The X-ray Crystallography Facility
What we do
The X-ray Crystallography Facility in the Organic Chemistry
Institute of the University of Zürich is an analytical service
laboratory which uses X-ray diffraction to determine the
three-dimensional, single-crystal structures of small molecules.
Organic compounds make up the bulk of the samples that are analysed,
although inorganic and organometallic compounds are also regularly
investigated.
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A typical diagram depicting the molecular structure of
one of our compounds, a thienothiazine carboxylate.
M. Kägi, G. Mloston, A. Linden and H. Heimgartner,
Helv. Chim. Acta 1994, 77, 1299-1312.
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Crystal structure analyses are carried out on a full-service basis
by the Manager, Dr. A. Linden
and the facility's laboratory assistant, Ms S. Blumentritt. While the majority of samples originate from within
the Institute, the facility also conducts analyses for researchers in
other departments of the University and for industrial customers, and
collaborates with academic colleagues at several external
institutions.
Samples are usually analysed on a first come, first served basis
with one structure being determined for each research group on a
cyclic system. Variations in this policy for operational efficiency
or urgent work are at the discretion of the Manager. When a structure
determination has been completed, the report, tables and diagrams are
placed on a Macintosh server which is accessible via AppleTalk from
all Macintosh computers within the institute.
A one-semester graduate
course in small-molecule crystallography is offered every year.
It comprises lectures in the basic theory of crystallography, as well
as extensive hands-on practical experience involving crystal
mounting, data collection, solving and refining a structure and
exposure to a range of problems that can be encountered during a
structural analysis.
Read about the history
of crystallography at the University of Zürich.
Services
The X-ray Crystallography Facility offers the following range of
services associated with single crystal structure analyses of small
molecules:
- Advice on growing
diffraction-quality single crystals and evaluation of crystal
quality.
- Evaluation and mounting of crystals, including moderately air
and moisture sensitive samples.
- Determination of unit cell parameters, crystal system and
space group.
- Data collection with Mo radiation using CCD detector
technology.
- Choice of data collection temperature from room temperature
down to 93 K (160 K is employed unless otherwise
requested).
- Absorption corrections (highly redundant symmetry-equivalent
reflections are recorded routinely so that a correction based on
the Blessing algorithm can be applied if needed and the crystal
faces are indexed when the material is strongly absorbing or the
Blessing correction shows that absorption corrections are
important).
- Structure solution using the powerful array of structure
solution programs that is available.
- Structure refinement.
- Determination of the absolute configuration when an
enantiomerically pure compound contains an element heavier than
Si.
- Preparation of molecular illustrations in colour or black
& white for publications, theses, slides or overhead
projection.
- Comprehensive analysis of the structural results, including
hydrogen bonding, unusual geometrical features, intermolecular
interactions, planes, ring puckering, etc.
- Preparation of a comprehensive report with full data
tables.
- Preparation of results for publication or the writing of a
complete paper when the structural results are to be published
separately.
- Searches in the Cambridge
Structural Database and the Inorganic
Crystal Structure Database.
- Tuition and guidance
in the use of the Cambridge Structural Database.
- Consultancy on matters relating to crystallography and
structural chemistry.
Resources
The hardware available for crystal structure analyses
includes:
- Nonius FR590 sealed tube 3 kW generator.
- Nonuis Kappa-axis four-cirgle goniometer with Nonius KappaCCD
electronic CCD area detector.
- MiraCol capillary collimator optics.
- Mo radiation.
- Oxford Cryostream 700 low temperature device for crystal
cooling (variable from -180 to +130 C).
- KappaCCD interface server PC (Windows 98) for control of the
diffractometer.
- Two PC host workstations (Linux) for control of the data
acquisition and data processing, as well as for structure solution
and refinement and molecular graphics.
- SGI Origin 200 computer system for structure solution and
refinement and molecular graphics.
- Macintosh G3 computer workstations.
- Access to the university's IBM SP2-550 computer cluster.
The software available includes:
- Nonius KappaCCD Collect data collection software system.
- Denzo-SMN software for frame integration, scaling and data
reduction.
- Nonius EvalCCD software. An alternative package for frame
integration, scaling and data reduction, which is particularly
useful for handling twins.
- Nonius MaXus Structure Determination Program - a complete
package for structure solution and refinement, molecular graphics
and preparation of reports and tables.
- teXsan 1.10 (Unix version) from Molecular Structure
Corporation. A complete package for data reduction, structure
solution and refinement, molecular graphics and preparation of
reports and tables.
- SHELXL-97 for structure refinement.
- CRYSTALS for structure refinement.
- XTAL 3.6 for structure refinement.
- A full range of structure solution programs, including
SHELXS-97, DIRDIF-94, SIR-92, MULTAN and SnB.
- PLATON for comprehensive analysis of the structural
results.
- ORTEP-II & -III, PLUTO, Chem-Ray and CHARON for molecular
graphics.
Crystallographic and other databases that are accessible:
Crystallographic and other journals:
Some Other Useful Crystallography Links
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Last update: 2-May-2005 /AL
Institute of Organic Chemistry, University of Zurich,
Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
