17
1 Hybrid QM/MM Methods: Treating Electronic Phenomena …
7. Zeglis BM, Pierre VC, Barton JK (2007) Metallointercalators and metalloinsertors. Chem
Commun 44:4565–4579
8. Ortmans I, Elias B, Kelly JM, Moucheron C, Kirsch-De Mesmaeker A (2004)
[RU(TAP) 2 (dppz)]
2+
: a DNA intercalating complex, which luminesces strongly in water and
under goes photo-induced proton-coupled electron transfer with guanosine-5'-monophosphate.
Dalton Trans 33:668–676
9. Monari A, Rivail J-L, Assfeld X (2013) Theoretical modelling of large molecular systems.
Advances in the local self consistent field method for mixed quantum mechanics/molecular
mechanics calculations. Acc Chem Res 46:596–603
10. Monard G, Merz KM Jr (1999) Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems. Acc Chem Rev 32:904–911
11. Lin H, Truhlar DG (2007) QM/MM: what we have learned, where are we, and where do we
go from here? Theor Chem Acc 117:185–199
12. Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Ang Chem Int
48:1198–1229
13. Gordon MS, Fedorov DG, Pruitt SR, Slipchenko IV (2012) Fragmentation methods: a route
to accurate calculations on large molecules Chem Rev 112:632–613
14. Dixon SL, Merz KM Jr (1996) Semiempirical molecular-orbital calculations with linear system size scaling. J Chem Phys 104:6643–6649
15. Daniels AD, Millam JM, Scuseria GE (1997) Semiempirical methods with conjugate gradient density matrix search to replace diagonalization for molecular systems contianing thousands of atoms. J Chem Phys 107:425–431
16. Yang W, Lee TS (1995) A density matrix divide-and-conquer approach for electronic structure calculations of large molecules. J Chem Phys 103:5674–5678
17. Monard G, Bernal-Uruchurtu MI, van der Vaart A, Merz KM Jr, Ruiz-Lopèz MF (2005)
Simulation of liquid water using semiempirical hamiltonina and the divide and conquer approach. J Phys Chem A 109:3425–3432
18. Tarek M, Delemotte L (2013) Omega currents in voltage-gated ion channels: what can we
learn from uncovering the voltage-sensing mechanism using MD simulations? Acc Chem
Res. doi:10.1021/ar300290u
19. Warshel A, Levitt M (1976) Theoretical studies of enzymatic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozime. J Mol Biol
103:227–249
20. Assfeld X, Rivail J-L (1996) Quantum chemical computations on parts of large molecules:
the ab initio local self consistent field method. Chem Phys Lett 263:100–106
21. Jensen, F (2007) Introduction to quantum chemistry, 2nd edn. Wiley, New York
22. Piela L (2007) Ideas of quantum chemistry. Elsevier, Amsterdam
23. Cramer CJ (2004) Essentials of computational chemistry, 2nd edn. Wiley, New York
24. van Gunsteren WF, Berendsen HJC (1987) Groningen Molecular Simulation (GROMOS)
library manual. Biomos, Groningen
25. Allinger NL, Yuh YH, Lii JH (1989) Molecular mechanics. The MM3 force field for hydrocarbons. J Am Chem Soc 111:8551–8566
26. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE. III, DeBolt S, Ferguson D,
Seibel G, Kollman P (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to
simulate structural and energetic properties of molecules. Comput Phys Commun 91:1–41
27. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S,
Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau F. TK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC,
Stote R, Straub J, Watanabe W, Wiórkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom
empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B
102:3586–3616
28. Dang LX, Chang T-M (1997) Molecular dynamics study of water clusters, liquid and liquid–
vapor interface of water with many-body potentials. J Chem Phys 106:8149–8159
1 Hybrid QM/MM Methods: Treating Electronic Phenomena …
7. Zeglis BM, Pierre VC, Barton JK (2007) Metallointercalators and metalloinsertors. Chem
Commun 44:4565–4579
8. Ortmans I, Elias B, Kelly JM, Moucheron C, Kirsch-De Mesmaeker A (2004)
[RU(TAP) 2 (dppz)]
2+
: a DNA intercalating complex, which luminesces strongly in water and
under goes photo-induced proton-coupled electron transfer with guanosine-5'-monophosphate.
Dalton Trans 33:668–676
9. Monari A, Rivail J-L, Assfeld X (2013) Theoretical modelling of large molecular systems.
Advances in the local self consistent field method for mixed quantum mechanics/molecular
mechanics calculations. Acc Chem Res 46:596–603
10. Monard G, Merz KM Jr (1999) Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems. Acc Chem Rev 32:904–911
11. Lin H, Truhlar DG (2007) QM/MM: what we have learned, where are we, and where do we
go from here? Theor Chem Acc 117:185–199
12. Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Ang Chem Int
48:1198–1229
13. Gordon MS, Fedorov DG, Pruitt SR, Slipchenko IV (2012) Fragmentation methods: a route
to accurate calculations on large molecules Chem Rev 112:632–613
14. Dixon SL, Merz KM Jr (1996) Semiempirical molecular-orbital calculations with linear system size scaling. J Chem Phys 104:6643–6649
15. Daniels AD, Millam JM, Scuseria GE (1997) Semiempirical methods with conjugate gradient density matrix search to replace diagonalization for molecular systems contianing thousands of atoms. J Chem Phys 107:425–431
16. Yang W, Lee TS (1995) A density matrix divide-and-conquer approach for electronic structure calculations of large molecules. J Chem Phys 103:5674–5678
17. Monard G, Bernal-Uruchurtu MI, van der Vaart A, Merz KM Jr, Ruiz-Lopèz MF (2005)
Simulation of liquid water using semiempirical hamiltonina and the divide and conquer approach. J Phys Chem A 109:3425–3432
18. Tarek M, Delemotte L (2013) Omega currents in voltage-gated ion channels: what can we
learn from uncovering the voltage-sensing mechanism using MD simulations? Acc Chem
Res. doi:10.1021/ar300290u
19. Warshel A, Levitt M (1976) Theoretical studies of enzymatic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozime. J Mol Biol
103:227–249
20. Assfeld X, Rivail J-L (1996) Quantum chemical computations on parts of large molecules:
the ab initio local self consistent field method. Chem Phys Lett 263:100–106
21. Jensen, F (2007) Introduction to quantum chemistry, 2nd edn. Wiley, New York
22. Piela L (2007) Ideas of quantum chemistry. Elsevier, Amsterdam
23. Cramer CJ (2004) Essentials of computational chemistry, 2nd edn. Wiley, New York
24. van Gunsteren WF, Berendsen HJC (1987) Groningen Molecular Simulation (GROMOS)
library manual. Biomos, Groningen
25. Allinger NL, Yuh YH, Lii JH (1989) Molecular mechanics. The MM3 force field for hydrocarbons. J Am Chem Soc 111:8551–8566
26. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE. III, DeBolt S, Ferguson D,
Seibel G, Kollman P (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to
simulate structural and energetic properties of molecules. Comput Phys Commun 91:1–41
27. MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S,
Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau F. TK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC,
Stote R, Straub J, Watanabe W, Wiórkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom
empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B
102:3586–3616
28. Dang LX, Chang T-M (1997) Molecular dynamics study of water clusters, liquid and liquid–
vapor interface of water with many-body potentials. J Chem Phys 106:8149–8159