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This study explores the disordered 3D structure of the Cu-Pt complex, highlighting the role of statistical disorder and diffuse scattering in understanding its partial ordering. It discusses preliminary data retrieval from the Oxford Diffraction instrument and the analysis of X-ray diffraction data using Jana2006 and Superflip software. A detailed assessment of the refined structure elucidates the coordination of copper and the positioning of the ligand chains. The iterative process of modeling and refining occupancies is illustrated, showcasing the significance of complete structural formulation, including hydrogen atoms.
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Example 4.1 - PtCu Disordered 3d structure
statistical disorder: no structured diffuse scattering partial ordering -> structured diffuse scattering 2-fold supercell 3-fold supercell
Steps with Example 3 • Preliminary informationFiles from Oxford Diffraction instrumentComposition [Cu(CH3-NH-CH2-CH2-NH2)2] [Pt(CN)4] • Reading of dataJana2006 reads jobname.hkl and jobname.sum. The second file will be soon replaced by the experimental CIF file. • Solution with SuperflipSuperflip returns a fragment of the structure • Completing structure model from difference Fourier map Labeling in all examples is only informative. It depends on the Superflip result and way of solution!
Where is the chain CH3-NH-CH2-CH2-NH2 ? Coordination of copper before splitting atoms Coordination of copper after splitting atoms. R=2.2%
Refined occupancies and distances to copper indicate that C4 and C6 are probably nitrogenthat C6’ is probably carbonthat in position of C2 two atoms coincide
CH3-NH-CH2-CH2-NH2 The chains surround copper from two sides. The two possibilities have the same occupancy because they are symmetry equivalent.
Final model without hydrogensAssigning proper chemical typesSplitting C2Fixing occupancies
Adding hydrogen atomsCH3 and CH2 are fixed by geometryNH and NH2 are found in difference Fourier and refined R=1.8%
