Low-Temperature Neutron Diffraction Structures ofN-Glycoprotein Linkage Models and Analogues: Structure Refinement and Trifurcated Hydrogen Bonds

2011 ◽  
Vol 133 (26) ◽  
pp. 10042-10045 ◽  
Author(s):  
Gianluca Cioci ◽  
Amrita Srivastava ◽  
Duraikkannu Loganathan ◽  
Sax A. Mason ◽  
Serge Pérez ◽  
...  
Keyword(s):  
Low Temperature ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Structure Refinement ◽  
Linkage Models

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

2001 ◽  
Vol 57 (6) ◽  
pp. 833-841 ◽  
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.

Neutron Diffraction Study of Aromatic Hydrogen Bonds: 5-Ethynyl-5H-dibenzo[a,d]cyclohepten-5-ol at 20K

1997 ◽  
Vol 53 (5) ◽  
pp. 843-848 ◽  
Author(s):  
T. Steiner ◽  
S. A. Mason ◽  
M. Tamm
Keyword(s):  
Crystal Structure ◽  
Low Temperature ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Neutron Diffraction Study ◽  
Hydroxyl Group ◽  
Intermolecular Hydrogen Bonds ◽  
Ethynyl Group ◽  
Compound C ◽  
Aromatic Hydrogen

The neutron diffraction crystal structure of the title compound, C17H12O, was determined at 20 K. One of the benzyl groups accepts intermolecular hydrogen bonds from a hydroxyl and an ethynyl group, one to each face of the ring. The bond donated by the hydroxyl group points almost linearly to an aromatic C atom with a H...C separation of 2.339 (6) Å. The bond donated by the ethynyl group points to the aromatic midpoint M with a H...M separation of 2.587 (5) Å. The average acetylenic C—H bond length determined by low- temperature neutron diffraction is only 1.062 (6) Å, appreciably shorter than observed for chemically different C—H bonds.

Hirshfeld atom refinement for modelling strong hydrogen bonds

2014 ◽  
Vol 70 (5) ◽  
pp. 483-498 ◽  
Author(s):  
Magdalena Woińska ◽  
Dylan Jayatilaka ◽  
Mark A. Spackman ◽  
Alison J. Edwards ◽  
Paulina M. Dominiak ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Atom ◽  
Low Temperature ◽  
Hydrogen Bonds ◽  
Neutron Diffraction ◽  
Electron Density ◽  
Diffraction Experiment ◽  
Neutron Diffraction Experiment ◽  
X Ray ◽  
Atom Model

High-resolution low-temperature synchrotron X-ray diffraction data of the salt L-phenylalaninium hydrogen maleate are used to test the new automated iterative Hirshfeld atom refinement (HAR) procedure for the modelling of strong hydrogen bonds. The HAR models used present the first examples ofZ′ > 1 treatments in the framework of wavefunction-based refinement methods. L-Phenylalaninium hydrogen maleate exhibits several hydrogen bonds in its crystal structure, of which the shortest and the most challenging to model is the O—H...O intramolecular hydrogen bond present in the hydrogen maleate anion (O...O distance is about 2.41 Å). In particular, the reconstruction of the electron density in the hydrogen maleate moiety and the determination of hydrogen-atom properties [positions, bond distances and anisotropic displacement parameters (ADPs)] are the focus of the study. For comparison to the HAR results, different spherical (independent atom model, IAM) and aspherical (free multipole model, MM; transferable aspherical atom model, TAAM) X-ray refinement techniques as well as results from a low-temperature neutron-diffraction experiment are employed. Hydrogen-atom ADPs are furthermore compared to those derived from a TLS/rigid-body (SHADE) treatment of the X-ray structures. The reference neutron-diffraction experiment reveals a truly symmetric hydrogen bond in the hydrogen maleate anion. Only with HAR is it possible to freely refine hydrogen-atom positions and ADPs from the X-ray data, which leads to the best electron-density model and the closest agreement with the structural parameters derived from the neutron-diffraction experiment,e.g.the symmetric hydrogen position can be reproduced. The multipole-based refinement techniques (MM and TAAM) yield slightly asymmetric positions, whereas the IAM yields a significantly asymmetric position.

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].

Low temperature neutron diffraction data for CeCo0.86Ge2

2005 ◽  
Vol 387 (1-2) ◽  
pp. L8-L10 ◽  
Author(s):  
A. Gil ◽  
B. Penc ◽  
J. Hernandez-Velasco ◽  
E. Wawrzyńska ◽  
A. Szytuła
Keyword(s):  
Low Temperature ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Neutron Diffraction Data

Low Temperature Neutron Diffraction Data for CeCo0.86Ge2.

ChemInform ◽  
2005 ◽  
Vol 36 (15) ◽  
Author(s):  
A. Gil ◽  
B. Penc ◽  
J. Hernandez-Velasco ◽  
E. Wawrzynska ◽  
A. Szytula
Keyword(s):  
Low Temperature ◽  
Neutron Diffraction ◽  
Diffraction Data ◽  
Neutron Diffraction Data

Infrared spectra of the ammonium ion in crystals. Part VIII. Spectroscopic criteria of highly-bent hydrogen bonds

1980 ◽  
Vol 58 (9) ◽  
pp. 867-874 ◽  
Author(s):  
Osvald Knop ◽  
Wolfgang J. Westerhaus ◽  
Michael Falk
Keyword(s):  
Low Temperature ◽  
Hydrogen Bonds ◽  
Infrared Spectra ◽  
Room Temperature ◽  
Ammonium Ion ◽  
Temperature Transition ◽  
Increasing Temperature

Available evidence suggests that (1) the stretching frequencies of highly-bent hydrogen bonds decrease with increasing temperature, regardless of whether the bonds are static or dynamic in character, to a single acceptor or to several competing acceptors; and (2) departures from symmetric trifurcation (or bifurcation) toward asymmetric situations lower the stretching frequency. In further support of these criteria isotopic probe ion spectra between 10 K and room temperature have been obtained for taurine and for trigonal (NH4)2MF6 (M = Si, Ge, Sn, Ti). Evidence of a low-temperature transition at 100(10) K in trigonal (NH4)2SnF6 is presented, and existence of the previously reported transition at 38.6 K in trigonal (NH4)2SiF6 is confirmed. Symmetry changes associated with these transitions are discussed.

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