Ab Initio Structure Solution from Powder Diffraction Data: A Comprehensive Approach - Prof, Study notes of Crystallography

Download Ab Initio Structure Solution from Powder Diffraction Data: A Comprehensive Approach - Prof and more Study notes Crystallography in PDF only on Docsity! 1 Angus P. Wilkinson School of Chemistry and Biochemistry Georgia Institute of Technology Ab initio structure solution from powder diffraction data Outline The problem General procedure Instrument selection An example - Ga2(HPO3)3.4H2O Recent developments How far can we go ? 2 The problem Single crystals not available: – Synthesis route does not provide crystals. – Material undergoes a phase transition that destroys single crystals. Rietveld refinement requires a model. Standard structure solution methods require integrated intensities. – We have to live with overlap or get smart. Ab initio structure solution through the ages Powder diffraction data has long been used for structure solution. – Most of the early successes were with simple structures » Some atom positions fixed by density and space group - α UF5 Zachariasen » Model building can be useful – Patterson and direct methods were adopted later » Early examples include, β Pu by Zachariasen and Ellinger in 1963. 5 Choice of instrument Many powder ab initios are carried out using high resolution laboratory diffractometers. Synchrotron data can give you a lot of extra information. Neutron diffractometers have been used in special cases. Combined X-ray and neutron data sets are becoming increasingly popular. Ab initio structure solution of Ga2(HPO3)3.4H2O 6 Strategy Index lab X-ray data set using Treor – a = 8.13Å, b = 10.02Å, c = 7.70Å, β = 111.5o Get supporting information – TGA shows weight loss of ~ 15% at about 180oC – 31P MAS NMR shows three distinct phosphorus sites – SHG demonstrates non-centrosymmetric Assign unit cell contents – On basis of above plus an estimate of the density, Ga2(HPO3)3.3H2O and Z = 2. Collect synchrotron X-ray pattern. – Used beam line X7A at NSLS, λ = 1.29915(2)Å – Collected data in range 6 < 2θ < 75o – Capillary sample Assign space group on the basis of systematic absences and SHG. Use the Le Bail method within GSAS to extract 551 structure factors. Input Fs into CRYSTALS. 7 Run SHELXS-86 TREF – produced two large peaks in E map, presumably Ga. Difference Fourier maps calculated with CRYSTALS located two phosphorus and two oxygen atoms. Use GSAS for combined Rietveld / Fourier maps to locate 10 more oxygen atoms. Low temperature neutron data was collected at NIST so the hydrogen positions could be located. – A deuterated sample was used Use the x-ray model as a starting point for neutron refinement. – The fit was lousy ! Locate as many deuterons as possible using geometric arguments. Refine model and locate additional oxygen and several deuterons. Final model – 29 atoms in the asymmetric unit. – 132 positional parameters. 10 Approaches to simulated annealing Refine the model with respect to the diffraction pattern. – Solovyov et al., Mat. Sci. For. 133-136, 195 (1993) Refine the model using bond-strength bond-length relationships. – Limited applicability. May get more than one structure. – Pannetier et al., Nature 346, 343 (1990). Refine the model with respect to a geometric cost function. – Shows a lot of promise for zeolitic materials. – Deem and Newsam, JACS 114, 7198 (1992). 11 What are the limits to ab initio structure solution ? If you can refine it, you should be able to solve it!