An introduction of chemical structure coding in the X-ray Powder Diffraction File

2000 ◽  
Vol 15 (1) ◽  
pp. 38-41
Author(s):  
Wei Lianhu ◽  
Xiao Yunde ◽  
Zhang Jinbei ◽  
Lin ShaoFan
Keyword(s):  
Powder Diffraction ◽  
Chemical Structure ◽  
Computer Application ◽  
Improved Method ◽  
Powder Diffraction File ◽  
X Ray ◽  
Chemical Structures ◽  
And Topology ◽  
Connection Table ◽  
Almost All

A special computer storage method for chemical structures is illustrated in this article. With an improved method of two-dimensional connection table and topology, we can fit almost all chemical structures and display them very conveniently. We have used this method in the PDF (X-Ray Powder Diffraction File) database, which contains many special structures.Key words: database, computer application, chemical structure

scholarly journals Crystal structure of pimecrolimus Form B, C43H68ClNO11

2021 ◽  
Vol 36 (1) ◽  
pp. 35-42
Author(s):  
Shivang Bhaskar ◽  
Joseph T. Golab ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Density Functional ◽  
Van Der Waals Interactions ◽  
Powder Diffraction File ◽  
X Ray ◽  
Weak Intermolecular Interactions ◽  
Significant Difference ◽  
Atomic Coordinates ◽  
Solid State Conformation

The crystal structure of pimecrolimus Form B has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Pimecrolimus crystallizes in the space group P21 (#4) with a = 15.28864(7), b = 13.31111(4), c = 10.95529(5) Å, β = 96.1542(3)°, V = 2216.649(9) Å3, and Z = 2. Although there are an intramolecular six-ring hydrogen bond and some larger chain and ring patterns, the crystal structure is dominated by van der Waals interactions. There is a significant difference between the conformation of the Rietveld-refined and the DFT-optimized structures in one portion of the macrocyclic ring. Although weak, intermolecular interactions are apparently important in determining the solid-state conformation. The powder pattern is included in the Powder Diffraction File™ (PDF®) as entry 00-066-1619. This study provides the atomic coordinates to be added to the PDF entry.

Crystal structure of ziprasidone hydrochloride monohydrate, C21H22Cl2N4OS(H2O)

2015 ◽  
Vol 30 (3) ◽  
pp. 192-198
Author(s):  
James A. Kaduk ◽  
Kai Zhong ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Powder Diffraction ◽  
Density Functional ◽  
Minimum Energy ◽  
Strong Hydrogen Bond ◽  
Powder Diffraction File ◽  
X Ray ◽  
Hydrochloride Monohydrate ◽  
Positively Charged

The crystal structure of ziprasidone hydrochloride monohydrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Ziprasidone hydrochloride monohydrate crystallizes in space group P-1 (#2) with a = 7.250 10(3), b = 10.986 66(8), c = 14.071 87(14) Å, α = 83.4310(4), β = 80.5931(6), γ = 87.1437(6)°, V = 1098.00(1) Å3, and Z = 2. The ziprasidone conformation in the solid state is very close to the minimum energy conformation. The positively-charged nitrogen in the ziprasidone makes a strong hydrogen bond with the chloride anion. The water molecule makes two weaker bonds to the chloride, and acts as an acceptor in an N–H⋯O hydrogen bond. The powder pattern is included in the Powder Diffraction File™ as entry 00-064-1492.

Crystal structure of oxybutynin hydrochloride hemihydrate, C22H32NO3Cl(H2O)0.5

2019 ◽  
Vol 34 (1) ◽  
pp. 50-58
Author(s):  
James A. Kaduk ◽  
Nicholas C. Boaz ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Hydroxyl Group ◽  
Layered Crystal ◽  
Powder Diffraction File ◽  
X Ray ◽  
Layered Crystal Structure ◽  
Oxybutynin Hydrochloride

The crystal structure of oxybutynin hydrochloride hemihydrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Oxybutynin hydrochloride hemihydrate crystallizes in space group I2/a (#15) with a = 14.57266(8), b = 8.18550(6), c = 37.16842(26) Å, β = 91.8708(4)°, V = 4421.25(7) Å3, and Z = 8. The compound exhibits X-ray-induced photoreduction of the triple bond. Prominent in the layered crystal structure is the N–H⋅⋅⋅Cl hydrogen bond between the cation and anion, as well as O–H⋅⋅⋅Cl hydrogen bonds from the water molecule and hydroxyl group of the oxybutynin cation. C–H⋅⋅⋅Cl hydrogen bonds also contribute to the crystal energy, and help determine the conformation of the cation. The powder pattern is included in the Powder Diffraction File™ as entry 00-068-1305.

Qualitative phase analysis system for crystalline mixtures based on X-ray powder diffraction file

2004 ◽  
Vol 19 (4) ◽  
pp. 340-346
Author(s):  
YuanYuan Qiao ◽  
YunFei Xi ◽  
DongTao Zhuo ◽  
Ji Jun Wang ◽  
ShaoFan Lin
Keyword(s):  
Phase Analysis ◽  
Powder Diffraction ◽  
Identification System ◽  
Phase Identification ◽  
Powder Diffraction File ◽  
X Ray ◽  
Analysis System ◽  
Qualitative Phase ◽  
Full Peak

A qualitative phase identification system for crystalline mixtures is presented. The system provides up to five-phase qualitative identification using up to nine-peak filtration, and additive full peak matching based on the powder diffraction file of ICDD. It was implemented using Microsoft Visual C++, and runs under most common Windows systems. Screenshots and examples are included.

Crystal structure of minocycline hydrochloride dihydrate form A, C23H28N3O7Cl (H2O)2

2018 ◽  
Vol 34 (1) ◽  
pp. 59-65
Author(s):  
Austin M. Wheatley ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Density Functional ◽  
Hydroxyl Group ◽  
Water Molecules ◽  
Powder Diffraction File ◽  
X Ray ◽  
Dimethyl Amine ◽  
Minocycline Hydrochloride ◽  
Amine Groups

The crystal structure of minocycline hydrochloride dihydrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Minocycline hydrochloride dihydrate crystallizes in space groupP212121(#19) witha= 7.40772(1),b= 14.44924(3),c= 22.33329(4) Å,V= 2390.465(12) Å3, andZ= 4. The minocycline cation is a zwitterion: both dimethylamino groups are protonated and one hydroxyl group is ionized. A potential ambiguity in the orientation of the amide group was resolved by considering Rietveld refinement residuals and displacement coefficients, as well as DFT energies. The crystal structure is dominated by hydrogen bonds. Both water molecules and a hydroxyl group act as donors to the chloride anion. Both protonated dimethyl amine groups act as donors to the ionized hydroxyl group. Several intramolecular O–H···O hydrogen groups help determine the conformation of the cation. The powder pattern is included in the Powder Diffraction File™ as entry 00-066-1606.

Crystal structure of bretylium tosylate (Bretylol®), C18H24BrNO3S

2018 ◽  
Vol 33 (4) ◽  
pp. 298-302
Author(s):  
Austin M. Wheatley ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Double Layers ◽  
Powder Diffraction Data ◽  
Powder Diffraction File ◽  
X Ray ◽  
Polar Interactions ◽  
Normal Hydrogen

The crystal structure of bretylium tosylate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Bretylium tosylate crystallizes in space group C2/c (#15) with a = 32.6238(4), b = 12.40353(14), c = 9.93864(12) Å, β = 101.4676(10), V = 3941.39(5) Å3, and Z = 8. The sample exhibited visible decomposition in the X-ray beam. The unusual displacement ellipsoid of the Br atom probably indicates that the decomposition in the beam involves the Br atom. The crystal structure can be viewed as layered parallel to the bc plane. The layers are double, the center consisting of the cation/anion polar interactions and the outer surface of the double layers consists of hydrocarbon interactions. In the absence of normal hydrogen bond donors, the only hydrogen bonds in the bretylium tosylate structure are C–H…O hydrogen bonds. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

Developments in formulation analyses by powder diffraction analysis

2006 ◽  
Vol 21 (2) ◽  
pp. 105-110 ◽  
Author(s):  
T. G. Fawcett ◽  
J. Faber ◽  
F. Needham ◽  
S. N. Kabekkodu ◽  
C. R. Hubbard ◽  
...  
Keyword(s):  
Diffraction Analysis ◽  
Powder Diffraction ◽  
Phase Identification ◽  
Powder Diffraction File ◽  
X Ray ◽  
Comprehensive Database ◽  
Crystallographic Databases ◽  
Digital Pattern ◽  
Speed And Accuracy

Developments in X-ray analysis hardware and software have combined to dramatically improve the throughput, speed, and accuracy of formulation analyses. We will focus on a complimentary development, the growth and application of a comprehensive database based on the Powder Diffraction File™ (PDF®). The PDF is an edited and standardized combination of several crystallographic databases with ∼497 000 published entries. The comprehensive nature of this database, combined with phase identification and digital pattern simulations, was used to identify complex formulations with crystalline and noncrystalline ingredients. We will show how these parallel developments enhance the ability to correctly identify complex formularies.

Crystal structure of methylprednisolone acetate form II, C24H32O6

2018 ◽  
Vol 33 (1) ◽  
pp. 44-48
Author(s):  
Austin M. Wheatley ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Powder Diffraction ◽  
Density Functional ◽  
Hydroxyl Groups ◽  
Methylprednisolone Acetate ◽  
Powder Diffraction File ◽  
X Ray ◽  
Bond Network ◽  
Acetate Form

The crystal structure of methylprednisolone acetate form II, C24H32O6, has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Methylprednisolone acetate crystallizes in space group P212121 (#19) with a = 8.17608(2), b = 9.67944(3), c = 26.35176(6) Å, V = 2085.474(6) Å3, and Z = 4. Both hydroxyl groups act as hydrogen bond donors, resulting in a two-dimensional hydrogen bond network in the ab plane. C–H⋯O hydrogen bonds also contribute to the crystal energy. The powder pattern is included in the Powder Diffraction File™ as entry 00-065-1412.

Evaluation of Reference X-ray Diffraction Patterns in the ICDD Powder Diffraction File

1990 ◽  
Vol 34 ◽  
pp. 369-376
Author(s):  
G. J. McCarthy ◽  
J. M. Holzer ◽  
W. M. Syvinski ◽  
K. J. Martin ◽  
R. G. Garvey
Keyword(s):  
Powder Diffraction ◽  
X Ray Diffraction ◽  
Powder Diffraction File ◽  
Cd Rom ◽  
X Ray ◽  
Binary Oxides ◽  
Diffraction Patterns ◽  
Input Format ◽  
Good Agreement

AbstractProcedures and tools for evaluation of reference x-ray powder patterns in the JCPDSICDD Powder Diffraction File are illustrated by a review of air-stable binary oxides. The reference patterns are evaluated using an available microcomputer version of the NBS*A1DS83 editorial program and PDF patterns retrieved directly from the CD-ROM in the program's input format. The patterns are compared to calculated and experimental diffractograms. The majority of the oxide patterns have been found to be in good agreement with the calculated and observed diffractograms, but are often missing some weak reflections routinely observed with a modern diffractometer. These weak reflections are added to the PDF pattern. For the remainder of the phases, patterns are redetermined.

Crystal structure of bumetanide, C17H20N2O5S

2019 ◽  
Vol 34 (2) ◽  
pp. 189-195
Author(s):  
Samantha C. Diulus ◽  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Powder Diffraction ◽  
Density Functional ◽  
Double Layers ◽  
Powder Diffraction Data ◽  
Powder Diffraction File ◽  
Molecular Conformations ◽  
X Ray ◽  
Phenyl Rings ◽  
Triclinic Structure

The crystal structure of bumetanide has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Bumetanide crystallizes in space group P-1 (#2) with a = 5.00168(4), b = 9.22649(3), c = 19.59924(14) Å, α = 80.7941(5), β = 82.8401(7), γ = 86.8148(7)°, V = 885.268(9) Å3, and Z = 2. The crystal structure is layered with the double layers parallel to the ab plane. The exterior of the layer is composed of hydrocarbon portions of the molecule, both phenyl rings and butyl side chains. The central portion of the bilayer contains the hydrogen-bonding regions, both the carboxylic acid dimers and the hydrogen bonds involving the sulfonamide groups. The molecular conformations of bumetanide in this current triclinic structure and the previously-determined monoclinic polymorph FEDGON are very similar, as are the energies of the two polymorphs. The powder pattern is included in the Powder Diffraction File™ as entry 00-066-1609.

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