Structural investigation ofN,N′-methylenebisacrylamideviaX-ray diffraction assisted by crystal structure prediction

2015 ◽  
Vol 48 (2) ◽  
pp. 550-557 ◽  
Author(s):  
Claudia Graiff ◽  
Daniele Pontiroli ◽  
Laura Bergamonti ◽  
Chiara Cavallari ◽  
Pier Paolo Lottici ◽  
...  

The crystal structure ofN,N′-methylenebisacrylamide was determined through the geometry optimization of the molecular unit with density functional theory and conformational analysis, and then through the calculation of the packingviaa crystal structure prediction protocol, based on lattice energy minimization. All the calculated structures were ranked, comparing their powder pattern with the laboratory low-quality X-ray diffraction data. Rietveld refinement of the best three proposed structures allowed the most probable crystal arrangement of the molecules to be obtained. This approach was essential for disentangling the twinning problems affecting the single-crystal X-ray diffraction data, collected on samples obtainedviarecrystallization of powder, which definitely confirmed the predicted model. It was found thatN,N′-methylenebisacrylamide shows a monoclinic structure in the space groupC2/c, with lattice parametersa= 17.822 (12),b= 4.850 (3),c= 19.783 (14) Å, β = 102.370 (9)°,V= 1670 (2) Å3. Two strong interactions between the amide protons and the carbonyl groups of neighbouring molecules were found along thebaxis, determining the crystal growth in the form of wires in this direction. This work provides a further example of how computational methods may help to investigate low-quality molecular crystals with standard diffraction techniques.

2018 ◽  
Vol 34 (1) ◽  
pp. 74-75
Author(s):  
J. A. Kaduk ◽  
K. Zhong ◽  
T. N. Blanton ◽  
S. Gates-Rector ◽  
T. G. Fawcett

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.


2004 ◽  
Vol 126 (22) ◽  
pp. 7071-7081 ◽  
Author(s):  
Maryjane Tremayne ◽  
Leanne Grice ◽  
James C. Pyatt ◽  
Colin C. Seaton ◽  
Benson M. Kariuki ◽  
...  

2019 ◽  
Vol 19 (11) ◽  
pp. 6058-6066 ◽  
Author(s):  
Doris E. Braun ◽  
Arianna Rivalta ◽  
Andrea Giunchi ◽  
Natalia Bedoya-Martinez ◽  
Benedikt Schrode ◽  
...  

2021 ◽  
pp. 1-3
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton

The crystal structure of pazopanib hydrochloride Form 1 has been refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Pazopanib hydrochloride crystallizes in space group P-1 (#2) with a = 8.45008(6), b = 8.71310(12), c = 16.05489(35) Å, α = 79.5996(9), β = 86.4784(5), γ = 87.3764(3)°, V = 1159.724(9) Å3, and Z = 2. The crystal structure is essentially identical to that of CSD Refcode CEVYEK. There are four strong N–H⋯Cl hydrogen bonds to the chloride anion. Several additional weaker N–H⋯Cl and C–H⋯Cl hydrogen bonds are also present. A variety of C–H⋯O, C–H⋯N, and N–H⋯S hydrogen bonds also contribute to the lattice energy. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.


2018 ◽  
Vol 18 (6) ◽  
pp. 3558-3568 ◽  
Author(s):  
Jennifer T. J. Freitas ◽  
Cristiane C. de Melo ◽  
Olímpia M. M. S. Viana ◽  
Fabio F. Ferreira ◽  
Antonio C. Doriguetto

2014 ◽  
Vol 70 (a1) ◽  
pp. C1442-C1442
Author(s):  
Karthikeyan Natarajan ◽  
Sathya Duraisamy ◽  
Sivakumar Kandasamy

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.


2021 ◽  
pp. 1-3
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton

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®).


CrystEngComm ◽  
2013 ◽  
Vol 15 (10) ◽  
pp. 1853-1859 ◽  
Author(s):  
Han Wu ◽  
Matthew Habgood ◽  
Julia E. Parker ◽  
Nik Reeves-McLaren ◽  
Jeremy K. Cockcroft ◽  
...  

2021 ◽  
pp. 1-6
Author(s):  
Joel W. Reid

Synchrotron powder diffraction data is presented for the monoclinic polymorph of dimethylarsinic acid, (CH3)2AsO(OH) (DMAV). Rietveld refinement with GSASII yielded lattice parameters of a = 15.9264(15) Å, b = 6.53999(8) Å, c = 11.3401(9) Å, and β = 125.8546(17)° (Z = 8, space group C2/c). The Rietveld-refined structure was compared with both a density functional theory (DFT)-optimized structure and the published, low-temperature single-crystal structure, and all three structures exhibited excellent agreement. The triclinic polymorph of DMAV was also DFT optimized with CRYSTAL17 to determine the positions of the hydrogen atoms. Monoclinic DMAV forms zigzag chains parallel to the b-axis with adjacent DMAV molecules connected by an O–H⋯O bond, whereas triclinic DMAV forms dimers connected by two O–H⋯O bonds.


Sign in / Sign up

Export Citation Format

Share Document