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Computational Analysis of Inorganic and Bioinorganic Nickel Complexes

  • Csilla Csiki
  • Karen M. Norenberg
  • Christina M. Shoemaker
  • Marc Zimmer
Part of the NATO ASI Series book series (ASHT, volume 41)

Abstract

The idea of using a mathematical model, based on the ball and spring concept, to describe the geometry of molecules, as is done in molecular mechanics (MM), has been in the literature for more than 50 years. However its use was fairly rare until the advent of relatively inexpensive workstations which has led to a large proliferation of MM programs and to the everyday use and acceptance of MM methods, especially in organic and bioorganic chemistry. Bioinorganic and inorganic MM calculations are less common and their use has been limited by a number of factors.

Keywords

Membered Ring Nickel Complex Cambridge Structural Database Chair Conformation Solid State Structure 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Nakamoto, K. Infrared and Raman Spectra of Inorganic and Coordination Compounds, 3rd ed.; Wiley: New York, 1978.Google Scholar
  2. 2.
    Vedani, A.; Dunitz, J.D. J. Am. Chem. Soc.1985, 107, 7653.CrossRefGoogle Scholar
  3. Hoops S.C., Anderson, K.W., and Merz, K.M. Jr. (1991) Force field design for metalloproteins, J. Am. Chem. Soc. 113, 8262–8270, and other papers in this book.CrossRefGoogle Scholar
  4. 3.
    Halcrow M.A., and Christou G. (1994) Biomimetic chemistry of nickel, Chem. Rev. 94, 2421 - 2481.CrossRefGoogle Scholar
  5. 4.
    Comba, P. (1993) The relationship between ligand structures, coordination stereochemistry, and electronic and thermodynamic properties, Coord. Chem. Rev. 123, 148.CrossRefGoogle Scholar
  6. Comba, P and Hambley, T.W. (1995) Molecular Modeling of Inorganic Compounds, VCH, Weinheim, Germany.Google Scholar
  7. 5.
    Martell, A.E., Hancock, R.D., and Motekaitis, R.J. (1994) Factors affecting stabilities of chelate, macrocyclic and macrobicyclic complexes in solution, Coord. Chem. Rev. 133, 39 - 65.CrossRefGoogle Scholar
  8. Hancock, R. D. (1990) Molecular mechanics calculations and metal ion recognition, Acc. Chem. Res. 23, 253 - 257.CrossRefGoogle Scholar
  9. 6.
    Hancock, R.D., Dobson, S.M., Evers, A., Wade, P., Ngwenya, M.P., Boeyens, J.C.A., and Wainwright, K.P. (1988) More rigid macrocyclic ligands that show metal ion size-based selectivity. A crystallographic, molecular mechanics, and formation constant study of the complexes of bridged cyclen, J. Am. Chem. Soc. 110, 2788 - 2794.CrossRefGoogle Scholar
  10. 7.
    Adam, K.R., Antolovich, M., Brigden, L.G., and Lindoy, L.F. (1991) Comparative molecular mechanics study of the low-spin nickel(II) complexes of an extended series of tetraaza macrocycles, J. Am. Chem. Soc. 113, 3346 - 3351.CrossRefGoogle Scholar
  11. 8.
    Drew, M.G.B., Jutson, N.J., Mitchell, P.C.H., Potter, R.J., and Thompsett, D. (1993) Experimental and computer modelling studies of carbon-supported metal complexes, J. Chem. Soc. Faraday Trans. 89, 3963 - 3973.CrossRefGoogle Scholar
  12. 9.
    Song, X.-Z., Jentzen, W., Jia, S.-L., Jaquinod, L., Nurco, D.J., Medforth, C.J., Smith, K.M., and Shelnutt, J.A. (1996) Representation of nonplanar structures of nickel(II) 5,15-disubstituted porphyrins in terms of displacements along the lowest-frequency normal coordinates of the macrocycle, J. Am. Chem. Soc. 118, 12975 - 12988.CrossRefGoogle Scholar
  13. 10.
    Zimmer, M., and Crabtree, R.H. (1990) Bending of the reduced porphyrin of factor F430 can accomodate a trigonal-bipyramidal geometry at nickel: A conformational analysis of this nickel-containing tetrapyrrole, in relation to archaebacterial methanogenesis. J. Am. Chem. Soc. 112, 1062 - 1066.CrossRefGoogle Scholar
  14. Zimmer, M. (1993) Empirical force field analysis of the revised structure of coenzyme F430. Epimerization and geometry of the corphinoid tetrapyrrole, J. Biomol. Struct. & Dyn. 11, 203 - 214.CrossRefGoogle Scholar
  15. 11.
    Bernhardt, P.V., and Comba, P. (1993) Prediction and interpretation of electronic spectra of transition metal complexes via the combination of molecular mechanics and angular overlap model calculations, Inorg. Chem. 32, 2798 - 2803.CrossRefGoogle Scholar
  16. 12.
    Gugelchuk, M.M., and Houk, K.N. (1994) Stereoselective organometallic reactions; A force field study of pi-allyl intermediates in nickel(0)-catalyzed cycloadditions, J. Am. Chem. Soc. 116, 330 - 339.CrossRefGoogle Scholar
  17. 13.
    Norenberg, K.N., Shoemaker, C.M., and Zimmer, M. Molecular mechanics and cluster analysis of nicke(II) six-membered rings. J. Chem. Soc., Dalton Trans. In press.Google Scholar
  18. 14.
    Allen, F.H., and Kennard, O. (1993) 3D search and research using the Cambridge Structural Database, Chem. Design Automation News 8 31–37.Google Scholar
  19. 15.
    DaCruz, M.F., and Zimmer, M. (1996) Cluster and molecular mechanical analysis of the conformation of all six-membered cobalt(III) diamine rings in the Cambridge Structure Database, Inorg. Chem. 35, 2872 - 2877.CrossRefGoogle Scholar
  20. 16.
    Zimmer, M. (1995) Bioinorganic molecular mechanics, Chem. Rev. 95, 2629 - 2649.CrossRefGoogle Scholar
  21. 17.
    Hay, B. P. (1993) Methods for molecular mechanics modeling of coordination compounds, Coord Chem. Rev. 126, 177 - 236.CrossRefGoogle Scholar
  22. 18.
    Shenkin, P.S., and McDonald, D.Q. (1994) Cluster analysis of molecular conformations, J. Comp. Chem. 15, 899 - 916.CrossRefGoogle Scholar
  23. 19.
    Rawle, S.C., Clarke, A.J., Moore, P., and Alcock, N.W. (1992) Ligands designed to impose tetrahedral co-ordination; a convenient route to aminoethyl and aminopropyl pendant arm derivatives of 1,5,9triazacyclododecane, J. Chem. Soc., Dalton Trans. 1992, 2755–2757. CSD name = pakvus.CrossRefGoogle Scholar
  24. 20.
    Hancock, R.D. (1989) Molecular Mechanics, Prog. lnorg. Chem. 37187 - 291CrossRefGoogle Scholar
  25. 21.
    Wiberg K.B. and Boyd R.H. (1972) Application of strain energy minimization to the dynamics of conformational changes, J. Am. Chem. Soc. 94, 8426 - 8430.CrossRefGoogle Scholar
  26. Hancock, R.D., Drew, M.G.B., and Yates P.C. (1986) The close equivalence to earlier reported methods of a recently reported method of calculating hole sizes in macrocyclic ligands, J. Chem. Soc., Dalton Trans. 1986, 2505–2507.Google Scholar
  27. 22.
    V.B. Pett, L.L. Diaddario, E.R. Dockal, P.W. Corfield, C. Ceccarelli, M.D. Glick, L.A. Ochrymowycz and D.B. Rorabacher, Ring size effects on the structure of macrocyclic ligand complexes: copper(II) complexes with 12–16-membered cyclic tetrathia ethers Inorg. Chem. 22, 1983, 3661–3670.CrossRefGoogle Scholar
  28. 23.
    Blake, A.J., Reid G., and Schroeder, M. (1989) Platinum metal thioether macrocyclic complexes: Synthesis, electrochemistry, and single-crystal X-ray structures of cis-[RhC12L2]PF6and trans[RhC12L3]PF6L2=1,4,8,11-tetrathiacycIotetradecane, L3= 1,5,9,13-tetrathiacyclohexadecane, J. Chem. Soc., Dalton Trans. 1989, 1675.CrossRefGoogle Scholar
  29. 24.
    Desimone, R.E., Cragel, J.,Jr., Ilsley, W.H. and Glick, M.D. (1979) Structural chemistry of molybdenum complexes of cyclic polythiaethers:the crystal and molecular structure of ethoxido-oxobis(1,5,9,13-tetrashiacyclohexadecane)-.mu.-oxodimolybdenum(IV) trifluoromethanesulfonate hydrate, J. Coord. Chem. 9, 167 - 175.CrossRefGoogle Scholar
  30. 25.
    Hills, A., Hughes, D.L., Jimenez-Tenorio, M., Leigh, G.J., Houlton, A. and Silver, J.A. (1989) Large Moessbauer quadrupole splittings in high-spin iron(II) complexes: the structure of diiodo-1,5,9,13tetrathiacyclohexadecaneiron(II) (or 1,5,9,13-tetrathiacyclohexadecaneiron(II) diiodide) J. Chem. Soc., Chem. Comm. 1989, 1774 - 1775.CrossRefGoogle Scholar
  31. 26.
    Setzer, W.N., Tang, Y., Grant, G.J., and VanDerveer D.G. (1991) Synthesis and X-ray Crystal Structures of Heavy-Metal Complexes of 1,5,9,13-Tetrathiacyclohexadecane, Inorg. Chem. 30, 3652 - 3656.CrossRefGoogle Scholar
  32. 27.
    Mobley, H.L.T. and Hausinger, R.P. (1989) Microbial ureases: significance, regulation, and molecular characterization Microbiol. Rev. 53, 85–108.Google Scholar
  33. 28.
    Dixon, N.E., Gazzola, C., Blakeley, R.L., and Zerner, B. (1975) Jack bean urease (EC3.5.1.5). A metalloenzyme. A simple biological role for nickel? J. Am. Chem. Soc. 97, 4131 - 4132.CrossRefGoogle Scholar
  34. 29.
    Jabri, E., Carr, M.B., Hausinger, R.P., and Karplus, P.A. (1995) The crystal structure of urease from Klebsiella aerogenes, Science 268, 998 - 1004.CrossRefGoogle Scholar
  35. 30.
    Park, I.-S., and Hausinger, R.P. (1995) Requirement of carbon dioxide for in vitro assembly of the urease nickel metallocenter. Science 267, 1156 - 1158.CrossRefGoogle Scholar
  36. 31.
    Jabri, E., and Karplus, P.A. (1996) Structures of the Klebsiella aerogenes, urease apoenzyme and two acive-site mutants, Biochemistry 35, 10616 - 10626.CrossRefGoogle Scholar
  37. 32.
    Park, I.-S., Michel, L.O., Pearson, M.A., Jabri, E., Karplus, P.A., Wang, S., Dong, J., Scott, R.A. Koehler, B.P., Johnson, M.K., and Hausinger, R.P. (1996) Characterization of the mononickel metallocenter in H134A mutant urease, J. Bio. Chem. 271, 18632 - 18637.CrossRefGoogle Scholar
  38. 33.
    Park, I.-S., and Hausinger, R.P. (1996) Metal ion interactions with urease and ureD-urease apoproteins, Biochemistry 35, 5345 - 5352.CrossRefGoogle Scholar
  39. 34.
    Csiki, C., and Zimmer, M. (in press) Computational Design of Biomimetic Compounds: Urease an example, J. Mol. Struct.Google Scholar
  40. 35.
    Lippard S.J., and Berg J.M. (1994) Principles in Bioinorganic Chemistry, University Science Books: Mill Valley, CA.Google Scholar
  41. 36.
    Francis M.B., Finney N.S., and Jacobsen E.N. (1996) Combinatorial approach to the discovery of novel coordination complexes, J. Am. Chem. Soc. 118, 8983 - 8984.CrossRefGoogle Scholar
  42. 37.
    Allen F.H., and Kennard O. (1991) The development of versions 3 and 4 of the Cambridge Structural Database System, J. Chem. Inf. Comput. Sci. 37, 187 - 204.Google Scholar
  43. 38.
    Lippard, S.J. (1995) At last - the crystal structure of urease, Science 268, 996 - 997.CrossRefGoogle Scholar
  44. 39.
    Moncrief, M.B.C., Horn, L.G., Jabri, E., Karplus, P.A., Hausinger, R.P. (1995) Urease activity in the crystalline state, Protein Science 4, 2234 - 2236.CrossRefGoogle Scholar
  45. 40.
    Mohamadi, F., Richards, N.G.F., Guida, W.C. Liskamp, R., Lipton, M., Caulfield, C., Chang, C., Hendrickson, T. and Still, W.C. (1990) MacroModel-An integrated software system for modeling organic and bioorganic molecules using molecular mechanics J. Comp. Chem. 11, 440 - 467.Google Scholar
  46. 41.
    Ferguson, D.M., and Kollman P.A. (1991) Can the Lennard-Jones 6–12 function replace the 10–12 form in molecular mechanics calculations? J. Comp. Chem. 12, 620 - 626.CrossRefGoogle Scholar
  47. 42.
    McDonald, Q. and Still, W.C. (1992) AMBER* torsional parameters for the peptide backbone Tetrahedron Len. 33, 7743–7746.CrossRefGoogle Scholar
  48. 43.
    Hancock, R.D., Dobson, S.M., Evers, A., Wade, P.W., Ngwenya, M.P., Boeyens, J.C.A., and Wainwright, K.P. (1989) More rigid macrocyclic ligands that show metal ion size-based selectivity. A crystallographic, molecular mechanics, and formation constant study of the complexes of bridged cyclen, J. Am. Chem. Soc. 110, 2788 - 2794.CrossRefGoogle Scholar
  49. 44.
    Comba, P., and Zimmer, M. (1996) Inorganic molecular mechanics, J. Chem. Ed 73, 108 - 110.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 1997

Authors and Affiliations

  • Csilla Csiki
    • 1
  • Karen M. Norenberg
    • 1
  • Christina M. Shoemaker
    • 1
  • Marc Zimmer
    • 1
  1. 1.Chemistry DepartmentConnecticut CollegeNew LondonUSA

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