19
1 Hybrid QM/MM Methods: Treating Electronic Phenomena …
50. Dehez F, Soetens JC, Chipot C, Ángyán JG, Millot C (2000) Determination of distributed polarizabilities from a statistical analysis of induction energies. J Phys Chem A 104:1293–1303
51. Martin M, Aguilar M, Chalmet S, Ruiz-Lopez MF (2001) An iterative procedure to determinate Lennard–Jone parameters for their use in quantum mechanics/molecular mechanics
liquid state simulations. 284:607–614
52. Dehez F, Chipot C, Millot C, Ángyán JG (2001) Fast and accurate determination of induction energies: reduction of topologically distributed polarizability models. Chem Phys Lett
338:180–188
53. Thompson MA (1996) QM/MMpol: a consistent model for solute/solvent polarization. Application to the aqueous solvation and spectroscopy of formaldehyde, acetaldehyde and acetone. J Phys Chem 100:14492–14507
54. Jacquemin D, Perpète EA, Laurent AD, Assfeld X, Adamo C (2009) Spectral properties
of self-assembled squaraine–tetralactam: a theoretical assessment. Phys Chem Chem Phys
11:1258–1262
55. Laurent AD, Assfeld X (2010) Effect of the enhanced cyan fluorescent proteinic framework
on the UV/visible absorption spectra of some chromophores. Interdisc Sci Comput Life Sci
2:38–47
56. Monari A, Very T, Rivail J-L, Assfeld X (2012) A QM/MM study on the spinach plastocyanin: redox properties and absorption spectra. Comp Theoret Chem 990:119–125
57. Monari A, Very T, Rivail J-L, Assfeld X (2012) Effects of mutations on the absorption spectrum of copper proteins: a QM/MM study Theor Chem Acc 131:1221
58. Very T, Despax S, Hébraud P, Monari A, Assfeld X (2012) Spectral properties of polypyridyl
ruthenium complex intercalated in DNA: theoretical insights on the surrounding effects for
[Ru(dppz)(bpy) 2 ]
2+
. Phys Chem Chem Phys 14:12496–12504
59. Chantzis A, Very T, Monari A, Assfeld X (2012) Improved treatment of surrounding effects:
UV/vis absorption properties of a solvated Ru(II) complex. J Chem Theory Comp 8:1536
60. Etienne T, Very T, Perpète EA, Monari A, Assfeld X (2013) A QM/MM study of the absorption spectrum of harmane in water solution and interacting with DNA: the crucial role of
dynamic effects J Phys Chem B 117:4973–4980
61. Moreau Y, Loss P-F, Assfeld X (2004) Solvent effects on the asymmetric Diels–Alder reaction between cyclopentadiene and (–)-menthyl acrylate revisited with the three-layer hybrid
local self-consistent field/molecular mechanics/self-consistent reaction field method. Theor
Chem Acc 112: 228–239
62. Ferré N, Assfeld X (2002) Application of the local self-consistent-field method to core-ionized and core-excited molecules, polymers, and proteins: true orthogonality between ground
and excited states. J Chem Phys 117:4119–4125
63. Loos PF, Assfeld X (2007) Core-ionized and core-excited states of macromolecules. Int J
Quantum Chem 107:2243–2252
64. Ferré N, Assfeld X, Rivail J-L (2002) Specific force field determination for the hybrid ab
initio QM/MM LSCF method. J Comput Chem 23:610–624
65. Fornili A, Loos P-F, Sironi M, Assfeld X (2006) Frozen core orbitals as an alternative to
specific frontier bond potential in hybrid quantum mechanics/molecular mechanics methods.
Chem Phys Lett 427:236–240
66. Loos P-F, Fornili A, Sironi M, Assfeld X (2007) Removing extra frontier parameters in QM/
MM methods: a tentative with the local self-consistent field approach. Comput Lett 4:473–
486
67. Loos P-F, Assfeld X (2007) On the frontier bond location in the QM/MM description of peptides and proteins. AIP Conf Proc 963:308–315
68. Ferré N, Assfeld X (2003) A new three-layer hybrid method (LSCF/MM/Madelung) devoted
to the study of chemical reactivity in zeolites. Preliminary results. J Mol Struct (Theochem)
632:83–90
69. Loos PF, Assfeld X (2007) Self-consistent strictly localized orbitals. J Chem Theory Comput
3:1047–1053
1 Hybrid QM/MM Methods: Treating Electronic Phenomena …
50. Dehez F, Soetens JC, Chipot C, Ángyán JG, Millot C (2000) Determination of distributed polarizabilities from a statistical analysis of induction energies. J Phys Chem A 104:1293–1303
51. Martin M, Aguilar M, Chalmet S, Ruiz-Lopez MF (2001) An iterative procedure to determinate Lennard–Jone parameters for their use in quantum mechanics/molecular mechanics
liquid state simulations. 284:607–614
52. Dehez F, Chipot C, Millot C, Ángyán JG (2001) Fast and accurate determination of induction energies: reduction of topologically distributed polarizability models. Chem Phys Lett
338:180–188
53. Thompson MA (1996) QM/MMpol: a consistent model for solute/solvent polarization. Application to the aqueous solvation and spectroscopy of formaldehyde, acetaldehyde and acetone. J Phys Chem 100:14492–14507
54. Jacquemin D, Perpète EA, Laurent AD, Assfeld X, Adamo C (2009) Spectral properties
of self-assembled squaraine–tetralactam: a theoretical assessment. Phys Chem Chem Phys
11:1258–1262
55. Laurent AD, Assfeld X (2010) Effect of the enhanced cyan fluorescent proteinic framework
on the UV/visible absorption spectra of some chromophores. Interdisc Sci Comput Life Sci
2:38–47
56. Monari A, Very T, Rivail J-L, Assfeld X (2012) A QM/MM study on the spinach plastocyanin: redox properties and absorption spectra. Comp Theoret Chem 990:119–125
57. Monari A, Very T, Rivail J-L, Assfeld X (2012) Effects of mutations on the absorption spectrum of copper proteins: a QM/MM study Theor Chem Acc 131:1221
58. Very T, Despax S, Hébraud P, Monari A, Assfeld X (2012) Spectral properties of polypyridyl
ruthenium complex intercalated in DNA: theoretical insights on the surrounding effects for
[Ru(dppz)(bpy) 2 ]
2+
. Phys Chem Chem Phys 14:12496–12504
59. Chantzis A, Very T, Monari A, Assfeld X (2012) Improved treatment of surrounding effects:
UV/vis absorption properties of a solvated Ru(II) complex. J Chem Theory Comp 8:1536
60. Etienne T, Very T, Perpète EA, Monari A, Assfeld X (2013) A QM/MM study of the absorption spectrum of harmane in water solution and interacting with DNA: the crucial role of
dynamic effects J Phys Chem B 117:4973–4980
61. Moreau Y, Loss P-F, Assfeld X (2004) Solvent effects on the asymmetric Diels–Alder reaction between cyclopentadiene and (–)-menthyl acrylate revisited with the three-layer hybrid
local self-consistent field/molecular mechanics/self-consistent reaction field method. Theor
Chem Acc 112: 228–239
62. Ferré N, Assfeld X (2002) Application of the local self-consistent-field method to core-ionized and core-excited molecules, polymers, and proteins: true orthogonality between ground
and excited states. J Chem Phys 117:4119–4125
63. Loos PF, Assfeld X (2007) Core-ionized and core-excited states of macromolecules. Int J
Quantum Chem 107:2243–2252
64. Ferré N, Assfeld X, Rivail J-L (2002) Specific force field determination for the hybrid ab
initio QM/MM LSCF method. J Comput Chem 23:610–624
65. Fornili A, Loos P-F, Sironi M, Assfeld X (2006) Frozen core orbitals as an alternative to
specific frontier bond potential in hybrid quantum mechanics/molecular mechanics methods.
Chem Phys Lett 427:236–240
66. Loos P-F, Fornili A, Sironi M, Assfeld X (2007) Removing extra frontier parameters in QM/
MM methods: a tentative with the local self-consistent field approach. Comput Lett 4:473–
486
67. Loos P-F, Assfeld X (2007) On the frontier bond location in the QM/MM description of peptides and proteins. AIP Conf Proc 963:308–315
68. Ferré N, Assfeld X (2003) A new three-layer hybrid method (LSCF/MM/Madelung) devoted
to the study of chemical reactivity in zeolites. Preliminary results. J Mol Struct (Theochem)
632:83–90
69. Loos PF, Assfeld X (2007) Self-consistent strictly localized orbitals. J Chem Theory Comput
3:1047–1053