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

Nanosecond-Lived Excimer Observation in a Crystal of a Rhodium(I) Complex via Time-Resolved X-ray Laue Diffraction

The rare observation of transient Rh···Rh excimer formation in a single crystal is reported. The estimated excited-state lifetime at 100 K is 2 ns, which makes it the shortest-lived small-molecule species caught experimentally using the laser-pump/X-ray-probe time-resolved Laue method. Upon excitation with 390 nm laser light, the intermolecular Rh···Rh distance decreases from 3.379(4) to 3.19(1) Å, and the metal-metal contact gains more bonding character. On the basis of the experimental results and theoretical modeling, the structural changes determined with 100 ps time resolution reflect principally the S0 → S1 electronic transition.

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.

Photocrystallographic Studies on Transition Metal Nitrito Metastable Linkage Isomers: Manipulating the Metastable State

The design of solid-state materials whose properties and functions can be manipulated in a controlled manner by the application of light is an important objective in modern materials chemistry. When the material changes property or function, it is helpful if a simple measurable response, such as a change in color, can be detected. Potential applications for such materials are wide ranging, from data storage to smart windows. With the growing emphasis on solid-state materials that have two or more accessible energy states and which exhibit bistability, attention has turned to transition metal complexes that contain ambidentate ligands that can switch between linkage isomeric forms when activated by light. Suitable ligands that show promise in this area include nitrosyls, nitro groups, and coordinated sulfur dioxide molecules, each of which can coordinate to a metal center in more than one bonding mode. A nitrosyl normally coordinates through its N atom (η¹-NO) but when photoactivated can undergo isomerism and coordinate through its O atom (η¹-ON). At a molecular level, converting between these two configurations can act as an “on/off” switch. The analysis of such materials has been aided by the development of photocrystallographic techniques, which allow the full three-dimensional structure of a single crystal of a complex, under photoactivation, to be determined, when it is in either a metastable or short-lived excited state. The technique effectively brings the dimension of “time” to the crystallographic experiment and brings us closer to being able to watch solid-state processes occur in real time.

In this Account, we highlight the advances made in photocrystallography for studying solid-state, photoactivated linkage isomerism and describe the factors that favor the switching process and which allow complete switching between isomers. We demonstrate that control of temperature is key to achieving either a metastable state or an excited state with a specific lifetime. We draw our conclusions from published work on the formation of photoactivated metastable states for nitrosyl and sulfur dioxide complexes and from our own work on photoactivated switching between nitro and nitrito groups. We show that efficient switching between isomers is dependent on the wavelength of light used, on the temperature at which the experiment is carried out, on the flexibility of the crystal lattice, and on both the electronic and steric environment of the ambidentate ligand undergoing isomerism. We have designed and prepared a number of nitro/nitrito isomeric metal complexes that undergo reversible 100% conversion between the two forms at temperatures close to room temperature. Through our fine control over the generation of the metastable states, it should be possible to effectively “dial up” a suitable temperature to give a metastable or an excited state with a desired lifetime.

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.

Using Spectral Representation to Classify Proteins' Conformational States

Numerous proteins are molecular targets for drug action and hence are important in drug discovery. Structure-based computational drug discovery relies on detailed information regarding protein conformations for subsequent drug screening in silico. There are two key issues in analyzing protein conformations in virtual screening. The first considers the protein’s conformational change in response to physical and chemical conditions. The second is the protein’s atomic resolution reconstruction from X-ray crystallography or nuclear magnetic resonance (NMR) data. In this latter problem, information is needed regarding the sample’s position relative to the source of X-rays. Here, we introduce a new measure for classifying protein conformational states using spectral representation and Wigner’s D-functions. Predictions based on the new measure are in good agreement with conformational states of proteins. These results could also be applied to improve conformational alignment of the snapshots given by protein crystallography.

The dramatic development of X-ray photocrystallography over the past six decades

A short description of some of the paradigm-changing developments of the study of light-induced structural changes in molecular crystals is presented. The review is by no means comprehensive. The extensive literature on the subject should be consulted for further information.

Ultrafast X-Ray Crystallography and Liquidography

Time-resolved X-ray diffraction provides direct information on three-dimensional structures of reacting molecules and thus can be used to elucidate structural dynamics of chemical and biological reactions. In this review, we discuss time-resolved X-ray diffraction on small molecules and proteins with particular emphasis on its application to crystalline (crystallography) and liquid-solution (liquidography) samples. Time-resolved X-ray diffraction has been used to study picosecond and slower dynamics at synchrotrons and can now access even femtosecond dynamics with the recent arrival of X-ray free-electron lasers.

Application of advanced X-ray methods in life sciences

BACKGROUND

Synchrotron radiation (SR) sources provide diverse X-ray methods for the investigation of structure-function relationships in biological macromolecules.

SCOPE OF REVIEW

Recent developments in SR sources and in the X-ray tools they offer for life sciences are reviewed. Specifically, advances in macromolecular crystallography, small angle X-ray solution scattering, X-ray absorption and fluorescence spectroscopy, and imaging are discussed with examples.

MAJOR CONCLUSIONS

SR sources offer a range of X-ray techniques that can be used in a complementary fashion in studies of biological systems at a wide range of resolutions from atomic to cellular scale. Emerging applications of X-ray techniques include the characterization of disordered proteins, noncrystalline and nonequilibrium systems, elemental imaging of tissues, cells and organs, and detection of time-resolved changes in molecular structures.

GENERAL SIGNIFICANCE

X-ray techniques are in the center of hybrid approaches that are used to gain insight into complex problems relating to biomolecular mechanisms, disease and possible therapeutic solutions. This article is part of a Special Issue entitled "Science for Life". Guest Editors: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.

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.

Using synchrotrons and XFELs for time-resolved X-ray crystallography and solution scattering experiments on biomolecules

Time-resolved structural information is key to understand the mechanism of biological processes, such as catalysis and signalling. Recent developments in X-ray sources as well as data collection and analysis methods are making routine time-resolved X-ray crystallography and solution scattering experiments a real possibility for structural biologists. Here we review the information that can be obtained from these techniques and discuss the considerations that must be taken into account when designing a time-resolved experiment.