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CASE STUDY

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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.

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 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 polymorph consists

of a monoclinic unit cell (P21/c, Z=4) that

InaposterpresentedattheAbInitioModelinginSolidStateChemistry2004

conference,London,researchersreportedonthestructuredeterminationoftheC

polymorphofpalmiticacidfromconventionalX-raypowderdiffractiondata.Using

Accelrys’ReflexPlusandCASTEPsoftware,theywereabletovalidatetheresultsof

powderanalysisagainstthetheoreticalstructureoftheCpolymorphofpalmiticacid,

andsoestablishamethodtosolvethestructuresofthelongermembersofthefamily.

materials studio enables the complete workflow of structure solution from X-ray powder data in one integrated environment alongside atomistic simulation

CASE STUDY: MATEriAlS STUDio

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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

CASE STUDY: MATEriAlS STUDio

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CS-8067-1211

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.

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.