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  4. Does Z' equal 1 or 2? Enhanced powder NMR crystallography verification of a disordered room temperature crystal structure of a p38 inhibitor for chronic obstructive pulmonary disease
 
research article

Does Z' equal 1 or 2? Enhanced powder NMR crystallography verification of a disordered room temperature crystal structure of a p38 inhibitor for chronic obstructive pulmonary disease

Widdifield, Cory M.
•
Lill, Sten O. Nilsson
•
Broo, Anders
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2017
Physical Chemistry Chemical Physics

The crystal structure of the Form A polymorph of N-cyclopropyl-3-fluoro-4-methyl-5-[3-[[1-[2-[2-(methylamino) ethoxy] phenyl] cyclopropyl] amino]-2-oxo-pyrazin-1-yl] benzamide (i.e., AZD7624), determined using single-crystal X-ray diffraction (scXRD) at 100 K, contains two molecules in the asymmetric unit (Z' = 2) and has regions of local static disorder. This substance has been in phase IIa drug development trials for the treatment of chronic obstructive pulmonary disease, a disease which affects over 300 million people and contributes to nearly 3 million deaths annually. While attempting to verify the crystal structure using nuclear magnetic resonance crystallography (NMRX), we measured C-13 solid-state NMR (SSNMR) spectra at 295 K that appeared consistent with Z' = 1 rather than Z' = 2. To understand this surprising observation, we used multinuclear SSNMR (H-1, C-13, N-15), gauge-including projector augmented-wave density functional theory (GIPAW DFT) calculations, crystal structure prediction (CSP), and powder XRD (pXRD) to determine the room temperature crystal structure. Due to the large size of AZD7624 (ca. 500 amu, 54 distinct C-13 environments for Z' = 2), static disorder at 100 K, and (as we show) dynamic disorder at ambient temperatures, NMR spectral assignment was a challenge. We introduce a method to enhance confidence in NMR assignments by comparing experimental C-13 isotropic chemical shifts against site-specific DFT-calculated shift distributions established using CSP-generated crystal structures. The assignment and room temperature NMRX structure determination process also included measurements of C-13 shift tensors and the observation of residual dipolar coupling between C-13 and N-14. CSP generated ca. 90 reasonable candidate structures (Z' = 1 and Z' = 2), which when coupled with GIPAW DFT results, room temperature pXRD, and the assigned SSNMR data, establish Z' = 2 at room temperature. We find that the polymorphic Form A of AZD7624 is maintained at room temperature, although dynamic disorder is present on the NMR timescale. Of the CSP-generated structures, 2 are found to be fully consistent with the SSNMR and pXRD data; within this pair, they are found to be structurally very similar (RMSD16 = 0.30 angstrom). We establish that the CSP structure in best agreement with the NMR data possesses the highest degree of structural similarity with the scXRD-determined structure (RMSD16 = 0.17 angstrom), and has the lowest DFT-calculated energy amongst all CSP-generated structures with Z' = 2.

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Type
research article
DOI
10.1039/c7cp02349a
Web of Science ID

WOS:000404530600038

Author(s)
Widdifield, Cory M.
Lill, Sten O. Nilsson
Broo, Anders
Lindkvist, Maria
Pettersen, Anna
Ankarberg, Anna Svensk
Aldred, Peter
Schantz, Staffan
Emsley, Lyndon  
Date Issued

2017

Publisher

Royal Society of Chemistry

Published in
Physical Chemistry Chemical Physics
Volume

19

Issue

25

Start page

16650

End page

16661

Editorial or Peer reviewed

REVIEWED

Written at

OTHER

EPFL units
LRM  
Available on Infoscience
September 5, 2017
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/140221
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