A quantitative description of the ground-state wave function of Cu(A) by X-ray absorption spectroscopy: comparison to plastocyanin and relevance to electron transfer

In Solution Identification of the Lysine-Cysteine Redox Switch with a NOS Bridge in Transaldolase by Sulfur K-Edge X-ray Absorption Spectroscopy

A novel covalent post-translational modification (lysine-NOS-cysteine) was discovered in proteins, initially in the enzyme transaldolase of Neisseria gonorrhoeae (NgTAL) [Nature 2021, 593, 460-464], acting as a redox switch. The identification of this novel linkage in solution was unprecedented until now. We present detection of the NOS redox switch in solution using sulfur K-edge X-ray absorption spectroscopy (XAS). The oxidized NgTAL spectrum shows a distinct shoulder on the low-energy side of the rising edge, corresponding to a dipole-allowed transition from the sulfur 1s core to the unoccupied σ* orbital of the S-O group in the NOS bridge. This feature is absent in the XAS spectrum of reduced NgTAL, where Lys-NOS-Cys is absent. Our experimental and calculated XAS data support the presence of a NOS bridge in solution, thus potentially facilitating future studies on enzyme activity regulation mediated by the NOS redox switches, drug discovery, biocatalytic applications, and protein design.

Tuning the Type 1 Reduction Potential of Multicopper Oxidases: Uncoupling the Effects of Electrostatics and H-Bonding to Histidine Ligands

In multicopper oxidases (MCOs), the type 1 (T1) Cu accepts electrons from the substrate and transfers these to the trinuclear Cu cluster (TNC) where O₂ is reduced to H₂O. The T1 potential in MCOs varies from 340 to 780 mV, a range not explained by the existing literature. This study focused on the ∼350 mV difference in potential of the T1 center in Fet3p and Trametes versicolor laccase (TvL) that have the same 2His1Cys ligand set. A range of spectroscopies performed on the oxidized and reduced T1 sites in these MCOs shows that they have equivalent geometric and electronic structures. However, the two His ligands of the T1 Cu in Fet3p are H-bonded to carboxylate residues, while in TvL they are H-bonded to noncharged groups. Electron spin echo envelope modulation spectroscopy shows that there are significant differences in the second-sphere H-bonding interactions in the two T1 centers. Redox titrations on type 2-depleted derivatives of Fet3p and its D409A and E185A variants reveal that the two carboxylates (D409 and E185) lower the T1 potential by 110 and 255-285 mV, respectively. Density functional theory calculations uncouple the effects of the charge of the carboxylates and their difference in H-bonding interactions with the His ligands on the T1 potential, indicating 90-150 mV for anionic charge and ∼100 mV for a strong H-bond. Finally, this study provides an explanation for the generally low potentials of metallooxidases relative to the wide range of potentials of the organic oxidases in terms of different oxidized states of their TNCs involved in catalytic turnover.

Fully Delocalized Mixed-Valent Cu1.5 Cu1.5 Complex: Strong Cu-Cu interaction and Fast Electron Self-Exchange Rate Despite Large Structural Changes

A flexible macrocyclic ligand with two tridentate {CNC} compartments can host two Cu ions in reversibly interconvertible states, Cu^I Cu^I (1) and mixed-valent Cu^1.5 Cu^1.5 (2). They were characterized by XRD and multiple spectroscopic methods, including EPR, UV/Vis absorption and MCD, in combination with TD-DFT and CASSCF calculations. 2 features a short Cu⋅⋅⋅Cu distance (≈2.5 Å; compared to ≈4.0 Å in 1) and a very high delocalization energy of 13 000 cm^-1 , comparable to the mixed-valent state of the biological Cu_A site. Electron self-exchange between 1 and 2 is rapid despite large structural reorganization, and is proposed to proceed via a sequential mechanism involving an active conformer of 1, viz. 1'; the latter has been characterized by XRD. Such electron transfer (ET) process is reminiscent of the conformationally gated ET proposed for biological systems. This redox couple is a unique pair of flexible dicopper complexes, achieving fast electron self-exchange closely related to the function of the Cu_A site.

New Dinuclear Macrocyclic Copper(II) Complexes as Potentially Fluorescent and Magnetic Materials

Two dinuclear copper(II) complexes with macrocyclic Schiff bases K1 and K2 were prepared by the template reaction of (R)-(+)-1,1'-binaphthalene-2,2'-diamine and 2-hydroxy-5-methyl-1,3-benzenedicarboxaldehyde K1, or 4-tert-butyl-2,6-diformylphenol K2 with copper(II) chloride dihydrate. The compounds were characterized by spectroscopic methods. X-ray crystal structure determination and DFT calculations confirmed their geometry in solution and in the solid phase. Moreover, intermolecular interactions in the crystal structure of K2 were analyzed using 3D Hirshfeld surfaces and the related 2D fingerprint plots. The magnetic study revealed very strong antiferromagnetic CuII-CuII exchange interactions, which were supported by magneto-structural correlation and DFT calculations conducted within a broken symmetry (BS) framework. Complexes K1 and K2 exhibited luminescent properties that may be of great importance in the search for new OLEDs. Both K1 and K2 complexes showed emissions in the range of 392-424 nm in solutions at various polarities. Thin materials of the studied compounds were deposited on Si(111) by the spin-coating method or by thermal vapor deposition and studied by scanning electron microscopy (SEM/EDS), atomic force microscopy (AFM), and fluorescence spectroscopy. The thermally deposited K1 and K2 materials showed high fluorescence intensity in the range of 318-531 nm for K1/Si and 326-472 nm for the K2/Si material, indicating that they could be used in optical devices.

Europium-151 and iron-57 nuclear resonant vibrational spectroscopy of naturally abundant KEu(III)Fe(II)(CN)6 and Eu(III)Fe(III)(CN)6 complexes

We have performed and analyzed the first combined 151Eu and 57Fe nuclear resonant vibrational spectroscopy (NRVS) for naturally abundant KEu(III)[Fe(II)(CN)6] and Eu(III)[Fe(III)(CN)6] complexes. Comparison of the observed 151Eu vs.57Fe NRVS spectroscopic features confirms that Eu(III) in both KEu(III)[Fe(II)(CN)6] and Eu(III)[Fe(III)(CN)6] occupies a position outside the [Fe(CN)6] core and coordinates to the N atoms of the CN- ions, whereas Fe(III) or Fe(II) occupies the site inside the [Fe(CN)6]4- core and coordinates to the C atoms of the CN- ions. In addition to the spectroscopic interest, the results from this study provide invaluable insights for the design and evaluation of the nanoparticles of such complexes as potential cellular contrast agents for their use in magnetic resonance imaging. The combined 151Eu and 57Fe NRVS measurements are also among the first few explorations of bi-isotopic NRVS experiments.

Tracking energy scale variations from scan to scan in nuclear resonant vibrational spectroscopy: In situ correction using zero-energy position drifts ΔEi rather than making in situ calibration measurements

Nuclear resonant vibrational spectroscopy (NRVS) is an excellent modern vibrational spectroscopy, in particular, for revealing site-specific information inside complicated molecules, such as enzymes. There are two different concepts about the energy calibration for a beamline or a monochromator (including a high resolution monochromator): the absolute energy calibration and the practical energy calibration. While the former pursues an as-fine-as-possible and as-repeatable-as-possible result, the latter includes the environment influenced variation from scan to scan, which often needs an in situ calibration measurement to track. However, an in situ measurement often shares a weak beam intensity and therefore has a noisy NRVS spectrum at the calibration sample location, not leading to a better energy calibration/correction in most cases. NRVS users for a long time have noticed that there are energy drifts in the vibrational spectra's zero-energy positions from scan to scan (ΔE_i), but their trend has not been explored and utilized in the past. In this publication, after providing a brief introduction to the critical issue(s) in practical NRVS energy calibrations, we have evaluated the trend and the mechanism for these zero-energy drifts (ΔE_i) and explored their link to the energy scales (α_i) from scan to scan. Via detailed analyses, we have established a new stepwise procedure for carrying out practical energy calibrations, which includes the correction for the scan-dependent energy variations using ΔE_i values rather than running additional in situ calibration measurements. We also proved that one additional instrument-fixed scaling constant (α₀) exists to convert such "calibrated" energy axis (E') to the real energy axis (E_real). The "calibrated" real energy axis (E_real) has a preliminary error bar of ±0.1% (the 2σ_E divided by the vibrational energy position), which is 4-8 times better than that from the current practical energy calibration procedure.

Probing Physical Oxidation State by Resonant X-ray Emission Spectroscopy: Applications to Iron Model Complexes and Nitrogenase

The ability of resonant X-ray emission spectroscopy (XES) to recover physical oxidation state information, which may often be ambiguous in conventional X-ray spectroscopy, is demonstrated. By combining Kβ XES with resonant excitation in the XAS pre-edge region, resonant Kβ XES (or 1s3p RXES) data are obtained, which probe the 3dn+1 final-state configuration. Comparison of the non-resonant and resonant XES for a series of high-spin ferrous and ferric complexes shows that oxidation state assignments that were previously unclear are now easily made. The present study spans iron tetrachlorides, iron sulfur clusters, and the MoFe protein of nitrogenase. While 1s3p RXES studies have previously been reported, to our knowledge, 1s3p RXES has not been previously utilized to resolve questions of metal valency in highly covalent systems. As such, the approach presented herein provides chemists with means to more rigorously and quantitatively address challenging electronic-structure questions.

Electronic Structures and Reactivity Profiles of Aryl Nitrenoid-Bridged Dicopper Complexes

Dicopper complexes templated by dinucleating, pacman dipyrrin ligand scaffolds (Mesdmx, tBudmx: dimethylxanthine-bridged, cofacial bis-dipyrrin) were synthesized by deprotonation/metalation with mesitylcopper (CuMes; Mes: mesityl) or by transmetalation with cuprous precursors from the corresponding deprotonated ligand. Neutral imide complexes (Rdmx)Cu2(μ2-NAr) (R: Mes, tBu; Ar: 4-MeOC6H4, 3,5-(F3C)2C6H3) were synthesized by treatment of the corresponding dicuprous complexes with aryl azides. While one-electron reduction of (Mesdmx)Cu2(μ2-N(C6H4OMe)) with potassium graphite initiates an intramolecular, benzylic C-H amination at room temperature, chemical reduction of (tBudmx)Cu2(μ2-NAr) leads to isolable [(tBudmx)Cu2(μ2-NAr)]- product salts. The electronic structures of the thermally robust [(tBudmx)Cu2(μ2-NAr)]0/- complexes were assessed by variable-temperature electron paramagnetic resonance spectroscopy, X-ray absorption spectroscopy (Cu L2,3/K-edge, N K-edge), optical spectroscopy, and DFT/CASSCF calculations. These data indicate that the formally Class IIIA mixed valence complexes of the type [(Rdmx)Cu2(μ2-NAr)]- feature significant NAr-localized spin following reduction from electronic population of the [Cu2(μ2-NAr)] π* manifold, contrasting previous methods for engendering iminyl character through chemical oxidation. The reactivity of the isolable imido and iminyl complexes are examined for prototypical radical-promoted reactivity (e.g., nitrene transfer and H-atom abstraction), where the divergent reactivity is rationalized by the relative degree of N-radical character afforded from different aryl substituents.

Formation and Electronic Structure of an Atypical CuA Site

PmoD, a recently discovered protein from methane-oxidizing bacteria, forms a homodimer with a dicopper CuA center at the dimer interface. Although the optical and electron paramagnetic resonance (EPR) spectroscopic signatures of the PmoD CuA bear similarities to those of canonical CuA sites, there are also some puzzling differences. Here we have characterized the rapid formation (seconds) and slow decay (hours) of this homodimeric CuA site to two mononuclear Cu2+ sites, as well as its electronic and geometric structure, using stopped-flow optical and advanced paramagnetic resonance spectroscopies. PmoD CuA formation occurs rapidly and involves a short-lived intermediate with a λmax of 360 nm. Unlike other CuA sites, the PmoD CuA is unstable, decaying to two type 2 Cu2+ centers. Surprisingly, NMR data indicate that the PmoD CuA has a pure σu* ground state rather than the typical equilibrium between σu* and πu of all other CuA proteins. EPR, ENDOR, ESEEM, and HYSCORE data indicate the presence of two histidine and two cysteine ligands coordinating the CuA core in a highly symmetrical fashion. This report significantly expands the diversity and understanding of known CuA sites.

Fine Tuning of Functional Features of the CuA Site by Loop-Directed Mutagenesis

Here we report the spectroscopic and electrochemical characterization of three novel chimeric Cu_A proteins in which either one or the three loops surrounding the metal ions in the Thermus thermophilus protein have been replaced by homologous human and plant sequences while preserving the set of coordinating amino acids. These conservative modifications mimic basic differences between Cu_A sites from different organisms and allow for fine tuning the energy gap between alternative electronic ground states of Cu_A.. This results in a systematic modulation of thermodynamic and kinetic electron transfer (ET) parameters and in the selection of one of two possible redox-active molecular orbitals, which differ in the ET reorganization energy by a factor of 2. Moreover, the ET mechanism is found to be frictionally controlled, and the modifications introduced into the different chimeras do not affect the frictional activation parameter.

Dramatic Electronic Perturbations of CuA Centers via Subtle Geometric Changes

Cu_A is a binuclear copper site acting as electron entry port in terminal heme-copper oxidases. In the oxidized form, Cu_A is a mixed valence pair whose electronic structure can be described using a potential energy surface with two minima, σ_u* and π_u, that are variably populated at room temperature. We report that mutations in the first and second coordination spheres of the binuclear metallocofactor can be combined in an additive manner to tune the energy gap and, thus, the relative populations of the two lowest-lying states. A series of designed mutants span σ_u*/π_u energy gaps ranging from 900 to 13 cm^-1. The smallest gap corresponds to a variant with an effectively degenerate ground state. All engineered sites preserve the mixed-valence character of this metal center and the electron transfer functionality. An increase of the Cu-Cu distance less than 0.06 Å modifies the σ_u*/π_u energy gap by almost 2 orders of magnitude, with longer distances eliciting a larger population of the π_u state. This scenario offers a stark contrast to synthetic systems, as model compounds require a lengthening of 0.5 Å in the Cu-Cu distance to stabilize the π_u state. These findings show that the tight control of the protein environment allows drastic perturbations in the electronic structure of Cu_A sites with minor geometric changes.

L-edge sum rule analysis on 3d transition metal sites: from d10 to d0 and towards application to extremely dilute metallo-enzymes

According to L-edge sum rules, the number of 3d vacancies at a transition metal site is directly proportional to the integrated intensity of the L-edge X-ray absorption spectrum (XAS) for the corresponding metal complex. In this study, the numbers of 3d holes are characterized quantitatively or semi-quantitatively for a series of manganese (Mn) and nickel (Ni) complexes, including the electron configurations 3d10→ 3d0. In addition, extremely dilute (<0.1% wt/wt) Ni enzymes were examined by two different approaches: (1) by using a high resolution superconducting tunnel junction X-ray detector to obtain XAS spectra with a very high signal-to-noise ratio, especially in the non-variant edge jump region; and (2) by adding an inert tracer to the sample that provides a prominent spectral feature to replace the weak edge jump for intensity normalization. In this publication, we present for the first time: (1) L-edge sum rule analysis for a series of Mn and Ni complexes that include electron configurations from an open shell 3d0 to a closed shell 3d10; (2) a systematic analysis on the uncertainties, especially on that from the edge jump, which was missing in all previous reports; (3) a clearly-resolved edge jump between pre-L3 and post-L2 regions from an extremely dilute sample; (4) an evaluation of an alternative normalization standard for L-edge sum rule analysis. XAS from two copper (Cu) proteins measured using a conventional semiconductor X-ray detector are also repeated as bridges between Ni complexes and dilute Ni enzymes. The differences between measuring 1% Cu enzymes and measuring <0.1% Ni enzymes are compared and discussed. This study extends L-edge sum rule analysis to virtually any 3d metal complex and any dilute biological samples that contain 3d metals.

Oxygen Activation by Cu LPMOs in Recalcitrant Carbohydrate Polysaccharide Conversion to Monomer Sugars

Natural carbohydrate polymers such as starch, cellulose, and chitin provide renewable alternatives to fossil fuels as a source for fuels and materials. As such, there is considerable interest in their conversion for industrial purposes, which is evidenced by the established and emerging markets for products derived from these natural polymers. In many cases, this is achieved via industrial processes that use enzymes to break down carbohydrates to monomer sugars. One of the major challenges facing large-scale industrial applications utilizing natural carbohydrate polymers is rooted in the fact that naturally occurring forms of starch, cellulose, and chitin can have tightly packed organizations of polymer chains with low hydration levels, giving rise to crystalline structures that are highly recalcitrant to enzymatic degradation. The topic of this review is oxidative cleavage of carbohydrate polymers by lytic polysaccharide mono-oxygenases (LPMOs). LPMOs are copper-dependent enzymes (EC 1.14.99.53-56) that, with glycoside hydrolases, participate in the degradation of recalcitrant carbohydrate polymers. Their activity and structural underpinnings provide insights into biological mechanisms of polysaccharide degradation.

Theoretical Investigation of the Electronic Properties of Three Vanadium Phthalocyaninato (Pc) Based Complexes: PcV, PcVO, and PcVI

The electronic properties of three vanadium phthalocyaninato (Pc) based complexes (PcV, PcVO, and PcVI; I-III, respectively) were theoretically investigated and corresponding ^VL_2,3-edge XAS spectra modeled. Ground state (GS) DFT outcomes indicated that II is more stable than III by 141 kcal/mol; moreover, the Ziegler transition state method allowed us to estimate the PcV-X bond dissociation energy and to quantify σ/π contributions to the V-X interaction. As such, the Nalewajski-Mrozek V-X and V-N bond multiplicity indexes (V-O/V-I = 2.48/1.22; V-N = 0.64, 0.51, and 0.58 in I-III, respectively) state that the V-X bond strength and nature affect the V-N interaction. The coordination of X to V in the I → II/I → III reactions implies the transfer of two/one electrons from I to X. In both cases, the oxidation involves only the V ion; moreover, V 3d based orbitals from which electrons are transferred were identified. Literature ^I/IIL_2,3-edge XAS data were modeled by exploiting the DFT/ROCIS method. The same protocol was adopted to predict ^IIIL_2,3-edge XAS spectra. Theoretical results indicated that, along the whole series, spectral features lying at the lowest excitation energies (EEs) are mostly generated by states having the same GS spin multiplicity and involve 2p^V → SOMO (single occupied molecular orbital) single electronic excitations. XAS features at higher EEs include only states with the same GS spin multiplicity in I, while states with both ΔS = 0 and ΔS = +1 (S = total spin quantum number) are present in II and III with significant, in some cases prevailing, contributions from metal to ligand charge transfer (MLCT) excitations. Beyond the role played by MLCT transitions in determining XAS patterns, it is noteworthy that they involve only Pc-based empty orbitals with no participation of the X-based virtual levels.

Walking the seven lines: binuclear copper A in cytochrome c oxidase and nitrous oxide reductase

The enzymes nitrous oxide reductase (N2OR) and cytochrome c oxidase (COX) are constituents of important biological processes. N2OR is the terminal reductase in a respiratory chain converting N₂O to N₂ in denitrifying bacteria; COX is the terminal oxidase of the aerobic respiratory chain of certain bacteria and eukaryotic organisms transforming O₂ to H₂O accompanied by proton pumping. Different spectroscopies including magnetic resonance techniques, were applied to show that N2OR has a mixed-valent Cys-bridged [Cu^1.5+(CyS)₂Cu^1.5+] copper site, and that such a binuclear center, called CuA, does also exist in COX. A sequence motif shared between the CuA center of N2OR and the subunit II of COX raises the issue of a putative evolutionary relationship of the two enzymes. The suggestion of a binuclear CuA in COX, with one unpaired electron delocalized between two equivalent Cu nuclei, was difficult to accept originally, even though regarded as a clever solution to many experimental observations. This minireview in honor of Helmut Sigel traces several of the critical steps forward in understanding the nature of CuA in N2OR and COX, and discusses its unique electronic features to some extent including the contributions made by the development of methodology and the discovery of a novel multi-copper enzyme. Left: X-band (9.130 GHz) and C-band (4.530 GHz, 1st harmonic display of experimental spectrum) EPR spectra of bovine heart cytochrome c oxidase, recorded at 20K. Right: Ribbon presentation of the CuA domain in cytochrome c oxidase and nitrous oxide reductase.

[Cu6 (NGuaS)6 ]2+ and its oxidized and reduced derivatives: Confining electrons on a torus

The hexanuclear thioguanidine mixed-valent copper complex cation [Cu₆ (NGuaS)₆ ]⁺² (NGuaS = o-SC₆ H₄ NC(NMe₂ )₂ ) and its oxidized/reduced states are theoretically analyzed by means of density functional theory (DFT) (TPSSh + D3BJ/def2-TZV (p)). A detailed bonding analysis using overlap populations is performed. We find that a delocalized Cu-based ring orbital serves as an acceptor for donated S p electrons. The formed fully delocalized orbitals give rise to a confined electron cloud within the Cu₆ S₆ cage which becomes larger on reduction. The resulting strong electrostatic repulsion might prevent the fully reduced state. Experimental UV/Vis spectra are explained using time-dependent density functional theory (TD-DFT) and analyzed with a natural transition orbital analysis. The spectra are dominated by MLCTs within the Cu₆ S₆ core over a wide range but LMCTs are also found. The experimental redshift of the reduced low energy absorption band can be explained by the clustering of the frontier orbitals. © 2017 Wiley Periodicals, Inc.

Iron L2,3-Edge X-ray Absorption and X-ray Magnetic Circular Dichroism Studies of Molecular Iron Complexes with Relevance to the FeMoco and FeVco Active Sites of Nitrogenase

Herein, a systematic study of a series of molecular iron model complexes has been carried out using Fe L_2,3-edge X-ray absorption (XAS) and X-ray magnetic circular dichroism (XMCD) spectroscopies. This series spans iron complexes of increasing complexity, starting from ferric and ferrous tetrachlorides ([FeCl₄]^−/2–), to ferric and ferrous tetrathiolates ([Fe(SR)₄]^−/2–), to diferric and mixed-valent iron–sulfur complexes [Fe₂S₂R₄]^2–/3–. This test set of compounds is used to evaluate the sensitivity of both Fe L_2,3-edge XAS and XMCD spectroscopy to oxidation state and ligation changes. It is demonstrated that the energy shift and intensity of the L_2,3-edge XAS spectra depends on both the oxidation state and covalency of the system; however, the quantitative information that can be extracted from these data is limited. On the other hand, analysis of the Fe XMCD shows distinct changes in the intensity at both L₃ and L₂ edges, depending on the oxidation state of the system. It is also demonstrated that the XMCD intensity is modulated by the covalency of the system. For mononuclear systems, the experimental data are correlated with atomic multiplet calculations in order to provide insights into the experimental observations. Finally, XMCD is applied to the tetranuclear heterometal–iron–sulfur clusters [MFe₃S₄]^3+/2+ (M = Mo, V), which serve as structural analogues of the FeMoco and FeVco active sites of nitrogenase. It is demonstrated that the XMCD data can be utilized to obtain information on the oxidation state distribution in complex clusters that is not readily accessible for the Fe L_2,3-edge XAS data alone. The advantages of XMCD relative to standard K-edge and L_2,3-edge XAS are highlighted. This study provides an important foundation for future XMCD studies on complex (bio)inorganic systems.

A systematic Fe L_2,3-edge X-ray absorption (XAS) and X-ray magnetic circular dichroism (XMCD) study of iron tetrachlorides ([FeCl₄]^−/2−), iron tetrathiolates ([Fe(SR)₄]^−/2−), diferric and mixed-valent iron−sulfur dimers [Fe₂S₂R₄]^2−/3− and heterometal−iron−sulfur tetramers [MFe₃S₄]^3+/2+ (M = Mo, V) is reported. The changes in XAS and XMCD energies and intensities across this set of complexes are presented together with atomic multiplet calculations. The advantages of XMCD as an electronic structure probe of complex clusters are highlighted.

K- and L-edge X-ray Absorption Spectroscopy (XAS) and Resonant Inelastic X-ray Scattering (RIXS) Determination of Differential Orbital Covalency (DOC) of Transition Metal Sites

Continual advancements in the development of synchrotron radiation sources have resulted in X-ray based spectroscopic techniques capable of probing the electronic and structural properties of numerous systems. This review gives an overview of the application of metal K-edge and L-edge X-ray absorption spectroscopy (XAS), as well as K resonant inelastic X-ray scattering (RIXS), to the study of electronic structure in transition metal sites with emphasis on experimentally quantifying 3d orbital covalency. The specific sensitivities of K-edge XAS, L-edge XAS, and RIXS are discussed emphasizing the complementary nature of the methods. L-edge XAS and RIXS are sensitive to mixing between 3d orbitals and ligand valence orbitals, and to the differential orbital covalency (DOC), that is, the difference in the covalencies for different symmetry sets of the d orbitals. Both L-edge XAS and RIXS are highly sensitive to and enable separation of and donor bonding and back bonding contributions to bonding. Applying ligand field multiplet simulations, including charge transfer via valence bond configuration interactions, DOC can be obtained for direct comparison with density functional theory calculations and to understand chemical trends. The application of RIXS as a probe of frontier molecular orbitals in a heme enzyme demonstrates the potential of this method for the study of metal sites in highly covalent coordination sites in bioinorganic chemistry.

Spin-Polarization-Induced Preedge Transitions in the Sulfur K-Edge XAS Spectra of Open-Shell Transition-Metal Sulfates: Spectroscopic Validation of σ-Bond Electron Transfer

Sulfur K-edge X-ray absorption spectroscopy (XAS) spectra of the monodentate sulfate complexes [MII(itao)(SO4)(H2O)0,1] (M = Co, Ni, Cu) and [Cu(Me6tren)(SO4)] exhibit well-defined preedge transitions at 2479.4, 2479.9, 2478.4, and 2477.7 eV, respectively, despite having no direct metal-sulfur bond, while the XAS preedge of [Zn(itao)(SO4)] is featureless. The sulfur K-edge XAS of [Cu(itao)(SO4)] but not of [Cu(Me6tren)(SO4)] uniquely exhibits a weak transition at 2472.1 eV, an extraordinary 8.7 eV below the first inflection of the rising K-edge. Preedge transitions also appear in the sulfur K-edge XAS of crystalline [MII(SO4)(H2O)] (M = Fe, Co, Ni, and Cu, but not Zn) and in sulfates of higher-valent early transition metals. Ground-state density functional theory (DFT) and time-dependent DFT (TDDFT) calculations show that charge transfer from coordinated sulfate to paramagnetic late transition metals produces spin polarization that differentially mixes the spin-up (α) and spin-down (β) spin orbitals of the sulfate ligand, inducing negative spin density at the sulfate sulfur. Ground-state DFT calculations show that sulfur 3p character then mixes into metal 4s and 4p valence orbitals and various combinations of ligand antibonding orbitals, producing measurable sulfur XAS transitions. TDDFT calculations confirm the presence of XAS preedge features 0.5-2 eV below the rising sulfur K-edge energy. The 2472.1 eV feature arises when orbitals at lower energy than the frontier occupied orbitals with S 3p character mix with the copper(II) electron hole. Transmission of spin polarization and thus of radical character through several bonds between the sulfur and electron hole provides a new mechanism for the counterintuitive appearance of preedge transitions in the XAS spectra of transition-metal oxoanion ligands in the absence of any direct metal-absorber bond. The 2472.1 eV transition is evidence for further radicalization from copper(II), which extends across a hydrogen-bond bridge between sulfate and the itao ligand and involves orbitals at energies below the frontier set. This electronic structure feature provides a direct spectroscopic confirmation of the through-bond electron-transfer mechanism of redox-active metalloproteins.

Optical response of the Cu2 S2 diamond core in Cu2II(NGuaS)2 Cl2

Density functional theory (DFT) and time-dependent DFT calculations are presented for the dicopper thiolate complex Cu2 (NGuaS)2 Cl2 [NGuaS=2-(1,1,3,3-tetramethylguanidino) benzenethiolate] with a special focus on the bonding mechanism of the Cu2 S2 Cl2 core and the spectroscopic response. This complex is relevant for the understanding of dicopper redox centers, for example, the CuA center. Its UV/Vis absorption is theoretically studied and found to be similar to other structural CuA models. The spectrum can be roughly divided in the known regions of metal d-d absorptions and metal to ligand charge transfer regions. Nevertheless the chloride ions play an important role as electron donors, with the thiolate groups as electron acceptors. The bonding mechanism is dissected by means of charge decomposition analysis which reveals the large covalency of the Cu2 S2 diamond core mediated between Cu dz2 and S-S π and π* orbitals forming Cu-S σ bonds. Measured resonant Raman spectra are shown for 360- and 720-nm excitation wavelength and interpreted using the calculated vibrational eigenmodes and frequencies. The calculations help to rationalize the varying resonant behavior at different optical excitations. Especially the phenylene rings are only resonant for 720 nm. © 2016 Wiley Periodicals, Inc.

Metal-interacted histidine dimer: an ETS-NOCV and XANES study

We have analyzed the metal coordination in a histidine dimer, hydrated with a water molecule, based on the extended transition state scheme with the theory of natural orbitals for chemical valence (ETS-NOCV).

Electronic structure of CuTPP and CuTPP(F) complexes: a combined experimental and theoretical study II

CuTPP and CuTPP(F) thick films deposited on Au(111) have been studied by coupling NEXAFS spectroscopy at the ^C/N/FK-edges and ^CuL_2,3-edges and spin-unrestricted TD-DFT calculations.

Anisotropic covalency contributions to superexchange pathways in type one copper active sites

Type one (T1) Cu sites deliver electrons to catalytic Cu active sites: the mononuclear type two (T2) Cu site in nitrite reductases (NiRs) and the trinuclear Cu cluster in the multicopper oxidases (MCOs). The T1 Cu and the remote catalytic sites are connected via a Cys-His intramolecular electron-transfer (ET) bridge, which contains two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the Cys and the His. The high covalency of the T1 Cu-S(Cys) bond is shown here to activate the T1 Cu site for hole superexchange via occupied valence orbitals of the bridge. This covalency-activated electronic coupling (H(DA)) facilitates long-range ET through both pathways. These pathways can be selectively activated depending on the geometric and electronic structure of the T1 Cu site and thus the anisotropic covalency of the T1 Cu-S(Cys) bond. In NiRs, blue (π-type) T1 sites utilize P1 and green (σ-type) T1 sites utilize P2, with P2 being more efficient. Comparing the MCOs to NiRs, the second-sphere environment changes the conformation of the Cys-His pathway, which selectively activates HDA for superexchange by blue π sites for efficient turnover in catalysis. These studies show that a given protein bridge, here Cys-His, provides different superexchange pathways and electronic couplings depending on the anisotropic covalencies of the donor and acceptor metal sites.

The role of protein dynamics and thermal fluctuations in regulating cytochrome c/cytochrome c oxidase electron transfer

In this overview we present recent combined electrochemical, spectroelectrochemical, spectroscopic and computational studies from our group on the electron transfer reactions of cytochrome c and of the primary electron acceptor of cytochrome c oxidase, the CuA site, in biomimetic complexes. Based on these results, we discuss how protein dynamics and thermal fluctuations may impact on protein ET reactions, comment on the possible physiological relevance of these results, and finally propose a regulatory mechanism that may operate in the Cyt/CcO electron transfer reaction in vivo. This article is part of a Special Issue entitled: 18th European Bioenergetic Conference.

L-edge X-ray absorption spectroscopy and DFT calculations on Cu2O2 species: direct electrophilic aromatic attack by side-on peroxo bridged dicopper(II) complexes

The hydroxylation of aromatic substrates catalyzed by coupled binuclear copper enzymes has been observed with side-on-peroxo-dicopper(II) (P) and bis-μ-oxo-dicopper(III) (O) model complexes. The substrate-bound-O intermediate in [Cu(II)2(DBED)2(O)2](2+) (DBED = N,N'-di-tert-butyl-ethylenediamine) was shown to perform aromatic hydroxylation. For the [Cu(II)2(NO2-XYL)(O2)](2+) complex, only a P species was spectroscopically observed. However, it was not clear whether this O-O bond cleaves to proceed through an O-type structure along the reaction coordinate for hydroxylation of the aromatic xylyl linker. Accurate evaluation of these reaction coordinates requires reasonable quantitative descriptions of the electronic structures of the P and O species. We have performed Cu L-edge XAS on two well-characterized P and O species to experimentally quantify the Cu 3d character in their ground state wave functions. The lower per-hole Cu character (40 ± 6%) corresponding to higher covalency in the O species compared to the P species (52 ± 4%) reflects a stronger bonding interaction of the bis-μ-oxo core with the Cu(III) centers. DFT calculations show that 10-20% Hartree-Fock (HF) mixing for P and ~38% for O species are required to reproduce the Cu-O bonding; for the P species this HF mixing is also required for an antiferromagnetically coupled description of the two Cu(II) centers. B3LYP (with 20% HF) was, therefore, used to calculate the hydroxylation reaction coordinate of P in [Cu(II)2(NO2-XYL)(O2)](2+). These experimentally calibrated calculations indicate that the electrophilic attack on the aromatic ring does not involve formation of a Cu(III)2(O(2-))2 species. Rather, there is direct electron donation from the aromatic ring into the peroxo σ* orbital of the Cu(II)2(O2(2-)) species, leading to concerted C-O bond formation with O-O bond cleavage. Thus, species P is capable of direct hydroxylation of aromatic substrates without the intermediacy of an O-type species.

Redox-state sensing by hydrogen bonds in the CuA center of cytochrome c oxidase

Cytochrome c oxidases (CcO) couple electron transfer to active proton translocation through a gated mechanism that minimizes energy losses by preventing protons from flowing backwards or leaking. Such a complex mechanism requires that information about the redox and protonation states of the different centers be transmitted between different parts of the oxidase. Here we report a network of residues located around the electron entry point of CcO, the CuA site in subunit II, that experience collective pH equilibria around neutral pH. This network starts at the occluded side of the CuA site and extends to the interface between subunits I and II of the CcO, where the proton exit is located and through which electrons flow into subunit I. One of the residues in this network is directly involved in a hydrogen bond to one of the CuA ligands, whose strength is highly sensitive to the redox state of the metal center. We propose that this interaction mediates the transmission of redox changes from ET centers to other functional regions of the oxidase, and possibly also in other similar machineries, as part of their gating and regulatory mechanisms.

Axial interactions in the mixed-valent CuA active site and role of the axial methionine in electron transfer

Within Cu-containing electron transfer active sites, the role of the axial ligand in type 1 sites is well defined, yet its role in the binuclear mixed-valent CuA sites is less clear. Recently, the mutation of the axial Met to Leu in a CuA site engineered into azurin (CuA Az) was found to have a limited effect on E(0) relative to this mutation in blue copper (BC). Detailed low-temperature absorption and magnetic circular dichroism, resonance Raman, and electron paramagnetic resonance studies on CuA Az (WT) and its M123X (X = Q, L, H) axial ligand variants indicated stronger axial ligation in M123L/H. Spectroscopically validated density functional theory calculations show that the smaller ΔE(0) is attributed to H2O coordination to the Cu center in the M123L mutant in CuA but not in the equivalent BC variant. The comparable stabilization energy of the oxidized over the reduced state in CuA and BC (CuA ∼ 180 mV; BC ∼ 250 mV) indicates that the S(Met) influences E(0) similarly in both. Electron delocalization over two Cu centers in CuA was found to minimize the Jahn-Teller distortion induced by the axial Met ligand and lower the inner-sphere reorganization energy. The Cu-S(Met) bond in oxidized CuA is weak (5.2 kcal/mol) but energetically similar to that of BC, which demonstrates that the protein matrix also serves an entatic role in keeping the Met bound to the active site to tune down E(0) while maintaining a low reorganization energy required for rapid electron transfer under physiological conditions.

Iron L-edge X-ray absorption spectroscopy of oxy-picket fence porphyrin: experimental insight into Fe-O2 bonding

The electronic structure of the Fe-O(2) center in oxy-hemoglobin and oxy-myoglobin is a long-standing issue in the field of bioinorganic chemistry. Spectroscopic studies have been complicated by the highly delocalized nature of the porphyrin, and calculations require interpretation of multideterminant wave functions for a highly covalent metal site. Here, iron L-edge X-ray absorption spectroscopy, interpreted using a valence bond configuration interaction multiplet model, is applied to directly probe the electronic structure of the iron in the biomimetic Fe-O(2) heme complex [Fe(pfp)(1-MeIm)O(2)] (pfp ("picket fence porphyrin") = meso-tetra(α,α,α,α-o-pivalamidophenyl)porphyrin or TpivPP). This method allows separate estimates of σ-donor, π-donor, and π-acceptor interactions through ligand-to-metal charge transfer and metal-to-ligand charge transfer mixing pathways. The L-edge spectrum of [Fe(pfp)(1-MeIm)O(2)] is further compared to those of [Fe(II)(pfp)(1-MeIm)(2)], [Fe(II)(pfp)], and [Fe(III)(tpp)(ImH)(2)]Cl (tpp = meso-tetraphenylporphyrin) which have Fe(II)S = 0, Fe(II)S = 1, and Fe(III)S = 1/2 ground states, respectively. These serve as references for the three possible contributions to the ground state of oxy-pfp. The Fe-O(2) pfp site is experimentally determined to have both significant σ-donation and a strong π-interaction of the O(2) with the iron, with the latter having implications with respect to the spin polarization of the ground state.

Electron transfer interactome of cytochrome C

Lying at the heart of many vital cellular processes such as photosynthesis and respiration, biological electron transfer (ET) is mediated by transient interactions among proteins that recognize multiple binding partners. Accurate description of the ET complexes – necessary for a comprehensive understanding of the cellular signaling and metabolism – is compounded by their short lifetimes and pronounced binding promiscuity. Here, we used a computational approach relying solely on the steric properties of the individual proteins to predict the ET properties of protein complexes constituting the functional interactome of the eukaryotic cytochrome c (Cc). Cc is a small, soluble, highly-conserved electron carrier protein that coordinates the electron flow among different redox partners. In eukaryotes, Cc is a key component of the mitochondrial respiratory chain, where it shuttles electrons between its reductase and oxidase, and an essential electron donor or acceptor in a number of other redox systems. Starting from the structures of individual proteins, we performed extensive conformational sampling of the ET-competent binding geometries, which allowed mapping out functional epitopes in the Cc complexes, estimating the upper limit of the ET rate in a given system, assessing ET properties of different binding stoichiometries, and gauging the effect of domain mobility on the intermolecular ET. The resulting picture of the Cc interactome 1) reveals that most ET-competent binding geometries are located in electrostatically favorable regions, 2) indicates that the ET can take place from more than one protein-protein orientation, and 3) suggests that protein dynamics within redox complexes, and not the electron tunneling event itself, is the rate-limiting step in the intermolecular ET. Further, we show that the functional epitope size correlates with the extent of dynamics in the Cc complexes and thus can be used as a diagnostic tool for protein mobility.

A number of vital cellular processes such as respiration, photosynthesis, and multifarious metabolic conversions rely on a long-range electron transfer (ET) among protein molecules. Full understanding of the biological ET requires accurate description of the redox protein complexes, which is hampered by their pronounced mobility and short lifetimes. Here we used a simple computational approach to predict the ET properties of the physiological protein complexes of cytochrome c (Cc) – a small electron carrier that coordinates the electron flow among different redox partners. By performing extensive conformational sampling of the possible binding geometries, we mapped out functional epitopes in the Cc complexes and assessed their ET properties. Our study suggests that protein dynamics within redox complexes is the rate-limiting step in the intermolecular ET and indicates that the functional epitope size correlates with the extent of dynamics in the Cc complexes. We believe that the latter finding can be used as a diagnostic tool for protein mobility and expect that this work will engender future studies of the intermolecular ET in biological networks.

Alternative ground states enable pathway switching in biological electron transfer

Electron transfer is the simplest chemical reaction and constitutes the basis of a large variety of biological processes, such as photosynthesis and cellular respiration. Nature has evolved specific proteins and cofactors for these functions. The mechanisms optimizing biological electron transfer have been matter of intense debate, such as the role of the protein milieu between donor and acceptor sites. Here we propose a mechanism regulating long-range electron transfer in proteins. Specifically, we report a spectroscopic, electrochemical, and theoretical study on WT and single-mutant Cu(A) redox centers from Thermus thermophilus, which shows that thermal fluctuations may populate two alternative ground-state electronic wave functions optimized for electron entry and exit, respectively, through two different and nearly perpendicular pathways. These findings suggest a unique role for alternative or "invisible" electronic ground states in directional electron transfer. Moreover, it is shown that this energy gap and, therefore, the equilibrium between ground states can be fine-tuned by minor perturbations, suggesting alternative ways through which protein-protein interactions and membrane potential may optimize and regulate electron-proton energy transduction.

Spectroscopic and DFT studies of second-sphere variants of the type 1 copper site in azurin: covalent and nonlocal electrostatic contributions to reduction potentials

The reduction potentials (E(0)) of type 1 (T1) or blue copper (BC) sites in proteins and enzymes with identical first coordination spheres around the redox active copper ion can vary by ~400 mV. Here, we use a combination of low-temperature electronic absorption and magnetic circular dichroism, electron paramagnetic resonance, resonance Raman, and S K-edge X-ray absorption spectroscopies to investigate a series of second-sphere variants--F114P, N47S, and F114N in Pseudomonas aeruginosa azurin--which modulate hydrogen bonding to and protein-derived dipoles nearby the Cu-S(Cys) bond. Density functional theory calculations correlated to the experimental data allow for the fractionation of the contributions to tuning E(0) into covalent and nonlocal electrostatic components. These are found to be significant, comparable in magnitude, and additive for active H-bonds, while passive H-bonds are mostly nonlocal electrostatic in nature. For dipoles, these terms can be additive to or oppose one another. This study provides a methodology for uncoupling covalency from nonlocal electrostatics, which, when coupled to X-ray crystallographic data, distinguishes specific local interactions from more long-range protein/active interactions, while affording further insight into the second-sphere mechanisms available to the protein to tune the E(0) of electron-transfer sites in biology.

Stable Cu(II) and Cu(I) mononuclear intermediates in the assembly of the CuA center of Thermus thermophilus cytochrome oxidase

CuA is a dinuclear mixed-valence center located in subunit 2 of the ba(3)-type cytochrome oxidase from Thermus thermophilus. The assembly of this site within the periplasmic membrane is believed to be mediated by the copper chaperones Sco and/or PCuAC, but the biological mechanisms are still poorly understood, thereby stimulating interest in the mechanisms of CuA formation from inorganic ions. The formulation of the CuA center as an electron-delocalized Cu(1.5)-Cu(1.5) system implicates both Cu(II) and Cu(I) states in the metalation process. In earlier work we showed that selenomethionine (SeM) substitution of the coordinated M160 residue provided a ligand-directed probe for studying the copper coordination environment via the Se XAS signal, which was particularly useful for interrogating the Cu(I) states where other spectroscopic probes are absent. In the present study we have investigated the formation of mixed-valence CuA and its M160SeM derivative by stopped-flow UV-vis, EPR, and XAS at both Cu and Se edges, while the formation of fully reduced di-Cu(I) CuA has been studied by XAS alone. Our results establish the presence of previously undetected mononuclear intermediates and show important differences from the metalation reactions of purple CuA azurin. XAS spectroscopy at Cu and Se edges has allowed us to extend mechanistic inferences to formation of the di-Cu(I) state which may be more relevant to biological CuA assembly. In particular, we find that T. thermophilus CuA assembles more rapidly than reported for other CuA systems and that the dominant intermediate along the pathway to mixed-valence is a new green species with λ(max) = 460 nm. This intermediate has been isolated in a homogeneous state and shown to be a mononuclear Cu(II)-(His)(Cys)(2) species with no observable Cu(II)-(Met) interaction. Reduction with dithionite generates its Cu(I) homologue which is again mononuclear but now shows a strong interaction with the Met160 thioether. The results are discussed within the framework of the "coupled distortion" model for Cu(II) thiolates and their relevance to biological metalation reactions of the CuA center.

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.