Radosław Kamiński

Statistical analysis of multipole-model-derived structural parameters and charge-density properties from high-resolution X-ray diffraction experiments.

A comprehensive analysis of various properties derived from multiple high-resolution X-ray diffraction experiments is reported. A total of 13 charge-density-quality data sets of α-oxalic acid dihydrate (C2H2O4·2H2O) were subject to Hansen-Coppens-based modelling of electron density. The obtained parameters and properties were then statistically analysed yielding a clear picture of their variability across the different measurements. Additionally, a computational approach (CRYSTAL and PIXEL programs) was utilized to support and examine the experimental findings. The aim of the study was to show the real accuracy and interpretation limits of the charge-density-derived data. An investigation of raw intensities showed that most of the reflections (60-70%) fulfil the normality test and the lowest ratio is observed for weak reflections. It appeared that unit-cell parameters are determined to the order of 10(-3) Å (for cell edges) and 10(-2) ° (for angles), and compare well with the older studies of the same compound and with the new 100 K neutron diffraction data set. Fit discrepancy factors are determined within a 0.5% range, while the residual density extrema are about ±0.16 (3) e Å(-3). The geometry is very well reproducible between different data sets. Regarding the multipole model, the largest errors are present on the valence shell charge-transfer parameters. In addition, symmetry restrictions of multipolar parameters, with respect to local coordinate systems, are well preserved. Standard deviations for electron density are lowest at bond critical points, being especially small for the hydrogen-bonded contacts. The same is true for kinetic and potential energy densities. This is also the case for the electrostatic potential distribution, which is statistically most significant in the hydrogen-bonded regions. Standard deviations for the integrated atomic charges are equal to about 0.1 e. Dipole moments for the water molecule are comparable with the ones presented in various earlier studies. The electrostatic energies should be treated rather qualitatively. However, they are quite well correlated with the PIXEL results.

LASER - a program for response-ratio refinement of time-resolved diffraction data

The program LASER2010 is described. It is specifically designed for the refinement of externally induced structural changes in crystalline solids, including time-resolved laser-pump X-ray probe experiments. The refinement is based on the measured relative intensity changes rather than on the integrated reflection intensities.

CLUSTERGEN: a program for molecular cluster generation from crystallographic data

A new program, CLUSTERGEN, for molecular cluster generation is introduced. CLUSTERGEN provides the quantum mechanics/molecular mechanics (QM/MM) input files for program packages such as ADF [Baerends et al. (2012). Vrije Universiteit, Amsterdam, The Netherlands] and GAUSSIAN [Frisch et al. (2009). Gaussian Inc., Pittsburgh, Pennsylvania, USA]. Additionally, it prints out a standard CRYSTAL [Dovesi et al. (2009). University of Turin, Italy] input and, in general, facilitates file-format manipulation. The CLUSTERGEN program is supported by an extensive manual and a user-friendly graphical interface. The code is freely available and carefully commented, which makes it easily modifiable. Exemplary applications of CLUSTERGEN concerning QM/MM calculations and derivation of nucleus-independent chemical shift indices are demonstrated.

Data scaling and temperature calibration in time-resolved photocrystallographic experiments

Experiments in which structural changes in crystals are induced by pulsed-laser exposure involve an increase in sample temperature due to the dissipation of the deposited excess energy. The heat increase is especially pronounced when a large number of pulses is needed, as in pseudo-steady-state experiments conducted at conventional sources, but not negligible in synchrotron studies in which very short laser exposures may be adequate. The relative scaling of the light-ON and light-OFF data and the correction for temperature differences between the two sets are discussed.

An experimental charge density of HEPES.

We report the experimental charge density of HEPES [4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid], which is a common buffering agent. The structure was refined using the Hansen-Coppens formalism. The ability of the HEPES molecule to form stable intermolecular interactions and intermolecular hydrogen bonds in the crystal structure is discussed in terms of its buffering properties. The protonation mode observed in the crystal structure is different from that expected in solution, suggesting that additional factors must be taken into consideration in order to explain the solution properties of the compound. As ordered HEPES molecules are found in the active sites of proteins in several protein crystal structures, our results will allow for quantitative analysis of the electrostatic potential of the interacting surfaces of those proteins.

Shedding Light on the Photochemistry of Coinage-Metal Phosphorescent Materials: A Time-Resolved Laue Diffraction Study of an AgI–CuI 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.

Anharmonicity and isomorphic phase transition: a multi-temperature X-ray single-crystal and powder diffraction study of 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole

Multi-temperature single-crystal and powder diffraction experiments on 1-(2′-aminophenyl)-2-methyl-4-nitroimidazole show that this crystal undergoes an isomorphic phase transition with the coexistence of two phase domains over a wide temperature range. The anharmonic approach was the only way to model the resulting disorder.

On R factors for dynamic structure crystallography

In studies of dynamic changes in crystals in which induced metastable species may have lifetimes of microseconds or less, refinements are most sensitive if based on the changes induced in the measured intensities. Agreement factors appropriate for such refinements, based on the ratios of the intensities before and after the external perturbation is applied, are discussed and compared with R factors commonly applied in static structure crystallography.

Optimizing the accuracy and precision of the single-pulse Laue technique for synchrotron photo-crystallography.

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.

Macrocyclic Multicenter Complexes of Nickel and Copper of Increasing Complexity

Multicenter (bi-, tri-, and tetranuclear) tetraazamacrocyclic complexes were self-assembled from Ni and Cu tetraazamacrocyclic mononuclear units and α,ω-diamines as building blocks. The structures of all compounds studied were proved by spectroscopic methods (ESI MS and NMR spectroscopy). Electrochemical experiments revealed reversible one-electron electrode processes at each of the Ni(2+) and Cu(2+) centers with formation of metal cations in oxidation state +3. Long linkers allow bi- and trinuclear complexes with noninteracting metal centers to be obtained. In the case of the short linkers (e.g. ethylenediamine) higher, trinuclear species are formed as major product. The structures of the bis- and tris-macrocyclic systems were confirmed by single-crystal X-ray diffraction. The tris-macrocyclic systems form cations in the shape of triangles partially filled with counterions and solvent molecules. The cations form positively charged layers, which interact in the crystal lattice with the neighboring negatively charged layers of anions. In solution, the trinuclear complexes exhibit strong host-guest interactions with 9,10-dimethyltriptycene due to complementarity of shape and size of this guest molecule. The association constants were determined by NMR spectroscopy and voltammetry, and very good agreement was obtained. The structural flexibility of the tetranuclear complex with long linkers allows for attractive interactions between the metal-complexing macrocycles that result in folding of the molecule. On the contrary, no folding is possible in the case of short linkers consisting of two CH(2) groups.