The LaueUtil toolkit for Laue photocrystallography. I. Rapid orientation matrix determination for intermediate-size-unit-cell Laue data

Axial vs equatorial: Capturing the intramolecular charge transfer state geometry in conformational polymorphic crystals of a donor-bridge-acceptor dyad in nanosecond-time-scale

Two conformational polymorphs of a donor-bridge-acceptor (D-B-A) dyad, p-(CH3)2N-C6H4-(CH2)2-(1-pyrenyl)/PyCHDMA, were studied, where the electron donor (D) moiety p-(CH3)2N-C6H4/DMA is connected through a bridging group (B), -CH2-CH2-, to the electron acceptor (A) moiety pyrene. Though molecular dyads like PyCHDMA have the potential to change solar energy into electrical current through the process of photoinduced intramolecular charge transfer (ICT), the major challenge is the real-time investigation of the photoinduced ICT process in crystals, necessary to design solid-state optoelectronic materials. The time-correlated single photon counting (TCSPC) measurements with the single crystals showed that the ICT state lifetime of the thermodynamic form, PyCHDMA1 (pyrene and DMA: axial), is ∼3 ns, whereas, for the kinetic form, PyCHDMA20 (pyrene and DMA: equatorial), it is ∼7 ns, while photoexcited with 375 nm radiation. The polymorphic crystals were photo-excited and subsequently probed with a pink Laue x-ray beam in time-resolved x-ray diffraction (TRXRD) measurements. The TRXRD results suggest that in the ICT state, due to electron transfer from the tertiary N-atom in DMA moiety to the bridging group and pyrene moiety, a decreased repulsion between the lone-pair and the bond-pair at N-atom induces planarity in the C-N-(CH3)2 moiety, in both polymorphs. The Natural Bond Orbital calculations and partial atomic charge analysis by Hirshfeld partitioning also corroborated the same. Although the interfragment charge transfer (IFCT) analysis using the TDDFT results showed that for the charge transfer excitation in both conformers, the electrons were transferred from the DMA moiety to mostly the pyrene moiety, the bridging group has little role to play in that.

Short- vs. long-range elastic distortion: structural dynamics of a [2 × 2] tetrairon(II) spin crossover grid complex observed by time-resolved X-Ray crystallography

Spin crossover complexes (SCO) are among the most studied molecular switches due to their potential use in displays, sensors, actuators and memory components. A prerequisite to using these materials is the understanding of the structural changes following the spin transition at out-of-equilibrium conditions. So far, out-of-equilibrium studies in SCO solids have been focused on mononuclear complexes, though a growing number of oligonuclear SCO complexes showing cooperative effects are being reported. Here, we use time-resolved pink Laue crystallography to study the out-of-equilibrium dynamics of a [2 × 2] tetranuclear metallogrid of the form [FeII4LMe4](BF4)4·2MeCN ([LMe]- = 4-methyl-3,5-bis{6-(2,2'-bipyridyl)}pyrazolate). The out-of-equilibrium spin state switching induced by a ps laser pulse demonstrates that the metallogrid exhibits a multi-step response similar to that reported for mononuclear complexes. Contrary to the mononuclear complexes, the metallogrid shows two types of elastic distortions at different time scales. The first is a short-range distortion that propagates over the entire Fe4 grid complex during the ps time scale, and it is caused by the rearrangement of the coordination sphere of the photo-switching ion and the constant feedback between strongly linked metal ions. The second is a long-range distortion caused by the anisotropic expansion of the lattice during the ns time scale, observed in mononuclear materials. The structural analysis demonstrates that the long-range prevails over the short-range distortion, inducing the largest deformation of both the entire grid and the coordination sphere of each metal ion. The present study sheds light on the out-of -equilibrium dynamics of a non-cooperative oligonuclear complex.

Indexing of diffraction patterns for determination of crystal orientations

The task of determining the orientations of crystals is usually performed by indexing reflections detected on diffraction patterns. The well known underlying principle of indexing methods is universal: they are based on matching experimental scattering vectors to some vectors of the reciprocal lattice. Despite this, the standard attitude has been to devise algorithms applicable to patterns of a particular type. This paper provides a broader perspective. A general approach to indexing of diffraction patterns of various types is presented. References are made to formally similar problems in other research fields, e.g. in computational geometry, computer science, computer vision or star identification. Besides a general description of available methods, concrete algorithms are presented in detail and their applicability to patterns of various types is demonstrated; a program based on these algorithms is shown to index Kikuchi patterns, Kossel patterns and Laue patterns, among others.

Instrument-model refinement in normalized reciprocal-vector space for X-ray Laue diffraction

A simple yet efficient instrument-model refinement method for X-ray diffraction data is presented and discussed. The method is based on least-squares minimization of differences between respective normalized (i.e. unit length) reciprocal vectors computed for adjacent frames. The approach was primarily designed to work with synchrotron X-ray Laue diffraction data collected for small-molecule single-crystal samples. The method has been shown to work well on both simulated and experimental data. Tests performed on simulated data sets for small-molecule and protein crystals confirmed the validity of the proposed instrument-model refinement approach. Finally, examination of data sets collected at both BioCARS 14-ID-B (Advanced Photon Source) and ID09 (European Synchrotron Radiation Facility) beamlines indicated that the approach is capable of retrieving goniometer parameters (e.g. detector distance or primary X-ray beam centre) reliably, even when their initial estimates are rather inaccurate.

Seed-skewness algorithm for X-ray diffraction signal detection in time-resolved synchrotron Laue photocrystallography

A one-dimensional seed-skewness algorithm adapted for X-ray diffraction signal detection is presented and discussed. The method, primarily designed for photocrystallographic time-resolved Laue data processing, was shown to work well for the type of data collected at the Advanced Photon Source and European Synchrotron Radiation Facility. Nevertheless, it is also applicable in the case of standard single-crystal X-ray diffraction data. The reported algorithm enables reasonable separation of signal from the background in single one-dimensional data vectors as well as the capability to determine small changes of reflection shapes and intensities resulting from exposure of the sample to laser light. Otherwise, the procedure is objective, and relies only on skewness computation and its subsequent minimization. The new algorithm was proved to yield comparable results to the Kruskal-Wallis test method [Kalinowski, J. A. et al. (2012). J. Synchrotron Rad. 19, 637], while the processing takes a similar amount of time. Importantly, in contrast to the Kruskal-Wallis test, the reported seed-skewness approach does not need redundant input data, which allows for faster data collections and wider applications. Furthermore, as far as the structure refinement is concerned, the reported algorithm leads to the excited-state geometry closest to the one modelled using the quantum-mechanics/molecular-mechanics approach reported previously [Jarzembska, K. N. et al. (2014). Inorg. Chem. 53, 10594], when the t and s algorithm parameters are set to the recommended values of 0.2 and 3.0, respectively.

pinkIndexer - a universal indexer for pink-beam X-ray and electron diffraction snapshots

A crystallographic indexing algorithm, pinkIndexer, is presented for the analysis of snapshot diffraction patterns. It can be used in a variety of contexts including measurements made with a monochromatic radiation source, a polychromatic source or with radiation of very short wavelength. As such, the algorithm is particularly suited to automated data processing for two emerging measurement techniques for macromolecular structure determination: serial pink-beam X-ray crystallography and serial electron crystallography, which until now lacked reliable programs for analyzing many individual diffraction patterns from crystals of uncorrelated orientation. The algorithm requires approximate knowledge of the unit-cell parameters of the crystal, but not the wavelengths associated with each Bragg spot. The use of pinkIndexer is demonstrated by obtaining 1005 lattices from a published pink-beam serial crystallography data set that had previously yielded 140 indexed lattices. Additionally, in tests on experimental serial crystallography diffraction data recorded with quasi-monochromatic X-rays and with electrons the algorithm indexed more patterns than other programs tested.

On the Nature of Luminescence Thermochromism of Multinuclear Copper(I) Benzoate Complexes in the Crystalline State

A model luminescent [(PhCO2)4Cu4] (Cu4) complex in the crystalline state was investigated via combined crystallographic and spectroscopic techniques contributed substantially by theoretical modelling. The complex appeared to exhibit luminescence thermochromism, i.e., red phosphorescence at room temperature which changes to green when lowering the temperature to 90 K. The low-energy emissive state was assigned as a cluster-centred triplet, 3CC. The emission from this state predicted in TDDFT (~635 nm) matches the experimental red band observed at 660–715 nm. In contrast, the nature of the high-energy “green” band was less straightforward. The next reached cluster-centred triplet excited state occurred to be energetically close to the experimental value of ~545 nm. The two excited states also exhibit significant metal-to-ligand and ligand-to-metal charge transfer characteristics, especially for solid-state distorted geometries. In both cases the cluster core was expected to become notably contracted when compared to the ground state. Time-resolved photocrystallographic results supported the computationally predicted core contraction upon excitation. Additionally, the differences between the spectroscopic behaviour of the related tetra- and hexanuclear copper(I) complexes, Cu4 and Cu6 (i.e., [(PhCO2)6Cu6]) in the crystalline state were discussed and examined. It appeared that crystal packing may constitute an important factor as far as the lack of luminescence thermochromism in the latter case is concerned. Synopsis: Structure–property relationships characterising a model luminescent [(PhCO2)4Cu4] (Cu4) complex in the crystalline state were investigated via combined crystallographic and spectroscopic techniques contributed by theoretical modelling, and compared with the properties of the related [(PhCO2)6Cu6] (Cu6) complex.

Exploring the structural changes on excitation of a luminescent organic bromine-substituted complex by in-house time-resolved pump-probe diffraction

The structural changes accompanying the excitation of the luminescent dibromobenzene derivative, 1,4-dibromo-2,5-bis(octyloxy)benzene, have been measured by in-house monochromatic time-resolved (TR) diffraction at 90 K. Results show an increment of the very short intermolecular Br•••Br contact distance from 3.290 Å to 3.380 Å. Calculations show the Br…Br interaction to be strongly repulsive in both the Ground and Excited states but significantly relaxed by the lengthening of the contact distance on excitation. The stability of the crystals is attributed to the many weak C-H···Br and C-H···π intermolecular interactions. The study described is the first practical application of In-House Time-Resolved diffraction, made possible by the continuing increase in the brightness of X-ray sources and the sensitivity of our detectors.

Analysis of multicrystal pump-probe data sets. II. Scaling of ratio data sets

Two methods for scaling of multicrystal data collected in time-resolved photocrystallography experiments are discussed. The WLS method is based on a weighted least-squares refinement of laser-ON/laser-OFF intensity ratios. The other, previously applied, is based on the average absolute system response to light exposure. A more advanced application of these methods for scaling within a data set, necessary because of frequent anisotropy of light absorption in crystalline samples, is proposed. The methods are applied to recently collected synchrotron data on the tetra-nuclear compound Ag2Cu2L4 with L = 2-diphenylphosphino-3-methylindole. A statistical analysis of the weighted least-squares refinement residual terms is performed to test the importance of the scaling procedure.

New methods in time-resolved Laue pump-probe crystallography at synchrotron sources

Newly developed methods for time-resolved studies using the polychromatic and in particular the pink-Laue technique, suitable for medium and small-size unit cells typical in chemical crystallography, are reviewed. The order of the sections follows that of a typical study, starting with a description of the pink-Laue technique, followed by the strategy of data collection for analysis with the RATIO method. Novel procedures are described for spot integration, orientation matrix determination for relatively sparse diffraction patterns, scaling of multi-crystal data sets, use of Fourier maps for initial assessment and analysis of results, and least-squares refinement of photo-induced structural and thermal changes. In the calculation of Fourier maps a ground-state structure model, typically based on monochromatic results, is employed as reference, and the laser-ON structure factors for the Fourier summations are obtained by multiplying the reference ground-state structure factors by the square root of the experimental ON/OFF ratios. A schematic of the procedure followed is included in the conclusion section.

Shedding light on the photochemistry of coinage-metal phosphorescent materials: a time-resolved Laue diffraction study of an Ag(I)-Cu(I) tetranuclear complex

The triplet excited state of a new crystalline form of a tetranuclear coordination d(10)-d(10)-type complex, Ag2Cu2L4 (L = 2-diphenylphosphino-3-methylindole ligand), containing Ag(I) and Cu(I) metal centers has been explored using the Laue pump-probe technique with ≈80 ps time resolution. The relatively short lifetime of 1 μs is accompanied by significant photoinduced structural changes, as large as the Ag1···Cu2 distance shortening by 0.59(3) Å. The results show a pronounced strengthening of the argentophilic interactions and formation of new Ag···Cu bonds on excitation. Theoretical calculations indicate that the structural changes are due to a ligand-to-metal charge transfer (LMCT) strengthening the Ag···Ag interaction, mainly occurring from the methylindole ligands to the silver metal centers. QM/MM optimizations of the ground and excited states of the complex support the experimental results. Comparison with isolated molecule optimizations demonstrates the restricting effect of the crystalline matrix on photoinduced distortions. The work represents the first time-resolved Laue diffraction study of a heteronuclear coordination complex and provides new information on the nature of photoresponse of coinage metal complexes, which have been the subject of extensive studies.

On the assessment of time-resolved diffraction results

Data collected during dynamic structure pump-probe crystallography experiments require appropriate indicators of agreement and tools to visualize the electron-density distribution changes. Agreement factors based on the ratio of intensities R with and without the external perturbation are shown to be analogous to the R1 and wR2 R factors widely used in standard crystallographic refinements. The η-based R factors, normalized by the average relative intensity change, are significantly larger than R-based values. It is shown that the relative intensity change η-based R factors are not suitable for comparing different data sets. Fourier photodifference maps allow the visualization of the externally induced structural changes in the crystal, but also can be used during refinement to observe residual peaks not yet accounted for by the model and thus monitor the progress of the refinement. The photodeformation maps are a complementary tool to confirm the validity of the final model. Photodeformation maps with equalized laser-on and laser-off thermal motion are used to highlight the structural changes.

The LaueUtil toolkit for Laue photocrystallography. II. Spot finding and integration

A spot-integration method is described which does not require prior indexing of the reflections. It is based on statistical analysis of the values from each of the pixels on successive frames, followed for each frame by morphological analysis to identify clusters of high value pixels which form an appropriate mask corresponding to a reflection peak. The method does not require prior assumptions such as fitting of a profile or definition of an integration box. The results are compared with those of the seed-skewness method which is based on minimizing the skewness of the intensity distribution within a peak's integration box. Applications in Laue photocrystallography are presented.

Restricted photochemistry in the molecular solid state: structural changes on photoexcitation of Cu(I) phenanthroline metal-to-ligand charge transfer (MLCT) complexes by time-resolved diffraction

The excited-state structure of [Cu(I)[(1,10-phenanthroline-N,N') bis(triphenylphosphine)] cations in their crystalline [BF(4)] salt has been determined at both 180 and 90 K by single-pulse time-resolved synchrotron experiments with the modified polychromatic Laue method. The two independent molecules in the crystal show distortions on MLCT excitation that differ in magnitude and direction, a difference attributed to a pronounced difference in the molecular environment of the two complexes. As the excited states differ, the decay of the emission is biexponential with two strongly different lifetimes, the longer lifetime, assigned to the more restricted molecule, becoming more prevalent as the temperature increases. Standard deviations in the current Laue study are very much lower than those achieved in a previous monochromatic study of a Cu(I) 2,9-dimethylphenanthroline substituted complex ( J. Am. Chem. Soc. 2009 , 131 , 6566 ), but the magnitudes of the shifts on excitation are similar, indicating that lattice restrictions dominate over the steric effect of the methyl substitution. Above all, the study illustrates emphatically that molecules in solids have physical properties different from those of isolated molecules and that their properties depend on the specific molecular environment. This conclusion is relevant for the understanding of the properties of molecular solid-state devices, which are increasingly used in current technology.