Crystal structure determination from conventional X-ray powder diffraction data of polycrystalline materials

Chemicals case study Industry Sector Pharmaceutical Organization Universitat de Barcelona Accelrys Ltd Institute for Materials Research, University of Salford Key Product X-Cell Reflex Plus (containing Powder Solve) CASTEP Accelrys European Headquarters 334 Cambridge Science Park Cambridge, CB4 0WN, UK Tel: +44 1223 228500 Accelrys Asia Headquarters Nishi-shimbashi TS Bldg 11F Nishi-shimbashi 3-3-1, Minato-ku, Tokyo, 105-0003, Japan Tel: +81 3 3578 3861 Accelrys Corporate Headquarters 10188 Telesis Court, Suite 100 San Diego, CA 92121 United States Tel: +1 858 799 5000 Page 1 of 2 Crystal structure determination from conventional X-ray powder diffraction data of polycrystalline materials E. Moreno, C. Conesa-Moratilla, T. Calvet, M. A. Cuevas-Diarte, I. Morrison. 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 validaat 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. 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 significaantl 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 CH3(CH2)14COOH. 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 polymoorp consists of a monoclinic unit cell (P21/c, Z=4) that contains two dimers held together by hydrogen bonds. In this form, the hydrocarbon chains assume an all-transconformation3. 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 refinemeen 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 spec-􀁓 Figure 1: Structure obtained after optimizatiio with CASTEP (K 1x4x2 PW480eV cutoff GGA-PBE) and X-ray powder diffraction comparisso with experimental data.Chemicals case study continued Page 2 of 2 ified 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 calculattions78 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 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 con siderations · 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. 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. 7. Hohenberg, P., Kohn,W., Phys. Rev.1964, 136, B864-871. 8. Kohn,W., Sham, L., Phys. Rev. 1965, 140, A1133-1138. 9. Delley, B., J. Chem. Phys.1990, 92, 508-517. 10. Delley, B., J. Chem. Phys. 2000,113, 7756-7764. Crystal structure determination from conventional X-ray powder diffraction data of polycrystalline materials 􀁓 Figure 2: Structure obtained after Rietveld refinement and X-ray powder diffraction comparriso with experimental data