Exploiting EXAFS and XANES for time-resolved molecular structures in liquids

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 photoelectron spectroscopy of photoexcited aqueous ferrioxalate

The photochemistry of metal-organic compounds in solution is determined by both intra- and inter-molecular relaxation processes after photoexcitation. Understanding its prime mechanisms is crucial to optimise the reactive paths and control their outcome. Here we investigate the photoinduced dynamics of aqueous ferrioxalate ([Fe^III(C₂O₄)₃]^3-) upon 263 nm excitation using ultrafast liquid phase photoelectron spectroscopy (PES). The initial step is found to be a ligand-to-metal electron transfer, occuring on a time scale faster than our time resolution (≲30 fs). Furthermore, we observe that about 25% of the initially formed ferrous species population are lost in ∼2 ps. Cast in the contest of previous ultrafast infrared and X-ray spectroscopic studies, we suggest that upon prompt photoreduction of the metal centre, the excited molecules dissociate in <140 fs into the pair of CO₂ and [(CO₂)Fe^II(C₂O₄)₂]^3- fragments, with unity quantum yield. About 25% of these pairs geminately recombine in ∼2 ps, due to interaction with the solvent molecules, reforming the ground state of the parent ferric molecule.

X-ray multi-probe data acquisition: A novel technique for laser pump x-ray transient absorption spectroscopy

We report the development and implementation of a novel data acquisition (DAQ) technique for synchrotron-based laser pump X-ray Transient Absorption (XTA) spectroscopy, called X-ray Multi-Probe DAQ (XMP DAQ). This technique utilizes high performance analog to digital converters and home-built software to efficiently measure and process the XTA signal from all x-ray pulses between laser excitations. XMP DAQ generates a set of time resolved x-ray absorption spectra at thousands of different pump-probe time delays simultaneously. Two distinct XMP DAQ schemes are deployed to accommodate different synchrotron storage ring filling patterns. Current Integration (CI) DAQ is a quasi-analog technique that implements a fitting procedure to extract the time resolved absorption intensity from the averaged fluorescence detector response. The fitting procedure eliminates issues associated with small drifts in the voltage baseline and greatly enhances the accuracy of the technique. Photon Counting (PC) DAQ is a binary technique that uses a time resolved histogram to calculate the XTA spectrum. While PC DAQ is suited to measure XTA data with closely spaced x-ray pulses (∼10 ns) and a low count rate (<1 detected photon/pulse), CI DAQ works best for widely spaced pulses (tens of ns or greater) with a high count rate (>1 detected photon/pulse). XMP DAQ produces a two-dimensional XTA dataset, enabling efficient quantitative analysis of photophysical and photochemical processes from the sub-nanosecond timescale to 100 μs and longer.

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 Kβ 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.

Toward time-resolved laser T-jump/X-ray probe spectroscopy in aqueous solutions

Most chemical and biochemical reactions in nature and in industrial processes are driven by thermal effects that bring the reactants above the energy barrier for reaction. In aqueous solutions, this process can also be triggered by the laser driven temperature jump (T-jump) method, in which the water vibrational (stretch, bend, or combination) modes are excited by a short laser pulse, leading to a temperature increase in the irradiated volume within a few picoseconds. The combination of the laser T-jump with X-ray spectroscopic probes would add element-specificity as well as sensitivity to the structure, the oxidation state, and the spin state of the intermediates of reactions. Here, we present preliminary results of a near infrared pump/X-ray absorption spectroscopy probe to study the ligand exchange of an octahedral aqueous Cobalt complex, which is known to pass through intermediate steps yielding tetrahedral chlorinated as final species. The structural changes of the chemical reaction are monitored with great sensitivity, even in the presence of a mild local increase in temperature. This work opens perspectives for the study of non-light-driven reactions using time-resolved X-ray spectroscopic methods.

Localized holes and delocalized electrons in photoexcited inorganic perovskites: Watching each atomic actor by picosecond X-ray absorption spectroscopy

We report on an element-selective study of the fate of charge carriers in photoexcited inorganic CsPbBr₃ and CsPb(ClBr)₃ perovskite nanocrystals in toluene solutions using time-resolved X-ray absorption spectroscopy with 80 ps time resolution. Probing the Br K-edge, the Pb L₃-edge, and the Cs L₂-edge, we find that holes in the valence band are localized at Br atoms, forming small polarons, while electrons appear as delocalized in the conduction band. No signature of either electronic or structural changes is observed at the Cs L₂-edge. The results at the Br and Pb edges suggest the existence of a weakly localized exciton, while the absence of signatures at the Cs edge indicates that the Cs⁺ cation plays no role in the charge transport, at least beyond 80 ps. This first, time-resolved element-specific study of perovskites helps understand the rather modest charge carrier mobilities in these materials.

Tracking reaction dynamics in solution by pump–probe X-ray absorption spectroscopy and X-ray liquidography (solution scattering)

TRXL and TRXAS are powerful techniques for real-time probing of structural and electronic dynamics of photoinduced reactions in solution phase.

Identifying the major intermediate species by combining time-resolved X-ray solution scattering and X-ray absorption spectroscopy

Identifying the intermediate species along a reaction pathway is a first step towards a complete understanding of the reaction mechanism, but often this task is not trivial. There has been a strong on-going debate: which of the three intermediates, the CHI2 radical, the CHI2-I isomer, and the CHI2(+) ion, is the dominant intermediate species formed in the photolysis of iodoform (CHI3)? Herein, by combining time-resolved X-ray liquidography (TRXL) and time-resolved X-ray absorption spectroscopy (TR-XAS), we present strong evidence that the CHI2 radical is dominantly formed from the photolysis of CHI3 in methanol at 267 nm within the available time resolution of the techniques (∼20 ps for TRXL and ∼100 ps for TR-XAS). The TRXL measurement, conducted using the time-slicing scheme, detected no CHI2-I isomer within our signal-to-noise ratio, indicating that, if formed, the CHI2-I isomer must be a minor intermediate. The TR-XAS transient spectra measured at the iodine L1 and L3 edges support the same conclusion. The present work demonstrates that the application of these two complementary time-resolved X-ray methods to the same system can provide a detailed understanding of the reaction mechanism.

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.

Detailed Characterization of a Nanosecond-Lived Excited State: X-ray and Theoretical Investigation of the Quintet State in Photoexcited [Fe(terpy)2]2

Theoretical predictions show that depending on the populations of the Fe 3d _xy , 3d _xz , and 3d _yz orbitals two possible quintet states can exist for the high-spin state of the photoswitchable model system [Fe(terpy)₂]²⁺. The differences in the structure and molecular properties of these ⁵B₂ and ⁵E quintets are very small and pose a substantial challenge for experiments to resolve them. Yet for a better understanding of the physics of this system, which can lead to the design of novel molecules with enhanced photoswitching performance, it is vital to determine which high-spin state is reached in the transitions that follow the light excitation. The quintet state can be prepared with a short laser pulse and can be studied with cutting-edge time-resolved X-ray techniques. Here we report on the application of an extended set of X-ray spectroscopy and scattering techniques applied to investigate the quintet state of [Fe(terpy)₂]²⁺ 80 ps after light excitation. High-quality X-ray absorption, nonresonant emission, and resonant emission spectra as well as X-ray diffuse scattering data clearly reflect the formation of the high-spin state of the [Fe(terpy)₂]²⁺ molecule; moreover, extended X-ray absorption fine structure spectroscopy resolves the Fe-ligand bond-length variations with unprecedented bond-length accuracy in time-resolved experiments. With ab initio calculations we determine why, in contrast to most related systems, one configurational mode is insufficient for the description of the low-spin (LS)-high-spin (HS) transition. We identify the electronic structure origin of the differences between the two possible quintet modes, and finally, we unambiguously identify the formed quintet state as ⁵E, in agreement with our theoretical expectations.

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.

Solvation dynamics monitored by combined X-ray spectroscopies and scattering: photoinduced spin transition in aqueous [Fe(bpy)3]2+

We have studied the photoinduced low spin (LS) to high spin (HS) conversion of aqueous Fe(bpy)₃ with pulse-limited time resolution. In a combined setup permitting simultaneous X-ray diffuse scattering (XDS) and spectroscopic measurements at a MHz repetition rate we have unraveled the interplay between intramolecular dynamics and the intermolecular caging solvent response with 100 ps time resolution. On this time scale the ultrafast spin transition including intramolecular geometric structure changes as well as the concomitant bulk solvent heating process due to energy dissipation from the excited HS molecule are long completed. The heating is nevertheless observed to further increase due to the excess energy between HS and LS states released on a subnanosecond time scale. The analysis of the spectroscopic data allows precise determination of the excited population which efficiently reduces the number of free parameters in the XDS analysis, and both combined permit extraction of information about the structural dynamics of the first solvation shell.

A wavelet analysis for the X-ray absorption spectra of molecules

We present a Wavelet transform analysis for the X-ray absorption spectra of molecules. In contrast to the traditionally used Fourier transform approach, this analysis yields a 2D correlation plot in both R- and k-space. As a consequence, it is possible to distinguish between different scattering pathways at the same distance from the absorbing atom and between the contributions of single and multiple scattering events, making an unambiguous assignment of the fine structure oscillations for complex systems possible. We apply this to two previously studied transition metal complexes, namely iron hexacyanide in both its ferric and ferrous form, and a rhenium diimine complex, [ReX(CO)(3)(bpy)], where X = Br, Cl, or ethyl pyridine (Etpy). Our results demonstrate the potential advantages of using this approach and they highlight the importance of multiple scattering, and specifically the focusing phenomenon to the extended X-ray absorption fine structure (EXAFS) spectra of these complexes. We also shed light on the low sensitivity of the EXAFS spectrum to the Re-X scattering pathway.

L2,3-edge x-ray absorption near-edge spectroscopy analysis of photoisomerism in solid ruthenium-sulfur dioxide complexes

Ru L(2,3) edge x-ray absorption near-edge spectroscopy spectra of four compounds [Ru(SO(2))(NH(3))(4)X]Y (X =  water, Y = (±)-camphorsulfonate(2); X =water, Y = tosylate(2); X =isonicotinamide, Y = tosylate(2); X =pyridine, Y = triflate(2)) are reported before and after optical excitation, which causes photoinduced linkage isomerism of the SO(2) ligand. Principal component analysis reveals consistent changes in the spectra upon photoisomerization, suggesting a partial oxidation of the Ru ion. These results demonstrate that x-ray absorption near-edge spectroscopy is an effective means of probing photoinduced linkage isomerism.

Hydrophobicity with atomic resolution: Steady-state and ultrafast X-ray absorption and molecular dynamics studies

Static and time-resolved X-ray absorption spectroscopy (XAS) is used to probe the solvent shell structure around iodide and iodine. In particular, we characterize the changes observed upon electron abstraction of aqueous iodide, which reflects the transition from hydrophilic to hydrophobic solvation after impulsive electron abstraction from iodide. The static spectrum of aqueous iodide, which is analyzed using quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, indicates that the hydrogens of the closest water molecules point toward the iodide, as expected for hydrophilic solvation. In addition, these simulations demonstrate a small anisotropy in the solvent shell. Following electron abstraction, most of the water molecules move away from iodine, while one comes closer to form a complex with it that survives for 3–4 ps. This lifetime is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform a hydrogen bond network in the hydrophobic solvation shell.

Understanding the electronic structure of 4d metal complexes: from molecular spinors to L-edge spectra of a di-Ru catalyst

L(2,3)-edge X-ray absorption spectroscopy (XAS) has demonstrated unique capabilities for the analysis of the electronic structure of di-Ru complexes such as the blue dimer cis,cis-[Ru(III)(2)O(H(2)O)(2)(bpy)(4)](4+) water oxidation catalyst. Spectra of the blue dimer and the monomeric [Ru(NH(3))(6)](3+) model complex show considerably different splitting of the Ru L(2,3) absorption edge, which reflects changes in the relative energies of the Ru 4d orbitals caused by hybridization with a bridging ligand and spin-orbit coupling effects. To aid the interpretation of spectroscopic data, we developed a new approach, which computes L(2,3)-edges XAS spectra as dipole transitions between molecular spinors of 4d transition metal complexes. This allows for careful inclusion of the spin-orbit coupling effects and the hybridization of the Ru 4d and ligand orbitals. The obtained theoretical Ru L(2,3)-edge spectra are in close agreement with experiment. Critically, existing single-electron methods (FEFF, FDMNES) broadly used to simulate XAS could not reproduce the experimental Ru L-edge spectra for the [Ru(NH(3))(6)](3+) model complex nor for the blue dimer, while charge transfer multiplet (CTM) calculations were not applicable due to the complexity and low symmetry of the blue dimer water oxidation catalyst. We demonstrated that L-edge spectroscopy is informative for analysis of bridging metal complexes. The developed computational approach enhances L-edge spectroscopy as a tool for analysis of the electronic structures of complexes, materials, catalysts, and reactive intermediates with 4d transition metals.

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.

Excited-state molecular structures captured by X-ray transient absorption spectroscopy: a decade and beyond

Transient molecular structures along chemical reaction pathways are important for predicting molecular reactivity, understanding reaction mechanisms, as well as controlling reaction pathways. During the past decade, X-ray transient absorption spectroscopy (XTA, or LITR-XAS, laser-initiated X-ray absorption spectroscopy), analogous to the commonly used optical transient absorption spectroscopy, has been developed. XTA uses a laser pulse to trigger a fundamental chemical process, and an X-ray pulse(s) to probe transient structures as a function of the time delay between the pump and probe pulses. Using X-ray pulses with high photon flux from synchrotron sources, transient electronic and molecular structures of metal complexes have been studied in disordered media from homogeneous solutions to heterogeneous solution-solid interfaces. Several examples from the studies at the Advanced Photon Source in Argonne National Laboratory are summarized, including excited-state metalloporphyrins, metal-to-ligand charge transfer (MLCT) states of transition metal complexes, and charge transfer states of metal complexes at the interface with semiconductor nanoparticles. Recent developments of the method are briefly described followed by a future prospective of XTA. It is envisioned that concurrent developments in X-ray free-electron lasers and synchrotron X-ray facilities as well as other table-top laser-driven femtosecond X-ray sources will make many breakthroughs and realise dreams of visualizing molecular movies and snapshots, which ultimately enable chemical reaction pathways to be controlled.

Time-resolved structural studies of protein reaction dynamics: a smorgasbord of X-ray approaches

Time-resolved structural studies of proteins have undergone several significant developments during the last decade. Recent developments using time-resolved X-ray methods, such as time-resolved Laue diffraction, low-temperature intermediate trapping, time-resolved wide-angle X-ray scattering and time-resolved X-ray absorption spectroscopy, are reviewed.

Proteins undergo conformational changes during their biological function. As such, a high-resolution structure of a protein’s resting conformation provides a starting point for elucidating its reaction mechanism, but provides no direct information concerning the protein’s conformational dynamics. Several X-ray methods have been developed to elucidate those conformational changes that occur during a protein’s reaction, including time-resolved Laue diffraction and intermediate trapping studies on three-dimensional protein crystals, and time-resolved wide-angle X-ray scattering and X-ray absorption studies on proteins in the solution phase. This review emphasizes the scope and limitations of these complementary experimental approaches when seeking to understand protein conformational dynamics. These methods are illustrated using a limited set of examples including myoglobin and haemoglobin in complex with carbon monoxide, the simple light-driven proton pump bacteriorhodopsin, and the superoxide scavenger superoxide reductase. In conclusion, likely future developments of these methods at synchrotron X-ray sources and the potential impact of emerging X-ray free-electron laser facilities are speculated upon.

Picosecond and femtosecond X-ray absorption spectroscopy of molecular systems

The need to visualize molecular structure in the course of a chemical reaction, a phase transformation or a biological function has been a dream of scientists for decades. The development of time-resolved X-ray and electron-based methods is making this true. X-ray absorption spectroscopy is ideal for the study of structural dynamics in liquids, because it can be implemented in amorphous media. Furthermore, it is chemically selective. Using X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) in laser pump/X-ray probe experiments allows the retrieval of the local geometric structure of the system under study, but also the underlying photoinduced electronic structure changes that drive the structural dynamics. Recent developments in picosecond and femtosecond X-ray absorption spectroscopy applied to molecular systems in solution are reviewed: examples on ultrafast photoinduced processes such as intramolecular electron transfer, low-to-high spin change, and bond formation are presented.