235
15. Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Angew Chem Int Ed
48(7):1198–1229. doi:10.1002/anie.200802019
16. de Vivo M (2011) Bridging quantum mechanics and structure-based drug design. Front Biosci 16(1):1619–1633. doi:10.2741/3809
17. Lodola A, de Vivo M (2012) The increasing role of QM/MM in drug discovery. Adv Prot
Chem Struct Biol 87:337–362. doi:10.1016/B978-0-12-398312-1.00011-1
18. Cavalli A, Carloni P, Recanatini M (2006) Target-related applications of first principles quantum chemical methods in drug design. Chem Rev 106(9):3497–3519. doi:10.1021/cr050579p
19. Hu L, Söderhjelm P, Ryde U (2013) Accurate reaction energies in proteins obtained by
combining QM/MM and large QM calculations. J Chem Theor Comput 9(1):640–649.
doi:10.1021/ct3005003
20. Zalesny R, Papadopoulos MG, Mezey PG, Leszczynski J (eds) (2011) Linear-scaling techniques in computational chemistry and physics. In: Challenges advances computational
chemistry physics, vol 13. Springer, Dordrecht. doi:10.1007/978-90-481-2853-2
21. Whitten JL (1973) Coulombic potential energy integrals and approximations. J Chem Phys
58(10):4496–4501. doi:10.1063/1.1679012
22. Baerends EJ, Ellis DE, Ros P (1973) Self-consistent molecular Hartree–Fock–Slater calculations I. The computational procedure. Chem Phys 2(1):41–51. doi:10.1016/03010104(73)80059-X
23. Dunlap BI, Connolly JWD, Sabin JR (1979) On some approximations in applications of Xα
theory. J Chem Phys 71(8):3396–3402. doi:10.1063/1.438728
24. Dunlap BI, Connolly JWD, Sabin JR (1979) On first-row diatomic molecules and local density models. J Chem Phys 71(12):4993–4999. doi:10.1063/1.438313
25. Feyereisen M, Fitzgerald G, Komornicki A (1993) Use of approximate integrals in ab initio theory. An application in MP2 energy calculations. Chem Phys Lett 208 359–363.
doi:10.1016/0009-2614(93)87156-W
26. Eichkorn K, Weigend F, Treutler O, Ahlrichs R (1997) Auxiliary basis sets for main row
atoms and transition metals and their use to approximate Coulomb potentials. Theor Chem
Acc 97(1-4):119–124. doi:10.1007/s002140050244
27. Weigend F, Häser M, Patzelt H, Ahlrichs R (1998) RI-MP2: optimized auxiliary basis sets
and demonstration of efficiency. Chem Phys Lett 294(1–3):143–152. doi:10.1016/S00092614(98)00862-8
28. Furche F, Ahlrichs R, Hättig C, Klopper W, Sierka M, Weigend F (2013) Turbomole. WIREs
Comput Mol Sci. doi:10.1002/wcms.1162
29. Neese F (2012) The ORCA program system. WIREs Comput Mol Sci 2(1):73–78.
doi:10.1002/wcms.81
30. Aguirre D, Chifotides HT, Angeles-Boza AM, Chouai A, Turro C, Dunbar KR (2009) Redox-regulated inhibition of T7 RNA polymerase via establishment of disulfide linkages by
substituted Dppz dirhodium(I, II) complexes. Inorg Chem 48(10):4435–4444. doi:10.1021/
ic900164j
31. Villar JAFP, Lima FTD, C.L. Veber, A.R.M. Oliveira, A.K. Calgarotto, S. Marangoni, da Silva
SL (2008) Synthesis and evaluation of nitrostyrene derivative compounds, new snake venom
phospholipase A2 inhibitors. Toxicon 51(8):1467–1478. doi:10.1016/j.toxicon.2008.03.023
32. Parameswari AR, Kumaradhas P (2013) Exploring the conformation, charge density distribution and the electrostatic properties of galanthamine molecule in the active site of AChE
using DFT and AIM theory. Int J Quant Chem 113(8):1200–1208. doi:10.1002/qua.24251
33. Silva JRA, Lameira J, Alves CN (2012) Insights for design of Trypanosoma cruzi GAPDH
inhibitors: a QM/MM MD study of 1,3-bisphospo-d-glyceric acid analogs. Int J Quant Chem
112(20):3398–3402. doi:10.1002/qua.24253
34. Negri M, Recanatini M, Hartmann RW (2011) Computational investigation of the binding
mode of bis(hydroxylphenyl) arenes in 17β-HSD1: molecular dynamics simulations, MMPBSA free energy calculations, and molecular electrostatic potential maps. J Comp Aid Mol
Des 25(9):795–811. doi:10.1007/s10822-011-9464-7
7 Density Functional Theory Calculations of Enzyme–Inhibitor …
15. Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Angew Chem Int Ed
48(7):1198–1229. doi:10.1002/anie.200802019
16. de Vivo M (2011) Bridging quantum mechanics and structure-based drug design. Front Biosci 16(1):1619–1633. doi:10.2741/3809
17. Lodola A, de Vivo M (2012) The increasing role of QM/MM in drug discovery. Adv Prot
Chem Struct Biol 87:337–362. doi:10.1016/B978-0-12-398312-1.00011-1
18. Cavalli A, Carloni P, Recanatini M (2006) Target-related applications of first principles quantum chemical methods in drug design. Chem Rev 106(9):3497–3519. doi:10.1021/cr050579p
19. Hu L, Söderhjelm P, Ryde U (2013) Accurate reaction energies in proteins obtained by
combining QM/MM and large QM calculations. J Chem Theor Comput 9(1):640–649.
doi:10.1021/ct3005003
20. Zalesny R, Papadopoulos MG, Mezey PG, Leszczynski J (eds) (2011) Linear-scaling techniques in computational chemistry and physics. In: Challenges advances computational
chemistry physics, vol 13. Springer, Dordrecht. doi:10.1007/978-90-481-2853-2
21. Whitten JL (1973) Coulombic potential energy integrals and approximations. J Chem Phys
58(10):4496–4501. doi:10.1063/1.1679012
22. Baerends EJ, Ellis DE, Ros P (1973) Self-consistent molecular Hartree–Fock–Slater calculations I. The computational procedure. Chem Phys 2(1):41–51. doi:10.1016/03010104(73)80059-X
23. Dunlap BI, Connolly JWD, Sabin JR (1979) On some approximations in applications of Xα
theory. J Chem Phys 71(8):3396–3402. doi:10.1063/1.438728
24. Dunlap BI, Connolly JWD, Sabin JR (1979) On first-row diatomic molecules and local density models. J Chem Phys 71(12):4993–4999. doi:10.1063/1.438313
25. Feyereisen M, Fitzgerald G, Komornicki A (1993) Use of approximate integrals in ab initio theory. An application in MP2 energy calculations. Chem Phys Lett 208 359–363.
doi:10.1016/0009-2614(93)87156-W
26. Eichkorn K, Weigend F, Treutler O, Ahlrichs R (1997) Auxiliary basis sets for main row
atoms and transition metals and their use to approximate Coulomb potentials. Theor Chem
Acc 97(1-4):119–124. doi:10.1007/s002140050244
27. Weigend F, Häser M, Patzelt H, Ahlrichs R (1998) RI-MP2: optimized auxiliary basis sets
and demonstration of efficiency. Chem Phys Lett 294(1–3):143–152. doi:10.1016/S00092614(98)00862-8
28. Furche F, Ahlrichs R, Hättig C, Klopper W, Sierka M, Weigend F (2013) Turbomole. WIREs
Comput Mol Sci. doi:10.1002/wcms.1162
29. Neese F (2012) The ORCA program system. WIREs Comput Mol Sci 2(1):73–78.
doi:10.1002/wcms.81
30. Aguirre D, Chifotides HT, Angeles-Boza AM, Chouai A, Turro C, Dunbar KR (2009) Redox-regulated inhibition of T7 RNA polymerase via establishment of disulfide linkages by
substituted Dppz dirhodium(I, II) complexes. Inorg Chem 48(10):4435–4444. doi:10.1021/
ic900164j
31. Villar JAFP, Lima FTD, C.L. Veber, A.R.M. Oliveira, A.K. Calgarotto, S. Marangoni, da Silva
SL (2008) Synthesis and evaluation of nitrostyrene derivative compounds, new snake venom
phospholipase A2 inhibitors. Toxicon 51(8):1467–1478. doi:10.1016/j.toxicon.2008.03.023
32. Parameswari AR, Kumaradhas P (2013) Exploring the conformation, charge density distribution and the electrostatic properties of galanthamine molecule in the active site of AChE
using DFT and AIM theory. Int J Quant Chem 113(8):1200–1208. doi:10.1002/qua.24251
33. Silva JRA, Lameira J, Alves CN (2012) Insights for design of Trypanosoma cruzi GAPDH
inhibitors: a QM/MM MD study of 1,3-bisphospo-d-glyceric acid analogs. Int J Quant Chem
112(20):3398–3402. doi:10.1002/qua.24253
34. Negri M, Recanatini M, Hartmann RW (2011) Computational investigation of the binding
mode of bis(hydroxylphenyl) arenes in 17β-HSD1: molecular dynamics simulations, MMPBSA free energy calculations, and molecular electrostatic potential maps. J Comp Aid Mol
Des 25(9):795–811. doi:10.1007/s10822-011-9464-7
7 Density Functional Theory Calculations of Enzyme–Inhibitor …