High-pressure Single-crystal Diffraction Research Articles

High-pressure single-crystal diffraction at the ANSTO Australian Synchrotron

High-pressure single-crystal diffraction at the ANSTO Australian Synchrotron

High-pressure single-crystal diffraction at the Australian Synchrotron.

A new high-pressure single-crystal diffraction setup has been designed and implemented at the Australian Synchrotron for collecting molecular and protein crystal structures. The setup incorporates a modified micro-Merrill-Bassett cell and holder designed specifically to fit onto the horizontal air-bearing goniometer, allowing high-pressure diffraction measurements to be collected with little to no modification of the beamline setup compared with ambient data collections. Compression data for the amino acid, L-threonine, and the protein, hen egg-white lysozyme, were collected, showcasing the capabilities of the setup.

High-Pressure Structural Behavior of para-Xylene

A high-pressure neutron powder diffraction study was conducted on perdeuterated para-xylene (C8D10). para-Xylene crystallizes in the monoclinic crystal system (space group P21/n) at ambient temperature and ca. 0.1 GPa. The structure is consistent with the known low-temperature form. No further phase transitions were observed in the pressure range 0.11(1)–4.72(2) GPa. A complementary high-pressure single-crystal diffraction experiment was performed on hydrogenous para-xylene confirming the assigned space group P21/n. An isothermal equation of state was obtained [bulk modulus, B0 = 3.5(4) GPa] and structural changes of the material have been investigated as a function of pressure. This experimental study is supported by dispersion-corrected density functional theory calculations.

Mapping completeness.

Tchoń & Makal [IUCrJ (2021), 8, 1006-1017] use numerical simulations to explore the dependence of data completeness on crystal orientation, X-ray energy and diamond anvil cell geometry for high-pressure diffraction experiments. Their completeness heat maps for different Laue classes can be used to guide optimization of high-pressure single-crystal diffraction experiments.

High-Pressure Crystallography as a Guide in the Design of Single-Molecule Magnets.

Single-molecule magnet materials owe their function to the presence of significant magnetic anisotropy, which arises from the interplay between the ligand field and spin-orbit coupling, and this is responsible for setting up an energy barrier for magnetic relaxation. Therefore, chemical control of magnetic anisotropy is a central challenge in the quest to synthesize new molecular nanomagnets with improved properties. There have been several reports of design principles targeting such control; however, these principles rely on idealized geometries, which are rarely obtained in crystal structures. Here, we present the results of high-pressure single-crystal diffraction on the single-ion magnet, Co(SPh)4(PPh4)2, in the pressure range of 0-9.2 GPa. Upon pressurization a sequence of small geometrical distortions of the central CoS4 moeity are observed, enabling a thorough analysis of the magneto-structural correlations. The magneto-structural correlations are investigated by theoretical analyses of the pressure-dependent experimental molecular structures. We observed a significant increase in the magnitude of the zero-field splitting parameter D, from -54.6 cm-1 to -89.7 cm-1, which was clearly explained from the reduction of the energy difference between the essential dxy and dx2-y2 orbitals, and structurally assigned to the change of an angle of compression of the CoS4 moeity.

Pressure-and temperature induced phase transitions, piezochromism, NLC behaviour and pressure controlled Jahn-Teller switching in a Cu-based framework.

In situ single-crystal diffraction and spectroscopic techniques have been used to study a previously unreported Cu-framework bis[1-(4-pyridyl)butane-1,3-dione]copper(ii) (CuPyr-I). CuPyr-I was found to exhibit high-pressure and low-temperature phase transitions, piezochromism, negative linear compressibility, and a pressure induced Jahn–Teller switch, where the switching pressure was hydrostatic media dependent.

Low-pressure ferroelastic phase transition in rutile-type AX2 minerals: cassiterite (SnO2), pyrolusite (MnO2) and sellaite (MgF2)

The structural behaviour of cassiterite (SnO2), pyrolusite (MnO2) and sellaite (MgF2), i.e. AX2-minerals, has been investigated at room temperature by in situ high-pressure single-crystal diffraction, up to 14 GPa, using a diamond anvil cell. Such minerals undergo a ferroelastic phase transition, from rutile-like structure (SG: P42/mnm) to CaCl2-like structure (SG: Pnnm), at ≈ 10.25, 4.05 and 4.80 GPa, respectively. The structural evolution under pressure has been described by the trends of some structure parameters that are other than zero in the region of the low-symmetry phase’s stability. In particular, three tilting-angles (ω, ω′, ABS) and the metric distortion of the cation-centred octahedron (quantified via the difference between apical-anion and equatorial-anion distances Δ|Xax−Xeq|) are used to express the atoms’ readjustment, i.e. relaxation, taking place in the CaCl2-like structures under pressure. The crystallographic investigation presented is complemented with an analysis of the energy involved in the phase transition using the Landau formalism and adopting the following definition for the order parameter: Q = η11–η22, ηij being the spontaneous strain tensor. The dependence of ω, ω′, ABS and Δ|Xax−Xeq| on Q allows determination of a correlation between geometrical deformation parameter and energy. Lastly, the relaxation mechanisms that exploits ω, ω′, ABS and Δ|Xax−Xeq| may be related to the ionic degree of bonding, the latter modelled via quantum mechanics and Bader theory. Sellaite, the mineral exhibiting the highest degree of ionic bonding among those investigated, tends to accomplish relaxation through pure rotation of the octahedron, rather than a metric distortion (Δ|Xax−Xeq|), which would shorten inter-atomic distances thus increasing repulsion between anions.

A high-pressure single-crystal-diffraction experimental system at 4W2 beamline of BSRF.

Information on the structural evolution of materials under high pressure is of great importance for understanding the properties of materials exhibited under high pressure. High-pressure powder diffraction is widely used to investigate the structure evolution of materials at such pressure. Unfortunately, powder diffraction data are usually insufficient for retrieving the atomic structures, with high-pressure single-crystal diffraction being more desirable for such a purpose. Here, a high-pressure single-crystal diffraction experimental system developed recently at beamline 4W2 of Beijing Synchrotron Radiation Facility (BSRF) is reported. The design and operation of this system are described with emphasis on special measures taken to allow for the special circumstance of high-pressure single-crystal diffraction. As an illustration, a series of diffraction datasets were collected on a single crystal of LaB6 using this system under various pressures (from ambient pressure to 39.1 GPa). The quality of the datasets was found to be sufficient for structure solution and subsequent refinement.

High Pressure Single Crystal Diffraction at PX^2.

In this report we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell (DAC) at the GSECARS 13-BM-C beamline at the Advanced Photon Source. The DAC program at 13-BM-C is part of the Partnership for Extreme Xtallography (PX^2) project. BX-90 type DACs with conical-type diamond anvils and backing plates are recommended for these experiments. The sample chamber should be loaded with noble gas to maintain a hydrostatic pressure environment. The sample is aligned to the rotation center of the diffraction goniometer. The MARCCD area detector is calibrated with a powder diffraction pattern from LaB6. The sample diffraction peaks are analyzed with the ATREX software program, and are then indexed with the RSV software program. RSV is used to refine the UB matrix of the single crystal, and with this information and the peak prediction function, more diffraction peaks can be located. Representative single crystal diffraction data from an omphacite (Ca0.51Na0.48)(Mg0.44Al0.44Fe2+0.14Fe3+0.02)Si2O6 sample were collected. Analysis of the data gave a monoclinic lattice with P2/n space group at 0.35 GPa, and the lattice parameters were found to be: a = 9.496 ±0.006 Å, b = 8.761 ±0.004 Å, c = 5.248 ±0.001 Å, β = 105.06 ±0.03º, α = γ = 90º.

High Pressure Single Crystal Diffraction at PX^2

In this report we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell (DAC) at the GSECARS 13-BM-C beamline at the Advanced Photon Source. The DAC program at 13-BM-C is part of the Partnership for Extreme Xtallography (PX^2) project. BX-90 type DACs with conical-type diamond anvils and backing plates are recommended for these experiments. The sample chamber should be loaded with noble gas to maintain a hydrostatic pressure environment. The sample is aligned to the rotation center of the diffraction goniometer. The MARCCD area detector is calibrated with a powder diffraction pattern from LaB6. The sample diffraction peaks are analyzed with the ATREX software program, and are then indexed with the RSV software program. RSV is used to refine the UB matrix of the single crystal, and with this information and the peak prediction function, more diffraction peaks can be located. Representative single crystal diffraction data from an omphacite (Ca0.51Na0.48)(Mg0.44Al0.44Fe2+0.14Fe3+0.02)Si2O6 sample were collected. Analysis of the data gave a monoclinic lattice with P2/n space group at 0.35 GPa, and the lattice parameters were found to be: a = 9.496 ±0.006 Å, b = 8.761 ±0.004 Å, c = 5.248 ±0.001 Å, β = 105.06 ±0.03º, α = γ = 90º.

High pressure single-crystal synchrotron X-ray diffraction technique

A lot of great work has been done since the high pressure research carried out on synchrotron radiation facility almost 40 years ago. The history of high pressure single-crystal diffraction research on synchrotron radiation facility has also been more than 20 years. Recently, with the development of synchrotron X-ray optical techniques and high pressure technology, especially the invention and improvement of large opening diamond anvil cell (DAC), high pressure single-crystal X-ray diffraction (HPSXRD) method has become more and more popular in high pressure studies. The HPSXRD can be used to perform structure determination and refinement to obtain the information about lattice parameter, space group, atomic coordinate and site occupation. Compared with powder X-ray diffraction, the HPSXRD can not only obtain the three-dimensional diffraction information of samples, but also have much better signal-to-noise ratio. Furthermore, the HPSXRD data can be used to study the electron density distribution to obtain more information about chemical bonds and electron distribution. In this work, we introduce the HPSXRD method in synchrotron radiation facilities, including the knowledge of single-crystal X-ray diffraction experimental system, DAC for HPSXRD, sample loading, and HPSXRD data processing.

Determining complex crystal structures from high pressure single-crystal diffraction data collected on synchrotron sources

As part of a Long Term Project, single-crystal diffraction techniques have been developed for use at the high pressure beamlines ID09 and ID27 at the European Synchrotron Radiation Facility, and have been utilised to determine the crystal structures of various high pressure phases, including those with incommensurate structures, at both high and low temperatures. The same techniques have also been used to determine the structures of high pressure phases at the SRS, Diamond and Petra-III synchrotron sources. In this paper, we describe technical details of the methods developed, and describe some of the considerations necessary for planning experiments and collecting and processing the data. We then illustrate the quality of data that can be obtained, and the complexity of the structures that can be refined, using recent results obtained from complex high pressure phases of N2 and Ba.

Indexing of multi-particle diffraction data in a high-pressure single-crystal diffraction experiment

High-pressure single-crystal diffraction experiments often suffer from the crushing of single crystals due to the application of high pressure. Consequently, only diffraction data resulting from several particles in random orientations is available, which cannot be routinely indexed by commonly used methods designed for single-crystal data. A protocol is proposed to index such diffraction data. The techniques of powder pattern indexing are first used to propose the possible lattice parameters, and then a genetic algorithm is applied to determine the orientation of the reciprocal lattice for each of the particles. This protocol has been verified experimentally.

High pressure studies of metal organic framework materials

This paper gives a brief overview of our recent work in the field of high pressure structural studies of metal organic framework materials. These are nanoporous materials which have found widespread application in the fields of gas separation and storage. Pressure provides a convenient tool to modify pore size and content without the need to alter the material chemically. Our techniques (high pressure single crystal diffraction and density functional theory) have allowed us to determine how the molecular frameworks change as a function of external pressure. The results have been surprising.

Compressibility of protoamphibole: A high-pressure single-crystal diffraction study of protomangano-ferro-anthophyllite

The high-pressure behavior of protoamphibole (space group Pnmn) was studied by in situ singlecrystal X-ray diffraction on a sample of protomangano-ferro-anthophyllite with formula (Mn 1.39 Fe 0.59 ) (Fe 3.98 Mg 1.02 )Si 8 O 22 (OH) 2 , from Yokone-Yama, Awano Town, Tochigi Prefecture, Japan. Unit-cell parameters were collected at various pressures up to 9 GPa, and structural refinements were obtained from data collected at several pressures up to 7 GPa. Fitting the P-V data to a third-order Birch- Murnaghan equation of state (EoS) gives the following parameters: K T0 = 64(1) GPa, K′ = 7.0(4), and V 0 = 926.4(4) Å 3 . Axial moduli are: K 0a = 30.7(8) GPa, K′ a = 10.8(5), and a 0 = 9.430(2) Å; K 0b = 109(4) GPa, K′ b = 2.7(8), and b 0 = 18.364(4) Å; K 0c = 94(5), GPa, K′ c = 4(1), and c 0 = 5.354(2) Å. The corresponding axial compressibilities (10 -3 GPa -1 ) are β a = 10.9(3), β b = 3.1(1), and β c = 3.5(2), and indicate that the HP behavior of protomangano-ferro-anthophyllite is highly anisotropic, the highest compressibility being along [100]. No discontinuous behavior or polymorphic transitions were observed in the pressure range studied. Structural refinements show that M1, M2, and M3 polyhedra have similar compressibilities, owing to their similar composition. M4 (72% Mn, 28% Fe) is a highly distorted site and is slightly softer than the other octahedra. The major movements in the tetrahedral ribbon concern kinking of the double chain, bending along the [100] direction through the empty A site, and tetrahedral rotation, necessary to maintain coherence with the octahedral layer. The kinking angle of O5-O6-O5, which in air is 179.1(2)°, decreases to 174(2)° at 6.9 GPa. The T1-O7-T1 angle changes from 143.8(3)° to 134(5)° at 6.9 GPa, and the tetrahedral rotation α increases from 0.2(2)° to 4(2)°.

Estimation of polyhedral compressibilities and structural evolution of GdFeO3-type perovskites at high pressures

A new approach based on the bond-valence matching relation is developed to predict the detailed structural evolution of GdFeO(3)-type perovskites at high pressure from knowledge of the room-pressure structure and the high-pressure unit-cell parameters alone. The evolution of perovskite structures estimated in this way is in good agreement with the structure refinements available from high-pressure single-crystal diffraction measurements of a number of perovskites. The method is then extended to predict the structure of MgSiO(3) perovskite at pressures for which no single-crystal structural data are available and the results are compared to ab initio quantum calculations of MgSiO(3) perovskite up to 120 GPa.

Rigid unit modes at high pressure: an explorative study of a fibrous zeolite-like framework with EDI topology

We report a comparative study on the high pressure (HP) structural behaviour of a fibrous zeolite (with EDI topology) on the basis of rigid unit modes (RUM) modelling and previously published single-crystal X-ray diffraction. HP single-crystal diffraction data lead to a more precise determination of the elastic parameters (axial and volume compressibilities) useful to define the equation-of-state under isothermal conditions, and the structural refinements are useful to describe the main deformation mechanisms of the Si/Al framework and extra-framework content at high pressure. The RUM modelling is applied to simulate the compressive behaviour of the framework, under hydrostatic and non-hydrostatic conditions, using a minimum number of parameters, and to describe the deformation mechanism intuitively in terms of the rotations of the SiO4 polyhedra. The local and global P-induced deformation mechanisms of the Si/Al framework observed in experiment (channel ellipticity, SBU rotation) are well reproduced by RUM modelling. The simulation of uniaxial compression (non-hydrostatic conditions) shows an interesting result on the structural behaviour. This comparative study tests the reliability of the RUM modelling in open-framework silicates with a complicated crystal structure.

NEW INSTRUMENTATION FOR HIGH-PRESSURE SINGLE CRYSTAL DIFFRACTION AT ISIS

The newly installed, much-improved single-crystal diffractometer, SXD at ISIS, received its first neutrons in May 2001. The detector area now covers slightly more than 2re steradians in solid angle. High-pressure research using single crystals is becoming an increasingly important part of the user programme and thus, efforts are underway to provide a new sample environment as well as state-of-the-art data analysis software to open new opportunities in high-pressure single-crystal diffraction. Recently, a new gas-pressure cell with pressures up to 0.5 GPa has been successfully commissioned. First results from a series of molecular compounds containing short hydrogen bonds are presented. More recent developments at ISIS include a sapphire anvil cell for pressures up to 8 GPa, which has been successfully tested on the GEM powder diffractometer. It will shortly also be tested on SXD, as well as a modified Paris-Edinburgh cell to take 5-l5mm3 single-crystal samples to pressures of more than lOGPa.

High-pressure single-crystal X-ray diffraction facilities on station 9.8 at the SRS Daresbury Laboratory--hydrogen location in the high-pressure structure of ethanol.

A new high-pressure single-crystal diffraction facility has been constructed on station 9.8 at the Synchrotron Radiation Source, Daresbury Laboratory, for a range of studies on a variety of systems of relevance to physics, chemistry and materials science that would otherwise prove intractable with conventional laboratory-based methods. The station has been equipped with a modified Enraf-Nonius CAD4 four-circle diffractometer for high-pressure studies which can be conveniently, and rapidly, interchanged with the Bruker SMART CCD area-detector system when more routine ambient-pressure diffraction work is to be undertaken. This rapid change-over has been achieved by permanently mounting the CAD4 on its own jacking table, formerly used for the station's white-beam diffraction mode, which allows the alignment of the SMART diffractometer to remain undisturbed when the CAD4 is in use. Early results on the test low-melting-point compound ethanol (CH3CH2OH) reveal that excellent refined structures can be obtained, including the location and refinement of the H atoms, demonstrating that one of the original, and major, objectives of the station has been accomplished.

Compression of cadmium orthosilicate, Cd2SiO4: a high-pressure single-crystal diffraction study

AbstractThe compression of cadmium orthosilicate, Cd2SiO4, was studied by high-pressure single-crystal diffraction carried out in a diamond-anvil cell. The equation of state at room temperature (third-order Birch-Murnaghan:V0= 695.71(3) Å3,K0.298= 119.2(5) GPa,K′ = = 6.17(4)) was determined from unit-cell volume data to 9.51 GPa. Compression of the orthorhombic structure (Fddd,Z= 8) was found to be anisotropic with relative compressibilities of 2.10:1.00:4.77 for thea,b, andcaxes. The variation of the lattice parameters with pressure is described by:a/a0= 0.99989(7) − 3.10(3) × × 10−GPa−1×P+ 8.2(3) × 10−5GPa−2×P2;b/b0= = 1.00007(8) − 8.8(9) × l0−2GPa−1×P;c/c0= 1.00001(5) − 4.16(3) × 10−3GPa−1×P+ 6.5(2) × 10−5GPa−2×P2. Crystal structures were determined at pressures of 3.01 GPa, 5.44 GPa, and 8.69 GPa. The anisotropy of the unit-cell compression is controlled by the distortion of the CdO6and SiO4polyhedra due to their unusual interconnection through shared edges. Cation-cation repulsion between Cd and Si atoms, which results in short and long Cd–O bonds, was found also to be responsible for unusual compressional behaviour related to the strength of the bond: the shorter the Cd–O bond the higher its compressibility. The large uniaxial distortion of the silicate tetrahedron is responsible for the relatively higher compressibility along thecaxis. The compressional differences between theaandbaxis result from the compressional anisotropy of the CdO6octahedron.