scholarly journals Structural Refinement of Carbimazole by NMR Crystallography

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4577
Author(s):  
Andrea Scarperi ◽  
Giovanni Barcaro ◽  
Aleksandra Pajzderska ◽  
Francesca Martini ◽  
Elisa Carignani ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Geometry Optimization ◽  
Optimization Methods ◽  
2D Nmr ◽  
Dimensional Structure ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
Hydrogen Atoms ◽  
X Ray ◽  
Nmr Crystallography

The characterization of the three-dimensional structure of solids is of major importance, especially in the pharmaceutical field. In the present work, NMR crystallography methods are applied with the aim to refine the crystal structure of carbimazole, an active pharmaceutical ingredient used for the treatment of hyperthyroidism and Grave’s disease. Starting from previously reported X-ray diffraction data, two refined structures were obtained by geometry optimization methods. Experimental 1H and 13C isotropic chemical shift measured by the suitable 1H and 13C high-resolution solid state NMR techniques were compared with DFT-GIPAW calculated values, allowing the quality of the obtained structure to be experimentally checked. The refined structure was further validated through the analysis of 1H-1H and 1H-13C 2D NMR correlation experiments. The final structure differs from that previously obtained from X-ray diffraction data mostly for the position of hydrogen atoms.

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.

Structural refinement of nano BaTiO3powder using X-ray diffraction data

2004 ◽  
Vol 39 (13) ◽  
pp. 4363-4366 ◽  
Author(s):  
Yong-Il Kim ◽  
Seung-Hoon Nahm ◽  
Maeng-Joon Jung
Keyword(s):  
Diffraction Data ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
X Ray

Powder X-ray diffraction of Metastudtite, (UO2)O2(H2O)2

2016 ◽  
Vol 31 (1) ◽  
pp. 71-72 ◽  
Author(s):  
Mark A. Rodriguez ◽  
Philippe E. Weck ◽  
Joshua D. Sugar ◽  
Thomas J. Kulp
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
First Principles ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Unit Cells

There has been some confusion in the published literature concerning the structure of Metastudtite (UO2)O2(H2O)2 where differing unit cells and space groups have been cited for this compound. Owing to the absence of a refined structure for Metastudtite, Weck et al. (2012) have documented a first-principles study of Metastudtite using density functional theory (DFT). Their model presents the structure of Metastudtite as an orthorhombic (space group Pnma) structure with lattice parameters of a = 8.45, b = 8.72, and c = 6.75 Å. A Powder Diffraction File (PDF) database entry has been allocated for this hypothetical Metastudtite phase based on the DFT modeling (see 01-081-9033) and aforementioned Dalton Trans. manuscript. We have obtained phase pure powder X-ray diffraction data for Metastudtite and have confirmed the model of Weck et al. via Rietveld refinement (see Figure 1). Structural refinement of this powder diffraction dataset has yielded updated refined parameters. The new cell has been determined as a = 8.411(1), b = 8.744(1), and c = 6.505(1) Å; cell volume = 478.39 Å3. There are only subtle differences between the refined structure and that of the first-principles model derived from DFT. Notably, the b-axis is significantly contracted in the final refinement as compared with DFT. There were also subtle changes to the U1, O1, and O3 atom positions. Tabulated powder diffraction data (d's and I's) for the Metastudtite have been derived from the refined model and these new values can serve to augment the PDF entry 01-081-9033 with a more updated entry based on observed X-ray powder diffraction data.

Structural investigation ofN,N′-methylenebisacrylamideviaX-ray diffraction assisted by crystal structure prediction

2015 ◽  
Vol 48 (2) ◽  
pp. 550-557 ◽  
Author(s):  
Claudia Graiff ◽  
Daniele Pontiroli ◽  
Laura Bergamonti ◽  
Chiara Cavallari ◽  
Pier Paolo Lottici ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Diffraction Data ◽  
Structure Prediction ◽  
Density Functional ◽  
Geometry Optimization ◽  
Lattice Energy ◽  
Strong Interactions ◽  
Crystal Structure Prediction ◽  
X Ray Diffraction ◽  
X Ray

The crystal structure ofN,N′-methylenebisacrylamide was determined through the geometry optimization of the molecular unit with density functional theory and conformational analysis, and then through the calculation of the packingviaa crystal structure prediction protocol, based on lattice energy minimization. All the calculated structures were ranked, comparing their powder pattern with the laboratory low-quality X-ray diffraction data. Rietveld refinement of the best three proposed structures allowed the most probable crystal arrangement of the molecules to be obtained. This approach was essential for disentangling the twinning problems affecting the single-crystal X-ray diffraction data, collected on samples obtainedviarecrystallization of powder, which definitely confirmed the predicted model. It was found thatN,N′-methylenebisacrylamide shows a monoclinic structure in the space groupC2/c, with lattice parametersa= 17.822 (12),b= 4.850 (3),c= 19.783 (14) Å, β = 102.370 (9)°,V= 1670 (2) Å3. Two strong interactions between the amide protons and the carbonyl groups of neighbouring molecules were found along thebaxis, determining the crystal growth in the form of wires in this direction. This work provides a further example of how computational methods may help to investigate low-quality molecular crystals with standard diffraction techniques.

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.

Structural refinement of RE2ACu2O6 from powder X-ray diffraction data (RE=La, Nd, A=Sr, Ca)

1999 ◽  
Vol 313 (3-4) ◽  
pp. 285-293 ◽  
Author(s):  
H Deng ◽  
C Dong ◽  
H Chen ◽  
F Wu ◽  
S.L Jia ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Structural Refinement ◽  
X Ray Diffraction ◽  
X Ray

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.

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