Abstract
Parametrization of a molecular-mechanics program to include terms specific for five- and six-coordinate transition metal complexes is applied to heme complexes. The principal new feature peculiar to five and six coordination is a term that represents the effect of electron-pair repulsion modified by the ligand electronegativity and takes into account the different possible structures of complexes. The model system takes into account the structural differences of the fixing centre in the haemoglobin subunits. The customary proximal histidine is added. The macrocycle heme IX is wholly considered in our model. The calculations show clearly that certain conformations of heme IX–histidine models are much more favourable than others for fixing O2. From the O2 binding in haemoglobin and myoglobin and in simple Fe porphyrin models it is concluded that the bent O2 ligand is best viewed as bound superoxide, O2 −. Rotation of axial ligands are practically free. A small modification of the model in both crystal and protein matrix affects the orientation of the ligands in experimental systems.
Similar content being viewed by others
References
M.F. Perutz: Proc. R. Soc. London, B 208, 135 (1980).
M.F. Perutz, G. Fermi, B. Luisi, B. Shaanan, and R.C. Liddington: Acc. Chem. Res. 20, 309 (1987).
K.G. Welinder: Curr. Opin. Struct. Biol. 2, 388 (1992).
B.G. Malmström: Chem. Rev. 90, 1247 (1990).
M. Sono, M.P. Roach, E.D. Coulter, and J.H. Dawson: Chem. Rev. 96, 2841 (1996).
J. Barber and B. Andersson: Nature (London) 370, 31 (1994).
C.L. Drennan, S. Huang, J.T. Drummond, R.G. Matthews, and M.L. Ludwig: Science 266, 1669 (1994).
M.A. Halcrow and G. Christou: Chem. Rev. 94, 2421 (1994).
M. Momenteau and C.A. Reed: Chem. Rev. 94, 659 (1994).
A. Dedieu, M.-M. Rohmer, and A. Veillard: Adv. Quantum Chem. 16, 43 (1982).
M.-M. Rohmer, A. Dedieu, and A. Veillard: Chem. Phys. 77, 449 (1983).
M.-M. Rohmer: Chem. Phys. Lett. 116, 44 (1985).
N. Li, Z. Su, P. Coppens, and J. Landrum: J. Am. Chem. Soc. 112, 7294 (1990).
T.G. Spiro and P.M. Kozlowski: J. Biol. Inorg. Chem. 2, 516 (1997).
T.G. Spiro and P.M. Kozlowski: J. Am. Chem. Soc. 120, 4524 (1998).
T. Vangberg, D.F. Bocian, and A. Ghosh: J. Biol. Inorg. Chem. 2, 526 (1997).
P. Jewsbury, S. Yamamoto, T. Minato, M. Saito, and T. Kitagawa: J. Am. Chem. Soc. 116, 11586 (1994).
P. Jewsbury, S. Yamamoto, T. Minato, M. Saito, and T. Kitagawa: J. Phys. Chem. 99, 12677 (1995).
A. Ghosh and D.F. Bocian: J. Phys. Chem. 100, 6363 (1996).
E. Sigfridsson and U. Ryde: J. Biol. Inorg. Chem. 4, 99 (1999).
C. Rovira, P. Ballone, and M. Parrinello: Chem. Phys. Lett. 271, 247 (1997).
C. Rovira, K. Kunc, J. Hutter, P. Ballone, and M. Parrinello: J. Phys. Chem. A 101, 8914 (1997).
C. Rovira, K. Kunc, J. Hutter, P. Ballone, and M. Parrinello: Int. J. Quantum Chem. 69, 31 (1998).
C. Rovira and M. Parrinello: Chem. Eur. J. 5, 250 (1999).
C. Rovira, P. Carloni, and M. Parrinello: J. Phys. Chem. B 103, 7031 (1999).
R. Salzmann, M.T. McMahon, N. Godbout, L.K. Sanders, M. Wojdelski, and E. Oldfield: J. Am. Chem. Soc. 121, 3818 (1999).
N. Godbout, L.K. Sanders, R. Salzmann, R.H. Havlin, M. Wojdelski, and E. Oldfield: J. Am. Chem. Soc. 121, 3829 (1999).
G. Loew and M. Dupuis: J. Am. Chem. Soc. 118, 10584 (1996).
D.L. Harris and G.H. Loew: J. Am. Chem. Soc. 118, 10588 (1996).
D. Harris, G. Loew, and L. Waskell: J. Am. Chem. Soc. 120, 4308 (1998).
D.E. Woon and G.H. Loew: J. Phys. Chem. A 102, 10380 (1998).
O. Zakharieva, M. Grodzicki, A.X. Trautwein, C. Veeger, and I.M.C.M. Rietgens: J. Biol. Inorg. Chem. 1, 192 (1996).
M.T. Green: J. Am. Chem. Soc. 120, 10772 (1998).
G.B. Jameson, G.A. Rodley, W.T. Robinson, R.R. Gagne, C.A. Reed, and J.P. Collman: Inorg. Chem. 17, 850 (1978).
G.B. Jameson, F.S. Molinaro, J.A. Ibers, J.P. Collman, J.I. Brauman, E. Rose, and K.S. Suslick: J. Am. Chem. Soc. 102, 3224 (1980).
F. Maseras: New J. Chem. 22, 327 (1998).
J.-D. Maréchal, G. Barea, F. Maseras, A. Lledó s, L. Mouawad, and D. Pérahia: J. Comput. Chem. 21, 282 (2000).
R. Salzmann, C.J. Ziegler, N. Godbout, M.T. McMahon, K.S. Suslick, and E. Oldfield: J. Am. Chem. Soc. 120, 11323 (1998).
S. Han, K. Cho, and J. Ihm: Phys. Rev. E 59, 2218 (1999).
K. Kim, J. Fettinger, J.L. Sessler, M. Cyr, J. Hugdahl, J.P. Collman, and J.A. Ibers: J. Am. Chem. Soc. 111, 403 (1989).
M.P. Johansson, M.R.A. Blomberg, D. Sundholm, and M. Wikström: Biochim. Biophys. Acta 1553, 183 (2002).
M.P. Johansson, D. Sundholm, G. Gerfen, and M. Wikström: J. Am. Chem. Soc. 124, 11771 (2002).
F. Torrens, M. Ruiz-Ló pez, C. Cativiela, J.I. García, and J.A. Mayoral: Tetrahedron 48, 5209 (1992).
F. Torrens: Mol. Simul. 24, 391 (2000).
N.L. Allinger: J. Am. Chem. Soc. 99, 8127 (1977).
F. Torrens: Polyhedron 22, 1091 (2003).
B.T. Thole: Chem. Phys. 59, 341 (1981).
T.L. Hill: J. Chem. Phys. 16, 399 (1948).
J.A. Deiters, J.C. Gallucci, T.E. Clark, and R.R. Holmes: J. Am. Chem. Soc. 99, 5461 (1977).
H. Yow and L.S. Bartell: J. Mol. Struct. 15, 209 (1973).
F. Torrens: J. Phys. Org. Chem. 15, 742 (2002).
R.S. Mulliken: J. Chem. Phys. 2, 782 (1934).
J.E. Huheey: J. Phys. Chem. 69, 3284 (1965).
R.T. Sanderson: Science 114, 670 (1951).
R.S. Mulliken, C.A. Rieke, D. Orloff, and H. Orloff: J. Chem. Phys. 17, 1248 (1949).
C. Joachim, G. Treboux, and H. Tang: A model conformational flip-flop molecular switch. In Molecular Electronics: Science and Technology, AIP Conference Proceedings Vol. 262, AIP, New York (1992), pp. 107-117.
A.I. Vogel: J. Chem. Soc. 1833 (1948).
N. Gresh, P. Claverie, and A. Pullman: Int. J. Quantum Chem. Symp. 13, 243 (1979).
A.K. Rappé, C.J. Casewit, K.S. Colwell, W.A. Goddard III, and W.M. Skiff: J. Am. Chem. Soc. 114, 10024 (1992).
M. Momenteau, W.R. Scheidt, C.W. Eigenbrot, and C.A. Reed: J. Am. Chem. Soc. 110, 1207 (1988).
J.J. Weiss: Nature (London) 202, 83 (1964).
H.P. Misra and I. Fridovich: J. Biol. Chem. 247, 6960 (1972).
L. Pauling: Proc. Natl. Acad. Sci. USA 74, 2612 (1977).
M.J.S. Dewar, E.G. Zoebisch, E.F. Healy, and J.J.P. Stewart: J. Am. Chem. Soc. 107, 3902 (1985).
R. Huber, O. Epp, and H. Formanek: J. Mol. Biol. 52, 349 (1970).
E.A. Padian and W.E. Love: J. Biol. Chem. 249, 4067 (1974).
J.C. Norvell, A.C. Nunes, and B.P. Schoenborn: Science 190, 568 (1975).
W.R. Scheidt and K. Hatano: Acta Crystallogr. Sect. C 47, 2201 (1991).
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Torrens, F. An Improved Force Field for O2, CO and CN Binding to Metalloporphyrins. Journal of Inclusion Phenomena 49, 37–46 (2004). https://doi.org/10.1023/B:JIPH.0000031111.00613.4c
Issue Date:
DOI: https://doi.org/10.1023/B:JIPH.0000031111.00613.4c