Short-lived metal-centered excited state initiates iron-methionine photodissociation in ferrous cytochrome c

Efficient Spin-Adapted Implementation of Multireference Algebraic Diagrammatic Construction Theory. I. Core-Ionized States and X-ray Photoelectron Spectra

We present an efficient implementation of multireference algebraic diagrammatic construction theory (MR-ADC) for simulating core-ionized states and X-ray photoelectron spectra (XPS). Taking advantage of spin adaptation, automatic code generation, and density fitting, our implementation can perform calculations for molecules with more than 1500 molecular orbitals, incorporating static and dynamic correlation in the ground and excited electronic states. We demonstrate the capabilities of MR-ADC methods by simulating the XPS spectra of substituted ferrocene complexes and azobenzene isomers. For the ground electronic states of these molecules, the XPS spectra computed using the extended second-order MR-ADC method (MR-ADC(2)-X) are in a very good agreement with available experimental results. We further show that MR-ADC can be used as a tool for interpreting or predicting the results of time-resolved XPS measurements by simulating the core ionization spectra of azobenzene along its photoisomerization, including the XPS signatures of excited states and the minimum energy conical intersection. This work is the first in a series of publications reporting the efficient implementations of MR-ADC methods.

Time-Resolved X-ray Emission Spectroscopy and Synthetic High-Spin Model Complexes Resolve Ambiguities in Excited-State Assignments of Transition-Metal Chromophores: A Case Study of Fe-Amido Complexes

To fully harness the potential of abundant metal coordination complex photosensitizers, a detailed understanding of the molecular properties that dictate and control the electronic excited-state population dynamics initiated by light absorption is critical. In the absence of detectable luminescence, optical transient absorption (TA) spectroscopy is the most widely employed method for interpreting electron redistribution in such excited states, particularly for those with a charge-transfer character. The assignment of excited-state TA spectral features often relies on spectroelectrochemical measurements, where the transient absorption spectrum generated by a metal-to-ligand charge-transfer (MLCT) electronic excited state, for instance, can be approximated using steady-state spectra generated by electrochemical ligand reduction and metal oxidation and accounting for the loss of absorptions by the electronic ground state. However, the reliability of this approach can be clouded when multiple electronic configurations have similar optical signatures. Using a case study of Fe(II) complexes supported by benzannulated diarylamido ligands, we highlight an example of such an ambiguity and show how time-resolved X-ray emission spectroscopy (XES) measurements can reliably assign excited states from the perspective of the metal, particularly in conjunction with accurate synthetic models of ligand-field electronic excited states, leading to a reinterpretation of the long-lived excited state as a ligand-field metal-centered quintet state. A detailed analysis of the XES data on the long-lived excited state is presented, along with a discussion of the ultrafast dynamics following the photoexcitation of low-spin Fe(II)-Namido complexes using a high-spin ground-state analogue as a spectral model for the 5T2 excited state.

A comparative review of time-resolved x-ray and electron scattering to probe structural dynamics

The structure of molecules, particularly the dynamic changes in structure, plays an essential role in understanding physical and chemical phenomena. Time-resolved (TR) scattering techniques serve as crucial experimental tools for studying structural dynamics, offering direct sensitivity to molecular structures through scattering signals. Over the past decade, the advent of x-ray free-electron lasers (XFELs) and mega-electron-volt ultrafast electron diffraction (MeV-UED) facilities has ushered TR scattering experiments into a new era, garnering significant attention. In this review, we delve into the basic principles of TR scattering experiments, especially focusing on those that employ x-rays and electrons. We highlight the variations in experimental conditions when employing x-rays vs electrons and discuss their complementarity. Additionally, cutting-edge XFELs and MeV-UED facilities for TR x-ray and electron scattering experiments and the experiments performed at those facilities are reviewed. As new facilities are constructed and existing ones undergo upgrades, the landscape for TR x-ray and electron scattering experiments is poised for further expansion. Through this review, we aim to facilitate the effective utilization of these emerging opportunities, assisting researchers in delving deeper into the intricate dynamics of molecular structures.

Stimulated X-ray emission spectroscopy

We describe an emerging hard X-ray spectroscopy technique, stimulated X-ray emission spectroscopy (S-XES). S-XES has the potential to characterize the electronic structure of 3d transition metal complexes with spectral information currently not reachable and might lead to the development of new ultrafast X-ray sources with properties beyond the state of the art. S-XES has become possible with the emergence of X-ray free-electron lasers (XFELs) that provide intense femtosecond X-ray pulses that can be employed to generate a population inversion of core-hole excited states resulting in stimulated X-ray emission. We describe the instrumentation, the various types of S-XES, the potential applications, the experimental challenges, and the feasibility of applying S-XES to characterize dilute systems, including the Mn4Ca cluster in the oxygen evolving complex of photosystem II.

Situating the phosphonated calixarene-cytochrome C association by molecular dynamics simulations

Protein-calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as "molecular glue." Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding.

Iron Kβ X-ray Emission Spectroscopy: The Origin of Spectral Features from Atomic to Molecular Systems Using Multi-configurational Calculations

Kβ X-ray emission spectroscopy (XES) is widely used to fingerprint the local spin of transition-metal ions, including in pump-probe experiments, to identify excited states or in chemical and biological reactions to characterize short-lived intermediates. In this study, the spectra of ferrous and ferric complexes for various spin states were measured experimentally and described theoretically through restricted active space (RAS) calculations including dynamic correlations. Through the RAS calculations from simple atomic models to complex molecular systems, spectral effects such as the exchange interactions, crystal-field strength, and covalent orbital mixing were evaluated and discussed. The calculations find that only the spectral features of low-spin cases show a dependence on the crystal-field strength, particularly for ferrous low spin. The effect of the covalent orbital mixing strength on the first moment of the Kβ1,3 main line and the Kβ1,3-Kβ' energy splitting is quantitatively described. Clear relationships are found within a given nominal spin but less between different spin states, which calls for careful selection of reference spectra in future experiments. This study further advances our understanding of the correlation between changes in experimental spectral features and their corresponding electronic structure information.

Exploring fingerprints of ultrafast structural dynamics in molecular solutions with an X-ray laser

We apply ultrashort X-ray laser pulses to track optically excited structural dynamics of [Ir2(dimen)4]2+ molecules in solution. In our exploratory study we determine angular correlations in the scattered X-rays, which comprise a complex fingerprint of the ultrafast dynamics. Model-assisted analysis of the experimental correlation data allows us to elucidate various aspects of the photoinduced changes in the excited molecular ensembles. We unambiguously identify that in our experiment the photoinduced transition dipole moments in [Ir2(dimen)4]2+ molecules are oriented perpendicular to the Ir-Ir bond. The analysis also shows that the ground state conformer of [Ir2(dimen)4]2+ with a larger Ir-Ir distance is mostly responsible for the formation of the excited state. We also reveal that the ensemble of solute molecules can be characterized with a substantial structural heterogeneity due to solvent influence. The proposed X-ray correlation approach offers an alternative path for studies of ultrafast structural dynamics of molecular ensembles in the liquid and gas phases.

Solution phase high repetition rate laser pump x-ray probe picosecond hard x-ray spectroscopy at the Stanford Synchrotron Radiation Lightsource

We present a dedicated end-station for solution phase high repetition rate (MHz) picosecond hard x-ray spectroscopy at beamline 15-2 of the Stanford Synchrotron Radiation Lightsource. A high-power ultrafast ytterbium-doped fiber laser is used to photoexcite the samples at a repetition rate of 640 kHz, while the data acquisition operates at the 1.28 MHz repetition rate of the storage ring recording data in an alternating on-off mode. The time-resolved x-ray measurements are enabled via gating the x-ray detectors with the 20 mA/70 ps camshaft bunch of SPEAR3, a mode available during the routine operations of the Stanford Synchrotron Radiation Lightsource. As a benchmark study, aiming to demonstrate the advantageous capabilities of this end-station, we have conducted picosecond Fe K-edge x-ray absorption spectroscopy on aqueous [FeII(phen)3]2+, a prototypical spin crossover complex that undergoes light-induced excited spin state trapping forming an electronic excited state with a 0.6-0.7 ns lifetime. In addition, we report transient Fe Kβ main line and valence-to-core x-ray emission spectra, showing a unique detection sensitivity and an excellent agreement with model spectra and density functional theory calculations, respectively. Notably, the achieved signal-to-noise ratio, the overall performance, and the routine availability of the developed end-station have enabled a systematic time-resolved science program using the monochromatic beam at the Stanford Synchrotron Radiation Lightsource.

The role of basicity in selective C-H bond activation by transition metal-oxidos

The development of (bio)catalysts capable of selectively activating strong C-H bonds is a continuing challenge in modern chemistry. In both metalloenzymes and synthetic systems capable of activating C-H bonds, transition metal-oxido intermediates serve as the active species for reactivity whose thermodynamic properties influence the bond strengths they are capable of activating. In this Frontier article, we present current ideas of how the basicity of transition metal-oxidos impacts their reactivity with C-H bonds and present new opportunities within this field. We highlight recent insights into the role basicity plays in the activation process and its influence on mechanism, as well as the important role that secondary coordination sphere effects, such as hydrogen bonds, in tuning the basicity of the metal-oxido species is discussed.

Interactions of ultrashort laser pulses with hemoglobin: Photophysical aspects and potential applications

Hemoglobin (Hb), a life-sustaining and highly abundant erythrocyte protein, is not readily fluorescent. A few studies have already reported Two-Photon Excited Fluorescence (TPEF) of Hb, however, the mechanisms through which Hb becomes fluorescent upon interaction with ultrashort laser pulses are not completely understood. Here, we characterized photophysically this interaction on Hb thin film and erythrocytes using fluorescence spectroscopy upon single-photon/two-photon absorption, and UV-VIS single-photon absorption spectroscopy. A gradual increase of the fluorescence intensity, ending up with saturation, is observed upon prolonged exposure of Hb thin layer and erythrocytes to ultrashort laser pulses at 730 nm. When compared to protoporphyrin IX (PpIX) and oxidized Hb by H₂O₂, TPEF spectra from a thin Hb film and erythrocytes showed good mutual agreement, broad peaking at 550 nm, supporting hemoglobin undergoes degradation and that same fluorescent specie(s) originating from the heme moiety are generated. The uniform square shaped patterns of the fluorescent photoproduct exhibited the same level of the fluorescence intensity even after 12 weeks from the formation, indicating high photoproduct stability. We finally demonstrated the full potential of the formed Hb photoproduct with TPEF scanning microscopy towards spatiotemporally controlled micropatterning in HTF and single human erythrocyte labelling and tracking in the whole blood.

Ferricyanide photo-aquation pathway revealed by combined femtosecond Kβ main line and valence-to-core x-ray emission spectroscopy

Reliably identifying short-lived chemical reaction intermediates is crucial to elucidate reaction mechanisms but becomes particularly challenging when multiple transient species occur simultaneously. Here, we report a femtosecond x-ray emission spectroscopy and scattering study of the aqueous ferricyanide photochemistry, utilizing the combined Fe Kβ main and valence-to-core emission lines. Following UV-excitation, we observe a ligand-to-metal charge transfer excited state that decays within 0.5 ps. On this timescale, we also detect a hitherto unobserved short-lived species that we assign to a ferric penta-coordinate intermediate of the photo-aquation reaction. We provide evidence that bond photolysis occurs from reactive metal-centered excited states that are populated through relaxation of the charge transfer excited state. Beyond illuminating the elusive ferricyanide photochemistry, these results show how current limitations of Kβ main line analysis in assigning ultrafast reaction intermediates can be circumvented by simultaneously using the valence-to-core spectral range.

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.

Origin of the Second-Order Proton Catalysis of Ferriin Reduction in Belousov-Zhabotinsky Reactions: Density Functional Studies of Ferroin and Ferriin Aggregates with Outer Sphere Ligands Sulfate, Bisulfate, and Sulfuric Acid

The detailed mechanisms of Belousov-Zhabotinsky oscillating reactions continue to present grand challenges, even after half a century of study. The origin of the pH dependence of the oscillation pattern had never been rigorously identified. In our recent kinetic study of one of the key Belousov-Zhabotinsky reactions, the iron-catalyzed bromate oxidation of malonic acid, compelling agreement between experiments and kinetic simulations was achieved only with the inclusion of second-order proton catalysis of the reduction of the [Fe(phen)₃]³⁺ species. After exhausting all other avenues in search of an explanation of this proton catalysis, we considered the possibility that the parent iron-phenanthroline complexes could aggregate with neutral and anionic outer sphere ligands (OSLs) in the highly concentrated sulfuric acid solution, and we hypothesized that OSL protonation would increase the capacity of the aggregated complex to oxidize the organic fuel. We performed potential energy surface analyses at the SMD(APFD/6-311G*) level of complexes of the types [Fe(phen)₃(SO₄^2-)_m(HSO₄^-)_n(H₂SO₄)_o]^(c-2m-n)+ for ferriin (c = 3) and ferroin (c = 2) aggregated with m sulfate, n bisulfate, and o sulfuric acid OSLs. We present structures of the OSL aggregates, develop a nomenclature for their description, and characterize their electronic structure. The structural chemistry provides the foundation to discuss the ferroin/ferriin redox couple with emphasis on the relationship between the vertical electron affinities of ferriin aggregates and their OSL protonation states. For proton catalysis to manifest itself, double-protonation paths that are slightly endergonic should be present, and proton affinities of aggregated OSLs allow the identification of such double-protonation chains. As a first test of our mechanistic proposal for the second-order proton catalysis of the Belousov-Zhabotinsky reaction, the results presented here provide compelling evidence in support of the importance of outer sphere ligation of the iron catalyst.

Reaction dynamics studied via femtosecond X-ray liquidography at X-ray free-electron lasers

X-ray free-electron lasers (XFELs) provide femtosecond X-ray pulses suitable for pump–probe time-resolved studies with a femtosecond time resolution. Since the advent of the first XFEL in 2009, recent years have witnessed a great number of applications with various pump–probe techniques at XFELs. Among these, time-resolved X-ray liquidography (TRXL) is a powerful method for visualizing structural dynamics in the liquid solution phase. Here, we classify various chemical and biological molecular systems studied via femtosecond TRXL (fs-TRXL) at XFELs, depending on the focus of the studied process, into (i) bond cleavage and formation, (ii) charge distribution and electron transfer, (iii) orientational dynamics, (iv) solvation dynamics, (v) coherent nuclear wavepacket dynamics, and (vi) protein structural dynamics, and provide a brief review on each category. We also lay out a plausible roadmap for future fs-TRXL studies for areas that have not been explored yet.

Femtosecond X-ray liquidography using X-ray free-electron lasers (XFELs) visualizes various aspects of reaction dynamics.

Hydrogen/Deuterium Exchange Measurements May Provide an Incomplete View of Protein Dynamics: a Case Study on Cytochrome c

Many aspects of protein function rely on conformational fluctuations. Hydrogen/deuterium exchange (HDX) mass spectrometry (MS) provides a window into these dynamics. Despite the widespread use of HDX-MS, it remains unclear whether this technique provides a truly comprehensive view of protein dynamics. HDX is mediated by H-bond-opening/closing events, implying that HDX methods provide an H-bond-centric view. This raises the question if there could be fluctuations that leave the H-bond network unaffected, thereby rendering them undetectable by HDX-MS. We explore this issue in experiments on cytochrome c (cyt c). Compared to the Fe(II) protein, Fe(III) cyt c shows enhanced deuteration on both the distal and proximal sides of the heme. Previous studies have attributed the enhanced dynamics of Fe(III) cyt c to the facile and reversible rupture of the distal M80-Fe(III) bond. Using molecular dynamics (MD) simulations, we conducted a detailed analysis of various cyt c conformers. Our MD data confirm that rupture of the M80-Fe(III) contact triggers major reorientation of the distal Ω loop. Surprisingly, this event takes place with only miniscule H-bonding alterations. In other words, the distal loop dynamics are almost "HDX-silent". Moreover, distal loop movements cannot account for enhanced dynamics on the opposite (proximal) side of the heme. Instead, enhanced deuteration of Fe(III) cyt c is attributed to sparsely populated conformers where both the distal (M80) and proximal (H18) coordination bonds have been ruptured, along with opening of numerous H-bonds on both sides of the heme. We conclude that there can be major structural fluctuations that are only weakly coupled to changes in H-bonding, making them virtually impossible to track by HDX-MS. In such cases, HDX-MS may provide an incomplete view of protein dynamics.

The Quest to Simulate Excited-State Dynamics of Transition Metal Complexes

This Perspective describes current computational efforts in the field of simulating photodynamics of transition metal complexes. We present the typical workflows and feature the strengths and limitations of the different contemporary approaches. From electronic structure methods suitable to describe transition metal complexes to approaches able to simulate their nuclear dynamics under the effect of light, we give particular attention to build a bridge between theory and experiment by critically discussing the different models commonly adopted in the interpretation of spectroscopic experiments and the simulation of particular observables. Thereby, we review all the studies of excited-state dynamics on transition metal complexes, both in gas phase and in solution from reduced to full dimensionality.

Capturing photochemical and photophysical transformations in iron complexes with ultrafast X-ray spectroscopy and scattering

Light-driven chemical transformations provide a compelling approach to understanding chemical reactivity with the potential to use this understanding to advance solar energy and catalysis applications. Capturing the non-equilibrium trajectories of electronic excited states with precision, particularly for transition metal complexes, would provide a foundation for advancing both of these objectives. Of particular importance for 3d metal compounds is characterizing the population dynamics of charge-transfer (CT) and metal-centered (MC) electronic excited states and understanding how the inner coordination sphere structural dynamics mediate the interaction between these states. Recent advances in ultrafast X-ray laser science has enabled the electronic excited state dynamics in 3d metal complexes to be followed with unprecedented detail. This review will focus on simultaneous X-ray emission spectroscopy (XES) and X-ray solution scattering (XSS) studies of iron coordination and organometallic complexes. These simultaneous XES-XSS studies have provided detailed insight into the mechanism of light-induced spin crossover in iron coordination compounds, the interaction of CT and MC excited states in iron carbene photosensitizers, and the mechanism of Fe-S bond dissociation in cytochrome c.