Direct determination of the complete set of iron normal modes in a porphyrin-imidazole model for carbonmonoxy-heme proteins: [Fe(TPP)(CO)(1-MeIm)

Detailed Fe vibrational spectra have been obtained for the heme model complex [Fe(TPP)(CO)(1-MeIm)] using a new, highly selective and quantitative technique, Nuclear Resonance Vibrational Spectroscopy (NRVS). This spectroscopy measures the complete vibrational density of states for iron atoms, from which normal modes can be calculated via refinement of the force constants. These data and mode assignments can reveal previously undetected vibrations and are useful for validating predictions based on optical spectroscopies and density functional theory, for example. Vibrational modes of the iron porphyrin-imidazole compound [Fe(TPP)(CO)(1-MeIm)] have been determined by refining normal mode calculations to NRVS data obtained at an X-ray synchrotron source. Iron dynamics of this compound, which serves as a useful model for the active site in the six-coordinate heme protein, carbonmonoxy-myoglobin, are discussed in relation to recently determined dynamics of a five-coordinate deoxy-myoglobin model, [Fe(TPP)(2-MeHIm)]. For the first time in a six-coordinate heme system, the iron-imidazole stretch mode has been observed, at 226 cm(-)(1). The heme in-plane modes with large contributions from the nu(42), nu(49), nu(50), and nu(53) modes of the core porphyrin are identified. In general, the iron modes can be attributed to coupling with the porphyrin core, the CO ligand, the imidazole ring, and/or the phenyl rings. Other significant findings are the observation that the porphyrin ring peripheral substituents are strongly coupled to the iron doming mode and that the Fe-C-O tilting and bending modes are related by a negative interaction force constant.     

Intermolecular dynamics in crystalline iron octaethylporphyrin (FeOEP)

The new technique of nuclear resonance vibrational spectroscopy (NRVS) has increased the range and quality of dynamical data from Fe-containing molecules that when combined with Raman and infrared spectroscopies impose stricter constraints on normal mode simulations, especially at lower frequencies. Going beyond the usual single molecule approximation, a classical normal-mode analysis that includes intermolecular coupling and the full crystalline symmetry is found to produce a better fit with fewer free parameters for the heme compound iron octaethylporphyrin (FeOEP), using NRVS data from polycrystalline material. Off-diagonal force constants were completely unnecessary, indicating that their role in previous single molecule fits was just to emulate intermolecular coupling. Sound velocities deduced from the calculated phonon dispersion curves are compared to NRVS measurements to further constrain the intermolecular force constants. The NRVS data by themselves are insufficient to rigorously determine all unknown force constants for molecules of this size, but the improved crystal model fit indicates the necessity of including intermolecular interactions for normal-mode analyses.     

Normal-mode analysis of FeCl4- and Fe2S2Cl42- via vibrational mössbauer, resonance Raman, and FT-IR spectroscopies

[NEt(4)][FeCl(4)], [P(C(6)H(5))(4)][FeCl(4)], and [NEt(4)](2)[Fe(2)S(2)Cl(4)] have been examined using (57)Fe nuclear resonance vibrational spectroscopy (NRVS). These complexes serve as simple models for Fe-S clusters in metalloproteins. The (57)Fe partial vibrational density of states (PVDOS) spectra were interpreted by computation of the normal modes assuming Urey-Bradley force fields, using additional information from infrared and Raman spectra. Previously published force constants were used as initial values; the new constraints from NRVS frequencies and amplitudes were then used to refine the force field parameters in a nonlinear least-squares analysis. The normal-mode calculations were able to quantitatively reproduce both the frequencies and the amplitudes of the intramolecular-mode (57)Fe PVDOS. The optimized force constants for bending, stretching, and nonbonded interactions agree well with previously reported values. In addition, the NRVS technique also allowed clear observation of anion-cation lattice modes below 100 cm(-1) that are nontrivial to observe by conventional spectroscopies. These features were successfully reproduced, either by assuming whole-body motions of point-mass anions and cations or by simulations using all of the atoms in the unit cell. The advantages of a combined NRVS, Raman, and IR approach to characterization of Fe-S complexes are discussed.     

Dynamics of an [Fe4S4(SPh)4]2- cluster explored via IR, Raman, and nuclear resonance vibrational spectroscopy (NRVS)-analysis using 36S substitution, DFT calculations, and empirical force fields

We have used four vibrational spectroscopies--FT-IR, FT-Raman, resonance Raman, and 57Fe nuclear resonance vibrational spectroscopy (NRVS)--to study the normal modes of the Fe-S cluster in [(n-Bu)4N]2[Fe4S4(SPh)4]. This [Fe4S4(SR)4]2- complex serves as a model for the clusters in 4Fe ferredoxins and high-potential iron proteins (HiPIPs). The IR spectra exhibited differences above and below the 243 K phase transition. Significant shifts with 36S substitution into the bridging S positions were also observed. The NRVS results were in good agreement with the low temperature data from the conventional spectroscopies.The NRVS spectra were interpreted by normal mode analysis using optimized Urey-Bradley force fields (UBFF) as well as from DFT theory. For the UBFF calculations, the parameters were refined by comparing calculated and observed NRVS frequencies and intensities. The frequency shifts after 36S substitution were used as an additional constraint. A D 2d symmetry Fe4S4S'4 model could explain most of the observed frequencies, but a better match to the observed intensities was obtained when the ligand aromatic rings were included for a D 2d Fe4S4(SPh)4 model. The best results were obtained using the low temperature structure without symmetry constraints. In addition to stretching and bending vibrations, low frequency modes between approximately 50 and 100 cm(-1) were observed. These modes, which have not been seen before, are interpreted as twisting motions with opposing sides of the cube rotating in opposite directions. In contrast with a recent paper on a related Fe4S4 cluster, we find no need to assign a large fraction of the low frequency NRVS intensity to 'rotational lattice modes'. We also reassign the 430 cm(-1) band as primarily an elongation of the thiophenolate ring, with approximately 10% terminal Fe-S stretch character. This study illustrates the benefits of combining NRVS with conventional Raman and IR analysis for characterization of Fe-S centers. DFT theory is shown to provide remarkable agreement with the experimental NRVS data. These results provide a reference point for the analysis of more complex Fe-S clusters in proteins.     

Fe vibrational spectroscopy of myoglobin and cytochrome f

The Fe vibrational density of states (VDOS) has been determined for the heme proteins deoxymyoglobin, metmyoglobin, and cytochrome f in the oxidized and reduced states, using nuclear resonance vibrational spectroscopy (NRVS). For cytochrome f in particular, the NRVS spectrum is compared with multiwavelength resonance Raman spectra to identify those Raman modes with significant Fe displacement. Modes not seen by Raman due to optical selection rules appear in the NRVS spectrum. The mean Fe force constant extracted from the VDOS illustrates how Fe dynamics varies among these four monoheme proteins, and is correlated with oxidation and spin state trends seen in model heme compounds. The protein's contribution to Fe motion is dominant at low frequencies, where coupling to the backbone tightly constrains Fe displacements in cytochrome f, in contrast to enhanced heme flexibility in myoglobin.     

Characterization of the Fe site in iron-sulfur cluster-free hydrogenase (Hmd) and of a model compound via nuclear resonance vibrational spectroscopy (NRVS)

We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron site in the iron-sulfur cluster-free hydrogenase Hmd from the methanogenic archaeon Methanothermobacter marburgensis. The spectra have been interpreted by comparison with a cis-(CO)2-ligated Fe model compound, Fe(S2C2H4)(CO)2(PMe3)2, as well as by normal mode simulations of plausible active site structures. For this model complex, normal mode analyses both from an optimized Urey-Bradley force field and from complementary density functional theory (DFT) calculations produced consistent results. For Hmd, previous IR spectroscopic studies found strong CO stretching modes at 1944 and 2011 cm(-1), interpreted as evidence for cis-Fe(CO)2 ligation. The NRVS data provide further insight into the dynamics of the Fe site, revealing Fe-CO stretch and Fe-CO bend modes at 494, 562, 590, and 648 cm(-1), consistent with the proposed cis-Fe(CO)2 ligation. The NRVS also reveals a band assigned to Fe-S stretching motion at approximately 311 cm(-1) and another reproducible feature at approximately 380 cm(-1). The (57)Fe partial vibrational densities of states (PVDOS) for Hmd can be reasonably well simulated by a normal mode analysis based on a Urey-Bradley force field for a five-coordinate cis-(CO)2-ligated Fe site with additional cysteine, water, and pyridone cofactor ligands. A "truncated" model without a water ligand can also be used to match the NRVS data. A final interpretation of the Hmd NRVS data, including DFT analysis, awaits a three-dimensional structure for the active site.     

Normal mode analysis of Pyrococcus furiosus rubredoxin via nuclear resonance vibrational spectroscopy (NRVS) and resonance raman spectroscopy

We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe(S(cys))(4) site in reduced and oxidized rubredoxin (Rd) from Pyrococcus furiosus (Pf). The oxidized form has also been investigated by resonance Raman spectroscopy. In the oxidized Rd NRVS, strong asymmetric Fe-S stretching modes are observed between 355 and 375 cm(-1); upon reduction these modes shift to 300-320 cm(-1). This is the first observation of Fe-S stretching modes in a reduced Rd. The peak in S-Fe-S bend mode intensity is at approximately 150 cm(-1) for the oxidized protein and only slightly lower in the reduced case. A third band occurs near 70 cm(-1) for both samples; this is assigned primarily as a collective motion of entire cysteine residues with respect to the central Fe. The (57)Fe partial vibrational density of states (PVDOS) were interpreted by normal mode analysis with optimization of Urey-Bradley force fields. The three main bands were qualitatively reproduced using a D(2)(d) Fe(SC)(4) model. A C(1) Fe(SCC)(4) model based on crystallographic coordinates was then used to simulate the splitting of the asymmetric stretching band into at least 3 components. Finally, a model employing complete cysteines and 2 additional neighboring atoms was used to reproduce the detailed structure of the PVDOS in the Fe-S stretch region. These results confirm the delocalization of the dynamic properties of the redox-active Fe site. Depending on the molecular model employed, the force constant K(Fe-S) for Fe-S stretching modes ranged from 1.24 to 1.32 mdyn/A. K(Fe-S) is clearly diminished in reduced Rd; values from approximately 0.89 to 1.00 mdyn/A were derived from different models. In contrast, in the final models the force constants for S-Fe-S bending motion, H(S-Fe-S), were 0.18 mdyn/A for oxidized Rd and 0.15 mdyn/A for reduced Rd. The NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.     

Symmetry properties of vibrational modes in mesoporphyrin IX dimethyl ester investigated by polarization-sensitive resonance Raman and CARS spectroscopy

The symmetry properties of selected vibrational modes of mesoporphyrin IX dimethyl ester (MP-IX-DME) in solution are investigated under different electronic resonance conditions. The Raman band parameters of the macrocycle modes nu(2), nu(10), nu(11), and nu(19) are determined from a quantitative analysis of polarized spontaneous resonance Raman (RR) and polarization-sensitive (PS) multiplex coherent anti-Stokes Raman scattering (CARS) spectra obtained with pre-resonant B band and resonant Qx band excitation, respectively. Additionally, the molecular geometry and the vibrational modes of MP-IX-DME are calculated by employing density functional theory (DFT) on the B3LYP/6-31G(d) level. Both the DFT-derived structure and the Raman spectroscopic parameters of MP-IX-DME indicate minor deviations from an ideal D2h macrocycle symmetry. To assess the influence of the beta substitution pattern on the in-plane symmetry, calculated normal-mode vectors and several experimentally detected parameters, such as peak positions, depolarization ratios, and coherent phases, are analyzed. The effects of the macrocycle substitution pattern are different for the selected vibrational modes: nu(2) in particular is very sensitive to subtle perturbations of the in-plane symmetry. The considerable activity of totally symmetric vibrations observed in the PS CARS spectra of MP-IX-DME and the correlation of mode symmetries with coherent phases confirm earlier PS CARS results on octaethylporphine (OEP) acquired under the same electronic resonance conditions.     

High‐Frequency Fe–H Vibrations in a Bridging Hydride Complex Characterized by NRVS and DFT

High‐spin iron species with bridging hydrides have been detected in species trapped during nitrogenase catalysis, but there are few general methods of evaluating Fe?H bonds in high‐spin multinuclear iron systems. An ⁵⁷Fe nuclear resonance vibrational spectroscopy (NRVS) study on an Fe(μ‐H)₂Fe model complex reveals Fe?H stretching vibrations for bridging hydrides at frequencies greater than 1200 cm^?1. These isotope‐sensitive vibrational bands are not evident in infrared (IR) spectra, showing the power of NRVS for identifying hydrides in this high‐spin iron system. Complementary density functional theory (DFT) calculations elucidate the normal modes of the rhomboidal iron hydride core.     

Quantitative vibrational dynamics of iron in nitrosyl porphyrins

We use quantitative experimental and theoretical approaches to characterize the vibrational dynamics of the Fe atom in porphyrins designed to model heme protein active sites. Nuclear resonance vibrational spectroscopy (NRVS) yields frequencies, amplitudes, and directions for 57Fe vibrations in a series of ferrous nitrosyl porphyrins, which provide a benchmark for evaluation of quantum chemical vibrational calculations. Detailed normal mode predictions result from DFT calculations on ferrous nitrosyl tetraphenylporphyrin Fe(TPP)(NO), its cation [Fe(TPP)(NO)]+, and ferrous nitrosyl porphine Fe(P)(NO). Differing functionals lead to significant variability in the predicted Fe-NO bond length and frequency for Fe(TPP)(NO). Otherwise, quantitative comparison of calculated and measured Fe dynamics on an absolute scale reveals good overall agreement, suggesting that DFT calculations provide a reliable guide to the character of observed Fe vibrational modes. These include a series of modes involving Fe motion in the plane of the porphyrin, which are rarely identified using infrared and Raman spectroscopies. The NO binding geometry breaks the four-fold symmetry of the Fe environment, and the resulting frequency splittings of the in-plane modes predicted for Fe(TPP)(NO) agree with observations. In contrast to expectations of a simple three-body model, mode energy remains localized on the FeNO fragment for only two modes, an N-O stretch and a mode with mixed Fe-NO stretch and FeNO bend character. Bending of the FeNO unit also contributes to several of the in-plane modes, but no primary FeNO bending mode is identified for Fe(TPP)(NO). Vibrations associated with hindered rotation of the NO and heme doming are predicted at low frequencies, where Fe motion perpendicular to the heme is identified experimentally at 73 and 128 cm-1. Identification of the latter two modes is a crucial first step toward quantifying the reactive energetics of Fe porphyrins and heme proteins.     

Quantum chemistry-based analysis of the vibrational spectra of five-coordinate metalloporphyrins [M(TPP)Cl

Vibrational properties of the five-coordinate porphyrin complexes [M(TPP)(Cl)] (M = Fe, Mn, Co) are analyzed in detail. For [Fe(TPP)(Cl)] (1), a complete vibrational data set is obtained, including nonresonance (NR) Raman, and resonance Raman (RR) spectra at multiple excitation wavelengths as well as IR spectra. These data are completely assigned using density functional (DFT) calculations and polarization measurements. Compared to earlier works, a number of bands are reassigned in this one. These include the important, structure-sensitive band at 390 cm(-1), which is reassigned here to the totally symmetric nu(breathing)(Fe-N) vibration for complex 1. This is in agreement with the assignments for [Ni(TPP)]. In general, the assignments are on the basis of an idealized [M(TPP)]+ core with D(4h) symmetry. In this Work, small deviations from D(4h) are observed in the vibrational spectra and analyzed in detail. On the basis of the assignments of the vibrational spectra of 1, [Mn(TPP)(Cl)] (2), and diamagnetic [Co(TPP)(Cl)] (3), eight metal-sensitive bands are identified. Two of them correspond to the nu(M-N) stretching modes with B(1g) and Eu symmetries and are assigned here for the first time. The shifts of the metal sensitive modes are interpreted on the basis of differences in the porphyrin C-C, C-N, and M-N distances. Besides the porphyrin core vibrations, the M-Cl stretching modes also show strong metal sensitivity. The strength of the M-Cl bond in 1-3 is further investigated. From normal coordinate analysis (NCA), force constants of 1.796 (Fe), 0.932 (Mn), and 1.717 (Co) mdyn/A are obtained for 1-3, respectively. The weakness of the Mn-Cl bond is attributed to the fact that it only corresponds to half a sigma bond. Finally, RR spectroscopy is used to gain detailed insight into the nature of the electronically excited states. This relates to the mechanism of resonance enhancement and the actual nature of the enhanced vibrations. It is of importance that anomalous polarized bands (A(2g) vibrations), which are diagnostic for vibronic mixing, are especially useful for this purpose.     

Single-atom test of all-atom empirical potentials: Fe in myoglobin

The measured Fe vibrational density of states in deoxy-myoglobin, obtained from nuclear resonance vibrational spectroscopy, is compared to results from a normal-mode analysis using an all-atom empirical potential. Substantial disagreement reveals that for this one atom, the empirical potential does not accurately describe the actual forces. A Green function technique is developed to calculate the iron vibrational spectrum of deoxy-myoglobin by coupling the independently calculated heme and globin normal modes; nonbonded interactions between the heme molecule and the protein are essential for a good fit to the measurements. A projection of the eigenvectors from this potential onto the displacements induced by binding of CO demonstrates that normal modes over a broad range centered around 50-150 cm(-1) may drive the ligand-induced structural changes.     

3D Motions of Iron in Six‐Coordinate {FeNO}7 Hemes by Nuclear Resonance Vibration Spectroscopy

The vibrational spectrum of a six‐coordinate nitrosyl iron porphyrinate, monoclinic [Fe(TpFPP)(1‐MeIm)(NO)] (TpFPP=tetra‐para‐fluorophenylporphyrin; 1‐MeIm=1‐methylimidazole), has been studied by oriented single‐crystal nuclear resonance vibrational spectroscopy (NRVS). The crystal was oriented to give spectra perpendicular to the porphyrin plane and two in‐plane spectra perpendicular or parallel to the projection of the FeNO plane. These enable assignment of the FeNO bending and stretching modes. The measurements reveal that the two in‐plane spectra have substantial differences that result from the strongly bonded axial NO ligand. The direction of the in‐plane iron motion is found to be largely parallel and perpendicular to the projection of the bent FeNO on the porphyrin plane. The out‐of‐plane Fe‐N‐O stretching and bending modes are strongly mixed with each other, as well as with porphyrin ligand modes. The stretch is mixed with v₅₀ as was also observed for dioxygen complexes. The frequency of the assigned stretching mode of eight Fe‐X‐O (X=N, C, and O) complexes is correlated with the Fe?XO bond lengths. The nature of highest frequency band at ≈560 cm^?1 has also been examined in two additional new derivatives. Previously assigned as the Fe?NO stretch (by resonance Raman), it is better described as the bend, as the motion of the central nitrogen atom of the FeNO group is very large. There is significant mixing of this mode. The results emphasize the importance of mode mixing; the extent of mixing must be related to the peripheral phenyl substituents.     

Theoretical analysis of the terahertz spectrum of the high explosive PETN.

The experimental solid-state terahertz (THz) spectrum (3 to 120 cm(-1)) of the high explosive pentaerythritol tetranitrate (PETN, C(5)H(6)N(4)O(12)) has been modeled using solid-state density functional theory (DFT) calculations. Solid-state DFT, employing the BP density functional, is in best qualitative agreement with the features in the previously reported THz spectrum. The crystal environment of PETN includes numerous intermolecular hydrogen-bonding interactions that contribute to large (up to 80 cm(-1)) calculated shifts in molecular normal-mode positions in the solid state. Comparison of the isolated-molecule and solid-state normal-mode calculations for a series of density functionals reveals the extent to which the inclusion of crystal-packing interactions and the relative motions between molecules are required for correctly reproducing the vibrational structure of solid-state THz spectra. The THz structure below 120 cm(-1) is a combination of both intermolecular (relative rotations and translations) and intramolecular (torsions, large amplitude motions) vibrational motions. Vibrational-mode analyses indicate that the first major feature (67.2 cm(-1)) in the PETN THz spectrum contains all of the optical rotational and translational cell modes and no internal (molecular) vibrational modes.     

Vibrational spectra of the trifluoromethylsulfinate anion and scaled quantum mechanical force fields for CF3SO2- and CF3SeO2-

The infrared and Raman spectra of KCF(3)SO(2) were obtained and the observed spectral features assigned to the expected normal modes of vibration. Besides, the vibrational properties of the CF(3)SO(2)(-) and CF(3)SeO(2)(-) related anions were studied by means of density functional theory (DFT) techniques. After obtaining the optimized geometrical parameters and conformations, the vibrational wavenumbers and the associated force constants were calculated. The original force fields in cartesian coordinates were transformed to local symmetry coordinates and subsequently scaled to reproduce the experimental wavenumbers. Some trends observed in the force constants of the studied species and of the related CF(3)SO(3)(-) anion could be explained by the differences in geometrical parameters.     

Direct probe of iron vibrations elucidates NO activation of heme proteins

We use nuclear resonance vibrational spectroscopy (NRVS) to identify the Fe-NO stretching frequency in the NO adduct of myoglobin (MbNO) and in the related six-coordinate porphyrin Fe(TPP)(1-MeIm)(NO). Frequency shifts observed in MbNO Raman spectra upon isotopic substitution of Fe or the nitrosyl nitrogen confirm and extend the NRVS results. In contrast with previous assignments, the Fe-NO frequency of these six-coordinate complexes lies 70-100 cm-1 lower than in the analogous five-coordinate nitrosyl complexes, indicating a significant weakening of the Fe-NO bond in the presence of a trans imidazole ligand. This result supports proposed mechanisms for NO activation of heme proteins and underscores the value of NRVS as a direct probe of metal reactivity in complex biomolecules.     

First-principles-based calculations of vibrational normal modes in polyatomic materials with translational symmetry: application to PETN molecular crystal

Numerical studies of vibrational energy transport and associated (non)linear infrared and Raman response in polyatomic materials require knowledge of the multidimensional vibrational potential-energy surface and the ability to perform normal-mode analysis on that potential. The presence of translational symmetry, as in crystals, leads to the observed dispersion of the unit cell normal modes and has to be accounted for in calculations of energy transfer rates and other spectroscopic quantities. Here we report on the implementation of a computational approach that combines the generalized supercell method and density functional theory electronic structure calculations to investigate the vibrational structure in translationally symmetric materials containing relatively large numbers of atoms in the unit cell (58 atoms in the present study). The method is applied to calculate the phonon and vibron dispersion relations and the vibrational density of states in pentaerythritol tetranitrate (PETN) molecular crystal which is an important energetic material. The results set the stage for future investigations of vibrational energy transport and associated nonlinear spectroscopic signatures in this class of materials.     

Extended X-ray absorption fine structure and nuclear resonance vibrational spectroscopy reveal that NifB-co, a FeMo-co precursor, comprises a 6Fe core with an interstitial light atom

NifB-co, an Fe-S cluster produced by the enzyme NifB, is an intermediate on the biosynthetic pathway to the iron molybdenum cofactor (FeMo-co) of nitrogenase. We have used Fe K-edge extended X-ray absorption fine structure (EXAFS) spectroscopy together with (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to probe the structure of NifB-co while bound to the NifX protein from Azotobacter vinelandii. The spectra have been interpreted in part by comparison with data for the completed FeMo-co attached to the NafY carrier protein: the NafY:FeMo-co complex. EXAFS analysis of the NifX:NifB-co complex yields an average Fe-S distance of 2.26 A and average Fe-Fe distances of 2.66 and 3.74 A. Search profile analyses reveal the presence of a single Fe-X (X = C, N, or O) interaction at 2.04 A, compared to a 2.00 A Fe-X interaction found in the NafY:FeMo-co EXAFS. This suggests that the interstitial light atom (X) proposed to be present in FeMo-co has already inserted at the NifB-co stage of biosynthesis. The NRVS exhibits strong bands from Fe-S stretching modes peaking around 270, 315, 385, and 408 cm(-1). Additional intensity at approximately 185-200 cm(-1) is interpreted as a set of cluster "breathing" modes similar to those seen for the FeMo-cofactor. The strength and location of these modes also suggest that the FeMo-co interstitial light atom seen in the crystal structure is already in place in NifB-co. Both the EXAFS and NRVS data for NifX:NifB-co are best simulated using a Fe 6S 9X trigonal prism structure analogous to the 6Fe core of FeMo-co, although a 7Fe structure made by capping one trigonal 3S terminus with Fe cannot be ruled out. The results are consistent with the conclusion that the interstitial light atom is already present at an early stage in FeMo-co biosynthesis prior to the incorporation of Mo and R-homocitrate.     

Applications of X-ray absorption spectroscopy to biologically relevant metal-based chemistry

Recent developments in the understanding of the biosynthesis of the active site of the nitrogenase enzyme, the structure of the iron centre of [Fe]-hydrogenase and the structure and biomimetic chemistry of the [FeFe] hydrogenase H-cluster as deduced by application of X-ray spectroscopy are reviewed. The techniques central to this work include X-ray absorption spectroscopy either in the form of extended X-ray absorption fine structure (EXAFS), X-ray absorption near-edge structure (XANES) and nuclear resonant vibrational spectroscopy (NRVS). Examples of the advances in the understanding of the chemistry of the system through integration of a range of spectroscopic and computational techniques with X-ray spectroscopy are highlighted. The critical role played by ab initio calculation of structural and spectroscopic properties of transition-metal compounds using density functional theory (DFT) is illustrated both by the calculation of nuclear resonance vibrational spectroscopy (NRVS) spectra and the structures and spectra of intermediates through the catalytic reactions of hydrogenase model compounds.