CY6205: Basic Concepts in X-ray Crystallography and Data Refinements

Course Objective: The learners will be able to: Explain the basic aspects of crystallography Refine X-ray single crystal data using WingX/SHELXL, Olex, Apex software Extract valuable structural parameters using different software by refining the experimental raw-data Write an account on crystallographic data of their samples

Course Content: A historical introduction to molecular structure determination. Single crystal, amorphous crystalline material, differences, crystallization methods and driving forces for single crystal formation, role of solvents and their polarity on crystallization, cryo-crystallization. Iso-energy surface plots for intermolecular interactions. Difference between single crystal and quasi-crystal. The effect of twining of crystals. Congruent, Crystallographic symmetry operations, Miller indices and crystallographic direction, crystallographic point group in three dimensions, 32-point groups of Johann Friedrich Christian Hessel. Laue classes, crystal systems, primitive and non-primitive lattices, reciprocal lattice, Bravais lattice, space groups, what does a space group infer about the organizations of lattice points in three-dimensional space. Operations of symmetry elements in each crystal system. Hermann–Mauguin notation and Schoenflies notations. Relationship between them. X-ray, generation of X-ray, X-ray sources, X-ray single crystal diffraction, Braggs law, Laue equations, scattering factor, structure factor, relation between them, systematic absences, special position and normal position in space lattice, what is R-factor. Selection of single crystal, crystal mounting, determination of unit cell parameters, data-collection, data reduction, data integration, data refinements. Least square method, heavy atom methods and Patterson’s map for phase problem. Data reduction in different space group leading to INS, RES and CIF files. Structure visualization by Mercury and Diamond. Preparation of ORTEP pictures and packing diagram. X-ray single crystal data refinements using WingX/SHELXL, Olex, Apex software. Preparation of crystallographic table, physical significance of these parameters, generation of table of bond lengths and angles by PUBLCIF. Introduction to X-ray charge density experiments and correlation with QTAIM (Brader’s theory). Powder X-ray diffraction pattern, indexing of powder pattern, identifying the lattice planes. Basis of Rietveld refinement.

Text Books:

1. Ziacovazzo, C.; Monaco H. L.; Viterbo, D.; Scordari, F.; Gilli, G.; Zanotti, G.; Catti, M. Fundamentals of crystallography. Edited by Ziacovazzo, C. Third edition. IUCr Texts on Crystallography No. 15, IUCr/Oxford University Press, 2011. ISBN 978-0-19-957365-3

2. Woolfson, M. M.; An introduction to X-ray crystallography. Second Edition, Cambridge University Press, 1997. ISBN 0 521 41271 4 (hardcover). – ISBN 0 521 42359 7 

3. Gatti, C.; Macchi, P. Modern Charge-Density Analysis. Springer Science & Business Media. ISBN9048138361, 9789048138364. Dordrecht: Springer Netherlands, 2012.