Erratum: Hanbury Brown-Twiss Interferometry at a Free-Electron Laser [Phys. Rev. Lett. 111, 034802 (2013)].

This corrects the article DOI: 10.1103/PhysRevLett.111.034802.

Time-resolved pump and probe x-ray absorption fine structure spectroscopy at beamline P11 at PETRA III.

We report about the development and implementation of a new setup for time-resolved X-ray absorption fine structure spectroscopy at beamline P11 utilizing the outstanding source properties of the low-emittance PETRA III synchrotron storage ring in Hamburg. Using a high intensity micrometer-sized X-ray beam in combination with two positional feedback systems, measurements were performed on the transition metal complex fac-Tris[2-phenylpyridinato-C2,N]iridium(III) also referred to as fac-Ir(ppy)3. This compound is a representative of the phosphorescent iridium(III) complexes, which play an important role in organic light emitting diode (OLED) technology. The experiment could directly prove the anticipated photoinduced charge transfer reaction. Our results further reveal that the temporal resolution of the experiment is limited by the PETRA III X-ray bunch length of ∼103 ps full width at half maximum (FWHM).

A micro-patterned silicon chip as sample holder for macromolecular crystallography experiments with minimal background scattering.

At low emittance synchrotron sources it has become possible to perform structure determinations from the measurement of multiple microcrystals which were previously considered too small for diffraction experiments. Conventional mounting techniques do not fulfill the requirements of these new experiments. They significantly contribute to background scattering and it is difficult to locate the crystals, making them incompatible with automated serial crystallography. We have developed a micro-fabricated sample holder from single crystalline silicon with micropores, which carries up to thousands of crystals and significantly reduces the background scattering level. For loading, the suspended microcrystals are pipetted onto the chip and excess mother liquor is subsequently soaked off through the micropores. Crystals larger than the pore size are retained and arrange themselves according to the micropore pattern. Using our chip we were able to collect 1.5 Å high resolution diffraction data from protein microcrystals with sizes of 4 micrometers and smaller.

Hanbury Brown-Twiss interferometry at a free-electron laser.

We present measurements of second- and higher-order intensity correlation functions (so-called Hanbury Brown-Twiss experiment) performed at the free-electron laser (FEL) FLASH in the non-linear regime of its operation. We demonstrate the high transverse coherence properties of the FEL beam with a degree of transverse coherence of about 80% and degeneracy parameter of the order 10(9) that makes it similar to laser sources. Intensity correlation measurements in spatial and frequency domain gave an estimate of the FEL average pulse duration of 50 fs. Our measurements of the higher-order correlation functions indicate that FEL radiation obeys Gaussian statistics, which is characteristic to chaotic sources.

Impact of ultrafast electronic damage in single-particle x-ray imaging experiments.

In single-particle coherent x-ray diffraction imaging experiments, performed at x-ray free-electron lasers (XFELs), samples are exposed to intense x-ray pulses to obtain single-shot diffraction patterns. The high intensity induces electronic dynamics on the femtosecond time scale in the system, which can reduce the contrast of the obtained diffraction patterns and adds an isotropic background. We quantify the degradation of the diffraction pattern from ultrafast electronic damage by performing simulations on a biological sample exposed to x-ray pulses with different parameters. We find that the contrast is substantially reduced and the background is considerably strong only if almost all electrons are removed from their parent atoms. This happens at fluences of at least one order of magnitude larger than provided at currently available XFEL sources.

Spatial and temporal coherence properties of single free-electron laser pulses.

The experimental characterization of the spatial and temporal coherence properties of the free-electron laser in Hamburg (FLASH) at a wavelength of 8.0 nm is presented. Double pinhole diffraction patterns of single femtosecond pulses focused to a size of about 10×10 µm(2) were measured. A transverse coherence length of 6.2 ± 0.9 µm in the horizontal and 8.7 ± 1.0 µm in the vertical direction was determined from the most coherent pulses. Using a split and delay unit the coherence time of the pulses produced in the same operation conditions of FLASH was measured to be 1.75 ± 0.01 fs. From our experiment we estimated the degeneracy parameter of the FLASH beam to be on the order of 10(10) to 10(11), which exceeds the values of this parameter at any other source in the same energy range by many orders of magnitude.

Coherence properties of individual femtosecond pulses of an x-ray free-electron laser.

Measurements of the spatial and temporal coherence of single, femtosecond x-ray pulses generated by the first hard x-ray free-electron laser, the Linac Coherent Light Source, are presented. Single-shot measurements were performed at 780 eV x-ray photon energy using apertures containing double pinholes in "diffract-and-destroy" mode. We determined a coherence length of 17 µm in the vertical direction, which is approximately the size of the focused Linac Coherent Light Source beam in the same direction. The analysis of the diffraction patterns produced by the pinholes with the largest separation yields an estimate of the temporal coherence time of 0.55 fs. We find that the total degree of transverse coherence is 56% and that the x-ray pulses are adequately described by two transverse coherent modes in each direction. This leads us to the conclusion that 78% of the total power is contained in the dominant mode.

X-ray holographic microscopy with zone plates applied to biological samples in the water window using 3rd harmonic radiation from the free-electron laser FLASH.

The imaging of hydrated biological samples - especially in the energy window of 284-540 eV, where water does not obscure the signal of soft organic matter and biologically relevant elements - is of tremendous interest for life sciences. Free-electron lasers can provide highly intense and coherent pulses, which allow single pulse imaging to overcome resolution limits set by radiation damage. One current challenge is to match both the desired energy and the intensity of the light source. We present the first images of dehydrated biological material acquired with 3rd harmonic radiation from FLASH by digital in-line zone plate holography as one step towards the vision of imaging hydrated biological material with photons in the water window. We also demonstrate the first application of ultrathin molecular sheets as suitable substrates for future free-electron laser experiments with biological samples in the form of a rat fibroblast cell and marine biofouling bacteria Cobetia marina.

Coherent diffraction of a single virus particle: the impact of a water layer on the available orientational information.

Coherent diffractive imaging using x-ray free-electron lasers (XFELs) may provide a unique opportunity for high-resolution structural analysis of single particles sprayed from an aqueous solution into the laser beam. As a result, diffraction images are measured from randomly oriented objects covered by a water layer. We analyze theoretically how the thickness of the covering water layer influences the structural and orientational information contained in the recorded diffraction images. This study has implications for planned experiments on single-particle imaging with XFELs.

Theoretical estimation for correlations of diffraction patterns from objects differently oriented in space.

Coherent diffraction imaging of single biomolecules is expected to open unique opportunities for studies of non-crystalline samples. There are, however, still many technical and physical issues that need to be resolved in a more quantitative manner, especially if one aims for structural information at high resolution. Signal recorded from an object after a single shot is low. As primarily proposed in Spence and Doak (2004) and Huldt et al. (2003), averaging over the diffraction patterns from many different shots is necessary, in order to achieve a signal-to-noise ratio sufficient for image reconstruction. The images of the randomly oriented molecules have to be sorted out in order to identify those corresponding to the similar spatial orientations of the objects. This procedure is called the classification of diffraction images. Here we approach the classification in the framework of pattern-to-pattern correlations, and analyse theoretically the correlations between diffraction images of differently oriented objects.

Energetics, ionization, and expansion dynamics of atomic clusters irradiated with short intense vacuum-ultraviolet pulses.

Kinetic equations are used to model the dynamics of Xe clusters irradiated with short, intense vacuum-ultraviolet pulses. Various cluster size and pulse fluences are considered. It is found that the highly charged ions observed in the experiments are mainly due to Coulomb explosion of the outer cluster shell. Ions within the cluster core predominantly recombine with plasma electrons, forming a large fraction of neutral atoms. To our knowledge, our model is the first and only one that gives an accurate description of all of the experimental data collected from atomic clusters at 100 nm photon wavelength.

Coherent-pulse 2D crystallography using a free-electron laser x-ray source.

Coherent diffractive imaging for the reconstruction of a two-dimensional (2D) finite crystal structure with a single pulse train of free-electron laser radiation at 7.97 nm wavelength is demonstrated. This measurement shows an advance on traditional coherent imaging techniques by applying it to a periodic structure. It is also significant that this approach paves the way for the imaging of the class of specimens which readily form 2D, but not three-dimensional crystals. We show that the structure is reconstructed to the detected resolution, given an adequate signal-to-noise ratio.

Charge-density study on cyclosporine A.

Two single-crystal X-ray diffraction data sets of cyclosporine A were measured to high resolution using synchrotron radiation at temperatures of 5 and 90 K. They allowed an accurate determination of its molecular and electronic structure. Three electron-density models based on pseudoatom scattering factors were compared in terms of derived bond topological properties and in terms of electron-density differences on a grid. In one model multipole parameters were freely refined, whereas in the other two models the density was built up from fixed database parameters from the invariom database and University at Buffalo Databank. The data quality not only allowed benchmarking of the quality of both databases with the refined density, but also judgement of the feasibility of a multipole refinement of a larger oligopeptide structure such as cyclosporine A. Both databases performed equally well and reproduced the experimentally determined charge density satisfactorily.

Charge-density studies of energetic materials: CL-20 and FOX-7.

Experimental electron densities and derived properties have been determined for the two energetic materials CL-20 (3,5,9,11-tetraacetyl-14-oxo-1,3,5,7,9,11-hexaazapentacyclo-[5.5.3.02,6.04,10.08,12]pentadecane), and FOX-7 (1,1-diamino-2,2-dinitroethylene) from single-crystal diffraction. Synchrotron data extending to high scattering angles were measured at low temperature. Low figures-of-merit and excellent residuals were obtained. The Hansen & Coppens multipole-model electron density was compared with results from theoretical calculations via structure factors simulating an experiment. Chemical bonding in the molecules is discussed and a topological analysis gives insight especially into the character of those bonds that are thought to play a key role in the decomposition of the molecules. A comparison of theoretical and experimental electrostatic potentials shows no obvious evidence supporting earlier findings on other nitroheterocyclic molecules that electron-density maxima near the C-NO(2) bonds mapped on the electron-density isosurface can be correlated with impact sensitivities. For FOX-7 periodic Hartree-Fock calculations were performed to investigate the influence of the crystal field on the electron density distribution.

The structure of the hexagonal crystal form of hen egg-white lysozyme.

The three-dimensional structure of hen egg-white lysozyme (HEWL) in a hexagonal crystal form has been determined and refined to 1.46 A resolution. This hexagonal crystal form crystallizes from a saturated sodium nitrate solution at pH 8.4. The crystals belong to space group P6(1)22, with unit-cell parameters a = b = 85.64, c = 67.93 A. A total of 165 water molecules, 16 nitrate ions and five sodium ions were located in the electron-density map. The hexagonal crystal form exhibits a higher solvent content and a higher degree of disorder than other crystal forms of lysozyme. The flexibility of the protein depends on the crystal packing, although some residue ranges are flexible in all native HEWL crystal forms.

Synthesis and antibacterial study of unsaturated Mannich ketones.

Several Mannich ketones of 2-arylmethylenecycloalkanones were synthesised using the classical acid-catalysed Mannich reaction. Antibacterial activity of these new water-soluble compounds was reported against Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, Staphylococcus saprophyticus, Micrococcus luteus and Bacillus subtilis standard strains. Human cell line cytotoxicity of our new compounds was evaluated against HeLa cell lines. Some compounds showed low cytotoxicity (41.52 nM mL(-1) for 14 and 46.60 nM mL(-1) for 18) and proved to be efficient antibacterial agents against the Gram-positive strains. Minimum inhibitory concentrations varied from 1.56 to 100 microg mL(-1). The mechanism of action was examined, too.

Approximate solution of the Takagi-Taupin equations for a semi-infinite crystal in the three-beam Laue-Laue case.

An analytical approximate solution of the Takagi-Taupin equations for a symmetrical three-beam Laue-Laue case in a perfect non-absorbing semi-infinite crystal slab has been obtained. The expression, a second-order expansion, is valid for situations where the effective crystal thickness does not exceed half the actual extinction length and it is shown to be in perfect agreement with the full numerical solution of the fundamental equations.

Expeditious synthesis and chromatographic resolution of (+)- and (-)-trans-1-benzylcyclohexan-1,2-diamine hydrochlorides.

The hitherto unknown (-)- and (+)-1-benzylcyclohexan-1,2-diamine hydrochlorides 4a. HCl and 4b. HCl were synthesized by means of diastereoselective alpha-iminoamine rearrangement with subsequent imine reduction and hydrogenolysis. The relative trans-configuration as well as the absolute (1S,2R) and (1R,2S) configurations of 4a and 4b, respectively, were elucidated on the basis of an X-ray analysis of 3b. HCl. The enantiomeric excess (ee) values of the title compounds (>99%) were determined by chiral HPLC on a Chirex (D) Penicillamine column.

Potential for biomolecular imaging with femtosecond X-ray pulses.

Sample damage by X-rays and other radiation limits the resolution of structural studies on non-repetitive and non-reproducible structures such as individual biomolecules or cells. Cooling can slow sample deterioration, but cannot eliminate damage-induced sample movement during the time needed for conventional measurements. Analyses of the dynamics of damage formation suggest that the conventional damage barrier (about 200 X-ray photons per A2 with X-rays of 12 keV energy or 1 A wavelength) may be extended at very high dose rates and very short exposure times. Here we have used computer simulations to investigate the structural information that can be recovered from the scattering of intense femtosecond X-ray pulses by single protein molecules and small assemblies. Estimations of radiation damage as a function of photon energy, pulse length, integrated pulse intensity and sample size show that experiments using very high X-ray dose rates and ultrashort exposures may provide useful structural information before radiation damage destroys the sample. We predict that such ultrashort, high-intensity X-ray pulses from free-electron lasers that are currently under development, in combination with container-free sample handling methods based on spraying techniques, will provide a new approach to structural determinations with X-rays.

Properties of an electron-density map derived from a limited number of experimentally determined triplet phases.

In a previous communication [Weckert et al. (1999). Acta Cryst. D55, 1320-1328], the feasibility of the measurement of a large set of triplet phases by three-beam interference was demonstrated. This paper reports the methodology for the calculation of an electron-density map from this limited amount of experimental phase information and the map's properties with respect to model building and refinement. The tetragonal form of hen egg-white lysozyme (HEWL) was chosen as a test structure for the development of this method. The quality of the electron-density map obtained from all measured triplet phases allows a straightforward and nearly complete interpretation. The starting model was refined to a final R value of 17.4%. In a second step, the minimum number of phased reflections needed for the interpretation of an electron-density map was investigated, applying criteria based on |F| and resolution.