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 of initial masks to identify appropriate reflection footprints. 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.
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.
photocrystallography; X-ray diffraction; X-ray detection; CCD; Laue method; spot integration; background estimate; statistical analysis; image filtering
We report the spin state photo-switching dynamics in two polymorphs of a spin-crossover molecular complex triggered by a femtosecond laser flash, as determined by combining femtosecond optical pump-probe spectroscopy and picosecond X-ray diffraction techniques,. The light-driven transformations in the two polymorphs are compared. Combining both techniques and tracking how the X-ray data correlate with optical signals allows understanding of how electronic and structural degrees of freedom couple and play their role when the switchable molecules interact in the active crystalline medium. The study sheds light on crossing the border between femtochemistry at the molecular scale and femtoswitching at the material scale
The excited state structure of [Cu(1)[(1,10-phenanthroline-N,N’) bis(triphenylphosphine)] cations in their crystalline [BF4] salt has been determined at both 180 and 90K 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 which 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 bi-exponential 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 dimethyl-phenanthroline substituted complex (J. Am. Chem. Soc.
2009, 131, 6566), but the magnitude of the shifts on excitation is 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.
A new method for determination of the orientation matrix of Laue X-ray data is presented. The method is based on matching of the patterns of central reciprocal lattice rows projected on a unit sphere centered on the origin of the reciprocal lattice of the Laue data set with the corresponding pattern of a monochromatic data set on the same material.
A new method for determination of the orientation matrix of Laue X-ray data is presented. The method is based on matching of the experimental patterns of central reciprocal lattice rows projected on a unit sphere centered on the origin of the reciprocal lattice with the corresponding pattern of a monochromatic data set on the same material. This technique is applied to the complete data set and thus eliminates problems often encountered when single frames with a limited number of peaks are to be used for orientation matrix determination. Application of the method to a series of Laue data sets on organometallic crystals is described. The corresponding program is available under a Mozilla Public License-like open-source license.
LaueUtil; Laue photocrystallography; orientation matrix determination; computer programs
A modified Laue technique suitable for time-resolved diffraction is described in which profile-independent integration is used, the RATIO method is applied and multi-crystal data are normalized to a common scale. The method is applied in single-pulse pump–probe studies of a binuclear Rh complex, showing Rh—Rh bond shortening of 0.136 (8) Å on excitation.
A modified Laue method is shown to produce excited-state structures at atomic resolution of a quality competitive with those from monochromatic experiments. The much faster data collection allows the use of only one or a few X-ray pulses per data frame, which minimizes crystal damage caused by laser exposure of the samples and optimizes the attainable time resolution. The method has been applied to crystals of the α-modification of Rh2(μ-PNP)2(PNP)2 (BPh4)2 [PNP = CH3N(P(OCH3)2)2, Ph = phenyl]. The experimental results show a shortening of the Rh—Rh distance in the organometallic complex of 0.136 (8) Å on excitation and are quantitatively supported by quantum-mechanical (QM)/molecular-mechanics (MM) theoretical calculations which take into account the confining effect of the crystal environment, but not by theoretical results on the isolated complex, demonstrating the defining effect of the crystal matrix.
Laue techniques; single-pulse diffraction; quantum-mechanical/molecular-mechanics calculations; QM/MM calculations; time-resolved X-ray crystallography
The polychromatic Laue technique has been applied in 100 ps delay synchrotron pump–probe experiments of the triplet excited state of a Rh(I) dinuclear complex. The observed contraction of the Rh–Rh distance of 0.154 (13) Å is less than predicted by a series of theoretical calculations, a difference attributed to the constraining effect of the crystal lattice.
The accuracy achieved in single-pulse pump-probe Laue experiments at beamline 14-ID at APS is estimated to be 3–4%.
The accuracy that can be achieved in single-pulse pump-probe Laue experiments is discussed. It is shown that with careful tuning of the experimental conditions a reproducibility of the intensity ratios of equivalent intensities obtained in different measurements of 3–4% can be achieved. The single-pulse experiments maximize the time resolution that can be achieved and, unlike stroboscopic techniques in which the pump-probe cycle is rapidly repeated, minimize the temperature increase due to the laser exposure of the sample.
single-pulse diffraction; accuracy; Laue method; RATIO method; photo-crystallography
Excited-state geometries determined by time-resolved synchrotron diffraction are summarized with emphasis on their comparison with a series of theoretical results. The relative merits of monochromatic and polychromatic (Laue) techniques are discussed.
Definitive experimental results on the geometry of fleeting species are at the time of writing still limited to monochromatic data collection, but methods for modifications of the polychromatic Laue data to increase their accuracy and their suitability for pump–probe experiments have been implemented and are reviewed. In the monochromatic experiments summarized, excited-state conversion percentages are small when neat crystals are used, but are higher when photoactive species are embedded in an inert framework in supramolecular crystals. With polychromatic techniques and increasing source brightness, smaller samples down to tenths of a micrometre or less can be used, increasing homogeneity of exposure and the fractional population of the excited species. Experiments described include a series of transition metal complexes and a fully organic example involving excimer formation. In the final section, experimental findings are compared with those from theoretical calculations on the isolated species. Qualitative agreement is generally obtained, but the theoretical results are strongly dependent on the details of the calculation, indicating the need for further systematic analysis.
pump–probe experiments; time-resolved diffraction; excited-state molecular geometries; excimers
We report the direct observation of a bent geometry for a non-stabilized nitrile imine in a metal-coordination crystal. The photoinduced tetrazole ring rupture to release N2 appears to depend on the size of voids around the N3-N4 bond in the crystal lattice. We further observed the selective formation of 1,3-addition product when a reactive nitrile imine was photo-generated in water. Taken together, the bent nitrile imine geometry agrees with the 1,3-dipolar structure, a transient reactive species that mediates the photoinduced 1,3-dipolar cycloaddition in the aqueous medium.
The electrostatic component of the enzyme/inhibitor interaction of a wide range influenza neuraminidases and inhibitors has been analyzed using transferable aspherical-atom densities from a recently compiled databank. Results are subdivided into the contributions of individual active-site residues and different functional groups of the inhibitors, and the effect of the Arg292→Lys mutation is considered.
Although electrostatic interactions contribute only a part of the interaction energies between macromolecules, unlike dispersion forces they are highly directional and therefore dominate the nature of molecular packing in crystals and in biological complexes and contribute significantly to differences in inhibition strength among related enzyme inhibitors. In the reported study, a wide range of complexes of influenza neuraminidases with inhibitor molecules (sialic acid derivatives and others) have been analyzed using charge densities from a transferable aspherical-atom data bank. The strongest interactions of the residues are with the acidic group at the C2 position of the inhibitor (∼−300 kJ mol−1 for —COO− in non-aromatic inhibitors, ∼−120–210 kJ mol−1 for —COO− in aromatic inhibitors and ∼−450 kJ mol−1 for —PO3
2−) and with the amino and guanidine groups at C4 (∼−250 kJ mol−1). Other groups contribute less than ∼100 kJ mol−1. Residues Glu119, Asp151, Glu227, Glu276 and Arg371 show the largest variation in electrostatic energies of interaction with different groups of inhibitors, which points to their important role in the inhibitor recognition. The Arg292→Lys mutation reduces the electrostatic interactions of the enzyme with the acidic group at C2 for all inhibitors that have been studied (SIA, DAN, 4AM, ZMR, G20, G28, G39 and BCZ), but enhances the interactions with the glycerol group at C6 for inhibitors that contain it. This is in agreement with the lower level of resistance of the mutated virus to glycerol-containing inhibitors compared with the more hydrophobic derivatives.
electrostatic interaction energy; aspherical-atom databank; enzyme–substrate complexes; influenza neuraminidase
Corrigendum to Acta Cryst. (2007), E63, m2596.
The acknowledgement in the paper by Pearsal, Gembicky, Dominiak, Larsen & Coppens [Acta Cryst. (2007), E63, m2596] is extended and an omitted reference is added.
A RATIO method for analysis of intensity changes in time-resolved pump–probe Laue diffraction experiments is described.
A RATIO method for analysis of intensity changes in time-resolved pump–probe Laue diffraction experiments is described. The method eliminates the need for scaling the data with a wavelength curve representing the spectral distribution of the source and removes the effect of possible anisotropic absorption. It does not require relative scaling of series of frames and removes errors due to all but very short term fluctuations in the synchrotron beam.
Laue diffraction; time-resolved diffraction; ratio method; data reduction