Introduction to X-ray Structure Analysis: Applied Crystallography Course

1. CHEMISTRY 69600 APPLIED CRYSTALLOGRAPHY SPRING 2011 The Chemistry 69600 Special Topics Course in Applied Crystallography is designed to introduce chemists to the technique of x-ray structure analysis. Most topics are covered in only enough depth so that the experiment can be understood. The course is taught in a computer lab so students can have hands on experience using software. Instructor: Phillip Fanwick 234 WTHR 44572 pfanwick@purdue.edu Text: NONE Website: http://xraylab.chem.purdue.edu/chm696.htm Course Prerequisites: 1. A basic knowledge of point group symmetry. 2. Minimal knowledge in matrix mathematics Course Requirements: 1. Attend Lectures 2. Complete all homework sets 3. Collect data and solve a crystal structure in the laboratory

2. Topics to be Covered: 1. A brief overview of crystallography and its relationship to other analytical methods. 2. Crystals, lattices; non-orthogonal coordinate systems: 3. From point groups to space groups, Hermann-Mauguin Notation 4. Symmetry, centering; unit cell selection, space group determination, and more Hermann-Mauguin Notation. 5. The nature of x-rays; X-ray generation. 6. Scattering and diffraction. 7. Fourier synthesis and non-linear least squares refinement. 8. Data collection and reduction; cameras, diffractometers; growing,selecting and mounting crystals. 9. Solving the structure--Patterson and Direct Methods. 10. Refinement in practice--SHELX. 11. Out of the Norm--absolute configuration and disorder 12. Molecular Graphics. 13. Finishing the Structure; crystallographic statistics. 14. Crystallographic databases.

3. Some other comments The basic idea of the course is to provide an introduction to crystallography Give some insight into what goes on in the crystallography lob Build physical not mathematical models wherever possible Do not derive information that can readily be looked up. However, it is important to know where to find it. I am not training crystallographers but chemists who can use and understand crystallography

4. Important Analytical Techniques It can be argued that since 1950 the two principal analytical techniques that have advanced chemistry are: 1. NMR 2. X-ray Crystallography Yet while NMR has become central to chemical education, crystallography remains almost unknown.

5. Cambridge Structural Database This is a database of all crystallographic structures that contain at least one organic carbon atom. In general there is one entry per compound per publication. Date Number of Entries 1983 52,363 1990 104,380 2001 251,515 Present 591,860 (544,565 compounds)

6. Why crystallography is not taught. The theory is too difficult. The instrumentation is too expensive. Lack of instructors. No course to place it in.

8. Objectives A major problem in crystallographic education is the failure to decide what we want students to be able to do with crystallography. There are a whole spectrum of possible objectives but very few are applicable to the typical chemist.

9. Objectives A major problem in crystallographic education is the failure to decide what we want students to be able to do with crystallography. There are a whole spectrum of possible objectives but very few are applicable to the typical chemist.

10. Objective 1 Know the Input and Output for the Crystallographic Experiment What are the sample requirements and needed initial information to conduct the experiment? What information is the product of the experiment?

11. Objective 2 Analyze and Work with Crystallographic Data. Understand bond distances and angles, their statistics and their relation to bonding Work with simple molecular graphics Read Crystallographic Information Files (CIF) Critically analyze crystallographic results.

12. Graphical Output

13. Derived Output Bond Distances and their s.u.'s Bond Angles and their s.u.'s Torsional Angles and s.u.'s Least Square Planes, angles between planes, and their s.u.'s From these can infer bond orders, types of bonding etc.

14. Input A crystal—good faces, transparent The crystal should be single—only one crystal. Size—appropriate to x-ray beam size. Typically 0.3mm on an edge. Since the x-ray beam has a definite size using crystals larger than the beam does not produce more intensity Shape is important as very thin plates or long needles do not put much crystal in the beam. Need to have an idea of what elements are present.

15. Some Comments on Crystals It would appear easy to get crystals for crystallography but it can be quite difficult. Some crystals do not grow to give suitable shape or produce layered or multiple crystals. Some compounds will never give crystals. Remember-- The quality of a structure can never be better than the quality of the crystals!!

16. Good Crystals

17. Workable Crystals

18. Unusable Crystals

19. Working with Crystallographic Data Like any other data, crystallographic results must be analyzed critically. Most chemists have no idea how to do this. This has lead to the idea that crystallographic results are always correct. It is also important that chemists determine what in the result is significant or interesting.

20. A Comment Any crystallographic result must agree with known chemistry. Generally when a structure produces an unbelievable result it is the structure that is incorrect “Extraordinary claims require extraordinary evidence”--Carl Sagan There are levels of quality in structures and marginal structures produce the most extraordinary claims

21. Crystallographic Information File All information from a structure is contained in the crystallographic information file (cif) The cif is formatted such that each datum has a definition (header) and then the entry. The headers are defined by the International Union of Crystallography (IUCr) committee called COMCIFS. Each definition is spelled out in a cif dictionary. This can be found at http://www.iucr.org/resources/cif/dictionaries/cif_core

22. Part of a CIF

23. CIF Dictionary

24. S.U.'s and comparisons Since there is an error in the measured data there are errors in the derived parameters These errors are expressed as standard uncertainties (s.u.'s) Two parameters are the same if they differ by less than 3 s.u.'s Two parameters are different if they differ by more than 3 s.u.'s

25. Other Cif Ideas loop_ _geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_1 _geom_bond_site_symmetry_2 _geom_bond_publ_flag Cl3 C3 1.739(3) . . ? Cl1 C1 1.739(2) . . ? O23 C24 1.364(3) . . ? O23 N22 1.407(3) . . ? N22 C21 1.309(3) . . ? F1 C7 1.321(3) . . ? C1 C6 1.373(3) . . ? C1 C2 1.398(3) . . ? F3 C7 1.313(3) . . ? F2 C7 1.317(3) . . ? C6 C5 1.398(3) . . ? C6 H6 0.9500 . . ? C4 C5 1.376(4) . . ? C4 C3 1.382(3) . . ? C4 H4 0.9500 . . ? C2 C3 1.399(3) . . ?

26. ORTEP Drawings ORTEP stands for Oak Ridge Thermal Ellipse Plotting program The original was written in 1956 by Carol Johnson at Oak Ridge Thermal Ellipse is an old term for atomic displacement parameter (adp) The adp's are very important in analyzing a structure.

27. ADP's and Motion

28. ADP's and Temperature

29. ADP's and Element Assignment The crystal structure is refined by calculating the data from a structural model and adjusting it to the observed data. The data intensity is related to the electron density. An assumption is that the atoms are located where the density is. The element type is assigned. If the number of electrons is mis-assigned then the atomic volume will be adjusted to get a better fit to the density

33. Disorder Not all crystals are perfectly ordered Crystal structure sees the average occupancy

34. Recent Result (H30)AlF4 reported Nothing obviously wrong Crystals grown from solution with pH 8.5 Actually (NH4)AlF4

35. Homework Read JACS December 1920 2419-2434—The Chemistry and Crystallography... Pay attention to what measurements were made. What instruments were used? How could this information be used? Make notes but nothing to hand in!! December 1920 Volume 42, Issue