Spin cascade and doming in ferric hemes: Femtosecond X-ray absorption and X-ray emission studies.

The structure-function relationship is at the heart of biology, and major protein deformations are correlated to specific functions. For ferrous heme proteins, doming is associated with the respiratory function in hemoglobin and myoglobins. Cytochrome c (Cyt c) has evolved to become an important electron-transfer protein in humans. In its ferrous form, it undergoes ligand release and doming upon photoexcitation, but its ferric form does not release the distal ligand, while the return to the ground state has been attributed to thermal relaxation. Here, by combining femtosecond Fe Kα and Kß X-ray emission spectroscopy (XES) with Fe K-edge X-ray absorption near-edge structure (XANES), we demonstrate that the photocycle of ferric Cyt c is entirely due to a cascade among excited spin states of the iron ion, causing the ferric heme to undergo doming, which we identify. We also argue that this pattern is common to a wide diversity of ferric heme proteins, raising the question of the biological relevance of doming in such proteins.

3D printed devices and infrastructure for liquid sample delivery at the European XFEL.

The Sample Environment and Characterization (SEC) group of the European X-ray Free-Electron Laser (EuXFEL) develops sample delivery systems for the various scientific instruments, including systems for the injection of liquid samples that enable serial femtosecond X-ray crystallography (SFX) and single-particle imaging (SPI) experiments, among others. For rapid prototyping of various device types and materials, sub-micrometre precision 3D printers are used to address the specific experimental conditions of SFX and SPI by providing a large number of devices with reliable performance. This work presents the current pool of 3D printed liquid sample delivery devices, based on the two-photon polymerization (2PP) technique. These devices encompass gas dynamic virtual nozzles (GDVNs), mixing-GDVNs, high-viscosity extruders (HVEs) and electrospray conical capillary tips (CCTs) with highly reproducible geometric features that are suitable for time-resolved SFX and SPI experiments at XFEL facilities. Liquid sample injection setups and infrastructure on the Single Particles, Clusters, and Biomolecules and Serial Femtosecond Crystallography (SPB/SFX) instrument are described, this being the instrument which is designated for biological structure determination at the EuXFEL.

Femtosecond X-ray spectroscopy of haem proteins.

We discuss our recently reported femtosecond (fs) X-ray emission spectroscopy results on the ligand dissociation and recombination in nitrosylmyoglobin (MbNO) in the context of previous studies on ferrous haem proteins. We also present a preliminary account of femtosecond X-ray absorption studies on MbNO, pointing to the presence of more than one species formed upon photolysis.

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

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.

Gold-Catalyzed C-S Aryl-Group Transfer in Zinc Finger Proteins.

Reaction of the Au-C N chelate [Au(bnpy)Cl2 ] with the full-length zinc finger (ZnF; ZnCys3 His) of HIV nucleocapsid protein NCp7 results in C-S aryl transfer from the AuIII organometallic species to a cysteine of the ZnF. The reaction is general and occurs even for finger 3 of the transcription factor Sp1, containing a ZnCys2 His2 coordination sphere. This reaction is the first demonstration of group transfer from a coordination compound to biologically important zinc fingers, and is especially noteworthy for the ZnCys2 His2 transcription factors. The work expands the corpus of organometallic species which can efficiently modify biomolecules through C-atom transfer. The electronic features of the gold compound leading to this unexpected reaction were explored by X-ray absorption spectroscopy.

Experimental and theoretical correlations between vanadium K-edge X-ray absorption and Kß emission spectra.

A series of vanadium compounds was studied by K-edge X-ray absorption (XAS) and K[Formula: see text] X-ray emission spectroscopies (XES). Qualitative trends within the datasets, as well as comparisons between the XAS and XES data, illustrate the information content of both methods. The complementary nature of the chemical insight highlights the success of this dual-technique approach in characterizing both the structural and electronic properties of vanadium sites. In particular, and in contrast to XAS or extended X-ray absorption fine structure (EXAFS), we demonstrate that valence-to-core XES is capable of differentiating between ligating atoms with the same identity but different bonding character. Finally, density functional theory (DFT) and time-dependent DFT calculations enable a more detailed, quantitative interpretation of the data. We also establish correction factors for the computational protocols through calibration to experiment. These hard X-ray methods can probe vanadium ions in any oxidation or spin state, and can readily be applied to sample environments ranging from solid-phase catalysts to biological samples in frozen solution. Thus, the combined XAS and XES approach, coupled with DFT calculations, provides a robust tool for the study of vanadium atoms in bioinorganic chemistry.

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.

Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy.

We present an iron K-edge X-ray absorption study of carboxymyoglobin (MbCO), nitrosylmyoglobin (MbNO), oxymyoglobin (MbO2), cyanomyoglobin (MbCN), aquomet myoglobin (metMb) and unligated myoglobin (deoxyMb) in physiological media. The analysis of the XANES region is performed using the full-multiple scattering formalism, implemented within the MXAN package. This reveals trends within the heme structure, absent from previous crystallographic and X-ray absorption analysis. In particular, the iron-nitrogen bond lengths in the porphyrin ring converge to a common value of about 2 Å, except for deoxyMb whose bigger value is due to the doming of the heme. The trends of the Fe-Nε (His93) bond length is found to be consistent with the effect of ligand binding to the iron, with the exception of MbNO, which is explained in terms of the repulsive trans effect. We derive a high resolution description of the relative geometry of the ligands with respect to the heme and quantify the magnitude of the heme doming in the deoxyMb form. Finally, time-dependent density functional theory is used to simulate the pre-edge spectra and is found to be in good agreement with the experiment. The XAS spectra typically exhibit one pre-edge feature which arises from transitions into the unoccupied dσ and dπ - πligand* orbitals. 1s → dπ transitions contribute weakly for MbO2, metMb and deoxyMb. However, despite this strong Fe d contribution these transitions are found to be dominated by the dipole (1s → 4p) moment due to the low symmetry of the heme environment.

High-resolution molybdenum K-edge X-ray absorption spectroscopy analyzed with time-dependent density functional theory.

X-ray absorption spectroscopy (XAS) is a widely used experimental technique capable of selectively probing the local structure around an absorbing atomic species in molecules and materials. When applied to heavy elements, however, the quantitative interpretation can be challenging due to the intrinsic spectral broadening arising from the decrease in the core-hole lifetime. In this work we have used high-energy resolution fluorescence detected XAS (HERFD-XAS) to investigate a series of molybdenum complexes. The sharper spectral features obtained by HERFD-XAS measurements enable a clear assignment of the features present in the pre-edge region. Time-dependent density functional theory (TDDFT) has been previously shown to predict K-pre-edge XAS spectra of first row transition metal compounds with a reasonable degree of accuracy. Here we extend this approach to molybdenum K-edge HERFD-XAS and present the necessary calibration. Modern pure and hybrid functionals are utilized and relativistic effects are accounted for using either the Zeroth Order Regular Approximation (ZORA) or the second order Douglas-Kroll-Hess (DKH2) scalar relativistic approximations. We have found that both the predicted energies and intensities are in excellent agreement with experiment, independent of the functional used. The model chosen to account for relativistic effects also has little impact on the calculated spectra. This study provides an important calibration set for future applications of molybdenum HERFD-XAS to complex catalytic systems.

Atomic-scale observation of solvent reorganization influencing photoinduced structural dynamics in a copper complex photosensitizer.

Photochemical reactions in solution are governed by a complex interplay between transient intramolecular electronic and nuclear structural changes and accompanying solvent rearrangements. State-of-the-art time-resolved X-ray solution scattering has emerged in the last decade as a powerful technique to observe solute and solvent motions in real time. However, disentangling solute and solvent dynamics and how they mutually influence each other remains challenging. Here, we simultaneously measure femtosecond X-ray emission and scattering to track both the intramolecular and solvation structural dynamics following photoexcitation of a solvated copper photosensitizer. Quantitative analysis assisted by molecular dynamics simulations reveals a two-step ligand flattening strongly coupled to the solvent reorganization, which conventional optical methods could not discern. First, a ballistic flattening triggers coherent motions of surrounding acetonitrile molecules. In turn, the approach of acetonitrile molecules to the copper atom mediates the decay of intramolecular coherent vibrations and induces a further ligand flattening. These direct structural insights reveal that photoinduced solute and solvent motions can be intimately intertwined, explaining how the key initial steps of light harvesting are affected by the solvent on the atomic time and length scale. Ultimately, this work takes a step forward in understanding the microscopic mechanisms of the bidirectional influence between transient solvent reorganization and photoinduced solute structural dynamics.

Ultrafast Jahn-Teller Photoswitching in Cobalt Single-Ion Magnets.

Single-ion magnets (SIMs) constitute the ultimate size limit in the quest for miniaturizing magnetic materials. Several bottlenecks currently hindering breakthroughs in quantum information and communication technologies could be alleviated by new generations of SIMs displaying multifunctionality. Here, ultrafast optical absorption spectroscopy and X-ray emission spectroscopy are employed to track the photoinduced spin-state switching of the prototypical complex [Co(terpy)2 ]2+ (terpy = 2,2':6',2″-terpyridine) in solution phase. The combined measurements and their analysis supported by density functional theory (DFT), time-dependent-DFT (TD-DFT) and multireference quantum chemistry calculations reveal that the complex undergoes a spin-state transition from a tetragonally elongated doublet state to a tetragonally compressed quartet state on the femtosecond timescale, i.e., it sustains ultrafast Jahn-Teller (JT) photoswitching between two different spin multiplicities. Adding new Co-based complexes as possible contenders in the search for JT photoswitching SIMs will greatly widen the possibilities for implementing magnetic multifunctionality and eventually controlling ultrafast magnetization with optical photons.

Ultrafast Energy Transfer from Photoexcited Tryptophan to the Haem in Cytochrome c.

We report femtosecond Fe K-edge absorption (XAS) and nonresonant X-ray emission (XES) spectra of ferric cytochrome C (Cyt c) upon excitation of the haem (>300 nm) or mixed excitation of the haem and tryptophan (<300 nm). The XAS and XES transients obtained in both excitation energy ranges show no evidence for electron transfer processes between photoexcited tryptophan (Trp) and the haem, but rather an ultrafast energy transfer, in agreement with previous ultrafast optical fluorescence and transient absorption studies. The reported (J. Phys. Chem. B 2011, 115 (46), 13723-13730) decay times of Trp fluorescence in ferrous (∼350 fs) and ferric (∼700 fs) Cyt c are among the shortest ever reported for Trp in a protein. The observed time scales cannot be rationalized in terms of Förster or Dexter energy transfer mechanisms and call for a more thorough theoretical investigation.

Ultrafast X-ray absorption studies of the structural dynamics of molecular and biological systems in solution.

We review our recent studies of excited state structures and dynamics of chemical and biological systems with pico- and femtosecond X-ray absorption spectroscopy in the liquid phase.

L-edge XANES analysis of photoexcited metal complexes in solution.

Ultrafast X-ray absorption spectroscopy is a powerful tool to observe electronic and geometric structures of short-lived reaction intermediates. The ab initio FEFF9 code is applied to simulate the Pt L(3)-edge XANES spectrum of the photocatalytic diplatinum molecule [Pt(2)(P(2)O(5)H(2))(4)](4-) and the photo-induced changes that occur therein. The spectra are interpreted within a XAFS-like scattering theoretical framework (bound-continuum transitions) or in terms of a final-state local l-projected density of states (LDOS) (bound-bound transitions). By using a novel Bayesian fitting procedure, we show that the ground-state structures obtained independently from the XANES and EXAFS regions of the spectrum are in good agreement with each other. The semi-quantitative result obtained for the Pt-Pt contraction in the excited state is in line with recently published values. The improved theoretical treatment of inelastic losses has shown to result in more accurate peak positions in the above-continuum region of the spectrum which is an important prerequisite for obtaining quantitative structural information from (time-resolved) XANES spectra.

Evaluation of cobalt complexes with tripod ligands for zinc finger targeting.

Cobalt complexes have been demonstrated to target zinc fingers, as shown by investigations of Doxovir, the trade name of the [CoIII(acacen)(2-Me-Imz)2]+ drug in clinical trials. Mechanistic studies indicate zinc finger disruption by metal coordination to His residues. Other than Doxovir, a few studies have investigated other ligands and geometries for cobalt complexes for zinc finger targeting. Tripod ligands demonstrated good zinc and cobalt chelation. In this manuscript, we report the ability of CoII and CoIII complexes of tri(2-pyridylmethyl)amine and N,N-di(2-pyridylmethyl)glycinate to disrupt zinc fingers. The results obtained by mass spectrometry and X-ray absorption spectroscopy demonstrate that the complexes were able to remove zinc from the zinc fingers. The product was oxidised apo-peptide. In contrast, the ligands themselves were able to remove zinc, and they did not promote oxidation, resulting in free Cys residues. Cobalt finger adducts were not detected for the complexes with tripod ligands unless they were coordinated to planar ligands such as salen or acacen. Studies of the interactions of cobalt complexes with amino acids demonstrated that tripod ligands promote the cysteine reaction, while the salen ligands promote histidine coordination, demonstrating a different mechanism of action. The results reported here are significant for better understanding and further design of zinc finger targeting compounds.

Femtosecond X-ray emission study of the spin cross-over dynamics in haem proteins.

In haemoglobin the change from the low-spin (LS) hexacoordinated haem to the high spin (HS, S = 2) pentacoordinated domed deoxy-myoglobin (deoxyMb) form upon ligand detachment from the haem and the reverse process upon ligand binding are what ultimately drives the respiratory function. Here we probe them in the case of Myoglobin-NO (MbNO) using element- and spin-sensitive femtosecond Fe Kα and Kß X-ray emission spectroscopy at an X-ray free-electron laser (FEL). We find that the change from the LS (S = 1/2) MbNO to the HS haem occurs in ~800 fs, and that it proceeds via an intermediate (S = 1) spin state. We also show that upon NO recombination, the return to the planar MbNO ground state is an electronic relaxation from HS to LS taking place in ~30 ps. Thus, the entire ligand dissociation-recombination cycle in MbNO is a spin cross-over followed by a reverse spin cross-over process.

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.

Tracking multiple components of a nuclear wavepacket in photoexcited Cu(I)-phenanthroline complex using ultrafast X-ray spectroscopy.

Disentangling the strong interplay between electronic and nuclear degrees of freedom is essential to achieve a full understanding of excited state processes during ultrafast nonadiabatic chemical reactions. However, the complexity of multi-dimensional potential energy surfaces means that this remains challenging. The energy flow during vibrational and electronic relaxation processes can be explored with structural sensitivity by probing a nuclear wavepacket using femtosecond time-resolved X-ray Absorption Near Edge Structure (TR-XANES). However, it remains unknown to what level of detail vibrational motions are observable in this X-ray technique. Herein we track the wavepacket dynamics of a prototypical [Cu(2,9-dimethyl-1,10-phenanthroline)2]+ complex using TR-XANES. We demonstrate that sensitivity to individual wavepacket components can be modulated by the probe energy and that the bond length change associated with molecular breathing mode can be tracked with a sub-Angstrom resolution beyond optical-domain observables. Importantly, our results reveal how state-of-the-art TR-XANES provides deeper insights of ultrafast nonadiabatic chemical reactions.

Comparative electronic structures of nitrogenase FeMoco and FeVco.

An investigation of the active site cofactors of the molybdenum and vanadium nitrogenases (FeMoco and FeVco) was performed using high-resolution X-ray spectroscopy. Synthetic heterometallic iron-sulfur cluster models and density functional theory calculations complement the study of the MoFe and VFe holoproteins using both non-resonant and resonant X-ray emission spectroscopy. Spectroscopic data show the presence of direct iron-heterometal bonds, which are found to be weaker in FeVco. Furthermore, the interstitial carbide is found to perturb the electronic structures of the cofactors through highly covalent Fe-C bonding. The implications of these conclusions are discussed in light of the differential reactivity of the molybdenum and vanadium nitrogenases towards various substrates. Possible functional roles for both the heterometal and the interstitial carbide are detailed.

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.