Low-energy spectrum of iron-sulfur clusters directly from many-particle quantum mechanics

Nature Chemistry

Volumn 6, Issue 10, 2014, Pages 927-933

  Sharma, Sandeep ^a   Sivalingam, Kantharuban ^b   Neese, Frank ^b   Chan, Garnet Kin Lic ^a  

^a PRINCETON UNIVERSITY   (United States)

^b MAX PLANCK INSTITUTE FOR CHEMICAL ENERGY CONVERSION   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

IRON; SULFUR;

CATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; DIMERIZATION; QUANTUM THEORY; THERMODYNAMICS;

CATALYSIS; DIMERIZATION; IRON; MODELS, MOLECULAR; QUANTUM THEORY; SULFUR; THERMODYNAMICS;

EID: 84908513305     PISSN: 17554330     EISSN: 17554349     Source Type: Journal    
DOI: 10.1038/nchem.2041     Document Type: Article

References (58)

1. Beinert, H., Holm, R. H. & Münck, E. Iron-sulfur clusters: nature's modular, multipurpose structures. Science 277, 653-659 (1997).
2. Johnson, D. C., Dean, D. R., Smith, A. D. & Johnson, M. K. Structure, function, and formation of biological iron-sulfur clusters. Annu. Rev. Biochem. 74, 247-281 (2005).
3. Noodleman, L., Peng, C. Y., Case, D. A. & Mouesca, J. M. Orbital interactions, electron delocalization and spin coupling in iron-sulfur clusters. Coord. Chem. Rev. 144, 199-244 (1995).
4. Zener, C. Interaction between the d-shells in the transition metals. II. Ferromagnetic compounds of manganese with perovskite structure. Phys. Rev. 82, 403-405 (1951).
5. Anderson, P.W. & Hasegawa, H. Considerations on double exchange. Phys. Rev. 100, 675-681 (1955).
6. Girerd, J-J. Electron transfer between magnetic ions in mixed valence binuclear systems. J. Chem. Phys. 79, 1766-1775 (1983).
7. Noodleman, L. & Baerends, E. J. Electronic structure, magnetic properties, ESR, and optical spectra for 2-iron ferredoxin models by LCAO-X? valence bond theory. J. Am. Chem. Soc. 106, 2316-2327 (1984).
8. Noodleman, L. & Davidson, E. R. Ligand spin polarization and antiferromagnetic coupling in transition metal dimers. Chem. Phys. 109, 131-143 (1986).
9. Papaefthymiou, V., Girerd, J. J., Moura, I., Moura, J. J. G. & Münck, E. Moessbauer study of D. gigas ferredoxin II and spin-coupling model for Fe3S4 cluster with valence delocalization. J. Am. Chem. Soc. 109, 4703-4710 (1987).
10. Blondin, G. & Girerd, J. J. Interplay of electron exchange and electron transfer in metal polynuclear complexes in proteins or chemical models. Chem. Rev. 90, 1359-1376 (1990).
11. Borshch, S. A., Kotov, I. N. & Bersuker, I. B. A vibronic model for exchangecoupled mixed-valence dimers. Chem. Phys. Lett. 111, 264-270 (1984).
12. Labeguerie, P. et al. Is it possible to determine rigorous magnetic Hamiltonians in spin s = 1 systems from density functional theory calculations? J. Chem. Phys. 129, 154110 (2008).
13. Gibson, J. F., Hall, D. O., Thornley, J. H. & Whatley, F. R. The iron complex in spinach ferredoxin. Proc. Natl Acad. Sci. USA 56, 987-990 (1966).
14. Brintzinger, H., Palmer, G. & Sands, R. H. On the ligand field of iron in ferredoxin from spinach chloroplasts and related nonheme iron enzymes. Proc. Natl Acad. Sci. USA 55, 397-404 (1966).
15. Rius, G. & Lamotte, B. Single-crystal ENDOR study of an 57Fe-enriched iron-sulfur [Fe4S4]3+ cluster. J. Am. Chem. Soc. 111, 2464-2469 (1989).
16. Mouesca, J. M., Lamotte, B. & Rius, G. Comparison between spin population distributions in two different [Fe4S4]3+ clusters by proton ENDOR in single crystals of a synthetic model compound. J. Inorg. Biochem. 43, 251-270 (1991).
17. Bertini, I., Briganti, F., Luchinat, C., Scozzafava, A. & Sola, M. Proton NMR spectroscopy and the electronic structure of the high potential iron-sulfur protein from Chromatium vinosum. J. Am. Chem. Soc. 113, 1237-1245 (1991).
18. Banci, L. et al. Proton NMR spectra of oxidized high-potential iron-sulfur protein (HiPIP) from Rhodocyclus gelatinosus. A model for oxidized HiPIPs. Inorg. Chem. 30, 4517-4524 (1991).
19. Papaefthymiou, V., Millar, M. M. & Muenck, E. Moessbauer and EPR studies of a synthetic analog for the iron-sulfur Fe4S4 core of oxidized and reduced highpotential iron proteins. Inorg. Chem. 25, 3010-3014 (1986).
20. Kappl, R., Ebelshäuser, M., Hannemann, F., Bernhardt, R. & Hüttermann, J. Probing electronic and structural properties of the reduced [2Fe-2S] cluster by orientation-selective 1H ENDOR spectroscopy: adrenodoxin versus Rieske iron-sulfur protein. Appl. Magn. Reson. 30, 427-459 (2006).
21. Maurice, R., Guihery, N., Bastardis, R. & De Graaf, C. Rigorous extraction of the anisotropic multispin Hamiltonian in bimetallic complexes from the exact electronic Hamiltonian. J. Chem. Theor. Comput. 6, 55-65 (2009).
22. Noodleman, L., Norman, J. G., Osborne, J. H., Aizman, A. & Case, D. A. Models for ferredoxins: electronic structures of iron-sulfur clusters with one, two, and four iron atoms. J. Am. Chem. Soc. 107, 3418-3426 (1985).
23. Mouesca, J-M., Chen, J. L., Noodleman, L., Bashford, D. & Case, D. A. Density functional/Poisson-Boltzmann calculations of redox potentials for iron-sulfur clusters. J. Am. Chem. Soc. 116, 11898-11914 (1994).
24. Shoji, M. et al. Theory of chemical bonds in metalloenzymes III: full geometry optimization and vibration analysis of ferredoxin-type [2Fe-2S] cluster. Int. J. Quantum Chem. 107, 116-133 (2007).
25. Noodleman, L. Valence bond description of antiferromagnetic coupling in transition metal dimers. J. Chem. Phys. 74, 5737-5743 (1981).
26. Yamaguchi, K., Fueno, T., Ueyama, N., Akira, N. & Masaaki, O. Antiferromagnetic spin couplings between iron ions in ironsulfur clusters. A localized picture by the spin vector model. Chem. Phys. Lett. 164, 210-216 (1989).
27. Yamaguchi, K., Fueno, T., Ozaki, M., Ueyama, N. & Nakamura, A. A general spin-orbital (GSO) description of antiferromagnetic spin couplings between four irons in iron-sulfur clusters. Chem. Phys. Lett. 168, 56-62 (1990).
28. Neese, F. Prediction of molecular properties and molecular spectroscopy with density functional theory: from fundamental theory to exchange-coupling. Coord. Chem. Rev. 253, 526-563 (2009).
29. Miralles, J., Daudey, J-P. & Caballol, R. Variational calculation of small energy differences. The singlet-triplet gap in [Cu2Cl6]2. Chem. Phys. Lett. 198, 555-562 (1992).
30. Miralles, J., Castell, O., Caballol, R. & Malrieu, J-P. Specific CI calculation of energy differences: transition energies and bond energies. Chem. Phys. 172, 33-43 (1993).
31. Castell, O. & Caballol, R. Ab-initio configuration interaction calculation of the exchange coupling constant in hydroxo doubly bridged Cr(III) dimers. Inorg. Chem. 38, 668-673 (1999).
32. Cabrero, J., Ben Amor, N., De Graaf, C., Illas, F. & Caballol, R. Ab-initio study of the exchange coupling in oxalato-bridged Cu(II) dinuclear complexes. J. Phys. Chem. A 104, 9983-9989 (2000).
33. Hübner, O. & Sauer, J. The electronic states of Fe2S2 ?/0/+/2+. J. Chem. Phys. 116, 617-628 (2002).
34. Hastings, M. B. Entropy and entanglement in quantum ground states. Phys. Rev. B 76, 35114 (2007).
35. Verstraete, F., Murg, V. & Cirac, J. I. Matrix product states, projected entangled pair states, and variational renormalization group methods for quantum spin systems. Adv. Phys. 57, 143-224 (2008).
36. White, S. R. Density matrix formulation for quantum renormalization groups. Phys. Rev. Lett. 69, 2863 (1992).
37. White, S. R. & Martin, R. L. Ab initio quantum chemistry using the density matrix renormalization group. J. Chem. Phys. 110, 4127-4130 (1999).
38. Chan, G. K-L. & Sharma, S. The density matrix renormalization group in quantum chemistry. Annu. Rev. Phys. Chem. 62, 465-481 (2011).
39. Kurashige, Y., Chan, G. K-L. & Yanai, T. Entangled quantum electronic wavefunctions of the Mn4CaO5 cluster in photosystem II. Nature Chem. 5, 660-666 (2013).
40. Sharma, S. & Chan, G. K-L. Spin-adapted density matrix renormalization group algorithms for quantum chemistry. J. Chem. Phys. 136, 124121 (2012).
41. Chan, G. K. L. & Head-Gordon, M. Highly correlated calculations with a polynomial cost algorithm: a study of the density matrix renormalization group. J. Chem. Phys. 116, 4462-4476 (2002).
42. Zgid, D. & Nooijen, M. On the spin and symmetry adaptation of the density matrix renormalization group method. J. Chem. Phys. 128, 014107 (2008).
43. Moritz, G., Hess, B. A. & Reiher, M. Convergence behavior of the densitymatrix renormalization group algorithm for optimized orbital orderings. J. Chem. Phys. 122, 024107 (2005).
44. Kurashige, Y. & Yanai, T. High-performance ab initio density matrix renormalization group method: applicability to large-scale multireference problems for metal compounds. J. Chem. Phys. 130, 234114 (2009).
45. Legeza, Ö., Röder, J. & Hess, B. A. QC-DMRG study of the ionic-neutral curve crossing of LiF. Mol. Phys. 101, 2019-2028 (2003).
46. Marti, K. H., Ondik, I. M., Mortise, G. & Reiher, M. Density matrix renormalization group calculations on relative energies of transition metal complexes and clusters. J. Chem. Phys. 128, 014104 (2008).
47. Mayerle, J. J., Denmark, S. E., DePamphilis, B. V., Ibers, J. A. & Holm, R. H. Synthetic analogs of the active sites of iron-sulfur proteins. XI. Synthesis and properties of complexes containing the iron sulfide Fe2S2 core and the structures of bis[o-xylyl-?,-dithiolato-?-sulfido-ferrate(III)] and bis[ p-tolylthiolato-?-sulfido-ferrate(III)] dianions. J. Am. Chem. Soc. 97, 1032-1045 (1975).
48. Orme-Johnson, W. H. Iron-sulfur proteins: structure and function. Annu. Rev. Biochem. 42, 159-204 (1973).
49. Venkateswara Rao, P. & Holm, R. H. Synthetic analogues of the active sites of iron sulfur proteins. Chem. Rev. 104, 527-560 (2003).
50. Noodleman, L., Case, D., Mouesca, J-M. & Lamotte, B. Valence electron delocalization in polynuclear iron-sulfur clusters. J. Biol. Inorg. Chem. 1, 177-182 (1996).
51. Gillum,W. O., Frankel, R. B., Foner, S. & Holm, R. H. Synthetic analogues of the active sites of iron-sulfur proteins. XIII. Further electronic structural relationships between the analogues [Fe2S2(SR)4]2? and the active sites of oxidized 2Fe-2S proteins. Inorg. Chem. 15, 1095-1100 (1976).
52. Noodleman, L. & Case, D. A. Density-functional theory of spin polarization and spin coupling in iron-sulfur clusters. Adv. Inorg. Chem 38, 423-470 (1992).
53. Averill, B. A., Herskovitz, T., Holm, R. H. & Ibers, J. A. Synthetic analogs of the active sites of iron-sulfur proteins. II. Synthesis and structure of the tetra [mercapto-?3-sulfido-iron] clusters, [Fe4S4(SR)4]2-. J. Am. Chem. Soc. 95, 3523-3534 (1973).
54. Noodleman, L., Lovell, T., Liu, T., Himo, F. & Torres, R. A. Insights into properties and energetics of iron-sulfur proteins from simple clusters to nitrogenase. Curr. Opin. Chem. Biol. 6, 259-273 (2002).
55. Shaik, S., Kumar, D., De Visser, S. P., Altun, A. & Thiel, W. Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes. Chem. Rev. 105, 2279-2328 (2005).
56. Wodtke, A. M., Tully, J. C. & Auerbach, D. J. Electronically non-adiabatic interactions of molecules at metal surfaces: can we trust the Born-Oppenheimer approximation for surface chemistry? Int. Rev. Phys. Chem. 23, 513-539 (2004).
57. Lancaster, K. M. et al. X-ray emission spectroscopy evidences a central carbon in the nitrogenase iron-molybdenum cofactor. Science 334, 974-977 (2011).
58. Spatzal, T. et al. Evidence for interstitial carbon in nitrogenase FeMo cofactor. Science 334, 940 (2011).