Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion transport across bacterial membranes. We used an x-ray laser to study the subpicosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin. A series of structural snapshots with near-atomic spatial resolution and temporal resolution in the femtosecond regime show how the excited all-trans retinal samples conformational states within the protein binding pocket before passing through a twisted geometry and emerging in the 13-cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key facet of this stereoselective and efficient photochemical reaction.

Light-driven sodium pumps actively transport small cations across cellular membranes 1 .They are used by microbes to convert light into membrane potential and have become useful optogenetic tools with applications in neuroscience. While resting state structures of the prototypical sodium pump Krokinobacter eikastus rhodopsin 2 (KR2) have been solved 2,3 , it is unclear how structural alterations over time allow sodium translocation against a concentration gradient. Using the Swiss X-ray Free Electron Laser 4 , we have collected serial crystallographic data at ten pump-probe delays from femtoseconds to milliseconds. Highresolution structural snapshots throughout the KR2 photocycle show how retinal isomerization is completed on the femtosecond timescale and changes the local structure of the binding pocket in the early nanoseconds. Subsequent rearrangements and deprotonation of the retinal Schiff base open an electrostatic gate in microseconds. Structural and spectroscopic data in combination with quantum chemical calculations indicate transient binding of a sodium ion close to the retinal within one millisecond. In the last structural intermediate at 20 ms after activation, we identified a potential second sodium binding site close to the extracellular exit. These results provide direct molecular insight into the dynamics of active cation transport across biological membranes.

Historically, room-temperature structure determination was succeeded by cryo-crystallography to mitigate radiation damage. Here, we demonstrate that serial millisecond crystallography at a synchrotron beamline equipped with high-viscosity injector and high frame-rate detector allows typical crystallographic experiments to be performed at room-temperature. Using a crystal scanning approach, we determine the high-resolution structure of the radiation sensitive molybdenum storage protein, demonstrate soaking of the drug colchicine into tubulin and native sulfur phasing of the human G protein-coupled adenosine receptor. Serial crystallographic data for molecular replacement already converges in 1,000–10,000 diffraction patterns, which we collected in 3 to maximally 82 minutes. Compared with serial data we collected at a free-electron laser, the synchrotron data are of slightly lower resolution, however fewer diffraction patterns are needed for de novo phasing. Overall, the data we collected by room-temperature serial crystallography are of comparable quality to cryo-crystallographic data and can be routinely collected at synchrotrons.

Conformational dynamics are essential for proteins to function. We adapted time-resolved serial crystallography developed at x-ray lasers to visualize protein motions using synchrotrons. We recorded the structural changes in the light-driven proton-pump bacteriorhodopsin over 200 milliseconds in time. The snapshot from the first 5 milliseconds after photoactivation shows structural changes associated with proton release at a quality comparable to that of previous x-ray laser experiments. From 10 to 15 milliseconds onwards, we observe large additional structural rearrangements up to 9 angstroms on the cytoplasmic side. Rotation of leucine-93 and phenylalanine-219 opens a hydrophobic barrier, leading to the formation of a water chain connecting the intracellular aspartic acid–96 with the retinal Schiff base. The formation of this proton wire recharges the membrane pump with a proton for the next cycle.

We show that the combination of X-ray scattering with a nanofocused beam and X-ray cross correlation analysis is an efficient means for the full structural characterization of mesocrystalline nanoparticle assemblies with a single experiment. We analyze several hundred diffraction patterns of individual sample locations, i.e. individual grains, to obtain a meaningful statistical distribution of the superlattice and atomic lattice ordering. Simultaneous small-and wide-angle X-ray scattering of the same sample location allows us to determine the structure and orientation of the superlattice as well as the angular correlation of the first two Bragg peaks of the atomic lattices, their orientation with respect to the superlattice, and the average orientational misfit due to local structural disorder. This experiment is particularly advantageous for synthetic mesocrystals made by the simultaneous self-assembly of colloidal nanocrystals and surfacefunctionalization with conductive ligands. While the structural characterization of such materials has been challenging so far, the present method now allows correlating mesocrystalline structure with optoelectronic properties. Mesocrystals (MC) are three-dimensional arrays of iso-oriented single-crystalline particles with an individual size between 1 -1000 nm. [1][2][3][4][5] Their physical properties are largely determined by structural coherence, for which the angular correlation between their individual atomic lattices and the underlying superlattice of nanocrystals (NC) is a key ingredient. 1,2 Colloidal NCs stabilized by organic surfactants have been shown to pose excellent building blocks for the design of synthetic MCs with tailored structural properties which are conveniently obtained by self-assembly of NCs from solution on a solid or liquid substrate by exploiting ligand-ligand 3 interactions. [6][7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24][25] Typically, the utilized ligands consist of wide-gap, bulky hydrocarbons which render the MCs insulating. [26][27][28][29][30][31][32][33] MCs obtained in this way exhibit average grain sizes of ~150 µm 2 , which enables a detailed characterization by electron and/or X-ray microscopy. 34 Since the optoelectronic properties of PbS NC ensembles bear many opportunities for applications in solar cells or photodetectors, a number of ligand exchange procedures with small organic or inorganic molecules as well as single atom passivation strategies have been developed, all of which greatly increase the carrier mobilities within the SL of NCs. 28,33,[35][36][37][38][39][40][41][42][43][44] Due to the short interparticle spacing imposed by these ligands, structural coherence is mostly lost in such superlattices, but in rare cases it has been demonstrated that significant long-range order and even mesocrystallinity can be preserved. 25,35,45 However, a persisting problem of these protocols is that they are prone to introduce defects in the superlattice structure with some degree of granularity and signifi...

The advent of accelerator-driven free-electron lasers (FEL) has opened new avenues for high-resolution structure determination via di raction methods that go far beyond conventional X-ray crystallography methods 1-10 . These techniques rely on coherent scattering processes that require the maintenance of first-order coherence of the radiation field throughout the imaging procedure. Here we show that higher-order degrees of coherence, displayed in the intensity correlations of incoherently scattered X-rays from an FEL, can be used to image two-dimensional objects with a spatial resolution close to or even below the Abbe limit. This constitutes a new approach towards structure determination based on incoherent processes 11,12 , including fluorescence emission or wavefront distortions, generally considered detrimental for imaging applications. Our method is an extension of the landmark intensity correlation measurements of Hanbury Brown and Twiss 13 to higher than second order, paving the way towards determination of structure and dynamics of matter in regimes where coherent imaging methods have intrinsic limitations 14 .The discovery by Hanbury Brown and Twiss of photon bunching of thermal light 15 and its application in astronomy to determine the angular diameter of stars by measuring spatial photon correlations 13 was a hallmark experiment for the development of modern quantum optics 16 . The subsequent quantum mechanical description of photon correlations by Glauber paved the way for a generalized concept of optical coherence 17 that is founded on the analysis of correlation functions of order m rather than the first-order coherence. For example, the spatial second-order photon correlation function g (2) (r 1 , r 2 ) expresses the probability to detect a photon at position r 1 given that a photon is recorded at position r 2 . In the case of two incoherent sources, g (2) (r 1 , r 2 ) displays a cosine modulation which oscillates at a spatial frequency depending on the source separation 18,19 . In this way interference fringes show up even in the complete absence of first-order coherence, allowing the extraction of structural information from incoherently emitting objects. This has been applied in Earth-bound stellar interferometry to measure the angular diameter of stars with 100-fold increased resolution 13 or to reveal the spatial and statistical properties of pulsed FEL sources 20,21 .Extending this concept to arbitrary arrangements of incoherently scattering emitters enables one to use intensity correlations for imaging applications. This has been demonstrated recently for one-dimensional arrays of emitters in the visible range of the spectrum [22][23][24] , where a spatial resolution even below the canonical Abbe limit has been achieved. Here we go still further and employ the method to image arbitrary two-dimensional incoherently scattering objects radiating in the vacuum ultraviolet. The extension from one dimension 24 to two dimensions is non-trivial and even unexpected in view of the tremendously enlarg...

We present a comprehensive experimental analysis of statistical properties of the self-amplified spontaneous emission free-electron laser (FEL) FLASH by means of Hanbury Brown and Twiss interferometry. The experiments were performed at FEL wavelengths of 5.5, 13.4, and 20.8 nm. We determined the second-order intensity correlation function for all wavelengths and different operation conditions of FLASH. In all experiments a high degree of spatial coherence (above 50%) was obtained. Our analysis performed in spatial and spectral domains provided us with the independent measurements of an average pulse duration of the FEL that were below 60 fs. To explain the complicated behavior of the second-order intensity correlation function we developed an advanced theoretical model that includes the presence of multiple beams and external positional jitter of the FEL pulses. By this analysis we determined that in one of the experiments external positional jitter was about 25% of the beam size. We envision that methods developed in our study will be used widely for analysis and diagnostics of FEL radiation.

The invention of optical lasers led to a revolution in the field of optics and to the creation of such fields of research as quantum optics. The reason was their unique statistical and coherence properties. The emerging, short-wavelength free-electron lasers (FELs) are sources of very bright coherent extreme-ultraviolet and X-ray radiation with pulse durations on the order of femtoseconds, and are presently considered to be laser sources at these energies. FELs are highly spatially coherent to the first-order but in spite of their name, behave statistically as chaotic sources. Here, we demonstrate experimentally, by combining Hanbury Brown and Twiss interferometry with spectral measurements that the seeded XUV FERMI FEL-2 source does indeed behave statistically as a laser. The results may be useful for quantum optics experiments and for the design and operation of next generation FEL sources.