Crystal Structure Solution of the Dark Red, Light Red and Orange Polymorphs of 5-Methyl-2-[(2-Nitro-4-Methylphenyl)Amino]-3-Thiophenecarbonitrile by High Resolution X-Ray Powder Diffraction and Simulated Annealing Techniques

The crystal structures of two compounds belonging to a group of theophylline derivatives have been solved by X-ray powder diffraction methods. Despite the fact that these compounds seemed to be rather simple (23 atoms in an asymmetric unit), the preferred orientation and dominant zone problems created very serious obstacles in the investigations, even for the most modern powder diffraction methods. The crystal structure of the first compound, 8-phenylazoxanthine, C14H14N6O2, was finally solved from laboratory diffractometer data, while in the case of the second compound, 8-(3-bromobenzylidene)xanthine, C15H14N5O2Br, it was not possible to reliably index its diffraction pattern until data had been collected at the high-resolution powder diffractometer ID31 at the ESRF Grenoble. The serious problems encountered during anab initiocrystal structure solution from powder data of these pharmaceutical samples are described and discussed.

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Sideroxylin from Miconia Ioneura: Monohydrate Crystal Structure from High Resolution X-Ray Powder Diffraction

Natural Product Communications ◽

10.1177/1934578x0800300516 ◽

2008 ◽

Vol 3 (5) ◽

pp. 1934578X0800300

Author(s):

Silvina Pagola ◽

María I. Tracanna ◽

Sara M. Amani ◽

Ana M. González ◽

Ana B. Raschi ◽

...

Keyword(s):

Crystal Structure ◽

Simulated Annealing ◽

Thermogravimetric Analysis ◽

High Resolution ◽

Powder Diffraction ◽

Room Temperature ◽

Simulated Annealing Algorithm ◽

Ethyl Acetate Extract ◽

X Ray ◽

Annealing Algorithm

High resolution X-ray powder diffraction has been used to obtain the crystal structure of sideroxylin ( 4H-1-Benzopyran-4-one,5-hydroxy-2-(4-hydroxyphenyl)-7-methoxy-6,8-dimethyl) monohydrate, (C18H16O5).H2O, isolated from the bioactive ethyl acetate extract of Miconia ioneura Griseb (Melastomataceae) leaves. The crystal structure was determined using direct space methodology based on the simulated annealing algorithm. Thermogravimetric analysis shows that the material dehydrates while heated from room temperature to ~150°C.

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Powder study of 3-azabicyclo[3.3.1]nonane-2,4-dione form 2

Acta Crystallographica Section E Structure Reports Online ◽

10.1107/s1600536806023312 ◽

2006 ◽

Vol 62 (7) ◽

pp. o3046-o3048 ◽

Cited By ~ 3

Author(s):

Ashley T Hulme ◽

Philippe Fernandes ◽

Alastair Florence ◽

Andrea Johnston ◽

Kenneth Shankland

Keyword(s):

Crystal Structure ◽

Simulated Annealing ◽

Hydrogen Bonds ◽

Powder Diffraction ◽

Title Compound ◽

Variable Temperature ◽

Polycrystalline Sample ◽

Asymmetric Unit ◽

X Ray ◽

Compound C

A polycrystalline sample of a new polymorph of the title compound, C8H11NO2, was produced during a variable-temperature X-ray powder diffraction study. The crystal structure was solved at 1.67 Å resolution by simulated annealing from laboratory powder data collected at 250 K. Subsequent Rietveld refinement yielded an R wp of 0.070 to 1.54 Å resolution. The structure contains two molecules in the asymmetric unit, which form a C 2 2(8) chain motif via N—H...O hydrogen bonds.

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Disordered crystal structure of pentamethylcyclopentadienylsodium as seen by high-resolution X-ray powder diffraction

Acta Crystallographica Section B Structural Science ◽

10.1107/s010876810101237x ◽

2001 ◽

Vol 57 (5) ◽

pp. 673-679 ◽

Cited By ~ 4

Author(s):

Consiglia Tedesco ◽

Robert E. Dinnebier ◽

Falk Olbrich ◽

Sander van Smaalen

Keyword(s):

Crystal Structure ◽

High Resolution ◽

Rietveld Refinement ◽

Powder Diffraction ◽

Lattice Parameters ◽

Space Group ◽

X Ray ◽

Disordered Crystal

The crystal structure of pentamethylcyclopentadienylsodium, [NaC10H15] (NaCp*), has been determined from high-resolution X-ray powder diffraction. The compound crystallizes in space group Cmcm with lattice parameters a = 4.61030 (3), b = 16.4621 (3), c = 14.6751 (2) Å, V = 1113.77 (4) Å3 (Z = 4). NaCp* forms polymeric multidecker chains along the a axis. The Rietveld refinement (Rp = 0.050 and RF = 0.163) shows that the Cp* moieties occupy, with disorder, two different orientations rotated away from the eclipsed conformation by ±13.8°.

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Crystal structure solution of an elusive polymorph of Dibenzylsquaramide

Powder Diffraction ◽

10.1017/s0885715613000821 ◽

2013 ◽

Vol 28 (S2) ◽

pp. S470-S480 ◽

Cited By ~ 6

Author(s):

Anna Portell ◽

Xavier Alcobé ◽

Latévi M. Lawson Daku ◽

Radovan Černý ◽

Rafel Prohens

Keyword(s):

Crystal Structure ◽

Powder Diffraction ◽

Diffraction Data ◽

Structural Features ◽

Powder Diffraction Data ◽

Asymmetric Unit ◽

X Ray ◽

The Third ◽

Group Assignment ◽

Structure Solution

The crystal structure of the third polymorph of dibenzylsquaramide (Portell, A. et al., 2009), (fig. 1) has been determined from laboratory X-ray powder diffraction data by means of direct space methods using the computing program FOX. (Favre-Nicolin and Černý, 2002) The structure resolution has not been straightforward due to several difficulties on the indexing process and in the space group assignment. The asymmetric unit contains two different conformers, which has implied an additional difficulty during the Rietveld (Rietveld, 1969) refinement. All these issues together with particular structural features of disquaramides are discussed.

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Combined Rietveld and stereochemical restraint refinement of a protein crystal structure

Journal of Applied Crystallography ◽

10.1107/s002188989901064x ◽

1999 ◽

Vol 32 (6) ◽

pp. 1084-1089 ◽

Cited By ~ 44

Author(s):

R. B. Von Dreele

Keyword(s):

Crystal Structure ◽

High Resolution ◽

Single Crystal ◽

Powder Diffraction ◽

Diffraction Data ◽

Tertiary Structure ◽

Protein Crystal ◽

Powder Diffraction Data ◽

X Ray ◽

Protein Crystal Structure

By combining high-resolution X-ray powder diffraction data and stereochemical restraints, Rietveld refinement of protein crystal structures has been shown to be feasible. A refinement of the 1261-atom protein metmyoglobin was achieved by combining 5338 stereochemical restraints with a 4648-step (dmin= 3.3 Å) powder diffraction pattern to give the residualsRwp= 2.32%,Rp= 1.66%,R(F2) = 3.10%. The resulting tertiary structure of the protein is essentially identical to that obtained from previous single-crystal studies.

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Crystal structure solution for the A 6 B 2O17 (A = Zr, Hf; B = Nb, Ta) superstructure

Acta Crystallographica Section B Structural Science Crystal Engineering and Materials ◽

10.1107/s2052520619001963 ◽

2019 ◽

Vol 75 (2) ◽

pp. 227-234 ◽

Cited By ~ 4

Author(s):

Scott J. McCormack ◽

Waltraud M. Kriven

Keyword(s):

Crystal Structure ◽

Powder Diffraction ◽

Neutron Powder Diffraction ◽

X Ray ◽

Order And Disorder ◽

Solid Solution Range ◽

Structure Solution ◽

Compositional Variations ◽

Structural Mechanisms

Zr6Ta2O17, Hf6Nb2O17 and Hf6Ta2O17 crystal structure solutions have been solved using synchrotron X-ray powder diffraction and neutron powder diffraction in conjunction with simulated annealing, charge flipping and Rietveld refinement. These structures have been shown to be isomorphous with the Zr6Nb2O17 superstructure, leading to the classification of the A 6 B 2O17 (A = Zr, Hf; B = Nb, Ta) orthorhombic compound family with symmetry Ima2 (No. 46). The asymmetrical structural units of cation-centred oxygen polyhedra used to build the structure are as follows: (i) one set of symmetry-equivalent six-coordinated polyhedra, (ii) three sets of symmetry-equivalent seven-coordinated polyhedra and (iii) one set of symmetry-equivalent eight-coordinated polyhedra. The potential for cation order and disorder was discussed in terms of cation atomic number contrast in X-ray and neutron powder diffraction as well as the bond valence method. In addition, the structural mechanisms for experimentally observed compositional variations within the solid solution range can be attributed to the addition or removal of a set of symmetry-equivalent seven-coordinated polyhedra accompanied by corresponding oxygen tilts within the A 6 B 2O17 structure.

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Crystal structure of brigatinib Form A (Alunbrig®), C29H39ClN7O2P

Powder Diffraction ◽

10.1017/s0885715621000518 ◽

2021 ◽

pp. 1-8

Author(s):

Ryan L. Hodge ◽

James A. Kaduk ◽

Amy M. Gindhart ◽

Thomas N. Blanton

Keyword(s):

Crystal Structure ◽

Powder Diffraction ◽

Density Functional ◽

Phosphoryl Group ◽

Powder Diffraction Data ◽

Factor Solution ◽

Powder Diffraction File ◽

Functional Theory ◽

X Ray ◽

Structure Solution

The crystal structure of brigatinib Form A has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Brigatinib Form A crystallizes in space group P-1 (#2) with a = 9.59616(20), b = 10.9351(3), c = 14.9913(6) Å, α = 76.1210(13), β = 79.9082(11), γ = 74.0802(6)°, V = 1458.497(15) Å3, and Z = 2. Structure solution was complicated by the lowest cost factor solution having an unreasonable conformation of the dimethylphosphoryl group. The second-best structure yielded a better refinement. The crystal structure is characterized by alternating layers of aliphatic and aromatic portions of the molecules along the b-axis. Strong N–H⋯N hydrogen bonds link the molecules into pairs, with a graph set R2,2(8). There is a strong intramolecular N–H⋯O hydrogen bond to the phosphoryl group, which determines the orientation of this group. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

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