3D atomic structure from a single X-ray free electron laser pulse.

X-ray Free Electron Lasers (XFEL) are cutting-edge pulsed x-ray sources, whose extraordinary pulse parameters promise to unlock unique applications. Several new methods have been developed at XFELs; however, no methods are known, which allow ab initio atomic level structure determination using only a single XFEL pulse. Here, we present experimental results, demonstrating the determination of the 3D atomic structure from data obtained during a single 25 fs XFEL pulse. Parallel measurement of hundreds of Bragg reflections was done by collecting Kossel line patterns of GaAs and GaP. To the best of our knowledge with these measurements, we reached the ultimate temporal limit of the x-ray structure solution possible today. These measurements open the way for obtaining crystalline structures during non-repeatable fast processes, such as structural transformations. For example, the atomic structure of matter at extremely non-ambient conditions or transient structures formed in irreversible physical, chemical, or biological processes may be captured in a single shot measurement during the transformation. It would also facilitate time resolved pump-probe structural studies making them significantly shorter than traditional serial crystallography.

Formation of Paramagnetic Defects in the Synthesis of Silicon Carbide.

Silicon carbide (SiC) is a very promising platform for quantum information processing, as it can host room temperature solid state defect quantum bits. These room temperature quantum bits are realized by paramagnetic silicon vacancy and divacancy defects in SiC that are typically introduced by irradiation techniques. However, irradiation techniques often introduce unwanted defects near the target quantum bit defects that can be detrimental for the operation of quantum bits. Here, we demonstrate that by adding aluminum precursor to the silicon and carbon sources, quantum bit defects are created in the synthesis of SiC without any post treatments. We optimized the synthesis parameters to maximize the paramagnetic defect concentrations-including already established defect quantum bits-monitored by electron spin resonance spectroscopy.

Amino-Termination of Silicon Carbide Nanoparticles.

Silicon carbide nanoparticles (SiC NPs) are promising inorganic molecular-sized fluorescent biomarkers. It is imperative to develop methods to functionalize SiC NPs for certain biological applications. One possible route is to form amino groups on the surface, which can be readily used to attach target biomolecules. Here, we report direct amino-termination of aqueous SiC NPs. We demonstrate the applicability of the amino-terminated SiC NPs by attaching bovine serum albumin as a model for functionalization. We monitor the optical properties of the SiC NPs in this process and find that the fluorescence intensity is very sensitive to surface termination. Our finding may have implications for a few nanometers sized SiC NPs containing paramagnetic color centers with optically read electron spins.

Comparison of EMC and CM methods for orienting diffraction images in single-particle imaging experiments.

In single-particle imaging (SPI) experiments, diffraction patterns of identical particles are recorded. The particles are injected into the X-ray free-electron laser (XFEL) beam in random orientations. The crucial step of the data processing of SPI is finding the orientations of the recorded diffraction patterns in reciprocal space and reconstructing the 3D intensity distribution. Here, two orientation methods are compared: the expansion maximization compression (EMC) algorithm and the correlation maximization (CM) algorithm. To investigate the efficiency, reliability and accuracy of the methods at various XFEL pulse fluences, simulated diffraction patterns of biological molecules are used.

Enhancement of X-ray-Excited Red Luminescence of Chromium-Doped Zinc Gallate via Ultrasmall Silicon Carbide Nanocrystals.

X-ray-activated near-infrared luminescent nanoparticles are considered as new alternative optical probes due to being free of autofluorescence, while both their excitation and emission possess a high penetration efficacy in vivo. Herein, we report silicon carbide quantum dot sensitization of trivalent chromium-doped zinc gallate nanoparticles with enhanced near-infrared emission upon X-ray and UV-vis light excitation. We have found that a ZnGa2O4 shell is formed around the SiC nanoparticles during seeded hydrothermal growth, and SiC increases the emission efficiency up to 1 order of magnitude due to band alignment that channels the excited electrons to the chromium ion.

Incorporating particle symmetry into orientation determination in single-particle imaging.

In coherent-diffraction-imaging experiments X-ray diffraction patterns of identical particles are recorded. The particles are injected into the X-ray free-electron laser (XFEL) beam in random orientations. If the particle has symmetry, finding the orientation of a pattern can be ambiguous. With some modifications, the correlation-maximization method can find the relative orientations of the diffraction patterns for the case of symmetric particles as well. After convergence, the correlation maps show the symmetry of the particle and can be used to determine the symmetry elements and their orientations. The C factor, slightly modified for the symmetric case, can indicate the consistency of the assembled three-dimensional intensity distribution.

Harnessing no-photon exciton generation chemistry to engineer semiconductor nanostructures.

Production of semiconductor nanostructures with high yield and tight control of shape and size distribution is an immediate quest in diverse areas of science and technology. Electroless wet chemical etching or stain etching can produce semiconductor nanoparticles with high yield but is limited to a few materials because of the lack of understanding the physical-chemical processes behind. Here we report a no-photon exciton generation chemistry (NPEGEC) process, playing a key role in stain etching of semiconductors. We demonstrate NPEGEC on silicon carbide polymorphs as model materials. Specifically, size control of cubic silicon carbide nanoparticles of diameter below ten nanometers was achieved by engineering hexagonal inclusions in microcrystalline cubic silicon carbide. Our finding provides a recipe to engineer patterned semiconductor nanostructures for a broad class of materials.

Coherent diffraction imaging: consistency of the assembled three-dimensional distribution.

The short pulses of X-ray free-electron lasers can produce diffraction patterns with structural information before radiation damage destroys the particle. From the recorded diffraction patterns the structure of particles or molecules can be determined on the nano- or even atomic scale. In a coherent diffraction imaging experiment thousands of diffraction patterns of identical particles are recorded and assembled into a three-dimensional distribution which is subsequently used to solve the structure of the particle. It is essential to know, but not always obvious, that the assembled three-dimensional reciprocal-space intensity distribution is really consistent with the measured diffraction patterns. This paper shows that, with the use of correlation maps and a single parameter calculated from them, the consistency of the three-dimensional distribution can be reliably validated.

Crystal structure of the 4 + 2 cyclo-adduct of photooxidized anthracene and C60 fullerene.

The structure of the title compound, 5,6-[(1R,10S)-2,9-dioxatri-cyclo-[8.6.0(3,8).0(11,16)]hexa-decane-1,10-di-yl]-(C60-Ih)[5,6]fullerene methane-dithione 0.1-solvate, C74H10O2·0.1CS2, has tetra-gonal (P42/n) symmetry at 100 K. It has a unique eight-membered ring, with two incorporated O atoms in place of the original central ring of the anthracene. The distortion of the mol-ecular geometry around the cyclo-adduct bonds corresponds to that seen in related fullerene derivatives. Close packing of the adduct forms cavities partially filled with disordered carbon di-sulfide solvent mol-ecule. The 41% occupancy of the cavities yields an overall 1:0.103 adduct-solvent ratio. Reaction steps are described as light-assisted singlet-oxygen generation, peroxide, epoxide and dioxocin derivative formation and the final step of thermally activated cyclo-addition.

Selection and orientation of different particles in single particle imaging.

The short pulses of X-ray free electron lasers can produce diffraction patterns with structural information before radiation damage destroys the particle. The particles are injected into the beam in random orientations and they should be identical. However, in real experimental conditions it is not always possible to have identical particles. In this paper we show that the correlation maximization method, developed earlier, is able to select identical particles from a mixture and find their orientations simultaneously.

Atomic structure of a single large biomolecule from diffraction patterns of random orientations.

The short and intense pulses of the new X-ray free electron lasers, now operational or under construction, may make possible diffraction experiments on single molecule-sized objects with high resolution, before radiation damage destroys the sample. In a single molecule imaging (SMI) experiment thousands of diffraction patterns of single molecules with random orientations are recorded. One of the most challenging problems of SMI is how to assemble these noisy patterns of unknown orientations into a consistent single set of diffraction data. Here we present a new method which can solve the orientation problem of SMI efficiently even for large biological molecules and in the presence of noise. We show on simulated diffraction patterns of a large protein molecule, how the orientations of the patterns can be found and the structure to atomic resolution can be solved. The concept of our algorithm could be also applied to experiments where images of an object are recorded in unknown orientations and/or positions like in cryoEM or tomography.

Common arc method for diffraction pattern orientation.

Very short pulses of X-ray free-electron lasers opened the way to obtaining diffraction signal from single particles beyond the radiation dose limit. For three-dimensional structure reconstruction many patterns are recorded in the object's unknown orientation. A method is described for the orientation of continuous diffraction patterns of non-periodic objects, utilizing intensity correlations in the curved intersections of the corresponding Ewald spheres, and hence named the common arc orientation method. The present implementation of the algorithm optionally takes into account Friedel's law, handles missing data and is capable of determining the point group of symmetric objects. Its performance is demonstrated on simulated diffraction data sets and verification of the results indicates a high orientation accuracy even at low signal levels. The common arc method fills a gap in the wide palette of orientation methods.

Orientational ordering and low-temperature libration in the rotor-stator cocrystals of fullerenes and cubane.

Cocrystals of cubane and fullerenes, C60-cubane and C70-cubane, show distinct rotational ordering transitions. We studied the corresponding structural changes with temperature-dependent X-ray diffraction and the thermodynamics of the phase transitions with adiabatic microcalorimetry and differential scanning calorimetry. C60-cubane has one phase transition around 130 K from a high-temperature fcc phase with freely rotating C60 to a low-temperature orthorombic phase in which the fullerene rotation is frozen. The corresponding enthalpy change is approximately 1170 J/mol, and the entropy change is 9.6 J/(mol K). C70-cubane has two phase transitions. Around 380 K, the high-temperature fcc phase with freely rotating C70 transforms into a bct phase in which the C70 rotates uniaxially around an axis that precesses around the c direction with a full opening angle of 40 degree. Around 170 K, the uniaxial rotation also freezes out, with an accompanying structural transition to monoclinic and enthalpy and entropy changes of 620 J/mol and 8.7 J/(mol K), respectively. The low-temperature specific heat was analyzed in terms of the Debye-Einstein model to estimate the librational energies of the fullerenes and Debye temperatures. We found very similar values for the two cocrystals, approximately Elib = 2.2 meV and TDebye = 23 K. For reference, we also measured the specific heats of pure C60 and C70 and found Elib = 2.96 meV and TDebye = 32 K for C60 and Elib = 1.9 meV and TDebye = 20 K for C70.

Rotor-stator molecular crystals of fullerenes with cubane.

Cubane (C8H8) and fullerene (C60) are famous cage molecules with shapes of platonic or archimedean solids. Their remarkable chemical and solid-state properties have induced great scientific interest. Both materials form polymorphic crystals of molecules with variable orientational ordering. The idea of intercalating fullerene with cubane was raised several years ago but no attempts at preparation have been reported. Here we show that C60 and similarly C70 form high-symmetry molecular crystals with cubane owing to topological molecular recognition between the convex surface of fullerenes and the concave cubane. Static cubane occupies the octahedral voids of the face-centred-cubic structures and acts as a bearing between the rotating fullerene molecules. The smooth contact of the rotor and stator molecules decreases significantly the temperature of orientational ordering. These materials have great topochemical importance: at elevated temperatures they transform to high-stability covalent derivatives although preserving their crystalline appearance. The size-dependent molecular recognition promises selective formation of related structures with higher fullerenes and/or substituted cubanes.