Powder X-ray diffraction of capecitabine, C15H22FN3O6

2019 ◽  
Vol 34 (3) ◽  
pp. 282-283 ◽  
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Diffraction Data ◽  
Density Functional ◽  
National Laboratory ◽  
Argonne National Laboratory ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Acta Cryst ◽  
X Ray ◽  
Data Density ◽  
Structure Determinations

Capecitabine (Xeloda) is a chemotherapy drug used to treat breast, gastric, and colorectal cancers. Commercial capecitabine crystallizes in the orthorhombic space group P212121 (#19) with a = 5.20587(3), b = 9.52324(4), c = 34.79574(21) Å, V = 1725.062(12) Å3, and Z = 4. A reduced cell search in the Cambridge Structural Database (Groom C. R., Bruno, I. J., Lightfoot, M. P., and Ward, S. C. (2016) Crystallogr. Sect. B: Struct. Sci., Cryst. Eng. Mater.72, 171–179) yielded three previous structure determinations (Rohlicek, J., Husak, M., Gavenda, A., Jegorov, A., Kratochvil, B., and Fitch, A. (2016). Acta Cryst. Sect. E: Crystallgr. Commun.72, 879–880, BOVDUM; Malińska, M., Krzeczyński, P., Czerniec-Michalik, E., Trzcińska, K., Cmoch, P., Kutner, A., and Woźniak, K. (2014). J. Pharm. Sci.103, 587–593, BOVDUM01 and BOVDUM02), using synchrotron powder data and later single crystal data at two temperatures. In this work, the sample was ordered from United States Pharmacopeial Convention (lot # G0J205), and analyzed as-received. The room temperature (295 K) crystal structure was refined using synchrotron (λ = 0.413914 Å) powder diffraction data, density functional theory (DFT), and Rietveld refinement techniques. Hydrogen positions were included as part of the structure, and were re-calculated during the refinement. The diffraction data were collected on a beamline 11-BM at the Advanced Photon Source, Argonne National Laboratory and the powder X-ray diffraction pattern of the compound is provided. The agreement of the Rietveld-refined and DFT-optimized structures is poorest in the pentyl side chain, consistent with the disorder observed previously.

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.

Powder X-ray diffraction of bendamustine hydrochloride monohydrate, C16H22Cl2N3O2Cl·H2O

2018 ◽  
Vol 34 (1) ◽  
pp. 74-75
Author(s):  
J. A. Kaduk ◽  
K. Zhong ◽  
T. N. Blanton ◽  
S. Gates-Rector ◽  
T. G. Fawcett
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Diffraction Data ◽  
Density Functional ◽  
Argonne National Laboratory ◽  
Lymphocytic Leukemia ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hydrochloride Monohydrate

Bendamustine hydrochloride monohydrate (marketed as Treanda®) is a nitrogen mustard purine analog alkylator used in the treatment of chronic lymphocytic leukemia (CLL) and non-Hodgkin lymphomas. Commercial bendamustine hydrochloride monohydrate crystallizes in the monoclinic space group P21/c (14), with a = 4.71348(4) Å, b = 47.5325(3) Å, c = 8.97458 (5) Å, β = 96.6515(8)°, V = 1997.161(23) Å3, and Z = 4. A reduced cell search in the Cambridge Structural Database yielded a previously reported crystal structure (Allen, 2002), which did not include hydrogens (Reck, 2006). In this work, the sample was ordered from Santa Cruz Biotechnology, and analyzed as received. The room-temperature crystal structure was refined using synchrotron (λ = 0.413896 Å) powder diffraction data, density functional theory (DFT), and Rietveld refinement techniques. Hydrogen positions were included as part of the structure, and recalculated during the refinement. The diffraction data were collected on beamline BM-11 at the Advanced Photon Source, Argonne National Laboratory. Figure 1 shows the powder X-ray diffraction pattern of the compound. The pattern is included in the Powder Diffraction File as entry 00-064-1508.

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.

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.

scholarly journals Purification, crystallization and preliminary crystallographic analysis of a 4-thiouridine synthetase–RNA complex

2013 ◽  
Vol 69 (4) ◽  
pp. 421-424 ◽  
Author(s):  
Peter-Thomas Naumann ◽  
Charles T. Lauhon ◽  
Ralf Ficner
Keyword(s):  
Diffraction Data ◽  
Thermotoga Maritima ◽  
Crystallographic Analysis ◽  
X Ray Diffraction ◽  
Unit Cell Parameters ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters ◽  
Dependent Modification ◽  
Rna Complex

The sulfurtransferase 4-thiouridine synthetase (ThiI) is involved in the ATP-dependent modification of U8 in tRNA. ThiI fromThermotoga maritimawas cloned, overexpressed and purified. A complex comprising ThiI and a truncated tRNA was prepared and crystallized, and X-ray diffraction data were collected to a resolution of 3.5 Å. The crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 102.9,b= 112.8,c= 132.8 Å.

scholarly journals Powder X-ray diffraction of trimethoprim Form I, C14H18N4O3

2020 ◽  
Vol 35 (1) ◽  
pp. 69-70
Author(s):  
Jerry Hong ◽  
Joseph T. Golab ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Room Temperature ◽  
The United States ◽  
Unit Cell ◽  
Cell Length ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Determinations ◽  
Unit Cell Length

Trimethoprim crystallizes in the triclinic space group P-1 (#2) with a = 10.5085(3), b = 10.5417(2), c = 8.05869(13) Å, α = 101.23371(21), β = 112.1787(3), γ = 112.6321(4)°, V = 743.729 Å3, and Z = 2. A reduced cell search in the Cambridge Structural Database yielded three previous structure determinations, using data collected at 100 K, 173 K, and room temperature. In this work, the sample was ordered from the United States Pharmacopeial Convention (USP) 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 techniques. We found similar hydrogen bonding patterns with the previous determinations. In addition, we identified two C–H⋯O hydrogen bonds, which also contribute to the crystal energy. When comparing the previously reported trimethoprim structure determinations, the unit cell length lattice parameters were found to contract at lower temperatures, particularly 100 K. All structures show reasonable agreement, with unit cell length differences ranging between 0.05 and 0.15 Å. The diffraction data for this study were collected on beamline 11-BM at the Advanced Photon Source, and the powder X-ray diffraction pattern of the compound has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

Na2Si3O7: an incommensurate structure with crenel-type modulation functions, refined from a twinned crystal

2006 ◽  
Vol 62 (3) ◽  
pp. 440-446 ◽  
Author(s):  
Hannes Krüger ◽  
Volker Kahlenberg ◽  
Karen Friese
Keyword(s):  
Diffraction Data ◽  
Title Compound ◽  
Crystal Chemical ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Left Handed ◽  
Sodium Cations ◽  
Incommensurate Structure ◽  
Orthorhombic Cell

The structure of metastable, incommensurately modulated Na2Si3O7 has been determined from single-crystal X-ray diffraction data. In contrast to previous investigations which stated that the compound crystallizes in an orthorhombic space group, this study shows that the compound is monoclinic with a pseudo-orthorhombic cell and is affected by twinning. The structure is described in the (3 + 1)-dimensional superspace. Crenel-type modulation functions are used to account for an aperiodic sequence of right- and left-handed zweier single chains of silicate tetrahedra. The modulation mainly affects one of the two symmetrically independent tetrahedral chains, which are connected to build up [Si3O7]2− layers. Sodium cations are coordinated by five oxygen ligands and provide linkage between adjacent tetrahedral sheets. Distortions of the silicate tetrahedra and crystal chemical relationships of the title compound to sodium and lithium di- and metasilicates are discussed in detail.

The location of p-dichlorobenzene in a single crystal of zeolite H-ZSM-5 at high sorbate loading

1996 ◽  
Vol 52 (1) ◽  
pp. 140-144 ◽  
Author(s):  
H. van Koningsveld ◽  
J. C. Jansen ◽  
H. van Bekkum
Keyword(s):  
Single Crystal ◽  
Cross Sections ◽  
Unit Cell ◽  
Molecular Axis ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Acta Cryst ◽  
Elliptical Cross ◽  
X Ray ◽  
Structural Aspects

The crystal structure of a high-loaded complex of H-ZSM-5 with eight molecules of p-dichlorobenzene per unit cell has been solved by single-crystal X-ray diffraction. The orthorhombic space group P212121 with a = 20.102 (6), b = 19.797 (9), c = 13.436 (3) Å and V = 5347 (3) Å3 has four Si23.92Al0.08O48.2C6H4Cl2 units per unit cell. Dx = 2.164 Mg m−3, λ(MoKα) = 0.71073 Å and μ(Mo Kα) = 0.876 mm−1. The final R(wR) = 0.046 (0.039), w = 1/σ 2(F), for 6090 observed reflections with I > 1.0σ(I) measured at 293 K. The straight channel parallel to [010] is slightly corrugated. The elliptical cross sections have limiting apertures of 6.0 × 4.9 Å (r oxygen = 1.35 Å). The sinusoidal channel parallel to [100] is elliptical with major and minor axes of 6.1 × 4.8 Å, respectively. One of the two independent p-dichlorobenzene molecule lies at the intersection of the straight and sinusoidal channels with its long molecular axis almost parallel to (100) and deviating ~8° from [010]. The second p-dichlorobenzene molecule is in the sinusoidal channel. Its long molecular axis deviates almost 7° from [100] and is practically parallel to (010). The structural aspects are in all details comparable to those in the high-loaded H-ZSM-5/p-xylene complex [van Koningsveld, Tuinstra, van Bekkum & Jansen (1989). Acta Cryst. B45, 423–431] , except for the main interaction forces between the p-dichlorobenzene molecules at the channel intersection.

scholarly journals Maximum a posteriori estimation of crystallographic phases in X-ray diffraction tomography

2015 ◽  
Vol 373 (2043) ◽  
pp. 20140392 ◽  
Author(s):  
Doĝa Gürsoy ◽  
Tekin Biçer ◽  
Jonathan D. Almer ◽  
Raj Kettimuthu ◽  
Stuart R. Stock ◽  
...  
Keyword(s):  
National Laboratory ◽  
Spinous Process ◽  
Argonne National Laboratory ◽  
Three Dimensional ◽  
Polycrystalline Materials ◽  
Reconstruction Method ◽  
Diffraction Tomography ◽  
A Posteriori ◽  
X Ray Diffraction ◽  
X Ray

A maximum a posteriori approach is proposed for X-ray diffraction tomography for reconstructing three-dimensional spatial distribution of crystallographic phases and orientations of polycrystalline materials. The approach maximizes the a posteriori density which includes a Poisson log-likelihood and an a priori term that reinforces expected solution properties such as smoothness or local continuity. The reconstruction method is validated with experimental data acquired from a section of the spinous process of a porcine vertebra collected at the 1-ID-C beamline of the Advanced Photon Source, at Argonne National Laboratory. The reconstruction results show significant improvement in the reduction of aliasing and streaking artefacts, and improved robustness to noise and undersampling compared to conventional analytical inversion approaches. The approach has the potential to reduce data acquisition times, and significantly improve beamtime efficiency.

Structure and conformational analysis of a bidentate pro-ligand, C21H34N2S2, from powder synchrotron diffraction data and solid-state DFTB calculations

2009 ◽  
Vol 65 (5) ◽  
pp. 639-646 ◽  
Author(s):  
Edward E. Ávila ◽  
Asiloé J. Mora ◽  
Gerzon E. Delgado ◽  
Ricardo R. Contreras ◽  
Luis Rincón ◽  
...  
Keyword(s):  
Solid State ◽  
Diffraction Data ◽  
Density Functional ◽  
Simulated Annealing Algorithm ◽  
Theoretical Calculations ◽  
Tight Binding ◽  
Van Der Waals Interactions ◽  
Am1 Calculations ◽  
X Ray Diffraction ◽  
X Ray

The molecular and crystalline structure of ethyl 1′,2′,3′,4′,4a′,5′,6′,7′-octahydrodispiro[cyclohexane-1,2′-quinazoline-4′,1′′-cyclohexane]-8′-carbodithioate (I) was solved and refined from powder synchrotron X-ray diffraction data. The initial model for the structural solution in direct space using the simulated annealing algorithm implemented in DASH [David et al. (2006). J. Appl. Cryst. 39, 910–915] was obtained performing a conformational study on the fused six-membered rings of the octahydroquinazoline system and the two spiran cyclohexane rings of (I). The best model was chosen using experimental evidence from 1H and 13C NMR [Contreras et al. (2001). J. Heterocycl. Chem. 38, 1223–1225] in combination with semi-empirical AM1 calculations. In the refined structure the two spiran rings have the chair conformation, while both of the fused rings in the octahydroquinazoline system have half-chair conformations compared with in-vacuum density-functional theory (DFT) B3LYP/6-311G*, DFTB (density-functional tight-binding) theoretical calculations in the solid state and other related structures from X-ray diffraction data. Compound (I) presents weak intramolecular hydrogen bonds of the type N—H...S and C—H...S, which produce delocalization of the electron density in the generated rings described by graph symbols S(6) and S(5). Packing of the molecules is dominated by van der Waals interactions.

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