Phonon density of states measured by inelastic nuclear resonant scattering

Exploring the oxidation behavior of undiluted and diluted iron particles for energy storage: Mössbauer spectroscopic analysis and kinetic modeling

Iron is an abundant and non-toxic element that holds great potential as energy carrier for large-scale and long-term energy storage. While from a general viewpoint iron oxidation is well-known, the detailed kinetics of oxidation for micrometer sized particles are missing, but required to enable large-scale utilization for energy production. In this work, iron particles are subjected to temperature-programmed oxidation. By dilution with boron nitride a sintering of the particles is prevented enabling to follow single particle effects. The mass fractions of iron and its oxides are determined for different oxidation times using Mössbauer spectroscopy. On the basis of the extracted phase compositions obtained at different times and temperatures (600-700 °C), it can be concluded that also for particles the oxidation follows a parabolic rate law. The parabolic rate constants are determined in this transition region. Knowledge of the particle size distribution and its consideration in modeling the oxidation kinetics of iron powder has proven to be crucial.

Phonon energy dissipation in friction between black phosphorus layers

Herein, we employ molecular dynamics simulations to decode the friction properties and phonon energy dissipation between black phosphorus layers. The observations reveal the influence of three factors, temperature, velocity, and normal load, on the friction force of monolayer/bilayer black phosphorus. Specifically, friction is negatively correlated with layer thickness and temperature, and positively correlated with velocity and normal load. The change in friction force is further explained in terms of frictional energy dissipation, and supplemented by the height of potential barriers as well as the number of excited phonons. From the phonon spectrum analysis, the phonon number at the contact interface is found to be higher than that at the non-contact interface. This is due to the larger distance of the contact interface atoms deviate from their equilibrium positions, resulting in higher total energy generated by more intense oscillations, and therefore contributes greater to friction.

Coupling Effect of Structural Lubrication and Thermal Excitation on Phononic Friction

This work investigates the coupling effect of structural lubrication and thermal excitation on phononic friction between black phosphorus (BP) layers. As the rotation angle increases from commensurate to incommensurate states, the friction gradually decreases at any temperature. However, the role of temperature in friction depends on commensurability. For a rotation angle less than 10°, increasing temperature leads to a decrease in friction due to thermal excitation. Conversely, when the rotation angle exceeds 10°, elevated temperature results in an increase in friction due to the effect of thermal collision. At a critical rotation angle of 10°, higher temperatures lead to reduced friction through thermal lubrication at low speeds, and at large speeds, the thermal excitation duration becomes so short that the role of thermal lubrication is weakened, and instead thermal collision dominates. Further research reveals that BP's ability to withstand different maximum speeds is also determined by commensurability. Finally, a method to measure the sliding period length of a rotated tip through an unrotated substrate potential energy topography is proposed and simply verified by using the phonon spectrum.

Reactive high-spin iron(IV)-oxo sites through dioxygen activation in a metal-organic framework

In nature, nonheme iron enzymes use dioxygen to generate high-spin iron(IV)=O species for a variety of oxygenation reactions. Although synthetic chemists have long sought to mimic this reactivity, the enzyme-like activation of O2 to form high-spin iron(IV) = O species remains an unrealized goal. Here, we report a metal-organic framework featuring iron(II) sites with a local structure similar to that in α-ketoglutarate-dependent dioxygenases. The framework reacts with O2 at low temperatures to form high-spin iron(IV) = O species that are characterized using in situ diffuse reflectance infrared Fourier transform, in situ and variable-field Mössbauer, Fe Kβ x-ray emission, and nuclear resonance vibrational spectroscopies. In the presence of O2, the framework is competent for catalytic oxygenation of cyclohexane and the stoichiometric conversion of ethane to ethanol.

Collective motion in hcp-Fe at Earth's inner core conditions

Earth's inner core is predominantly composed of solid iron (Fe) and displays intriguing properties such as strong shear softening and an ultrahigh Poisson's ratio. Insofar, physical mechanisms to explain these features coherently remain highly debated. Here, we have studied longitudinal and shear wave velocities of hcp-Fe (hexagonal close-packed iron) at relevant pressure-temperature conditions of the inner core using in situ shock experiments and machine learning molecular dynamics (MLMD) simulations. Our results demonstrate that the shear wave velocity of hcp-Fe along the Hugoniot in the premelting condition, defined as T/Tm (Tm: melting temperature of iron) above 0.96, is significantly reduced by ~30%, while Poisson's ratio jumps to approximately 0.44. MLMD simulations at 230 to 330 GPa indicate that collective motion with fast diffusive atomic migration occurs in premelting hcp-Fe primarily along [100] or [010] crystallographic direction, contributing to its elastic softening and enhanced Poisson's ratio. Our study reveals that hcp-Fe atoms can diffusively migrate to neighboring positions, forming open-loop and close-loop clusters in the inner core conditions. Hcp-Fe with collective motion at the inner core conditions is thus not an ideal solid previously believed. The premelting hcp-Fe with collective motion behaves like an extremely soft solid with an ultralow shear modulus and an ultrahigh Poisson's ratio that are consistent with seismic observations of the region. Our findings indicate that premelting hcp-Fe with fast diffusive motion represents the underlying physical mechanism to help explain the unique seismic and geodynamic features of the inner core.

Nuclear Resonance Vibrational Spectroscopy Definition of Peroxy Intermediates in Catechol Dioxygenases: Factors that Determine Extra- versus Intradiol Cleavage

The extradiol dioxygenases (EDOs) and intradiol dioxygenases (IDOs) are nonheme iron enzymes that catalyze the oxidative aromatic ring cleavage of catechol substrates, playing an essential role in the carbon cycle. The EDOs and IDOs utilize very different FeII and FeIII active sites to catalyze the regiospecificity in their catechol ring cleavage products. The factors governing this difference in cleavage have remained undefined. The EDO homoprotocatechuate 2,3-dioxygenase (HPCD) and IDO protocatechuate 3,4-dioxygenase (PCD) provide an opportunity to understand this selectivity, as key O2 intermediates have been trapped for both enzymes. Nuclear resonance vibrational spectroscopy (in conjunction with density functional theory calculations) is used to define the geometric and electronic structures of these intermediates as FeII-alkylhydroperoxo (HPCD) and FeIII-alkylperoxo (PCD) species. Critically, in both intermediates, the initial peroxo bond orientation is directed toward extradiol product formation. Reaction coordinate calculations were thus performed to evaluate both the extra- and intradiol O-O cleavage for the simple organic alkylhydroperoxo and for the FeII and FeIII metal catalyzed reactions. These results show the FeII-alkylhydroperoxo (EDO) intermediate undergoes facile extradiol O-O bond homolysis due to its extra e-, while for the FeIII-alkylperoxo (IDO) intermediate the extradiol cleavage involves a large barrier and would yield the incorrect extradiol product. This prompted our evaluation of a viable mechanism to rearrange the FeIII-alkylperoxo IDO intermediate for intradiol cleavage, revealing a key role in the rebinding of the displaced Tyr447 ligand in this rearrangement, driven by the proton delivery necessary for O-O bond cleavage.

Isotopic enrichment in lanthanide coordination complexes: contribution to single-molecule magnets and spin qudit insights

Lanthanide Single-Molecule Magnets (SMMs) fascinate the scientific community due to their plethora of potential applications ranging from data storage to spintronic devices and quantum computing. This review article proposes a comprehensive description of the influence of the nuclear spin, i.e. hyperfine interaction, on the magnetic properties of lanthanide SMMs and on quantum information processing of qudit. This influence is analysed for non-Kramers and Kramers lanthanide SMMs as well as for the electronic distribution of the electron in 4f orbitals i.e. oblate and prolate ions. Then the role of magnetic interactions in isotopically enriched polynuclear Dy(III) SMMs is discussed. Finally the possible effect of superhyperfine interaction due to the nuclear spin of elements originating from the surrounding of the lanthanide centre is analyzed. The effect of nuclear spin on the dynamics of the lanthanide SMMs is demonstrated using different techniques such as magnetometry, muon spectroscopy (μ-SR), and Mössbauer and Resonance Vibrational Spectroscopies.

Heme protonation affects iron-NO binding in the NO transport protein nitrophorin

The nitrophorins (NPs) comprise an unusual group of heme proteins with stable ferric heme iron nitric oxide (Fe-NO) complexes. They are found in the salivary glands of the blood-sucking kissing bug Rhodnius prolixus, which uses the NPs to transport the highly reactive signaling molecule NO. Nuclear resonance vibrational spectroscopy (NRVS) of both isoform NP2 and a mutant NP2(Leu132Val) show, after addition of NO, a strong structured vibrational band at around 600 cm^-1, which is due to modes with significant Fe-NO bending and stretching contribution. Based on a hybrid calculation method, which uses density functional theory and molecular mechanics, it is demonstrated that protonation of the heme carboxyl groups does influence both the vibrational properties of the Fe-NO entity and its electronic ground state. Moreover, heme protonation causes a significant increase of the gap between the highest occupied and lowest unoccupied molecular orbital by almost one order of magnitude leading to a stabilization of the Fe-NO bond.

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

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

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

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

Phonon confinement and interface lattice dynamics of ultrathin high-k rare earth sesquioxide films: the case of Eu2O3 on YSZ(001)

The spatial confinement of atoms at surfaces and interfaces significantly alters the lattice dynamics of thin films, heterostructures and multilayers. Ultrathin films with high dielectric constants (high-k) are of paramount interest for applications as gate layers in current and future integrated circuits. Here we report a lattice dynamics study of high-k Eu₂O₃ films with thicknesses of 21.3, 2.2, 1.3, and 0.8 nm deposited on YSZ(001). The Eu-partial phonon density of states (PDOS), obtained from nuclear inelastic scattering, exhibits broadening of the phonon peaks accompanied by up to a four-fold enhancement of the number of low-energy states compared to the ab initio calculated PDOS of a perfect Eu₂O₃ crystal. Our analysis demonstrates that while the former effect reflects the reduced phonon lifetimes observed in thin films due to scattering from lattice defects, the latter phenomenon arises from an ultrathin EuO layer formed between the thin Eu₂O₃ film and the YSZ(001) substrate. Thus, our work uncovers another potential source of vibrational anomalies in thin films and multilayers, which has to be cautiously considered.

Mechanisms of O2 Activation by Mononuclear Non-Heme Iron Enzymes

Two major subclasses of mononuclear non-heme ferrous enzymes use two electron-donating organic cofactors (α-ketoglutarate or pterin) to activate O₂ to form Fe^IV═O intermediates that further react with their substrates through hydrogen atom abstraction or electrophilic aromatic substitution. New spectroscopic methodologies have been developed, enabling the study of the active sites in these enzymes and their oxygen intermediates. Coupled to electronic structure calculations, the results of these spectroscopies provide fundamental insight into mechanism. This Perspective summarizes the results of these studies in elucidating the mechanism of dioxygen activation to form the Fe^IV═O intermediate and the geometric and electronic structure of this intermediate that enables its high reactivity and selectivity in product formation.

Nuclear Resonance Vibrational Spectroscopy: A Modern Tool to Pinpoint Site-Specific Cooperative Processes

Nuclear resonant vibrational spectroscopy (NRVS) is a synchrotron radiation (SR)-based nuclear inelastic scattering spectroscopy that measures the phonons (i.e., vibrational modes) associated with the nuclear transition. It has distinct advantages over traditional vibration spectroscopy and has wide applications in physics, chemistry, bioinorganic chemistry, materials sciences, and geology, as well as many other research areas. In this article, we present a scientific and figurative description of this yet modern tool for the potential users in various research fields in the future. In addition to short discussions on its development history, principles, and other theoretical issues, the focus of this article is on the experimental aspects, such as the instruments, the practical measurement issues, the data process, and a few examples of its applications. The article concludes with introduction to non-57Fe NRVS and an outlook on the impact from the future upgrade of SR rings.

Lattice Dynamics and Structural Phase Transitions in Eu2O3

Using the density functional theory, we study the structural and lattice dynamical properties of europium sesquioxide (Eu₂O₃) in the cubic, trigonal, and monoclinic phases. The obtained lattice parameters and energies of the Raman modes show a good agreement with the available experimental data. The Eu-partial phonon density of states calculated for the cubic structure is compared with the nuclear inelastic scattering data obtained from a 20 nm thick Eu₂O₃ film deposited on a YSZ substrate. A small shift of the experimental spectrum to higher energies results from a compressive strain induced by the substrate. On the basis of lattice and phonon properties, we analyze the mechanisms of structural transitions between different phases of Eu₂O₃.

The phase transitions of rare-earth sesquioxide Eu₂O₃ are very complicated. Analyzing dynamical properties of this compound for experimentally observed C-, A-, and B-type phases and extracting key symmetry elements common for these phases, we describe transition mechanisms and their sequence. Our DFT first-principles predictions are supported by the nuclear inelastic scattering measurements.

Operando NRIXS and XAFS Investigation of Segregation Phenomena in Fe-Cu and Fe-Ag Nanoparticle Catalysts during CO2 Electroreduction

Operando nuclear resonant inelastic X‐ray scattering (NRIXS) and X‐ray absorption fine‐structure spectroscopy (XAFS) measurements were used to gain insight into the structure and surface composition of FeCu and FeAg nanoparticles (NPs) during the electrochemical CO₂ reduction (CO₂RR) and to extract correlations with their catalytic activity and selectivity. The formation of a core–shell structure during CO₂RR for FeAg NPs was inferred from the analysis of the operando NRIXS data (phonon density of states, PDOS) and XAFS measurements. Electrochemical analysis of the FeAg NPs revealed a faradaic selectivity of 36 % for CO in 0.1 M KHCO₃ at −1.1 V vs. RHE, similar to that of pure Ag NPs. In contrast, a predominant selectivity towards H₂ evolution is obtained in the case of the FeCu NPs, analogous to the results obtained for pure Fe NPs, although small Cu NPs have also been shown to favor H₂ production.

The Spectroscopy of Nitrogenases

Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.

Exploring the Vibrational Side of Spin-Phonon Coupling in Single-Molecule Magnets via 161 Dy Nuclear Resonance Vibrational Spectroscopy

Synchrotron-based nuclear resonance vibrational spectroscopy (NRVS) using the Mössbauer isotope 161 Dy has been employed for the first time to study the vibrational properties of a single-molecule magnet (SMM) incorporating DyIII , namely [Dy(Cy3 PO)2 (H2 O)5 ]Br3 ⋅2 (Cy3 PO)⋅2 H2 O ⋅2 EtOH. The experimental partial phonon density of states (pDOS), which includes all vibrational modes involving a displacement of the DyIII ion, was reproduced by means of simulations using density functional theory (DFT), enabling the assignment of all intramolecular vibrational modes. This study proves that 161 Dy NRVS is a powerful experimental tool with significant potential to help to clarify the role of phonons in SMMs.

The influence of phonon softening on the superconducting critical temperature of Sn nanostructures

The increase in superconducting transition temperature (T_C) of Sn nanostructures in comparison to bulk, was studied. Changes in the phonon density of states (PDOS) of the weakly coupled superconductor Sn were analyzed and correlated with the increase in T_C measured by magnetometry. The PDOS of all nanostructured samples shows a slightly increased number of low-energy phonon modes and a strong decrease in the number of high-energy phonon modes in comparison to the bulk Sn PDOS. The phonon densities of states, which were determined previously using nuclear resonant inelastic X-ray scattering, were used to calculate the superconducting transition temperature using the Allen-Dynes-McMillan (ADMM) formalism. Both the calculated as well as the experimentally determined values of T_C show an increase compared to the bulk superconducting transition temperature. The good agreement between these values indicates that phonon softening has a major influence on the superconducting transition temperature of Sn nanostructures. The influence of electron confinement effects appears to be minor in these systems.

High-pressure nuclear inelastic scattering with backscattering monochromatization

The capability to perform high-pressure low-temperature nuclear inelastic scattering on ¹²⁵Te and ¹²¹Sb with a sapphire backscattering monochromator is presented. This technique was applied to measure nuclear inelastic scattering in TeO₂ at pressures up to 10 GPa and temperatures down to 25 K. The evaluated partial Te densities of phonon states were compared with theoretical calculations and with Raman scattering measured under the same conditions. The high-pressure cell developed in this work can also be used for other techniques at pressures up to at least 100 GPa.

Phonon confinement and spin-phonon coupling in tensile-strained ultrathin EuO films

Reducing the material sizes to the nanometer length scale leads to drastic modifications of the propagating lattice excitations (phonons) and their interactions with electrons and magnons. In EuO, a promising material for spintronic applications in which a giant spin-phonon interaction is present, this might imply a reduction of the degree of spin polarization in thin films. Therefore, a comprehensive investigation of the lattice dynamics and spin-phonon interaction in EuO films is necessary for practical applications. We report a systematic lattice dynamics study of ultrathin EuO(001) films using nuclear inelastic scattering on the Mössbauer-active isotope 151Eu and first-principles theory. The films were epitaxially grown on YAlO3(110), which induces a tensile strain of ca. 2%. By reducing the EuO layer thickness from 8 nm to a sub-monolayer coverage, the Eu-partial phonon density of states (PDOS) reveals a gradual enhancement of the number of low-energy phonon states and simultaneous broadening and suppression of the peaks. These deviations from bulk features lead to significant anomalies in the vibrational thermodynamic and elastic properties calculated from the PDOS. The experimental results, supported by first-principles theory, unveil a reduction of the strength of the spin-phonon interaction in the tensile-strained EuO by a factor of four compared to a strain-free lattice.

Geometric and Electronic Structural Contributions to Fe/O2 Reactivity

While two classes of non-heme iron enzymes use ferric centers to activate singlet organic substrates for the spin forbidden reaction with ³O₂, most classes use high spin ferrous sites to activate dioxygen. These Fe^II active sites do not exhibit intense absorption bands and have an integer spin ground state thus are mostly EPR inactive. We have developed new spectroscopic methodologies that provide geometric and electronic structural insight into the ferrous centers and their interactions with cosubstrates for dioxygen activation and into the nature of the intermediates generated in these reactions. First, we present our variable-temperature variable-field magnetic circular dichroism (VTVH MCD) methodology to experimentally define the geometric and electronic structure of the high spin ferrous active site. Then, we focus on using Nuclear Resonance Vibrational Spectroscopy (NRVS, performed at SPring-8) to define geometric structure and VTVH MCD to define the electronic structure of the Fe^III-OOH and Fe^IV=O intermediates generated in O₂ activation and the spin state dependence of their frontier molecular orbitals (FMOs) in controlling reactivity. Experimentally validated reaction coordinates are derived for the anticancer drug bleomycin in its cleavage of DNA and for an alpha- ketoglutarate dependent dioxygenase in its selective halogenation over the thermodynamically favored hydroxylation of substrate.

Nuclear Resonance Vibrational Spectroscopy Definition of O2 Intermediates in an Extradiol Dioxygenase: Correlation to Crystallography and Reactivity

The extradiol dioxygenases are a large subclass of mononuclear nonheme Fe enzymes that catalyze the oxidative cleavage of catechols distal to their OH groups. These enzymes are important in bioremediation, and there has been significant interest in understanding how they activate O₂. The extradiol dioxygenase homoprotocatechuate 2,3-dioxygenase (HPCD) provides an opportunity to study this process, as two O₂ intermediates have been trapped and crystallographically defined using the slow substrate 4-nitrocatechol (4NC): a side-on Fe-O₂-4NC species and a Fe-O₂-4NC peroxy bridged species. Also with 4NC, two solution intermediates have been trapped in the H200N variant, where H200 provides a second-sphere hydrogen bond in the wild-type enzyme. While the electronic structure of these solution intermediates has been defined previously as Fe^III-superoxo-catecholate and Fe^III-peroxy-semiquinone, their geometric structures are unknown. Nuclear resonance vibrational spectroscopy (NRVS) is an important tool for structural definition of nonheme Fe-O₂ intermediates, as all normal modes with Fe displacement have intensity in the NRVS spectrum. In this study, NRVS is used to define the geometric structure of the H200N-4NC solution intermediates in HPCD as an end-on Fe^III-superoxo-catecholate and an end-on Fe^III-hydroperoxo-semiquinone. Parallel calculations are performed to define the electronic structures and protonation states of the crystallographically defined wild-type HPCD-4NC intermediates, where the side-on intermediate is found to be a Fe^III-hydroperoxo-semiquinone. The assignment of this crystallographic intermediate is validated by correlation to the NRVS data through computational removal of H200. While the side-on hydroperoxo semiquinone intermediate is computationally found to be nonreactive in peroxide bridge formation, it is isoenergetic with a superoxo catecholate species that is competent in performing this reaction. This study provides insight into the relative reactivities of Fe^III-superoxo and Fe^III-hydroperoxo intermediates in nonheme Fe enzymes and into the role H200 plays in facilitating extradiol catalysis.

A Nuclear Resonance Vibrational Spectroscopic Study of Oxy Myoglobins Reconstituted with Chemically Modified Heme Cofactors: Insights into the Fe-O2 Bonding and Internal Dynamics of the Protein

The molecular mechanism of O₂ binding to hemoglobin (Hb) and myoglobin (Mb) is a long-standing issue in the field of bioinorganic and biophysical chemistry. The nature of Fe-O₂ bond in oxy Hb and Mb had been extensively investigated by resonance Raman spectroscopy, which assigned the Fe-O₂ stretching bands at ∼570 cm^-1. However, resonance Raman assignment of the vibrational mode had been elusive due to the spectroscopic selection rule and to the limited information available about the ground-state molecular structure. Thus, nuclear resonance vibrational spectroscopy was applied to oxy Mbs reconstituted with ⁵⁷Fe-labeled native heme cofactor and two chemically modified ones. This advanced spectroscopy in conjunction with DFT analyses gave new insights into the nature of the Fe-O₂ bond of oxy heme by revealing the effect of heme peripheral substitutions on the vibrational dynamics of heme Fe atom, where the main Fe-O₂ stretching band of the native protein was characterized at ∼420 cm^-1.

SciPhon: a data analysis software for nuclear resonant inelastic X-ray scattering with applications to Fe, Kr, Sn, Eu and Dy

The synchrotron radiation technique of nuclear resonant inelastic X-ray scattering (NRIXS), also known as nuclear resonance vibrational spectroscopy or nuclear inelastic scattering, provides a wealth of information on the vibrational properties of solids. It has found applications in studies of lattice dynamics and elasticity, superconductivity, heme biochemistry, seismology, isotope geochemistry and many other fields. It involves probing the vibrational modes of solids by using the nuclear resonance of Mössbauer isotopes such as ⁵⁷Fe, ⁸³Kr, ¹¹⁹Sn, ¹⁵¹Eu and ¹⁶¹Dy. After data reduction, it provides the partial phonon density of states of the Mössbauer isotope that is investigated, as well as many other derived quantities such as the mean force constant of the chemical bonds and the Debye velocity. The data reduction is, however, not straightforward and involves removal of the elastic peak, normalization and Fourier-Log transformation. Furthermore, some of the quantities derived are highly sensitive to details in the baseline correction. A software package and several novel procedures to streamline and hopefully improve the reduction of the NRIXS data generated at sector 3ID of the Advanced Photon Source have been developed. The graphical user interface software is named SciPhon and runs as a Mathematica package. It is easily portable to other platforms and can be easily adapted for reducing data generated at other beamlines. Several tests and comparisons are presented that demonstrate the usefulness of this software, whose results have already been used in several publications. Here, the SciPhon software is used to reduce Kr, Sn, Eu and Dy NRIXS data, and potential implications for interpreting natural isotopic variations in those systems are discussed.

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.

Terminal Hydride Species in [FeFe]-Hydrogenases Are Vibrationally Coupled to the Active Site Environment

A combination of nuclear resonance vibrational spectroscopy (NRVS), FTIR spectroscopy, and DFT calculations was used to observe and characterize Fe-H/D bending modes in CrHydA1 [FeFe]-hydrogenase Cys-to-Ser variant C169S. Mutagenesis of cysteine to serine at position 169 changes the functional group adjacent to the H-cluster from a -SH to -OH, thus altering the proton transfer pathway. The catalytic activity of C169S is significantly reduced compared to that of native CrHydA1, presumably owing to less efficient proton transfer to the H-cluster. This mutation enabled effective capture of a hydride/deuteride intermediate and facilitated direct detection of the Fe-H/D normal modes. We observed a significant shift to higher frequency in an Fe-H bending mode of the C169S variant, as compared to previous findings with reconstituted native and oxadithiolate (ODT)-substituted CrHydA1. On the basis of DFT calculations, we propose that this shift is caused by the stronger interaction of the -OH group of C169S with the bridgehead -NH- moiety of the active site, as compared to that of the -SH group of C169 in the native enzyme.

NRVS Studies of the Peroxide Shunt Intermediate in a Rieske Dioxygenase and Its Relation to the Native FeII O2 Reaction

The Rieske dioxygenases are a major subclass of mononuclear nonheme iron enzymes that play an important role in bioremediation. Recently, a high-spin FeIII-(hydro)peroxy intermediate (BZDOp) has been trapped in the peroxide shunt reaction of benzoate 1,2-dioxygenase. Defining the structure of this intermediate is essential to understanding the reactivity of these enzymes. Nuclear resonance vibrational spectroscopy (NRVS) is a recently developed synchrotron technique that is ideal for obtaining vibrational, and thus structural, information on Fe sites, as it gives complete information on all vibrational normal modes containing Fe displacement. In this study, we present NRVS data on BZDOp and assign its structure using these data coupled to experimentally calibrated density functional theory calculations. From this NRVS structure, we define the mechanism for the peroxide shunt reaction. The relevance of the peroxide shunt to the native FeII/O2 reaction is evaluated. For the native FeII/O2 reaction, an FeIII-superoxo intermediate is found to react directly with substrate. This process, while uphill thermodynamically, is found to be driven by the highly favorable thermodynamics of proton-coupled electron transfer with an electron provided by the Rieske [2Fe-2S] center at a later step in the reaction. These results offer important insight into the relative reactivities of FeIII-superoxo and FeIII-hydroperoxo species in nonheme Fe biochemistry.

Sterically Stabilized Terminal Hydride of a Diiron Dithiolate

The kinetically robust hydride [t-HFe₂(Me₂pdt)(CO)₂(dppv)₂]⁺ ([t-H1]⁺) (Me₂pdt^2- = Me₂C(CH₂S^-)₂; dppv = cis-1,2-C₂H₂(PPh₂)₂) and related derivatives were prepared with ⁵⁷Fe enrichment for characterization by NMR, FT-IR, and NRVS. The experimental results were rationalized using DFT molecular modeling and spectral simulations. The spectroscopic analysis was aimed at supporting assignments of Fe-H vibrational spectra as they relate to recent measurements on [FeFe]-hydrogenase enzymes. The combination of bulky Me₂pdt^2- and dppv ligands stabilizes the terminal hydride with respect to its isomerization to the 5-16 kcal/mol more stable bridging hydride ([μ-H1]⁺) with t_1/2(313.3 K) = 19.3 min. In agreement with the nOe experiments, the calculations predict that one methyl group in [t-H1]⁺ interacts with the hydride with a computed CH···HFe distance of 1.7 Å. Although [t-H⁵⁷1]⁺ exhibits multiple NRVS features in the 720-800 cm^-1 region containing the bending Fe-H modes, the deuterated [t-D⁵⁷1]⁺ sample exhibits a unique Fe-D/CO band at ∼600 cm^-1. In contrast, the NRVS spectra for [μ-H⁵⁷1]⁺ exhibit weaker bands near 670-700 cm^-1 produced by the Fe-H-Fe wagging modes coupled to Me₂pdt^2- and dppv motions.

NRVS for Fe in Biology: Experiment and Basic Interpretation

For over 20 years, nuclear resonance vibrational spectroscopy (NRVS) has been used to study vibrational dynamics of iron-containing materials. With the only selection rule being iron motion, ⁵⁷Fe NRVS has become an excellent tool to study iron-containing enzymes. Over the past decade, considerable progress has been made in the study of complex metalloenzymes using NRVS. Iron cofactors in heme-containing globins; [2Fe2S], [3Fe4S], [4Fe4S] proteins; the [NiFe] and [FeFe] hydrogenases; and nitrogenases have been explored in a fashion not possible through traditional vibrational spectroscopy. In this chapter, we discuss the basics of NRVS, a strategy to perform NRVS, and a discussion of the application of NRVS on rubredoxin and [FeFe] hydrogenase.

A compact membrane-driven diamond anvil cell and cryostat system for nuclear resonant scattering at high pressure and low temperature

A new miniature panoramic diamond anvil cell (mini-pDAC) as well as a unique gas membrane-driven mechanism is developed and implemented to measure electronic, magnetic, vibrational, and thermodynamic properties of materials using the nuclear resonant inelastic X-ray scattering (NRIXS) and the synchrotron Mössbauer spectroscopy (SMS) simultaneously at high pressure (over Mbar) and low temperature (T < 10 K). The gas membrane system allows in situ pressure tuning of the mini-pDAC at low temperature. The mini-pDAC fits into a specially designed compact liquid helium flow cryostat system to achieve low temperatures, where liquid helium flows through the holder of the mini-pDAC to cool the sample more efficiently. The system has achieved sample temperatures as low as 9 K. Using the membrane, sample pressures of up to 1.4 Mbar have been generated from this mini-pDAC. The instrument has been routinely used at 3-ID, Advanced Photon Source, for NRIXS and SMS studies. The same instrument can easily be used for other X-ray techniques, such as X-ray radial diffraction, X-ray Raman scattering, X-ray emission spectroscopy, and X-ray inelastic scattering under high pressure and low temperature. In this paper, technical details of the mini-pDAC, membrane engaging mechanism, and the cryostat system are described, and some experimental results are discussed.

Reaction Coordinate Leading to H2 Production in [FeFe]-Hydrogenase Identified by Nuclear Resonance Vibrational Spectroscopy and Density Functional Theory

[FeFe]-hydrogenases are metalloenzymes that reversibly reduce protons to molecular hydrogen at exceptionally high rates. We have characterized the catalytically competent hydride state (Hhyd) in the [FeFe]-hydrogenases from both Chlamydomonas reinhardtii and Desulfovibrio desulfuricans using 57Fe nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT). H/D exchange identified two Fe-H bending modes originating from the binuclear iron cofactor. DFT calculations show that these spectral features result from an iron-bound terminal hydride, and the Fe-H vibrational frequencies being highly dependent on interactions between the amine base of the catalytic cofactor with both hydride and the conserved cysteine terminating the proton transfer chain to the active site. The results indicate that Hhyd is the catalytic state one step prior to H2 formation. The observed vibrational spectrum, therefore, provides mechanistic insight into the reaction coordinate for H2 bond formation by [FeFe]-hydrogenases.

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.

Spectroscopic and Computational Investigations of Ligand Binding to IspH: Discovery of Non-diphosphate Inhibitors

Isoprenoid biosynthesis is an important area for anti-infective drug development. One isoprenoid target is (E)-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate (HMBPP) reductase (IspH), which forms isopentenyl diphosphate and dimethylallyl diphosphate from HMBPP in a 2H+ /2e- reduction. IspH contains a 4 Fe-4 S cluster, and in this work, we first investigated how small molecules bound to the cluster by using HYSCORE and NRVS spectroscopies. The results of these, as well as other structural and spectroscopic investigations, led to the conclusion that, in most cases, ligands bound to IspH 4 Fe-4 S clusters by η1 coordination, forming tetrahedral geometries at the unique fourth Fe, ligand side chains preventing further ligand (e.g., H2 O, O2 ) binding. Based on these ideas, we used in silico methods to find drug-like inhibitors that might occupy the HMBPP substrate binding pocket and bind to Fe, leading to the discovery of a barbituric acid analogue with a Ki value of ≈500 nm against Pseudomonas aeruginosa IspH.

Peroxide Activation for Electrophilic Reactivity by the Binuclear Non-heme Iron Enzyme AurF

Binuclear non-heme iron enzymes activate O₂ for diverse chemistries that include oxygenation of organic substrates and hydrogen atom abstraction. This process often involves the formation of peroxo-bridged biferric intermediates, only some of which can perform electrophilic reactions. To elucidate the geometric and electronic structural requirements to activate peroxo reactivity, the active peroxo intermediate in 4-aminobenzoate N-oxygenase (AurF) has been characterized spectroscopically and computationally. A magnetic circular dichroism study of reduced AurF shows that its electronic and geometric structures are poised to react rapidly with O₂. Nuclear resonance vibrational spectroscopic definition of the peroxo intermediate formed in this reaction shows that the active intermediate has a protonated peroxo bridge. Density functional theory computations on the structure established here show that the protonation activates peroxide for electrophilic/single-electron-transfer reactivity. This activation of peroxide by protonation is likely also relevant to the reactive peroxo intermediates in other binuclear non-heme iron enzymes.

A luminescent Pt2Fe spin crossover complex

A heterotrinuclear luminescent [Pt₂Fe] spin crossover (SCO) complex was developed, synthesized, and investigated.

High-pressure studies with x-rays using diamond anvil cells

Pressure profoundly alters all states of matter. The symbiotic development of ultrahigh-pressure diamond anvil cells, to compress samples to sustainable multi-megabar pressures; and synchrotron x-ray techniques, to probe materials' properties in situ, has enabled the exploration of rich high-pressure (HP) science. In this article, we first introduce the essential concept of diamond anvil cell technology, together with recent developments and its integration with other extreme environments. We then provide an overview of the latest developments in HP synchrotron techniques, their applications, and current problems, followed by a discussion of HP scientific studies using x-rays in the key multidisciplinary fields. These HP studies include: HP x-ray emission spectroscopy, which provides information on the filled electronic states of HP samples; HP x-ray Raman spectroscopy, which probes the HP chemical bonding changes of light elements; HP electronic inelastic x-ray scattering spectroscopy, which accesses high energy electronic phenomena, including electronic band structure, Fermi surface, excitons, plasmons, and their dispersions; HP resonant inelastic x-ray scattering spectroscopy, which probes shallow core excitations, multiplet structures, and spin-resolved electronic structure; HP nuclear resonant x-ray spectroscopy, which provides phonon densities of state and time-resolved Mössbauer information; HP x-ray imaging, which provides information on hierarchical structures, dynamic processes, and internal strains; HP x-ray diffraction, which determines the fundamental structures and densities of single-crystal, polycrystalline, nanocrystalline, and non-crystalline materials; and HP radial x-ray diffraction, which yields deviatoric, elastic and rheological information. Integrating these tools with hydrostatic or uniaxial pressure media, laser and resistive heating, and cryogenic cooling, has enabled investigations of the structural, vibrational, electronic, and magnetic properties of materials over a wide range of pressure-temperature conditions.

Anomalous Lattice Dynamics of EuSi_{2} Nanoislands: Role of Interfaces Unveiled

We report a systematic lattice dynamics study of EuSi_{2} films and nanoislands by in situ nuclear inelastic scattering on ^{151}Eu and ab initio theory. The Eu-partial phonon density of states of the nanoislands exhibits anomalous excess of phonon states at low and high energies, not present in the bulk and at the EuSi_{2}(001) surface. We demonstrate that atomic vibrations along the island-substrate interface give rise to phonon states both at low and high energies, while atomic vibrations across the island-island interface result in localized high-energy phonon modes.

High-resolution monochromator for iron nuclear resonance vibrational spectroscopy of biological samples

A new high-resolution monochromator for 14.4-keV X-rays has been designed and developed for the Fe nuclear resonance vibrational spectroscopy of biological samples. Higher flux and stability are especially important for measuring biological samples, because of the very weak signals produced due to the low concentrations of Fe-57. A 24% increase in flux while maintaining a high resolution below 0.9 meV is achieved in the calculation by adopting an asymmetric reflection of Ge, which is used as the first crystal of the three-bounce high-resolution monochromator. The small cost resulting from a 20% increase of the exit beam size is acceptable to our biological applications. The higher throughput of the new design has been experimentally verified. A fine rotation mechanics that that combines a weak-link hinge with a piezoelectric actuator was used for controlling the photon energy of the monochromatic beam. The resulting stability is sufficient to preserve the intrinsic resolution.

O2 Activation by Non-Heme Iron Enzymes

The non-heme Fe enzymes are ubiquitous in nature and perform a wide range of functions involving O₂ activation. These had been difficult to study relative to heme enzymes; however, spectroscopic methods that provide significant insight into the correlation of structure with function have now been developed. This Current Topics article summarizes both the molecular mechanism these enzymes use to control O₂ activation in the presence of cosubstrates and the oxygen intermediates these reactions generate. Three types of O₂ activation are observed. First, non-heme reactivity is shown to be different from heme chemistry where a low-spin Fe^III-OOH non-heme intermediate directly reacts with substrate. Also, two subclasses of non-heme Fe enzymes generate high-spin Fe^IV═O intermediates that provide both σ and π frontier molecular orbitals that can control selectivity. Finally, for several subclasses of non-heme Fe enzymes, binding of the substrate to the Fe^II site leads to the one-electron reductive activation of O₂ to an Fe^III-superoxide capable of H atom abstraction and electrophilic attack.

Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites

Fe^III-(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here, we present the NRVS spectra of side-on Fe^III-peroxy and end-on Fe^III-hydroperoxy model complexes and assign these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe-O-O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of Fe^III-peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.

Hydrogenase Enzymes and Their Synthetic Models: The Role of Metal Hydrides

Hydrogenase enzymes efficiently process H2 and protons at organometallic FeFe, NiFe, or Fe active sites. Synthetic modeling of the many H2ase states has provided insight into H2ase structure and mechanism, as well as afforded catalysts for the H2 energy vector. Particularly important are hydride-bearing states, with synthetic hydride analogues now known for each hydrogenase class. These hydrides are typically prepared by protonation of low-valent cores. Examples of FeFe and NiFe hydrides derived from H2 have also been prepared. Such chemistry is more developed than mimicry of the redox-inactive monoFe enzyme, although functional models of the latter are now emerging. Advances in physical and theoretical characterization of H2ase enzymes and synthetic models have proven key to the study of hydrides in particular, and will guide modeling efforts toward more robust and active species optimized for practical applications.

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.

A strenuous experimental journey searching for spectroscopic evidence of a bridging nickel-iron-hydride in [NiFe] hydrogenase

Direct spectroscopic evidence for a hydride bridge in the Ni-R form of [NiFe] hydrogenase has been obtained using iron-specific nuclear resonance vibrational spectroscopy (NRVS). The Ni-H-Fe wag mode at 675 cm(-1) is the first spectroscopic evidence for a bridging hydride in Ni-R as well as the first iron-hydride-related NRVS feature observed for a biological system. Although density function theory (DFT) calculation assisted the determination of the Ni-R structure, it did not predict the Ni-H-Fe wag mode at ∼ 675 cm(-1) before NRVS. Instead, the observed Ni-H-Fe mode provided a critical reference for the DFT calculations. While the overall science about Ni-R is presented and discussed elsewhere, this article focuses on the long and strenuous experimental journey to search for and experimentally identify the Ni-H-Fe wag mode in a Ni-R sample. As a methodology, the results presented here will go beyond Ni-R and hydrogenase research and will also be of interest to other scientists who use synchrotron radiation for measuring dilute samples or weak spectroscopic features.

Phonons in Ultrathin Oxide Films: 2D to 3D Transition in FeO on Pt(111)

The structural and magnetic properties of ultrathin FeO(111) films on Pt(111) with thicknesses from 1 to 16 monolayers (MLs) were studied using the nuclear inelastic scattering of synchrotron radiation. A distinct evolution of vibrational characteristics with thickness, revealed in the phonon density of states (PDOS), shows a textbook transition from 2D to 3D lattice dynamics. For the thinnest films of 1 and 2 ML, the low-energy part of the PDOS followed a linear ∝E dependence in energy that is characteristic for two-dimensional systems. This dependence gradually transforms with thickness to the bulk ∝E^{2} relationship. Density-functional theory phonon calculations perfectly reproduced the measured 1-ML PDOS within a simple model of a pseudomorphic FeO/Pt(111) interface. The calculations show that the 2D PDOS character is due to a weak coupling of the FeO film to the Pt(111) substrate. The evolution of the vibrational properties with an increasing thickness is closely related to a transient long-range magnetic order and stabilization of an unusual structural phase.