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.     

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 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.     

How nitrogenase shakes--initial information about P-cluster and FeMo-cofactor normal modes from nuclear resonance vibrational spectroscopy (NRVS)

Nitrogenase catalyzes a reaction critical for life, the reduction of N(2) to 2NH(3), yet we still know relatively little about its catalytic mechanism. We have used the synchrotron technique of (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the dynamics of the Fe-S clusters in this enzyme. The catalytic site FeMo-cofactor exhibits a strong signal near 190 cm(-)(1), where conventional Fe-S clusters have weak NRVS. This intensity is ascribed to cluster breathing modes whose frequency is raised by an interstitial atom. A variety of Fe-S stretching modes are also observed between 250 and 400 cm(-)(1). This work is the first spectroscopic information about the vibrational modes of the intact nitrogenase FeMo-cofactor and P-cluster.     

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.     

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.     

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.     

Anharmonic vibrational frequency shifts upon interaction of phenol+ with the open shell ligand O2. The performance of DFT methods versus MP2

Anharmonic vibrational frequency shifts of the phenol(+) O-H stretching mode upon complex formation with the open-shell ligand O(2) were computed at several DFT and MP2 levels of theory, with various basis sets, up to 6-311++G(2df,2pd). It was found that all DFT levels of theory significantly outperform the MP2 method with this respect. The best agreement with the experimental frequency shift for the hydrogen-bonded minimum on the potential energy surfaces was obtained with the HCTH/407 functional (-93.7 cm(-1) theoretical vs -86 cm(-1) experimental), which is a significant improvement over other, more standard DFT functionals (such as, e.g., B3LYP, PBE1PBE), which predict too large downshifts (-139.9 and -147.7 cm(-1), respectively). Good agreement with the experiment was also obtained with the mPW1B95 functional proposed by Truhlar et al. (-109.2 cm(-1)). We have attributed this trend due to the corrected long-range behavior of the HCTH/407 and mPW1B95 functionals, despite the fact that they have been designed primarily for other purposes. MP2 method, even with the largest basis set used, manages to reproduce only less than 50% of the experimentally detected frequency downshift for the hydrogen-bonded dimer. This was attributed to the much more significant spin contamination of the reference HF wave function (compared to DFT Kohn-Sham wave functions), which was found to be strongly dependent on the O-H stretching vibrational coordinate. All DFT levels of theory outperform MP2 in the case of computed anharmonic OH stretching frequency shifts upon ionization of the neutral phenol molecule as well. Besides the hydrogen-bonded minimum, DFT levels of theory also predict existence of two other minima, corresponding to stacked arrangement of the phenol(+) and O(2) subunits. mPW1B95 and PBE1PBE functionals predict a very slight blue shift of the phenol(+) O-H stretching mode in the case of stacked dimer with the nearly perpendicular orientation of oxygen molecule with respect to the phenolic ring, which is entirely of electrostatic origin, in agreement with the experimental observations of an additional band in the IR photodissociation spectra of phenol(+)-O(2) dimer [Patzer, A.; Knorke, H.; Langer, J.; Dopfer, O. Chem. Phys. Lett. 2008, 457, 298]. The structural features of the minima on the studied PESs were discussed in details as well, on the basis of NBO and AIM analyses.     

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.     

Synthesis, X-ray crystallographic characterization, and electronic structure studies of a di-azide iron(III) complex: implications for the azide adducts of iron(III) superoxide dismutase

We have synthesized and characterized, using X-ray crystallographic, spectroscopic, and computational techniques, a six-coordinate diazide Fe (3+) complex, LFe(N 3) 2 (where L is the tetradentate ligand 7-diisopropyl-1,4,7-triazacyclononane-1-acetic acid), that serves as a model of the azide adducts of Fe (3+) superoxide dismutase (Fe (3+)SOD). While previous spectroscopic studies revealed that two distinct azide-bound Fe (3+)SOD species can be obtained at cryogenic temperatures depending on protein and azide concentrations, the number of azide ligands coordinated to the Fe (3+) ion in each species has been the subject of some controversy. In the case of LFe(N 3) 2, the electronic absorption and magnetic circular dichroism spectra are dominated by two broad features centered at 21 500 cm (-1) (approximately 4000 M (-1) cm (-1)) and approximately 30 300 cm (-1) (approximately 7400 M (-1) cm (-1)) attributed to N3 (-) --> Fe (3+) charge transfer (CT) transitions. A normal coordinate analysis of resonance Raman (RR) data obtained for LFe(N 3) 2 indicates that the vibrational features at 363 and 403 cm (-1) correspond to the Fe-N 3 stretching modes (nu Fe-N3) associated with the two different azide ligands and yields Fe-N 3 force constants of 1.170 and 1.275 mdyne/A, respectively. RR excitation profile data obtained with laser excitation between 16,000 and 22,000 cm (-1) reveal that the nu Fe-N3 modes at 363 and 403 cm (-1) are preferentially enhanced upon excitation in resonance with the N 3 (-) --> Fe (3+) CT transitions at lower and higher energies, respectively. Consistent with this result, density functional theory electronic structure calculations predict a larger stabilization of the molecular orbitals of the more strongly bound azide due to increased sigma-symmetry orbital overlap with the Fe 3d orbitals, thus yielding higher N 3 (-) --> Fe (3+) CT transition energies. Comparison of our data obtained for LFe(N 3) 2 with those reported previously for the two azide adducts of Fe (3+)SOD provides compelling evidence that a single azide is coordinated to the Fe (3+) center in each protein species.     

Raman study of molecular dynamics of inorganic fluoroxidizers in nonaqueous solutions: part 4. Xenon tetrafluoride and xenon hexafluoride in hydrogen fluoride

Raman spectra of XeF4 and XeF6 in the nonaqueous HF solutions at various concentrations and vibrational spectra of the [XeF5]+ cation in the solid state and in the HF solutions over a wide range of vibrational frequencies have been studied. The assignments of the observed vibrational bands of the [XeF5]+ cation and XeF6-HF system has been made. A number of associates or solvates being formed as a result of the donor-acceptor interaction between Lewis base and Lewis acid has been shown to exist alongside with ionized monomeric and polymeric modifications of XeF6 in the HF solution such as ([XeF5]+ F-)n (n = 1, 2, 4). The contours of the nu1(A1g) band of XeF4 with frequency 552 cm(-1) and bands of stretching modes of ([XeF5]+ F-)n (n = 1, 2, 4) with frequency in the range of 600-670 cm(-1) are analysed. The correlation functions of the vibrational and rotational relaxation as well as the corresponding characteristic time for these processes have been calculated. A conclusion has been driven at that it is vibrational dephasing that makes the major contribution to the formation of ([XeF5]+ F)4 and ([XeF5]+ F-)2 band contours, while in the case of [XeF5]+ F- and XeF4 the contributions of vibrational dephasing and rotational relaxation nearly coincide.     

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.     

New members of a class of iron-thiolate-nitrosyl compounds: trinuclear iron-thiolate-nitrosyl complexes containing Fe(3)S(6) core

The neutral trinuclear iron-thiolate-nitrosyl, [(ON)Fe(mu-S,S-C(6)H(4))](3) (1), and its oxidation product, [(ON)Fe(mu-S,S-C(6)H(4))](3)[PF(6)] (2), were synthesized and characterized by IR, X-ray diffraction, X-ray absorption, electron paramagnetic resonance (EPR), and magnetic measurement. The five-coordinated, square pyramidal geometry around each iron atom in complex 1 remains intact when complex 1 is oxidized to yield complex 2. Magnetic measurements and EPR results show that there is only one unpaired electron in complex 1 (S(total) = 1/2) and no unpaired electron (S(total) = 0) in 2. The detailed geometric comparisons between complexes 1 and 2 provide understanding of the role that the unpaired electron plays in the chemical bonding of this trinuclear complex. Significant shortening of the Fe-Fe, Fe-N, and Fe-S distances around Fe(1) is observed when complex 1 is oxidized to 2. This result implicates that the removal of the unpaired electron does induce the strengthening of the Fe-Fe, Fe-N, and Fe-S bonds in the Fe(1) fragment. A significant shift of the nuNO stretching frequency from 1751 cm(-1) (1) to 1821, 1857 cm(-1) (2) (KBr) also indicates the strengthening of the N-O bonds in complex 2. The EPR, X-ray absorption, magnetic measurements, and molecular orbital calculations lead to the conclusion that the unpaired electron in complex 1 is mainly allocated in the Fe(1) fragment and is best described as {Fe(1)NO}7, so that the unpaired electron is delocalized between Fe and NO via d-pi* orbital interaction; some contributions from [Fe(2)NO] and [Fe(3)NO] as well as the thiolates associated with Fe (1) are also realized. According to MO calculations, the spin density of complex 1 is predominantly located at the Fe atoms with 0.60, -0.15, and 0.25 at Fe(1), Fe(2), and Fe(3), respectively.     

Ligand K-edge X-ray absorption spectroscopy and DFT calculations on [Fe3S4]0,+ clusters: delocalization, redox, and effect of the protein environment

Ligand K-edge XAS of an [Fe3S4]0 model complex is reported. The pre-edge can be resolved into contributions from the mu(2)S(sulfide), mu(3)S(sulfide), and S(thiolate) ligands. The average ligand-metal bond covalencies obtained from these pre-edges are further distributed between Fe(3+) and Fe(2.5+) components using DFT calculations. The bridging ligand covalency in the [Fe2S2]+ subsite of the [Fe3S4]0 cluster is found to be significantly lower than its value in a reduced [Fe2S2] cluster (38% vs 61%, respectively). This lowered bridging ligand covalency reduces the superexchange coupling parameter J relative to its value in a reduced [Fe2S2]+ site (-146 cm(-1) vs -360 cm(-1), respectively). This decrease in J, along with estimates of the double exchange parameter B and vibronic coupling parameter lambda2/k(-), leads to an S = 2 delocalized ground state in the [Fe3S4]0 cluster. The S K-edge XAS of the protein ferredoxin II (Fd II) from the D. gigas active site shows a decrease in covalency compared to the model complex, in the same oxidation state, which correlates with the number of H-bonding interactions to specific sulfur ligands present in the active site. The changes in ligand-metal bond covalencies upon redox compared with DFT calculations indicate that the redox reaction involves a two-electron change (one-electron ionization plus a spin change of a second electron) with significant electronic relaxation. The presence of the redox inactive Fe(3+) center is found to decrease the barrier of the redox process in the [Fe3S4] cluster due to its strong antiferromagnetic coupling with the redox active Fe2S2 subsite.     

Structural, electronic, and vibrational characterization of Fe-HNO porphyrinates by density functional theory

A recent report of the structural and vibrational properties of heme-bound HNO in myoglobin, MbHNO, revealed a long Fe-N(HNO) bond with the hydrogen atom bonded to the coordinated N atom. The Fe-N(H)-O moiety was reported to exhibit an unusually high Fe-N(HNO) stretching frequency relative to those of the corresponding [FeNO]6 and [FeNO]7 porphyrinates, despite the Fe-N(HNO) bond being longer than either of its Fe-N(NO) counterparts. Herein, we present results from density functional theory calculations of an active site model of MbHNO that support the previous assignment and clarify this seemingly contradictory result. The results are consistent with the experimental evidence for a ground-state Fe-N(H)-O structure having a long Fe-N(HNO) bond and a uniquely high nu(Fe)(-)(N(HNO)) frequency. This high frequency is the result of the correspondingly low reduced mass of the normal mode, which is largely attributable to significant motion of the N-bound hydrogen atom. Additionally, the calculations show the Fe-N(H)O bonding in this complex to be remarkably insensitive to whether the HNO and ImH ligand planes are parallel or perpendicular. This is attributed to insensitivities of the Fe-L(axial) characters of molecular orbitals to the relative HNO and ImH orientation in both the parallel and perpendicular conformers.     

Structure of protonated carbon dioxide clusters: infrared photodissociation spectroscopy and ab initio calculations

The infrared photodissociation spectra (IRPD) in the 700 to 4000 cm(-1) region are reported for H+ (CO2)n clusters (n = 1-4) and their complexes with argon. Weakly bound Ar atoms are attached to each complex upon cluster formation in a pulsed electric discharge/supersonic expansion cluster source. An expanded IRPD spectrum of the H+ (CO2)Ar complex, previously reported in the 2600-3000 cm(-1) range [Dopfer, O.; Olkhov, R.V.; Roth, D.; Maier, J.P. Chem. Phys. Lett. 1998, 296, 585-591] reveals new vibrational resonances. For n = 2 to 4, the vibrational resonances involving the motion of the proton are observed in the 750 to 1500 cm(-1) region of the spectrum, and by comparison to the predictions of theory, the structure of the small clusters are revealed. The monomer species has a nonlinear structure, with the proton binding to the lone pair of an oxygen. In the dimer, this nonlinear configuration is preserved, with the two CO2 units in a trans configuration about the central proton. Upon formation of the trimer, the core CO2 dimer ion undergoes a rearrangement, producing a structure with near C2v symmetry, which is preserved upon successive CO2 solvation. While the higher frequency asymmetric CO2 stretch vibrations are unaffected by the presence of the weakly attached Ar atom, the dynamics of the shared proton motions are substantially altered, largely due to the reduction in symmetry of each complex. For n = 2 to 4, the perturbation due to Ar leads to blue shifts of proton stretching vibrations that involve motion of the proton mostly parallel to the O-H+-O axis of the core ion. Moreover, proton stretching motions perpendicular to this axis exhibit smaller shifts, largely to the red. Ab initio (MP2) calculations of the structures, complexation energies, and harmonic vibrational frequencies are also presented, which support the assignments of the experimental spectra.     

New perspectives on iron-ligand vibrations of oxyheme complexes

We report our studies of the vibrational dynamics of iron for three imidazole-ligated oxyheme derivatives that mimic the active sites of histidine-ligated heme proteins complexed with dioxygen. The experimental vibrational data are obtained from nuclear resonance vibrational spectroscopy (NRVS) measurements conducted on both powder samples and oriented single crystals, and which includes several in-plane (ip) and out-of-plane (oop) measurements. Vibrational spectral assignments have been made through a combination of the oriented sample spectra and predictions based on density functional theory (DFT) calculations. The two Fe-O(2) modes that have been previously observed by resonance Raman spectroscopy in heme proteins are clearly shown to be very strongly mixed and are not simply either a bending or stretching mode. In addition, a third Fe-O(2) mode, not previously reported, has been identified. The long-sought Fe-Im stretch, not observed in resonance Raman spectra, has been identified and compared with the frequencies observed for the analogous CO and NO species. The studies also suggest that the in-plane iron motion is anisotropic and is controlled by the orientation of the Fe-O(2) group and not sensitive to the in-plane Fe-N(p) bonds and/or imidazole orientations.     

Transformation and structural discrimination between the neutral {Fe(NO)2}10 dinitrosyliron complexes (DNICs) and the anionic/cationic {Fe(NO)2}9 DNICs

Reaction of Fe(CO)2(NO)2 and sparteine/tetramethylethylenediamine (TMEDA) in tetrahydrofuran afforded the electron paramagnetic resonance (EPR)-silent, neutral {Fe(NO)2}10 dinitrosyliron complexes (DNICs) [(sparteine)Fe(NO)2] (1) and [(TMEDA)Fe(NO)2] (2), respectively. The stable and isolable anionic {Fe(NO)2}9 DNIC [(S(CH2)3S)Fe(NO)2]- (4), with a bidentate alkylthiolate coordinated to a {Fe(NO)(2)} motif, was prepared by the reaction of [S(CH2)3S]2- and the cationic {Fe(NO)2}9 [(sparteine)Fe(NO)2]+ (3) obtained from the reaction of complex 1 and [NO][BF4] in CH(3)CN. Transformation from the neutral complex 1 to the anionic complex 4 was verified via the cationic complex 3. Here complex 3 acts as an {Fe(NO)2}-donor reagent in the presence of thiolates. The EPR spectra of complexes 3 and 4 exhibit an isotropic signal with g = 2.032 and 2.031 at 298 K, respectively, the characteristic g value of {Fe(NO)2}9 DNICs. On the basis of N-O/Fe-N(O) bond lengths of the single-crystal X-ray structures of the {Fe(NO)2}9/{Fe(NO)2}10 DNICs, the oxidation level of the {Fe(NO)2} core of DNICs can be unambiguously assigned. The mean N-O distances falling in the range of 1.214(6)-1.189(4) A and the Fe-N(O) bond distances in the range of 1.650(7)-1.638(3) A are assigned as the neutral {Fe(NO)(2)}(10) DNICs. In contrast, the mean N-O bond distances ranging from 1.178(3) to 1.160(6) A and the mean Fe-N(O) bond distances ranging from 1.695(3) to 1.661(4) A are assigned as the anionic/neutral/cationic {Fe(NO)2}9 DNICs. In addition, an EPR spectrum in combination with the IR nu(NO) (the relative position of the nu(NO) stretching frequencies and their difference Deltanu(NO)) spectrum may serve as an efficient tool for discrimination of the existence of the anionic/cationic/neutral {Fe(NO)2}9 DNICs and the neutral {Fe(NO)2}10 DNICs.     

Computational studies on the A cluster of acetyl-coenzyme A synthase: geometric and electronic properties of the NiFeC species and mechanistic implications

DFT computational studies on the A cluster of acetyl-coenzyme A synthase are presented and discussed. They aim at evaluating possible A cluster models to settle the ongoing controversy about the nature of the proximal metal site in the catalytically active form of the cluster, recently proposed to be either Ni or Cu. Two possible models for the NiFeC species are considered, [Fe4S4]2+-Ni+CO-Ni2+ and [Fe4S4]2+-Cu+CO-Ni+. While for the former the computed 57Fe, 61Ni, and 13C hyperfine coupling parameters agree reasonably well with corresponding experimental values, for the latter model this agreement is very poor because the actual charge distribution is [Fe4S4]+-Cu+CO-Ni2+. Together, our results provide compelling evidence that the catalytically active A cluster contains Ni rather than Cu at the proximal metal site. Computations on the Ared2 state proposed to be part of the catalytic cycle (Darnault, C.; Volbeda, A.; Kim, E. J.; Legrand, P.; Vernède, X.; Lindahl, P. A.; Fontecilla-Camps, J. C. Nat. Struct. Biol. 2003, 10, 271-279) yield [Fe4S4]+-Ni+-Ni2+, hinting toward a Ni+/Ni3+ redox couple being involved in the methylation reaction.     

Infrared spectroscopy of discrete uranyl anion complexes

The Free-Electron Laser for Infrared Experiments (FELIX) was used to study the wavelength-resolved multiple photon photodissociation of discrete, gas-phase uranyl (UO22+) complexes containing a single anionic ligand (A), with or without ligated solvent molecules (S). The uranyl antisymmetric and symmetric stretching frequencies were measured for complexes with general formula [UO2A(S)n]+, where A was hydroxide, methoxide, or acetate; S was water, ammonia, acetone, or acetonitrile; and n = 0-3. The values for the antisymmetric stretching frequency for uranyl ligated with only an anion ([UO2A]+) were as low or lower than measurements for [UO2]2+ ligated with as many as five strong neutral donor ligands and are comparable to solution-phase values. This result was surprising because initial DFT calculations predicted values that were 30-40 cm(-1) higher, consistent with intuition but not with the data. Modification of the basis sets and use of alternative functionals improved computational accuracy for the methoxide and acetate complexes, but calculated values for the hydroxide were greater than the measurement regardless of the computational method used. Attachment of a neutral donor ligand S to [UO2A]+ produced [UO2AS]+, which produced only very modest changes to the uranyl antisymmetric stretch frequency, and did not universally shift the frequency to lower values. DFT calculations for [UO2AS]+ were in accord with trends in the data and showed that attachment of the solvent was accommodated by weakening of the U-anion bond as well as the uranyl. When uranyl frequencies were compared for [UO2AS]+ species having different solvent neutrals, values decreased with increasing neutral nucleophilicity.