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Molecular Structure Laboratory

Chemical Crystallography 613


Molecular Structure Laboratory / Education / Chemical Crystallography 613 Updated: April 24, 2018

  • Course Description
  • Crystallographic Problems
  • Advanced crystallographic Problems

Instructors: Ilia A. Guzei (iguzei@chem.wisc.edu) and Lawrence F. Dahl (dahl@chem.wisc.edu)
Course Materials: Handouts, Web pages.
Suggested Texts: "Crystal Structure Determination" by Werner Massa (ISBN 3-540-20644-2), "Foundations of Crystallography with Computer Applications" by Maureen M. Julian (ISBN 978-1-4200-6075-1).

            The course is designed for individuals who desire to acquire basic crystallographic knowledge, mathematical foundations of diffraction principles, and hands-on experience in operation of diffractometers, computer software, and crystal structure determination.  The course provides the concepts of crystallographic analysis including point/space group symmetry, the use of reciprocal lattice to understand diffraction by crystals, and crystallographic experiment design.
Modern single-crystal X-ray diffraction is the most powerful and unambiguous analytical method for the absolute structural elucidation of solids.  The chemistry department is equipped with two state-of-the-art area-detector CCD diffractometers, which  allow complete stereochemical characterizations of over 90% of non-macromolecular compounds within 1-2 days.  This analytical tool enables researchers to ascertain both stoichiometeries and absolute configurations of small-to-large size compounds.  This course is particularly important for a student interested in comprehending and evaluating the countless structure determinations given in the literature.  In addition, it provides an excellent foundation for the determination and/or interpretation of protein structures and would be extremely valuable as an introduction to protein crystallography.
A large portion of the second part of the course will take place in the departmental computer laboratory for the students to learn the practical aspects of crystal structure analysis.  An additional session will be include a hands-on practicum at the X-ray diffraction facility. These sessions will cover: (1) selection and mounting of single crystals on a diffractometer; (2) use of diffractometers for data-collection; (3) use of SHELXTL/OLEX2 computer program packages for processing X-ray data, structural solution and refinement, and preparation of publication quality reports; (4) important topics such as establishing absolute structure (e.g., molecular chirality) for non-centrosymmetric space groups, interpretation of inter-/intramolecular hydrogen bonding interactions, and analysis of molecular conformations; (5) use of the Cambridge Structural Database, which contains over 500,000 structures.
During the course each student will solve a number of crystal structures (at least one research sample may be submitted by the student) and will give a brief presentation on an individually assigned crystallographic study.

The course provides minor Chemistry credit of 3 hours for all disciplines within Chemistry (analytical, chemical biology, inorganic, materials, organic, physical) and for outside departments (Biochemistry, Engineering, Food Science, Geology, Materials Science, and Physics).  Undergraduate and non-dissertator graduate students will have to register for the course.  For questions please contact Dr. Guzei and/or Prof. Dahl.

Crystallographic Problems (download all)

Proposed (and intentionally misleading) Structures Unit cell data

Diffraction data

Theme
aspirin.p4p aspirin.hkl Hydrogen atom positions
one.p4p one.hkl Connectivity
two.p4p two.hkl Special position
vitaminC.p4p vitaminC.hkl Hydrogen atom positions
three.p4p three.hkl Proton transfer
four.p4p four.hkl Direct methods failure
five.p4p five.hkl Enantiomers and diastereomers
six six.p4p six.hkl Structure building
seven.p4p seven.hkl Special position and disorder
eight.p4p eight.hkl Unexpected composition
nine nine.p4p nine.hkl Positional disorder
ten ten.p4p ten.hkl Connectivity
structure11 Structure11.p4p Structure11.hkl Atomic identities and solvent disorder
ferrocene.p4p ferrocene.hkl Space group assignment and disorder

These structures have been selected to demonstrate advanced refinement techniques with programs OLEX2 and SHELXL. The zip file contains data files and instructions.

Proposed Structure Unit cell data

Diffraction data

Theme
Example0.ins Example0.hkl Structure solution
Example1.res Example1.hkl Atom identification, SQUEEZE
Example2.res Example2.hkl

Idealized geometry;

Acta C - idealized geometry library

Example3.res Example3.hkl

CF3 disorder.

RIGU paper.

Example4.res Example4.hkl Br/Cl disorder
Example5.res Example5.hkl Part -1 example video
Example6.res Example6.hkl tBu disorder illustrates modes FIT and SPLIT as well as SADI/RIGU commands. Original paper.
Example7.res Example7.hkl Easy SPLIT
Example8.res Example8.hkl Water molecules and GROW. Easy example
Example9.res Example9.hkl Involved toluene disorder. SQUEEZE
Ylid_twin.p4p Ylid_twin.mul Twinned ylid data
Example10.p4p Example10.hkl Easy split example
Quartz Quartz.p4p Quartz.raw High symmetry
ZnCl2 + Na(Ph4B) Example11.p4p Example11.mul Twin

Many thanks to Dr. Carla Slebodnick (example1), Charlotte Stern (3,4), and Prof. Len Barbour (5-7).

 


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