 (1999)
78. Lin, H., Truhlar, D.G.: QM/MM: what have we learned, where are we, and where do we go
from here? Theor. Chem. Acc. 117(2), 185–199 (2007)
79. Senn, H.M., Thiel, W.: QM/MM methods for biological systems. Top. Curr. Chem. 268,
173290 (2007)
80. Hayashi, S., Ohmine, I.: Proton transfer in bacteriorhodopsin: structure, excitation, IR
spectra, and potential energy surface analyses by an ab initio QM/MM method. J. Phys.
Chem. B 104, 10678–10691 (2000)
81. Schreiber, M., Buß, V., Sugihara, M.: Exploring the opsin shift with ab initio methods:
geometry and counterion effects on the electronic spectrum of retinal. J. Chem. Phys. 119
(23), 12045–12048 (2003)
82. Reed, A.E., Weinstock, R.B., Weinhold, F.: Natural population analysis. J. Chem. Phys. 83
(2), 735–746 (1985)
62
M. Wanko and A. Rubio