Harriott Nowell

I19, the small-molecule single-crystal diffraction beamline at Diamond Light Source.

The dedicated small-molecule single-crystal X-ray diffraction beamline (I19) at Diamond Light Source has been operational and supporting users for over three years. I19 is a high-flux tunable-wavelength beamline and its key details are described in this article. Much of the work performed on the beamline involves structure determination from small and weakly diffracting crystals. Other experiments that have been supported to date include structural studies at high pressure, studies of metastable species, variable-temperature crystallography, studies involving gas exchange in porous materials and structural characterizations that require analysis of the diffuse scattering between Bragg reflections. A range of sample environments to facilitate crystallographic studies under non-ambient conditions are available as well as a number of options for automation. An indication of the scope of the science carried out on the beamline is provided by the range of highlights selected for this paper.

Methyl group librations in sterically hindered dimethylnaphthalene molecules: neutron diffraction studies of 1,8-dimethylnaphthalene between 50 and 200 K

The structure of 1,8-dimethylnaphthalene has been studied by variable temperature single crystal neutron diffraction. The location of the two methyl groups on the same side of the naphthalene ring leads to substantial steric effects, notably a hindering of the methyl group librations. This steric effect appears to dominate over the alternative possibility of coupled motions of these groups. The results are compared directly with those from the related compound n 1,5-dimethylnaphthalene where there is no possibility of methyl group coupled motions, but also less severe steric hindrance.

ExtSym: a program to aid space‐group determination from powder diffraction data

Once unit-cell dimensions have been determined from a powder diffraction data set and therefore the crystal system is known (e.g. orthorhombic), the method presented by Markvardsen, David, Johnson & Shankland [Acta Cryst. (2001), A57, 47-54] can be used to generate a table ranking the extinction symbols of the given crystal system according to probability. Markvardsen et al. tested a computer program (ExtSym) implementing the method against Pawley refinement outputs generated using the TF12LS program [David, Ibberson & Matthewman (1992). Report RAL-92-032. Rutherford Appleton Laboratory, Chilton, Didcot, Oxon, UK]. Here, it is shown that ExtSym can be used successfully with many well known powder diffraction analysis packages, namely DASH [David, Shankland, van de Streek, Pidcock, Motherwell & Cole (2006). J. Appl. Cryst. 39, 910-915], FullProf [Rodriguez-Carvajal (1993). Physica B, 192, 55-69], GSAS [Larson & Von Dreele (1994). Report LAUR 86-748. Los Alamos National Laboratory, New Mexico, USA], PRODD [Wright (2004). Z. Kristallogr. 219, 1-11] and TOPAS [Coelho (2003). Bruker AXS GmbH, Karlsruhe, Germany]. In addition, a precise description of the optimal input for ExtSym is given to enable other software packages to interface with ExtSym and to allow the improvement/modification of existing interfacing scripts. ExtSym takes as input the powder data in the form of integrated intensities and error estimates for these intensities. The output returned by ExtSym is demonstrated to be strongly dependent on the accuracy of these error estimates and the reason for this is explained. ExtSym is tested against a wide range of data sets, confirming the algorithm to be very successful at ranking the published extinction symbol as the most likely

Crystal engineering urea organic acid hydrogen bonded networks with solvent inclusion properties

Nine hydrogen bonded networks of N-phenylurea and 5-nitroisophthalic acid, with solvent inclusion properties, have been engineered and their thermal stabilities studied. Solvent guests of methanol, ethanol, acetonitrile, acetone, THF, ethyl acetate and water have been included into the hydrogen bonded host networks in pockets and channels via interaction with a carboxylic acid group of the host. Two non-solvated N-phenylurea 5-nitroisophthalic acid complexes (NS1 2:1 and NS2 1:1) were also formed. Thermal studies of the inclusion materials revealed guest release and conversion to NS1, in all but one case, and conversion of one non-solvated form to the other (NS2 to NS1). The carboxylic acid:amide hydrogen bond synthon R22(8) was shown to be a robust synthon for network formation whilst guest molecules are suggested to have a role in templating the overall network geometry.

Facilities for small-molecule crystallography at synchrotron sources

Although macromolecular crystallography is a widely supported technique at synchrotron radiation facilities throughout the world, there are, in comparison, only very few beamlines dedicated to small-molecule crystallography. This limited provision is despite the increasing demand for beamtime from the chemical crystallography community and the ever greater overlap between systems that can be classed as either small macromolecules or large small molecules. In this article, a very brief overview of beamlines that support small-molecule single-crystal diffraction techniques will be given along with a more detailed description of beamline I19, a dedicated facility for small-molecule crystallography at Diamond Light Source.

Multiple-data-set Rietveld analysis using isotopes in powder neutron diffraction. 2. Positional and anisotropic thermal displacement parameter determinations in CuO (tenorite) at 2 K and 300 K

The technique of isotope-substitution neutron diffraction (ISND) and combined-data-set Rietveld analysis from powder neutron data of crystalline materials is presented and compared with single-data-set powder refinement methods. The rationale behind improvements in the precision and accuracy of the refined model as a result of reduction in parameter correlation in the least-squares technique is described. The improvements are demonstrated practically through a study of isotopically copper-substituted tenorite, CuO, at 2 and 300 K. Typically, the estimated errors on structural parameters from the combined analysis technique are 30% lower than separate single-data-set analyses. Comparison of the precision and accuracy of the structural models obtained from this investigation with previous single-crystal X-ray studies are also presented.

Tuning charge-assisted and weak hydrogen bonds in molecular complexes of the proton sponge DMAN by acid co-former substitution

Nine new molecular complexes of the proton sponge 1,8-bis(dimethylamino)naphthalene (DMAN) with substituted benzoic acid co-formers have been engineered with varying component stoichiometries (1u2006:u20061, 1u2006:u20062 or 1u2006:u20063). These complexes are all ionic in nature, following proton transfer between the acid co-former and DMAN; the extracted proton is held by DMAN in all instances in an intramolecular [N–H⋯N]+ hydrogen bond. A number of structural features are common to all complexes and are found to be tunable in a predictable way using systematic acid co-former substitution. These features include charge-assisted hydrogen bonds formed between acid co-formers in hydrogen bonding motifs consistent with complex stoichiometry, and weak hydrogen bonds which facilitate the crystal packing of DMAN and acid co-former components into a regular motif. Possible crystal structure tuning by co-former substitution can aid the rational design of such materials, offering the potential to target solid-state properties that may be influenced by these interactions.

0.48 Angstrom 3,5-Dinitrobenzoic Acid (3,5-Dnba) C2/C Polymorph Single Crystal X-Ray Diffraction Data Set Recorded At Diamond Light Source I19-1

Data set from 3,5-dinitrobenzoic acid (3,5-DNBA) C2/c polymorphxa0recorded during in house research (DLS proposal: NR18193). Each run is saved as a single compressed tar file for convenience, runs 1, 2, 3 correspond to 3 x 170 degree omega scans at phi 0, 120, 240 degrees with 2-theta of 30 degrees, run 4 phi scan at 2-theta 0, runs 5-8 omega scans at 2-theta 55 degrees, giving data to 0.48A.nnxa0nnNow including scale factor graph & report from processing

Imaging H-atom behaviour on I19, Diamond Light Source

The short data collection times in the recently upgraded experiments hutch 1 (EH1) equipped with a Pilatus 2M detector provides potential for the study of finer detail of crystal structure and its evolution; either as a function of an external variable, such as temperature, or across a set of related materials. In particular, the evolving behaviour of hydrogen atoms (H-atoms) across hydrogen bonds is of interest, enabling charge and energy transfer in a range of biological and chemical systems. [1] The study of this behaviour therefore allows insight into how it may be targeted and tuned in future materials.

Single crystal synchrotron X-ray diffraction for imaging hydrogen bond evolution

Hydrogen bonding is a valuable intermolecular interaction in “engineering” solid-state materials. This is because of the directionality and relative strength (1) of these bonds. Hydrogen bonds enable charge and energy transfer, via H-bond evolution, in a range of biological and chemical systems (2). Recent work has demonstrated that single crystal X-ray diffraction can be used to image the evolution of hydrogen bonds, including variable temperature proton migration and proton disorder processes. In particular, in a recent study of the temperature dependent proton disorder in hydrogen bonded 3,5-dinitrobenzoic acid (3,5-DNBA) dimers, the proton disorder deduced from data collected on an X-ray laboratory source is in agreement with that found from neutron data (3). This work focuses on variable temperature single crystal synchrotron X-ray diffraction, for the imaging of evolving hydrogen bonds. The development of appropriate methodology is important here, particularly as previous studies have involved laboratory X-ray sources only. Results will be presented from variable temperature data collections on I19, at the Diamond Light Source, and on beamline 11.3.1, at the Advanced Light Source (ALS), on systems such as 3,5-DNBA and co-crystals of benzimidazole, both exhibiting proton disorder across hydrogen bonding interactions. Synchrotron X-ray diffraction measurements have also been used to follow the change in the position of a proton within an intramolecular [N—H•••N]+ hydrogen bond across a range of proton-sponge molecular complexes. Importantly, it has been possible to visualise the evolving hydrogen atom position in Fourier difference electron density maps generated from the synchrotron data. In particular, for the 35-DNBA study, the clearest picture of the evolving hydrogen atom position is observed in those generated from data collected at the ALS; even clearer than that observed in X-ray laboratory and neutron measurements on the same system.