Department of Chemistry

Queen's University
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DEPARTMENT OF

Chemistry

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X-ray Crystallography

  • X-ray Crystallography Machine

    X-ray Crystallography Machine

  • Analysis being done in the X-ray Crystallography Lab

    Analysis being done in the X-ray Crystallography Lab

  • Close in shot of the X-ray Crystallography Machine

    Close in shot of the X-ray Crystallography Machine

  • Inspection in the X-ray Crystallography Lab

    Inspection in the X-ray Crystallography Lab

Location

Department of Chemistry
Chernoff Hall Room 107
Queen's University
90 Bader Lane
Kingston, Ontario, Canada K7L 3N6
Phone: 613-533-6000 ext.74474
Fax: 613-533-6669

Hours

Monday to Friday
9:00 AM - 5:00 PM

Work Order form (DOC, 369KB).

Crystallography is the science of the arrangement of atoms in molecules and of the arrangement of molecules with respect to each other:

 Crystallography borders, naturally, on pure physics, chemistry, biology, mineralogy, technology and also on mathematics, but is distinguished by being concerned with the methods and results of investigating the arrangement of atoms in matter, particularly when that arrangement has regular features [Paul P. Ewald, Acta Crystallographica (1948), 1, 2].

The X-ray Crystallography Facility as part of the Department of Chemistry provides single crystal X-ray (for small molecules) for Chemistry, Material Sciences etc.. The facility is used by departmental members, but is also available for academic users from other departments within and other academic and industrial institutions outside Queen’s University.

Note: Crystals, which cannot be measured on this instrument because they are too small, can be sent  to the Canadian Light source in Saskatoon, SK. The data sets will be collected remotely and processed in-house.

Contact Information

 Gabreille Schatte

Dr. Gabriele Schatte
Instrumentation Manager
Email: gabriele.schatte@chem.queensu.ca
 

 

Determination of a Structure

The following flow chart provides an overview of the steps in the determination of a structure:

X-Ray Flowchart

The analysis of a single crystal X-ray structure results in:

a) Bond distance, bond angles and torsion angles between atoms;

b) Determination of the absolute conformation;

c) Identification of solvent molecules present in crystal lattice;

d) Identification of intra- and/or inter-molecular interactions (e.g. hydrogen bonding).

e) Packing diagrams, which show the arrangement of the molecules within unit cells and can reveal the presence of channels, voids, helices etc.

In addition, the X-ray powder pattern can be calculated and the results can be used to identify the bulk of material via X-ray powder diffraction.

Instrumentation

Crystal DiffractometerThe X-ray crystallography facility is equipped with a state-of-the-art Smart Apex2 D85 diffractometer. The diffractometer is equipped with a CCD based Apex2 detector cooled to -55 ºC using graphite 24monochromated Mo-Kαradiation {17.44 keV; λ(Mo Kα): 0.71073 Å} from a sealed fine-focus ceramic tube X-ray tube and a K780 X-ray generator.

The system uses a horizontal-oriented D8 3circle goniometer base with 2-theta, omega and phi drivesand a fixed chi stage with an angle of 54.74º.

A monocap collimator of 0.5 mm in diameter is used. The MonoCap™ collimator is an assembly of a single glass tube mounted into a metal holder. The glass tube works as an X-ray guide using the effect of total external reflection for focusing and collimating X-ray beams. Data collections can be performed at ambient or lower temperatures using the Oxford Cryosystems 700 Series Cryostream cooling system (temperature range: 90 to 300 K).

Note: Crystals, which cannot be measured on this instrument because they are too small, can be sent to the Canadian Lightsource in Saskatoon, SK. The data sets will be collected remotely and processed in-house.

Software

The following suites of programs are installed on the client computer:

APEX2 – Software controlling the diffractometer, used for data collection and data processing. Designed by Bruker AXS.

WinGX - A MS-Windows based system of programs for solving, refining and analyzing single crystal X-ray diffraction data for small molecules. Has a very user-friendly GUI. Louis Farrgia's WinGX - Tutorials and Examples - software downloads

Olex2 - Program for small-molecule structure solution and refinement. It also includes many useful tools for structure analysis, archiving and report genera¬tion. http://www.olex2.org/

Platon - Program is designed as a Multipurpose Crystallographic Tool: routines for standard geometrical calculations (bonds distances, angles, torsions, planes, rings, intra- and inter-molecular contacts), test programs for missing symmetry, voids in the lattice etc.), utility programs (cell transformations, SHELXL input file etc.), programs for structure validation. http://www.cryst.chem.uu.nl/platon/

SIR97, SIR2002, SIR2004, SIR2011, SHELXS - Programs for structure solution. http://www.ic.cnr.it/icnew/site/ and http://shelx.uni-ac.gwdg.de/SHELX/

Shelxle - graphical user interface for SHELXL (Sheldrick, G. M. (2008). Acta Cryst. A64, 112-122), program used for the refinement of small molecule structures.

Mercury – Program for .3D structure visualization and the exploration of crystal packing. http://www.ccdc.cam.ac.uk/Solutions/FreeSoftware/Pages/FreeMercury.aspx

CheckCIF, PublCIF and EnCIFer are useful for checking and manipulating CIF files.

Cambridge Crystallographic Database Centre (CCDC)

Services Offered
  • Advice on how to crystallize quality crystals suitable for X-ray diffraction
  • Mounting of crystals, including air, moisture and temperature sensitive samples
  • Determination of unit cell parameters
  • Accurate data collection at room or low temperature
  • Data reduction and absorption correction
  • Structure solution and refinement
  • Validation of the data
  • Detailed report with tables of coordinates and molecular geometry
  • Preparation of high quality molecular plots
  • Providing help with Cambridge Crystallographic Database
Service Packages and Fees

Service Packages

The X-ray Crystallography Facility offers the following services associated with single crystal structure analyses of small molecules. The estimated service hours are given behind the service packages:

PAK-1

Unit cell determination only.

PAK-2

Determination of the unit cell and collection of a data set. The data files will be sent electronically to the user/client.

PAK-3

X-ray data collection, structure solution and complete refinement of the structure. Preparation of a comprehensive report with complete experimental details and full tables of atomic coordinates, atomic displacement parameters, bond distances and angles, torsion angles. Preparation of one molecular illustration.

Optional Services

Available with the service package Pak-3:

  • Preparation of additional specialized molecular illustrations
  • Comprehensive analysis of the structural features, including hydrogen bonding, unusual geometrical features and intermolecular interactions
  • Preparation of results for publication if it is intended to publish them in the open literature
  • Preparation of results for publication if it is intended to publish them in the open literature

Fees

Internal users

  • PAK-1: $20 per hour
  • PAK-2: $150 (Note: Unsuccessful attempt of data collection: service hours *$20, 1 hr minimum and 5hr maximum)
  • PAK-3: $230
  • Optional Service: service hours * $20

External academic users

  • PAK-1: $30 per hour
  • PAK-2: $200 (Note: Unsuccessful attempt of data collection: service hours *$20, 1 hr minimum and 5hr maximum)
  • PAK-3: $400
  • Optional Service: service hours * $30

Industrial users

  • PAK-1: $100 per hour
  • PAK-2: $300 (Note: Unsuccessful attempt of data collection: service hours *$20, 1 hr minimum and 5hr maximum)
  • PAK-3: $600
  • Optional Service: service hours * $40