Trans-to-cis isomerization, the key reaction in photoactive proteins, cannot usually occur through the standard one-bond-flip mechanism. Due to spatial constraints imposed by a protein environment, isomerization is likely to proceed via a “volume-conserving” mechanism in which highly-choreographed atomic motions are expected, the details of which have not yet been directly observed. Here we employ time-resolved X-ray crystallography to structurally visualize isomerization of the p-coumaric acid chromophore in photoactive yellow protein with 100 picosecond time resolution and 1.6 Å spatial resolution. The structure of the earliest intermediate (IT) resembles a highly-strained transition state in which the torsion angle is located halfway between the trans and cis isomers. The reaction trajectory of IT bifurcates into two structurally distinct cis intermediates via hula-twist and bicycle-pedal pathways. The bifurcating reaction pathways can be controlled by weakening the hydrogen bond between the chromophore and an adjacent residue via E46Q mutation, which switches off the bicycle-pedal pathway.

The making and breaking of atomic bonds are essential processes in chemical reactions. Although the ultrafast dynamics of bond breaking have been studied intensively using time-resolved techniques, it is very difficult to study the structural dynamics of bond making, mainly because of its bimolecular nature. It is especially difficult to initiate and follow diffusion-limited bond formation in solution with ultrahigh time resolution. Here we use femtosecond time-resolved X-ray solution scattering to visualize the formation of a gold trimer complex, [Au(CN)2(-)]3 in real time without the limitation imposed by slow diffusion. This photoexcited gold trimer, which has weakly bound gold atoms in the ground state, undergoes a sequence of structural changes, and our experiments probe the dynamics of individual reaction steps, including covalent bond formation, the bent-to-linear transition, bond contraction and tetramer formation with a time resolution of ∼500 femtoseconds. We also determined the three-dimensional structures of reaction intermediates with sub-ångström spatial resolution. This work demonstrates that it is possible to track in detail and in real time the structural changes that occur during a chemical reaction in solution using X-ray free-electron lasers and advanced analysis of time-resolved solution scattering data.

We have studied the reaction dynamics for HgI2 in methanol by using time-resolved x-ray diffraction (TRXD). Although numerous time-resolved spectroscopic studies have provided ample information about the early dynamics of HgI 2, a comprehensive reaction mechanism in the solution phase spanning from picoseconds up to microseconds has been lacking. Here we show that TRXD can provide this information directly and quantitatively. Picosecond optical pulses triggered the dissociation of HgI 2, and 100-ps-long x-ray pulses from a synchrotron probed the evolving structures over a wide temporal range. To theoretically explain the diffracted intensities, the structural signal from the solute, the local structure around the solute, and the hydrodynamics of bulk solvents were considered in the analysis. The results in this work demonstrate that the determination of transient states in solution is strongly correlated with solvent energetics, and TRXD can be used as an ultrafast calorimeter. It also is shown that a manifold of structural channels can be resolved at the same time if the measurements are accurate enough and that global analysis is applied. The rate coefficients for the reactions were obtained by fitting our model against the experimental data in one global fit including all q-values and time delays. The comparison between all putative reaction channels confirms that two-body dissociation is the dominant dissociation pathway. After this primary bond breakage, two parallel channels proceed. Transient HgI associates nongeminately with an iodine atom to form HgI 2, and I2 is formed by nongeminate association of two iodine atoms.HgI2 ͉ hydrodynamics ͉ liquid phase ͉ molecular structural dynamics ͉ transient structure T he knowledge of temporally varying molecular structures during ultrafast processes is vital in understanding the mechanism and function of molecular reaction. During the last decades, the dynamics of molecular reactions have been investigated by numerous spectroscopic techniques with femtosecond time resolution. However, the direct determination, at atomic resolution, of the structural dynamics involved in such processes can only be obtained by time-resolved x-ray (1-5), electron diffraction (6-9) and x-ray absorption spectroscopy (10, 11) acting as atomic probes. The methodology of time-resolved x-ray͞electron diffraction is similar to ultrafast optical pumpprobe experiment: a femtosecond laser pulse triggers a reaction in the molecules, and a delayed electron or x-ray pulse, rather than an optical pulse as in optical spectroscopy, probes the structural evolution. The changes in the nuclear coordinates are directly recorded by varying the time delay between the laser and the x-ray͞electron pulse.Because the scattering cross section of hard x-rays is 6 orders of magnitude lower than for electrons (12, 13), time-resolved x-ray diffraction (TRXD) can penetrate condensed samples such as liquids. In the condensed phase, the dynamics are not only determined by the potential energy surfaces of the reactantp...

Fundamental studies of chemical reactions often draw molecular dynamics along a reaction coordinate in a calculated or suggested potential energy surface (PES) 1-5 . But fully mapping such dynamics experimentally, by following all nuclear motions in a timeresolved manner, that is the motions of wavepackets, is challenging and has not even been realized for the simple stereotypical bimolecular reaction 6-8 of A-B + C → A + B-C. Here we report such tracking of vibrational wavepacket trajectories during photo-induced bond formation in the gold trimer complex [Au(CN)2 -]3 in an aqueous solution, using femtosecond x-ray solution scattering (liquidography 9-12 ) at x-ray free electron lasers 13,14 . We find that the complex forms from an assembly of three monomers A, B and C clustered together through non-covalent interactions 15,16 and with the distance between A and B shorter than between B and C. Tracking of the wavepacket in three-dimensional nuclear coordinates (RAB, RBC, and RAC) reveals that within the first 60 fs after photoexcitation, a covalent bond forms between A and B to give A-B + C. The second covalent bond, between B and C, subsequently forms within 360 fs to give a linear and covalently-bonded trimer complex A-B-C. The trimer exhibits harmonic vibrations that we are also able to map, and unambiguously assign to specific normal modes using only the experimental data. More intense x-rays can in principle visualize the motion of not only highly-scattering atoms such as gold but also of lighter atoms such as carbon and nitrogen, which will open the door for the direct tracking of the atomic motions involved in many chemical reactions.The [Au(CN)2 -]3 complex has served as a valuable model system for studying photoinitiated processes in solution. Irradiation with ultraviolet light excites it from the ground state (S0) to the singlet state (S1), which within 20 fs undergoes intersystem crossing to reach a triplet excited state (T1') 18 . A further transition from T1' to another triplet excited state (T1) then occurs with a time constant of 1~2 ps, completing formation of covalent bonds and transformation of the complex from a bent to a linear structure 9,17,18 (see the Supplementary Information (SI) for details of the notations of electronic states).Formation of the bonds could involve any of the three possible candidate trajectories sketched in Fig. 1b. The equilibrium structure in the ground state determines the position of the

This Communication reports simultaneous tracking of structural and kinetic information for the photoinduced elimination reaction of 1,2-diiodotetrafluoroethane in solution by transient X-ray diffraction. The transient structure of .CF2CF2I is determined to be a classical mixture whereas .CH2CH2I is bridged. Compared with the gas phase reaction, the secondary dissociation of .CF2CF2I into C2F4 and I is slowed down by a factor of 6 in solution. Transient X-ray diffraction offers a complementary method for capturing transient structures in solution which might be invisible or "optically silent" in time-resolved optical spectroscopy.

Ionic species often play important roles in chemical reactions occurring in water and other solvents, but it has been elusive to determine the solvent-dependent molecular structure with atomic resolution. The triiodide ion has a molecular structure that sensitively changes depending on the type of solvent and its symmetry can be broken by strong solute-solvent interaction. Here, by applying pump-probe x-ray solution scattering, we characterize the exact molecular structure of I(3)(-) ion in water, methanol, and acetonitrile with subangstrom accuracy. The data reveal that I(3)(-) ion has an asymmetric and bent structure in water. In contrast, the ion keeps its symmetry in acetonitrile, while the symmetry breaking occurs to a lesser extent in methanol than in water. The symmetry breaking of I(3)(-) ion is reproduced by density functional theory calculations using 34 explicit water molecules, confirming that the origin of the symmetry breaking is the hydrogen-bonding interaction between the solute and solvent molecules.

Ultrafast (ps) time-resolved X-ray scattering was used to study the structural dynamics of Ru(3)(CO)(12) in cyclohexane after photolysis at 260 nm. Two intermediates form after 100 ps at the onset of the reaction: Ru(3)(CO)(10) for the CO loss channel and Ru(3)(CO)(11)(mu-CO) for the metal-metal cleavage channel. In our previous study at 390 nm, by contrast, three intermediates were observed simultaneously at the onset of the reaction that all relax back to Ru(3)(CO)(12) with different lifetimes. The major difference between photolysis at 260 and 390 nm is that in the first case Ru(3)(CO)(10)(mu-CO) is formed by bimolecular recombination of Ru(3)(CO)(10) with a free CO in 50 ns, whereas in the second case it forms directly from Ru(3)(CO)(12) at the onset of the reaction. The differences between the photofragmentation pathways are related to the absorption bands available at the two wavelengths. The extrema in the difference radial distribution functions (RDFs) are unambiguously assigned by decomposing the total signal into contributions from the solutes, the solvent and the solute-solvent cross-terms, and also contributions from each candidate species. The difference RDFs reveal the depletion of Ru-Ru bonds (2.88 A) in the initial Ru(3)(CO)(12) molecule and formation of Ru(3)(CO)(10) as the major photoproduct. The high-resolution X-ray (88 keV) scattering pattern of pure liquid C(6)H(12) indicates that the solvent dynamics at early time delays is due to broadening of the intermolecular interatomic correlations at constant volume, whereas during thermal expansion at longer time delays, it results from shifts in these correlations.

We introduced phenyl and naphthyl groups onto various positions of dual cores. Of the synthesized compounds, Na-AP-Na was found to exhibit the highest EL device efficiency of 5.46 cd A−1.