Metal–thiolate bonds in bioinorganic chemistry

Metal–thiolate active sites play major roles in bioinorganic chemistry. The MSthiolate bonds can be very covalent, and involve different orbital interactions. Spectroscopic features of these active sites (intense, low‐energy charge transfer transitions) reflect the high covalency of the MSthiolate bonds. The energy of the metal–thiolate bond is fairly insensitive to its ionic/covalent and π/σ nature as increasing MS covalency reduces the charge distribution, hence the ionic term, and these contributions can compensate. Thus, trends observed in stability constants (i.e., the Irving–Williams series) mostly reflect the dominantly ionic contribution to bonding of the innocent ligand being replaced by the thiolate. Due to high effective nuclear charges of the CuII and FeIII ions, the cupric– and ferric–thiolate bonds are very covalent, with the former having strong π and the latter having more σ character. For the blue copper site, the high π covalency couples the metal ion into the protein for rapid directional long range electron transfer. For rubredoxins, because the redox active molecular orbital is π in nature, electron transfer tends to be more localized in the vicinity of the active site. Although the energy of hydrogen bonding of the protein environment to the thiolate ligands tends to be fairly small, H‐bonding can significantly affect the covalency of the metal–thiolate bond and contribute to redox tuning by the protein environment. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1415–1428, 2006

[1]  M G Rossmann,et al.  Studies of asymmetry in the three-dimensional structure of lobster D-glyceraldehyde-3-phosphate dehydrogenase. , 1977, The Journal of biological chemistry.

[2]  Richard H. Holm,et al.  Synthetic analogues of the active sites of iron-sulfur proteins. , 2004 .

[3]  István Mayer,et al.  Charge, bond order and valence in the AB initio SCF theory , 1983 .

[4]  Michael Meot-Ner,et al.  The ionic hydrogen bond. , 2005, Chemical reviews.

[5]  S. I. Gorelsky,et al.  Mechanism of N2O reduction by the mu4-S tetranuclear CuZ cluster of nitrous oxide reductase. , 2006, Journal of the American Chemical Society.

[6]  E. Solomon,et al.  Single-crystal spectral studies of Fe(SR)4- [R = 2,3,5,6,-(Me)4C6H]: the electronic structure of the ferric tetrathiolate active site , 1990 .

[7]  H. Bartunik,et al.  Accuracy and precision in protein structure analysis: restrained least-squares refinement of the structure of poplar plastocyanin at 1.33 A resolution. , 1992, Acta crystallographica. Section B, Structural science.

[8]  S. Takamizawa,et al.  Novel Rubredoxin Model Tetrathiolato Iron(II) and Cobalt(II) Complexes Containing Intramolecular Single and Double NH.S Hydrogen Bonds. , 1998, Inorganic chemistry.

[9]  J. Salgado,et al.  The crystal structure of nickel(II)-azurin. , 1995, European journal of biochemistry.

[10]  J. Kovacs Synthetic analogues of cysteinate-ligated non-heme iron and non-corrinoid cobalt enzymes. , 2004, Chemical reviews.

[11]  H. Gray,et al.  Preparation and spectroscopic studies of cobalt(II) derivatives of blue copper proteins. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Edward I. Solomon,et al.  Ligand K-edge x-ray absorption spectroscopy: Covalency of ligand-metal bonds , 2005 .

[13]  Susan L. Cohen,et al.  Spectroscopic and Theoretical Studies of the Unusual EPR Parameters of Distorted Tetrahedral Cupric Sites:' Correlations to X-ray Spectral Features of Core Levels , 1987 .

[14]  G. Schneider,et al.  Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold. , 1997, Structure.

[15]  Edward I. Solomon,et al.  X-ray absorption spectroscopic studies of the blue copper site: Metal and ligand K-edge studies to probe the origin of the EPR hyperfine splitting in plastocyanin , 1993 .

[16]  H. Gray,et al.  Electronic absorption spectra of M(II)(Met121X) azurins (MCo, Ni, Cu; XLeu, Gly, Asp, Glu): charge-transfer energies and reduction potentials , 1992 .

[17]  Hideaki Umeyama,et al.  The origin of hydrogen bonding. An energy decomposition study , 1977 .

[18]  A. Gewirth,et al.  Electronic structure of plastocyanin: excited state spectral features , 1988 .

[19]  Gernot Frenking,et al.  Investigation of Donor-Acceptor Interactions: A Charge Decomposition Analysis Using Fragment Molecular Orbitals , 1995 .

[20]  P. Kollman,et al.  Atomic charges derived from semiempirical methods , 1990 .

[21]  Arvi Rauk,et al.  On the calculation of bonding energies by the Hartree Fock Slater method , 1977 .

[22]  Kazuo Kitaura,et al.  A new energy decomposition scheme for molecular interactions within the Hartree‐Fock approximation , 1976 .

[23]  A detailed analysis of the charge-transfer bands of a blue copper protein. Studies of the nickel(II), manganese(II), and cobalt(II) derivatives of azurin , 1979 .

[24]  Timothy Lovell,et al.  Density functional and reduction potential calculations of Fe4S4 clusters. , 2003, Journal of the American Chemical Society.

[25]  Stuart A. Rice,et al.  Inorganic Electronic Spectroscopy , 1968 .

[26]  K. Hodgson,et al.  INVESTIGATION OF IRON-SULFUR COVALENCY IN RUBREDOXINS AND A MODEL SYSTEM USING SULFUR K-EDGE X-RAY ABSORPTION SPECTROSCOPY , 1998 .

[27]  Sa-Ouk Kang,et al.  Crystal structure of nickel-containing superoxide dismutase reveals another type of active site. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[28]  D. Chong Recent Advances in Density Functional Methods Part III , 2002 .

[29]  M. Halcrow,et al.  Biomimetic Chemistry of Nickel , 1994 .

[30]  Robert K Szilagyi,et al.  Electronic structures of metal sites in proteins and models: contributions to function in blue copper proteins. , 2004, Chemical reviews.

[31]  S. I. Gorelsky,et al.  Spectroscopic and DFT investigation of [M{HB(3,5-iPr2pz)3}(SC6F5)] (M = Mn, Fe, Co, Ni, Cu, and Zn) model complexes: periodic trends in metal-thiolate bonding. , 2005, Inorganic chemistry.

[32]  R. Chakrabarti,et al.  Characterization of a human peptide deformylase: implications for antibacterial drug design. , 2003, Biochemistry.

[33]  Mark S. Gordon,et al.  Energy Decomposition Analyses for Many-Body Interaction and Applications to Water Complexes , 1996 .

[34]  R. J. Williams,et al.  Order of Stability of Metal Complexes , 1948, Nature.

[35]  R. Huber,et al.  Characterization and crystal structure of zinc azurin, a by-product of heterologous expression in Escherichia coli of Pseudomonas aeruginosa copper azurin. , 1992, European journal of biochemistry.

[36]  Pierre Kennepohl,et al.  Electronic structure contributions to electron-transfer reactivity in iron-sulfur active sites: 3. Kinetics of electron transfer. , 2003, Inorganic chemistry.

[37]  Edward I. Solomon,et al.  Electronic structure and bonding of the blue copper site in plastocyanin , 1985 .

[38]  Y. Moro-oka,et al.  X-ray structure of thiolatocopper(II) complexes bearing close spectroscopic similarities to blue copper proteins , 1992 .

[39]  Isao Endo,et al.  Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms , 1998, Nature Structural Biology.

[40]  Mark Earl Casida,et al.  In Recent Advances in Density-Functional Methods , 1995 .

[41]  L. Curtiss,et al.  Intermolecular interactions from a natural bond orbital, donor-acceptor viewpoint , 1988 .

[42]  M. Murata,et al.  X-ray crystal structure analysis of plastocyanin at 2.7 Å resolution , 1978, Nature.

[43]  G. Scuseria,et al.  An efficient implementation of time-dependent density-functional theory for the calculation of excitation energies of large molecules , 1998 .

[44]  H. Nar,et al.  The metal site of Pseudomonas aeruginosa azurin, revealed by a crystal structure determination of the co(II) derivative and co‐EPR spectroscopy , 1997, Proteins.

[45]  M. E. Casida Time-Dependent Density Functional Response Theory for Molecules , 1995 .

[46]  K. Okamoto,et al.  Structural and spectroscopic characterization of first-row transition metal(II) substituted blue copper model complexes with hydrotris(pyrazolyl)borate. , 2005, Inorganic chemistry.

[47]  K. Hodgson,et al.  Sulfur K-edge XAS and DFT calculations on P450 model complexes: effects of hydrogen bonding on electronic structure and redox potentials. , 2005, Journal of the American Chemical Society.

[48]  D. Rees,et al.  Structures of the superoxide reductase from Pyrococcus furiosus in the oxidized and reduced states. , 2000, Biochemistry.

[49]  R. J. P. Williams,et al.  637. The stability of transition-metal complexes , 1953 .