Chemical interactions and dynamics with femtosecond X-ray spectroscopy and the role of X-ray free-electron lasers

Probing the Dynamic Landscape: From Static to Time-Resolved X-Ray Absorption Spectroscopy to Investigate Copper Redox Chemistry in Neurodegenerative Disorders

Copper (Cu), with its ability to exist in various oxidation states, notably Cu(I) and Cu(II), plays a crucial role in diverse biological redox reactions. This includes its involvement in pathways associated with oxidative stress in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Transmissible Spongiform Encephalopathies. This paper offers an overview of X-ray Absorption Spectroscopy (XAS) studies designed to elucidate the interactions between Cu ions and proteins or peptides associated with these neurodegenerative diseases. The emphasis lies on XAS specificity, revealing the local coordination environment, and on its sensitivity to Cu oxidation states. Furthermore, the paper focuses on XAS applications targeting the characterization of intermediate reaction states and explores the opportunities arising from recent advancements in time-resolved XAS at ultrabright synchrotron and Free Electron Laser radiation sources.

Perspective: multi-configurational methods in bio-inorganic chemistry

Transition metal ions play crucial roles in the structure and function of numerous proteins, contributing to essential biological processes such as catalysis, electron transfer, and oxygen binding. However, accurately modeling the electronic structure and properties of metalloproteins poses significant challenges due to the complex nature of their electronic configurations and strong correlation effects. Multiconfigurational quantum chemistry methods are, in principle, the most appropriate tools for addressing these challenges, offering the capability to capture the inherent multi-reference character and strong electron correlation present in bio-inorganic systems. Yet their computational cost has long hindered wider adoption, making methods such as density functional theory (DFT) the method of choice. However, advancements over the past decade have substantially alleviated this limitation, rendering multiconfigurational quantum chemistry methods more accessible and applicable to a wider range of bio-inorganic systems. In this perspective, we discuss some of these developments and how they have already been used to answer some of the most important questions in bio-inorganic chemistry. We also comment on ongoing developments in the field and how the future of the field may evolve.

Excited-State Identification of a Nickel-Bipyridine Photocatalyst by Time-Resolved X-ray Absorption Spectroscopy

Photoassisted catalysis using Ni complexes is an emerging field for cross-coupling reactions in organic synthesis. However, the mechanism by which light enables and enhances the reactivity of these complexes often remains elusive. Although optical techniques have been widely used to study the ground and excited states of photocatalysts, they lack the specificity to interrogate the electronic and structural changes at specific atoms. Herein, we report metal-specific studies using transient Ni L- and K-edge X-ray absorption spectroscopy of a prototypical Ni photocatalyst, (dtbbpy)Ni(o-tol)Cl (dtb = 4,4'-di-tert-butyl, bpy = bipyridine, o-tol = ortho-tolyl), in solution. We unambiguously confirm via direct experimental evidence that the long-lived (∼5 ns) excited state is a tetrahedral metal-centered triplet state. These results demonstrate the power of ultrafast X-ray spectroscopies to unambiguously elucidate the nature of excited states in important transition-metal-based photocatalytic systems.

In situ X-ray spectroscopies beyond conventional X-ray absorption spectroscopy on deciphering dynamic configuration of electrocatalysts

Realizing viable electrocatalytic processes for energy conversion/storage strongly relies on an atomic-level understanding of dynamic configurations on catalyst-electrolyte interface. X-ray absorption spectroscopy (XAS) has become an indispensable tool to in situ investigate dynamic natures of electrocatalysts but still suffers from limited energy resolution, leading to significant electronic transitions poorly resolved. Herein, we highlight advanced X-ray spectroscopies beyond conventional XAS, with emphasis on their unprecedented capabilities of deciphering key configurations of electrocatalysts. The profound complementarities of X-ray spectroscopies from various aspects are established in a probing energy-dependent "in situ spectroscopy map" for comprehensively understanding the solid-liquid interface. This perspective establishes an indispensable in situ research model for future studies and offers exciting research prospects for scientists and spectroscopists.

Core Excitations of Uranyl in Cs2UO2Cl4 from Relativistic Embedded Damped Response Time-Dependent Density Functional Theory Calculations

X-ray spectroscopies, by their high selectivity and sensitivity to the chemical environment around the atoms probed, provide significant insights into the electronic structures of molecules and materials. Interpreting experimental results requires reliable theoretical models, accounting for environmental, relativistic, electron correlation, and orbital relaxation effects in a balanced manner. In this work, we present a protocol for the simulation of core excited spectra with damped response time-dependent density functional theory based on the Dirac-Coulomb Hamiltonian (4c-DR-TD-DFT), in which environmental effects are accounted for through the frozen density embedding (FDE) method. We showcase this approach for the uranium M4- and L3-edges and oxygen K-edge of the uranyl tetrachloride (UO2Cl42-) unit as found in a host Cs2UO2Cl4 crystal. We have found that the 4c-DR-TD-DFT simulations yield excitation spectra that very closely match the experiment for the uranium M4-edge and the oxygen K-edge, with good agreement for the broad experimental spectra for the L3-edge. By decomposing the complex polarizability in terms of its components, we have been able to correlate our results with angle-resolved spectra. We have observed that for all edges, but in particular the uranium M4-edge, an embedded model in which the chloride ligands are replaced by an embedding potential reproduces rather well the spectral profile obtained for UO2Cl42-. Our results underscore the importance of the equatorial ligands to simulating core spectra at both uranium and oxygen edges.

X-FAST: A versatile, high-throughput, and user-friendly XUV femtosecond absorption spectroscopy tabletop instrument

We present the X-FAST (XUV Femtosecond Absorption Spectroscopy Tabletop) instrument at the University of Wisconsin-Madison. The instrument produces femtosecond extreme ultraviolet photon pulses via high-harmonic generation in the range of 40-72 eV, as well as optical pump pulses for transient-absorption experiments. The system implements a gas-cooled sample cell that enables studying the dynamics of thermally sensitive thin-film samples. This paper provides potential users with specifications of the optical, vacuum, data acquisition, and sample cooling systems of the X-FAST instrument, along with performance metrics and data of an ultrafast laser-induced phase transition in a Ni2MnGa Heusler thin film.

Watching Excited State Dynamics with Optical and X-ray Probes: The Excited State Dynamics of Aquocobalamin and Hydroxocobalamin

Femtosecond time-resolved X-ray absorption (XANES) at the Co K-edge, X-ray emission (XES) in the Co Kβ and valence-to-core regions, and broadband UV-vis transient absorption are combined to probe the femtosecond to picosecond sequential atomic and electronic dynamics following photoexcitation of two vitamin B₁₂ compounds, hydroxocobalamin and aquocobalamin. Polarized XANES difference spectra allow identification of sequential structural evolution involving first the equatorial and then the axial ligands, with the latter showing rapid coherent bond elongation to the outer turning point of the excited state potential followed by recoil to a relaxed excited state structure. Time-resolved XES, especially in the valence-to-core region, along with polarized optical transient absorption suggests that the recoil results in the formation of a metal-centered excited state with a lifetime of 2-5 ps. This combination of methods provides a uniquely powerful tool to probe the electronic and structural dynamics of photoactive transition-metal complexes and will be applicable to a wide variety of systems.

Photoinduced bond oscillations in ironpentacarbonyl give delayed synchronous bursts of carbonmonoxide release

Early excited state dynamics in the photodissociation of transition metal carbonyls determines the chemical nature of short-lived catalytically active reaction intermediates. However, time-resolved experiments have not yet revealed mechanistic details in the sub-picosecond regime. Hence, in this study the photoexcitation of ironpentacarbonyl Fe(CO)₅ is simulated with semi-classical excited state molecular dynamics. We find that the bright metal-to-ligand charge-transfer (MLCT) transition induces synchronous Fe-C oscillations in the trigonal bipyramidal complex leading to periodically reoccurring release of predominantly axial CO. Metaphorically the photoactivated Fe(CO)₅ acts as a CO geyser, as a result of dynamics in the potential energy landscape of the axial Fe-C distances and non-adiabatic transitions between manifolds of bound MLCT and dissociative metal-centered (MC) excited states. The predominant release of axial CO ligands and delayed release of equatorial CO ligands are explained in a unified mechanism based on the σ^*(Fe-C) anti-bonding character of the receiving orbital in the dissociative MC states.

The photodissociation of transition metal carbonyls is involved in catalysis and synthetic processes. Here the authors, using semi-classical excited state molecular dynamics, observe details of the early stage dynamics in the photodissociation of Fe(CO)₅, including synchronous bursts of CO at periodic intervals of 90 femtoseconds.

Femtosecond X-ray Spectroscopy Directly Quantifies Transient Excited-State Mixed Valency

Quantifying charge delocalization associated with short-lived photoexcited states of molecular complexes in solution remains experimentally challenging, requiring local element specific femtosecond experimental probes of time-evolving electron transfer. In this study, we quantify the evolving valence hole charge distribution in the photoexcited charge transfer state of a prototypical mixed valence bimetallic iron-ruthenium complex, [(CN)₅Fe^IICNRu^III(NH₃)₅]^-, in water by combining femtosecond X-ray spectroscopy measurements with time-dependent density functional theory calculations of the excited-state dynamics. We estimate the valence hole charge that accumulated at the Fe atom to be 0.6 ± 0.2, resulting from excited-state metal-to-metal charge transfer, on an ∼60 fs time scale. Our combined experimental and computational approach provides a spectroscopic ruler for quantifying excited-state valency in solvated complexes.

Development of an experimental apparatus to observe ultrafast phenomena by tender X-ray absorption spectroscopy at PAL-XFEL

Understanding the ultrafast dynamics of molecules is of fundamental importance. Time-resolved X-ray absorption spectroscopy (TR-XAS) is a powerful spectroscopic technique for unveiling the time-dependent structural and electronic information of molecules that has been widely applied in various fields. Herein, the design and technical achievement of a newly developed experimental apparatus for TR-XAS measurements in the tender X-ray range with X-ray free-electron lasers (XFELs) at the Pohang Accelerator Laboratory XFEL (PAL-XFEL) are described. Femtosecond TR-XAS measurements were conducted at the Ru L3-edge of well known photosensitizer tris(bipyridine)ruthenium(II) chloride ([Ru(bpy)3]2+) in water. The results indicate ultrafast photoinduced electron transfer from the Ru center to the ligand, which demonstrates that the newly designed setup is applicable for monitoring ultrafast reactions in the femtosecond domain.

Femtosecond X-ray Liquidography Visualizes Wavepacket Trajectories in Multidimensional Nuclear Coordinates for a Bimolecular Reaction

ConspectusVibrational wavepacket motions on potential energy surfaces are one of the critical factors that determine the reaction dynamics of photoinduced reactions. The motions of vibrational wavepackets are often discussed in the interpretation of observables measured with various time-resolved vibrational or electronic spectroscopies but mostly in terms of the frequencies of wavepacket motions, which are approximated by normal modes, rather than the actual positions of the wavepacket. Although the time-dependent positions (that is, the trajectory) of wavepackets are hypothesized or drawn in imagined or calculated potential energy surfaces, it is not trivial to experimentally determine the trajectory of wavepackets, especially in multidimensional nuclear coordinates for a polyatomic molecule. Recently, we performed a femtosecond X-ray liquidography (solution scattering) experiment on a gold trimer complex (GTC), [Au(CN)₂^-]₃, in water at X-ray free-electron lasers (XFELs) and elucidated the time-dependent positions of vibrational wavepackets from the Franck-Condon region to equilibrium structures on both excited and ground states in the course of the formation of covalent bonds between gold atoms.Bond making is an essential process in chemical reactions, but it is challenging to keep track of detailed atomic movements associated with bond making because of its bimolecular nature that requires slow diffusion of two reaction parties to meet each other. Bond formation in the solution phase has been elusive because the diffusion of the reactants limits the reaction rate of a bimolecular process, making it difficult to initiate and track the bond-making processes with an ultrafast time resolution. In principle, if the bimolecular encounter can be controlled to overcome the limitation caused by diffusion, the bond-making processes can be tracked in a time-resolved manner, providing valuable insight into the bimolecular reaction mechanism. In this regard, GTC offers a good model system for studying the dynamics of bond formation in solution. Au(I) atoms in GTC exhibit a noncovalent aurophilic interaction, making GTC an aggregate complex without any covalent bond. Upon photoexcitation of GTC, an electron is excited from an antibonding orbital to a bonding orbital, leading to the formation of covalent bonds among Au atoms. Since Au atoms in the ground state of GTC are located in close proximity within the same solvent cage, the formation of Au-Au covalent bonds occurs without its reaction rate being limited by diffusion through the solvent.Femtosecond time-resolved X-ray liquidography (fs-TRXL) data revealed that the ground state has an asymmetric bent structure. From the wavepacket trajectory determined in three-dimensional nuclear coordinates (two internuclear distances and one bond angle), we found that two covalent bonds are formed between three Au atoms of GTC asynchronously. Specifically, one covalent bond is formed first for the shorter Au-Au pair (of the asymmetric and bent ground-state structure) in 35 fs, and subsequently, the other covalent bond is formed for the longer Au-Au pair within 360 fs. The resultant trimer complex has a symmetric and linear geometry, implying the occurrence of bent-to-linear transformation concomitant with the formation of two equivalent covalent bonds, and exhibits vibrations that can be unambiguously assigned to specific normal modes based on the wavepacket trajectory, even without the vibrational frequencies provided by quantum calculation.

Using X-ray free-electron lasers for spectroscopy of molecular catalysts and metalloenzymes

The metal centres in metalloenzymes and molecular catalysts are responsible for the rearrangement of atoms and electrons during complex chemical reactions, and they enable selective pathways of charge and spin transfer, bond breaking/making and the formation of new molecules. Mapping the electronic structural changes at the metal sites during the reactions gives a unique mechanistic insight that has been difficult to obtain to date. The development of X-ray free-electron lasers (XFELs) enables powerful new probes of electronic structure dynamics to advance our understanding of metalloenzymes. The ultrashort, intense and tunable XFEL pulses enable X-ray spectroscopic studies of metalloenzymes, molecular catalysts and chemical reactions, under functional conditions and in real time. In this Technical Review, we describe the current state of the art of X-ray spectroscopy studies at XFELs and highlight some new techniques currently under development. With more XFEL facilities starting operation and more in the planning or construction phase, new capabilities are expected, including high repetition rate, better XFEL pulse control and advanced instrumentation. For the first time, it will be possible to make real-time molecular movies of metalloenzymes and catalysts in solution, while chemical reactions are taking place.

XABOOM: An X-ray Absorption Benchmark of Organic Molecules Based on Carbon, Nitrogen, and Oxygen 1s → π* Transitions

The performance of several standard and popular approaches for calculating X-ray absorption spectra at the carbon, nitrogen, and oxygen K-edges of 40 primarily organic molecules up to the size of guanine has been evaluated, focusing on the low-energy and intense 1s → π* transitions. Using results obtained with CVS-ADC(2)-x and fc-CVS-EOM-CCSD as benchmark references, we investigate the performance of CC2, ADC(2), ADC(3/2), and commonly adopted density functional theory (DFT)-based approaches. Here, focus is on precision rather than on accuracy of transition energies and intensities-in other words, we target relative energies and intensities and the spread thereof, rather than absolute values. The use of exchange-correlation functionals tailored for time-dependent DFT calculations of core excitations leads to error spreads similar to those seen for more standard functionals, despite yielding superior absolute energies. Long-range corrected functionals are shown to perform particularly well compared to our reference data, showing error spreads in energy and intensity of 0.2-0.3 eV and ∼10%, respectively, as compared to 0.3-0.6 eV and ∼20% for a typical pure hybrid. In comparing intensities, state mixing can complicate matters, and techniques to avoid this issue are discussed. Furthermore, the influence of basis sets in high-level ab initio calculations is investigated, showing that reasonably accurate results are obtained with the use of 6-311++G**. We name this benchmark suite as XABOOM (X-ray absorption benchmark of organic molecules) and provide molecular structures and ground-state self-consistent field energies and spectroscopic data. We believe that it provides a good assessment of electronic structure theory methods for calculating X-ray absorption spectra and will become useful for future developments in this field.

An assessment of different electronic structure approaches for modeling time-resolved x-ray absorption spectroscopy

We assess the performance of different protocols for simulating excited-state x-ray absorption spectra. We consider three different protocols based on equation-of-motion coupled-cluster singles and doubles, two of them combined with the maximum overlap method. The three protocols differ in the choice of a reference configuration used to compute target states. Maximum-overlap-method time-dependent density functional theory is also considered. The performance of the different approaches is illustrated using uracil, thymine, and acetylacetone as benchmark systems. The results provide guidance for selecting an electronic structure method for modeling time-resolved x-ray absorption spectroscopy.

The five-analyzer point-to-point scanning crystal spectrometer at ESRF ID26

X-ray emission spectroscopy in a point-to-point focusing geometry using instruments that employ more than one analyzer crystal poses challenges with respect to mechanical design and performance. This work discusses various options for positioning the components and provides the formulas for calculating their relative placement. Ray-tracing calculations were used to determine the geometrical contributions to the energy broadening including the source volume as given by the beam footprint on the sample. The alignment of the instrument is described and examples are given for the performance.

Ultrafast structural dynamics of in-cage isomerization of diiodomethane in solution

Despite extensive studies on the isomer species formed by photodissociation of haloalkanes in solution, the molecular structure of the precursor of the isomer, which is often assumed to be a vibrationally hot isomer formed from the radical pair, and its in-cage isomerization mechanism remain elusive. Here, the structural dynamics of CH₂I₂ upon 267 nm photoexcitation in methanol were probed with femtosecond X-ray solution scattering at an X-ray free-electron laser. The determined molecular structure of the transiently formed species that converts to the CH₂I–I isomer has the I–I distance of 4.17 Å, which is longer than that of the isomer (3.15 Å) by more than 1.0 Å and the mean-squared displacement of 0.45 Ų, which is about 100 times larger than those of typical regular chemical bonds. These unusual structural characteristics are consistent with either a vibrationally hot form of the CH₂I–I isomer or the loosely-bound radical pair (CH₂I˙⋯I˙).

The structural dynamics of in-cage isomerization of CH₂I₂ and the unusual structure of the loosely-bound isomer precursor were unveiled with femtosecond X-ray liquidography (solution scattering).

XANES Measurements for Studies of Adsorbed Protein Layers at Liquid Interfaces

X-ray absorption near edge structure (XANES) spectra for protein layers adsorbed at liquid interfaces in a Langmuir trough have been recorded for the first time. We studied the parkin protein (so-called E3 ubiquitin ligase), which plays an important role in pathogenesis of Parkinson disease. Parkin contains eight Zn binding sites, consisting of cysteine and histidine residues in a tetracoordinated geometry. Zn K-edge XANES spectra were collected in the following two series: under mild radiation condition of measurements (short exposition time) and with high X-ray radiation load. XANES fingerprint analysis was applied to obtain information on ligand environments around zinc ions. Two types of zinc coordination geometry were identified depending on X-ray radiation load. We found that, under mild conditions, local zinc environment in our parkin preparations was very similar to that identified in hemoglobin, treated with a solution of ZnCl₂ salt. Under high X-ray radiation load, considerable changes in the zinc site structure were observed; local zinc environment appeared to be almost identical to that defined in Zn-containing enzyme alkaline phosphatase. The formation of a similar metal site in unrelated protein molecules, observed in our experiments, highlights the significance of metal binding templates as essential structural modules in protein macromolecules.

Characterizing electronic and atomic structures for amorphous and molecular metal oxide catalysts at functional interfaces by combining soft X-ray spectroscopy and high-energy X-ray scattering

Amorphous thin film materials and heterogenized molecular catalysts supported on electrode and other functional interfaces are widely investigated as promising catalyst formats for applications in solar and electrochemical fuels catalysis. However the amorphous character of these catalysts and the complexity of the interfacial architectures that merge charge transport properties of electrode and semiconductor supports with discrete sites for multi-step catalysis poses challenges for probing mechanisms that activate and tune sites for catalysis. This minireview discusses advances in soft X-ray spectroscopy and high-energy X-ray scattering that provide opportunities to resolve interfacial electronic and atomic structures, respectively, that are linked to catalysis. This review discusses how these techniques can be partnered with advances in nanostructured interface synthesis for combined soft X-ray spectroscopy and high-energy X-ray scattering analyses of thin film and heterogenized molecular catalysts. These combined approaches enable opportunities for the characterization of both electronic and atomic structures underlying fundamental catalytic function, and that can be applied under conditions relevant to device applications.

Vibronic coherence evolution in multidimensional ultrafast photochemical processes

The complex choreography of electronic, vibrational, and vibronic couplings used by photoexcited molecules to transfer energy efficiently is remarkable, but an unambiguous description of the temporally evolving vibronic states governing these processes has proven experimentally elusive. We use multidimensional electronic-vibrational spectroscopy to identify specific time-dependent excited state vibronic couplings involving multiple electronic states, high-frequency vibrations, and low-frequency vibrations which participate in ultrafast intersystem crossing and subsequent relaxation of a photoexcited transition metal complex. We discover an excited state vibronic mechanism driving long-lived charge separation consisting of an initial electronically-localized vibrational wavepacket which triggers delocalization onto two charge transfer states after propagating for ~600 femtoseconds. Electronic delocalization consequently occurs through nonadiabatic internal conversion driven by a 50 cm^-1 coupling resulting in vibronic coherence transfer lasting for ~1 picosecond. This study showcases the power of multidimensional electronic-vibrational spectroscopy to elucidate complex, non-equilibrium energy and charge transfer mechanisms involving multiple molecular coordinates.

Elucidation of the photoaquation reaction mechanism in ferrous hexacyanide using synchrotron x-rays with sub-pulse-duration sensitivity

Ligand substitution reactions are common in solvated transition metal complexes, and harnessing them through initiation with light promises interesting practical applications, driving interest in new means of probing their mechanisms. Using a combination of time-resolved x-ray absorption spectroscopy and hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations and x-ray absorption near-edge spectroscopy calculations, we elucidate the mechanism of photoaquation in the model system iron(ii) hexacyanide, where UV excitation results in the exchange of a CN^- ligand with a water molecule from the solvent. We take advantage of the high flux and stability of synchrotron x-rays to capture high precision x-ray absorption spectra that allow us to overcome the usual limitation of the relatively long x-ray pulses and extract the spectrum of the short-lived intermediate pentacoordinated species. Additionally, we determine its lifetime to be 19 (±5) ps. The QM/MM simulations support our experimental findings and explain the ∼20 ps time scale for aquation as involving interconversion between the square pyramidal (SP) and trigonal bipyramidal pentacoordinated geometries, with aquation being only active in the SP configuration.

The measurement of ultrafast electronic and structural dynamics with X-rays

In this theme issue, leading researchers discuss recent work on the measurement of ultrafast electronic and structural dynamics in matter using a new generation of short duration X-ray photon sources. These photon sources, based upon high harmonic generation from lasers and X-ray free-electron lasers, look set to have a high impact on ultrafast science. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.