A Structural Model of the Type 1 Copper Protein Active Site: N2S(thiolate)S(thioether) Ligation in a Cu(II) Complex

Molecular Mechanism of Substrate Oxidation in Lytic Polysaccharide Monooxygenases: Insight from Theoretical Investigations

Lytic polysaccharide monooxygenases (LPMOs) are copper enzymes that today comprise a large enzyme superfamily, grouped into the distinct members AA9-AA17 (with AA12 exempted). The LPMOs have the potential to facilitate the upcycling of biomass waste products by boosting the breakdown of cellulose and other recalcitrant polysaccharides. The cellulose biopolymer is the main component of biomass waste and thus comprises a large, unexploited resource. The LPMOs work through a catalytic, oxidative reaction whose mechanism is still controversial. For instance, the nature of the intermediate performing the oxidative reaction is an open question, and the same holds for the employed co-substrate. Here we review theoretical investigations addressing these questions. The applied theoretical methods are usually based on quantum mechanics (QM), often combined with molecular mechanics (QM/MM). We discuss advantages and disadvantages of the employed theoretical methods and comment on the interplay between theoretical and experimental results.

Long-Range Charge Delocalization Mediates the Ultrafast Ligand-to-Metal Charge Transfer Dynamics at the Cu2+-Active Site in Azurin

The blue color metalloprotein in azurin has traditionally been attributed to the intense cysteine-to-Cu²⁺ ligand-to-metal charge transfer transition centered at 628 nm. Although resonance Raman measurements of the Cu²⁺ active site have implied that the LMCT transition electronically couples to the protein scaffold well beyond its primary metal-ligand coordination shell, the structural extent of this electronic coupling and visualization of the protein-mediated charge transfer dynamics have remained elusive. Here, using femtosecond broadband transient absorption and impulsive Raman spectroscopy, we provide direct evidence for a rapid relaxation between two distinct charge transfer states, having different spatial delocalization, within ∼300 fs followed by recombination of charges in subpicosecond time scales. We invoke the formation of a protein-centered radical cation, possibly Trp48 or a Phe residue, within 100 fs substantiating the long-range electronic coupling for the first time beyond the traditional copper active site. The Raman spectra of the excited CT state show the presence of protein-centric vibrations along with the vibrational modes assigned to the copper active site. Our results demonstrate a large delocalization length scale of the initially populated CT state, thereby highlighting the possibility of exploiting azurin photochemistry for energy conversion techniques.

Targeting the reactive intermediate in polysaccharide monooxygenases

Lytic polysaccharide monooxygenases (LPMOs) are copper metalloenzymes that can enhance polysaccharide depolymerization through an oxidative mechanism, making them interesting for the production of biofuel from cellulose. However, the details of this activation are unknown; in particular, the nature of the intermediate that attacks the glycoside C-H bond in the polysaccharide is not known, and a number of different species have been suggested. The homolytic bond-dissociation energy (BDE) has often been used as a descriptor for the bond-activation power, especially for inorganic model complexes. We have employed quantum-chemical cluster calculations to estimate the BDE for a number of possible LPMO intermediates to bridge the gap between model complexes and the actual LPMO active site. The calculated BDEs suggest that the reactive intermediate is either a Cu(II)-oxyl, a Cu(III)-oxyl, or a Cu(III)-hydroxide, which indicate that O-O bond breaking occurs before the C-H activation step.

A mechanistic investigation of the photoinduced, copper-mediated cross-coupling of an aryl thiol with an aryl halide

Photoinduced, copper-catalyzed cross-coupling can offer a complementary approach to thermal (non-photoinduced) methods for generating C-X (X = C, N, O, S, etc.) bonds. In this report, we describe the first detailed mechanistic investigation of one of the processes that we have developed, specifically, the (stoichiometric) coupling of a copper-thiolate with an aryl iodide. In particular, we focus on the chemistry of a discrete [CuI(SAr)2]- complex (Ar = 2,6-dimethylphenyl), applying a range of techniques, including ESI-MS, cyclic voltammetry, transient luminescence spectroscopy, optical spectroscopy, DFT calculations, Stern-Volmer analysis, EPR spectroscopy, actinometry, and reactivity studies. The available data are consistent with the viability of a pathway in which photoexcited [CuI(SAr)2]-* serves as an electron donor to an aryl iodide to afford an aryl radical, which then reacts in cage with the newly generated copper(II)-thiolate to furnish the cross-coupling product in a non-chain process.

C-Nitrosation of a β-diketiminate ligand in copper(ii) complex

Copper(ii) complex of a β-diketiminate ligand, upon reaction with nitric oxide, affords C-nitrosation of the ligand.

Prodigiosin analogue designed for metal coordination: stable zinc and copper pyrrolyldipyrrins

The pyrrolyldipyrrin motif is found in several naturally occurring prodigiosin pigments. The potential roles of the interactions of prodigiosins with transition metals and the properties of metal-bound pyrrolyldipyrrins, however, have been difficult to assess because of the very limited number of well-characterized stable complexes. Here, we show that the introduction of a meso-aryl substituent and an ethyl ester group during the sequential assembly of the three heterocycles affords a pyrrolyldipyrrin of enhanced coordinating abilities when compared to that of natural prodigiosins. UV-visible absorption studies indicate that this ligand promptly binds Zn(II) ions with 2:1 ligand-to-metal stoichiometry and Cu(II) ions with 1:1 stoichiometry. Notably, no addition of base is required for the formation of the resulting stable complexes. The crystal structures reveal that whereas the tetrahedral zinc center engages two nitrogen donors on each ligand, the pseudosquare planar copper complex features coordination of all three pyrrolic nitrogen atoms and employs the ester group as a neutral ligand. This first example of coordination of a redox-active transition metal within a fully conjugated pyrrolyldipyrrin framework was investigated spectroscopically by electron paramagnetic resonance to show that the 1:1 metal-to-ligand ratio found in the crystal structure is also maintained in solution.

Assessment of Quantum Mechanical Methods for Copper and Iron Complexes by Photoelectron Spectroscopy

Broken-symmetry density functional theory (BS-DFT) calculations are assessed for redox energetics [Cu(SCH₃)₂]^1–/0, [Cu(NCS)₂]^1–/0, [FeCl₄]^1–/0, and [Fe(SCH₃)₄]^1–/0 against vertical detachment energies (VDE) from valence photoelectron spectroscopy (PES), as a prelude to studies of metalloprotein analogs. The M06 and B3LYP hybrid functionals give VDE that agree with the PES VDE for the Fe complexes, but both underestimate it by ∼400 meV for the Cu complexes; other hybrid functionals give VDEs that are an increasing function of the amount of Hartree–Fock (HF) exchange and so cannot show good agreement for both Cu and Fe complexes. Range-separated (RS) functionals appear to give a better distribution of HF exchange since the negative HOMO energy is approximately equal to the VDEs but also give VDEs dependent on the amount of HF exchange, sometimes leading to ground states with incorrect electron configurations; the LRC-ωPBEh functional reduced to 10% HF exchange at short-range give somewhat better values for both, although still ∼150 meV too low for the Cu complexes and ∼50 meV too high for the Fe complexes. Overall, the results indicate that while HF exchange compensates for self-interaction error in DFT calculations of both Cu and Fe complexes, too much may lead to more sensitivity to nondynamical correlation in the spin-polarized Fe complexes.

DNA-binding studies and antioxidant activities of two-, three- and four-coordinate silver(i) complexes containing bis(2-benzimidazolyl)aniline derivatives

Three novel structure Ag(i) complexes have been synthesized and characterized. The three ligands and Ag(i) complexes bind to DNA in an intercalation mode. The Ag(i) complexes have stronger ability of antioxidation for hydroxyl radical and superoxide radical.

Inner- and outer-sphere metal coordination in blue copper proteins

Blue copper proteins (BCPs) comprise classic cases of Nature's profound control over the electronic structures and chemical reactivity of transition metal ions. Early studies of BCPs focused on their inner coordination spheres, that is, residues that directly coordinate Cu. Equally important are the electronic and geometric perturbations to these ligands provided by the outer coordination sphere. In this tribute to Hans Freeman, we review investigations that have advanced the understanding of how inner-sphere and outer-sphere coordination affects biological Cu properties.

Type 1 copper site synthetic model complexes with increased redox potentials

Reactions of NaSCPh(3) with (R(3)tacn)Cu(OTf)(2) (R is Me, iPr; tacn is 1,4,7-triazacyclononane; OTf is CF(3)SO(3)(-)) yield blue complexes identified as ((R(3)tacn)CuSCPh(3))(OTf) on the basis of UV-vis, resonance Raman, and electron paramagnetic resonance (EPR) spectroscopy and electrospray ionization mass spectrometry. These complexes exhibit spectroscopic properties typical of type 1 copper sites in proteins, including diagnostic Sπ → Cu(d(x(2)-y(2))) ligand-to-metal charge transfer transitions at approximately 610-630 nm and small A(||) values in EPR spectra of less than 100 × 10(-4) cm(-1). Cyclic voltammetry experiments revealed redox potentials for the complexes similar to those of several low-potential type 1 copper proteins (e.g., azurin, stellacyanin) and approximately 0.5 V higher than those of previously reported model compounds. Thus, the new complexes mimic key aspects of both the structure and the function of type 1 copper sites.

1,3-Bis(1-methyl-1H-benzimidazol-2-yl)-2-oxapropane

In the title mol­ecule, C₁₈H₁₈N₄O, the dihedral angle between the mean planes of the two benzimidazole ring systems is 61.5 (1)°.

Synthesis and spectral studies of copper complexes using a N-octylated bis benzimidazole diamide ligand

Monomeric Cu(II) and Cu(I) complexes bound to a tetradentate bis-benzimidazole diamide ligand N,N'-bis(N-octyl benzimidazolyl-2yl)(methyl)pentane diamide (O-GBGA) have been isolated and characterized. X-Band EPR spectra of the copper(II) complexes in CH2Cl2 were recorded in a frozen solution as solvent at liquid nitrogen temperature. Solution spectra typically indicate a d(x2-y2) ground state (g||>g⊥>2.0023) and show less than four nuclear hyperfine lines with broadening of g⊥ line in some cases, thus indicating distorted tetragonal geometry. One of the copper(II) complexes shows a five line N-SHF structure (16±1G) implying the binding of imine nitrogen of the benzimidazole to copper ion. α2 ranges from 0.57-0.97 indicating considerable amount of covalent character in Cu-L bond. Anodic shifts in E1/2 values indicate the retention of anion in the coordination sphere of Cu(II), E1/2 values becoming anodic in the order C6H5COO-<SCN-<Cl-. The fluorescence quantum yield of complexes was found to be lower than that of the ligand O-GBGA (Φ=0.029) and the relative fluorescence data reveals that fluorescence of such compounds could distinguish between small and large anions.

Aqua-[1,3-bis-(benzimidazol-2-yl)-2-oxapropane]-diethano-lmanganese(II) dipicrate ethanol disolvate

In the title complex, [Mn(C₁₆H₁₄N₄O)(C₂H₅OH)₂(H₂O)](C₆H₂N₃O₇)₂·2C₂H₅OH, the Mn^II ion is in a distorted octa­hedral coordination environment, defined by an MnN₂O₄ donor set. The 1,3-bis­(benz­imid­azol-2-yl)-2-oxapropane ligand is tridentate. In the crystal structure, inter­molecular N—H⋯O and O—H⋯O hydrogen bonds link the components into a three-dimensional network. The O atoms of one of the nitro groups are disordered over two sets of sites with refined occupancies of 0.577 (11) and 0.423 (11).

Spectroscopic and computational studies of a series of high-spin Ni(II) thiolate complexes

The electronic structures of a series of high-spin Ni(II)-thiolate complexes of the form [PhTt(tBu)]Ni(SR) (R = CPh(3), 2; C(6)F(5), 3; C(6)H(5), 4; PhTt(tBu) = phenyltris((tert-butylthio)methyl)borate) have been characterized using a combined spectroscopic and computational approach. Resonance Raman (rR) spectroscopic data reveal that the nu(Ni-SR) vibrational feature occurs between 404 and 436 cm(-1) in these species. The corresponding rR excitation profiles display a striking de-enhancement behavior because of interference effects involving energetically proximate electronic excited states. These data were analyzed in the framework of time-dependent Heller theory to obtain quantitative insight into excited state nuclear distortions. The electronic absorption and magnetic circular dichroism spectra of 2-4 are characterized by numerous charge transfer (CT) transitions. The dominant absorption feature, which occurs at approximately 18,000 cm(-1) in all three complexes, is assigned as a thiolate-to-Ni CT transition involving molecular orbitals that are of pi-symmetry with respect to the Ni-S bond, reminiscent of the characteristic absorption feature of blue copper proteins. Density functional theory computational data provide molecular orbital descriptions for 2-4 and allow for detailed assignments of the key spectral features. A comparison of the results obtained in this study to those reported for similar Ni-thiolate species reveals that the supporting ligand plays a secondary role in determining the spectroscopic properties, as the electronic structure is primarily determined by the metal-thiolate bonding interaction.

Synthesis and structures of isopropyl-β-diketiminato copper(I) complexes

The reaction of N,N′-diisopropyl-2-amino-4-iminopent-2-ene (nacnaci-PrH, 1) either with CuOt-Bu or with a mixture of mesityl copper and 10% CuOt-Bu afforded, in the presence of PPh3, CN(C6Me2H3), or MeCN, the Lewis base coordinated complexes nacnaci-PrCuPPh3·0.5 C6H14 (2), nacnaci-PrCuCN(C6Me2H3) (3), and nacnaci-PrCu(NCMe) (4). Compounds 2, 3, and 4 were characterized by single-crystal X-ray diffraction studies. Compound 4 afforded two species in deuterated benzene in a 2:1 ratio, which were assigned to {nacnaci-PrCu}2(μ-NCMe) and nacnaci-PrCuNCMe (4). Upon addition of 5 equiv. of MeCN, the two sets collapsed into that of 4. No copper complexes were formed in the presence of styrene, stilbene, or diphenylacetylene.

N-[3-(2,6-Dimethylanilino)-1-methylbut-2-enylidene]-2,6-dimethylanilinium chloride

The title salt, C₂₁H₂₇N₂⁺·Cl⁻ resulted from the condensation between 2,6-dimethyl­aniline and acetyl­acetone in acidified ethanol. The bulky cation is stabilized in a β-imino­enamine tautomeric form, and presents a W-shaped conformation. The benzene rings are arranged almost parallel, with a dihedral angle of 6.58 (4)° between the mean planes. Both N—H groups in the cation form strong hydrogen bonds with two symmetry-related chloride anions. The resulting supra­molecular structure is a one dimensional polymer running along [001], alternating cations and anions. The π–π inter­action observed in the mol­ecule, characterized by a centroid–centroid separation of 4.298 (4) Å, is thus extended to the chains, with separations of 5.222 (4) Å between benzene rings of neighbouring cations in the crystal.

Chemical issues addressing the construction of the distal Ni[cysteine-glycine-cysteine]2- site of acetyl CoA synthase: why not copper?

The discovery of the metallopeptide Ni(Cysteine-Glycine-Cysteine)(2-), Ni(CGC)(2-), in the A-cluster active site of Acetyl CoA Synthase has prompted the synthesis of many small molecule models which employ M(N(2)S(2)) complexes as metalloligands. In vitro studies have shown that nickel incorporates into the N(2)S(2) binding pocket even when copper is in the enzyme growth medium, while copper is preferentially taken up in the proximal site, displacing the catalytically active nickel. (Darnault, C.; Volbeda, A.; Kim, E.J.; Legrand, P.; Vernede, X.; Lindahl, P.A.; Fontecilla-Camps, J.C. Nat. Struct. Biol. 2003, 10, 271-279.) The work herein has been designed to address the chemical viability of copper(II) within the tripeptide N(2)S(2) ligand set. To this end, a series of CuN(2)S(2)(2-) complexes, the resin-bound, O-Cu(CGC)(2-) (A) and free Cu(CGC)(2-) (B) complexes, as well as Cu(ema)(2-) (C) and Cu(emi)(2-) (D) dianions, have been characterized by UV-vis, electron paramagnetic resonance (EPR), and electrospray ionization mass spectrometry (ESI-MS) spectroscopies, cyclic voltammetry (CV), and, where appropriate, X-ray diffraction studies, and compared to the Ni(II) congeners. EPR spectroscopic results have indicated that, in frozen N,N-dimethylformamide (DMF) solution, the copper complexes are distorted square planar structures with nitrogen and sulfur donors. This is consistent with X-ray diffraction measurements which also show copper(II) in a distorted square planar environment that is bereft of CuN(2)S(2)(2-) intermolecular interactions. Density-functional theory (DFT) calculations resulted in optimized structures that are consistent with crystallographic data and indicated highest occupied molecular orbital (HOMO)-singly occupied molecular orbital (SOMO) gaps of 5.01 and 4.68 eV for C and D, respectively. Optimized structures of Ni(ema)(2-) and Ni(emi)(2-) share the same basic characteristics as the copper(II) congeners. Electrochemical characterization of C and D resulted in a reversible Cu(III/II) couple at -1.20 V and - 1.40 V, respectively. Reactivity studies with Rh(CO)(2)(+) show similar donor capabilities for complexes A-D. Analysis of A shows that transmetalation does not occur. From competitive metal uptake studies on immobilized tripeptide it is concluded that the N(2)S(2)(4-) ligating unit has a slight preference for Cu(2+) over Ni(2+) and that the biosynthetic pathway responsible for constructing the distal site of ACS must be selective for nickel insertion or copper exclusion, or both.