scholarly journals Towards accurate and precise positions of hydrogen atoms bonded to heavy metal atoms

2021 ◽  
Author(s):  
Magdalena Woińska ◽  
Michał L. Chodkiewicz ◽  
Krzysztof Woźniak
Keyword(s):  
Heavy Metal ◽  
Diffraction Data ◽  
Metal Hydride ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Hydride Complexes ◽  
Heavy Atoms ◽  
Metal Atoms ◽  
Transition Metal Hydride

Positions and anisotropic thermal motion of H-Atoms bound to heavy atoms in transition-metal hydride complexes were successfully refined using Hirshfeld Atom Refinement (HAR) against low resolution X-ray diffraction data.

The first proof of protonated anion tetrahedra in the tsumcorite-type compounds

2004 ◽  
Vol 68 (5) ◽  
pp. 757-767 ◽  
Author(s):  
T. Mihajlović ◽  
H. Effenberger
Keyword(s):  
Crystal Structure ◽  
Hydrothermal Synthesis ◽  
Single Crystal ◽  
Diffraction Data ◽  
Title Compound ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Synthetic Compounds ◽  
X Ray

AbstractHydrothermal synthesis produced the new compound SrCo2(AsO4)(AsO3OH)(OH)(H2O). The compound belongs to the tsumcorite group (natural and synthetic compounds with the general formula M(1)M(2)2(XO4)2(H2O,OH)2; M(1)1+,2+,3+ = Na, K, Rb, Ag, NH4, Ca, Pb, Bi, Tl; M(2)2+,3+ = Al, Mn3+, Fe3+, Co, Ni, Cu, Zn; and X5+,6+ = P, As, V, S, Se, Mo). It represents (1) the first Sr member, (2) the until now unknown [7]-coordination for the M(1) position, (3) the first proof of (partially) protonated arsenate groups in this group of compounds, and (4) a new structure variant.The crystal structure of the title compound was determined using single-crystal X-ray diffraction data. The compound is monoclinic, space group P21/a, with a = 9.139(2), b = 12.829(3), c = 7.522(2) Å, β = 114.33(3)°, V = 803.6(3) Å3, Z = 4 [wR2 = 0.065 for 3530 unique reflections]. The hydrogen atoms were located experimentally.

X-ray diffraction data and Rietveld refinement of CuGaxIn1-xSe2 (x=0.15 and 0.50)

2010 ◽  
Vol 25 (3) ◽  
pp. 253-257 ◽  
Author(s):  
E. J. Friedrich ◽  
R. Fernández-Ruiz ◽  
J. M. Merino ◽  
M. León
Keyword(s):  
Rietveld Refinement ◽  
Diffraction Data ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray ◽  
Zinc Blende ◽  
Metal Atoms ◽  
Tetragonal Crystal ◽  
Unit Cells ◽  
Type Crystal

X-ray powder diffraction data for CuGa0.15In0.85Se2 and CuGa0.50In0.50Se2 are reported. Indexing of the X-ray diffraction powder pattern and the Rietveld refinement confirmed that these compounds crystallize in the tetragonal crystal system, with space group I-42d (No. 122) and lattice parameters of a=5.7528(2) Å and c=11.5225(3) Å for CuGa0.15In0.85Se2 and a=5.6847(1) Å and c=11.2817(1) Å for CuGa0.50In0.50Se2. The CuGaxIn1−xSe2 system presents the chalcopyrite type crystal structure (CuFeS2) and corresponds to two stacked zinc-blende unit cells. The metal atoms Cu, In, and Ga are regularly ordered in the unit cell. Every Se atom is tetrahedrally bonded to two Cu and two In and Ga atoms.

scholarly journals Ultra-high resolution neutron and X-ray crystallography: structure of crambin

2014 ◽  
Vol 70 (a1) ◽  
pp. C1206-C1206
Author(s):  
Julian Chen ◽  
Bryant Hanson ◽  
S Fisher ◽  
Paul Langan ◽  
Andrey Kovalevsky ◽  
...  
Keyword(s):  
High Resolution ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
High Resolution Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Density Maps ◽  
Anisotropic Temperature ◽  
Exchange Patterns

Neutron diffraction data to 1.1 Å was collected on a crystal of the small protein crambin at the Protein Crystallography Station (PCS) at Los Alamos, the highest resolution neutron structure of a protein to date, and a technical benchmark for the instrument. 95 % of the hydrogen atoms in the protein structure were resolved. The data allowed for the refinement of anisotropic temperature factors for selected deuterium atoms within the protein. Hydrogen bonding networks ambiguous in room temperature, ultra-high resolution (0.84 Å) electron density maps are clarified in the nuclear density maps. The ultra-high resolution data also reveals unusual H/D exchange patterns and novel chemistry in the side chains and protein backbone. Complementary X-ray diffraction data was collected at 19-ID at the Advanced Photon Source, with extensive re-configuration of the beamline to allow for operation at higher energy settings.

Two crystal structures of 10,10′-(l,4-phenylene-dimethylidene)-bis-9,10-H-anthracenone

1992 ◽  
Vol 200 (3-4) ◽  
Author(s):  
G. Dewald ◽  
M. Hanack ◽  
E.-M. Peters ◽  
L. Walz
Keyword(s):  
Crystal Structures ◽  
Diffraction Data ◽  
Molecular Structures ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
Space Group ◽  
X Ray ◽  
Crystal And Molecular Structures

AbstractThe crystal and molecular structures of dimorphic 10,10′-(1,4-phenylene-dimethylidene)-bis-9,10-H-anthracenone (1) have been determined using X-ray diffraction data. The compound crystallizes either in the monoclinic space groupSince all non-hydrogen atoms are of pure

TAAM: a reliable and user friendly tool for hydrogen-atom location using routine X-ray diffraction data

2020 ◽  
Vol 76 (3) ◽  
pp. 296-306 ◽  
Author(s):  
Kunal Kumar Jha ◽  
Barbara Gruza ◽  
Prashant Kumar ◽  
Michal Leszek Chodkiewicz ◽  
Paulina Maria Dominiak
Keyword(s):  
Neutron Diffraction ◽  
Diffraction Data ◽  
Structure Refinement ◽  
X Rays ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Bond Lengths ◽  
Atom Model ◽  
User Friendly

Hydrogen is present in almost all of the molecules in living things. It is very reactive and forms bonds with most of the elements, terminating their valences and enhancing their chemistry. X-ray diffraction is the most common method for structure determination. It depends on scattering of X-rays from electron density, which means the single electron of hydrogen is difficult to detect. Generally, neutron diffraction data are used to determine the accurate position of hydrogen atoms. However, the requirement for good quality single crystals, costly maintenance and the limited number of neutron diffraction facilities means that these kind of results are rarely available. Here it is shown that the use of Transferable Aspherical Atom Model (TAAM) instead of Independent Atom Model (IAM) in routine structure refinement with X-ray data is another possible solution which largely improves the precision and accuracy of X—H bond lengths and makes them comparable to averaged neutron bond lengths. TAAM, built from a pseudoatom databank, was used to determine the X—H bond lengths on 75 data sets for organic molecule crystals. TAAM parametrizations available in the modified University of Buffalo Databank (UBDB) of pseudoatoms applied through the DiSCaMB software library were used. The averaged bond lengths determined by TAAM refinements with X-ray diffraction data of atomic resolution (d min ≤ 0.83 Å) showed very good agreement with neutron data, mostly within one single sample standard deviation, much like Hirshfeld atom refinement (HAR). Atomic displacements for both hydrogen and non-hydrogen atoms obtained from the refinements systematically differed from IAM results. Overall TAAM gave better fits to experimental data of standard resolution compared to IAM. The research was accompanied with development of software aimed at providing user-friendly tools to use aspherical atom models in refinement of organic molecules at speeds comparable to routine refinements based on spherical atom model.

scholarly journals Hydrogen atoms in bridging positions from quantum crystallographic refinements: influence of hydrogen atom displacement parameters on geometry and electron density

CrystEngComm ◽  
2020 ◽  
Vol 22 (28) ◽  
pp. 4778-4789 ◽  
Author(s):  
Lorraine A. Malaspina ◽  
Anna A. Hoser ◽  
Alison J. Edwards ◽  
Magdalena Woińska ◽  
Michael J. Turner ◽  
...  
Keyword(s):  
Hydrogen Atom ◽  
Electron Density ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Atom Displacement

Hydrogen atom positions can be obtained accurately from X-ray diffraction data of hydrogen maleate salts via Hirshfeld atom refinement.

An unprecedented structural phase transition in struvite-type compounds: dimorphism of KMgAsO4(H2O)6

2019 ◽  
Vol 74 (1) ◽  
pp. 9-14
Author(s):  
Matthias Weil
Keyword(s):  
Crystal Structure ◽  
Phase Transition ◽  
Diffraction Data ◽  
Structural Changes ◽  
Structural Phase ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Continuous Type ◽  
Reversible Phase Transition

AbstractThe crystal structure of struvite-type KMgAsO4(H2O)6 has been redetermined from single crystal X-ray diffraction data at room temperature. The previous structure model based on powder X-ray diffraction data was confirmed with higher precision and accuracy and with all hydrogen atoms located. KMgAsO4(H2O)6 undergoes a reversible phase transition of the continuous type at 263(2) K, changing the symmetry from orthorhombic to monoclinic. The corresponding Pnm21→P1121 symmetry reduction is of a translationengleiche type with index 2 and was monitored by temperature-dependent powder X-ray diffraction measurements. Such a phase transition is unprecedented for struvite-type compounds. The crystal structure of the monoclinic polymorph was determined from a two-domain crystal at 100 K. Except for the motion of one of the water molecules towards stronger hydrogen-bonding interactions, structural changes between the two polymorphs are small.

Powder X-ray diffraction of levothyroxine sodium pentahydrate, C15H10I4NNaO4(H2O)5

2015 ◽  
Vol 30 (4) ◽  
pp. 370-371
Author(s):  
J.A. Kaduk ◽  
K. Zhong ◽  
T.N. Blanton ◽  
S. Gates ◽  
T.G. Fawcett
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Room Temperature ◽  
Levothyroxine Sodium ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Synchrotron Powder Diffraction

The room-temperature crystal structure of levothyroxine sodium pentahydrate has been refined using synchrotron powder diffraction data. The compound crystallizes in space group P1 (#1) with a = 8.2489(4), b = 9.4868(5), c = 15.8298(6) Å, α = 84.1387(4), β = 83.1560(3), γ = 85.0482(3) deg, V = 1220.071(9) Å3, and Z = 2. Hydrogen atoms (missing from the previously-reported structure) were included.

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