Fate of transient isomer of CH2I2: Mechanism and origin of ionic photoproducts formation unveiled by time-resolved x-ray liquidography

Extracting Kinetics and Thermodynamics of Molecules without Heavy Atoms via Time-Resolved Solvent Scattering Signals

Time-resolved X-ray liquidography (TRXL) has emerged as a powerful technique for studying the structural dynamics of small molecules and macromolecules in liquid solutions. However, TRXL has limited sensitivity for small molecules containing light atoms only, whose signal has lower contrast compared with the signal from solvent molecules. Here, we present an alternative approach to bypass this limitation by detecting the change in solvent temperature resulting from a photoinduced reaction. Specifically, we analyzed the heat dynamics of TRXL data obtained from p-hydroxyphenacyl diethyl phosphate (HPDP). This analysis enabled us to experimentally determine the number of intermediates and their respective enthalpy changes, which can be compared to theoretical enthalpies to identify the intermediates. This work demonstrates that TRXL can be used to uncover the kinetics and reaction pathways for small molecules without heavy atoms even if the scattering signal from the solute molecules is buried under the strong solvent scattering signal.

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.

Structural Dynamics of C2F4I2 in Cyclohexane Studied via Time-Resolved X-ray Liquidography

The halogen elimination of 1,2-diiodoethane (C2H4I2) and 1,2-diiodotetrafluoroethane (C2F4I2) serves as a model reaction for investigating the influence of fluorination on reaction dynamics and solute-solvent interactions in solution-phase reactions. While the kinetics and reaction pathways of the halogen elimination reaction of C2H4I2 were reported to vary substantially depending on the solvent, the solvent effects on the photodissociation of C2F4I2 remain to be explored, as its reaction dynamics have only been studied in methanol. Here, to investigate the solvent dependence, we conducted a time-resolved X-ray liquidography (TRXL) experiment on C2F4I2 in cyclohexane. The data revealed that (ⅰ) the solvent dependence of the photoreaction of C2F4I2 is not as strong as that observed for C2H4I2, and (ⅱ) the nongeminate recombination leading to the formation of I2 is slower in cyclohexane than in methanol. We also show that the molecular structures of the relevant species determined from the structural analysis of TRXL data provide an excellent benchmark for DFT calculations, especially for investigating the relevance of exchange-correlation functionals used for the structural optimization of haloalkanes. This study demonstrates that TRXL is a powerful technique to study solvent dependence in the solution phase.

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.

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).

Observing the Structural Evolution in the Photodissociation of Diiodomethane with Femtosecond Solution X-Ray Scattering

Resolving the structural dynamics of the initial steps of chemical reactions is challenging. We report the femtosecond time-resolved wide-angle x-ray scattering of the photodissociation of diiodomethane in cyclohexane. The data reveal with structural detail how the molecule dissociates into radicals, how the radicals collide with the solvent, and how they form the photoisomer. We extract how translational and rotational kinetic energy is dispersed into the solvent. We also find that 85% of the primary radical pairs are confined to their original solvent cage and discuss how this influences the downstream recombination reactions.

Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data

In the past few decades, prediction of macromolecular structures beyond the native conformation has been aided by the development of molecular dynamics (MD) protocols aimed at exploration of the energetic landscape of proteins. Yet, the computed structures do not always agree with experimental observables, calling for further development of the MD strategies to bring the computations and experiments closer together. Here, we report a scalable, efficient MD simulation approach that incorporates an x-ray solution scattering signal as a driving force for the conformational search of stable structural configurations outside of the native basin. We further demonstrate the importance of inclusion of the hydration layer effect for a precise description of the processes involving large changes in the solvent exposed area, such as unfolding. Utilization of the graphics processing unit allows for an efficient all-atom calculation of scattering patterns on-the-fly, even for large biomolecules, resulting in a speed-up of the calculation of the associated driving force. The utility of the methodology is demonstrated on two model protein systems, the structural transition of lysine-, arginine-, ornithine-binding protein and the folding of deca-alanine. We discuss how the present approach will aid in the interpretation of dynamical scattering experiments on protein folding and association.