Introducing SpectraFit: An Open-Source Tool for Interactive Spectral Analysis.

In chemistry, analyzing spectra through peak fitting is a crucial task that helps scientists extract useful quantitative information about a sample's chemical composition or electronic structure. To make this process more efficient, we have developed a new open-source software tool called SpectraFit. This tool allows users to perform quick data fitting using expressions of distribution and linear functions through the command line interface (CLI) or Jupyter Notebook, which can run on Linux, Windows, and MacOS, as well as in a Docker container. As part of our commitment to good scientific practice, we have introduced an output file-locking system to ensure the accuracy and consistency of information. This system collects input data, results data, and the initial fitting model in a single file, promoting transparency, reproducibility, collaboration, and innovation. To demonstrate SpectraFit's user-friendly interface and the advantages of its output file-locking system, we are focusing on a series of previously published iron-sulfur dimers and their XAS spectra. We will show how to analyze the XAS spectra via CLI and in a Jupyter Notebook by simultaneously fitting multiple data sets using SpectraFit. Additionally, we will demonstrate how SpectraFit can be used as a black box and white box solution, allowing users to apply their own algorithms to engineer the data further. This publication, along with its Supporting Information and the Jupyter Notebook, serves as a tutorial to guide users through each step of the process. SpectraFit will streamline the peak fitting process and provide a convenient, standardized platform for users to share fitting models, which we hope will improve transparency and reproducibility in the field of spectroscopy.

Sulfur-Ligated [2Fe-2C] Clusters as Synthetic Model Systems for Nitrogenase.

Metal clusters featuring carbon and sulfur donors have coordination environments comparable to the active site of nitrogenase enzymes. Here, we report a series of di-iron clusters supported by the dianionic yldiide ligands, in which the Fe sites are bridged by two µ2-C atoms and four pendant S donors.The [L2Fe2] (L = {[Ph2P(S)]2C}2-) cluster is isolable in two oxidation levels, all-ferrous Fe2II and mixed-valence FeIIFeIII. The mixed-valence cluster displays two peaks in the Mössbauer spectra, indicating slow electron transfer between the two sites. The addition of the Lewis base 4-dimethylaminopyridine to the Fe2II cluster results in coordination with only one of the two Fe sites, even in the presence of an excess base. Conversely, the cluster reacts with 8 equiv of isocyanide tBuNC to give a monometallic complex featuring a new C-C bond between the ligand backbone and the isocyanide. The electronic structure descriptions of these complexes are further supported by X-ray absorption and resonant X-ray emission spectroscopies.

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

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

Elucidation of Structure-Activity Correlations in a Nickel Manganese Oxide Oxygen Evolution Reaction Catalyst by Operando Ni L-Edge X-ray Absorption Spectroscopy and 2p3d Resonant Inelastic X-ray Scattering.

Herein, we report the synthesis and electrochemical oxygen evolution experiments for a graphene-supported Ni3MnO4 catalyst. The changes that occur at the Ni active sites during the electrocatalyic oxygen evolution reaction (OER) were elucidated by a combination of operando Ni L-edge X-ray absorption spectroscopy (XAS) and Ni 2p3d resonant inelastic X-ray scattering (RIXS). These data are compared to reference measurements on NiO, ß-Ni(OH)2, ß-NiOOH, and γ-NiOOH. Through this comparative analysis, we are able to show that under alkaline conditions (0.1 M KOH), the oxides of the Ni3MnO4 catalyst are converted to hydroxides. At the onset of catalysis (1.47 V), the ß-Ni(OH)2-like phase is oxidized and converted to a dominantly γ-NiOOH phase. The present study thus challenges the notion that the ß-NiOOH phase is the active phase in OER and provides further evidence that the γ-NiOOH phase is catalytically active. The ability to use Ni L-edge XAS and 2p3d RIXS to provide a rational basis for structure-activity correlations is highlighted.

From Ylides to Doubly Yldiide-Bridged Iron(II) High Spin Dimers via Self-Protolysis.

A synthetic strategy for the preparation of novel doubly yldiide bridged iron(II) high spin dimers ([(µ2-C)FeL]2, L = N(SiMe3)2, Mesityl) has been developed. This includes the synthesis of ylide-iron(II) monomers [(Ylide)FeL2] via adduct formation. Subsequent self-protolysis at elevated temperatures by in situ deprotonation of the ylide ligands results in a dimerization reaction forming the desired bridging µ2-C yldiide ligands in [(µ2-C)FeL]2. The comprehensive structural and electronic analysis of dimers [(µ2-C)FeL]2, including NMR, Mössbauer, and X-ray spectroscopy, as well as X-ray crystallography, SQUID, and DFT calculations, confirm their high-spin FeII configurations. Interestingly, the Fe2C2 cores display very acute Fe-C-Fe angles (averaged: 78.6(2)°) resulting in short Fe···Fe distances (averaged: 2.588(2) Å). A remarkably strong antiferromagnetic coupling between the Fe centers has been identified. Strongly polarized Fe-C bonds are observed where the negative charge is mostly centered at the µ2-C yldiide ligands.

Spectroscopic and Quantum Chemical Investigation of Benzene-1,2-dithiolate-Coordinated Diiron Complexes with Relevance to Dinitrogen Activation.

In this work, a benzene-1,2-dithiolate (bdt) pentamethylcyclopentadienyl di-iron complex [Cp*Fe(µ-η2:η4-bdt)FeCp*] and its [Cp*Fe(bdt)(X)FeCp*] analogues (where X = N2H2, N2H3-, H-, NH2-, NHCH3-, or NO+) were investigated through spectroscopic and computational studies. These complexes are of relevance as model systems for dinitrogen activation in nitrogenase and share with its active site the presence of iron, sulfur ligands, and a very flexible electronic structure. On the basis of a combination of X-ray emission spectroscopy (XES), X-ray crystallography, Mössbauer, NMR, and EPR spectroscopy, the geometric and electronic structure of the series has been experimentally elucidated. All iron atoms were found to be in a local low-spin configuration. When no additional X ligand is bound, the bdt ligand is tilted and features a stabilizing π-interaction with one of the iron atoms. The number of lone-pair orbitals provided by the nitrogen-containing species is crucial to the overall electronic structure. When only one lone-pair is present and the iron atoms are bridged by one atom, a three-center bond occurs, and a direct Fe-Fe bond is absent. If the bridging atom provides two lone-pairs, then an Fe-Fe bond is formed. A recurring theme for all ligands is σ-donation into the unoccupied eg manifolds of both iron atoms and back-donation from the t2g manifolds into the ligand π* orbitals. The latter results in a weakening of the double bond of the bound ligand, and in the case of NO+, it results in a weakening of all bonds that comprise triple bond. The electron-rich thiolates further amplify this effect and can also serve as bases for proton binding. While the above observations have been made for the studied di-iron complexes, they may be of relevance for the active site in nitrogenase, where a similar N2 binding mode may occur allowing for the simultaneous weakening of the N2 σ bond and π bonds.

Probing the Valence Electronic Structure of Low-Spin Ferrous and Ferric Complexes Using 2p3d Resonant Inelastic X-ray Scattering (RIXS).

Understanding the detailed electronic structure of transition metal ions is essential in numerous areas of inorganic chemistry. In particular, the ability to map out the many particle d-d spectrum of a transition metal catalyst is key to understanding and predicting reactivity. However, from a practical perspective, there are often experimental limitations on the ability to determine the energetic ordering, and multiplicity of all the excited states. These limitations derive in part from parity and spin-selection rules, as well as from the limited energy range of many standard laboratory instruments. Herein, we demonstrate the ability of 2p3d resonant inelastic X-ray scattering (RIXS) to obtain detailed insights into the many particle spectrum of simple inorganic molecular iron complexes. The present study focuses on low-spin ferrous and ferric iron complexes, including [FeIII/II(tacn)2]3+/2+ and [FeIII/II(CN)6]3-/4-. This series thus allows us to assess the contribution of d-count and ligand donor type, by comparing the purely σ-donating tacn ligand to the π-accepting cyanide. In order to highlight the conceptual difference between RIXS and traditional optical spectroscopy, we compare first RIXS results with UV-vis and magnetic circular dichroism spectroscopy. We then highlight the ability of 2p3d RIXS to (1) separate d-d transitions from charge transfer transitions and (2) to determine the many particle d-d spectrum over a much wider energy range than is possible by optical spectroscopy. Our experimental results are correlated with semiempirical multiplet simulations and ab initio complete active space self-consistent field calculations in order to obtain detailed assignments of the excited states. These results show that Δ S = 1, and possibly Δ S = 2, transitions may be observed in 2p3d RIXS spectra. Hence, this methodology has great promise for future applications in all areas of transition metal inorganic chemistry.

Electronic Spectra of Iron-Sulfur Complexes Measured by 2p3d RIXS Spectroscopy.

Iron sulfur (FeS) proteins perform a wide range of biological functions including electron transfer and catalysis. Understanding the complex reactivity of these systems requires a detailed understanding of their electronic properties, which are encoded in the low-energy d-d excited states. Here we demonstrate that iron L-edge 2p3d resonant inelastic X-ray scattering (RIXS) can measure d-d excitation spectra in a series of monomeric, dimeric, and tetrameric FeS model complexes. RIXS provides advantages over traditional optical spectroscopies, because it is capable of measuring low-energy electronic excitations (0-10 000 cm-1) and spin-flip transitions. RIXS reveals the dense manifold of d-d excited states in dimeric [2Fe-2S] and tetrameric [MFe3S4]2+ (M = V or Mo) complexes resulting from covalency and exchange coupling. These results support recent ab initio theoretical predictions that FeS clusters possess a much greater number of low-lying excited states than predicted by model Hamiltonians.

Measurement of the Ligand Field Spectra of Ferrous and Ferric Iron Chlorides Using 2p3d RIXS.

Ligand field spectra provide direct information about the electronic structure of transition metal complexes. However, these spectra are difficult to measure by conventional optical techniques due to small cross sections for d-to-d transitions and instrumental limitations below 4000 cm-1. 2p3d resonant inelastic X-ray scattering (RIXS) is a second order process that utilizes dipole allowed 2p to 3d transitions to access d-d excited states. The measurement of ligand field excitation spectra by RIXS is demonstrated for a series of tetrahedral and octahedral Fe(II) and Fe(III) chlorides, which are denoted Fe(III)-Td, Fe(II)-Td, Fe(III)-Oh, and Fe(II)-Oh. The strong 2p spin-orbit coupling allows the measurement of spin forbidden transitions in RIXS spectroscopy. The Fe(III) spectra are dominated by transitions from the sextet ground state to quartet excited states, and the Fe(II) spectra contain transitions to triplet states in addition to the spin allowed 5Γ â†’ 5Γ transition. Each experimental spectrum is simulated using a ligand field multiplet model to extract the ligand field splitting parameter 10Dq and the Racah parameters B and C. The 10Dq values for Fe(III)-Td, Fe(II)-Td, and Fe(III)-Oh are found to be -0.7, -0.32, and 1.47 eV, respectively. In the case of Fe(II)-Oh, a single 10Dq parameter cannot be assigned because Fe(II)-Oh is a coordination polymer exhibiting axially compressed Fe(II)Cl 6 units. The 5T → 5E transition is split by the axial compression resulting in features at 0.51 and 0.88 eV. The present study forms the foundation for future applications of 2p3d RIXS to molecular iron sites in more complex systems, including iron-based catalysts and enzymes.

Measuring Spin-Allowed and Spin-Forbidden d-d Excitations in Vanadium Complexes with 2p3d Resonant Inelastic X-ray Scattering.

Spectroscopic probes of the electronic structure of transition metal-containing materials are invaluable to the design of new molecular catalysts and magnetic systems. Herein, we show that 2p3d resonant inelastic X-ray scattering (RIXS) can be used to observe both spin-allowed and (in the VIII case) spin-forbidden d-d excitation energies in molecular vanadium complexes. The spin-allowed d-d excitation energies determined by 2p3d RIXS are in good agreement with available optical data. In V(acac)3, a previously undetected spin-forbidden singlet state has been observed. The presence of this feature provides a ligand-field independent signature of VIII. It is also shown that d-d excitations may be obtained for porphyrin complexes. This is generally prohibitive using optical approaches due to intense porphyrin π-to-π* transitions. In addition, the intensities of charge-transfer features in 2p3d RIXS spectroscopy are shown to be a clear indication of metal-ligand covalency. The utility of 2p3d RIXS for future studies of complex inorganic systems is highlighted.

X-ray Absorption and Emission Spectroscopic Studies of [L2Fe2S2](n) Model Complexes: Implications for the Experimental Evaluation of Redox States in Iron-Sulfur Clusters.

Herein, a systematic study of [L2Fe2S2](n) model complexes (where L = bis(benzimidazolato) and n = 2-, 3-, 4-) has been carried out using iron and sulfur K-edge X-ray absorption (XAS) and iron Kß and valence-to-core X-ray emission spectroscopies (XES). These data are used as a test set to evaluate the relative strengths and weaknesses of X-ray core level spectroscopies in assessing redox changes in iron-sulfur clusters. The results are correlated to density functional theory (DFT) calculations of the spectra in order to further support the quantitative information that can be extracted from the experimental data. It is demonstrated that due to canceling effects of covalency and spin state, the information that can be extracted from Fe Kß XES mainlines is limited. However, a careful analysis of the Fe K-edge XAS data shows that localized valence vs delocalized valence species may be differentiated on the basis of the pre-edge and K-edge energies. These findings are then applied to existing literature Fe K-edge XAS data on the iron protein, P-cluster, and FeMoco sites of nitrogenase. The ability to assess the extent of delocalization in the iron protein vs the P-cluster is highlighted. In addition, possible charge states for FeMoco on the basis of Fe K-edge XAS data are discussed. This study provides an important reference for future X-ray spectroscopic studies of iron-sulfur clusters.