Mechanisms Whereby Mononuclear Copper Proteins Functionalize Organic Substrates

Access to a Cu(II)-O-Cu(II) motif: spectroscopic properties, solution structure, and reactivity

We report a complex with a rare Cu(II)-O-Cu(II) structural motif that is stable at room temperature, which allows its in-depth characterization by a variety of spectroscopic methods. Interest in such compounds is fueled by the recent discovery that a Cu(II)-O-Cu(II) species on the surface of Cu-ZSM-5 is capable of oxidizing methane to methanol, and this in turn ties into mechanistic discussions on the methane oxidation at the dicopper site within the particulate methane monooxygenase. For the synthesis of our Cu2O complex we have developed a novel, neutral ligand system, FurNeu, exhibiting two N-(N',N'-dimethylaminoethyl)(2-pyridylmethyl)amino binding pockets connected by a dibenzofuran spacer. The reaction of FurNeu with CuCl yielded [FurNeu](Cu2(μ-Cl))(CuCl2), 1, demonstrating the geometric potential of the ligand to stabilize Cu-X-Cu moieties. A Cu(I) precursor with weakly coordinating anions was chosen in the next step, namely [Cu(NCCH3)4]OTf, which led to the formation of [FurNeu](Cu(NCCH3))2(OTf)2, 3. Treatment of 3 with O2 or PhIO led to identical green solutions, whose UV-vis spectra were markedly different from the one displayed by [FurNeu](Cu)2(OTf)4, 4, prepared independently from FurNeu and Cu(OTf)2. Further investigations including PhIO consumption experiments, NMR and UV-vis spectroscopy, HR-ESI mass spectrometry, and protonation studies led to the identification of the green product as [FurNeu](Cu2(μ-O))(OTf)2, 5. DOSY NMR spectroscopy confirmed its monomeric character. Over longer periods of time 5 decomposes to give [Cu(picoloyl)2], formed through an oxidative N-dealkylation reaction followed by further oxidation of the ligand. Due to its slow decomposition reaction, all attempts to crystallize 5 failed. However, its structure in solution could be determined by EXAFS analysis in combination with DFT calculations, which revealed a Cu-O-Cu angle that amounts to 105.17°. Moreover, TDDFT calculations helped to rationalize the UV-vis absorptions of 5. The reactivity of complex 5 with 2,4-di-tert-butylphenol, DTBP, was also investigated; the initially formed biphenol product, TBBP, was found to further react in the presence of excessive O2 to yield 2,4,7,9-tetra-tert-butyloxepino[2,3-b]benzofuran, TBOBF, via an intermediate diphenoquinone. It turned out that 5, or its precursor 3, can even be employed as a catalyst for the oxidation of DTBP to TBBP or for the oxidation of TBBP to TBOBF.

Transcriptome analysis of cytoplasmic male sterility and restoration in CMS-D8 cotton

A global view of differential expression of genes in CMS-D8 of cotton was presented in this study which will facilitate the understanding of cytoplasmic male sterility in cotton. Cytoplasmic male sterility (CMS) is a maternally inherited trait in higher plants which is incapable of producing functional pollen. However, the male fertility can be restored by one or more nuclear-encoded restorer genes. A genome-wide transcriptome analysis of CMS and restoration in cotton is currently lacking. In this study, Affymetrix GeneChips© Cotton Genome Array containing 24,132 transcripts was used to compare differentially expressed (DE) genes of flower buds at the meiosis stage between CMS and its restorer cotton plants conditioned by the D8 cytoplasm. A total of 458 (1.9 %) of DE genes including 127 up-regulated and 331 down-regulated ones were identified in the CMS-D8 line. Quantitative RT-PCR was used to validate 10 DE genes selected from seven functional categories. The most frequent DE gene group was found to encode putative proteins involved in cell wall expansion, such as pectinesterase, pectate lyase, pectin methylesterase, glyoxal oxidase, polygalacturonase, indole-3-acetic acid-amino synthetase, and xyloglucan endo-transglycosylase. Genes in cytoskeleton category including actin, which plays a key role in cell wall expansion, cell elongation and cell division, were also highly differentially expressed between the fertile and CMS plants. This work represents the first study in utilizing microarray to identify CMS-related genes by comparing overall DE genes between fertile and CMS plants in cotton. The results provide evidence that many CMS-associated genes are mainly involved in cell wall expansion. Further analysis will be required to elucidate the molecular mechanisms of male sterility which will facilitate the development of new hybrid cultivars in cotton.

Structural snapshots from the oxidative half-reaction of a copper amine oxidase: implications for O2 activation

The mechanism of molecular oxygen activation is the subject of controversy in the copper amine oxidase family. At their active sites, copper amine oxidases contain both a mononuclear copper ion and a protein-derived quinone cofactor. Proposals have been made for the activation of molecular oxygen via both a Cu(II)-aminoquinol catalytic intermediate and a Cu(I)-semiquinone intermediate. Using protein crystallographic freeze-trapping methods under low oxygen conditions combined with single-crystal microspectrophotometry, we have determined structures corresponding to the iminoquinone and semiquinone forms of the enzyme. Methylamine reduction at acidic or neutral pH has revealed protonated and deprotonated forms of the iminoquinone that are accompanied by a bound oxygen species that is likely hydrogen peroxide. However, methylamine reduction at pH 8.5 has revealed a copper-ligated cofactor proposed to be the semiquinone form. A copper-ligated orientation, be it the sole identity of the semiquinone or not, blocks the oxygen-binding site, suggesting that accessibility of Cu(I) may be the basis of partitioning O2 activation between the aminoquinol and Cu(I).

Isolation of a 2-hydroxytetrahydrofuran complex from copper-promoted hydroxylation of THF

A complex of a binucleating macrocyclic ligand comprising a [Cu(II)(μ-OH)Na](2+) core reacts with CuI in THF/CH3CN to yield a novel species with a deprotonated 2-hydroxytetrahydrofuran (THF-2-ol) bridging between Cu(II) and Na(I) ions. The complexes were characterized by X-ray crystallography, electron paramagnetic resonance spectroscopy, and electrospray ionization mass spectrometry. (18)O-labeling studies support incorporation of the O atom from μ-OH into the coordinated THF-2-ol ligand.

Synthesis, characterization and equilibrium studies of some potential antimicrobial and antitumor complexes of Cu(II), Ni(II), Zn(II) and Cd(II) ions involving 2-aminomethylbenzimidazole and glycine

The ternary complexes of Cu(II), Zn(II), Ni(II) and Cd(II) with 2-aminomethylbenzimidazole (AMBI) and glycine as a representative example of amino acids have been isolated and characterized by elemental analyses, IR, ESR, UV-vis, magnetic moment, molar conductance and (1)H NMR spectra. AMBI behaves as neutral bidentate ligands with coordination through imidazole and amino group nitrogens while the glycine amino acid behaves as a monodenate anion with coordination involving the amino group and carboxylate oxygen after deprotonation. The magnetic and spectral data indicates a square planar geometry for both Cu(2+) and Ni(2+) complexes and a tetrahedral geometry for both Zn(2+) and Cd(2+) complexes. The isolated chelates have been screened for their antifungal and antibacterial activities using the disc diffusion method. A cytotoxicity of the compounds against colon (HCT116) and larynx (HEP2) cancer cells have been studied. The stability constants of ternary M-AMBI-Gly complexes were determined potentiometrically in aqueous solution at I=0.1 mol dm(-3) NaCl.

Building reactive copper centers in human carbonic anhydrase II

Reengineering metalloproteins to generate new biologically relevant metal centers is an effective a way to test our understanding of the structural and mechanistic features that steer chemical transformations in biological systems. Here, we report thermodynamic data characterizing the formation of two type-2 copper sites in carbonic anhydrase and experimental evidence showing one of these new, copper centers has characteristics similar to a variety of well-characterized copper centers in synthetic models and enzymatic systems. Human carbonic anhydrase II is known to bind two Cu(2+) ions; these binding events were explored using modern isothermal titration calorimetry techniques that have become a proven method to accurately measure metal-binding thermodynamic parameters. The two Cu(2+)-binding events have different affinities (K a approximately 5 × 10(12) and 1 × 10(10)), and both are enthalpically driven processes. Reconstituting these Cu(2+) sites under a range of conditions has allowed us to assign the Cu(2+)-binding event to the three-histidine, native, metal-binding site. Our initial efforts to characterize these Cu(2+) sites have yielded data that show distinctive (and noncoupled) EPR signals associated with each copper-binding site and that this reconstituted enzyme can activate hydrogen peroxide to catalyze the oxidation of 2-aminophenol.

A high-valent heterobimetallic [Cu(III)(μ-O)2Ni(III)]2+ core with nucleophilic oxo groups

A heterobimetallic CuNi bis(μ-oxo) diamond core is shown to possess nucleophilic oxo groups, and has been demonstrated for the first time as a viable intermediate during the deformylation of fatty aldehydes by cyanobacterial aldehyde decarbonylase.

Crystal structure and computational characterization of the lytic polysaccharide monooxygenase GH61D from the Basidiomycota fungus Phanerochaete chrysosporium

Carbohydrate structures are modified and degraded in the biosphere by a myriad of mostly hydrolytic enzymes. Recently, lytic polysaccharide mono-oxygenases (LPMOs) were discovered as a new class of enzymes for cleavage of recalcitrant polysaccharides that instead employ an oxidative mechanism. LPMOs employ copper as the catalytic metal and are dependent on oxygen and reducing agents for activity. LPMOs are found in many fungi and bacteria, but to date no basidiomycete LPMO has been structurally characterized. Here we present the three-dimensional crystal structure of the basidiomycete Phanerochaete chrysosporium GH61D LPMO, and, for the first time, measure the product distribution of LPMO action on a lignocellulosic substrate. The structure reveals a copper-bound active site common to LPMOs, a collection of aromatic and polar residues near the binding surface that may be responsible for regio-selectivity, and substantial differences in loop structures near the binding face compared with other LPMO structures. The activity assays indicate that this LPMO primarily produces aldonic acids. Last, molecular simulations reveal conformational changes, including the binding of several regions to the cellulose surface, leading to alignment of three tyrosine residues on the binding face of the enzyme with individual cellulose chains, similar to what has been observed for family 1 carbohydrate-binding modules. A calculated potential energy surface for surface translation indicates that P. chrysosporium GH61D exhibits energy wells whose spacing seems adapted to the spacing of cellobiose units along a cellulose chain.

A square-pyramidal copper(II) complex with strong intramolecular hydrogen bonds: diaqua(N,N'-dimethylformamide-κO)bis[2-(diphenylphosphoryl)benzoato-κO]copper(II)

In the title Cu(II) complex, [Cu(C19H14O3P)2(C3H7NO)(H2O)2], the molecule is bisected by a twofold axis relating the two 2-(diphenylphosphoryl)benzoate (ODPPB) ligands. The asymmetric unit consists of a Cu(II) metal centre on the symmetry axis, an ODPPB ligand, one water ligand and one dimethylformamide (DMF) ligand (disordered around the twofold axis). The Cu(II) ion has fivefold coordination provided by two carboxylate O atoms from two ODPPB ligands, two O atoms from two coordinated water molecules and another O atom from a (disordered) DMF molecule, giving a CuO5 square-pyramidal coordination geometry. The ODPPB ligand adopts a terminal monocoordinated mode with two free O atoms forming two strong intramolecular hydrogen bonds with the coordinated water molecules, which may play a key role in the stability of the molecular structure, as shown by the higher release temperature for the coordinated water molecules than for the coordinated DMF molecule. The optical absorption properties of powder samples of the title compound have also been studied.

Enhanced catalytic four-electron dioxygen (O2) and two-electron hydrogen peroxide (H2O2) reduction with a copper(II) complex possessing a pendant ligand pivalamido group

A copper complex, [(PV-tmpa)Cu(II)](ClO4)2 (1) [PV-tmpa = bis(pyrid-2-ylmethyl){[6-(pivalamido)pyrid-2-yl]methyl}amine], acts as a more efficient catalyst for the four-electron reduction of O2 by decamethylferrocene (Fc*) in the presence of trifluoroacetic acid (CF3COOH) in acetone as compared with the corresponding copper complex without a pivalamido group, [(tmpa)Cu(II)](ClO4)2 (2) (tmpa = tris(2-pyridylmethyl)amine). The rate constant (k(obs)) of formation of decamethylferrocenium ion (Fc*(+)) in the catalytic four-electron reduction of O2 by Fc* in the presence of a large excess CF3COOH and O2 obeyed first-order kinetics. The k(obs) value was proportional to the concentration of catalyst 1 or 2, whereas the k(obs) value remained constant irrespective of the concentration of CF3COOH or O2. This indicates that electron transfer from Fc* to 1 or 2 is the rate-determining step in the catalytic cycle of the four-electron reduction of O2 by Fc* in the presence of CF3COOH. The second-order catalytic rate constant (k(cat)) for 1 is 4 times larger than the corresponding value determined for 2. With the pivalamido group in 1 compared to 2, the Cu(II)/Cu(I) potentials are -0.23 and -0.05 V vs SCE, respectively. However, during catalytic turnover, the CF3COO(-) anion present readily binds to 2 shifting the resulting complex's redox potential to -0.35 V. The pivalamido group in 1 is found to inhibit anion binding. The overall effect is to make 1 easier to reduce (relative to 2) during catalysis, accounting for the relative k(cat) values observed. 1 is also an excellent catalyst for the two-electron two-proton reduction of H2O2 to water and is also more efficient than is 2. For both complexes, reaction rates are greater than for the overall four-electron O2-reduction to water, an important asset in the design of catalysts for the latter.

Temperature-independent catalytic two-electron reduction of dioxygen by ferrocenes with a copper(II) tris[2-(2-pyridyl)ethyl]amine catalyst in the presence of perchloric acid

Selective two-electron plus two-proton (2e(-)/2H(+)) reduction of O(2) to hydrogen peroxide by ferrocene (Fc) or 1,1'-dimethylferrocene (Me(2)Fc) in the presence of perchloric acid is catalyzed efficiently by a mononuclear copper(II) complex, [Cu(II)(tepa)](2+) (1; tepa = tris[2-(2-pyridyl)ethyl]amine) in acetone. The E(1/2) value for [Cu(II)(tepa)](2+) as measured by cyclic voltammetry is 0.07 V vs Fc/Fc(+) in acetone, being significantly positive, which makes it possible to use relatively weak one-electron reductants such as Fc and Me(2)Fc for the overall two-electron reduction of O(2). Fast electron transfer from Fc or Me(2)Fc to 1 affords the corresponding Cu(I) complex [Cu(I)(tepa)](+) (2), which reacts at low temperature (193 K) with O(2), however only in the presence of HClO(4), to afford the hydroperoxo complex [Cu(II)(tepa)(OOH)](+) (3). A detailed kinetic study on the homogeneous catalytic system reveals the rate-determining step to be the O(2)-binding process in the presence of HClO(4) at lower temperature as well as at room temperature. The O(2)-binding kinetics in the presence of HClO(4) were studied, demonstrating that the rate of formation of the hydroperoxo complex 3 as well as the overall catalytic reaction remained virtually the same with changing temperature. The apparent lack of activation energy for the catalytic two-electron reduction of O(2) is shown to result from the existence of a pre-equilibrium between 2 and O(2) prior to the formation of the hydroperoxo complex 3. No further reduction of [Cu(II)(tepa)(OOH)](+) (3) by Fc or Me(2)Fc occurred, and instead 3 is protonated by HClO(4) to yield H(2)O(2) accompanied by regeneration of 1, thus completing the catalytic cycle for the two-electron reduction of O(2) by Fc or Me(2)Fc.

Interdomain long-range electron transfer becomes rate-limiting in the Y216A variant of tyramine β-monooxygenase

The enzyme tyramine β-monooxygenase (TβM) belongs to a small eukaryotic family of physiologically important mononuclear dicopper monooxygenases. The properties of this family include noncoupled mononuclear copper centers ~11 Å apart, with Cu(M) performing C-H and O(2) activation and Cu(H) functioning as an electron storage site [Klinman, J. P. (2006) J. Biol. Chem. 281, 3013-3016]. A conserved tyrosine (Y216 in TβM) is positioned between the copper domains and is associated with Cu(H) (through an interaction with a Cu(H)-coordinating histidine). Mutations at Y216 (to W, I, and A) indicate little or no difference in electron paramagnetic resonance spectra, while X-ray absorption spectroscopy studies show only a very small decrease in distance between Cu(M) and its Met471 ligand in reduced enzyme. High-performance liquid chromatography assays demonstrate that turnover of substrate is complete with Y216W and Y216I, whereas Y216A undergoes a secondary inactivation that is linked to oxidation of ligands at Cu(M). Steady-state kinetic and isotope effect measurements were investigated. The significantly elevated K(m,Tyr) for Y216A, together with a very large (D)(k(cat)/K(m,Tyr)) of ~12, indicates a major impact on the binding of substrate at the Cu(M) site. The kinetic and isotopic parameters lead to estimated rate constants for C-H bond cleavage, dissociation of substrate from the Cu(M) site, and, in the case of Y216A, the rate of electron transfer (ET) from Cu(H) to Cu(M). These studies uncover a rate-limiting ET within the solvent-filled interface and lead to a paradigm shift in our understanding of the mononuclear dicopper monooxygenases.

Copper-, palladium-, and platinum-containing complexes of an asymmetric dinucleating ligand

The coordination chemistry of an asymmetric dinucleating hexadentate ligand LH(2) comprising neutral alkyltriamine and potentially dianionic dicarboxamido-pyridyl donor sets with copper, palladium, and platinum has been explored. Monometallic, dicopper, and heterodinuclear Cu-Pd and -Pt complexes have been prepared and characterized, including by NMR, EPR, UV-vis, and IR spectroscopy and X-ray crystallography. For example, the monometallic complexes [(LH(2))MCl]X (M = Cu, X = OTf; M = Pd or Pt, X = Cl) were prepared, wherein the metal(II) ions are coordinated to the triamine portion and the pyridyldicarboxamide is unperturbed. Treatment of LH(2) with [MesCu](x) (Mes = mesityl) provided a monocopper(I) complex, again with the metal coordinated only to the trialkylamine donor set. Reaction of [(LH(2))CuCl]OTf with NaOMe resulted in an unexpected migration of the copper(II)-chloride fragment to the pyridyldicarboxamide site to yield Na[LCuCl], from which a dicopper complex LCu(2)Cl(2) and mixed-metal complexes LCu(Cl)M(Cl) (M = Pd, Pt) were prepared by addition of CuCl(2) or MCl(2), respectively. The heterodinuclear complexes were also prepared by addition of CuCl(2) to [(LH(2))MCl]Cl.

Kinetics and thermodynamics of formation and electron-transfer reactions of Cu-O2 and Cu2-O2 complexes

The kinetics and thermodynamics of formation of Cu(II)-superoxo (Cu-O2) complexes by the reaction of Cu(I) complexes with dioxygen (O2) and the reduction of Cu(II)-superoxo complexes to dinuclear Cu-peroxo complexes are discussed. In the former case, electron transfer from a Cu(I) complex to O2 occurs concomitantly with binding of O2•- to the corresponding Cu(II) species. This is defined as an inner-sphere Cu(II) ion-coupled electron transfer process. Electron transfer from another Cu(I) complex to preformed Cu(II)-superoxo complexes also occurs concomitantly with binding of the the Cu(II)-peroxo species with the Cu(II) species to produce the dinuclear Cu-peroxo (Cu2-O2) complexes. The kinetics and thermodynamics of outer-sphere electron-transfer reduction of Cu2-O2 complexes are also been discussed in light of the Marcus theory of outer-sphere electron transfer.

Structural and electron paramagnetic resonance (EPR) characterization of novel vanadium(V/IV) complexes with hydroquinonate-iminodiacetate ligands exhibiting “noninnocent” activity

Reaction of KVO3 with 2-[N,N'-(carboxymethyl)aminomethyl]-5-methylhydroquinone (H4mecah) in aqueous solution at pH 8.2 results in the isolation of mononuclear K2[VV(O)2{Hmecah(-3)}]·2H2O complex. On the other hand, reaction with the 2-[N,N'-(carboxymethyl)aminomethyl]-5-tert-butylhydroquinone (H4tbutcah) under the same conditions gives the tetranuclear mixed-valent complex K6[{VVO(μ-O)VIVO}{μ-tbutbicah(-6)}]2·10.5H2O (H6tbutbicah, 2,2'-({2-[bis(carboxymethyl)amino]-3,6-dihydroxy-4-methylbenzyl}azanediyl)diacetic acid). The structures of both complexes were determined by single-crystal X-ray crystallography. The coordination environment of vanadium ions in both complexes is octahedral, with four out of the six positions to be occupied by the two cis carboxylate oxygens, one hydroquinonate oxygen, and one amine nitrogen atoms of the ligands’ tripod binding sites. The importance of the chelate ring strains in the stabilization of the p-semiquinone radical is also discussed. A protonation of the ligated to vanadium(IV) ion hydroquinonate oxygen at low pH was revealed by continuous wave (cw) X-band electron paramagnetic resonance (EPR) and UV–vis spectroscopies.

Coordination chemistry and reactivity of a cupric hydroperoxide species featuring a proximal H-bonding substituent

At -90 °C in acetone, a stable hydroperoxo complex [(BA)Cu(II)OOH](+) (2) (BA, a tetradentate N(4) ligand possessing a pendant -N(H)CH(2)C(6)H(5) group) is generated by reacting [(BA)Cu(II)(CH(3)COCH(3))](2+) with only 1 equiv of H(2)O(2)/Et(3)N. The exceptional stability of 2 is ascribed to internal H-bonding. Species 2 is also generated in a manner not previously known in copper chemistry, by adding 1.5 equiv of H(2)O(2) (no base) to the cuprous complex [(BA)Cu(I)](+). The broad implications for this finding are discussed. Species 2 slowly converts to a μ-1,2-peroxodicopper(II) analogue (3) characterized by UV-vis and resonance Raman spectroscopies. Unlike a close analogue not possessing internal H-bonding, 2 affords no oxidative reactivity with internal or external substrates. However, 2 can be protonated to release H(2)O(2), but only with HClO(4), while 1 equiv Et(3)N restores 2.

Inactivation of Met471Cys tyramine β-monooxygenase results from site-specific cysteic acid formation

Tyramine β-monooxygenase (TβM), the insect homologue of dopamine β-monooxygenase, is a neuroregulatory enzyme that catalyzes the β-hydroxylation of tyramine to yield octopamine. Mutation of the methionine (Met) ligand to Cu(M) of TβM, Met471Cys, yielded a form of TβM that is catalytically active but susceptible to inactivation during turnover [Hess, C. R., Wu, Z., Ng, A., Gray, E. E., McGuirl, M. M., and Klinman, J. P. (2008) J. Am. Chem. Soc. 130, 11939-11944]. Further, although the wild-type (WT) enzyme undergoes coordination of Met471 to Cu(M) in its reduced form, the generation of Met471Cys almost completely eliminates this interaction [Hess, C. R., Klinman, J. P., and Blackburn, N. J. (2010) J. Biol. Inorg. Chem. 15, 1195-1207]. The aim of this study is to identify the chemical consequence of the poor ability of Cys to coordinate Cu(M). We show that Met471Cys TβM is ~5-fold more susceptible to inactivation than the WT enzyme in the presence of the cosubstrate/reductant ascorbate and that this process is not facilitated by the substrate tyramine. The resulting 50-fold smaller ratio for turnover to inactivation in the case of Met471Cys prevents full turnover of the substrate under all conditions examined. Liquid chromatography-tandem mass spectrometry analysis of proteolytic digests of inactivated Met471Cys TβM leads to the identification of cysteic acid at position 471. While both Met and Cys side chains are expected to be similarly subject to oxidative damage in proteins, the enhanced reactivity of Met471Cys toward solution oxidants in TβM is attributed to its weaker interaction with Cu(I)(M).

Discovery of a metalloenzyme-like cooperative catalytic system of metal nanoclusters and catechol derivatives for the aerobic oxidation of amines

We have discovered a new class of cooperative catalytic system, consisting of heterogeneous polymer-immobilized bimetallic Pt/Ir alloyed nanoclusters (NCs) and 4-tert-butylcatechol, for the aerobic oxidation of amines to imines under ambient conditions. After optimization, the desired imines were obtained in good to excellent yields with broad substrate scope. The reaction rate was determined to be first-order with respect to the substrate and catechol and zero-order for the alloyed Pt/Ir NC catalyst. Control studies revealed that both the heterogeneous NC catalyst and 4-tert-butylcatechol are essential and act cooperatively to facilitate the aerobic oxidation under mild conditions.

[Analysis of enzymatic reactions by quantum chemical calculations]

Density functional theory (DFT) is now extensively used as a research tool for the investigation of structure and reactivity of biological systems; however, its high computational demands still restrict the applicability of DFT to systems of a few tens up to one hundred atoms. A combined quantum mechanical/molecular mechanical (QM/MM) approach is applicable as an important method to study whole enzyme systems more than ten thousands atoms. We have investigated methane monooxygenase, dopamenie β-monooxygenase, tyrosinase, B12 dependent diol dehydratase, etc. using DFT and QM/MM calculations. In particular, we have done some computational mutation analyses about the amino acid residues at the active site of diol dehydratase. Our DFT and QM/MM calculations can correctly describe the structures and activation barriers of intermediates and transition states in the protein environment, and therefore, we successfully revealed the catalytic role of amino acid residues at the active site of diol dehydratase. Predicted relative activities of mutants are consistent with experimentally observed reaction rates. These results encourage us to apply QM/MM research to enzymatic reactions, functional analysis of active-site residues, and rational design of enzymes with new catalytic functions.

X-ray absorption near-edge spectroscopy in bioinorganic chemistry: Application to M-O2 systems

Metal K-edge X-ray absorption spectroscopy (XAS) has been extensively applied to bioinorganic chemistry to obtain geometric structure information on metalloprotein and biomimetic model complex active sites by analyzing the higher energy extended X-ray absorption fine structure (EXAFS) region of the spectrum. In recent years, focus has been on developing methodologies to interpret the lower energy K-pre-edge and rising-edge regions (XANES) and using it for electronic structure determination in complex bioinorganic systems. In this review, the evolution and progress of 3d-transition metal K-pre-edge and rising-edge methodology development is presented with particular focus on applications to bioinorganic systems. Applications to biomimetic transition metal-O₂ intermediates (M = Fe, Co, Ni and Cu) are reviewed, which demonstrate the power of the method as an electronic structure determination technique and its impact in understanding the role of supporting ligands in tuning the electronic configuration of transition metal-O₂ systems.