N–O bond cleavage mechanism(s) in nitrous oxide reductase

  • Mehmed Z. ErtemEmail author
  • Christopher J. CramerEmail author
  • Fahmi HimoEmail author
  • Per E. M. SiegbahnEmail author
Original Paper


Quantum chemical calculations of active-site models of nitrous oxide reductase (N2OR) have been undertaken to elucidate the mechanism of N–O bond cleavage mediated by the supported tetranuclear Cu4S core (CuZ) found in the enzymatic active site. Using either a minimal model previously employed by Gorelsky et al. (J. Am. Chem. Soc. 128:278–290, 2006) or a more extended model including key residue side chains in the active-site second shell, we found two distinct mechanisms. In the first model, N2O binds to the fully reduced CuZ in a bent μ-(1,3)-O,N bridging fashion between the CuI and CuIV centers and subsequently extrudes N2 while generating the corresponding bridged μ-oxo species. In the second model, substrate N2O binds loosely to one of the coppers of CuZ in a terminal fashion, i.e., using only the oxygen atom; loss of N2 generates the same μ-oxo copper core. The free energies of activation predicted for these two alternative pathways are sufficiently close to one another that theory does not provide decisive support for one over the other, posing an interesting problem with respect to experiments that might be designed to distinguish between the two. Effects of nearby residues and active-site water molecules are also explored.


Density functional theory Molecular modeling Electronic structure Transition state 



F.H. gratefully acknowledges financial support from the Swedish Research Council (grants 621-2009-4736 and 622-2009-371) and computer time from the PDC Center for High Performance Computing. C.J.C. and M.Z.E. thank the US National Science Foundation (CHE09-52054) for funding, and William B. Tolman for stimulating discussion.


  1. 1.
    Berks BC, Ferguson SJ, Moir JWB, Richardson DJ (1995) Biochim Biophys Acta Bioenerg 1232:97–173Google Scholar
  2. 2.
    Zumft W (1997) Microbiol Mol Biol Rev 61:533–616PubMedGoogle Scholar
  3. 3.
    Prudencio M, Pereira AS, Tavares P, Besson S, Cabrito I, Brown K, Samyn B, Devreese B, Van Beeumen J, Rusnak F, Fauque G, Moura JJG, Tegoni M, Cambillau C, Moura I (2000) Biochemistry 39:3899–3907PubMedCrossRefGoogle Scholar
  4. 4.
    Brown K, Tegoni M, Prudencio M, Pereira AS, Besson S, Moura JJ, Moura I, Cambillau C (2000) Nat Struct Mol Biol 7:191–195CrossRefGoogle Scholar
  5. 5.
    Brown K, Djinovic-Carugo K, Haltia T, Cabrito I, Saraste M, Moura JG, Moura I, Tegoni M, Cambillau C (2000) J Biol Chem 275:41133–41136PubMedCrossRefGoogle Scholar
  6. 6.
    Rasmussen T, Berks BC, Sanders-Loehr J, Dooley DM, Zumft WG, Thomson AJ (2000) Biochemistry 39:12753–12756PubMedCrossRefGoogle Scholar
  7. 7.
    Haltia T, Brown K, Tegoni M, Cambillau C, Saraste M, Mattila K, Djinovic-Carugo K (2003) Biochem J 369:77–88PubMedCrossRefGoogle Scholar
  8. 8.
    Holm RH, Kennepohl P, Solomon EI (1996) Chem Rev 96:2239–2314PubMedCrossRefGoogle Scholar
  9. 9.
    Ferguson-Miller S, Babcock GT (1996) Chem Rev 96:2889–2908PubMedCrossRefGoogle Scholar
  10. 10.
    Farrar JA, Neese F, Lappalainen P, Kroneck PMH, Saraste M, Zumft WG, Thomson AJ (1996) J Am Chem Soc 118:11501–11514CrossRefGoogle Scholar
  11. 11.
    Charnock JM, Dreusch A, Korner H, Neese F, Nelson J, Kannt A, Michel H, Garner CD, Kroneck PMH, Zumft WG (2000) Eur J Biochem 267:6509CrossRefGoogle Scholar
  12. 12.
    Zumft WG (2005) J Mol Microbiol Biotechnol 10:154–166PubMedCrossRefGoogle Scholar
  13. 13.
    Alvarez ML, Ai J, Zumft W, Sanders-Loehr J, Dooley DM (2001) J Am Chem Soc 123:576–587PubMedCrossRefGoogle Scholar
  14. 14.
    Dell’Acqua S, Pauleta SR, Moura I, Moura JJG (2011) J Biol Inorg Chem 16:183–194PubMedCrossRefGoogle Scholar
  15. 15.
    Dooley DM, Moog RS, Zumft WG (1987) J Am Chem Soc 109:6730–6735CrossRefGoogle Scholar
  16. 16.
    Dooley DM, McGuirl MA, Rosenzweig AC, Landin JA, Scott RA, Zumft WG, Devlin F, Stephens PJ (1991) Inorg Chem 30:3006–3011CrossRefGoogle Scholar
  17. 17.
    Farrar JA, Zumft WG, Thomson AJ (1998) Proc Natl Acad Sci USA 95:9891–9896PubMedCrossRefGoogle Scholar
  18. 18.
    Chen P, Cabrito I, Moura JJG, Moura I, Solomon EI (2002) J Am Chem Soc 124:10497–10507PubMedCrossRefGoogle Scholar
  19. 19.
    Chen P, DeBeer George S, Cabrito I, Antholine WE, Moura JJG, Moura I, Hedman B, Hodgson KO, Solomon EI (2002) J Am Chem Soc 124:744–745PubMedCrossRefGoogle Scholar
  20. 20.
    Ghosh S, Gorelsky SI, Chen P, Cabrito I, Moura JJG, Moura I, Solomon EI (2003) J Am Chem Soc 125:15708–15709PubMedCrossRefGoogle Scholar
  21. 21.
    Chan JM, Bollinger JA, Grewell CL, Dooley DM (2004) J Am Chem Soc 126:3030–3031PubMedCrossRefGoogle Scholar
  22. 22.
    Gorelsky SI, Ghosh S, Solomon EI (2006) J Am Chem Soc 128:278–290PubMedCrossRefGoogle Scholar
  23. 23.
    Bar-Nahum I, Gupta AK, Huber SM, Ertem MZ, Cramer CJ, Tolman WB (2009) J Am Chem Soc 131:2812–2814PubMedCrossRefGoogle Scholar
  24. 24.
    Schrödinger (2000) Jaguar 5.5. Schrödinger, PortlandGoogle Scholar
  25. 25.
    Becke A (1993) J Chem Phys 98:5648–5652CrossRefGoogle Scholar
  26. 26.
    Lee C, Yang W, Parr R (1988) Phys Rev B 37:785–789CrossRefGoogle Scholar
  27. 27.
    Hay P, Wadt W (1985) J Chem Phys 82:299–310CrossRefGoogle Scholar
  28. 28.
    Reiher M, Salomon O, Hess B (2001) Theor Chem Acc 107:48–55CrossRefGoogle Scholar
  29. 29.
    Salomon O, Reiher M, Hess B (2002) J Chem Phys 117:4729–4737CrossRefGoogle Scholar
  30. 30.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian 03, revision D.01. Gaussian, WallingfordGoogle Scholar
  31. 31.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Mennucci B, Petersson GA, Nakatsuji H, Caricato M, Li X, Hratchian HP, Izmaylov AF, Bloino J, Zheng G, Sonnenberg JL, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Montgomery JA, Peralta JE, Ogliaro F, Bearpark M, Heyd JJ, Brothers E, Kudin KN, Staroverov VN, Kobayashi R, Normand J, Raghavachari K, Rendell A, Burant JC, Iyengar SS, Tomasi J, Cossi M, Rega N, Millam JM, Klene M, Knox JE, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Martin RL, Morokuma K, Zakrzewski VG, Voth GA, Salvador P, Dannenberg JJ, Dapprich S, Daniels AD, Farkas Ö, Foresman JB, Ortiz JV, Cioslowski J, Fox DJ (2010) Gaussian 09, revision A.02. Gaussian, WallingfordGoogle Scholar
  32. 32.
    Grimme S (2004) J Comput Chem 25:1463–1473PubMedCrossRefGoogle Scholar
  33. 33.
    Grimme S (2006) J Comput Chem 27:1787–1799PubMedCrossRefGoogle Scholar
  34. 34.
    De Marothy S (2011) XYZViewer a locally developed software for molecular visualization and simple property calculations. Stockholm University, StockholmGoogle Scholar
  35. 35.
    Tannor D, Marten B, Murphy R, Friesner R, Sitkoff D, Nicholls A, Ringalda M, Goddard W, Honig B (1994) J Am Chem Soc 116:11875–11882CrossRefGoogle Scholar
  36. 36.
    Marten B, Kim K, Cortis C, Friesner R, Murphy R, Ringnalda M, Sitkoff D, Honig B (1996) J Phys Chem 100:11775–11788CrossRefGoogle Scholar
  37. 37.
    Zhao Y, Truhlar DG (2006) J Chem Phys 125:194101PubMedCrossRefGoogle Scholar
  38. 38.
    Dolg M, Wedig U, Stoll H, Preuss H (1987) J Chem Phys 86:866–872CrossRefGoogle Scholar
  39. 39.
    Hehre WJ, Radom L, Schleyer PvR, Pople JA (1986) Ab initio molecular orbital theory. Wiley, New YorkGoogle Scholar
  40. 40.
    Cramer CJ (2004) Essentials of computational chemistry: theories and models. Wiley, ChichesterGoogle Scholar
  41. 41.
    Marenich AV, Cramer CJ, Truhlar DG (2009) J Phys Chem B 113:6378–6396PubMedCrossRefGoogle Scholar
  42. 42.
    Heisenberg WZ (1928) Physik 49:619–636CrossRefGoogle Scholar
  43. 43.
    Dirac PAM (1929) Proc R Soc Lond Ser A 123:714–733CrossRefGoogle Scholar
  44. 44.
    Yamaguchi K, Jensen F, Dorigo A, Houk KN (1988) Chem Phys Lett 149:537–542CrossRefGoogle Scholar
  45. 45.
    Soda T, Kitagawa Y, Onishi T, Takano Y, Shigeta Y, Nagao H, Yoshioka Y, Yamaguchi K (2000) Chem Phys Lett 319:223–230CrossRefGoogle Scholar
  46. 46.
    Noodleman L (1981) J Chem Phys 74:5737–5743CrossRefGoogle Scholar
  47. 47.
    Hu P, Zhang Y (2006) J Am Chem Soc 128:1272–1278PubMedCrossRefGoogle Scholar
  48. 48.
    Senn H, Thiel S, Thiel W (2005) J Chem Theory Comput 1:494–505CrossRefGoogle Scholar
  49. 49.
    Senn HM, Kaestner J, Breidung J, Thiel W (2009) Can J Chem Rev Can Chim 87:1322–1337CrossRefGoogle Scholar
  50. 50.
    Minenkov Y, Occhipinti G, Jensen VR (2009) J Phys Chem A 113:11833–11844PubMedCrossRefGoogle Scholar
  51. 51.
    Siegbahn PEM, Blomberg MRA, Chen S (2010) J Chem Theory Comput 6:2040–2044CrossRefGoogle Scholar
  52. 52.
    Harvey JN (2010) Faraday Discuss 145:487–505CrossRefGoogle Scholar
  53. 53.
    McMullin CL, Jover J, Harvey JN, Fey N (2010) Dalton Trans 39:10833–10836PubMedCrossRefGoogle Scholar
  54. 54.
    Lonsdale R, Harvey JN, Mulholland AJ (2010) J Phys Chem Lett 1:3232–3237CrossRefGoogle Scholar
  55. 55.
    Osuna S, Swart M, Sola M (2011) J Phys Chem A 115:3491–3496PubMedCrossRefGoogle Scholar
  56. 56.
    Zheng J, Zhao Y, Truhlar DG (2007) J Chem Theory Comput 3:569–582CrossRefGoogle Scholar
  57. 57.
    Cramer CJ, Gour JR, Kinal A, Wtoch M, Piecuch P, Shahi ARM, Gagliardi L (2008) J Phys Chem A 112:3754–3767PubMedCrossRefGoogle Scholar
  58. 58.
    Torker S, Merki D, Chen P (2008) J Am Chem Soc 130:4808–4814PubMedCrossRefGoogle Scholar
  59. 59.
    Zhao Y, Truhlar DG (2008) Theor Chem Acc 120:215–241CrossRefGoogle Scholar
  60. 60.
    Zhao Y, Truhlar DG (2008) Acc Chem Res 41:157–167PubMedCrossRefGoogle Scholar
  61. 61.
    Korth M, Grimme S (2009) J Chem Theory Comput 5:993–1003CrossRefGoogle Scholar
  62. 62.
    Zhao Y, Truhlar DG (2009) J Chem Theory Comput 5:324–333CrossRefGoogle Scholar
  63. 63.
    Reed AE, Weinstock RB, Weinhold F (1985) J Chem Phys 83:735–746CrossRefGoogle Scholar

Copyright information

© SBIC 2012

Authors and Affiliations

  1. 1.Department of Chemistry and Supercomputing InstituteUniversity of MinnesotaMinneapolisUSA
  2. 2.Department of Organic Chemistry, Arrhenius LaboratoryStockholm UniversityStockholmSweden
  3. 3.Department of Biochemistry and Biophysics, Arrhenius LaboratoryStockholm UniversityStockholmSweden

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