Covalent bond lengthening in hydroxyl groups involved in three-center and in cooperative hydrogen bonds. Analysis of low-temperature neutron diffraction data

The crystal structure of Sr(OH)2·8H2O has been determined at 20, 100 and 200 K from neutron diffraction data. The structure consists of double layers of H2O and OH− ions separated by Sr2+ along the c axis. The Sr2+ ions are eight-coordinated by water O atoms in a square antiprism configuration. Each H2O molecule is engaged in three hydrogen bonds. The OH− ions form chains of acceptor and donor bonds along the fourfold axis with O atoms engaged in four bonds with H2O molecules, such that both non-equivalent O atoms have square-pyramidal environments of five H atoms and the overall bonding configurations of distorted octahedra.

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Hydrogen positions and thermal expansion in lizardite-1T from Elba; a low-temperature study using Rietveld refinement of neutron diffraction data

American Mineralogist ◽

10.2138/am-1996-9-1008 ◽

1996 ◽

Vol 81 (9-10) ◽

pp. 1111-1116 ◽

Cited By ~ 23

Author(s):

M. Gregorkiewitz ◽

B. Lebech ◽

M. Mellini ◽

C. Viti

Keyword(s):

Thermal Expansion ◽

Low Temperature ◽

Neutron Diffraction ◽

Rietveld Refinement ◽

Diffraction Data ◽

Neutron Diffraction Data ◽

Temperature Study

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Structure, proton incorporation and transport properties of ceramic proton conductor Ba(Ce0.7Zr0.2Yb0.1)O3-δ

MRS Proceedings ◽

10.1557/proc-835-k1.4 ◽

2004 ◽

Vol 835 ◽

Author(s):

Yaping Li ◽

Alexander I. Kolesnikov ◽

James W. Richardson ◽

Chendong Zuo ◽

Tae H. Lee ◽

...

Keyword(s):

Neutron Diffraction ◽

Diffraction Data ◽

Inelastic Neutron Scattering ◽

Proton Conductor ◽

Inelastic Neutron ◽

Solid State Reactions ◽

Hydroxyl Groups ◽

Neutron Diffraction Data ◽

Vapor Pressures ◽

Structure Phase Transition

ABSTRACTDense ceramics with composition Ba(Ce0.7Zr0.2Yb0.1)O3-β (BCZY) were synthesized by solid state reactions, and their structures were characterized by Rietveld refinements of time-of-flight (TOF) neutron diffraction data collected for the samples at high-temperature and controlled atmospheres. The structure phase transition from orthorhombic Imma to cubic Pm3m was observed at the temperature between 500 and 700°C and in flowing 100ppm H2/Ar gases. At 900°C, the sample was subsequently exposed to different oxygen partial pressures (pO2, ranging from ∼10−17 to ∼10−23 atm) and water vapor pressures (pH2O) up to ∼0.18 atm. The expansion of lattice parameters of BCZY, instead of following the normally expected relationship with pO2, was actually correlated with the increase of pH2O, implying proton incorporation into the structures. The presence of H-containing species in the structure was confirmed by comparing both inelastic neutron scattering spectra and neutron diffraction data collected for dry and “wet” samples at 10K. The observed vibrational peaks at 104 and 150 meV and absence of a peak around 420 meV indicate the hydrogen occupation in the structure but the absence of any hydroxyl groups (hydrogen covalently bonded to oxygen). Electrical conductivities of BCZY were investigated at different temperatures in both dry and wet conditions.

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Opening and Narrowing of the Water H—O—H Angle by Hydrogen-Bonding Effects: Re-inspection of Neutron Diffraction Data

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768197018193 ◽

1998 ◽

Vol 54 (4) ◽

pp. 464-470 ◽

Cited By ~ 14

Author(s):

T. Steiner

Keyword(s):

Hydrogen Bonding ◽

Hydrogen Bonds ◽

Neutron Diffraction ◽

Diffraction Data ◽

Water Molecules ◽

Hydroxyl Groups ◽

Secondary Effects ◽

X Ray Diffraction ◽

X Ray ◽

Sample Average

For 71 water molecules donating two Ow—H...O hydrogen bonds, the correlation of the covalent H—O—H angle and the O...Ow...O angle is inspected from 49 well refined organic and organometallic neutron diffraction crystal structures. Compared to sample average, the water angle is opened for large and narrowed for small O...Ow...O angles. Notably, the H—O—H angle is widened compared with the gas phase value even for small O...Ow...O. Related behavior is observed for chloride anion acceptors. The correlation exhibits a considerable scatter which should not be interpreted as experimental inaccuracies, but as secondary effects. Possible secondary effects are multi-center hydrogen bonding and effects of coordination to the water O atom. In a comparative test, low-temperature X-ray diffraction data were shown to be completely unsuitable for this type of analysis. The dependence of the C—O—H angle on the C—O...O angle in hydrogen bonds donated by hydroxyl groups in carbohydrates is also shown.

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The incommensurately modulated structures of low-temperature labradorite feldspars: a single-crystal X-ray and neutron diffraction study

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520619017128 ◽

2020 ◽

Vol 76 (1) ◽

pp. 93-107

Author(s):

Shiyun Jin ◽

Huifang Xu ◽

Xiaoping Wang ◽

Ryan Jacobs ◽

Dane Morgan

Keyword(s):

Low Temperature ◽

Neutron Diffraction ◽

Single Crystal ◽

Diffraction Data ◽

Neutron Diffraction Study ◽

Neutron Diffraction Data ◽

X Ray Diffraction ◽

Subsolidus Phase ◽

X Ray ◽

Modulated Structures

Labradorite feldspars of the plagioclase solid solution series have been known for their complicated subsolidus phase relations and enigmatic incommensurately modulated structures. Characterized by the irrationally indexed e-reflections in the diffraction pattern, e-labradorite shows the largest variation in the incommensurate ordering states among the e-plagioclase structures. The strongly ordered low-temperature e-labradorite is one of the last missing pieces of the e-plagioclase puzzle. Nine plutonic and metamorphic labradorite feldspar samples from Canada, Ukraine, Minnesota (USA), Tanzania and Greenland with compositions ranging from An52.5 to An68 were studied with single-crystal X-ray diffraction. Two crystals from Labrador, Canada, and Duluth, MN, USA, with wide enough twin lamellae were analyzed with single-crystal neutron diffraction. The incommensurately modulated structures of e-plagioclase are refined for the first time with neutron diffraction data, which confirmed that the T—O distance modulation in the low-temperature e-plagioclase results from the Al–Si ordering in the framework. Detailed configurations of the M site are also observed in the structures refined from neutron diffraction data, which were not possible to see with X-ray diffraction data. The relation between the q-vectors and the mole% An composition is revealed for the entire compositional range of e-plagioclase, from An25 to An75. The previously proposed two-trend relation depending on the cooling rate and phase transition path is confirmed. A new classification of e-plagioclase (e α, e β and e γ) is proposed based on the q-vector of the structure, which makes it an independent character from the presence/absence of density modulation. New parameters are proposed to quantify the ordering states of these complicated aperiodic structures of e-plagioclases, such as the difference between 〈T1o—O〉 and 〈T1m—O〉 at phase t = 0.2 or the normalized intensity of the (071\bar 1) reflection.

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Cryo-neutron crystallographic data collection and preliminary refinement of left-handed Z-DNA d(CGCGCG)

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x1801066x ◽

2018 ◽

Vol 74 (10) ◽

pp. 603-609 ◽

Cited By ~ 2

Author(s):

Joel M. Harp ◽

Leighton Coates ◽

Brendan Sullivan ◽

Martin Egli

Keyword(s):

Low Temperature ◽

Data Collection ◽

Neutron Diffraction ◽

Diffraction Data ◽

Water Molecules ◽

X Rays ◽

Neutron Diffraction Data ◽

Oak Ridge ◽

Left Handed ◽

Z Dna

Crystals of left-handed Z-DNA [d(CGCGCG)]2 diffract X-rays to beyond 1 Å resolution, feature a small unit cell (∼18 × 31 × 44 Å) and are well hydrated, with around 90 water molecules surrounding the duplex in the asymmetric unit. The duplex shows regular hydration patterns in the narrow minor groove, on the convex surface and around sugar–phosphate backbones. Therefore, Z-DNA offers an ideal case to test the benefits of low-temperature neutron diffraction data collection to potentially determine the donor–acceptor patterns of first- and second-shell water molecules. Nucleic acid fragments pose challenges for neutron crystallography because water molecules are located on the surface rather than inside sequestered spaces such as protein active sites or channels. Water molecules can be expected to display dynamic behavior, particularly in cases where water is not part of an inner shell and directly coordinated to DNA atoms. Thus, nuclear density maps based on room-temperature diffraction data with a resolution of 1.6 Å did not allow an unequivocal determination of the orientations of water molecules. Here, cryo-neutron diffraction data collection for a Z-DNA crystal on the Macromolecular Neutron Diffractometer at the Spallation Neutron Source at Oak Ridge National Laboratory and the outcome of an initial refinement of the structure are reported. A total of 12 diffraction images were recorded with an exposure time of 3.5 h per image, whereby the crystal was static for each diffraction image with a 10° φ rotation between images. Initial refinements using these neutron data indicated the positions and orientations of 30 water molecules within the first hydration shell of the DNA molecule. This experiment constitutes a state-of-the-art approach and is the first attempt to our knowledge to determine the low-temperature neutron structure of a DNA crystal.

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Low-temperature crystal structure of the unconventional spin-triplet superconductor UTe2 from single-crystal neutron diffraction

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520619016950 ◽

2020 ◽

Vol 76 (1) ◽

pp. 137-143 ◽

Cited By ~ 4

Author(s):

Vladimir Hutanu ◽

Hao Deng ◽

Sheng Ran ◽

Wesley T. Fuhrman ◽

Henrik Thoma ◽

...

Keyword(s):

Crystal Structure ◽

Low Temperature ◽

Neutron Diffraction ◽

Single Crystal ◽

Diffraction Data ◽

Linear Thermal Expansion ◽

The Body ◽

Superconducting Transition ◽

Neutron Diffraction Data ◽

Spin Triplet

The crystal structure of a new superconductor UTe2 has been investigated using single-crystal neutron diffraction for the first time at the low temperature (LT) of 2.7 K, just above the superconducting transition temperature of ∼1.6 K, in order to clarify whether the orthorhombic structure of type Immm (No. 71), reported for the room-temperature (RT) structure persists down to the superconducting phase and can be considered as a parent symmetry for the development of spin-triplet superconductivity. In contrast to the previously reported phase transition at about 100 K [Stöwe (1996). J. Solid State Chem. 127, 202–210], our high-precision LT neutron diffraction data show that the body-centred RT symmetry is indeed maintained down to 2.7 K. No sign of a structural change from RT down to 2.7 K was observed. The most significant change depending on temperature was observed for the U ion position and the U–U distance along the c direction, implying its potential importance as a magnetic interaction path. No magnetic order could be deduced from the neutron diffraction data refinement at 2.7 K, consistent with bulk magnetometry. Assuming normal thermal evolution of the lattice parameters, moderately large linear thermal expansion coefficients of about α = 2.8 (7) × 10−5 K−1 are estimated.

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