Frederico A. Lima

A high-repetition rate scheme for synchrotron-based picosecond laser pump/x-ray probe experiments on chemical and biological systems in solution

We present the extension of time-resolved optical pump/x-ray absorption spectroscopy (XAS) probe experiments towards data collection at MHz repetition rates. The use of a high-power picosecond laser operating at an integer fraction of the repetition rate of the storage ring allows exploitation of up to two orders of magnitude more x-ray photons than in previous schemes based on the use of kHz lasers. Consequently, we demonstrate an order of magnitude increase in the signal-to-noise of time-resolved XAS of molecular systems in solution. This makes it possible to investigate highly dilute samples at concentrations approaching physiological conditions for biological systems. The simplicity and compactness of the scheme allows for straightforward implementation at any synchrotron beamline and for a wide range of x-ray probe techniques, such as time-resolved diffraction or x-ray emission studies.

Structural Determination of a Photochemically Active Diplatinum Molecule by Time‐Resolved EXAFS Spectroscopy

Metallica: A large contraction of the Pt-Pt bond in the triplet excited state of the photoreactive [Pt(2)(P(2)O(5)H(2))(4)](4-) ion is determined by time-resolved X-ray absorption spectroscopy (see picture). The strengthening of the Pt-Pt interaction is accompanied by a weakening of the ligand coordination bonds, resulting in an elongation of the platinum-ligand bond that is determined for the first time.

Solvent Induced Luminescence Quenching: Static and Time-Resolved X-Ray Absorption Spectroscopy of a Copper(I) Phenanthroline Complex

We present a static and picosecond X-ray absorption study at the Cu K-edge of bis(2,9-dimethyl-1,10-phenanthroline)copper(I) ([Cu(dmp)2](+); dmp = 2,9-dimethyl-1,10-phenanthroline) dissolved in acetonitrile and dichloromethane. The steady-state photoluminescence spectra in dichloromethane and acetonitrile are also presented and show a shift to longer wavelengths for the latter, which points to a stronger stabilization of the excited complex. The fine structure features of the static and transient X-ray spectra allow an unambiguous assignment of the electronic and geometric structure of the molecule in both its ground and excited (3)MLCT states. Importantly, the transient spectra are remarkably similar for both solvents, and the spectral changes can be rationalized using the optimized ground- and excited-state structures of the complex. The proposed assignment of the lifetime shortening of the excited state in donor solvents (acetonitrile) to a metal-centered exciplex is not corroborated here. Molecular dynamics simulations confirm the lack of complexation; however, in both solvents the molecules come close to the metal but undergo rapid exchange with the bulk. The shortening of the lifetime of the title complex and nine additional related complexes can be rationalized by the decrease in the (3)MLCT energy. Deviations from this trend may be explained by means of the effects of the dihedral angle between the ligand planes, the solvent, and the (3)MLCT-(1)MLCT energy gap.

Identification of a spin-coupled Mo(III) in the nitrogenase iron–molybdenum cofactor

Nitrogenase is a complex enzyme that catalyzes the formation of ammonia utilizing a MoFe7S9C cluster. The presence of a central carbon atom was recently revealed, finally completing the atomic level description of the active site. However, important prerequisites for understanding the mechanism – the total charge, metal oxidation states and electronic structure are unknown. Herein we present high-energy resolution fluorescence detected Mo K-edge X-ray absorption spectroscopy of nitrogenase. Comparison to FeMo model complexes of known oxidation state indicates that the Mo in the FeMo cofactor of nitrogenase is best described as Mo(III), in contrast to the universally accepted Mo(IV) assignment. The oxidation state assignment is supported by theoretical calculations, which reveal the presence of an unusual spin-coupled Mo(III) site. Although so far Mo(III) was not reported to occur in biology the suggestion raises interesting parallels with the known homogenous Mo catalysts for N2 reduction, where a Mo(III) compound is the N2-binding species. It also requires a reassignment of the Fe oxidation states in the cofactor.

X-ray absorption spectroscopy of ground and excited rhenium-carbonyl-diimine complexes: evidence for a two-center electron transfer.

Steady-state and picosecond time-resolved X-ray absorption spectroscopy is used to study the ground and lowest triplet states of [ReX(CO)(3)(bpy)](n+), X = Etpy (n = 1), Cl, or Br (n = 0). We demonstrate that the transient spectra at both the Re L(3)- and Br K-edges show the emergence of a pre-edge feature, absent in the ground-state spectrum, which is associated with the electron hole created in the highest occupied molecular orbital following photoexcitation. Importantly, these features have the same dynamics, confirming previous predictions that the low-lying excited states of these complexes involve a two-center charge transfer from both the Re and the ligand, X. We also demonstrate that the DFT optimized ground and excited structures allow us to reproduce the experimental XANES and EXAFS spectra. The ground-state structural refinement shows that the Br atom contributes very little to the latter, whereas the Re-C-O scattering paths are dominant due to the so-called focusing effect. For the excited-state spectrum, the Re-X bond undergoes one of the largest changes but still remains a weak contribution to the photoinduced changes of the EXAFS spectrum.

Photooxidation and photoaquation of iron hexacyanide in aqueous solution: A picosecond X-ray absorption study

We present a picosecond Fe K-edge absorption study of photoexcited ferrous and ferric hexacyanide in water under 355 and 266 nm excitation. Following 355 nm excitation, the transient spectra for the ferrous and ferric complexes exhibit a red shift of the edge reflecting an increased electron density at the Fe atom. For the former, an enhanced pre-edge transition is also observed. These observations are attributed to the aquated [Fe(CN)5OH2]3− species, based on quantum chemical calculations which also provide structural parameters. Upon 266 nm excitation of the ferric complex, a transient reminiscent of the aquated species is observed (appearance of a pre-edge feature and red shift of the edge) but it is different from that obtained under 355 nm excitation. This points to a new reaction channel occurring through an intermediate state lying between these two excitation energies. Finally, 266 nm excitation of the ferrous species is dominated by the photooxidation channel with formation of the ferric complex as main photoproduct. However, we observe an additional minor photoproduct, which is identical to the 266 nm generated photoproduct of the ferric species, suggesting that under our experimental conditions, the pump pulse photooxidises the ferrous complex and re-excites the primary ferric photoproduct.

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 Kβ 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 Kβ 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.

NO binding kinetics in myoglobin investigated by picosecond Fe K-edge absorption spectroscopy

Significance This work is the first demonstration, to our knowledge, of picosecond X-ray absorption spectroscopy to probe ligand binding to heme proteins in physiological media. By Fe K-edge absorption spectroscopy, we directly interrogate the active center of the protein, delivering insight into its electronic and geometric structure. In particular, we have investigated the evolution of the Fe center after photodissociation of NO from nitrosylmyoglobin (MbNO) and observed an intermediate over hundreds of picoseconds, which we propose to be the domed ligated form of MbNO that is formed on recombination of NO to the Fe atom. This work opens the way to a detailed investigation of metalloproteins using subpicosecond X-ray spectroscopy at free electron lasers. Diatomic ligands in hemoproteins and the way they bind to the active center are central to the protein’s function. Using picosecond Fe K-edge X-ray absorption spectroscopy, we probe the NO-heme recombination kinetics with direct sensitivity to the Fe-NO binding after 532-nm photoexcitation of nitrosylmyoglobin (MbNO) in physiological solutions. The transients at 70 and 300 ps are identical, but they deviate from the difference between the static spectra of deoxymyoglobin and MbNO, showing the formation of an intermediate species. We propose the latter to be a six-coordinated domed species that is populated on a timescale of ∼200 ps by recombination with NO ligands. This work shows the feasibility of ultrafast pump–probe X-ray spectroscopic studies of proteins in physiological media, delivering insight into the electronic and geometric structure of the active center.

Heart fossilization is possible and informs the evolution of cardiac outflow tract in vertebrates

Elucidating cardiac evolution has been frustrated by lack of fossils. One celebrated enigma in cardiac evolution involves the transition from a cardiac outflow tract dominated by a multi-valved conus arteriosus in basal actinopterygians, to an outflow tract commanded by the non-valved, elastic, bulbus arteriosus in higher actinopterygians. We demonstrate that cardiac preservation is possible in the extinct fish Rhacolepis buccalis from the Brazilian Cretaceous. Using X-ray synchrotron microtomography, we show that Rhacolepis fossils display hearts with a conus arteriosus containing at least five valve rows. This represents a transitional morphology between the primitive, multivalvar, conal condition and the derived, monovalvar, bulbar state of the outflow tract in modern actinopterygians. Our data rescue a long-lost cardiac phenotype (119-113 Ma) and suggest that outflow tract simplification in actinopterygians is compatible with a gradual, rather than a drastic saltation event. Overall, our results demonstrate the feasibility of studying cardiac evolution in fossils. DOI: http://dx.doi.org/10.7554/eLife.14698.001

Molybdenum L-Edge XAS Spectra of MoFe Nitrogenase†

A molybdenum L-edge X-ray absorption spectroscopy (XAS) study is presented for native and oxidized MoFe protein of nitrogenase as well as Mo-Fe model compounds. Recently collected data on MoFe protein (in oxidized and reduced forms) is compared to previously published Mo XAS data on the isolated FeMo cofactor in NMF solution and put in context of the recent Mo K-edge XAS study, which showed a MoIII assignment for the molybdenum atom in FeMoco. The L3-edge data are interpreted within a simple ligand-field model, from which a time-dependent density functional theory (TDDFT) approach is proposed as a way to provide further insights into the analysis of the molybdenum L3-edges. The calculated results reproduce well the relative spectral trends that are observed experimentally. Ultimately, these results give further support for the MoIII assignment in protein-bound FeMoco, as well as isolated FeMoco.