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Synthetic Models of Copper–Nitrosyl Species Proposed as Intermediates in Biological Denitrification

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Nitrosyl Complexes in Inorganic Chemistry, Biochemistry and Medicine II

Part of the book series: Structure and Bonding ((STRUCTURE,volume 154))

Abstract

Copper-containing nitrite reductase enzymes catalyze the reduction of nitrite to nitric oxide during denitrification, a key component of the global nitrogen cycle. Insights into the properties of proposed copper–nitrosyl intermediates have been obtained through studies of model complexes. Such complexes comprising both copper and nickel exhibit variable geometries and electronic structures that are influenced by the supporting ligands.

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Abbreviations

Ar:

Aryl

atm:

Atmosphere

Bpy:

2,2′-Bipyridyl

Bu:

Butyl

Cp:

Cyclopentadienyl

Cu-NiR:

Copper nitrite reductase enzyme

Cy:

Cyclohexyl

dmp:

2,9-Dimethyl-1,10-phenanthroline

ENDOR:

Electron-nuclear double resonance

EPR:

Electron paramagnetic resonance

equiv:

Equivalent(s)

ESI-MS:

Electrospray ionization mass spectrometry

Et:

Ethyl

h:

Hour(s)

His:

Histidine

Im:

Imidazole

iPr:

Isopropyl

IR:

Infrared spectroscopy

MCD:

Magnetic circular dichroism

Me:

Methyl

Mes:

Mesityl 2,4,6-trimethylphenyl (not methanesulfonyl)

min:

Minute(s)

mol:

Mole(s)

NMR:

Nuclear magnetic resonance

Ph:

Phenyl

py:

Pyridine

pz:

Pyrazolyl

rt:

Room temperature

s:

Second(s)

tBu:

tert-Butyl

THF:

Tetrahydrofuran

TMEDA:

N,N,N',N'-tetramethyl-1,2-ethylenediamine

Tol:

4-Methylphenyl

Tp:

Tris(pyrazolyl)hydroborate

UV–vis:

Ultraviolet–visible

XAS:

X-ray absorption spectroscopy

References

  1. Zumft WG (1997) Cell biology and molecular basis of denitrification. Microbiol Rev 61:533

    CAS  Google Scholar 

  2. Eady RR, Hasnain SS (2004) Denitrification. In: McCleverty JA, Meyer TJ (eds) Comprehensive coordination chemistry II, vol 8. Elsevier, Amsterdam, pp 759–786

    Chapter  Google Scholar 

  3. Wasser IM, de Vries S, Moënne-Loccoz P, Schröder I, Karlin KD (2002) Nitric oxide in biological denitrification: Fe/Cu metalloenzyme and metal complex NOx redox chemistry. Chem Rev 102:1201

    Article  CAS  Google Scholar 

  4. Campbell WH (1999) Nitrate reductase structure, function and regulation: bridging the gap between biochemistry and physiology. Annu Rev Plant Physiol Plant Mol Biol 50:277

    Article  CAS  Google Scholar 

  5. Moënne-Loccoz P, Richter O-MH, Huang H-W, Wasser IM, Ghiladi RA, Karlin KD, de Vries S (2000) Nitric oxide reductase from Paracoccus denitrificans contains an oxo-bridged heme/non-heme diiron center. J Am Chem Soc 122:9344

    Article  Google Scholar 

  6. Zumft W (2005) Nitric oxide reductases of prokaryotes with emphasis on the respiratory, heme-copper oxidase type. J Inorg Biochem 99:194

    Article  CAS  Google Scholar 

  7. Dell Acqua S, Pauleta SR, Moura I, Moura JJG (2011) The tetranuclear copper active site of nitrous oxide reductase: the CuZ center. J Biol Inorg Chem 16:183

    Article  CAS  Google Scholar 

  8. Averill BA (1996) Dissimilatory nitrite and nitric oxide reductases. Chem Rev 96:2951

    Article  CAS  Google Scholar 

  9. Merkle A, Lehnert N (2012) Binding and activation of nitrite and nitric oxide by copper nitrite reductase and corresponding model complexes. Dalton Trans 41:3355

    Article  CAS  Google Scholar 

  10. Suzuki S, Kataoka K, Yamaguchi K (2000) Metal coordination and mechanism of multicopper nitrite reductase. Acc Chem Res 33:728

    Article  CAS  Google Scholar 

  11. Antonyuk SV, Strange RW, Sawers G, Eady RR, Hasnain SS (2005) Atomic resolution structures of resting-state, substrate- and product-complexed Cu-nitrite reductase provide insight into catalytic mechanism. Proc Natl Acad Sci USA 102:12041

    Article  CAS  Google Scholar 

  12. Enemark JH, Feltham RD (1974) Principles of structure, bonding, and reactivity for metal nitrosyl complexes. Coor Chem Rev 13:339

    Article  CAS  Google Scholar 

  13. McCleverty JA (2004) Chemistry of nitric oxide relevant to biology. Chem Rev 104:403

    Article  CAS  Google Scholar 

  14. Hayton TW, Legzdins P, Sharp WB (2002) Coordination and organometallic chemistry of metal − NO complexes. Chem Rev 102:935

    Article  CAS  Google Scholar 

  15. Wijma HJ, Jeuken LJC, Verbeet MP, Armstrong FA, Canters GW (2006) A random-sequential mechanism for nitrite binding and active site reduction in copper-containing nitrite reductase. J Biol Chem 281:16340

    Article  CAS  Google Scholar 

  16. Ye RW, Toro-Suarez I, Tiedje JM, Averill BA (1991) H2 18O isotope exchange studies on the mechanism of reduction of nitric oxide and nitrite to nitrous oxide by denitrifying bacteria. J Biol Chem 266:12848

    CAS  Google Scholar 

  17. Tolman W (2006) Using synthetic chemistry to understand copper protein active sites: a personal perspective. J Biol Inorg Chem 11:261

    Article  CAS  Google Scholar 

  18. Kujime M, Fujii H (2006) Spectroscopic characterization of reaction intermediates in a model for copper nitrite reductase. Angew Chem Int Ed 45:1089

    Article  CAS  Google Scholar 

  19. Tocheva EI, Rosell FI, Mauk AG, Murphy MEP (2004) Side-on copper-nitrosyl coordination by nitrite reductase. Science 304:867

    Article  CAS  Google Scholar 

  20. Tocheva EI, Rosell FI, Mauk AG, Murphy MEP (2007) Stable copper-nitrosyl formation by nitrite reductase in either oxidation state. Biochemistry 46:12366

    Article  CAS  Google Scholar 

  21. Usov OM, Sun Y, Grigoryants VM, Shapleigh JP, Scholes CP (2006) EPR-ENDOR of the Cu(I)NO complex of nitrite reductase. J Am Chem Soc 128:13102

    Article  CAS  Google Scholar 

  22. Ghosh S, Dey A, Usov OM, Sun Y, Grigoryants VM, Scholes CP, Solomon EI (2007) Resolution of the spectroscopy versus crystallography issue for NO intermediates of nitrite reductase from Rhodobacter sphaeroides. J Am Chem Soc 129:10310

    Article  CAS  Google Scholar 

  23. Silaghi-Dumitrescu R (2006) Copper-containing nitrite reductase: a DFT study of nitrite and nitric oxide adducts. J Inorg Biochem 100:396

    Article  CAS  Google Scholar 

  24. Sundararajan M, Surendran R, Hillier IH (2006) How is NO bound to reduced copper nitrite reductase? A DFT study. Chem Phys Lett 418:96

    Article  CAS  Google Scholar 

  25. Periyasamy G, Sundararajan M, Hillier IH, Burton NA, McDouall JJW (2007) The binding of nitric oxide at the Cu(I) site of copper nitrite reductase and of inorganic models: DFT calculations of the energetics and EPR parameters of side-on and end-on structures. Phys Chem Chem Phys 9:2498

    Article  CAS  Google Scholar 

  26. Merkle AC, Lehnert N (2009) The side-on copper(I) nitrosyl geometry in copper nitrite reductase is due to steric interactions with isoleucine-257. Inorg Chem 48:11504

    Article  CAS  Google Scholar 

  27. Karlin KD (1993) Metalloenzymes, structural motifs, and inorganic models. Science 261:701

    Article  CAS  Google Scholar 

  28. Shelef M (1995) Selective catalytic reduction of NOx with N-free reductants. Chem Rev 95:209

    Article  CAS  Google Scholar 

  29. Paul PP, Tyeklar Z, Farooq A, Karlin KD, Liu S, Zubieta J (1990) Isolation and X-ray structure of a dinuclear copper-nitrosyl complex. J Am Chem Soc 112:2430

    Article  CAS  Google Scholar 

  30. Karlin KD, Hayes JC, Gultneh Y, Cruse RW, McKown JW, Hutchinson JP, Zubieta J (1984) Copper-mediated hydroxylation of an arene: model system for the action of copper monooxygenases. Structures of a binuclear copper(I) complex and its oxygenated product. J Am Chem Soc 106:2121

    Article  CAS  Google Scholar 

  31. Carrier SM, Ruggiero CE, Tolman WB, Jameson GB (1992) Synthesis and structural characterization of a mononuclear copper nitrosyl complex. J Am Chem Soc 114:4407

    Article  CAS  Google Scholar 

  32. Ruggiero CE, Carrier SM, Antholine WE, Whittaker JW, Cramer CJ, Tolman WB (1993) Synthesis and structural and spectroscopic characterization of mononuclear copper nitrosyl complexes: models for nitric oxide adducts of copper proteins and copper-exchanged zeolites. J Am Chem Soc 115:11285

    Article  CAS  Google Scholar 

  33. Ruggiero CE, Carrier SM, Tolman WB (1994) Reductive disproportionation of NO mediated by copper complexes: modeling N2O generation by copper proteins and heterogeneous catalysts. Angew Chem Int Ed Engl 33:895

    Article  Google Scholar 

  34. Schneider JL, Carrier SM, Ruggiero CE, Young VG Jr, Tolman WB (1998) Influences of ligand environment on the spectroscopic properties and disproportionation reactivity of copper-nitrosyl complexes. J Am Chem Soc 120:11408

    Article  CAS  Google Scholar 

  35. Fujisawa K, Tateda A, Miyashita Y, Okamoto K, Paulat F, Praneeth VKK, Merkle A, Lehnert N (2008) Structural and spectroscopic characterization of mononuclear copper(I) nitrosyl complexes: end-on versus side-on coordination of NO to copper(I). J Am Chem Soc 130:1205

    Article  CAS  Google Scholar 

  36. Mealli C, Arcus CS, Wilkinson JL, Marks TJ, Ibers JA (1976) Structural studies of copper(I) binding by hydrotris(1-pyrazolyl)borate and hydrotris(3,5-dimethyl-1-pyrazolyl)borate in the solid state and in solution. J Am Chem Soc 98:711

    Article  CAS  Google Scholar 

  37. Kitajima N, Fujisawa K, Fujimoto C, Moro-oka Y, Hashimoto S, Kitagawa T, Toriumi K, Tatsumi K, Nakamura A (1992) A new model for dioxygen binding in hemocyanin. Synthesis, characterization, and molecular structure of the μ-η22 peroxo dinuclear copper(II) complexes, [Cu(HB(3,5-R2pz)3)](O2) (R = i-Pr and Ph). J Am Chem Soc 114:1277

    Article  CAS  Google Scholar 

  38. Tomson NC, Crimmin MR, Petrenko T, Rosebrugh LE, Sproules S, Boyd WC, Bergman RG, DeBeer S, Toste FD, Wieghardt K (2011) A step beyond the Feltham–Enemark notation: spectroscopic and correlated ab Initio computational support for an antiferromagnetically coupled M(II)–(NO) − description of Tp*M(NO) (M = Co, Ni). J Am Chem Soc 133:18785

    Article  CAS  Google Scholar 

  39. Park GY, Deepalatha S, Puiu SC, D-H L, Mondal B, Sarjeant AAN, del Rio D, Pau MYM, Solomon EI, Karlin KD (2009) A peroxynitrite complex of copper: formation from a copper-nitrosyl complex, transformation to nitrite and exogenous phenol oxidative coupling or nitration. J Biol Inorg Chem 14:1301

    Article  CAS  Google Scholar 

  40. Mercer M, Fraser RTM (1963) Formation and dissociation of copper (II) nitrosyl complexes in non-aqueous solvents. J Inorg Nucl Chem 25:525

    Article  CAS  Google Scholar 

  41. Doyle MP, Siegfried B, Hammond JJ (1976) Oxidative deamination of primary amines by copper halide nitrosyls. The formation of geminal dihalides. J Am Chem Soc 98:1627

    Article  CAS  Google Scholar 

  42. Deters D, Weser U (1995) The analogous reaction of a diSchiff base coordinated copper and Cu2Zn2 superoxide dismutase with nitric oxide. Biometals 8:25

    Article  CAS  Google Scholar 

  43. Tran D, Ford PC (1996) Nitric oxide reduction of the copper (II) complex Cu(dmp)2 2+(dmp = 2,9-dimethyl-1,10-phenanthroline). Inorg Chem 35:2411

    Article  CAS  Google Scholar 

  44. Tran D, Skelton BW, White AH, Laverman LE, Ford PC (1998) Investigation of the nitric oxide reduction of the bis(2,9-dimethyl-1,10-phenanthroline) complex of copper(II) and the structure of [Cu(dmp)2(H2O)](CF3SO3)2. Inorg Chem 37:2505

    Article  CAS  Google Scholar 

  45. Sarma M, Singh A, Subrahmanyam Gupta G, Das G, Mondal B (2010) Nitric oxide reduction of copper(II) complex with tetradentate amine ligand followed by ligand transformation. Inorg Chim Acta 363:63

    Article  CAS  Google Scholar 

  46. Sarma M, Kalita A, Kumar P, Singh A, Mondal B (2010) Reduction of copper(II) complexes of tripodal ligands by nitric oxide and trinitrosation of the ligands. J Am Chem Soc 132:7846

    Article  CAS  Google Scholar 

  47. Sarma M, Mondal B (2011) Nitric oxide reduction of copper(II) complexes: spectroscopic evidence of copper(II) − nitrosyl intermediate. Inorg Chem 50:3206

    Article  CAS  Google Scholar 

  48. Kalita A, Kumar P, Deka RC, Mondal B (2012) First example of a Cu(I)–(η2-O, O)nitrite complex derived from Cu(II)–nitrosyl. Chem Commun 48:1251

    Article  CAS  Google Scholar 

  49. Kalita A, Kumar P, Mondal B (2012) Reaction of a copper(II)–nitrosyl complex with hydrogen peroxide: putative formation of a copper(I)–peroxynitrite intermediate. Chem Commun 48:4636

    Article  CAS  Google Scholar 

  50. Wright AM, Wu G, Hayton TW (2010) Structural characterization of a copper nitrosyl complex with a {CuNO}10 configuration. J Am Chem Soc 132:14336

    Article  CAS  Google Scholar 

  51. Kieber-Emmons M, Riordan C (2007) Dioxygen activation at monovalent nickel. Acc Chem Res 40:618

    Article  CAS  Google Scholar 

  52. Yao S, Driess M (2011) Lessons from isolable nickel(I) precursor complexes for small molecule activation. Acc Chem Res 45:276

    Article  Google Scholar 

  53. Harding DJ, Harding P, Adams H, Tuntulani T (2007) Synthesis and characterization of sterically hindered tris(pyrazolyl)borate Ni complexes. Inorg Chim Acta 360:3335

    Article  CAS  Google Scholar 

  54. Landry VK, Pang K, Quan SM, Parkin G (2007) Tetrahedral nickel nitrosyl complexes with tripodal [N3] and [Se3] donor ancillary ligands: structural and computational evidence that a linear nitrosyl is a trivalent ligand. Dalton Trans 820

    Google Scholar 

  55. Maffett LS, Gunter KL, Kreisel KA, Yap GPA, Rabinovich D (2007) Nickel nitrosyl complexes in a sulfur-rich environment: the first poly(mercaptoimidazolyl)borate derivatives. Polyhedron 26:4758

    Article  CAS  Google Scholar 

  56. Nieto I, Bontchev RP, Ozarowski A, Smirnov D, Krzystek J, Telser J, Smith JM (2009) Synthesis and spectroscopic investigations of four-coordinate nickel complexes supported by a strongly donating scorpionate ligand. Inorg Chim Acta 362:4449

    Article  CAS  Google Scholar 

  57. Muñoz SB III, Salvador B, Foster WK, Lin H-J, Margarit CG, Dickie DA, Smith JM (2012) Tris(carbene)borate ligands featuring imidazole-2-ylidene, benzimidazol-2-ylidene, and 1,3,4-triazol-2-ylidene donors. Evaluation of donor properties in four-coordinate {NiNO}10 complexes. Inorg Chem 51:12660

    Article  Google Scholar 

  58. Di Vaira M, Ghilardi CA, Sacconi L (1976) Synthesis and structural characterization of some nitrosyl complexes of iron, cobalt, and nickel with poly(tertiary phosphines and arsines). Inorg Chem 15:1555

    Article  Google Scholar 

  59. MacBeth CE, Thomas JC, Betley TA, Peters JC (2004) The coordination chemistry of “[BP3]NiX” platforms: targeting low-valent nickel sources as promising candidates to L3Ni=E and L3Ni≡E linkages. Inorg Chem 43:4645

    Article  CAS  Google Scholar 

  60. Wright AM, Wu G, Hayton TW (2011) Late-metal nitrosyl cations: synthesis and reactivity of [Ni(NO)(MeNO2)3][PF6]. Inorg Chem 50:11746

    Article  CAS  Google Scholar 

  61. Iluc VM, Miller AJM, Hillhouse GL (2005) Synthesis and characterization of side-bound aryldiazo and end-bound nitrosyl complexes of nickel. Chem Commun 5091

    Google Scholar 

  62. Wright AM, Wu G, Hayton TW (2012) Formation of N2O from a nickel nitrosyl: isolation of the cis-[N2O2]2– intermediate. J Am Chem Soc 134:9930

    Article  CAS  Google Scholar 

  63. Puiu SC, Warren TH (2003) Three-coordinate β-diketiminato nickel nitrosyl complexes from nickel(I)-lutidine and nickel(II)-alkyl precursors. Organometallics 22:3974

    Article  CAS  Google Scholar 

  64. Landry VK, Parkin G (2007) Synthesis and structural characterization of [BseMe]Ni(PPh3)(NO), a nickel complex with a bent nitrosyl ligand. Polyhedron 26:4751

    Article  CAS  Google Scholar 

  65. Fomitchev DV, Furlani TR, Coppens P (1998) Combined X-ray diffraction and density functional study of [Ni(NO)(η5-Cp*)] in the ground and light-induced metastable states. Inorg Chem 37:1519

    Article  CAS  Google Scholar 

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Correspondence to William B. Tolman .

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Salmon, D.J., Tolman, W.B. (2013). Synthetic Models of Copper–Nitrosyl Species Proposed as Intermediates in Biological Denitrification. In: Mingos, D. (eds) Nitrosyl Complexes in Inorganic Chemistry, Biochemistry and Medicine II. Structure and Bonding, vol 154. Springer, Berlin, Heidelberg. https://doi.org/10.1007/430_2013_93

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