Towards pump-probe single-crystal XFEL refinements for small-unit-cell systems.

Serial femtosecond crystallography for small-unit-cell systems has so far seen very limited application despite obvious scientific possibilities. This is because reliable data reduction has not been available for these challenging systems. In particular, important intensity corrections such as the partiality correction critically rely on accurate determination of the crystal orientation, which is complicated by the low number of diffraction spots for small-unit-cell crystals. A data reduction pipeline capable of fully automated handling of all steps of data reduction from spot harvesting to merged structure factors has been developed. The pipeline utilizes sparse indexing based on known unit-cell parameters, seed-skewness integration, intensity corrections including an overlap-based combined Ewald sphere width and partiality correction, and a dynamically adjusted post-refinement routine. Using the pipeline, data measured on the compound K4[Pt2(P2O5H2)4]·2H2O have been successfully reduced and used to solve the structure to an R1 factor of ∼9.1%. It is expected that the pipeline will open up the field of small-unit-cell serial femtosecond crystallography experiments and allow investigations into, for example, excited states and reaction intermediate chemistry.

Multipole electron densities and structural parameters from synchrotron powder X-ray diffraction data obtained with a MYTHEN detector system (OHGI).

Powder X-ray diffraction has some inherent advantages over traditional single-crystal X-ray diffraction in accurately determining electron densities and structural parameters due to the lower requirements for sample crystallinity, simpler corrections and measurement simultaneity. For some simple inorganic materials, it has been shown that these advantages can compensate for disadvantages such as peak overlap and error-prone background subtraction. Although it is challenging to extend powder X-ray diffraction-based electron-density studies to organic materials with significant peak overlap, previous results using a dedicated vacuum diffractometer with a large image-plate camera (AVID) demonstrated that it can be done. However, the vacuum setup with the off-line detector system was found to prohibit a widespread use. Fast microstrip detectors, which have been employed at a number of powder diffraction beamlines, have the potential to facilitate electron-density studies. Nevertheless, no electron-density studies even for materials with slight peak overlap have been performed with microstrip detectors. One of the most critical problems has been a difference in sensitivity between microstrip channels, which substantially defines the dynamic range of a detector. Recently, a robust approach to this problem has been developed and applied to a total scattering measurement system (OHGI) with 15 MYTHEN microstrip modules. In the present study, synchrotron powder X-ray diffraction data obtained with OHGI are evaulated in terms of multipole electron densities and structural parameters (atomic positions and displacement parameters). These results show that, even without a dedicated setup and perfect samples, electron-density modelling can be carried out on high-quality powder X-ray diffraction data. However, it was also found that the required prior information about the sample prohibits widespread use of the method. With the presently obtainable data quality, electron densities of molecular crystals in general are not reliably obtained from powder data, but it is an excellent, possibly superior, alternative to single-crystal measurements for small-unit-cell inorganic solids. If aspherical atomic scattering factors can be obtained from other means (multipole databases, theoretical calculations), then atomic positions (including for hydrogen) and anisotropic atomic displacement parameters (non-hydrogen atoms) of excellent accuracy can be refined from synchrotron powder X-ray diffraction data on organic crystals.

Multipole electron densities and atomic displacement parameters in urea from accurate powder X-ray diffraction.

Electron density determination based on structure factors obtained through powder X-ray diffraction has so far been limited to high-symmetry inorganic solids. This limit is challenged by determining high-quality structure factors for crystalline urea using a bespoke vacuum diffractometer with imaging plates. This allows the collection of data of sufficient quality to model the electron density of a molecular system using the multipole method. The structure factors, refined parameters as well as chemical bonding features are compared with results from the high-quality synchrotron single-crystal study by Birkedal et al. [Acta Cryst. (2004), A60, 371-381] demonstrating that powder X-ray diffraction potentially provides a viable alternative for electron density determination in simple molecular crystals where high-quality single crystals are not available.