accelrys.com CASE STUDY 1 Key Products • X-Cell • Reflex Plus (Containing Powder Solve • CASTEP Industry sector • Pharmaceutical Organizations • Universitat de Barcelona • Accelrys Ltd • Institute for Materials Research • University of Salford CRYSTAL STRUCTURE DETERMINATION FROM X-RAY POWDER DIFFRACTION DATA FOR POLYCRYSTALLINE MATERIALS E. Moreno, C. Conesa-Moratilla, T. Calvet, M. A. Cuevas- Diarte, I. Morrison. X-ray diffraction is one of the most powerful techniques for characterizing the structural properties of crystalline solids; single crystal X-ray diffraction, in particular, is widely used. Unfortunately, for many important crystalline solids it is difficult to grow a single crystal of sufficient size and quality for analysis by this method. High-quality polycrystalline samples are often easier to obtain, allowing the option of using powder diffraction patterns to determine crystal structures. However, the information content in such patterns is significantly reduced in comparison with single crystal X-ray diffraction, and data problems can make solving a crystal structure difficult. Palmitic acid is a long chain compound from the family of n-carboxylic acids with a general formula CH 3 (CH 2 ) 14 COOH. Four different forms, named A, B, E and C are mentioned in the literature. 1-2 The knowledge of the structure of compounds like these is crucial for gaining understanding of more complex systems such as polymers, or biological substances such as lipids. The C polymorph consists of a monoclinic unit cell (P2 1 /c, Z=4) that In a poster presented at the Ab Initio Modeling in Solid State Chemistry 2004 conference, London, researchers reported on the structure determination of the C polymorph of palmitic acid from conventional X-ray powder diffraction data. Using Accelrys’ Reflex Plus and CASTEP software, they were able to validate the results of powder analysis against the theoretical structure of the C polymorph of palmitic acid, and so establish a method to solve the structures of the longer members of the family. Materials Studio enables the complete workflow of structure solution from X-ray powder data in one integrated environment alongside atomistic simulation
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accelrys.com
CASE STUDY
1
Key Products
• X-Cell
• ReflexPlus(ContainingPowderSolve
• CASTEP
Industry sector
• Pharmaceutical
Organizations
• UniversitatdeBarcelona
• AccelrysLtd
• InstituteforMaterialsResearch
• UniversityofSalford
Crystal struCture determInatIOn frOm X-ray POwder dIffraCtIOn data fOr POlyCrystallIne materIals
E. Moreno, C. Conesa-Moratilla, T. Calvet, M. A. Cuevas-Diarte, I. Morrison.
materials studio enables the complete workflow of structure solution from X-ray powder data in one integrated environment alongside atomistic simulation
contains two dimers held together by hydrogen bonds. In this
form, the hydrocarbon chains assume an all-trans conformation3.
The powder diffraction pattern of the C polymorph of palmitic
acid was indexed with X-Cell4. Among others solutions, a
monoclinic unit cell (P21/c) was obtained, in agreement with
that in the literature. After Pawley refinement of the P21/c cell,
the structure solution was attempted by a direct space Monte
Carlo simulated-annealing approach, and full-profile comparison
method implemented in Powder Solve5. Following the global
optimization algorithm, the trial structures are continuously
generated by modifying specified degrees of freedom in order
to find the trial structure that yields the best agreement between
calculated and experimental patterns. In this case, the molecules
have been treated as a quasi-rigid body with one internal degree
of freedom involving the torsion angle between O-C1-C2-C3.
After the structure solution step, Rietveld6 refinement is
done. Usually the information contained in the pattern is not
enough to refine all the discrete atomic coordinates; instead,
the refinement has to be assessed considering the molecule
as a rigid body. In such cases, the use of first-principles DFT
calculations7-8 are a valuable tool to optimize the crystal structure,
since they provide fairly accurately atomic positions, which are
a valuable guidance in a subsequent Rietveld refinement.
Indexing, refinement and structure solution steps were carried out using the Reflex Plus software package for crystal structure determination from powder X-ray
figure 1: Structure obtained after optimization with CASTEP (K 1x4x2 PW480eV cutoff GGA-PBE) and X-ray powder diffraction comparison with experimental data.
figure 2: Structure obtained after Rietveld refinement and X-ray powder diffraction comparison with experimental dat
diffraction, implemented in the PC modeling environment Materials Studio. The input files for the DFT calculations were generated with CASTEP module, implemented in the same Materials Studio modeling environment.
In summary, elucidation of the crystal structure was possible with systematic use of software tools:
• Unit cell index with X-Cell2
• Space group determination, based on systematic absences and density considerations
• Pawley refinement
• Simulated annealing using PowderSolve (Reflex Plus)
• Structure refinement using the Rietveld method
• Optimization of atomic coordinates by DFT calculations using DMol3 or CASTEP
• Rietveld refinement with fixed atomic coordinates
The final structure was validated by comparing the results with those obtained by single crystal X-ray diffraction2.
To learn more about Materials Studio by Accelrys, go to
accelrys.com/materials-studio
referenCe
1. Moreno, E.; Calvet, T. et al, (Awaiting publication).
2. Von Sydow, E., Arkiv for Kemi; 1955, 9, 231-254.
3. Moreno, E., et al, (Awaiting publication).
4. Neumann, M.A., J. Appl. Cryst. 2003, 36, 356-365.
5. Engel, G. E., et al. J. Appl. Cryst. 1999. 32, 1169-1179.
6. Young, R. A., The Rietveld Method, Oxford University Press; Oxford, 1995.