메뉴 건너뛰기




Volumn 24, Issue 2, 2005, Pages 128-137

Development of parameter sets for semi-empirical MO calculations of transition metal systems: Iron parameters for iron-sulfur proteins

Author keywords

BFGS; Parameterization; PM3; Rubredoxins; Transition metals

Indexed keywords

COMPLEXATION; MATHEMATICAL MODELS; PROBABILITY DENSITY FUNCTION;

EID: 25444442590     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2005.07.001     Document Type: Conference Paper
Times cited : (19)

References (50)
  • 2
    • 0001531848 scopus 로고    scopus 로고
    • Protein control of redox potentials of iron-sulfur proteins
    • P.J. Stephens, D.R. Jollie, and A. Warshel Protein control of redox potentials of iron-sulfur proteins Chem. Rev. 96 1996 2491 2513
    • (1996) Chem. Rev. , vol.96 , pp. 2491-2513
    • Stephens, P.J.1    Jollie, D.R.2    Warshel, A.3
  • 3
    • 0011509370 scopus 로고    scopus 로고
    • Structural and functional aspects of metal sites in biology
    • R.H. Holm, P. Kennepohl, and E.I. Solomon Structural and functional aspects of metal sites in biology Chem. Rev. 96 1996 2239 2314
    • (1996) Chem. Rev. , vol.96 , pp. 2239-2314
    • Holm, R.H.1    Kennepohl, P.2    Solomon, E.I.3
  • 4
    • 0001164656 scopus 로고    scopus 로고
    • Probing the electronic structure of redox species and direct determination of intrinsic reorganization energies of electron transfer reactions
    • X.-B. Wang, and L.-S. Wang Probing the electronic structure of redox species and direct determination of intrinsic reorganization energies of electron transfer reactions J. Chem. Phys. 112 2000 6959 6962
    • (2000) J. Chem. Phys. , vol.112 , pp. 6959-6962
    • Wang, X.-B.1    Wang, L.-S.2
  • 6
    • 25444476660 scopus 로고    scopus 로고
    • The structure and spin-states of some Fe(III) mimics of nitrile hydratase, studied by DFT and ONIOM (DFT:PM3) calculations
    • C. Morgado, J.P. McNamara, I.H. Hillier, and M. Sundararajan The structure and spin-states of some Fe(III) mimics of nitrile hydratase, studied by DFT and ONIOM (DFT:PM3) calculations Mol. Phys. 103 2005 905 923
    • (2005) Mol. Phys. , vol.103 , pp. 905-923
    • Morgado, C.1    McNamara, J.P.2    Hillier, I.H.3    Sundararajan, M.4
  • 7
    • 84986527758 scopus 로고
    • IMOMM: A new integrated ab initio + molecular mechanics geometry optimisation scheme of equilibrium structures and transition states
    • F. Maseras, and K. Morokuma IMOMM: a new integrated ab initio + molecular mechanics geometry optimisation scheme of equilibrium structures and transition states J. Comput. Chem. 16 1995 1170 1179
    • (1995) J. Comput. Chem. , vol.16 , pp. 1170-1179
    • Maseras, F.1    Morokuma, K.2
  • 8
    • 0037473497 scopus 로고    scopus 로고
    • Geometry optimisation with QM/MM, ONIOM and other combined methods. Part I: Microiterations and constraints
    • T. Vreven, K. Morokuma, O. Farkas, H.B. Schlegel, and M.J. Frisch Geometry optimisation with QM/MM, ONIOM and other combined methods. Part I: microiterations and constraints J. Comput. Chem. 24 2003 760 769
    • (2003) J. Comput. Chem. , vol.24 , pp. 760-769
    • Vreven, T.1    Morokuma, K.2    Farkas, O.3    Schlegel, H.B.4    Frisch, M.J.5
  • 9
    • 0027125907 scopus 로고
    • A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations
    • J. Gao, and X. Xia A priori evaluation of aqueous polarization effects through Monte Carlo QM-MM simulations Science 258 1992 631 635
    • (1992) Science , vol.258 , pp. 631-635
    • Gao, J.1    Xia, X.2
  • 10
    • 84986513644 scopus 로고
    • A combined quantum mechanical and molecular potential for molecular dynamics simulations
    • M.J. Field, P.A. Basch, and M. Karplus A combined quantum mechanical and molecular potential for molecular dynamics simulations J. Comput. Chem. 11 1990 700 733
    • (1990) J. Comput. Chem. , vol.11 , pp. 700-733
    • Field, M.J.1    Basch, P.A.2    Karplus, M.3
  • 11
    • 84988129057 scopus 로고
    • Optimisation of parameters for semiempirical methods. Part I: Method
    • J.J.P. Stewart Optimisation of parameters for semiempirical methods. Part I: method J. Comput. Chem. 10 1989 209 220
    • (1989) J. Comput. Chem. , vol.10 , pp. 209-220
    • Stewart, J.J.P.1
  • 12
    • 84988073214 scopus 로고
    • Optimisation of parameters for semiempirical methods. Part II: Applications
    • J.J.P. Stewart Optimisation of parameters for semiempirical methods. Part II: applications J. Comput. Chem. 10 1989 221 264
    • (1989) J. Comput. Chem. , vol.10 , pp. 221-264
    • Stewart, J.J.P.1
  • 13
    • 84986525833 scopus 로고
    • Optimisation of parameters for semiempirical methods. Part III: Extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb and Bi
    • J.J.P. Stewart Optimisation of parameters for semiempirical methods. Part III: extension of PM3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb and Bi J. Comput. Chem. 12 1991 320 341
    • (1991) J. Comput. Chem. , vol.12 , pp. 320-341
    • Stewart, J.J.P.1
  • 14
    • 2542462121 scopus 로고    scopus 로고
    • Optimisation of parameters for semiempirical methods. Part IV: Extension of MNDO, AM1 and PM3 to more main group elements
    • J.J.P. Stewart Optimisation of parameters for semiempirical methods. Part IV: extension of MNDO, AM1 and PM3 to more main group elements J. Mol. Model 10 2004 155 164
    • (2004) J. Mol. Model , vol.10 , pp. 155-164
    • Stewart, J.J.P.1
  • 15
    • 0001379933 scopus 로고
    • Extension of the MNDO formalism to d orbitals: Integral approximations and preliminary numerical results
    • W. Thiel, and A.A. Voityuk Extension of the MNDO formalism to d orbitals: integral approximations and preliminary numerical results Theor. Chim. Acta 81 1992 391 404
    • (1992) Theor. Chim. Acta , vol.81 , pp. 391-404
    • Thiel, W.1    Voityuk, A.A.2
  • 16
    • 0000716157 scopus 로고    scopus 로고
    • Erratum. Extension of the MNDO formalism to d orbitals: Integral approximations and preliminary numerical results
    • W. Thiel, and A.A. Voityuk Erratum. Extension of the MNDO formalism to d orbitals: integral approximations and preliminary numerical results Theor. Chim. Acta 93 1996 315
    • (1996) Theor. Chim. Acta , vol.93 , pp. 315
    • Thiel, W.1    Voityuk, A.A.2
  • 17
    • 0034683926 scopus 로고    scopus 로고
    • Quo Vadis semiempirical MO-theory?
    • T. Clark Quo Vadis semiempirical MO-theory? J. Mol. Struct. (Theochem.) 530 2000 1 10
    • (2000) J. Mol. Struct. (Theochem.) , vol.530 , pp. 1-10
    • Clark, T.1
  • 18
    • 0002833182 scopus 로고
    • Parameterization of NDDO wavefunctions using genetic algorithms: An evolutionary approach to parameterizing potential energy surfaces and direct dynamics calculations of organic reactions
    • I. Rossi, and D.G. Truhlar Parameterization of NDDO wavefunctions using genetic algorithms: an evolutionary approach to parameterizing potential energy surfaces and direct dynamics calculations of organic reactions Chem. Phys. Lett. 233 1995 231 236
    • (1995) Chem. Phys. Lett. , vol.233 , pp. 231-236
    • Rossi, I.1    Truhlar, D.G.2
  • 19
    • 4143118105 scopus 로고    scopus 로고
    • Towards a quantum mechanical force field for carbohydrates: A reparameterized semi-empirical MO approach
    • J.P. McNamara, A.-M. Muslim, H. Abdel-Aal, H. Wang, I.H. Hillier, and R.A. Bryce Towards a quantum mechanical force field for carbohydrates: a reparameterized semi-empirical MO approach Chem. Phys. Lett. 394 2004 429 436
    • (2004) Chem. Phys. Lett. , vol.394 , pp. 429-436
    • McNamara, J.P.1    Muslim, A.-M.2    Abdel-Aal, H.3    Wang, H.4    Hillier, I.H.5    Bryce, R.A.6
  • 20
    • 1642396584 scopus 로고    scopus 로고
    • The use of methods involving semi-empirical molecular orbital theory to study the structure and reactivity of transition metal complexes
    • M. Mohr, J.P. McNamara, H. Wang, S.A. Rajeev, J. Ge, C.A. Morgado, and I.H. Hillier The use of methods involving semi-empirical molecular orbital theory to study the structure and reactivity of transition metal complexes Faraday Discuss. 124 2003 413 428
    • (2003) Faraday Discuss. , vol.124 , pp. 413-428
    • Mohr, M.1    McNamara, J.P.2    Wang, H.3    Rajeev, S.A.4    Ge, J.5    Morgado, C.A.6    Hillier, I.H.7
  • 22
    • 14644436405 scopus 로고    scopus 로고
    • A semi-empirical molecular orbital scheme to study electron transfer in iron-sulfur proteins
    • M. Sundararajan, J.P. McNamara, M. Mohr, H. Wang, and I.H. Hillier A semi-empirical molecular orbital scheme to study electron transfer in iron-sulfur proteins Biochem. Soc. Trans. 33 2005 20 21
    • (2005) Biochem. Soc. Trans. , vol.33 , pp. 20-21
    • Sundararajan, M.1    McNamara, J.P.2    Mohr, M.3    Wang, H.4    Hillier, I.H.5
  • 23
    • 0001242593 scopus 로고    scopus 로고
    • AM1/d parameters for molybdenum
    • A.A. Voityuk, and N. Rösch AM1/d parameters for molybdenum J. Phys. Chem. A 104 2000 4089 4093
    • (2000) J. Phys. Chem. a , vol.104 , pp. 4089-4093
    • Voityuk, A.A.1    Rösch, N.2
  • 24
    • 0022004980 scopus 로고
    • Electron transfers in chemistry and biology
    • R.A. Marcus, and N. Sutin Electron transfers in chemistry and biology Biochim. Biophys. Acta 811 1985 265 322
    • (1985) Biochim. Biophys. Acta , vol.811 , pp. 265-322
    • Marcus, R.A.1    Sutin, N.2
  • 26
    • 0001186035 scopus 로고    scopus 로고
    • PM3(tm) parameterisation using genetic algorithms
    • T.R. Cundari, J. Deng, and W. Fu PM3(tm) parameterisation using genetic algorithms Int. J. Quant. Chem. 77 2000 421 432
    • (2000) Int. J. Quant. Chem. , vol.77 , pp. 421-432
    • Cundari, T.R.1    Deng, J.2    Fu, W.3
  • 27
    • 0037075858 scopus 로고    scopus 로고
    • Sodium parameters for AM1 and PM3 optimised using a modified genetic algorithm
    • E.N. Brothers, and K.M. Merz Jr. Sodium parameters for AM1 and PM3 optimised using a modified genetic algorithm J. Phys. Chem. B 106 2002 2779 2785
    • (2002) J. Phys. Chem. B , vol.106 , pp. 2779-2785
    • Brothers, E.N.1    Merz Jr., K.M.2
  • 28
    • 0000675650 scopus 로고    scopus 로고
    • Modelling the bacterial photosynthetic reaction centre. Part 1: Magnesium parameters for the semiempirical AM1 method developed using a genetic algorithm
    • M.C. Hutter, J.R. Reimers, and N.S. Hush Modelling the bacterial photosynthetic reaction centre. Part 1: magnesium parameters for the semiempirical AM1 method developed using a genetic algorithm J. Phys. Chem. B 102 1998 8080 8090
    • (1998) J. Phys. Chem. B , vol.102 , pp. 8080-8090
    • Hutter, M.C.1    Reimers, J.R.2    Hush, N.S.3
  • 29
    • 0000732463 scopus 로고
    • A limited memory algorithm for bound constrained optimization
    • R.H. Byrd, P. Lu, J. Nocedal, and C. Zhu A limited memory algorithm for bound constrained optimization Siam. J. Sci. Comput. 16 1995 1190 1208
    • (1995) Siam. J. Sci. Comput. , vol.16 , pp. 1190-1208
    • Byrd, R.H.1    Lu, P.2    Nocedal, J.3    Zhu, C.4
  • 31
    • 24444468650 scopus 로고
    • Ground states of molecules. Part 38: The MNDO method. Approximations and parameters
    • M.J.S. Dewar, and W. Thiel Ground states of molecules. Part 38: the MNDO method. Approximations and parameters J. Am. Chem. Soc. 99 1977 4899 4907
    • (1977) J. Am. Chem. Soc. , vol.99 , pp. 4899-4907
    • Dewar, M.J.S.1    Thiel, W.2
  • 32
    • 0025390935 scopus 로고
    • MOPAC: A semiempirical molecular orbital program
    • J.J.P. Stewart MOPAC: a semiempirical molecular orbital program J. Comput. Aided Mol. Des. 4 1990 1 105
    • (1990) J. Comput. Aided Mol. Des. , vol.4 , pp. 1-105
    • Stewart, J.J.P.1
  • 34
    • 84987133043 scopus 로고
    • Additions and corrections. AM1: A new general purpose quantum mechanical molecular model
    • M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, and J.J.P. Stewart Additions and corrections. AM1: a new general purpose quantum mechanical molecular model J. Am. Chem. Soc. 115 1993 5348
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 5348
    • Dewar, M.J.S.1    Zoebisch, E.G.2    Healy, E.F.3    Stewart, J.J.P.4
  • 35
    • 25444478278 scopus 로고    scopus 로고
    • note
    • Eq. (8) differs from the one given in reference [23]; in the original publication, the factor of "2" was inadvertently omitted.
  • 36
    • 0001529855 scopus 로고
    • AM1 calculations for compounds containing boron
    • M.J.S. Dewar, C. Jie, and E.G. Zoebisch AM1 calculations for compounds containing boron Organometallics 7 1988 513 521
    • (1988) Organometallics , vol.7 , pp. 513-521
    • Dewar, M.J.S.1    Jie, C.2    Zoebisch, E.G.3
  • 37
    • 0242663009 scopus 로고    scopus 로고
    • Combined quantum chemistry and photoelectron spectroscopy study of the electronic structure and reduction potentials of rubredoxin redox site analogues
    • S. Niu, X.-B. Wang, J.A. Nicolas, L.-S. Wang, and T. Ichiye Combined quantum chemistry and photoelectron spectroscopy study of the electronic structure and reduction potentials of rubredoxin redox site analogues J. Phys. Chem. A 107 2003 2898 2907
    • (2003) J. Phys. Chem. a , vol.107 , pp. 2898-2907
    • Niu, S.1    Wang, X.-B.2    Nicolas, J.A.3    Wang, L.-S.4    Ichiye, T.5
  • 38
    • 0038664374 scopus 로고    scopus 로고
    • On the electronic structure of [1Fe] Fe-S complexes from anionic photoelectron spectroscopy
    • X. Yang, X.-B. Wang, Y.J. Fu, and L.-S. Wang On the electronic structure of [1Fe] Fe-S complexes from anionic photoelectron spectroscopy J. Phys. Chem. A 107 2003 1703 1709
    • (2003) J. Phys. Chem. a , vol.107 , pp. 1703-1709
    • Yang, X.1    Wang, X.-B.2    Fu, Y.J.3    Wang, L.-S.4
  • 40
    • 0035926249 scopus 로고    scopus 로고
    • Inner-sphere reorganisation energy of iron-sulfur clusters studied with theoretical methods
    • E. Sigfridsson, M.H.M. Olsson, and U. Ryde Inner-sphere reorganisation energy of iron-sulfur clusters studied with theoretical methods Inorg. Chem. 40 2001 2509 2519
    • (2001) Inorg. Chem. , vol.40 , pp. 2509-2519
    • Sigfridsson, E.1    Olsson, M.H.M.2    Ryde, U.3
  • 41
    • 0001752768 scopus 로고    scopus 로고
    • The Cambridge structural database: A quarter of a million crystal structures and rising
    • F.H. Allen The Cambridge structural database: a quarter of a million crystal structures and rising Acta Crystallogr. B 58 2002 380 388
    • (2002) Acta Crystallogr. B , vol.58 , pp. 380-388
    • Allen, F.H.1
  • 42
    • 1842583991 scopus 로고    scopus 로고
    • Hydrogenases: Active site puzzles and progress
    • F.A. Armstrong Hydrogenases: active site puzzles and progress Curr. Opin. Chem. Biol. 8 2004 133 140
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 133-140
    • Armstrong, F.A.1
  • 43
    • 0000189651 scopus 로고
    • Density-functional thermochemistry. Part III: The role of exact exchange
    • A.D. Becke Density-functional thermochemistry. Part III: the role of exact exchange J. Chem. Phys. 98 1993 5648 5652
    • (1993) J. Chem. Phys. , vol.98 , pp. 5648-5652
    • Becke, A.D.1
  • 44
    • 0038596731 scopus 로고
    • Results obtained with the correlation energy density functionals of Becke and Lee, Yang and Parr
    • B. Miehlich, A. Savin, H. Stoll, and H. Preuss Results obtained with the correlation energy density functionals of Becke and Lee, Yang and Parr Chem. Phys. Lett. 157 1989 200 206
    • (1989) Chem. Phys. Lett. , vol.157 , pp. 200-206
    • Miehlich, B.1    Savin, A.2    Stoll, H.3    Preuss, H.4
  • 45
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
    • C. Lee, W. Yang, and R.G. Parr Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density Phys. Rev. B 37 1988 785 789
    • (1988) Phys. Rev. B , vol.37 , pp. 785-789
    • Lee, C.1    Yang, W.2    Parr, R.G.3
  • 47
    • 4243553426 scopus 로고
    • Density-functional exchange-energy approximation with correct asymptotic behaviour
    • A.D. Becke Density-functional exchange-energy approximation with correct asymptotic behaviour Phys. Rev. A 38 1988 3098 3100
    • (1988) Phys. Rev. a , vol.38 , pp. 3098-3100
    • Becke, A.D.1
  • 48
    • 5944261746 scopus 로고
    • Density-functional approximation for the correlation energy of the inhomogeneous electron gas
    • J.P. Perdew Density-functional approximation for the correlation energy of the inhomogeneous electron gas Phys. Rev. B 33 1986 8822 8824
    • (1986) Phys. Rev. B , vol.33 , pp. 8822-8824
    • Perdew, J.P.1
  • 49
    • 0003056547 scopus 로고    scopus 로고
    • The origin of the problems with the PM3 core repulsion function
    • G.I. Csonka, and J.G. Ángyán The origin of the problems with the PM3 core repulsion function J. Mol. Struct. (Theochem.) 393 1997 31 38
    • (1997) J. Mol. Struct. (Theochem.) , vol.393 , pp. 31-38
    • Csonka, G.I.1    Ángyán, J.G.2
  • 50
    • 0035859440 scopus 로고    scopus 로고
    • A comparison of the inner-sphere reorganisation energies of cytochromes, iron-sulfur clusters and blue copper proteins
    • E. Sigfridsson, M.H.M. Olsson, and U. Ryde A comparison of the inner-sphere reorganisation energies of cytochromes, iron-sulfur clusters and blue copper proteins J. Phys. Chem. B 105 2001 5546 5552
    • (2001) J. Phys. Chem. B , vol.105 , pp. 5546-5552
    • Sigfridsson, E.1    Olsson, M.H.M.2    Ryde, U.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.