Unicellular organisms respond to a changing environment through physical and chemical sensory cascades. Sensory rhodopsin II (SRII) is a blue-light receptor, which initiates a negative phototaxis response in the host archaea. Here, we apply time-resolved X-ray solution scattering (TR-XSS) to characterize the mechanism of signal transduction by SRII and explore how light-induced structural changes are modified when SRII is in complex with its transducer protein (HtrII). TR-XSS difference data are modeled as arising from an outward movement of helices E and F in combination with modest changes associated with helices C and the extracellular regions of helices D and E. The magnitude of the displacement of helices E and F is similar irrespective of whether or not HtrII is present. In combination with structural predictions of the full SRII:HtrII complex, TR-XSS provides insight into how conformational changes may be communicated from SRII to the signaling domain of HtrII.

Roaming-mediated isomerization is a universal reaction mechanism in photochemistry, yet solvent-dependent pathways of roaming intermediates remain poorly understood, particularly for environmentally relevant halogen compounds involved in ozone depletion. Here, using femtosecond time-resolved X-ray solution scattering, we resolve the solvent-dependent roaming dynamics of CHBr3 in methanol and methylcyclohexane. By combining multi-method experimental analysis, machine learning-assisted ab initio molecular dynamics simulations, and density functional theory calculations, we uncover distinct solvent-steered reaction pathways. In methanol, roaming enhances solute-solvent interactions, leading to solvolysis before a stable isomer forms. In methylcyclohexane, roaming facilitates isomerization to a long-lived iso-CHBr2-Br product. Direct dissociation into CHBr2 + Br competes with both pathways in either solvent. By tracking bond-length oscillations and angular dynamics in real time, we visualize how the condensed-phase environment governs the branching ratio between competing pathways. Our findings establish solute-solvent interactions as key factors controlling roaming-mediated reactions in CHBr3, with broad implications for photochemical outcomes in solution.

Time-resolved x-ray solution scattering (TR-XSS) studies provide experimental probes of transient conformational states in macromolecules. Difference x-ray scattering curves from integral membrane proteins are predicted to be influenced by the presence of the surrounding detergent micelle. Here, we present time-dependent x-ray solution scattering data from visual rhodopsin when solubilized in two different detergents: the nonionic surfactant n-dodecyl-β-D-maltoside and the zwitterionic detergent 3-[(3-cholamidopropyl) dimethylammonio]-1-propanesulfonate. Both detergents produce micelles that surround rhodopsin, yet they have different composition, density and critical micelle concentrations and yield different x-ray scattering properties. Our theoretical framework is able to fit the experimental TR-XSS data for photoactivated rhodopsin in both detergents, yielding experimental verification of how x-ray scattering contrast from the detergent molecules influences difference x-ray scattering measurements from integral membrane proteins. These results increase confidence when modeling conformational changes of integral membrane proteins from an ensemble of predicted structures.

The structure and spin of photoexcited Fe2+(phen)3 in water are examined by x-ray scattering and x-ray emission spectroscopy with 100 ps time resolution. Excitation of the low-spin (LS) ground state (GS) to the charge transfer state 1MLCT* leads to the formation of a high-spin (HS) state that returns to the GS in 725 ps. Density functional theory (DFT) predicts a Fe–N bond elongation in HS by 0.19 Å in agreement with the scattering data. The angle between the ligands increases by 5.4° in HS, which allows the solvent to get 0.33 Å closer to Fe in spite of the expansion of the molecule. The rise in solvent temperature from the return of photoproducts to the GS is dominated by the formation dynamics of HS, 1MLCT* → HS, which is followed by a smaller rise from the HS → GS transition. The latter agrees with the 0.61 eV energy gap E(HS)−E(LS) calculated by DFT. However, the temperature rise from the 1MLCT → HS transition is greater than expected, by a factor of 2.1, which is explained by the re-excitation of nascent HS* by the 1.2 ps pump pulse. This hypothesis is supported by optical spectroscopy measurements showing that the 1.2 ps long pump pulse activates the HS* → 5MLCT* channel, which is followed by the ultrafast return to HS* via intersystem crossing. Finally, the spins of the photoproducts are monitored by the Kβ emission and the spectra confirm that the spins of LS and HS states are 0 and 2, respectively.

Time-resolved studies with temporal resolution that separate molecular level dynamics from macroscopic changes, allow clear distinction between the time scales of the different degrees of freedom involved. Cooperative molecular switching in the solid state is exemplified by spin crossover phenomenon in crystals of transition metal complexes. Here we show the existence of a delay between the crystalline volume increase, and the cooperative macroscopic switching of molecular state. Using 100 ps X-ray diffraction, we track the molecular spin state and the structure of the lattice during the photoinduced low spin to high spin transition in microcrystals of [Fe III (3-MeO-SalEen) 2 ]PF 6 . Model simulations explain the phenomenon with thermally activated kinetics governed by local energy barriers separating the molecular states. Such behaviour is different from that encountered in materials with no local energy barriers, where phase transformation can occur simultaneously with propagation of strain. Broadly, this motivates an optimised material design, scalable with size and intrinsic energetics.

Photolysis reaction pathways of [Au(III)Cl4]- in aqueous solution have been investigated by time-resolved X-ray absorption spectroscopy. Ultraviolet excitation directly breaks the Au-Cl bond in [Au(III)Cl4]- to form [Au(II)Cl3]- that becomes highly reactive within 79 ps. Disproportionation of [Au(II)Cl3]- generates [Au(I)Cl2]-, which is stable for ≤10 μs. In contrast, intense near-infrared lasers photolyze water to generate hydrated electrons, which then reduce [Au(III)Cl4]- to [Au(II)Cl3]- at 5 ns. Hydrated electrons further induce a chain reaction from [Au(II)Cl3]- to [Au(0)Cl]- by successively removing one Cl-. The zero-valency Au anions quickly polymerize and condense to form Au nanoparticles, which become the dominating product after 400 s. Our results reveal that the condensation of zero-valency Au starts with dimerization of gold clusters coordinated with chloride ions rather than direct condensation of pristine Au atoms.

Time-resolved x-ray solution scattering (TR-XSS) is a sub-field of structural biology, which observes secondary structural changes in proteins as they evolve along their functional pathways. While the number of distinct conformational states and their rise and decay can be extracted directly from TR-XSS experimental data recorded from light-sensitive systems, structural modeling is more challenging. This step often builds from complementary structural information, including secondary structural changes extracted from crystallographic studies or molecular dynamics simulations. When working with integral membrane proteins, another challenge arises because x-ray scattering from the protein and the surrounding detergent micelle interfere and these effects should be considered during structural modeling. Here, we utilize molecular dynamics simulations to explicitly incorporate the x-ray scattering cross term between a membrane protein and its surrounding detergent micelle when modeling TR-XSS data from photoactivated samples of detergent solubilized bacteriorhodopsin. This analysis provides theoretical foundations in support of our earlier approach to structural modeling that did not explicitly incorporate this cross term and improves agreement between experimental data and theoretical predictions at lower x-ray scattering angles.

The recombination of laser-dissociated iodine molecules dissolved in CCl4 is explored by time-resolved x-ray diffraction. The x-raypulses employed in our experiments were generated by the ESRF synchrotron in Grenoble. The solvent contribution to the measured signals was eliminated using appropriate experimental procedures. Motions of iodine atoms were then studied from 200 ps to 10 ps. Different relaxation processes are shown to operate in this time domain. It is proved that the iodine recombination follows two reaction paths, taking place in the electronic states X and A/A' of I2, respectively. In spite of widely different experimental approaches, laser optical and x-ray studies provide a similar picture of this prototype reaction.

Protein function depends critically on dynamics encoded into the native structure. Such structural dynamics are carefully coordinated to display the cooperativity and temporal timing necessary to execute the specific reaction. Determination of such key structural rearrangements requires monitoring protein reactions in real time. In this work, we used synchrotron-based time-resolved X-ray solution scattering (TR-XSS) to visualize structural changes in the Escherichia coli Adenylate kinase (AdK) enzyme upon laser-induced release of a protected ATP substrate. A 4.3-ms transient intermediate showed partial closing of both the ATP- and AMP-binding domains, which indicates a cooperative closing mechanism. The ATP-binding domain also showed local unfolding and breaking of an Arg131-Asp146 salt-bridge. Nuclear magnetic resonance (NMR) spectroscopy data identified similar unfolding in an Arg131Ala AdK mutant, which refolded upon forming a closed, substrate-binding, conformation. The observed structural dynamics are in agreement with a ‘cracking mechanism’ that has been proposed to underlie global structural transformation, such as allostery, in proteins. (in press, Science Advances)

The photoactivation mechanism of Os3(CO)12 at 400 nm is examined with time-resolved X-ray liquidography. The data reveal two pathways: the vibrational relaxation following an internal conversion to the electronic ground state and the ligand dissociation to form Os3(CO)11 with a ligand vacancy at the axial position.

This review focuses on how short X-ray pulses from synchrotrons and XFELs can be used to track light-induced structural changes in molecular complexes and proteins via the pump–probe method. The upgrade of the European Synchrotron Radiation Facility to a diffraction-limited storage ring, based on the seven-bend achromat lattice, and how it might boost future pump–probe experiments are described. We discuss some of the first X-ray experiments to achieve 100 ps time resolution, including the dissociation and in-cage recombination of diatomic molecules, as probed by wide-angle X-ray scattering, and the 3D filming of ligand transport in myoglobin, as probed by Laue diffraction. Finally, the use of femtosecond XFEL pulses to investigate primary chemical reactions, bond breakage and bond formation, isomerisation and electron transfer are discussed.

One of the main challenges in ultrafast material science is to trigger phase transitions with short pulses of light. Here we show how strain waves, launched by electronic and structural precursor phenomena, determine a coherent macroscopic transformation pathway for the semiconducting-to-metal transition in bistable Ti3O5 nanocrystals. Employing femtosecond powder X-ray diffraction, we measure the lattice deformation in the phase transition as a function of time. We monitor the early intra-cell distortion around the light absorbing metal dimer and the long range deformations governed by acoustic waves propagating from the laser-exposed Ti3O5 surface. We developed a simplified elastic model demonstrating that picosecond switching in nanocrystals happens concomitantly with the propagating acoustic wavefront, several decades faster than thermal processes governed by heat diffusion.

The induction of homogeneous and oriented ice nucleation has to date not been achieved. Here, we report induced nucleation of ice from millimeter sized supercooled water drops illuminated by ns-optical laser pulses well below the ionization threshold making use of particular laser beam configurations and polarizations. Employing a 100 ps synchrotron x-ray pulse 100 ns after each laser pulse, an unambiguous correlation was observed between the directions and the symmetry of the laser fields and that of the H-bonding arrays of the induced ice crystals. Moreover, an analysis of the x-ray diffraction data indicates that, in the main, the induced nucleation of ice is homogeneous at temperatures well above the observed and predicted values for supercooled water.

The biological function of proteins is critically dependent on dynamics inherent to the native structure. Such structural dynamics obey a predefined order and temporal timing to execute the specific reaction. Determination of the cooperativity of key structural rearrangements requires monitoring protein reactions in real time. In this work, we used time-resolved x-ray solution scattering (TR-XSS) to visualize structural changes in the Escherichia coli adenylate kinase (AdK) enzyme upon laser-induced activation of a protected ATP substrate. A 4.3-ms transient intermediate showed partial closing of both the ATP- and AMP-binding domains, which indicates a cooperative closing mechanism. The ATP-binding domain also showed local unfolding and breaking of an Arg131-Asp146 salt bridge. Nuclear magnetic resonance spectroscopy data identified similar unfolding in an Arg131Ala AdK mutant, which refolded in a closed, substrate-binding conformation. The observed structural dynamics agree with a “cracking mechanism” proposed to underlie global structural transformation, such as allostery, in proteins.

Sarco/endoplasmic reticulum Ca2+ ATPase (SERCA) transporters regulate calcium signaling by active calcium ion reuptake to internal stores. Structural transitions associated with transport have been characterized by x-ray crystallography, but critical intermediates involved in the accessibility switch across the membrane are missing. We combined time-resolved x-ray solution scattering (TR-XSS) experiments and molecular dynamics (MD) simulations for real-time tracking of concerted SERCA reaction cycle dynamics in the native membrane. The equilibrium [Ca2]E1 state before laser activation differed in the domain arrangement compared with crystal structures, and following laser-induced release of caged ATP, a 1.5-ms intermediate was formed that showed closure of the cytoplasmic domains typical of E1 states with bound Ca2+ and ATP. A subsequent 13-ms transient state showed a previously unresolved actuator (A) domain arrangement that exposed the ADP-binding site after phosphorylation. Hence, the obtained TR-XSS models determine the relative timing of so-far elusive domain rearrangements in a native environment.

An atomistic understanding of the photoinduced spin-state switching (PSS) within polynuclear systems of d(4)-d(7) transition metal ion complexes is required for their rational integration into light-driven reactions of chemical and biological interest. However, in contrast to mononuclear systems, the multidimensional dynamics of the PSS in solvated molecular arrays have not yet been elucidated due to the expected complications associated with the connectivity between the metal centers and the strong interactions with the surroundings. In this work, the PSS in a solvated triiron(II) metallogrid complex is characterized using transient optical absorption and X-ray emission spectroscopies on the femtosecond time scale. The complementary measurements reveal the photoinduced creation of energy-rich (hot) and long-lived quintet states, whose dynamics differ critically from their mononuclear congeners. This finding opens major prospects for developing novel schemes in solution-phase spin chemistry that are driven by the dynamic PSS process in compact oligometallic arrays.

Adenylate kinase (ADK) is a phosphotransferase that maintains energy homeostasis in cells by catalyzing the reversible transfer of a phosphoryl group from ATP to AMP to produce two ADPs. The protein consists of highly flexible ATP- and AMP-binding domains that undergo large conformational changes relative to the more static core domain during catalysis. The ADK protein has proven an excellent model system for both experimental and computational methods, but the coupling between conformation change and substrate binding and the timing of these events are not fully understood. We performed time-resolved X-ray solution scattering experiments using externally laser-triggered caged-ATP substrate to track ADK functional dynamics. The time-resolved X-ray data identified a kinetic state with a rise-time of 5.3 ms that upon computer simulation-driven structural refinement was shown to display significant closure of the ATP-binding domain, but with a fully open AMP-binding domain. Hence, this study shows that upon exposure to ATP, the initial response by the protein is starting to close its ATP-binding domain, while keeping the structural change in the AMP-binding domain on hold. The methodology holds promise to study relative order and timing of structural events in protein functional dynamics.

One of the most challenging tasks in biological science is to understand how a protein folds. In theoretical studies, the hypothesis adopting a funnel-like free-energy landscape has been recognized as a prominent scheme for explaining protein folding in views of both internal energy and conformational heterogeneity of a protein. Despite numerous experimental efforts, however, comprehensively studying protein folding with respect to its global conformational changes in conjunction with the heterogeneity has been elusive. Here we investigate the redox-coupled folding dynamics of equine heart cytochrome c (cyt-c) induced by external electron injection by using time-resolved X-ray solution scattering. A systematic kinetic analysis unveils a kinetic model for its folding with a stretched exponential behavior during the transition toward the folded state. With the aid of the ensemble optimization method combined with molecular dynamics simulations, we found that during the folding the heterogeneously populated ensemble of the unfolded state is converted to a narrowly populated ensemble of folded conformations. These observations obtained from the kinetic and the structural analyses of X-ray scattering data reveal that the folding dynamics of cyt-c accompanies many parallel pathways associated with the heterogeneously populated ensemble of unfolded conformations, resulting in the stretched exponential kinetics at room temperature. This finding provides direct evidence with a view to microscopic protein conformations that the cyt-c folding initiates from a highly heterogeneous unfolded state, passes through still diverse intermediate structures, and reaches structural homogeneity by arriving at the folded state.

A simple yet efficient instrument-model refinement method for X-ray diffraction data is presented and discussed. The method is based on least-squares minimization of differences between respective normalized (i.e. unit length) reciprocal vectors computed for adjacent frames. The approach was primarily designed to work with synchrotron X-ray Laue diffraction data collected for small-molecule single-crystal samples. The method has been shown to work well on both simulated and experimental data. Tests performed on simulated data sets for small-molecule and protein crystals confirmed the validity of the proposed instrument-model refinement approach. Finally, examination of data sets collected at both BioCARS 14-ID-B (Advanced Photon Source) and ID09 (European Synchrotron Radiation Facility) beamlines indicated that the approach is capable of retrieving goniometer parameters (e.g. detector distance or primary X-ray beam centre) reliably, even when their initial estimates are rather inaccurate.