Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis

2022 ◽  
Vol 78 (2) ◽  
Author(s):  
Sehrish Akram ◽  
Arshad Mehmood ◽  
Sajida Noureen ◽  
Maqsood Ahmed
Keyword(s):  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Single Crystal ◽  
Diffraction Data ◽  
Density Functional ◽  
Quantitative Estimation ◽  
Topological Analysis ◽  
Pyroglutamic Acid ◽  
X Ray Diffraction ◽  
X Ray

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

Synthesis, structural characterization, and hydrogen bonds of Co9(OH)14[SO4]2

2017 ◽  
Vol 72 (7) ◽  
pp. 505-510
Author(s):  
Hamdi Ben Yahia ◽  
Masahiro Shikano ◽  
Ilias Belharouak
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Single Crystal ◽  
Structural Characterization ◽  
Diffraction Data ◽  
Atmospheric Oxygen ◽  
Molar Ratio ◽  
X Ray Diffraction ◽  
X Ray ◽  
Triclinic System

AbstractThe new compound Co9(OH)14[SO4]2 was synthesized using a hydrothermal method from LiF, Na2SO3, and Co(CH3COO)2·4H2O in a molar ratio of 1:1:1 in the presence of atmospheric oxygen. Its crystal structure was determined from single crystal X-ray diffraction data. Co9(OH)14[SO4]2 crystallizes in the triclinic system, space group P1̅ with a=7.693(2) Å, b=8.318(2) Å, c=8.351(2) Å, α=82.375(5)°, β=77.832(4)°, γ=68.395(4)°, V=484.8(2) Å3, and Z=2. Its structure is composed of cobalt-containing sheets interconnected by SO4 tetrahedra. Bent and symmetrically trifurcated hydrogen bonds have been observed. Furthermore, structural similarities with hydrozincite and brucite minerals have been noticed.

scholarly journals Ab initio and DFT study on Cu (II) complex salicylate derivative

2014 ◽  
Vol 70 (a1) ◽  
pp. C1442-C1442
Author(s):  
Karthikeyan Natarajan ◽  
Sathya Duraisamy ◽  
Sivakumar Kandasamy
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Single Crystal ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray

X -ray diffraction becomes a routine process these decades for determining crystal structure of the materials. Most of the crystal structures solved nowadays is based on single crystal X-ray diffraction because it solves the crystal and molecular structures from small molecules to macro molecules without much human intervention. However it is difficult to grow single crystals of sufficient size and quality for conventional single-crystal X-ray diffraction studies. In such cases it becomes essential that structural information can be determined from powder diffraction data. With the recent developments in the direct-space approaches for structure solution, ab initio crystal structure analysis of molecular solids can be accomplished from X-ray powder diffraction data. It should be recalled that crystal structure determination from laboratory X-ray powder diffraction data is a far more difficult task than that of its single-crystal counterpart, particularly when the molecule possesses considerable flexibility or there are multiple molecules in the asymmetric unit. Salicylic acid and its derivatives used as an anti-inflammatory drug are known for its numerous medicinal applications. In our study, we synthesized mononuclear copper (II) complex of salicylate derivative. The structural characterization of the prepared compound was carried out using powder X-ray diffraction studies. Crystal structure of the compound has been solved by direct-space approach and refined by a combination of Rietveld method using TOPAS Academic V4.1. Density Functional Theory (DFT) calculations have to be carried in the solid state for the compound using GaussianW9.0 in the frame work of a generalized-gradient approximation (GGA). The geometry optimization was to be performed using B3LYP density functional theory. The atomic coordinates were taken from the final X-ray refinement cycle.

Powder X-ray diffraction of varenicline hydrogen tartrate Form B (Chantix®), (C13H14N3)(HC4H4O6)

2021 ◽  
pp. 1-3
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
Powder Diffraction File ◽  
Space Group ◽  
X Ray

The crystal structure of varenicline hydrogen tartrate Form B (Chantix®) has been refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Varenicline hydrogen tartrate Form B crystallizes in space group P212121 (#19) with a = 7.07616(2), b = 7.78357(2), c = 29.86149(7) Å, V = 1644.706(6) Å3, and Z = 4. The hydrogen bonds were identified and quantified. Hydrogen bonds link the cations and anions in zig-zag chains along the b-axis. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

scholarly journals NewM+,M3+-arsenates – the framework structures of AgM3+(HAsO4)2(M3+= Al, Ga) andM+GaAs2O7(M+= Na, Ag)

2017 ◽  
Vol 73 (5) ◽  
pp. 785-790 ◽  
Author(s):  
Karolina Schwendtner ◽  
Uwe Kolitsch
Keyword(s):  
Hydrogen Bonds ◽  
Single Crystal ◽  
Diffraction Data ◽  
Room Temperature ◽  
Three Dimensional ◽  
Structure Type ◽  
X Ray Diffraction ◽  
X Ray ◽  
Donor Acceptor ◽  
Anionic Framework

The crystal structures of hydrothermally synthesized silver(I) aluminium bis[hydrogen arsenate(V)], AgAl(HAsO4)2, silver(I) gallium bis[hydrogen arsenate(V)], AgGa(HAsO4)2, silver gallium diarsenate(V), AgGaAs2O7, and sodium gallium diarsenate(V), NaGaAs2O7, were determined from single-crystal X-ray diffraction data collected at room temperature. The first two compounds are representatives of the MCV-3 structure type known for KSc(HAsO4)2, which is characterized by a three-dimensional anionic framework of corner-sharing alternatingM3+O6octahedra (M= Al, Ga) and singly protonated AsO4tetrahedra. Intersecting channels parallel to [101] and [110] host the Ag+cations, which are positionally disordered in the Ga compound, but not in the Al compound. The hydrogen bonds are relatively strong, with O...O donor–acceptor distances of 2.6262 (17) and 2.6240 (19) Å for the Al and Ga compounds, respectively. The two diarsenate compounds are representatives of the NaAlAs2O7structure type, characterized by an anionic framework topology built ofM3+O6octahedra (M= Al, Ga) sharing corners with diarsenate groups, andM+cations (M= Ag) hosted in the voids of the framework. Both structures are characterized by a staggered conformation of the As2O7groups.

scholarly journals Powder X-ray diffraction of fluorometholone, C22H29FO4

2020 ◽  
Vol 35 (1) ◽  
pp. 71-72
Author(s):  
Diana Gonzalez ◽  
Joseph T. Golab ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
National Laboratory ◽  
Argonne National Laboratory ◽  
The United States ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray

Commercial fluorometholone, CAS #426-13-1, crystallizes in the monoclinic space group P21 (#4) with a = 6.40648(2), b = 13.43260(5), c = 11.00060(8) Å, β = 92.8203(5)°, V = 945.517(5) Å3, and Z = 2. A reduced cell search in the Cambridge Structural Database yielded one previous structure determination, using single-crystal data at 292 K. In this work, the sample was ordered from the United States Pharmacopeial Convention (Lot # R032K0) and analyzed as-received. The room temperature (295 K) crystal structure was refined using synchrotron (λ = 0.412826 Å) powder diffraction data and optimized using density functional theory (DFT) techniques. Hydrogen positions were included as a part of the structure and were re-calculated during the refinement. The diffraction data were collected on beamline 11-BM at the Advanced Photon Source, Argonne National Laboratory, and the powder X-ray diffraction pattern of the compound has been submitted to ICDD® for inclusion in the Powder Diffraction File™. The agreement of the Rietveld-refined and DFT-optimized structures is excellent; the root-mean-square Cartesian displacement is 0.060 Å. In addition to the O–H⋯O hydrogen bonds observed by Park et al. (Park, Y. J., Lee, M. Y., and Cho, S. I. (1992). “Fluorometholone,” J. Korean Chem. Soc. 36, 812–817), C–H⋯O hydrogen bonds contribute to the crystal energy.

Single-crystal investigation of Ce5AgxGe4−x (x = 0.1−1.08) with Sm5Ge4 type

2020 ◽  
Vol 75 (8) ◽  
pp. 765-768
Author(s):  
Bohdana Belan ◽  
Dorota Kowalska ◽  
Mariya Dzevenko ◽  
Mykola Manyako ◽  
Roman Gladyshevskii
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Diffraction Data ◽  
Binary Compound ◽  
Lattice Parameters ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray

AbstractThe crystal structure of the phase Ce5AgxGe4−x (x = 0.1−1.08) has been determined using single-crystal X-ray diffraction data for Ce5Ag0.1Ge3.9. This phase is isotypic with Sm5Ge4: space group Pnma (No. 62), Pearson code oP36, Z = 4, a = 7.9632(2), b = 15.2693(5), c = 8.0803(2) Å; R1 = 0.0261, wR2 = 0.0460, 1428 F2 values and 48 variables. The two crystallographic positions 8d and 4c show Ge/Ag mixing, leading to a slight increase in the lattice parameters as compared to those of the pure binary compound Ce5Ge4.

The modulated structure of Bi2Sr3−xCaxCu2O8: A commensurate model from single crystal X-ray diffraction data

1989 ◽  
Vol 161 (5-6) ◽  
pp. 598-606 ◽  
Author(s):  
G. Calestani ◽  
C. Rizzoli ◽  
M.G. Francesconi ◽  
G.D. Andreetti
Keyword(s):  
Single Crystal ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
Modulated Structure ◽  
X Ray

scholarly journals Crystallographic features of ammonium fluoroelpasolites: dynamic orientational disorder in crystals of (NH4)3HfF7 and (NH4)3Ti(O2)F5

2017 ◽  
Vol 73 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Anatoly A. Udovenko ◽  
Alexander A. Karabtsov ◽  
Natalia M. Laptash
Keyword(s):  
Single Crystal ◽  
Electron Density ◽  
Diffraction Data ◽  
Central Atom ◽  
X Ray Diffraction ◽  
Dynamic Nature ◽  
Orientational Disorder ◽  
High Quality ◽  
Structural Units ◽  
X Ray

A classical elpasolite-type structure is considered with respect to dynamically disordered ammonium fluoro-(oxofluoro-)metallates. Single-crystal X-ray diffraction data from high quality (NH4)3HfF7 and (NH4)3Ti(O2)F5 samples enabled the refinement of the ligand and cationic positions in the cubic Fm \bar 3 m (Z = 4) structure. Electron-density atomic profiles show that the ligand atoms are distributed in a mixed (split) position instead of 24e. One of the ammonium groups is disordered near 8c so that its central atom (N1) forms a tetrahedron with vertexes in 32f. However, a center of another group (N2) remains in the 4b site, whereas its H atoms (H2) occupy the 96k positions instead of 24e and, together with the H3 atom in the 32f position, they form eight spatial orientations of the ammonium group. It is a common feature of all ammonium fluoroelpasolites with orientational disorder of structural units of a dynamic nature.

The crystal structure of gypsum-II determined by single-crystal synchrotron X-ray diffraction data

2010 ◽  
Vol 95 (4) ◽  
pp. 655-658 ◽  
Author(s):  
S. Nazzareni ◽  
P. Comodi ◽  
L. Bindi ◽  
L. Dubrovinsky
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray

Refinement of the crystal structure of sieleckiite and revision of its symmetry

2017 ◽  
Vol 81 (4) ◽  
pp. 917-922
Author(s):  
Peter Elliott
Keyword(s):  
Crystal Structure ◽  
Synchrotron Radiation ◽  
Single Crystal ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
Aluminium Phosphate ◽  
Unit Cell Parameters ◽  
X Ray ◽  
Cell Parameters ◽  
Phosphate Mineral

AbstractThe crystal structure of the copper aluminium phosphate mineral sieleckiite, Cu3Al4(PO4)2 (OH)12·2H2O, from the Mt Oxide copper mine, Queensland, Australia was solved from single-crystal X-ray diffraction data utilizing synchrotron radiation. Sieleckiite has monoclinic rather than triclinic symmetry as previously reported and is space group C2/m with unit-cell parameters a = 11.711(2), b = 6.9233(14), c = 9.828(2) Å, β = 92.88(3)°, V = 795.8(3) Å3and Z = 2. The crystal structure, which has been refined to R1 = 0.0456 on the basis of 1186 unique reflections with Fo > 4σF, is a framework of corner-, edge- and face- sharing Cu and Al octahedra and PO4 tetrahedra.

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