High-pressure Crystallography Research Articles

The Ambiguous Origin of Thermochromism in Molecular Crystals of Dichalcogenides: Chalcogen Bonds versus Dynamic Se─Se/Te─Te Bonds.

We report thermochromism in crystals of diphenyl diselenide (dpdSe) and diphenyl ditelluride (dpdTe), which is at variance with the commonly known mechanisms of thermochromism in molecular crystals. Variable temperature neutron diffraction studies indicated no conformational change, tautomerization or phase transition between 100 K and 295 K. High-pressure crystallography studies indicated no associated piezochromism in dpdSe and dpdTe crystals. The evolution of the crystal structures and their electronic band structure with pressure and temperature reveal the contributions of intramolecular and intermolecular factors towards the origin of thermochromism - especially the intermolecular Se⋅⋅⋅Se and Te⋅⋅⋅Te chalcogen bonds and torsional modes of vibrations around the dynamic Se─Se and Te─Te bonds. Further, a co-crystal of dpdSe with iodine (dpdSe-I2) and an alloy crystal of dpdSe and dpdTe implied a predominantly intramolecular origin of the observed thermochromism associated with vibronic coupling.

High-pressure research and crystallography: the great unification

High-pressure research and crystallography: the great unification

The Promise and Challenge of High Pressure Macromolecular Crystallography

Since its introduction in the early 1970s, high pressure crystallography (HPX) has shown great potential for the investigation of different types of matter. Using diamond anvil cells, HPX is an emerging technique that has been rapidly implemented, making it available to biologists, and there is immense potential for utilizing this technique in biological systems in the future. At the molecular level, high-pressure crystallographic investigation provides information on structural characteristics that not only determine the native conformation of a protein but also the conformations with higher free-energy, thus revealing function-related structural changes and properties that can be modified as a result of pressurization. The increase in the number of crystal structures of different macromolecules determined under high pressure over the last five decades can be ascribed mainly to two factors: the emergence of high-pressure cells with very large, open angles, and the advent of third generation synchrotron sources. The use of high pressure crystallography as a research tool has been shown to contribute to the advancements in the basic fields of biochemistry (protein misfolding and aggregation), biophysics (protein stability), and biotechnology (food processing). Presently, with a growing interest in biomedicine and nanotechnology, this nonstandard method appears to be a valid instrument for probing more challenging and complex systems. In this review, we present the method, highlight a selection of recent applications, and describe challenges for high pressure macromolecular crystallography (HPMX).

Coordination Sphere Flexibility Leads to Elastic Deformation in a One-Dimensional Coordination Polymer Crystal

Coordination polymers exhibiting mechanical flexibility including elastic or plastic bending are rare. Here, we report an example of a mechanically flexible one-dimensional coordination polymer that shows elastic bending. Quantitative insights on the inter and intra-chain bonding as well as structural flexibility from a combination of techniques including variable temperature single crystal X-ray diffraction (XRD), high-pressure crystallography (ambient─15 GPa), synchrotron micro-XRD mapping of the bent crystal, and high-resolution synchrotron X-ray charge density analysis show that the helical coordination polymer behaves like a spring when subjected to external stimuli. Changes that occur with the variation of temperature, pressure, or bending, however, result in very different mechanistic changes. The exceptional coordination sphere flexibility rendered by the presence of Jahn–Teller distorted coordination bonds leads to the flexibility of the polymer.

Hierarchy of Intermolecular Interactions in Highly Luminescent Pyrenyl-Pyrazole-Aldehyde

The intricacies of the crystal structure and the hierarchy of intermolecular interactions in a highly luminescent pyrene-pyrazole-aldehyde (PPPcA) are hereby analyzed by means of experimental charge density analysis, periodic DFT calculations, and high-pressure crystallography. Luminescent properties of the material under pressure up to 6 GPa are reported. Several intermolecular interactions in the crystal structure of PPPcA are identified and found to be significant based on their energies and mechanical properties of the material, a pair of C–H···O hydrogen bonds in particular. However, the presence of any single strong intermolecular interaction cannot automatically warrant changes in luminescent properties of a crystal, as shown in the present case.

Equilibria between conformational states of the Ras oncogene protein revealed by high-pressure crystallography

Equilibria between conformational states of the Ras oncogene protein revealed by high-pressure crystallography

High-pressure high-temperature crystallography of silicon

High-pressure high-temperature crystallography of silicon

Materials synthesis at terapascal static pressures

Theoretical modelling predicts very unusual structures and properties of materials at extreme pressure and temperature conditions1,2. Hitherto, their synthesis and investigation above 200 gigapascals have been hindered both by the technical complexity of ultrahigh-pressure experiments and by the absence of relevant in situ methods of materials analysis. Here we report on a methodology developed to enable experiments at static compression in the terapascal regime with laser heating. We apply this method to realize pressures of about 600 and 900 gigapascals in a laser-heated double-stage diamond anvil cell3, producing a rhenium–nitrogen alloy and achieving the synthesis of rhenium nitride Re7N3—which, as our theoretical analysis shows, is only stable under extreme compression. Full chemical and structural characterization of the materials, realized using synchrotron single-crystal X-ray diffraction on microcrystals in situ, demonstrates the capabilities of the methodology to extend high-pressure crystallography to the terapascal regime.

High-pressure crystallography shows noble gas intervention into protein-lipid interaction and suggests a model for anaesthetic action

In this work we examine how small hydrophobic molecules such as inert gases interact with membrane proteins (MPs) at a molecular level. High pressure atmospheres of argon and krypton were used to produce noble gas derivatives of crystals of three well studied MPs (two different proton pumps and a sodium light-driven ion pump). The structures obtained using X-ray crystallography showed that the vast majority of argon and krypton binding sites were located on the outer hydrophobic surface of the MPs – a surface usually accommodating hydrophobic chains of annular lipids (which are known structural and functional determinants for MPs). In conformity with these results, supplementary in silico molecular dynamics (MD) analysis predicted even greater numbers of argon and krypton binding positions on MP surface within the bilayer. These results indicate a potential importance of such interactions, particularly as related to the phenomenon of noble gas-induced anaesthesia.

Sub-micrometer focusing setup for high-pressure crystallography at the Extreme Conditions beamline at PETRA III.

Scientific tasks aimed at decoding and characterizing complex systems and processes at high pressures set new challenges for modern X-ray diffraction instrumentation in terms of X-ray flux, focal spot size and sample positioning. Presented here are new developments at the Extreme Conditions beamline (P02.2, PETRA III, DESY, Germany) that enable considerable improvements in data collection at very high pressures and small scattering volumes. In particular, the focusing of the X-ray beam to the sub-micrometer level is described, and control of the aberrations of the focusing compound refractive lenses is made possible with the implementation of a correcting phase plate. This device provides a significant enhancement of the signal-to-noise ratio by conditioning the beam shape profile at the focal spot. A new sample alignment system with a small sphere of confusion enables single-crystal data collection from grains of micrometer to sub-micrometer dimensions subjected to pressures as high as 200 GPa. The combination of the technical development of the optical path and the sample alignment system contributes to research and gives benefits on various levels, including rapid and accurate diffraction mapping of samples with sub-micrometer resolution at multimegabar pressures.

Equilibria between conformational states of the Ras oncogene protein revealed by high pressure crystallography.

In this work, we experimentally investigate the allosteric transitions between conformational states on the Ras oncogene protein using high pressure crystallography. Ras protein is a small GTPase involved in central regulatory processes occurring in multiple conformational states. Ras acts as a molecular switch between active GTP-bound, and inactive GDP-bound states, controlling essential signal transduction pathways. An allosteric network of interactions between the effector binding regions and the membrane interacting regions is involved in Ras cycling. The conformational states which coexist simultaneously in solution possess higher Gibbs free energy than the ground state. Equilibria between these states can be shifted by applying pressure favouring conformations with lower partial molar volume, and has been previously analyzed by high-pressure NMR spectroscopy. High-pressure macromolecular crystallography (HPMX) is a powerful tool perfectly complementary to high-pressure NMR, allowing characterization at the molecular level with a high resolution the different allosteric states involved in the Ras cycling. We observe a transition above 300 MPa in the crystal leading to more stable conformers. Thus, we compare the crystallographic structures of Ras(wt)·Mg2+·GppNHp and Ras(D33K)·Mg2+·GppNHp at various high hydrostatic pressures. This gives insight into per-residue descriptions of the structural plasticity involved in allosteric equilibria between conformers. We have mapped out at atomic resolution the different segments of Ras protein which remain in the ground-state conformation or undergo structural changes, adopting excited-energy conformations corresponding to transient intermediate states. Such in crystallo phase transitions induced by pressure open the possibility to finely explore the structural determinants related to switching between Ras allosteric sub-states without any mutations nor exogenous partners.

Kilobytes of kilopascals: high-pressure depositions of the Cambridge Structural Database

The Cambridge Structural Database (CSD) is the largest repository of crystal structures of organic and metal–organic compounds, containing over 1.1 million entries. Over 3300 of the deposits are structures determined under high pressure, with the number being strongly affected by the experimental requirements of the high-pressure techniques. Nevertheless, it still presents a population sufficiently representative for statistical data mining. In this work, an in-depth analysis of this population is presented, showing where contributors of high-pressure depositions come from, which journals high-pressure structures are published in, and also providing information on some trends in high-pressure crystallography and how they have changed over the years elucidated from data collected in the CSD. The ultimate goal of this article is to bring the high-pressure crystallography content in the CSD to a wider audience of scientists.

Mapping high-pressure crystallography in a structural chemistry landscape

The remarkable growth in volume of high-pressure crystal structural chemistry depositions in the Cambridge Structure Database has been reported in a recent paper by Kaźmierczak & Patyk-Kaźmierczak [Acta Cryst. (2021), B77, 1012–1020].

In situ high-pressure nuclear magnetic resonance crystallography in one and two dimensions

Recent developments in in situ nuclear magnetic resonance (NMR) spectroscopy under extreme conditions have led to the observation of a wide variety of physical phenomena that are not accessible with standard high-pressure experimental probes. However, inherent di- or quadrupolar line broadening in diamond anvil cell (DAC)-based NMR experiments often limits detailed investigation of local atomic structures, especially if different phases or local environments coexist. Here, we describe our progress in the development of high-resolution NMR experiments in DACs using one- and two-dimensional homonuclear decoupling experiments at pressures up to the megabar regime. Using this technique, spectral resolutions of the order of 1 ppm and below have been achieved, enabling high-pressure structural analysis. Several examples are presented that demonstrate the wide applicability of this method for extreme conditions research.

Altering the magnetic ordering of Fe3Ga4 via thermal annealing and hydrostatic pressure

The effects of post-synthesis annealing temperature on arc-melted samples of Fe3Ga4 has been studied to investigate changes in crystallographic and magnetic properties induced by annealing. Results show a significant trend in the evolution of the (incommensurate spin density wave) ISDW-FM (ferromagnetic) transition temperature as a function of the refined unit cell volume in annealed samples. Strikingly, this trend allowed for the tuning of the transition temperature down to room-temperature (300 K) whilst maintaining a sharp transition in temperature, opening the door to the use of Fe3Ga4 in functional devices. Crystallographic analysis through Rietveld refinement of high-resolution x-ray diffraction data has showed that arc-melted stoichiometric Fe3Ga4 is multi-phase regardless of annealing temperature with a minor phase of FeGa3 decreasing in phase fraction at higher annealing temperature. In order to validate the trend in ISDW-FM transition temperature with regard to unit cell volume, high pressure magnetometry was performed. This showed that the FM-ISDW (~ 68 K) and ISDW-FM (~ 360 K) transition temperatures could be tuned, increased and decreased respectively, linearly with external pressure. Thus, external pressure and the ensuing crystallographic changes minimize the temperature range of the stability of the ISDW pointing toward the importance of structural properties on the mechanism for the formation of the intermediate ISDW phase. These results show how this model system can be tuned as well as highlighting the need for future high-pressure crystallography and related single crystal measurements to understand the mechanism and nature of the intermediate ISDW phase to be exploited in future devices.

High-pressure high-temperature crystallography of graphite intercalation compounds

High-pressure high-temperature crystallography of graphite intercalation compounds

High-pressure crystallography unlimited

High-pressure crystallography unlimited

Simultaneous quantitative recognition of all purines including N6-methyladenine via the host-guest interactions on a Mn-MOF

Simultaneous quantitative recognition of all purines including N6-methyladenine via the host-guest interactions on a Mn-MOF

Putting the Squeeze on Molecule-Based Magnets: Exploiting Pressure to Develop Magneto-Structural Correlations in Paramagnetic Coordination Compounds

The cornerstone of molecular magnetism is a detailed understanding of the relationship between structure and magnetic behaviour, i.e., the development of magneto-structural correlations. Traditionally, the synthetic chemist approaches this challenge by making multiple compounds that share a similar magnetic core but differ in peripheral ligation. Changes in the ligand framework induce changes in the bond angles and distances around the metal ions, which are manifested in changes to magnetic susceptibility and magnetisation data. This approach requires the synthesis of a series of different ligands and assumes that the chemical/electronic nature of the ligands and their coordination to the metal, the nature and number of counter ions and how they are positioned in the crystal lattice, and the molecular and crystallographic symmetry have no effect on the measured magnetic properties. In short, the assumption is that everything outwith the magnetic core is inconsequential, which is a huge oversimplification. The ideal scenario would be to have the same complex available in multiple structural conformations, and this is something that can be achieved through the application of external hydrostatic pressure, correlating structural changes observed through high-pressure single crystal X-ray crystallography with changes observed in high-pressure magnetometry, in tandem with high-pressure inelastic neutron scattering (INS), high-pressure electron paramagnetic resonance (EPR) spectroscopy, and high-pressure absorption/emission/Raman spectroscopy. In this review, which summarises our work in this area over the last 15 years, we show that the application of pressure to molecule-based magnets can (reversibly) (1) lead to changes in bond angles, distances, and Jahn–Teller orientations; (2) break and form bonds; (3) induce polymerisation/depolymerisation; (4) enforce multiple phase transitions; (5) instigate piezochromism; (6) change the magnitude and sign of pairwise exchange interactions and magnetic anisotropy, and (7) lead to significant increases in magnetic ordering temperatures.

A high-pressure macromolecular crystallography capability developed at CHESS

A high-pressure macromolecular crystallography capability developed at CHESS