20
A. Monari and X. Assfeld
70. Boys SF (1960) Construction of some molecular orbitals to be approximately invariant for
changes from one molecule to another. Rev Mod Phys 32:296–299
71. Monard G, Loos M, Théry V, Baka K, Rivail JL (1996) Hybrid classical quantum force field
for modeling very large molecules. Int J Quantum Chem 58:153–159
72. Foster JM, Boys SF (1960) Canonical configurational interaction procedure. Rev Mod Phys
32:300–302
73. Magnasco V, Perico A (1967) Uniform localization of atomic and molecular orbitals. I. J
Chem Phys 47:971–981
74. Weinstein H, Pauncz R (1968) Molecular orbital set determined by a localization procedure.
Symp Faraday Soc 2:23–31
75. Pipek J, Mezey PG (1989) A fast intrinsic localization procedure applicable for ab initio and
semiempirical linear combination of atomic orbital wave functions. J Chem Phys 90:4916–
4926
76. Fornili A, Moreau Y, Sironi M, Assfeld X (2006) On the suitability of strictly localized orbitals for hybrid QM/MM calculations. J Comput Chem 27:515–523
77. Sironi M, Famulari A (2000) An orthogonal approach to determine extremely localised molecular orbitals. Theor Chem Acc 103:417–422
78. Antonczak S, Monard G, Ruiz-López MF, Rivail J-L (1998) Modeling of peptide hydrolysis
by thermolysin. A semiempirical and QM/MM study. J Am Chem Soc. 120:8825–8833
79. Fornili A, Sironi M, Raimondi M (2003) Determination of extremely localized molecular
orbitals and their application to quantum mechanics/molecular mechanics methods and to the
study of intramolecular hydrogen bonding. J Mol Struct (Theochem) 632:157–172
80. Genoni A, Ghitti M, Pieraccini S, Sironi M (2005) A novel extremely localized molecular
orbitals based technique for the one-electron density matrix computation. Chem Phys Lett
415:256–260
81. Ruiz-Pernia J, Luk L, Garcia-Meseguer R, Marti S, Loveridge J, Tuñón I, Moliner V, Allemann R (2013) Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase. J Am Chem Soc. doi:10.1021/ja410519h
82. Luk L, Ruiz-Pernia J, Dawson W, Roca M, Loveridge J, Glowacki D, Harvey J, Mulholland
A, Tuñón I, Moliner V, Allemann R (2013) Unravelling the role of protein dynamics in dihydrofolate reductase catalysis. Proc Nat Acad Sci U S A 110:16344–16349
83. Jacquemin D, Mennucci B, Adamo C (2011) Excited-state calculations with TD-DFT: from
benchmarcks to simulations in complex environments. Phys Chem Chem Phys 13:16987–
16998
84. Gonzaléz L, Escudero D, Serrano-Andrés (2012) Progress and challenges in the calculation
of electronic excited states. Chem Phys Chem 13:28–51
85. Laurent AD, Jacquemin D (2013) TD-DFT benchmarks: a review. Int J Quant Chem.
doi:10.1002/qua.24438
86. Clark KM, Yu Y, Marshall NM, Sieracki NA, Nilges MJ, Blackburn NJ., van de Donk WA.,
Lu Y (2010) Transforming a blue copper into a red copper protein: engineering cystein and
homocystein into the axial position of azurin using site-directed mutagenesis and expressed
protein ligation. J Am Chem Soc 132:10093–10101
87. Abtouche S, Very T, Monari A, Brahimi M, Assfeld X (2013) Insights on the interactions of
polychlorobiphenyl with nucleic acid base. J Mol Model 19:581–588
A. Monari and X. Assfeld
70. Boys SF (1960) Construction of some molecular orbitals to be approximately invariant for
changes from one molecule to another. Rev Mod Phys 32:296–299
71. Monard G, Loos M, Théry V, Baka K, Rivail JL (1996) Hybrid classical quantum force field
for modeling very large molecules. Int J Quantum Chem 58:153–159
72. Foster JM, Boys SF (1960) Canonical configurational interaction procedure. Rev Mod Phys
32:300–302
73. Magnasco V, Perico A (1967) Uniform localization of atomic and molecular orbitals. I. J
Chem Phys 47:971–981
74. Weinstein H, Pauncz R (1968) Molecular orbital set determined by a localization procedure.
Symp Faraday Soc 2:23–31
75. Pipek J, Mezey PG (1989) A fast intrinsic localization procedure applicable for ab initio and
semiempirical linear combination of atomic orbital wave functions. J Chem Phys 90:4916–
4926
76. Fornili A, Moreau Y, Sironi M, Assfeld X (2006) On the suitability of strictly localized orbitals for hybrid QM/MM calculations. J Comput Chem 27:515–523
77. Sironi M, Famulari A (2000) An orthogonal approach to determine extremely localised molecular orbitals. Theor Chem Acc 103:417–422
78. Antonczak S, Monard G, Ruiz-López MF, Rivail J-L (1998) Modeling of peptide hydrolysis
by thermolysin. A semiempirical and QM/MM study. J Am Chem Soc. 120:8825–8833
79. Fornili A, Sironi M, Raimondi M (2003) Determination of extremely localized molecular
orbitals and their application to quantum mechanics/molecular mechanics methods and to the
study of intramolecular hydrogen bonding. J Mol Struct (Theochem) 632:157–172
80. Genoni A, Ghitti M, Pieraccini S, Sironi M (2005) A novel extremely localized molecular
orbitals based technique for the one-electron density matrix computation. Chem Phys Lett
415:256–260
81. Ruiz-Pernia J, Luk L, Garcia-Meseguer R, Marti S, Loveridge J, Tuñón I, Moliner V, Allemann R (2013) Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase. J Am Chem Soc. doi:10.1021/ja410519h
82. Luk L, Ruiz-Pernia J, Dawson W, Roca M, Loveridge J, Glowacki D, Harvey J, Mulholland
A, Tuñón I, Moliner V, Allemann R (2013) Unravelling the role of protein dynamics in dihydrofolate reductase catalysis. Proc Nat Acad Sci U S A 110:16344–16349
83. Jacquemin D, Mennucci B, Adamo C (2011) Excited-state calculations with TD-DFT: from
benchmarcks to simulations in complex environments. Phys Chem Chem Phys 13:16987–
16998
84. Gonzaléz L, Escudero D, Serrano-Andrés (2012) Progress and challenges in the calculation
of electronic excited states. Chem Phys Chem 13:28–51
85. Laurent AD, Jacquemin D (2013) TD-DFT benchmarks: a review. Int J Quant Chem.
doi:10.1002/qua.24438
86. Clark KM, Yu Y, Marshall NM, Sieracki NA, Nilges MJ, Blackburn NJ., van de Donk WA.,
Lu Y (2010) Transforming a blue copper into a red copper protein: engineering cystein and
homocystein into the axial position of azurin using site-directed mutagenesis and expressed
protein ligation. J Am Chem Soc 132:10093–10101
87. Abtouche S, Very T, Monari A, Brahimi M, Assfeld X (2013) Insights on the interactions of
polychlorobiphenyl with nucleic acid base. J Mol Model 19:581–588