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Lessons on O2 and NO bonding to heme from ab initio multireference/multiconfiguration and DFT calculations

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Abstract

This commentary focuses on the conceptual interpretation of the bonding of O2 and NO to heme in oxyheme and nitrosylheme complexes, using high-level ab initio complete active space self-consistent field (CASSCF)/molecular mechanical (MM), gas-phase CASSCF, and CASSCF followed by second-order perturbation theory (CASPT2) calculations as well as density functional theory (DFT) calculations. The commentary shows that expanding the complex multiconfigurational (MC) wave functions into valence bond (VB)-type configurations based on localized orbitals provides significant insight into bonding and precise definitions of oxidation states. Furthermore, the VB “reading” of the wave function unifies the descriptions of DFT and MC theories, reconciling controversies and surprises. In so doing, we demonstrate the impact of the protein bulk polarity and its hydrogen-bonding capability on the bonding. The insight provided by “reading” the VB content of the MC wave functions highlights the potential of this approach as a general paradigm in future computational bioinorganic chemistry. A great deal of insight lies in this road.

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Abbreviations

CASPT2:

Complete active space self-consistent field followed by second-order perturbation theory

CASSCF:

Complete active space self-consistent field

CASSCF(g):

Gas-phase CASSCF

CI:

Configuration interaction

CSF:

Configuration state function

DFT:

Density functional theory

GVB:

Generalized valence bond

Hb:

Hemoglobin

HO:

Heme oxygenase

Mb:

Myoglobin

MM:

Molecular mechanics

MR/MC:

Multireference/multiconfiguration

NOS:

Nitric oxide synthase

Por:

Porphine

QM:

Quantum mechanical

SAC:

Symmetry-adapted cluster

TCSCF:

Two-configuration self-consistent field

VB:

Valence bond

WFT:

Wave function theory

References

  1. Solomon EI, Scott RA, King RB (eds) (2009) Computational inorganic and bioinorganic chemistry. Wiley, New York

    Google Scholar 

  2. Senn HM, Thiel W (2009) Angew Chem Int Ed 48:1198–1229

    Article  CAS  Google Scholar 

  3. Shaik S, Cohen S, Wang Y, Chen H, Kumar D, Thiel W (2010) Chem Rev 110:949–1017

    Article  PubMed  CAS  Google Scholar 

  4. Siegbahn PEM (2006) J Biol Inorg Chem 11:695–701

    Article  PubMed  CAS  Google Scholar 

  5. Barbara K, Wennmohs F, Ye SF, Neese F (2007) Curr Opin Chem Biol 11:134–141

    Article  Google Scholar 

  6. Ryde U (2003) Curr Opin Chem Biol 7:136–142

    Article  PubMed  CAS  Google Scholar 

  7. Friesner RA, Guallar V (2005) Annu Rev Phys Chem 56:389–427

    Article  PubMed  CAS  Google Scholar 

  8. Ranaghan KE, Mulholland AJ (2010) Int Rev Phys Chem 29:65–133

    Google Scholar 

  9. Hu H, Yang WT (2008) Annu Rev Phys Chem 59:573–601

    Article  PubMed  CAS  Google Scholar 

  10. Chen H, Lai WZ, Shaik S (2011) J Phys Chem B 115:1727–1742

    Google Scholar 

  11. Chen H, Iketa-Saito M, Shaik S (2008) J Am Chem Soc 130:14778–14790

    Article  PubMed  CAS  Google Scholar 

  12. Chen H, Song JS, Lai WZ, Wu W, Shaik S (2010) J Chem Theory Comput 6:940–953

    Article  CAS  Google Scholar 

  13. Radoń M, Broclawik E, Pierloot K (2010) J Phys Chem B 114:1518–1528

    Article  PubMed  Google Scholar 

  14. Radoń M, Pierloot K (2008) J Phys Chem A 112:11824–11832

    Article  PubMed  Google Scholar 

  15. Jain R, Chan MK (2003) J Biol Inorg Chem 8:1–11

    Article  PubMed  CAS  Google Scholar 

  16. Oláh J, Harvey JN (2009) J Phys Chem A 113:7338–7345

    Article  PubMed  Google Scholar 

  17. Siegbahn PEM, Blomberg MRA, Chen SL (2010) J Chem Theory Comput 6:2040–2044

    Article  CAS  Google Scholar 

  18. Grimme S (2006) J Comput Chem 27:1787–1799

    Article  PubMed  CAS  Google Scholar 

  19. Cramer CJ, Truhlar DG (2009) Phys Chem Chem Phys 11:10757–10816

    Article  PubMed  CAS  Google Scholar 

  20. Scheidt WR, Barabanschikov A, Pavlik JW, Silvernail NJ, Sage JT (2010) Inorg Chem 49:6240–6252

    Article  PubMed  CAS  Google Scholar 

  21. Goodrich LE, Paulat F, Praneeth VKK, Lehnert N (2010) Inorg Chem 49:6293–6316

    Article  PubMed  CAS  Google Scholar 

  22. Springer BA, Sligar SG, Olson JS, Phillips GN Jr (1994) Chem Rev 94:699–714

    Article  CAS  Google Scholar 

  23. Perutz MF, Fermi G, Luisi B, Shaanan B, Liddington RC (1987) Acc Chem Res 20:309–321

    Article  CAS  Google Scholar 

  24. Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyckoff H, Phillips DC (1958) Nature 181:662–666

    Article  PubMed  CAS  Google Scholar 

  25. Perutz MF, Rossmann MG, Cullins AF, Muirhead H, Will G, North ACT (1960) Nature 185:416–422

    Article  PubMed  CAS  Google Scholar 

  26. Gamgee A (1901) Proc R Soc Lond 68:503–512

    Article  CAS  Google Scholar 

  27. Pauling L, Coryell CD (1936) Proc Natl Acad Sci USA 22:210–216

    Article  PubMed  CAS  Google Scholar 

  28. Griffith JS (1956) Proc R Soc Lond Ser A 235:23–36

    Article  CAS  Google Scholar 

  29. Gray HB (1971) Adv Chem Ser 100:365–389

    Article  Google Scholar 

  30. Jones RD, Summerville DA, Basolo F (1979) Chem Rev 79:139–179

    Article  CAS  Google Scholar 

  31. Collman JP, Gagne RR, Reed CA, Robinson WT, Rodley GA (1974) Proc Natl Acad Sci USA 71:1326–1329

    Article  PubMed  CAS  Google Scholar 

  32. Collman JP, Gagne RR, Reed CA, Halbert TR, Lang G, Robinson WT (1975) J Am Chem Soc 97:1427–1439

    Article  PubMed  CAS  Google Scholar 

  33. Phillips SEV (1978) Nature 273:247–248

    Article  PubMed  CAS  Google Scholar 

  34. Phillips SEV (1980) J Mol Biol 142:531–554

    Article  PubMed  CAS  Google Scholar 

  35. Phillips SEV, Schoenborn BP (1981) Nature 292:81–82

    Article  PubMed  CAS  Google Scholar 

  36. Shaanan B (1982) Nature 296:683–684

    Article  PubMed  CAS  Google Scholar 

  37. Shaanan B (1983) J Mol Biol 171:31–59

    Article  PubMed  CAS  Google Scholar 

  38. Weiss JJ (1964) Nature 202:83–84

    Article  PubMed  CAS  Google Scholar 

  39. Pauling L (1964) Nature 203:182–183

    Article  CAS  Google Scholar 

  40. Pauling L (1948) Stanford Med Bull 6:215–222

    PubMed  CAS  Google Scholar 

  41. McClure DS (1960) Radiation Res Suppl 2:218–242

    Google Scholar 

  42. Shaik S, Hiberty PC (2008) A chemist’s guide to valence bond theory. Wiley, Hoboken

    Google Scholar 

  43. Harcourt RD (1971) Int J Quantum Chem 5:479–495

    Article  CAS  Google Scholar 

  44. Harcourt RD (1972) Biopolymers 11:1551–1565

    Article  PubMed  CAS  Google Scholar 

  45. Harcourt RD (1973) Inorg Nucl Chem Lett 9:475–481

    Article  CAS  Google Scholar 

  46. Harcourt RD (1990) Chem Phys Lett 167:374–377

    Article  CAS  Google Scholar 

  47. Seno Y, Otsuka J, Matsuoka O, Fuchikam N (1972) J Phys Soc Jpn 33:1645–1660

    Article  CAS  Google Scholar 

  48. Otsuka J, Matsuoka O, Fuchikam N, Seno Y (1973) J Phys Soc Jpn 35:854–860

    Article  CAS  Google Scholar 

  49. Goddard WA III, Olafson BD (1975) Proc Natl Acad Sci USA 72:2335–2339

    Article  PubMed  CAS  Google Scholar 

  50. Olafson BD, Goddard WA III (1977) Proc Natl Acad Sci USA 74:1315–1319

    Article  PubMed  CAS  Google Scholar 

  51. Huynh BH, Case DA, Karplus M (1977) J Am Chem Soc 99:6103–6105

    Article  PubMed  CAS  Google Scholar 

  52. Case DA, Huynh BH, Karplus M (1979) J Am Chem Soc 101:4433–4453

    Article  CAS  Google Scholar 

  53. Lang G, Marshall W (1966) J Mol Biol 18:385–404

    Article  PubMed  CAS  Google Scholar 

  54. Lang G, Marshall W (1966) Proc Phys Soc 87:3–34

    Article  CAS  Google Scholar 

  55. Spartallan K, Lang G, Collman JP, Gagne RR, Reed CA (1975) J Chem Phys 63:5375–5382

    Article  Google Scholar 

  56. Weiss JJ (1964) Nature 203:183–183

    Google Scholar 

  57. Jensen KP, Roos BO, Ryde U (2005) J Inorg Biochem 99:45–54; Erratum: (2005) J Inorg Biochem 99:978

    Google Scholar 

  58. Ribas-Ariño J, Novoa JJ (2007) Chem Commun 3160–3162

  59. Hall MB, Newton JE (1984) Inorg Chem 23:4627–4632

    Article  Google Scholar 

  60. Bytheway I, Hall MB (1994) Chem Rev 94:639–658

    Article  CAS  Google Scholar 

  61. Loew GH, Kirchner RF (1975) J Am Chem Soc 97:7388–7390

    Article  PubMed  CAS  Google Scholar 

  62. Kirchner RF, Loew GH (1977) J Am Chem Soc 99:4639–4647

    Article  PubMed  CAS  Google Scholar 

  63. Herman ZS, Loew GH (1980) J Am Chem Soc 102:1815–1821

    Article  CAS  Google Scholar 

  64. Nakatsuji H, Hasegawa J, Ueda H, Hada M (1996) Chem Phys Lett 250:379–386

    Article  CAS  Google Scholar 

  65. Yamamoto S, Kashiwagi H (1989) Chem Phys Lett 161:85–89

    Article  CAS  Google Scholar 

  66. Yamamoto S, Kashiwagi H (1993) Chem Phys Lett 205:306–312

    Article  CAS  Google Scholar 

  67. Rovira C, Kunc K, Hutter J, Ballone P, Parrinello M (1997) J Phys Chem A 101:8914–8925

    Article  CAS  Google Scholar 

  68. Rovira C (2003) J Mol Struct (THEOCHEM) 632:309–321

    Article  CAS  Google Scholar 

  69. Unno M, Chen H, Kusama S, Shaik S, Ikeda-Saito M (2007) J Am Chem Soc 129:13394–13395

    Article  PubMed  CAS  Google Scholar 

  70. Jensen KP, Ryde U (2004) J Biol Chem 279:14561–14569

    Article  PubMed  CAS  Google Scholar 

  71. Franzen S (2002) Proc Natl Acad Sci USA 99:16754–16759

    Article  PubMed  CAS  Google Scholar 

  72. Nakashima H, Hasegawa JY, Nakatsuji H (2006) J Comput Chem 27:426–433

    Article  PubMed  CAS  Google Scholar 

  73. Sigfridsson E, Ryde U (1999) J Biol Inorg Chem 4:99–110

    Article  PubMed  CAS  Google Scholar 

  74. Blomberg LM, Blomberg MRA, Siegbahn PEM (2005) J Inorg Biochem 99:949–958

    Article  PubMed  CAS  Google Scholar 

  75. Strickland N, Harvey JN (2007) J Phys Chem B 111:841–852

    Article  PubMed  CAS  Google Scholar 

  76. Kaupp M, Rovira C, Parrinello M (2000) J Phys Chem B 104:5200–5208

    Article  CAS  Google Scholar 

  77. Vojtechovsky J, Chu K, Berendzen J, Sweet RM, Schlichting I (1999) Biophys J 77:2153–2174

    Article  PubMed  CAS  Google Scholar 

  78. Berg JM, Tymoczko JL, Stryer L (2007) Biochemistry, 6th edn. Freeman, New York

    Google Scholar 

  79. Olson JS, Mathews AJ, Rohlfs RJ, Springer BA, Egeberg KD, Sligar SG, Tame J, Renaud JP, Nagai K (1988) Nature 336:265–266

    Article  PubMed  CAS  Google Scholar 

  80. Braunstein D, Ansari A, Berendzen J, Cowen BR, Egeberg KD, Frauenfelder H, Hon MK, Ormos P, Sauke TB, Scfoll R, Schulte A, Sligar SG, Springer BA, Steinbach PJ, Young RD (1988) Proc Natl Acad Sci USA 85:8497–8501

    Article  PubMed  CAS  Google Scholar 

  81. Springer BA, Egeberg KD, Sligar SG, Rohlfs RJ, Mathews AJ, Olson JS (1989) J Biol Chem 264:3057–3060

    PubMed  CAS  Google Scholar 

  82. Rohlfs RJ, Mathews AJ, Carver TE, Olson JS, Springer BA, Egeberg KD, Sligar SG (1990) J Biol Chem 265:3168–3176

    PubMed  CAS  Google Scholar 

  83. Olson JS, Phillips GN Jr (1997) J Biol Inorg Chem 2:544–552

    Article  CAS  Google Scholar 

  84. Lim MH, Jackson TA, Anfinrud PA (1997) J Biol Inorg Chem 2:531–536

    Article  CAS  Google Scholar 

  85. Roos BO, Andersson K, Fülscher MP, Malmqvist PÅ, Serrano-Andrés L, Pierloot K, Merchán M (1996) Adv Chem Phys 93:219–331

    Article  CAS  Google Scholar 

  86. Sono M, Roach MP, Coulter ED, Dawson JH (1996) Chem Rev 96:2841–2887

    Article  PubMed  CAS  Google Scholar 

  87. Denisov IG, Makris TM, Sligar SG, Schlichting I (2005) Chem Rev 105:2253–2277

    Article  PubMed  CAS  Google Scholar 

  88. Rosen GM, Tsai P, Pou S (2002) Chem Rev 102:1191–1199

    Article  PubMed  CAS  Google Scholar 

  89. Colas C, Ortiz de Montellano PR (2003) Chem Rev 103:2305–2332

    Article  PubMed  CAS  Google Scholar 

  90. Unno M, Matsui T, Ikeda-Saito M (2007) Nat Prod Rep 24:553–570

    Article  PubMed  CAS  Google Scholar 

  91. Matsui T, Unno M, Ikeda-Saito M (2010) Acc Chem Res 43:240–247

    Article  PubMed  CAS  Google Scholar 

  92. Kühnel K, Derat E, Terner J, Shaik S, Schlichting I (2007) Proc Natl Acad Sci USA 104:99–104

    Article  PubMed  Google Scholar 

  93. Ignarro LJ (2000) In: Ignarro LJ (ed) Nitric oxide: biology and pathobiology. Academic Press, San Diego, pp 3–19

  94. McCleverty JA (2004) Chem Rev 104:403–418

    Article  PubMed  CAS  Google Scholar 

  95. Lehnert N, Scheidt WR (2010) Inorg Chem 49:6223–6225

    Article  PubMed  CAS  Google Scholar 

  96. Westcott BL, Enemark JL (1999) In: Solomon EI, Lever ABP (eds) Inorganic electronic structure and spectroscopy, vol 2. Wiley, New York, pp 403–450

  97. Sun N, Liu LV, Dey A, Villar-Acevedo G, Kovacs JA, Darensbourg MY, Hodgson KO, Hedman B, Solomon EI (2011) Inorg Chem 50:427–436

    Google Scholar 

  98. Ghosh A, Hopmann KH, Conradie J (2009) In: Solomon EI, Scott RA, King RB (eds) Computational inorganic and bioinorganic chemistry. Wiley, New York, pp 389–410

  99. Ghosh A (2005) Acc Chem Res 38:943–954

    Article  PubMed  CAS  Google Scholar 

  100. Conradie J, Ghosh A (2007) J Phys Chem B 111:12621–12624

    Article  PubMed  CAS  Google Scholar 

  101. Ghosh A (2006) J Biol Inorg Chem 11:712–724

    Article  PubMed  CAS  Google Scholar 

  102. Shaik S, Chen H, Janardanan D (2011) Nat Chem 3:19–27

    Article  PubMed  CAS  Google Scholar 

  103. Roos BO, Veryazov V, Conradie J, Taylor PR, Ghosh A (2008) J Phys Chem B 112:14099–14102

    Article  PubMed  CAS  Google Scholar 

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Acknowledgment

S.S. is supported by an ISF grant (53/09).

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Correspondence to Sason Shaik.

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Dedicated to Björn O. Roos, whose untimely death is a great loss to science.

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Shaik, S., Chen, H. Lessons on O2 and NO bonding to heme from ab initio multireference/multiconfiguration and DFT calculations. J Biol Inorg Chem 16, 841–855 (2011). https://doi.org/10.1007/s00775-011-0763-1

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  • DOI: https://doi.org/10.1007/s00775-011-0763-1

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