42. Andersson, K.: Different forms of the 0th-order hamiltonian in 2nd-order perturbation-theory
with a complete active space self-consistent-field reference function. Theor. Chim. Acta 91
(1–2), 31–46 (1995)
43. Neese, F.: A spectroscopy oriented configuration interaction procedure. J. Chem. Phys. 119,
9428–9443 (2003)
44. Neese, F., Petrenko, T., Ganyushin, D., Olbrich, G.: Advanced aspects of ab initio theoretical
optical spectroscopy of transition metal complexes: multiplets, spin-orbit coupling and
resonance Raman intensities. Coord. Chem. Rev. 251(3–4), 288–327 (2007)
45. Weber, W.: Ein neues semiempirisches NDDO-verfahren mit orthogonalisierungskorrekturen. Ph.D. thesis, Universita ¨t Zu ¨rich (1996)
46. Zerner, M.C., Ridley, J.: An intermediate neglect of differential overlap technique for
spectroscopy: pyrrole and the azines. Theor. Chim. Acta 32, 111 (1973)
47. Kolb, M.: Ein neues semiempirisches Verfahren auf Grundlage der NDDO Na ¨herung. Ph.D.
thesis, Universita ¨t Wuppertal (1991)
48. Tuttle, T., Thiel, W.: OMx-D: semiempirical methods with orthogonalization and dispersion
corrections. Implementation and biochemical application. Phys. Chem. Chem. Phys. 10(16),
2159–2166 (2008)
49. Paizs, B., Tajkhorshid, E., Suhai, S.: Electronic effects on the ground-state rotational barrier
of polyene Schiff bases: a molecular orbital study. J. Phys. Chem. B 103, 5388–5395 (1999)
50. Weber, W., Thiel, W.: Orthogonalisation corrections for semiempirical methods. Theor.
Chem. Acc. 103, 495–506 (2000)
51. Winget, P., Selcuki, C., Horn, A.H.C., Martin, B., Clark, T.: Towards a “next generation”
neglect of diatomic differential overlap based semiempirical molecular orbital technique.
Theor. Chem. Acc. 110(4), 254–266 (2003)
52. Zhou, H., Tajkhorshid, E., Frauenheim, T., Suhai, S., Elstner, M.: Performance of the AM1,
PM3, and SCC-DFTB methods in the study of conjugated Schiff base molecules. Chem.
Phys. 277, 91–103 (2002)
53. Silva-Junior, M.R., Thiel, W.: Benchmark of electronically excited states for semiempirical
methods: MNDO, AM1, PM3, OM1, OM2, OM3, INDO/S, and INDO/S2. J. Chem. Theory
Comput. 6(5), 1546–1564 (2010)
54. Wanko, M.: Optical excitations in biological systems: multiscale-simulation strategies and
applications to rhodopsins. Ph.D. dissertation, TU Braunschweig (2009). http://www.digibib.
tu-bs.de/?docid¼00030605
55. Keal, T., Wanko, M., Thiel, W.: Assessment of semiempirical methods for the photoisomerisation of a protonated Schiff base. Theor. Chem. Acc. 123(1), 145–156 (2009)
56. Wanko, M., Hoffmann, M., Strodel, P., Koslowski, A., Thiel, W., Neese, F., Frauenheim, T.,
Elstner, M.: Calculating absorption shifts for retinal proteins: computational challenges.
J. Phys. Chem. B 109, 3606–3615 (2005)
57. Warshel, A., Levitt, M.: Theoretical studies of enzymic reactions: dielectric, electrostatic and
steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103(2),
227–249 (1976)
58. Vreven, T., Morokuma, K.: The ONIOM (our own N-layered integrated molecular orbital +
molecular mechanics) method for the first singlet excited (S1) state photoisomerization path
of a retinal protonated Schiff base. J. Chem. Phys. 113, 2969 (2000)
59. Ferre, N., Olivucci, M.: The amide bond: pitfalls and drawbacks of the link atom scheme.
J. Mol. Struct. (Theochem) 632(71–82) (2003)
60. Jung, G., Werner, M., Schneider, M.: Efficient photoconversion distorts the fluorescence
lifetime of GFP in confocal microscopy: a model kinetic study on mutant Thr203Val.
ChemPhysChem 9(13), 1867–1874 (2008)
61. Ko ¨nig, P., Hoffmann, M., Frauenheim, T., Cui, Q.: A critical evaluation of different QM/MM
frontier treatments using SCC-DFTB as the QM method. J. Phys. Chem. B 109, 9082 (2005)
4 Theoretical Methods
61
with a complete active space self-consistent-field reference function. Theor. Chim. Acta 91
(1–2), 31–46 (1995)
43. Neese, F.: A spectroscopy oriented configuration interaction procedure. J. Chem. Phys. 119,
9428–9443 (2003)
44. Neese, F., Petrenko, T., Ganyushin, D., Olbrich, G.: Advanced aspects of ab initio theoretical
optical spectroscopy of transition metal complexes: multiplets, spin-orbit coupling and
resonance Raman intensities. Coord. Chem. Rev. 251(3–4), 288–327 (2007)
45. Weber, W.: Ein neues semiempirisches NDDO-verfahren mit orthogonalisierungskorrekturen. Ph.D. thesis, Universita ¨t Zu ¨rich (1996)
46. Zerner, M.C., Ridley, J.: An intermediate neglect of differential overlap technique for
spectroscopy: pyrrole and the azines. Theor. Chim. Acta 32, 111 (1973)
47. Kolb, M.: Ein neues semiempirisches Verfahren auf Grundlage der NDDO Na ¨herung. Ph.D.
thesis, Universita ¨t Wuppertal (1991)
48. Tuttle, T., Thiel, W.: OMx-D: semiempirical methods with orthogonalization and dispersion
corrections. Implementation and biochemical application. Phys. Chem. Chem. Phys. 10(16),
2159–2166 (2008)
49. Paizs, B., Tajkhorshid, E., Suhai, S.: Electronic effects on the ground-state rotational barrier
of polyene Schiff bases: a molecular orbital study. J. Phys. Chem. B 103, 5388–5395 (1999)
50. Weber, W., Thiel, W.: Orthogonalisation corrections for semiempirical methods. Theor.
Chem. Acc. 103, 495–506 (2000)
51. Winget, P., Selcuki, C., Horn, A.H.C., Martin, B., Clark, T.: Towards a “next generation”
neglect of diatomic differential overlap based semiempirical molecular orbital technique.
Theor. Chem. Acc. 110(4), 254–266 (2003)
52. Zhou, H., Tajkhorshid, E., Frauenheim, T., Suhai, S., Elstner, M.: Performance of the AM1,
PM3, and SCC-DFTB methods in the study of conjugated Schiff base molecules. Chem.
Phys. 277, 91–103 (2002)
53. Silva-Junior, M.R., Thiel, W.: Benchmark of electronically excited states for semiempirical
methods: MNDO, AM1, PM3, OM1, OM2, OM3, INDO/S, and INDO/S2. J. Chem. Theory
Comput. 6(5), 1546–1564 (2010)
54. Wanko, M.: Optical excitations in biological systems: multiscale-simulation strategies and
applications to rhodopsins. Ph.D. dissertation, TU Braunschweig (2009). http://www.digibib.
tu-bs.de/?docid¼00030605
55. Keal, T., Wanko, M., Thiel, W.: Assessment of semiempirical methods for the photoisomerisation of a protonated Schiff base. Theor. Chem. Acc. 123(1), 145–156 (2009)
56. Wanko, M., Hoffmann, M., Strodel, P., Koslowski, A., Thiel, W., Neese, F., Frauenheim, T.,
Elstner, M.: Calculating absorption shifts for retinal proteins: computational challenges.
J. Phys. Chem. B 109, 3606–3615 (2005)
57. Warshel, A., Levitt, M.: Theoretical studies of enzymic reactions: dielectric, electrostatic and
steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103(2),
227–249 (1976)
58. Vreven, T., Morokuma, K.: The ONIOM (our own N-layered integrated molecular orbital +
molecular mechanics) method for the first singlet excited (S1) state photoisomerization path
of a retinal protonated Schiff base. J. Chem. Phys. 113, 2969 (2000)
59. Ferre, N., Olivucci, M.: The amide bond: pitfalls and drawbacks of the link atom scheme.
J. Mol. Struct. (Theochem) 632(71–82) (2003)
60. Jung, G., Werner, M., Schneider, M.: Efficient photoconversion distorts the fluorescence
lifetime of GFP in confocal microscopy: a model kinetic study on mutant Thr203Val.
ChemPhysChem 9(13), 1867–1874 (2008)
61. Ko ¨nig, P., Hoffmann, M., Frauenheim, T., Cui, Q.: A critical evaluation of different QM/MM
frontier treatments using SCC-DFTB as the QM method. J. Phys. Chem. B 109, 9082 (2005)
4 Theoretical Methods
61