On the complex H-bonding network in paravauxite, Fe2+Al2(PO4)2(OH)2·8H2O: A single-crystal neutron diffraction study

AbstractThe crystal structure and the chemical composition of a paravauxite from the Siglo Veinte Mine, Llallagua, Bustillo Province, Potosi Department, Bolivia [Fe(Fe0.9162+Mn0.0162+Mg0.064Ca0.002)∑0.998Al(1)Al(2)Al2.005P(P1.998Si0.002)∑2O8(OH)2·8H2O, a = 5.242(1) Å, b = 10.569(2) Å, c = 6.970(2) Å, α = 106.78(3)°, β = 110.81(2)° and γ = 72.29(2)°, space group P], was investigated by single-crystal neutron diffraction and electron microprobe analysis in wavelength-dispersive mode. Neutron-intensity data were collected at 293 K and anisotropic structure refinement was performed. At the end of the refinement no peak larger than ±1.3 fm/Å3 was present in the final difference-Fourier map of the nuclear density. The final statistical index was R1 = 0.0495 for 194 refined parameters and 1678 unique reflections with Fo > 4σ(Fo). Eleven independent H sites (i.e. H(1), H(2), H(3), H(4A), H(4B), H(5), H(6), H(7), H(8), H(9A) and H(9B)), all at ∼1 Å from the respective O sites, were located successfully. H(4A) and H(4B) and H(9A) and H(9B) are two mutually exclusive subsite couples only 0.4−0.6 Å apart. The complex H-bonding scheme in the paravauxite structure is now well defined and 12 independent H bonds, with an energetically favourable bonding configuration, are described. A comparison between the previous experimental findings based on Raman and infrared spectroscopy and those obtained in this present study is carried out. Paravauxite provides the rare opportunity to investigate the H-bond configuration of coexisting hydroxyl groups and H2O molecules in minerals by single-crystal neutron diffraction. H2O is present as zeolitic (i.e. lying in the cavities) and non-zeolitic H2O (i.e. bonded to Al or Fe to form Al or Fe octahedra).

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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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Coexisting hydroxyl groups and H2O molecules in minerals: A single-crystal neutron diffraction study of eosphorite, MnAlPO4(OH)2{middle dot}H2O

American Mineralogist ◽

10.2138/am.2013.4438 ◽

2013 ◽

Vol 98 (7) ◽

pp. 1297-1301 ◽

Cited By ~ 6

Author(s):

G. D. Gatta ◽

G. Nenert ◽

P. Vignola

Keyword(s):

Neutron Diffraction ◽

Single Crystal ◽

Diffraction Study ◽

Neutron Diffraction Study ◽

Hydroxyl Groups

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Hydrogen-bond network in cyclodecaamylose hydrate at 20 K; neutron diffraction study of novel structural motifs band-flip and kink in α-(1→4)-D-glucoside oligosaccharides

Acta Crystallographica Section B Structural Science ◽

10.1107/s0108768101014288 ◽

2001 ◽

Vol 57 (6) ◽

pp. 833-841 ◽

Cited By ~ 9

Author(s):

K. Imamura ◽

O. Nimz ◽

J. Jacob ◽

D. Myles ◽

S. A. Mason ◽

...

Keyword(s):

Hydrogen Bonds ◽

Neutron Diffraction ◽

Diffraction Study ◽

Structure Refinement ◽

Neutron Diffraction Study ◽

The Other ◽

Water Molecules ◽

Hydroxyl Groups ◽

Neutron Density ◽

Asymmetric Unit

A single-crystal neutron diffraction study of cyclodecaamylose (CA10) was carried out at 20 K. CA10 crystallizes with 27.18 water molecules [(C6H10O5)10·27.18H2O] in space group C2 with unit-cell constants a = 29.31 (5), b = 9.976 (10), c = 19.34 (2) Å, β = 121.07 (2)°. The asymmetric unit contains a half molecule of CA10 and 13.59 water molecules, the other half being related by a crystallographic twofold rotation axis. All H atoms except two water H atoms could be located from difference neutron-density maps; structure refinement converged at R = 0.635. Two of the five CH2—O6 groups and one of the 15 O2, O3 hydroxyl groups of CA10 are twofold orientationally disordered. A total of 13.59 water molecules in the asymmetric unit are distributed over 23 positions; 20 of which are in the CA10 cavity, and the other three occupy intermolecular interstices. Of the 123 symmetry-independent hydrogen bonds, 25 (= 20%) are three-centered and 7 (= 6%) are four-centered. Water molecules and O—H groups of CA10 form an extended network with cooperative O—H...O—H...O—H hydrogen bonds. They are arranged in 11 polygons with three, four, five, six and eight O—H bonds and in homodromic, antidromic and heterodromic arrangements. Nine polygons are located within the cavity and the others are outside.

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First accurate location of two proton sites in tourmaline: A single-crystal neutron diffraction study of oxy-dravite

Mineralogical Magazine ◽

10.1180/minmag.2014.078.3.15 ◽

2014 ◽

Vol 78 (3) ◽

pp. 681-692 ◽

Cited By ~ 14

Author(s):

G. D. Gatta ◽

F. Bosi ◽

G. J. McIntyre ◽

H. Skogby

Keyword(s):

Neutron Diffraction ◽

Single Crystal ◽

Diffraction Study ◽

Structure Refinement ◽

Site Occupancy ◽

Bond Distance ◽

Neutron Diffraction Study ◽

Fold Axis ◽

Absorption Bands ◽

First Time

AbstractA single-crystal neutron diffraction study of oxy-dravite from Osarara (Narok district, Kenya) was performed. Intensity data were collected in Laue geometry at 10 K and anisotropic-structure refinement was undertaken. For the first time, two independent H sites were refined unambiguously for a mineral belonging to the tourmaline supergroup and located at 0.26, 0.13, 0.38 (labelled as H3, site occupancy ∼98%) and at 0, 0, 0.9 (labelled as H1, site occupancy ∼25%). The H-bonding scheme can thus be defined as follows: (1) the O at the O3 site acts as a ‘donor’ and the O at the O5 site as ‘acceptor’, the refined O3–H3 bond distance is 0.972(2) Å (and 0.9946 Å corrected for “riding motion”), H3⋯O5 = 2.263(2) Å, O3⋯O5 = 3.179(1) Å and O3–H3⋯O5 = 156.6(1)°; (2) the oxygen at the O1 site acts as a ‘donor’ and the O atoms at O4 and O5 as ‘acceptors’, the refined O1–H1 bond distance is 0.958(8) Å (and 0.9833 Å corrected for “riding motion”), H1⋯O4 = 2.858(6) Å, O1⋯O4 = 3.378(1) Å and O1–H1⋯O4 = 115.12(1)°, whereas H1⋯O5 = 2.886(6) Å, O1⋯O5 = 3.444(1) Å and O1–H1⋯O5 = 118.23(1)°. A further test refinement was performed with the H1 site out of the three-fold axis (at 0.02, 0.01, 0.90); this leads to O1–H1 = 0.995(8) Å (and 1.0112 Å corrected for “riding motion”), H1⋯O4 = 2.747(6) Å and O1–H1⋯O4 = 121.7(4)°, whereas H1⋯O5 = 2.654(9) Å and O1–H1⋯O5 = 136.5(6)°. Bond-valence analysis shows that the H-bonding strength involving O3 is stronger than that involving O1: ∼0.11 and <0.05 valence units, respectively.The refined angle between the O3–H3 vector and [0001] is 3.40(9)°. Such a small angle is in line with a pleochroic scheme for the OH-stretching absorption bands measured by infrared spectroscopy.

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