Role of C-H.cntdot..cntdot..cntdot.O hydrogen bonds in the coordination of water molecules. Analysis of neutron diffraction data

1993 ◽  
Vol 115 (11) ◽  
pp. 4540-4547 ◽  
Author(s):  
Thomas Steiner ◽  
Wolfram Saenger
Keyword(s):  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Water Molecules ◽  
Neutron Diffraction Data

Crystal engineering in the gem-alkynol family: the key role of water in the structure of 2,3,5,6-tetrabromo-trans-1,4-diethynyl-cyclohexa-2,5-diene-1,4-diol dihydrate determined by X-ray and neutron diffraction at 150 K

2001 ◽  
Vol 57 (4) ◽  
pp. 560-566 ◽  
Author(s):  
Clair Bilton ◽  
Judith A. K. Howard ◽  
N. N. L. Madhavi ◽  
Gautam R. Desiraju ◽  
Frank H. Allen ◽  
...  
Keyword(s):  
Low Temperature ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Crystal Engineering ◽  
Water Molecules ◽  
Neutron Diffraction Data ◽  
Acta Cryst ◽  
Parent Molecule ◽  
X Ray

The structure of the title compound has been determined using low-temperature (150 K) single-crystal X-ray and neutron diffraction data. Crystals adopt the uncommon space group P42/ncm and display a complex set of intermolecular interactions in which the water molecules play the crucial role: the water O-atom [O2(w)] accepts two hydrogen bonds and both water H atoms act as bifurcated donors. A set of O—H...O hydrogen bonds is formed around the 42 axis comprising (a) a cyclic tetrameric synthon involving four donor-H from two water molecules and two O(hydroxy) acceptors from two parent molecules, and (b) short discrete O(hydroxy)—H...O2(w) hydrogen bonds which link these tetramers along the c axis. Four Br...Br interactions [3.708 (1) Å] form cyclic Br4 tetramers around the \bar 4 axis and are linked to the O—H...O system via O2(w)—H...Br bonds with H...Br = 2.995 (2) Å. Finally, the O—H...O system is further linked to the parent molecules via C≡C...H...O2(w) bonds of 2.354 (3) Å. The supramolecular structure of the title hydrate is compared with that of the non-hydrated parent molecule, which also forms cyclic O—H...O bonded tetrameric synthons, and with its (non-hydrated) tetrachloro analogue, which forms cyclic tetrameric Cl4 synthons [Madhavi, Desiraju et al. (2000b). Acta Cryst. B56, 1063–1070].

Structure of strontium hydroxide octahydrate, Sr(OH)2·8H2O, at 20, 100 and 200 K from neutron diffraction

2005 ◽  
Vol 61 (4) ◽  
pp. 381-386 ◽  
Author(s):  
J. S. Ricci ◽  
R. C. Stevens ◽  
R. K. McMullan ◽  
W. T. Klooster
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Double Layers ◽  
Neutron Diffraction Data ◽  
Distorted Octahedra ◽  
Strontium Hydroxide ◽  
Fourfold Axis

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.

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

1998 ◽  
Vol 54 (4) ◽  
pp. 464-470 ◽  
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.

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

2018 ◽  
Vol 74 (10) ◽  
pp. 603-609 ◽  
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.

Determination of the number of water molecules in the proton pathway of bacteriorhodopsin using neutron diffraction data

2003 ◽  
Vol 32 (4) ◽  
pp. 392-401 ◽  
Author(s):  
Georgios Papadopoulos ◽  
Thomas Hau�
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Water Molecules ◽  
Neutron Diffraction Data
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