Browsing by Author "Parsons, S"

Now showing 1 - 16 of 16
  • No Thumbnail Available
    Item
    Accurate H-atom parameters for the two polymorphs of L-histi­dine at 5, 105 and 295 K
    (International Union of Crystallography, 2021-10-01) Novelli, G; McMonagle, CJ; Kleemiss, F; Probert, MR; Puschmann, H; Grabowsky, S; Maynard-Casely, HE; McIntyre, GJ; Parsons, S
    The crystal structure of the monoclinic polymorph of the primary amino acid L-histi­dine has been determined for the first time by single-crystal neutron diffraction, while that of the orthorhombic polymorph has been reinvestigated with an untwinned crystal, improving the experimental precision and accuracy. For each polymorph, neutron diffraction data were collected at 5, 105 and 295 K. Single-crystal X-ray diffraction experiments were also performed at the same temperatures. The two polymorphs, whose crystal packing is interpreted by intermolecular interaction energies calculated using the Pixel method, show differences in the energy and geometry of the hydrogen bond formed along the c direction. Taking advantage of the X-ray diffraction data collected at 5 K, the precision and accuracy of the new Hirshfeld atom refinement method im­ple­mented in NoSpherA2 were probed choosing various settings of the functionals and basis sets, together with the use of explicit clusters of molecules and enhanced rigid-body restraints for H atoms. Equivalent atomic coordinates and aniso­tropic displacement parameters were com­pared and found to agree well with those obtained from the corresponding neutron structural models.© International Union of Crystallography
  • No Thumbnail Available
    Item
    Accurate hydrogen parameters for the amino acid L-leucine
    (International Union of Crystallography, 2016-01) Binns, J; Parsons, S; McIntyre, GJ
    The structure of the primary amino acid L-leucine has been determined for the first time by neutron diffraction. This was made possible by the use of modern neutron Laue diffraction to overcome the previously prohibitive effects of crystal size and quality. The packing of the structure into hydrophobic and hydrophilic layers is explained by the intermolecular interaction energies calculated using the PIXEL method. Variable-temperature data collections confirmed the absence of phase transitions between 120 and 300 K in the single-crystal form. © International Union of Crystallography
  • Thumbnail Image
    Item
    Carbon molecules in space: a thermal equation of state study of solid hexamethylenetetramine
    (Australian Institute of Physics, 2020-02-04) Novelli, G; McIntyre, GJ; Maynard-Casely, HE; Marshall, WG; Kamenev, KV; Parsons, S
    Properties such as compressibility, thermo-elasticity and the energy landscape remain unknown for many organic compounds under conditions encountered on extraterrestrial planets and moons and in space. In this study, a thermal Equation of State (EoS) for the crystalline solid hexamethylenetetramine was determined by neutron powder diffraction in the temperature and pressure ranges of 113-480 K and 0-5 GPa, respectively. The material was chosen as a molecular model for its high symmetry and its property of remaining in the same phase throughout the experimental conditions selected to simulate the planetary environments. Equations of States (EoSs) show how the thermodynamic variables of temperature (T), pressure (P) and volume (V) are inter-related. The ideal gas law, PV = nRT, is an example of an EoS which is used as a simple but effective model to explain the properties of gases. More complex EoSs, where the assumption of ideality is relaxed, can be applied to solids in order to describe how the geometry and energy transform when they experience dramatic changes in their environment. Such information acquires enormous importance in planetary materials science, where scientists are trying to understand the fate of carbon, the fourth most abundant element in our galaxy, in the context of the origin of life and planetary environments. Despite the large heterogeneity of galactic and interstellar regions, the organic chemistry of the universe seems to follow common pathways. Molecules of high astrobiological and astrophysical relevance such as amino acids, polyaromatic hydrocarbons, and N-heterocycles have been identified across the solar system, but how they behave under such varied conditions is a question yet to be answered. Key to our approach was the determination of how the internal energy (U), entropy (S) and the Gibbs free energy (G) vary with pressure not only computationally, but also, and for the first time, experimentally. A new method has been developed, able to transform directly variable-PT crystallographic data into thermodynamic information. Although it is quite common to model thermal expansion at ambient pressure with a VTEoS, and compression at ambient temperature using a PV-EoS, determinations of PVT-EoSs are much less common, particularly for organic materials. This paucity of PTV-EoSs reflects the difficulty of varying pressure and temperature simultaneously in crystallographic experiments, especially at reduced temperatures. The task was addressed in this study by the variable-temperature insert for the Paris-Edinburgh press available on the PEARL instrument at the ISIS Neutron Spallation Source (UK). The results were successfully combined with periodic DFT (Figure 1) and other semiempirical calculations, where pressure and temperature can be included at little time cost, enabling the stability profile of the material to be understood, right down to the level of individual intermolecular interactions.
  • Thumbnail Image
    Item
    Development of high-pressure single-crystal neutron diffraction on the Laue diffractometer, KOALA, at OPAL
    (Australian Institute of Physics, 2016-02-04) Binns, J; McIntyre, GJ; Kamenev, KV; Moggach, S; Parsons, S
    Hydrogen bonds are one of the most important classes of intermolecular interaction, and accurate H-atom positions are critical for analysis of the energy terms which determine the thermodynamic stability of molecular crystals. At ambient pressure and low temperatures, H atoms can often be located by X-ray diffraction, and X-ray data can provide an accurate picture of the intermolecular contacts. High-pressure experiments do not afford this luxury. The high systematic errors introduced by the pressure cell and low completeness mean that H-atom positions are not revealed in X-ray Fourier maps. In some compounds H-atom positions can be inferred from the positions of other atoms, but this is not possible in all cases. Neutron diffraction data are much more sensitive to H than are X-ray data, and they are essential in cases where accurate H-atom location is important. Neutron powder patterns of complex molecular systems suffer from extensive peak overlap, and single-crystal diffraction therefore has a huge advantage; there is also no need to deuterate. The main disadvantage of neutron diffraction is that a large sample is usually required, which is at odds with the decreasing volumes possible with increasing pressure with existing pressure-cell materials. Modern neutron Laue diffraction and large moissanite anvil cells offer some respite 1, but complementing high-pressure X-ray data with high-pressure neutron data is still fraught with technical challenges to obtain identical conditions. Initial developmental experiments using a miniature diamond-anvil cell with a single crystal of size typical for X-ray diffraction on the KOALA Laue diffractometer at OPAL have shown the feasibility of the Laue technique for single-crystal neutron studies at high pressure. Remarkably, data completeness is similar to ambient-pressure measurements, despite the presence of the pressure cell. It is now possible to perform joint X-ray and neutron studies on the same sample under identical conditions.
  • No Thumbnail Available
    Item
    Effect of high pressure on the crystal structures of polymorphs of l-histidine
    (American Chemical Society, 2020-11-06) Novelli, G; Maynard-Casely, HE; McIntyre, GJ; Warren, MR; Parsons, S
    The effect of pressure on the crystal structures of the two ambient-pressure polymorphs of the amino acid l-histidine has been investigated. Single-crystal diffraction measurements, up to 6.60 GPa for the orthorhombic form I (P212121) and 6.85 GPa for the monoclinic form II (P21), show their crystal structures undergo isosymmetric single-crystal-to-single-crystal first-order phase transitions at 4.5 and 3.1 GPa to forms I′ and II′, respectively. Although the similarity in crystal packing and intermolecular interaction energies between the polymorphs is remarkable at ambient conditions, the manner in which each polymorph responds to pressure is different. Form II is found to be more compressible than form I, with bulk moduli of 11.6(6) GPa and 14.0(5) GPa, respectively. The order of compressibility follows the densities of the polymorphs at ambient conditions (1.450 and 1.439 g cm–3 for phases I and II, respectively). The difference is also related to the space-group symmetry, the softer monoclinic form having more degrees of freedom available to accommodate the change in pressure. In the orthorhombic form, the imidazole-based hydrogen atom involved in the H-bond along the c-direction swaps the acceptor oxygen atom at the transition to phase I′; the same swap occurs just after the phase transition in the monoclinic form and is also preceded by a bifurcation. Concurrently, the H-bond and the long-range electrostatic interaction along the b-direction form a three-centered H-bond at the I to I′ transition, while they swap their character during the II to II′ transition. The structural data were interpreted using periodic-density-functional theory, symmetry-adapted perturbation theory, and semiempirical Pixel calculations, which indicate that the transition is driven by minimization of volume, the intermolecular interactions generally being destabilized by the phase transitions. Nevertheless, volume calculations are used to show that networks of intermolecular contacts in both phases are very much less compressible than the interstitial void spaces, having bulk moduli similar to moderately hard metals. The volumes of the networks actually expand over the course of both phase transitions, with the overall unit-cell-volume decrease occurring through larger compression of interstitial void space. © 2020 American Chemical Society
  • Thumbnail Image
    Item
    High-pressure single-crystal neutron diffraction
    (Australian Institute of Physics, 2017-02-03) McIntyre, GJ; Binns, J; Parsons, S
    High-pressure neutron diffraction is always challenging, but it can offer several advantages over high-pressure X-ray diffraction to make meeting those challenges worthwhile. In addition to the usual higher sensitivity to low-X elements, notably hydrogen, and to magnetic moments, the low absorption by many pressure cell materials can yield greater reciprocal space coverage for single crystals. The low scattering power usually requires considerably larger sample volumes than with X-rays, but for the same reason the cell-wall materials can be quite thick. Common cell designs include He-gas cells and simple clamp cells, opposed piston cells (e.g. Bloch, McWhan), opposed-anvil cells (e.g. diamond anvil cell, Paris-Edinburgh cell), and multi-anvil cells, each adapted to sample volume, accessibility, pressure, and other external parameters, especially temperature, that suit the scientific question of interest. State-of-the-art experiments using each cell type will be described. A special challenge in high-pressure diffraction is to perform neutron and X-ray experiments on the same material under the same conditions. Previously, this meant using different cells and samples with achieving identical pressures largely a hit-or-miss affair. This has all changed with the recent demonstration on KOALA on the OPAL research reactor that modern neutron Laue diffraction can be performed on the same sample in the same diamond-anvil cell as used for laboratory X-ray experiments [1].
  • Thumbnail Image
    Item
    High-pressure single-crystal neutron diffraction
    (Australian Institute of Nuclear Science and Engineering, 2016-11-29) McIntyre, GJ; Binns, J; Parsons, S
    High-pressure neutron diffraction is always challenging, but it can offer several advantages over high-pressure X-ray diffraction to make meeting those challenges worthwhile. In addition to the usual higher sensitivity to low-X elements, notably hydrogen, and to magnetic moments, the low absorption by many pressure cell materials can yield greater reciprocal space coverage for single crystals. The low scattering power usually requires considerably larger sample volumes than with X-rays, but for the same reason the cell-wall materials can be quite thick. Common cell designs include He-gas cells and simple clamp cells, opposed piston cells (e.g. Bloch, McWhan), opposed-anvil cells (e.g. diamond anvil cell, Paris-Edinburgh cell), and multi-anvil cells, each adapted to sample volume, accessibility, pressure, and other external parameters, especially temperature, that suit the scientific question of interest. State-of-the art experiments using each cell type will be described. A special challenge in high-pressure diffraction is to perform neutron and X-ray experiments on the same material under the same conditions. Previously, this meant using different cells and samples with achieving identical pressures a hit-or-miss affair. This has all changed with the recent demonstration on KOALA on the OPAL research reactor that modern neutron Laue diffraction can be performed on the same sample in the same diamond-anvil cell as used for laboratory X-ray experiments [1].
  • Thumbnail Image
    Item
    Investigating carbon molecules with pressure-volume-temperature equations of state
    (Australian Nuclear Science and Technology Organisation, 2019-09-03) Novelli, G; McIntyre, GJ; Maynard-Casely, HE; Funnell, NP; Marshall, WG; Kamenev, KV; Parsons, S
    We are interested in intermolecular interactions which determine thermodynamic stability in crystalline solids and their response to changes in the external conditions. In no area is this information of more importance than in planetary materials science, where scientists are trying to understand the fate of carbon in the context of the origin of life and/or the varied planetary surfaces observed. Molecules of high astrobiological and astrophysical relevance, such as amino acids (1), polyaromatic hydrocarbons, and N-heterocycles (2), have been identified across the Universe but how they behave under such varying conditions is a question yet to be answered. Key to our approach is the determination of the internal-energy, entropy and the Gibbs free energy - not only computationally but also, and for the first time, experimentally. We have developed a new method that transforms variable-pressure (P)-temperature (T) crystallographic data into thermodynamic information. Equations of State (EoSs) are the models of choice to fit these data, describing how pressure, temperature, and volume (V) are inter related in solid phases. Although it is quite common to model thermal expansion at ambient pressure with a VT equation of state (EoS), and compression at ambient temperature using a PV-EoS, determinations of PVT-EoSs are much less common, particularly for molecular materials (3). The paucity of PVT-EoSs reflects the difficulty in varying pressure and temperature simultaneously in crystallographic experiments, especially at reduced temperatures. These difficulties are addressed by the variable temperature insert for the Paris-Edinburgh press available on the PEARL instrument at the ISIS Neutron Spallation Source (4) and by the cryofurnace for the Merrill-Bassett cell available on the KOALA instrument at the ANSTO OPAL reactor (5). The results can then be combined with Periodic DFT and other semi-empirical calculations, where pressure and temperature can be included at little time cost, enabling the stability profile of a material to be understood, right down to the level of individual intermolecular interactions. Many classes of structure-directing intermolecular interactions involve hydrogen atoms: hydrogen bonds are an obvious example, but hydrogens can also be involved in dispersion and electrostatic interactions. The responses of different kind of crystalline organics containing these interactions, such as hexamethylenetetramine, naphthalene, histidine, and alanine are to be studied using powder and single-crystal neutron diffraction up to 5 GPa and between 105-480 K. We are specifically using neutron diffraction for the experiments because of its sensitivity to locate hydrogen atoms. Additionally, the penetrating nature of neutron radiation means that complete, high-quality data can be obtained for samples in elaborate extreme-conditions environments.
  • No Thumbnail Available
    Item
    [Mn-6] under pressure: a combined crystallographic and magnetic study
    (Wiley-VCH Verlag Berlin, 2008-03) Prescimone, A; Milios, CJ; Moggach, S; Warren, JE; Lennie, AR; Sanchez-Benitez, J; Kamenev, KV; Bircher, R; Murrie, M; Parsons, S; Brechin, EK
    Folding under pressure: High-pressure crystallography of an Mn6 single-molecule magnet reveals dramatic changes in the intramolecular geometry of the magnetic core. These structural changes effect the magnetic properties of the molecule: the magnitude of the ferromagnetic exchange between the metals is decreased, and under extreme pressure switches to antiferromagnetic. © 2008, Wiley-VCH Verlag Berlin
  • No Thumbnail Available
    Item
    Neutron and high-pressure X-ray diffraction study of hydrogen-bonded ferroelectric rubidium hydrogen sulfate
    (International Union of Crystallography, 2016-01-01) Binns, J; McIntyre, GJ; Parsons, S
    The pressure- and temperature-dependent phase transitions in the ferroelectric material rubidium hydrogen sulfate (RbHSO4) are investigated by a combination of neutron Laue diffraction and high-pressure X-ray diffraction. The observation of disordered O-atom positions in the hydrogen sulfate anions is in agreement with previous spectroscopic measurements in the literature. Contrary to the mechanism observed in other hydrogen-bonded ferroelectric materials, H-atom positions are well defined and ordered in the paraelectric phase. Under applied pressure RbHSO4 undergoes a ferroelectric transition before transforming to a third, high-pressure phase. The symmetry of this phase is revised to the centrosymmetric space group P21/c, resulting in the suppression of ferroelectricity at high pressure. © International Union of Crystallography
  • Thumbnail Image
    Item
    A non-topological mechanism for negative linear compressibility
    (Royal Society of Chemistry, 2016-05-13) Binns, J; Kamenev, KV; Marriott, KER; McIntyre, GJ; Moggach, SA; Murrie, M; Parsons, S
    Negative linear compressibility (NLC), the increase in a unit cell length with pressure, is a rare phenomenon in which hydrostatic compression of a structure promotes expansion along one dimension. It is usually a consequence of crystal structure topology. We show that the source of NLC in the Co(II) citrate metal–organic framework UTSA-16 lies not in framework topology, but in the relative torsional flexibility of Co(II)-centred tetrahedra compared to more rigid octahedra.© Open Access CC BY Licence - The Royal Society of Chemistry 2016
  • No Thumbnail Available
    Item
    Phase transition sequences in tetra­methyl­ammonium tetra­chloro­metallates by x-ray diffraction and spectroscopic measurements
    (International Union of Crystallography, 2017-01) Binns, J; McIntyre, GJ; Barreda-Argüeso, JA; González, J; Aguado, F; Rodríguez, F; Valiente, R; Parsons, S
    The phase transition sequences of two members of the tetra­methyl­ammonium tetra­chloro­metallate(III) family of hybrid organic–inorganic salts have been determined and structurally characterized as a function of temperature for the first time. Unusually, a reduction in point-group symmetry with increasing temperature until reaching a cubic prototype phase is observed. Two additional intermediate phases are observed for Fe3+. First-principles calculations and the presence of short Cl...Cl contacts for Ga3+ suggest the [GaCl4]− anion to be conformationally hindered due to stronger lone-pair–σ-hole interactions. The conformationally more flexible Fe3+ structures show sublattice melting with the onset of rotational disorder in the [NMe4]+ cations occurring 40 K below the corresponding onset of rotational disorder in the [FeCl4]− sublattice. © International Union of Crystallography
  • Thumbnail Image
    Item
    Structural studies of phase transitions in hybrid organic-inorganic salts with temperature and pressure
    (Australian Institute of Physics, 2014-02-04) Binns, J; Parsons, S; Moggach, S; Valiente, R; McIntyre, GJ; Kamenev, KV
    The alkylammonium tetrachlorometallates have attracted significant attention for the numerous phase transitions observed in a relatively narrow range of temperatures and pressures as well as ferroelectric,-elastic and -magnetic behaviours. [1,2] Such simple organic salts could find possible applications as thin-film functional materials in low cost ferroelectric capacitors and RAM. With the exception of bis(tetramethylammonium) tetrachlorozincate(II) this class of materials has been subject to relatively little structural investigation, with a number of general phase sequences being determined from calorimetric and polarisation measurements. [3,4] While there are known to be ferroelectric phase transitions in many of these materials, the exact mechanism by which these simple organic salts exhibit such behaviour is unknown. We report on the phase sequences observed in two related materials: tetramethylammonium tetrachloroferrate(III) (TCF), and the previously unknown tetramethylammonium tetrachlorogallate(III) (TCG) which display re-entrant as well as plastic crystalline phases.
  • Thumbnail Image
    Item
    Towards joint high-pressure x-ray and neutron single-crystal diffraction
    (International Union of Crystallography, 2017-01) McIntyre, GJ; Binns, J; Kamenev, KV; Moggach, S; Parsons, S
    Diffraction methods can provide the highest-quality structural information about a crystal on the atomic scale and much work has been carried out to adapt X-ray and neutron diffraction techniques to a variety of challenging sample environments, including high-pressure. The ability to influence directly intermolecular distances makes high pressure one of the most important tools at our disposal for answering one of the big questions in chemistry - the prediction and control of solid-state structure. Modern neutron Laue diffractometers with large image-plate detectors permit extensive continuous sampling of reciprocal space with high resolution in the two-dimensional projection and a wide dynamic range with negligible bleeding of intense diffraction spots, qualities that are highly suited to high-pressure crystallography [1]. Here we show that high-pressure single-crystal neutron diffraction data can be collected using Laue diffraction from a sample of hexamine in a miniature diamond-anvil cell (mini-DAC) with no significant reductions in completeness or resolution [2]. The data are of similar quality, as judged by R-factors, geometric parameters, and estimated standard deviations, to those obtained at ambient pressures. This is achieved by the ability to measure diffracted intensity directly through the body of the mini-DAC. Joint high-pressure experiments using both X-ray and neutron diffraction on the same sample are now feasible using the mini-DAC and modern neutron Laue diffractometers like KOALA on the OPAL reactor. © International Union of Crystallography
  • Thumbnail Image
    Item
    Use of a miniature diamond-anvil cell in a joint x-ray and neutron high-pressure study on copper sulfate pentahydrate
    (International Union of Crystallography, 2022-01) Novelli, G; Kamenev, KV; Maynard-Casely, HE; Parsons, S; McIntyre, GJ
    Single-crystal X-ray and neutron diffraction data are usually collected using separate samples. This is a disadvantage when the sample is studied at high pressure because it is very difficult to achieve exactly the same pressure in two separate experiments, especially if the neutron data are collected using Laue methods where precise absolute values of the unit-cell dimensions cannot be measured to check how close the pressures are. In this study, diffraction data have been collected under the same conditions on the same sample of copper(II) sulfate pentahydrate, using a conventional laboratory diffractometer and source for the X-ray measurements and the Koala single-crystal Laue diffractometer at the ANSTO facility for the neutron measurements. The sample, of dimensions 0.40 × 0.22 × 0.20 mm3 and held at a pressure of 0.71 GPa, was contained in a miniature Merrill–Bassett diamond-anvil cell. The highly penetrating diffracted neutron beams passing through the metal body of the miniature cell as well as through the diamonds yielded data suitable for structure refinement, and compensated for the low completeness of the X-ray measurements, which was only 24% on account of the triclinic symmetry of the sample and the shading of reciprocal space by the cell. The two data-sets were combined in a single `XN' structure refinement in which all atoms, including H atoms, were refined with anisotropic displacement parameters. The precision of the structural parameters was improved by a factor of up to 50% in the XN refinement compared with refinements using the X-ray or neutron data separately. Published under an open-access licence.
  • Thumbnail Image
    Item
    Use of a miniature diamond-anvil cell in high-pressure single-crystal neutron Laue diffraction
    (International Union of Crystallography, 2016-05) Binns, J; Kamenev, KV; McIntyre, GJ; Moggach, SA; Parsons, S
    The first high-pressure neutron diffraction study in a miniature diamond-anvil cell of a single crystal of size typical for X-ray diffraction is reported. This is made possible by modern Laue diffraction using a large solid-angle image-plate detector. An unexpected finding is that even reflections whose diffracted beams pass through the cell body are reliably observed, albeit with some attenuation. The cell body does limit the range of usable incident angles, but the crystallographic completeness for a high-symmetry unit cell is only slightly less than for a data collection without the cell. Data collections for two sizes of hexamine single crystals, with and without the pressure cell, and at 300 and 150 K, show that sample size and temperature are the most important factors that influence data quality. Despite the smaller crystal size and dominant parasitic scattering from the diamond-anvil cell, the data collected allow a full anisotropic refinement of hexamine with bond lengths and angles that agree with literature data within experimental error. This technique is shown to be suitable for low-symmetry crystals, and in these cases the transmission of diffracted beams through the cell body results in much higher completeness values than are possible with X-rays. The way is now open for joint X-ray and neutron studies on the same sample under identical conditions. © International Union of Crystallography - Open Access