Insights into Proton Dynamics in a Photofunctional Salt‐Cocrystal Continuum: Single‐Crystal X‐ray, Neutron Diffraction, and Hirshfeld Atom Refinement

"The renaissance in Laue studies - at neutron sources - provides us with access to single crystal neutron diffraction data for synthetic compounds without requiring synthesis of prohibitively large amounts of compound or improbably large crystals. Such neutron diffraction studies provide vital data where proof of the presence or absence of hydrogen in particular locations is required and which cannot validly be proved by X-ray studies. Since the commissioning of KOALA at OPAL in 2009[1] we have obtained numerous data sets which demonstrate the vital importance of measuring data even where the extent of the diffraction pattern is at relatively low resolution - especially when compared to that obtainable for the same compound with X-rays. In the Laue experiment performed with a fixed radius detector, data reduction is only feasible for crystals in the ""goldilocks"" zone – where the unit cell is relatively large for the detector, a correspondingly low resolution diffraction pattern in which adjacent spots are less affected by overlap will yield more data against which a structure can be refined than a pattern of higher resolution – one where neighbouring spots overlap rendering both unusable (in our current methodology). Analogous application of powder neutron diffraction in such determinations is also considered. Single crystal neutron diffraction studies of several important compounds (up to 5KDa see figure below)[2] in which precise determination of hydride content by neutron diffraction was pivotal to the final formulation will be presented. The neutron data sets typically possess 20% or fewer unique data at substantially "lower resolution" than the corresponding X-ray data sets. Careful refinement clearly reveals chemical detail which is typically unexplored in related X-ray diffraction studies reporting high profile chemistry despite the synthetic route being one which hydride ought to be considered/excluded in product formulation."

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Accurate H-atom parameters for the two polymorphs of L-histidine at 5, 105 and 295 K

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s205252062100740x ◽

2021 ◽

Vol 77 (5) ◽

pp. 785-800

Author(s):

Giulia Novelli ◽

Charles J. McMonagle ◽

Florian Kleemiss ◽

Michael Probert ◽

Horst Puschmann ◽

...

Keyword(s):

Neutron Diffraction ◽

Single Crystal ◽

Diffraction Data ◽

Crystal Packing ◽

Basis Sets ◽

X Ray Diffraction ◽

X Ray ◽

Refinement Method ◽

Primary Amino ◽

Precision And Accuracy

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.

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H-bonding scheme in allactite: a combined single-crystal X-ray and neutron diffraction, optical absorption spectroscopy, FTIR and EPMA-WDS study

Mineralogical Magazine ◽

10.1180/minmag.2016.080.020 ◽

2016 ◽

Vol 80 (5) ◽

pp. 719-732 ◽

Cited By ~ 2

Author(s):

G. Diego Gatta ◽

Ferdinando Bosi ◽

Maria Teresa Fernandez Diaz ◽

Ulf Hålenius

Keyword(s):

Neutron Diffraction ◽

Optical Absorption ◽

Single Crystal ◽

Absorption Spectroscopy ◽

Structure Refinement ◽

Site Occupancy ◽

Optical Absorption Spectroscopy ◽

Hydroxyl Groups ◽

X Ray ◽

Bonding Scheme

AbsatractThe crystal chemistry of allactite from Långban, Värmland (Sweden) was investigated by single-crystal X-ray and neutron diffraction, optical absorption spectroscopy, Fourier-transform infra-red spectroscopy (FTIR) and electron microprobe analysis by wavelength-dispersive spectroscopy (EPMA-WDS). The optical spectra indicate the presence of Mn in valence state 2+ only. Assuming 16 O atoms per formula unit, arsenic as As5+and the (OH) content calculated by charge balance, the resulting formula based on the EPMA-WDS data is (Mn2+6.73Ca0.13Mg0.12Zn0.02)∑7.00(As5+)2.00O16H8, very close to the ideal composition Mn7(AsO4)2(OH)8. In the unpolarized FTIR spectrum of allactite, fundamental (OH)-stretching bands are observed at 3236, 3288, 3387, 3446, 3484, 3562 and 3570 cm–1, suggesting that a number of OH environments, with different hydrogen bond strengths, occur in the structure. The neutron structure refinement shows that four independent H sites occur in allactite with full site occupancy, all as members of hydroxyl groups. The complex hydrogen-bonding scheme in the allactite structure is now well defined, with at least nine hydrogen bonds energetically favourable with mono-, bi- and trifurcated configurations.

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Single-crystal neutron diffraction study of β-Cs3(HSO4)2[H2−x (S x P1−x )O4] (x ≃ 0.5) at 15 K

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768198013573 ◽

1999 ◽

Vol 55 (3) ◽

pp. 285-296 ◽

Cited By ~ 6

Author(s):

S. M. Haile ◽

W. T. Klooster

Keyword(s):

Neutron Diffraction ◽

Single Crystal ◽

Local Structure ◽

Unit Cell Volume ◽

Structural Models ◽

Neutron Diffraction Study ◽

Unit Cell ◽

Asymmetric Unit ◽

X Ray ◽

Anisotropic Displacement Parameters

The structure of β-Cs3(HSO4)2[H2−x (S x P1−x )O4] has been examined by single-crystal neutron diffraction at 15 K. The compound crystallizes in space group C2/c and contains four formula units in the unit cell, with lattice parameters a = 19.769 (9), b = 7.685 (2), c = 8.858 (3) Å and β = 100.60 (4)°. Refinement of P, S and H site occupancies indicated that the value of x (in the stoichiometry) is 0.500 (6). This, together with the unit-cell volume of 1322.8 (14) Å3, implies a density of 3.463 Mg m−3. The structure contains zigzag rows of XO4 anions, where X = P or S, that alternate, in a checkerboard fashion, with zigzag rows of Cs cations. Moreover, there is one proton site, H(3), with an occupancy of 0.25 and one X-atom site, X(1), that is occupied by 0.5 P and 0.5 S. These features are in general agreement with a previous X-ray structure determination carried out at 298 K. In contrast to the X-ray study, however, it was found that two different structural models adequately fit the diffraction data. In the first model, the proton vacancies and the P atoms were assumed to be randomly distributed over the H(3) and X(1) sites, respectively, and to have no impact on the local structure. In the second model, several atoms were assigned split occupancies over two neighboring sites, to reflect the presence or absence of a proton vacancy, and the presence of P or S on the X(1) site. Refinement assuming the first model, in which anisotropic displacement parameters for 12 of 14 atom sites in the asymmetric unit were employed, yielded residuals w R(F 2) = 0.084 and w R(F) = 0.038. For the second model, in which anisotropic displacement parameters were utilized for only the five atoms that were not split relative to the first model, the residuals were w R(F 2) = 0.081 and w R(F) = 0.036.

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