18
A. Monari and X. Assfeld
29. Dupuis M, Aida M, Kawashima Y, Hirao K (2002) A polarizable mixed hamiltonian model of
electronic structure for micro-solvated excited states. I energy and gradients formulation and
application to formaldehyde (
1
A 2 ) J Chem Phys 117:1242–1255
30. Gresh N, Andrés Cisneros G, Darden TA, Piquemal J-P (2007) Anisotropic, polarizable molecular mechanics studies of inter- and intramolecular interactions and ligand–macromolecule-complexes. A bottom-up strategy. J Chem Theory Comput 3:1960–1986
31. Field MJ, Bash PA, Kearplus M (1990) A combined quantum mechanical and molecular
mechanical potential for molecular dynamic simulations J Comput Chem 11:700–733
32. Kaminski GA, Jorgensen WL (1998) A quantum mechanical and molecular mechanical
method based on cm1a charges: applications to solvent effects on organic equilibria and
reactions. J Phys Chem B 102:1787–1796
33. Ferré N, Olivucci M (2003) The amide bond: pitfalls and drawback of the link atom scheme.
J Mol Struct (Theochem) 632:71–84
34. Antes I, Thiel W (1999) Adjusted connection atoms for combined quantum mechanical and
molecular mechanical methods. J Phys Chem A 103:9290–9295
35. Ranganathan S, Gready JE (1997) Hybrid quantum and molecular mechanical (QM/MM)
studies on the pyruvate to l-lactate interconversion in l-lactate dehydrogenase. J Phys Chem
B 101:5614–5618
36. Swart M (2003) AddRemove: a new link model for use in QM/MM studies. Int J Quantum
Chem 91:177–183
37. Das D, Eurenius KP, Billings EM, Sherwood P, Chatfield DC, Hodoscek M, Brook BR
(2002) Optimization of quantum mechanical molecular mechanical partitioning schemes:
Gaussian delocalization of molecular mechanical charges and the double link atom method.
J Chem Phys 117:10534–10547
38. Di Labio GA, Hurley MM, Christiansen PA (2002) Simple one-electron quantum capping potentials for use in hybrid QM/MM studies of biological molecules. J Chem Phys 116:9578–
9584
39. Zhang Y, Lee T-S, Yang W (1999) A pseudobond approach to combining quantum mechanical and molecular mechanical methods. J Chem Phys 110:46–54
40. Xiao C, Zhang Y (2007) Design-atom approach for quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons. J Chem Phys
127:124102
41. Ferenczy GG, Rivail J-L, Surjan PR, Naray-Szabo G (1992) NDDO fragment self-consistentfield approximation for large electronic systems. J Comput Chem 13:830–837
42. Théry V, Rinaldi D, Rivail J-L, Maigret B, Ferenczy GG (1994) Quantum mechanical computations on very large molecular systems: the local self-consistent field method. J Comput
Chem 15:269–282
43. Stewart JJP (1989) Optimization of parameters for semiempirical methods I. Method J Comput Chem 10:209–220
44. Gao G, Amara P, Alhambra C, Field MJ (1998) A generalized hybrid orbital (GHO) method
for the treatment of boundary atoms in combined QM/MM calculations. J Phys Chem A
102:4714–4721
45. Pu J, Gao J, Truhlar DG (2004) Generalized hybrid orbital (GHO) method for combining ab
initio Hartree–Fock wave functions with molecular mechanics. J Phys Chem A 108:632–650
46. Pu J, Gao J, Truhlar DG (2004) Combining self-consistent-charge density-functional tightbinding (SCC-DFTB) with molecular mechanics by the generalized hybrid orbital (GHO)
method. J Phys Chem A 108:5454–5463
47. Pu J, Truhlar DG (2005) Redristributed charge and dipole schemes for combined quantum
mechanical and molecular mechanical calculations J Phys Chem A 109:3991–4004
48. Maseras F, Morokuma K (1995) IMOMM, a new integrated ab initio + molecular mechanics
geometry optimization scheme of equilibrium structure and transition states. J Comput Chem
16:1170–1179
49. Celebi N, Ángyán JG, Dehez F, Millot C, Chipot C (2000) Distributed polarizabilities derived from induction energies: a finite perturbation approach. J Chem Phys 112:2709–2717
A. Monari and X. Assfeld
29. Dupuis M, Aida M, Kawashima Y, Hirao K (2002) A polarizable mixed hamiltonian model of
electronic structure for micro-solvated excited states. I energy and gradients formulation and
application to formaldehyde (
1
A 2 ) J Chem Phys 117:1242–1255
30. Gresh N, Andrés Cisneros G, Darden TA, Piquemal J-P (2007) Anisotropic, polarizable molecular mechanics studies of inter- and intramolecular interactions and ligand–macromolecule-complexes. A bottom-up strategy. J Chem Theory Comput 3:1960–1986
31. Field MJ, Bash PA, Kearplus M (1990) A combined quantum mechanical and molecular
mechanical potential for molecular dynamic simulations J Comput Chem 11:700–733
32. Kaminski GA, Jorgensen WL (1998) A quantum mechanical and molecular mechanical
method based on cm1a charges: applications to solvent effects on organic equilibria and
reactions. J Phys Chem B 102:1787–1796
33. Ferré N, Olivucci M (2003) The amide bond: pitfalls and drawback of the link atom scheme.
J Mol Struct (Theochem) 632:71–84
34. Antes I, Thiel W (1999) Adjusted connection atoms for combined quantum mechanical and
molecular mechanical methods. J Phys Chem A 103:9290–9295
35. Ranganathan S, Gready JE (1997) Hybrid quantum and molecular mechanical (QM/MM)
studies on the pyruvate to l-lactate interconversion in l-lactate dehydrogenase. J Phys Chem
B 101:5614–5618
36. Swart M (2003) AddRemove: a new link model for use in QM/MM studies. Int J Quantum
Chem 91:177–183
37. Das D, Eurenius KP, Billings EM, Sherwood P, Chatfield DC, Hodoscek M, Brook BR
(2002) Optimization of quantum mechanical molecular mechanical partitioning schemes:
Gaussian delocalization of molecular mechanical charges and the double link atom method.
J Chem Phys 117:10534–10547
38. Di Labio GA, Hurley MM, Christiansen PA (2002) Simple one-electron quantum capping potentials for use in hybrid QM/MM studies of biological molecules. J Chem Phys 116:9578–
9584
39. Zhang Y, Lee T-S, Yang W (1999) A pseudobond approach to combining quantum mechanical and molecular mechanical methods. J Chem Phys 110:46–54
40. Xiao C, Zhang Y (2007) Design-atom approach for quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons. J Chem Phys
127:124102
41. Ferenczy GG, Rivail J-L, Surjan PR, Naray-Szabo G (1992) NDDO fragment self-consistentfield approximation for large electronic systems. J Comput Chem 13:830–837
42. Théry V, Rinaldi D, Rivail J-L, Maigret B, Ferenczy GG (1994) Quantum mechanical computations on very large molecular systems: the local self-consistent field method. J Comput
Chem 15:269–282
43. Stewart JJP (1989) Optimization of parameters for semiempirical methods I. Method J Comput Chem 10:209–220
44. Gao G, Amara P, Alhambra C, Field MJ (1998) A generalized hybrid orbital (GHO) method
for the treatment of boundary atoms in combined QM/MM calculations. J Phys Chem A
102:4714–4721
45. Pu J, Gao J, Truhlar DG (2004) Generalized hybrid orbital (GHO) method for combining ab
initio Hartree–Fock wave functions with molecular mechanics. J Phys Chem A 108:632–650
46. Pu J, Gao J, Truhlar DG (2004) Combining self-consistent-charge density-functional tightbinding (SCC-DFTB) with molecular mechanics by the generalized hybrid orbital (GHO)
method. J Phys Chem A 108:5454–5463
47. Pu J, Truhlar DG (2005) Redristributed charge and dipole schemes for combined quantum
mechanical and molecular mechanical calculations J Phys Chem A 109:3991–4004
48. Maseras F, Morokuma K (1995) IMOMM, a new integrated ab initio + molecular mechanics
geometry optimization scheme of equilibrium structure and transition states. J Comput Chem
16:1170–1179
49. Celebi N, Ángyán JG, Dehez F, Millot C, Chipot C (2000) Distributed polarizabilities derived from induction energies: a finite perturbation approach. J Chem Phys 112:2709–2717