Picosecond sulfur K-edge X-ray absorption spectroscopy with applications to excited state proton transfer

UV photochemistry of the L-cystine disulfide bridge in aqueous solution investigated by femtosecond X-ray absorption spectroscopy

The photolysis of disulfide bonds is implicated in denaturation of proteins exposed to ultraviolet light. Despite this biological relevance in stabilizing the structure of many proteins, the mechanisms of disulfide photolysis are still contested after decades of research. Herein, we report new insight into the photochemistry of L-cystine in aqueous solution by femtosecond X-ray absorption spectroscopy at the sulfur K-edge. We observe homolytic bond cleavage upon ultraviolet irradiation and the formation of thiyl radicals as the single primary photoproduct. Ultrafast thiyl decay due to geminate recombination proceeds at a quantum yield of >80 % within 20 ps. These dynamics coincide with the emergence of a secondary product, attributed to the generation of perthiyl radicals. From these findings, we suggest a mechanism of perthiyl radical generation from a vibrationally excited parent molecule that asymmetrically fragments along a carbon-sulfur bond. Our results point toward a dynamic photostability of the disulfide bridge in condensed-phase.

Understanding Cysteine Chemistry Using Conventional and Serial X-Ray Protein Crystallography

Proteins that use cysteine residues for catalysis or regulation are widely distributed and intensively studied, with many biomedically important examples. Enzymes where cysteine is a catalytic nucleophile typically generate covalent catalytic intermediates whose structures are important for understanding mechanism and for designing targeted inhibitors. The formation of catalytic intermediates can change enzyme conformational dynamics, sometimes activating protein motions that are important for catalytic turnover. However, these transiently populated intermediate species have been challenging to structurally characterize using traditional crystallographic approaches. This review describes the use and promise of new time-resolved serial crystallographic methods to study cysteine-dependent enzymes, with a focus on the main (M^pro) and papain-like (PL^pro) cysteine proteases of SARS-CoV-2 as well as other examples. We review features of cysteine chemistry that are relevant for the design and execution of time-resolved serial crystallography experiments. In addition, we discuss emerging X-ray techniques such as time-resolved sulfur X-ray spectroscopy that may be able to detect changes in sulfur charge state and covalency during catalysis or regulatory modification. In summary, cysteine-dependent enzymes have features that make them especially attractive targets for new time-resolved serial crystallography approaches, which can reveal both changes to enzyme structure and dynamics during catalysis in crystalline samples.

Dissociation of Pyridinethiolate Ligands during Hydrogen Evolution Reactions of Ni-Based Catalysts: Evidence from X-ray Absorption Spectroscopy

The protonation of several Ni-centered pyridine-2-thiolate photocatalysts for hydrogen evolution is investigated using X-ray absorption spectroscopy (XAS). While protonation of the pyridinethiolate ligand was previously thought to result in partial dechelation from the metal at the pyridyl N site, we instead observe complete dissociation of the protonated ligand and replacement by solvent molecules. A combination of Ni K-edge and S K-edge XAS of the catalyst Ni(bpy)(pyS)₂ (bpy = 2,2′-bipyridine; pyS = pyridine-2-thiolate) identifies the structure of the fully protonated catalyst as a solvated [Ni(bpy)(DMF)₄]²⁺ (DMF = dimethylformamide) complex and the dissociated ligands as the N-protonated 2-thiopyridone (pyS-H). This surprising result is further supported by UV–vis absorption spectroscopy and DFT calculations and is demonstrated for additional catalyst structures and solvent environments using a combination of XAS and UV–vis spectroscopy. Following protonation, electrochemical measurements indicate that the solvated Ni bipyridine complex acts as the primary electron-accepting species during photocatalysis, resulting in separate protonated ligand and reduced Ni species. The role of ligand dissociation is considered in the larger context of the hydrogen evolution reaction (HER) mechanism. As neither the pyS-H ligand nor the Ni bipyridine complex acts as an efficient HER catalyst alone, the critical role of ligand coordination is highlighted. This suggests that shifting the equilibrium toward bound species by addition of excess protonated ligand (2-thiopyridone) may improve the performance of pyridinethiolate-containing catalysts.

Protonation of hydrogen-evolving Ni pyridinethiolate catalysts is investigated using X-ray absorption spectroscopy supported by UV−vis absorption spectroscopy and density functional theory. While pyridinethiolate ligand protonation was previously assumed to result in a partially coordinated species with a dissociated Ni−N bond, it is instead observed here to fully dissociate from the metal. The results are considered in the context of the electro- and photocatalytic hydrogen evolution reaction mechanisms of Ni pyridinethiolate complexes.

Anharmonic Motion in the Crystal Structure of 2-Mercaptopyridone

With the present study, we revise earlier results about the title compound 2-mercaptopyridone in which the deformation density was determined from an X–N study (X-ray, neutron diffraction) by Ohms et al., 1982. In the current X–X study (X-ray, X-ray), anharmonic motion parameters for the atoms were included and it resulted in a very clean deformation density map without the unexplainable features of the literature results. The presence of anharmonic effects is supported by a study of the thermal expansion in the temperature range 100–260 K. A topological study of the electron density confirms a bond length alternation in the six-membered ring. The calculation of the electrostatic potential indicates that the N–H⋯S hydrogen bond is an electrostatic interaction, and that other attractive intermolecular contacts are probably dispersive.

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.

Ligand-Field Effects in a Ruthenium(II) Polypyridyl Complex Probed by Femtosecond X-ray Absorption Spectroscopy

We employ femtosecond X-ray absorption spectroscopy of [Ru(m-bpy)₃]²⁺ (m-bpy = 6-methyl-2,2'-bipyridine) to elucidate the time evolution of the spin and charge density upon metal-to-ligand charge-transfer (MLCT) excitation. The core-level transitions at the Ru L₃-edge reveal a very short MLCT lifetime of 0.9 ps and relaxation to the lowest triplet metal-centered state (³MC) which exhibits a lifetime of about 300 ps. Time-dependent density functional theory relates ligand methylation to a lower ligand field strength that stabilizes the ³MC state. A quarter of the ³MLCT population appears to be trapped which may be attributed to intramolecular vibrational relaxation or further electron transfer to the solvent. Our results demonstrate that small changes in the ligand field allow control of the photophysical properties. Moreover, this study underscores the high information content of femtosecond L-edge spectroscopy as a probe of valence charge density and spin-state in 4d transition metals.

Probing competing relaxation pathways in malonaldehyde with transient X-ray absorption spectroscopy

Excited-state intramolecular hydrogen transfer (ESIHT) is a fundamental reaction relevant to chemistry and biology. Malonaldehyde is the simplest example of ESIHT, yet only little is known experimentally about its excited-state dynamics. Several competing relaxation pathways have been proposed, including internal conversion mediated by ESIHT and C[double bond, length as m-dash]C torsional motion as well as intersystem crossing. We perform an in silico transient X-ray absorption spectroscopy (TRXAS) experiment at the oxygen K-edge to investigate its potential to monitor the proposed ultrafast decay pathways in malonaldehyde upon photoexcitation to its bright S₂(ππ*) state. We employ both restricted active space perturbation theory and algebraic-diagrammatic construction for the polarization propagator along interpolated reaction coordinates as well as representative trajectories from ab initio multiple spawning simulations to compute the TRXAS signals from the lowest valence states. Our study suggests that oxygen K-edge TRXAS can distinctly fingerprint the passage through the H-transfer intersection and the concomitant population transfer to the S₁(nπ*) state. Potential intersystem crossing to T₁(ππ*) is detectable from reappearance of the double pre-edge signature and reversed intensities. Moreover, the torsional deactivation pathway induces transient charge redistribution from the enol side towards the central C-atom and manifests itself as substantial shifts of the pre-edge features. Given the continuous advances in X-ray light sources, our study proposes an experimental route to disentangle ultrafast excited-state decay channels in this prototypical ESIHT system and provides a pathway-specific mapping of the TRXAS signal to facilitate the interpretation of future experiments.

Ultrafast dynamics of photo-excited 2-thiopyridone: Theoretical insights into triplet state population and proton transfer pathways

Ultrafast non-adiabatic dynamics of the small heteroaromatic compound 2-thiopyridone has been studied with surface hopping simulations based on multi-configurational quantum chemistry. Initial excitation of the bright S 2 ( π , π * ) state is found to promptly relax to S 1 ( n ,   π * ) through in-plane motion. The subsequent dynamics are oppositely driven by out-of-plane motion, which results in both complex population transfers among all the available states and intersystem crossing predominantly through the "El-Sayed forbidden" S 1 ( n ,   π * ) to T 2 ( n ,   π * ) channel, through significant mixing of electronic excitation characters. Despite this complexity, the femto- to picosecond triplet population, expected from several spectroscopic measurements, is well described as a simple exponential decay of the singlet state manifold. No proton transfer is found in the reported trajectories, but two mechanisms for its possible mediation in previously reported experiments are proposed based on the observed structural dynamics: (i) ultrafast intra-molecular transfer driven by the initially coherent in-plane motion and (ii) inter-molecular solvent-mediated transfer driven by the out-of-plane modes that dominate the later motion.

Interdependent Electronic Structure, Protonation, and Solvatization of Aqueous 2-Thiopyridone

2-Thiopyridone (2-TP), a common model system for excited-state proton transfer, has been simulated in aqueous solution with ab initio molecular dynamics. The interplay of electronic structure, protonation, and solvatization is investigated by comparison of three differently protonated molecular forms and between the lowest singlet and triplet electronic states. An interdependence clearly manifests in the mixed-character T₁ state for the 2-TP form, systematic structural distortions of the 2-mercaptopyridine (2-MP) form, and photobase protolysis of the 2-TP^- form, in the aqueous phase. In comparison, simplified continuum models for the solvatization are found to be significantly inaccurate for several of the species. To facilitate future computational studies, we therefore present a minimal representative solvatization complex for each stable form and electronic state. Our findings demonstrate the importance of explicit solvatization of the compound and sets the stage for including it also in future studies.

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

X-ray free-electron lasers with intense, tuneable and short-pulse X-ray radiation are transformative tools for the investigation of transition-metal complexes and metalloproteins. This becomes apparent in particular when combining the experimental observables from X-ray spectroscopy with modern theoretical tools for calculations of electronic structures and X-ray spectra from first principles. The combination gives new insights into how charge and spin densities change in chemical reactions and how they determine reactivity. This is demonstrated for the investigations of structural dynamics with metal K-edge absorption spectroscopy, spin states in excited-state dynamics with metal 3p-3d exchange interactions, the frontier-orbital interactions in dissociation and substitution reactions with metal-specific X-ray spectroscopy, and studies of metal oxidation states with femtosecond pulses for 'probe-before-destroy' spectroscopy. The role of X-ray free-electron lasers is addressed with thoughts about how they enable 'bringing back together' different aspects of the same problem and this is thought to go beyond a conventional review paper where these aspects are formulated in italic font type in a prequel, an interlude and in a sequel. This article is part of the theme issue 'Measurement of ultrafast electronic and structural dynamics with X-rays'.

T1 Population as the Driver of Excited-State Proton-Transfer in 2-Thiopyridone

Excited-state proton transfer (ESPT) is a fundamental process in biomolecular photochemistry, but its underlying mediators often evade direct observation. We identify a distinct pathway for ESPT in aqueous 2-thiopyridone, by employing transient N 1s X-ray absorption spectroscopy and multi-configurational spectrum simulations. Photoexcitations to the singlet S₂ and S₄ states both relax promptly through intersystem crossing to the triplet T₁ state. The T₁ state, through its rapid population and near nanosecond lifetime, mediates nitrogen site deprotonation by ESPT in a secondary intersystem crossing to the S₀ potential energy surface. This conclusively establishes a dominant ESPT pathway for the system in aqueous solution, which is also compatible with previous measurements in acetonitrile. Thereby, the hitherto open questions of the pathway for ESPT in the compound, including its possible dependence on excitation wavelength and choice of solvent, are resolved.

UV-Photochemistry of the Disulfide Bond: Evolution of Early Photoproducts from Picosecond X-ray Absorption Spectroscopy at the Sulfur K-Edge

We have investigated dimethyl disulfide as the basic moiety for understanding the photochemistry of disulfide bonds, which are central to a broad range of biochemical processes. Picosecond time-resolved X-ray absorption spectroscopy at the sulfur K-edge provides unique element-specific insight into the photochemistry of the disulfide bond initiated by 267 nm femtosecond pulses. We observe a broad but distinct transient induced absorption spectrum which recovers on at least two time scales in the nanosecond range. We employed RASSCF electronic structure calculations to simulate the sulfur-1s transitions of multiple possible chemical species, and identified the methylthiyl and methylperthiyl radicals as the primary reaction products. In addition, we identify disulfur and the CH₂S thione as the secondary reaction products of the perthiyl radical that are most likely to explain the observed spectral and kinetic signatures of our experiment. Our study underscores the importance of elemental specificity and the potential of time-resolved X-ray spectroscopy to identify short-lived reaction products in complex reaction schemes that underlie the rich photochemistry of disulfide systems.

Structural dynamics upon photoexcitation-induced charge transfer in a dicopper(i)–disulfide complex

A study of structural evolution upon photoinduced charge transfer in a dicopper complex with biologically relevant sulfur coordination.