Quantitative vibrational dynamics of iron in nitrosyl porphyrins

Substituent Effects in Iron Porphyrin Catalysts for the Hydrogen Evolution Reaction

For a future hydrogen economy, non-precious metal catalysts for the water splitting reactions are needed that can be implemented on a global scale. Metal-nitrogen-carbon (MNC) catalysts with active sites constituting a metal center with fourfold coordination of nitrogen (MN₄ ) show promising performance, but an optimization rooted in structure-property relationships has been hampered by their low structural definition. Porphyrin model complexes are studied to transfer insights from well-defined molecules to MNC systems. This work combines experiment and theory to evaluate the influence of porphyrin substituents on the electronic and electrocatalytic properties of MN₄ centers with respect to the hydrogen evolution reaction (HER) in aqueous electrolyte. We found that the choice of substituent affects their utilization on the carbon support and their electrocatalytic performance. We propose an HER mechanism for supported iron porphyrin complexes involving a [Fe^II (P⋅)]^- radical anion intermediate, in which a porphinic nitrogen atom acts as an internal base. While this work focuses on the HER, the limited influence of a simultaneous interaction with the support and an aqueous electrolyte will likely be transferrable to other catalytic applications.

A Combined Spectroscopic and Computational Study on the Mechanism of Iron-Catalyzed Aminofunctionalization of Olefins Using Hydroxylamine Derived N-O Reagent as the "Amino" Source and "Oxidant"

Herein, we study the mechanism of iron-catalyzed direct synthesis of unprotected aminoethers from olefins by a hydroxyl amine derived reagent using a wide range of analytical and spectroscopic techniques (Mössbauer, Electron Paramagnetic Resonance, Ultra-Violet Visible Spectroscopy, X-ray Absorption, Nuclear Resonance Vibrational Spectroscopy, and resonance Raman) along with high-level quantum chemical calculations. The hydroxyl amine derived triflic acid salt acts as the “oxidant” as well as “amino” group donor. It activates the high-spin Fe(II) (S_t = 2) catalyst [Fe(acac)₂(H₂O)₂] (1) to generate a high-spin (S_t = 5/2) intermediate (Int I), which decays to a second intermediate (Int II) with S_t = 2. The analysis of spectroscopic and computational data leads to the formulation of Int I as [Fe(III)(acac)₂-N-acyloxy] (an alkyl-peroxo-Fe(III) analogue). Furthermore, Int II is formed by N–O bond homolysis. However, it does not generate a high-valent Fe(IV)(NH) species (a Fe(IV)(O) analogue), but instead a high-spin Fe(III) center which is strongly antiferromagnetically coupled (J = −524 cm^–1) to an iminyl radical, [Fe(III)(acac)₂-NH·], giving S_t = 2. Though Fe(NH) complexes as isoelectronic surrogates to Fe(O) functionalities are known, detection of a high-spin Fe(III)-N-acyloxy intermediate (Int I), which undergoes N–O bond cleavage to generate the active iron–nitrogen intermediate (Int II), is unprecedented. Relative to Fe(IV)(O) centers, Int II features a weak elongated Fe–N bond which, together with the unpaired electron density along the Fe–N bond vector, helps to rationalize its propensity for N-transfer reactions onto styrenyl olefins, resulting in the overall formation of aminoethers. This study thus demonstrates the potential of utilizing the iron-coordinated nitrogen-centered radicals as powerful reactive intermediates in catalysis.

Vibrational Perturbation of the [FeFe] Hydrogenase H-Cluster Revealed by 13C2H-ADT Labeling

[FeFe] hydrogenases are highly active catalysts for the interconversion of molecular hydrogen with protons and electrons. Here, we use a combination of isotopic labeling, ⁵⁷Fe nuclear resonance vibrational spectroscopy (NRVS), and density functional theory (DFT) calculations to observe and characterize the vibrational modes involving motion of the 2-azapropane-1,3-dithiolate (ADT) ligand bridging the two iron sites in the [2Fe]_H subcluster. A -¹³C²H₂- ADT labeling in the synthetic diiron precursor of [2Fe]_H produced isotope effects observed throughout the NRVS spectrum. The two precursor isotopologues were then used to reconstitute the H-cluster of [FeFe] hydrogenase from Chlamydomonas reinhardtii (CrHydA1), and NRVS was measured on samples poised in the catalytically crucial H_hyd state containing a terminal hydride at the distal Fe site. The ¹³C²H isotope effects were observed also in the H_hyd spectrum. DFT simulations of the spectra allowed identification of the ⁵⁷Fe normal modes coupled to the ADT ligand motions. Particularly, a variety of normal modes involve shortening of the distance between the distal Fe-H hydride and ADT N-H bridgehead hydrogen, which may be relevant to the formation of a transition state on the way to H₂ formation.

Spectroscopic discernibility of dopants and axial ligands in pyridinic FeN4 environments relevant to single-atom catalysts

Single-atom catalysts (SACs) activate small molecules, e.g. the oxygen reduction reaction is catalysed by FeNC materials. Because the nature of active site(s) in this type of SAC is unclear, spectroscopic and computational insights are needed to clarify the atomistic composition and electronic structure. Using quantum chemistry, we show that key features of [Fe{phen2A2}L]n+ complexes (A = CH, N with n = 0, A = O with n = 0, 2; L = OH-, Cl-) can be differentiated spectroscopically.

High-Frequency Fe-H and Fe-H2 Modes in a trans-Fe(η2-H2)(H) Complex: A Speed Record for Nuclear Resonance Vibrational Spectroscopy

Nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) are complementary tools for studying the vibrational and geometric structures of specific isotopically labeled molecular systems. Here we apply NRVS and DFT to characterize the trans-[57Fe(η2-H2)(H)(dppe)2][BPh4] [dppe = 1,2-bis(diphenylphosphino)ethane] complex. Heretofore, most NRVS observations have centered on the spectral region below 1000 cm-1, where the 57Fe signal is strongest. In this work, we show that state-of-the-art synchrotron facilities can extend the observable region to 2000 cm-1 and likely beyond, in measurements that require less than 1 day. The 57Fe-H stretch was revealed at 1915 cm-1, along with the asymmetric 57Fe-H2 stretch at 1774 cm-1. For a small fraction of the H2-dissociated product, the 57Fe-H stretch was detected at 1956 cm-1. The unique sensitivity to 57Fe motion and the isolated nature of the Fe-H/H2 stretching modes enabled NRVS to quantitatively analyze the sample composition.

Reactive mode composition factor analysis of transition states: the case of coupled electron-proton transfers

A simple method for the evaluation of the kinetic energy distribution within the reactive mode of a transition state (TS), denoted as the Reactive Mode Composition Factor (RMCF), is presented. It allows one to directly map the barrier properties onto the atomic-motion components of the reaction coordinate at the TS, which has potential to shed light onto some mechanistic features of a chemical process. To demonstrate the applicability of RMCF to reactivity, we link the kinetic energy distribution within a reactive mode with the asynchronicity (η) in C-H bond activation, as they both evolve in a series of coupled proton-electron transfer (CPET) reactions between Fe^IVO oxidants and 1,4-cyclohexadiene. RMCF shows how the earliness or lateness of a process manifests as a redistribution of kinetic energy in the reactive mode as a function of the free energy of reaction (ΔG₀) and η. Finally, the title analysis can be applied to predict H-atom tunneling contributions and kinetic isotope effects in a set of reactions, yielding a transparent rationalization based on the kinetic energy distributions in the reactive mode.

How Does a Heme Carbene Differ from Diatomic Ligated (NO, CO, and CN-) Analogues in the Axial Bond?

Compared to well studied diatomic ligands (NO, CN^-, CO), the axial bonds of carbene hemes is much less known although its significance in biological chemistry. The unusually large quadrupole splitting (Δ E_Q = +2.2 mm·s^-1) and asymmetric parameter (η = 0.9) of the five-coordinate heme carbene [Fe(TTP)(CCl₂)], which is the largest among all known low spin ferrohemes, has driven investigations by means of Mössbauer effect Nuclear Resonance Vibrational Spectroscopy (NRVS). Three distinct measurements on one single crystal (two in-plane and one out-of-plane) have demonstrated comprehensive vibrational structures including stretch (429) and bending modes (472 cm^-1) of the axial Fe-CCl₂, and revealed iron vibrational anisotropy in three orthogonal directions for the first time. Frontier orbital analysis especially comparisons with diatomic analogues (NO, CN^-, CO) suggest that CCl₂, similar to NO, has led to strong but anisotropic π bonding in a ligand-based "4C"-coordinate which induced the vibrational anisotropies and very large Mössbauer parameters. This is contrasted to CN^- and CO complexes which possess a porphyrin-based "4N"-coordinate electronic and vibrational structures due to inherent on-axis linear ligation.

What Can Be Learned from Nuclear Resonance Vibrational Spectroscopy: Vibrational Dynamics and Hemes

Nuclear resonance vibrational spectroscopy (NRVS; also known as nuclear inelastic scattering, NIS) is a synchrotron-based method that reveals the full spectrum of vibrational dynamics for Mössbauer nuclei. Another major advantage, in addition to its completeness (no arbitrary optical selection rules), is the unique selectivity of NRVS. The basics of this recently developed technique are first introduced with descriptions of the experimental requirements and data analysis including the details of mode assignments. We discuss the use of NRVS to probe ⁵⁷Fe at the center of heme and heme protein derivatives yielding the vibrational density of states for the iron. The application to derivatives with diatomic ligands (O₂, NO, CO, CN^–) shows the strong capabilities of identifying mode character. The availability of the complete vibrational spectrum of iron allows the identification of modes not available by other techniques. This permits the correlation of frequency with other physical properties. A significant example is the correlation we find between the Fe–Im stretch in six-coordinate Fe(XO) hemes and the trans Fe–N(Im) bond distance, not possible previously. NRVS also provides uniquely quantitative insight into the dynamics of the iron. For example, it provides a model-independent means of characterizing the strength of iron coordination. Prediction of the temperature-dependent mean-squared displacement from NRVS measurements yields a vibrational “baseline” for Fe dynamics that can be compared with results from techniques that probe longer time scales to yield quantitative insights into additional dynamical processes.

Coumarin centered copper(ii) complex with appended-imidazole as cancer chemotherapeutic agents against lung cancer: molecular insight via DFT-based vibrational analysis

Synthesis and structural characterization of the novel copper complex, DFT based vibrational analysis, DNA binding studies. In vitro cytotoxicity against A549 cancer cell lines and estimation of GSH, ROS, LPO levels, have been reported.

Vibrational dynamics (IR, Raman, NRVS) and a DFT study of a new antitumor tetranuclearstannoxane cluster, Sn(iv)-oxo-{di-o-vanillin} dimethyl dichloride

The vibrational dynamics of a newly synthesized tetrastannoxane was characterized with a combination of experimental (Raman, IR and tin-based nuclear resonance vibrational spectroscopy) and computational (DFT/B3LYP) methods, with an emphasis on the vibrations of the tin sites. The cytotoxic activity revealed a significant regression selectively against the human pancreatic cell lines.

Recent advances in biosynthetic modeling of nitric oxide reductases and insights gained from nuclear resonance vibrational and other spectroscopic studies

This Forum Article focuses on recent advances in structural and spectroscopic studies of biosynthetic models of nitric oxide reductases (NORs). NORs are complex metalloenzymes found in the denitrification pathway of Earth’s nitrogen cycle where they catalyze the proton-dependent two-electron reduction of nitric oxide (NO) to nitrous oxide (N₂O). While much progress has been made in biochemical and biophysical studies of native NORs and their variants, a clear mechanistic understanding of this important metalloenzyme related to its function is still elusive. We report herein UV–vis and nuclear resonance vibrational spectroscopy (NRVS) studies of mononitrosylated intermediates of the NOR reaction of a biosynthetic model. The ability to selectively substitute metals at either heme or nonheme metal sites allows the introduction of independent ⁵⁷Fe probe atoms at either site, as well as allowing the preparation of analogues of stable reaction intermediates by replacing either metal with a redox inactive metal. Together with previous structural and spectroscopic results, we summarize insights gained from studying these biosynthetic models toward understanding structural features responsible for the NOR activity and its mechanism. The outlook on NOR modeling is also discussed, with an emphasis on the design of models capable of catalytic turnovers designed based on close mimics of the secondary coordination sphere of native NORs.

New insights into nitric oxide reductases (NORs) are obtained. Using nuclear resonance vibrational spectroscopy, we probe both iron atoms in mononitrosylated intermediates of the NOR reaction in a biosynthetic protein model that reveal new insights into the structural and electronic features responsible for the NOR activity and its likely mechanism.

Comprehensive Fe-ligand vibration identification in {FeNO}6 hemes

Oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS) has been used to obtain all iron vibrations in two {FeNO}(6) porphyrinate complexes, five-coordinate [Fe(OEP)(NO)]ClO4 and six-coordinate [Fe(OEP)(2-MeHIm)(NO)]ClO4. A new crystal structure was required for measurements of [Fe(OEP)(2-MeHIm)(NO)]ClO4, and the new structure is reported herein. Single crystals of both complexes were oriented to be either parallel or perpendicular to the porphyrin plane and/or axial imidazole ligand plane. Thus, the FeNO bending and stretching modes can now be unambiguously assigned; the pattern of shifts in frequency as a function of coordination number can also be determined. The pattern is quite distinct from those found for CO or {FeNO}(7) heme species. This is the result of unchanging Fe-N(NO) bonding interactions in the {FeNO}(6) species, in distinct contrast to the other diatomic ligand species. DFT calculations were also used to obtain detailed predictions of vibrational modes. Predictions were consistent with the intensity and character found in the experimental spectra. The NRVS data allow the assignment and observation of the challenging to obtain Fe-Im stretch in six-coordinate heme derivatives. NRVS data for this and related six-coordinate hemes with the diatomic ligands CO, NO, and O2 reveal a strong correlation between the Fe-Im stretch and Fe-N(Im) bond distance that is detailed for the first time.

Structural characterization of CO-inhibited Mo-nitrogenase by combined application of nuclear resonance vibrational spectroscopy, extended X-ray absorption fine structure, and density functional theory: new insights into the effects of CO binding and the role of the interstitial atom

The properties of CO-inhibited Azotobacter vinelandii (Av) Mo-nitrogenase (N2ase) have been examined by the combined application of nuclear resonance vibrational spectroscopy (NRVS), extended X-ray absorption fine structure (EXAFS), and density functional theory (DFT). Dramatic changes in the NRVS are seen under high-CO conditions, especially in a 188 cm(-1) mode associated with symmetric breathing of the central cage of the FeMo-cofactor. Similar changes are reproduced with the α-H195Q N2ase variant. In the frequency region above 450 cm(-1), additional features are seen that are assigned to Fe-CO bending and stretching modes (confirmed by (13)CO isotope shifts). The EXAFS for wild-type N2ase shows evidence for a significant cluster distortion under high-CO conditions, most dramatically in the splitting of the interaction between Mo and the shell of Fe atoms originally at 5.08 Å in the resting enzyme. A DFT model with both a terminal -CO and a partially reduced -CHO ligand bound to adjacent Fe sites is consistent with both earlier FT-IR experiments, and the present EXAFS and NRVS observations for the wild-type enzyme. Another DFT model with two terminal CO ligands on the adjacent Fe atoms yields Fe-CO bands consistent with the α-H195Q variant NRVS. The calculations also shed light on the vibrational "shake" modes of the interstitial atom inside the central cage, and their interaction with the Fe-CO modes. Implications for the CO and N2 reactivity of N2ase are discussed.

Iron nitrosyl "natural" porphyrinates: does the porphyrin matter?

The synthesis and spectroscopic characterization of three five-coordinate nitrosyliron(II) complexes, [Fe(Porph)(NO)], are reported. These three nitrosyl derivatives, where Porph represents protoporphyrin IX dimethyl ester, mesoporphyrin IX dimethyl ester, or deuteroporphyrin IX dimethyl ester, display notable differences in their properties relative to the symmetrical synthetic porphyrins such as OEP and TPP. The N–O stretching frequencies are in the range of 1651–1660 cm^–1, frequencies that are lower than those of synthetic porphyrin derivatives. Mössbauer spectra obtained in both zero and applied magnetic field show that the quadrupole splitting values are slightly larger than those of known synthetic porphyrins. The electronic structures of these naturally occurring porphyrin derivatives are thus seen to be consistently different from those of the synthetic derivatives, the presumed consequence of the asymmetric peripheral substituent pattern. The molecular structure of [Fe(PPIX-DME)(NO)] has been determined by X-ray crystallography. Although disorder of the axial nitrosyl ligand limits the structural quality, this derivative appears to show the same subtle structural features as previously characterized five-coordinate nitrosyls.

The synthesis and characterization of three five-coordination {FeNO}₇ porphyrin derivatives based on natural porphyrin substitution patterns show that there are systematic differences compared to synthetic porphyrin derivatives with more symmetric substitution patterns. Characterization includes high-field Mössbauer spectroscopy and a crystal structure of the protoporphyrin IX dimethyl ester derivative.

Anisotropic iron motion in nitrosyl iron porphyrinates: natural and synthetic hemes

The vibrational spectra of two five-coordinate nitrosyl iron porphyrinates, [Fe(OEP)(NO)] (OEP = dianion of 2,3,7,8,12,13,17,18-octaethylporphyrin) and [Fe(DPIX)(NO)] (DPIX = deuteroporphyrin IX), have been studied by oriented single-crystal nuclear resonance vibrational spectroscopy. Single crystals (both are in the triclinic crystal system) were oriented to give vibrational spectra perpendicular to the porphyrin plane. Additionally, two orthogonal in-plane measurements that were also either perpendicular or parallel to the projection of the FeNO plane onto the porphyrin plane yield the complete set of vibrations with iron motion. In addition to cleanly enabling the assignment of the FeNO bending and stretching modes, the measurements reveal that the two in-plane spectra from the parallel and perpendicular in-plane directions for both compounds have substantial differences. The assignment of these in-plane vibrations were aided by density functional theory predictions. The differences in the two in-plane directions result from the strongly bonded axial NO ligand. The direction of the in-plane iron motion is thus found to be largely parallel and perpendicular to the projection of the FeNO plane on the porphyrin plane. These axial ligand effects on the in-plane iron motion are related to the strength of the axial ligand-to-iron bond.

Probing heme vibrational anisotropy: an imidazole orientation effect?

The complete iron vibrational spectrum of the five-coordinate high-spin complex [Fe(OEP)(2-MeHIm)], where OEP = octaethylporphyrinato and 2-MeHIm = 2-methylimidazole, has been obtained by oriented single-crystal nuclear resonance vibrational spectroscopy (NRVS) data. Measurements have been made in three orthogonal directions, which provides quantitative information for all iron motion. These experimental data, buttressed by density functional theory (DFT) calculations, have been used to define the effects of the axial ligand orientation. Although the axial imidazole removes the degeneracy in the in-plane vibrations, the imidazole orientation does not appear to control the direction of the in-plane iron motion. This is in contrast to the effect of the imidazolate ligand, as defined by DFT calculations, which does have substantial effects on the direction of the in-plane iron motion. The axial NO ligand has been found to have the strongest orientational effect (Angew. Chem., Int. Ed., 2010, 49, 4400). Thus the strength of the directional properties are in the order NO > imidazolate > imidazole, consistent with the varying strength of the Fe-ligand bond.

Quantitative vibrational dynamics of the metal site in a tin porphyrin: an IR, NRVS, and DFT study

We used a newer, synchrotron-based, spectroscopic technique (nuclear resonance vibrational spectroscopy, NRVS) in combination with a more traditional one (infrared absorption, IR) to obtain a complete, quantitative picture of the metal center vibrational dynamics in a six-coordinated tin porphyrin. From the NRVS (119)Sn site-selectivity and the sensitivity of the IR signal to (112)Sn/(119)Sn isotope substitution, we identified the frequency of the antisymmetric stretching of the axial bonds (290 cm(-1)) and all the other vibrations involving Sn. Experimentally authenticated density functional theory (DFT) calculations aid the data interpretation by providing detailed normal mode descriptions for each observed vibration. These results may represent a starting point toward the characterization of the local vibrational dynamics of the metallic site in tin porphyrins and compounds with related structures. The quantitative complementariness between IR, NRVS, and DFT is emphasized.

Elucidation of the Fe(IV)=O intermediate in the catalytic cycle of the halogenase SyrB2

Mononuclear non-haem iron (NHFe) enzymes catalyse a wide variety of oxidative reactions including halogenation, hydroxylation, ring closure, desaturation, and aromatic ring cleavage. These are highly important for mammalian somatic processes such as phenylalanine metabolism, production of neurotransmitters, hypoxic response, and the biosynthesis of natural products.^1–3 The key reactive intermediate in the catalytic cycles of these enzymes is an S = 2 Fe^IV=O species, which has been trapped for a number of NHFe enzymes^4–8 including the halogenase SyrB2, the subject of this study. Computational studies to understand the reactivity of the enzymatic NHFe Fe^IV=O intermediate^9–13 are limited in applicability due to the paucity of experimental knowledge regarding its geometric and electronic structures, which determine its reactivity. Synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) is a sensitive and effective method that defines the dependence of the vibrational modes of Fe on the nature of the Fe^IV=O active site.^14–16 Here we present the first NRVS structural characterisation of the reactive Fe^IV=O intermediate of a NHFe enzyme. This Fe^IV=O intermediate reacts via an initial H-atom abstraction step, with its subsquent halogenation (native) or hydroxylation (non-native) rebound reactivity being dependent on the substrate.¹⁷ A correlation of the experimental NRVS data to electronic structure calculations indicates that the substrate is able to direct the orientation of the Fe^IV=O intermediate, presenting specific frontier molecular orbitals (FMOs) which can activate the selective halogenation versus hydroxylation reactivity.

Effects of imidazole deprotonation on vibrational spectra of high-spin iron(II) porphyrinates

The effects of the deprotonation of coordinated imidazole on the vibrational dynamics of five-coordinate high-spin iron(II) porphyrinates have been investigated using nuclear resonance vibrational spectroscopy. Two complexes have been studied in detail with both powder and oriented single-crystal measurements. Changes in the vibrational spectra are clearly related to structural differences in the molecular structures that occur when imidazole is deprotonated. Most modes involving the simultaneous motion of iron and imidazolate are unresolved, but the one mode that is resolved is found at higher frequency in the imidazolates. These out-of-plane results are in accord with earlier resonance Raman studies of heme proteins. We also show the imidazole vs imidazolate differences in the in-plane vibrations that are not accessible to resonance Raman studies. The in-plane vibrations are at lower frequency in the imidazolate derivatives; the doming mode shifts are inconclusive. The stiffness, an experimentally determined force constant that averages the vibrational details to quantify the nearest-neighbor interactions, confirms that deprotonation inverts the relative strengths of axial and equatorial coordination.

Nuclear resonance vibrational spectroscopy and electron paramagnetic resonance spectroscopy of 57Fe-enriched [FeFe] hydrogenase indicate stepwise assembly of the H-cluster

The [FeFe] hydrogenase from Clostridium pasteurianum (CpI) harbors four Fe-S clusters that facilitate the transfer of an electron to the H-cluster, a ligand-coordinated six-iron prosthetic group that catalyzes the redox interconversion of protons and H(2). Here, we have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the iron centers in CpI, and we compare our data to that for a [4Fe-4S] ferredoxin as well as a model complex resembling the [2Fe](H) catalytic domain of the H-cluster. To enrich the hydrogenase with (57)Fe nuclei, we used cell-free methods to post-translationally mature the enzyme. Specifically, inactive CpI apoprotein with (56)Fe-labeled Fe-S clusters was activated in vitro using (57)Fe-enriched maturation proteins. This approach enabled us to selectively label the [2Fe](H) subcluster with (57)Fe, which NRVS confirms by detecting (57)Fe-CO and (57)Fe-CN normal modes from the H-cluster nonprotein ligands. The NRVS and iron quantification results also suggest that the hydrogenase contains a second (57)Fe-S cluster. Electron paramagnetic resonance (EPR) spectroscopy indicates that this (57)Fe-enriched metal center is not the [4Fe-4S](H) subcluster of the H-cluster. This finding demonstrates that the CpI hydrogenase retained an (56)Fe-enriched [4Fe-4S](H) cluster during in vitro maturation, providing unambiguous evidence of stepwise assembly of the H-cluster. In addition, this work represents the first NRVS characterization of [FeFe] hydrogenases.

Observation of the Fe-CN and Fe-CO vibrations in the active site of [NiFe] hydrogenase by nuclear resonance vibrational spectroscopy

Nuclear inelastic scattering of (57)Fe labeled [NiFe] hydrogenase is shown to give information on different states of the enzyme. It was thus possible to detect and assign Fe-CO and Fe-CN bending and stretching vibrations of the active site outside the spectral range of the Fe-S cluster normal modes.

Vibrational probes and determinants of the S = 0 ⇌ S = 2 spin crossover in five-coordinate [Fe(TPP)(CN)]-

The low-frequency vibrational characterization of the spin-crossover complex, five-coordinate cyano(tetraphenylporphyrinato)iron(II), [Fe(TPP)(CN)](-), is reported. Nuclear resonance vibrational spectroscopy has been used to measure all low-frequency vibrations involving iron at several temperatures; this yields vibrational spectra of both the low- (S = 0) and high-spin (S = 2) states. Multitemperature oriented single-crystal measurements facilitate assignments of the vibrational character of all modes and are consistent with the DFT-predicted spectra. The availability of the entire iron vibrational spectrum allows for the complete correlation of the modes between the two spin states. These data demonstrate that not only do the frequencies of the vibrations shift to lower values for the high-spin species as would be expected owing to the weaker bonds in the high-spin state, but also the mixing of iron modes with ligand modes changes substantially. Diagrams illustrating the changing character of the modes and their correlation are given. The reduced iron-ligand frequencies are the primary factor in the entropic stabilization of the high-spin state responsible for the spin crossover.

Nuclear resonance vibrational spectroscopy (NRVS) of rubredoxin and MoFe protein crystals

We have applied ⁵⁷Fe nuclear resonance vibrational spectroscopy (NRVS) for the first time to study the dynamics of Fe centers in Fe-S protein crystals, including oxidized wild type rubredoxin crystals from Pyrococcus furiosus, and the MoFe protein of nitrogenase from Azotobacter vinelandii. Thanks to the NRVS selection rule, selectively probed vibrational modes have been observed in both oriented rubredoxin and MoFe protein crystals. The NRVS work was complemented by extended X-ray absorption fine structure spectroscopy (EXAFS) measurements on oxidized wild type rubredoxin crystals from Pyrococcus furiosus. The EXAFS spectra revealed the Fe-S bond length difference in oxidized Pf Rd protein, which is qualitatively consistent with the X-ray crystal structure.

Photolability of NO in designed metal nitrosyls with carboxamido-N donors: a theoretical attempt to unravel the mechanism

During the past few years, photoactive metal nitrosyls (NO complexes of metals) have drawn attention as potential drugs for delivery of nitric oxide (NO) to biological targets under the control of light. Major success in this area has been achieved with designed metal nitrosyls derived from ligands that contain carboxamide group(s). A number of iron, manganese and ruthenium {MNO}(6) nitrosyls of such kind exhibit excellent NO photolability under low-power visible and near-IR light. The results of theoretical studies on these NO-donors have provided insight into (a) the electronic transitions that lead to photorelease of NO and (b) the structural features of the ligands that dictate the sensitivity of the nitrosyls to light of specific wavelengths. In addition, the results have afforded clear understanding of the electronic configurations of the various nitrosyls. This article highlights these results in a coherent manner. Good matches between the predicted and observed spectral features and NO photolability strongly suggest that theoretical studies should be an integral part of the smart design of such NO-donors in the future research.

Nuclear inelastic scattering and Mössbauer spectroscopy as local probes for ligand binding modes and electronic properties in proteins: vibrational behavior of a ferriheme center inside a β-barrel protein

In this work, we present a study of the influence of the protein matrix on its ability to tune the binding of small ligands such as NO, cyanide (CN(-)), and histamine to the ferric heme iron center in the NO-storage and -transport protein Nitrophorin 2 (NP2) from the salivary glands of the blood-sucking insect Rhodnius prolixus. Conventional Mössbauer spectroscopy shows a diamagnetic ground state of the NP2-NO complex and Type I and II electronic ground states of the NP2-CN(-) and NP2-histamine complex, respectively. The change in the vibrational signature of the protein upon ligand binding has been monitored by Nuclear Inelastic Scattering (NIS), also called Nuclear Resonant Vibrational Spectroscopy (NRVS). The NIS data thus obtained have also been calculated by quantum mechanical (QM) density functional theory (DFT) coupled with molecular mechanics (MM) methods. The calculations presented here show that the heme ruffling in NP2 is a consequence of the interaction with the protein matrix. Structure optimizations of the heme and its ligands with DFT retain the characteristic saddling and ruffling only if the protein matrix is taken into account. Furthermore, simulations of the NIS data by QM/MM calculations suggest that the pH dependence of the binding of NO, but not of CN(-) and histamine, might be a consequence of the protonation state of the heme carboxyls.

Nuclear resonance vibrational spectra of five-coordinate imidazole-ligated iron(II) porphyrinates

Nuclear resonance vibrational spectra have been obtained for six five-coordinate imidazole-ligated iron(II) porphyrinates, [Fe(Por)(L)] (Por = tetraphenylporphyrinate, octaethylporphyrinate, tetratolylporphyrinate, or protoporphyrinate IX and L = 2-methylimidazole or 1,2-dimethylimidazole). Measurements have been made on both powder and oriented crystal samples. The spectra are dominated by strong signals around 200-300 cm(-1). Although the in-plane and out-of-plane vibrations are seriously overlapped, oriented crystal spectra allow their deconvolution. Thus, oriented crystal experimental data, along with density functional theory (DFT) calculations, enable the assignment of key vibrations in the spectra. Molecular dynamics are also discussed. The nature of the Fe-N(Im) vibrations has been elaborated further than was possible from resonance Raman studies. Our study suggests that the Fe motions are coupled with the porphyrin core and peripheral groups motions. Both peripheral groups and their conformations have significant influence on the vibrational spectra (position and shape).

Predicting Nuclear Resonance Vibrational Spectra of [Fe(OEP)(NO)]

Nuclear Resonance Vibrational Spectroscopy (NRVS) is a sensitive vibrational probe for biologically important heme complexes. The exquisite sensitivity of the NRVS data to the electronic structure provides detailed insights into the nature of these interesting compounds, but requires highly accurate computational methods for the mode assignments. To determine the best combinations of density functionals and basis sets, a series of benchmark DFT calculations on the previously characterized complex [Fe(OEP)NO] (OEP(2-)=octaethylporphyrinatio dianion) were performed. A test set of 21 methodology combinations including 8 functionals (BP86, mPWPW91, B3LYP, PBE1PBE, M062X, M06L, LC-BP86 and ωB97X-D) and 5 basis set (VTZ, TZVP, Lanl2DZ for iron and 6-31G*, 6-31+G* for other atoms) was carried out to calculate electronic structures and vibrational frequencies. We also implemented the conversion of frequency calculations into orientation-selective mode composition factors (e(2)), which can used to simulate the Vibrational Density Of States (VDOS) using Gaussian normal distribution functions. These use a series of user-friendly scripts for their application to NRVS. The structures as well as the isotropic and anisotropic NRVS of [Fe(OEP)NO] obtained with the M06L functional with a variety of basis sets are found to best reproduce the available experimental data, followed by B3LYP/LanL2DZ calculations. Other density functionals and basis sets do not produce the same level of accuracy. The noticeably worse agreement between theory and experiment for the out-plane NRVS compared with the excellent performance of the M06L functional for the in-plane prediction is attributed to deficiencies of the physical model rather than the computational methodology.

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.

Spectroscopic identification of reactive porphyrin motions

Nuclear resonance vibrational spectroscopy (NRVS) reveals the vibrational dynamics of a Mössbauer probe nucleus. Here, (57)Fe NRVS measurements yield the complete spectrum of Fe vibrations in halide complexes of iron porphyrins. Iron porphine serves as a useful symmetric model for the more complex spectrum of asymmetric heme molecules that contribute to numerous essential biological processes. Quantitative comparison with the vibrational density of states (VDOS) predicted for the Fe atom by density functional theory calculations unambiguously identifies the correct sextet ground state in each case. These experimentally authenticated calculations then provide detailed normal mode descriptions for each observed vibration. All Fe-ligand vibrations are clearly identified despite the high symmetry of the Fe environment. Low frequency molecular distortions and acoustic lattice modes also contribute to the experimental signal. Correlation matrices compare vibrations between different molecules and yield a detailed picture of how heme vibrations evolve in response to (a) halide binding and (b) asymmetric placement of porphyrin side chains. The side chains strongly influence the energetics of heme doming motions that control Fe reactivity, which are easily observed in the experimental signal.

Dynamics of the [4Fe-4S] cluster in Pyrococcus furiosus D14C ferredoxin via nuclear resonance vibrational and resonance Raman spectroscopies, force field simulations, and density functional theory calculations

We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study oxidized and reduced forms of the [4Fe-4S] cluster in the D14C variant ferredoxin from Pyrococcus furiosus (Pf D14C Fd). To assist the normal-mode assignments, we conducted NRVS with D14C ferredoxin samples with (36)S substituted into the [4Fe-4S] cluster bridging sulfide positions, and a model compound without ligand side chains, (Ph(4)P)(2)[Fe(4)S(4)Cl(4)]. Several distinct regions of NRVS intensity are identified, ranging from "protein" and torsional modes below 100 cm(-1), through bending and breathing modes near 150 cm(-1), to strong bands from Fe-S stretching modes between 250 and ∼400 cm(-1). The oxidized ferredoxin samples were also investigated by resonance Raman (RR) spectroscopy. We found good agreement between NRVS and RR frequencies, but because of different selection rules, the intensities vary dramatically between the two types of spectra. The (57)Fe partial vibrational densities of states for the oxidized samples were interpreted by normal-mode analysis with optimization of Urey-Bradley force fields for local models of the [4Fe-4S] clusters. Full protein model calculations were also conducted using a supplemented CHARMM force field, and these calculations revealed low-frequency modes that may be relevant to electron transfer with Pf Fd partners. Density functional theory (DFT) calculations complemented these empirical analyses, and DFT was used to estimate the reorganization energy associated with the [Fe(4)S(4)](2+/+) redox cycle. Overall, the NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.

Fe-H/D stretching and bending modes in nuclear resonant vibrational, Raman and infrared spectroscopies: comparisons of density functional theory and experiment

Infrared, Raman, and nuclear resonant vibrational (NRVS) spectroscopies have been used to address the Fe-H bonding in trans-HFe(CO) iron hydride compound, HFe(CO)(dppe)2, dppe = 1,2-bis(diphenylphosphino)ethane. H and D isotopomers of the compound, with selective substitution at the metal-coordinated hydrogen, have been considered in order to address the Fe-H/D stretching and bending modes. Experimental results are compared to the normal mode analysis by density functional theory (DFT). The results are that (i) the IR spectrum does not clearly show Fe-H stretching or bending modes; (ii) Fe-H stretching modes are clear but weak in the Raman spectrum, and Fe-H bending modes are weak; (iii) NRVS 57Fe spectroscopy resolves Fe-H bending clearly, but Fe-H or Fe-D stretching is above its experimentally resolved frequency range. DFT calculations (with no scaling of frequencies) show intensities and peak locations that allow unambiguous correlations between observed and calculated features, with frequency errors generally less than 15 cm(-1). Prospects for using these techniques to unravel vibrational modes of protein active sites are discussed.

Dynamical transition in proteins and non-Gaussian behavior of low-frequency modes in self-consistent normal mode analysis

Self-consistent normal mode analysis (SCNMA) is applied to heme c type cytochrome f to study temperature-dependent protein motion. Classical normal mode analysis assumes harmonic behavior and the protein mean-square displacement has a linear dependence on temperature. This is only consistent with low-temperature experimental results. To connect the protein vibrational motions between low and physiological temperatures, we have incorporated a fitted set of anharmonic potentials into SCNMA. In addition, quantum harmonic-oscillator theory has been used to calculate the displacement distribution for individual vibrational modes. We find that the modes involving soft bonds exhibit significant non-Gaussian dynamics at physiological temperature, which suggests that it may be the cause of the non-Gaussian behavior of the protein motions probed by elastic incoherent neutron scattering. The combined theory displays a dynamical transition caused by the softening of few "torsional" modes in the low-frequency regime ( <50 cm(-1) or <6 meV or >0.6 ps). These modes change from Gaussian to a classical distribution upon heating. Our theory provides an alternative way to understand the microscopic origin of the protein dynamical transition.

Oriented single-crystal nuclear resonance vibrational spectroscopy of [Fe(TPP)(MI)(NO)]: quantitative assessment of the trans effect of NO

This paper presents oriented single-crystal Nuclear Resonance Vibrational Spectroscopy (NRVS) data for the six-coordinate (6C) ferrous heme-nitrosyl model complex [(57)Fe(TPP)(MI)(NO)] (1; TPP(2-) = tetraphenylporphyrin dianion; MI = 1-methylimidazole). The availability of these data enables for the first time the detailed simulation of the complete NRVS data, including the porphyrin-based vibrations, of a 6C ferrous heme-nitrosyl, using our quantum chemistry centered normal coordinate analysis (QCC-NCA). Importantly, the Fe-NO stretch is split by interaction with a porphyrin-based vibration into two features, observed at 437 and 472 cm(-1). The 437 cm(-1) feature is strongly out-of-plane (oop) polarized and shows a (15)N(18)O isotope shift of 8 cm(-1) and is therefore assigned to nu(Fe-NO). The admixture of Fe-N-O bending character is small. Main contributions to the Fe-N-O bend are observed in the 520-580 cm(-1) region, distributed over a number of in-plane (ip) polarized porphyrin-based vibrations. The main component, assigned to delta(ip)(Fe-N-O), is identified with the feature at 563 cm(-1). The Fe-N-O bend also shows strong mixing with the Fe-NO stretching internal coordinate, as evidenced by the oop NRVS intensity in the 520-580 cm(-1) region. Very accurate normal mode descriptions of nu(Fe-NO) and delta(ip)(Fe-N-O) have been obtained in this study. These results contradict previous interpretations of the vibrational spectra of 6C ferrous heme-nitrosyls where the higher energy feature at approximately 550 cm(-1) had usually been associated with nu(Fe-NO). Furthermore, these results provide key insight into NO binding to ferrous heme active sites in globins and other heme proteins, in particular with respect to (a) the effect of hydrogen bonding to the coordinated NO and (b) changes in heme dynamics upon NO coordination. [Fe(TPP)(MI)(NO)] constitutes an excellent model system for ferrous NO adducts of myoglobin (Mb) mutants where the distal histidine (His64) has been removed. Comparison to the reported vibrational data for wild-type (wt) Mb-NO then shows that the effect of H bonding to the coordinated NO is weak and mostly leads to a polarization of the pi/pi* orbitals of bound NO. In addition, the observation that delta(ip)(Fe-N-O) does not correlate well with nu(N-O) can be traced back to the very mixed nature of this mode. The Fe-N(imidazole) stretching frequency is observed at 149 cm(-1) in [Fe(TPP)(MI)(NO)], and spectral changes upon NO binding to five-coordinate ferrous heme active sites are discussed. The obtained high-quality force constants for the Fe-NO and N-O bonds of 2.57 and 11.55 mdyn/A can further be compared to those of corresponding 5C species, which allows for a quantitative analysis of the sigma trans interaction between the proximal imidazole (His) ligand and NO. This is key for the activation of the NO sensor soluble guanylate cyclase. Finally, DFT methods are calibrated against the experimentally determined vibrational properties of the Fe-N-O subunit in 1. DFT is in fact incapable of reproducing the vibrational energies and normal mode descriptions of the Fe-N-O unit well, and thus, DFT-based predictions of changes in vibrational properties upon heme modification or other perturbations of these 6C complexes have to be treated with caution.

Electronic structure and dynamics of nitrosyl porphyrins

Nitric oxide (NO) is a signaling molecule employed to regulate essential physiological processes. Thus, there is great interest in understanding the interaction of NO with heme, which is found at the active site of many proteins that recognize NO, as well as those involved in its creation and elimination. We summarize what we have learned from investigations of the structure, vibrational properties, and conformational dynamics of NO complexes with ferrous porphyrins, as well as computational investigations in support of these experimental studies. Multitemperature crystallographic data reveal variations in the orientational disorder of the nitrosyl ligand. In some cases, equilibria among NO orientations can be analyzed using the van't Hoff relationship and the free energy and enthalpy of the solid-state transitions evaluated experimentally. Density functional theory (DFT) calculations predict that intrinsic barriers to torsional rotation are smaller than thermal energies at physiological temperatures, and the coincidence of observed NO orientations with minima in molecular mechanics potentials indicates that nonbonded interactions with other chemical groups control the conformational freedom of the bound NO. In favorable cases, reduced disorder at low temperatures exposes subtle structural features including off-axis tilting of the Fe-NO bond and anisotropy of the equatorial Fe-N bonds. We also present the results of nuclear resonance vibrational spectroscopy measurements on oriented single crystals of [Fe(TPP)(NO)] and [Fe(TPP)(1-MeIm)(NO)]. These describe the anisotropic vibrational motion of iron in five- and six-coordinate heme-NO complexes and reveal vibrations of all Fe-ligand bonds as well as low-frequency molecular distortions associated with the doming of the heme upon ligand binding. A quantitative comparison with predicted frequencies, amplitudes, and directions facilitates identification of the vibrational modes but also suggests that commonly used DFT functionals are not fully successful at capturing the trans interaction between the axial NO and imidazole ligands. This supports previous conclusions that heme-NO complexes exhibit an unusual degree of variability with respect to the computational method, and we speculate that this variability hints at a genuine electronic instability that a protein can exploit to tune its reactivity. We anticipate that ongoing characterization of heme-NO complexes will deepen our understanding of their structure, dynamics, and reactivity.

Nuclear resonance vibrational spectroscopy applied to [Fe(OEP)(NO)]: the vibrational assignments of five-coordinate ferrous heme-nitrosyls and implications for electronic structure

This study presents Nuclear Resonance Vibrational Spectroscopy (NRVS) data on the five-coordinate (5C) ferrous heme-nitrosyl complex [Fe(OEP)(NO)] (1, OEP(2-) = octaethylporphyrinato dianion) and the corresponding (15)N(18)O labeled complex. The obtained spectra identify two isotope sensitive features at 522 and 388 cm(-1), which shift to 508 and 381 cm(-1), respectively, upon isotope labeling. These features are assigned to the Fe-NO stretch nu(Fe-NO) and the in-plane Fe-N-O bending mode delta(ip)(Fe-N-O), the latter has been unambiguously assigned for the first time for 1. The obtained NRVS data were simulated using our quantum chemistry centered normal coordinate analysis (QCC-NCA). Since complex 1 can potentially exist in 12 different conformations involving the FeNO and peripheral ethyl orientations, extended density functional theory (DFT) calculations and QCC-NCA simulations were performed to determine how these conformations affect the NRVS properties of [Fe(OEP)NO]. These results show that the properties and force constants of the FeNO unit are hardly affected by the conformational changes involving the ethyl substituents. On the other hand, the NRVS-active porphyrin-based vibrations around 340-360, 300-320, and 250-270 cm(-1) are sensitive to the conformational changes. The spectroscopic changes observed in these regions are due to selective mechanical couplings of one component of E(u)-type (in ideal D(4h) symmetry) porphyrin-based vibrations with the in-plane Fe-N-O bending mode. This leads to the observed variations in Fe(OEP) core mode energies and NRVS intensities without affecting the properties of the FeNO unit. The QCC-NCA simulated NRVS spectra of 1 show excellent agreement with experiment, and indicate that conformer F is likely present in the samples of this complex investigated here. The observed porphyrin-based vibrations in the NRVS spectra of 1 are also assigned based on the QCC-NCA results. The obtained force constants of the Fe-NO and N-O bonds are 2.83-2.94 (based on the DFT functional applied) and about 12.15 mdyn/A, respectively. The electronic structures of 5C ferrous heme-nitrosyls in different model complexes are then analyzed, and variations in their properties based on different porphyrin substituents are explained. Finally, the shortcomings of different DFT functionals in describing the axial FeNO subunit in heme-nitrosyls are elucidated.

Dynamics of Rhodobacter capsulatus [2FE-2S] ferredoxin VI and Aquifex aeolicus ferredoxin 5 via nuclear resonance vibrational spectroscopy (NRVS) and resonance Raman spectroscopy

We have used (57)Fe nuclear resonance vibrational spectroscopy (NRVS) to study the Fe(2)S(2)(Cys)(4) sites in oxidized and reduced [2Fe-2S] ferredoxins from Rhodobacter capsulatus (Rc FdVI) and Aquifex aeolicus (Aa Fd5). In the oxidized forms, nearly identical NRVS patterns are observed, with strong bands from Fe-S stretching modes peaking around 335 cm(-1), and additional features observed as high as the B(2u) mode at approximately 421 cm(-1). Both forms of Rc FdVI have also been investigated by resonance Raman (RR) spectroscopy. There is good correspondence between NRVS and Raman frequencies, but because of different selection rules, intensities vary dramatically between the two kinds of spectra. For example, the B(3u) mode at approximately 288 cm(-1), attributed to an asymmetric combination of the two FeS(4) breathing modes, is often the strongest resonance Raman feature. In contrast, it is nearly invisible in the NRVS, as there is almost no Fe motion in such FeS(4) breathing. NRVS and RR analysis of isotope shifts with (36)S-substituted into bridging S(2-) ions in Rc FdVI allowed quantitation of S(2-) motion in different normal modes. We observed the symmetric Fe-Fe stretching mode at approximately 190 cm(-1) in both NRVS and RR spectra. At still lower energies, the NRVS presents a complex envelope of bending, torsion, and protein modes, with a maximum at 78 cm(-1). The (57)Fe partial vibrational densities of states (PVDOS) were interpreted by normal-mode analysis with optimization of Urey-Bradley force fields. Progressively more complex D(2h) Fe(2)S(2)S'(4), C(2h) Fe(2)S(2)(SCC)(4), and C(1) Fe(2)S(2)(Cys)(4) models were optimized by comparison with the experimental spectra. After modification of the CHARMM22 all-atom force field by the addition of refined Fe-S force constants, a simulation employing the complete protein structure was used to reproduce the PVDOS, with better results in the low frequency protein mode region. This process was then repeated for analysis of data on the reduced FdVI. Finally, the degree of collectivity was used to quantitate the delocalization of the dynamic properties of the redox-active Fe site. The NRVS technique demonstrates great promise for the observation and quantitative interpretation of the dynamical properties of Fe-S proteins.