Research Guides

Department of Chemistry University of Oxford

Amber L. Thompson

We are one of the UK's leading high resolution X-ray crystallography groups. The laboratory is equipped with two state-of-the-art Oxford Diffraction dual microfocus Kappa geometry area detector diffractometers (top left) and two Nonius single wavelength Kappa CCD diffractometers.  All the diffractometers are capable of handling samples down to liquid nitrogen temperatures. Every student in the laboratory has their own high-specification PC, and other PCs are available to outside students. The Cambridge Crystallographic Database is installed on selected PCs.

The Laboratory houses the Single Crystal X-ray Analytical Service.  This symbiosis of the research and analytical activities means that the Service is supported by the research group, and the research group has access to an endless supply of interesting or difficult crystallographic problems.

The Laboratory has a high profile outside of Oxford, with members regularly being invited to speak at National and International meetings.

The Chemical Crystallography Service is run in two parts: the analytical service and the "DIY" service which includes some 40 trained "users".  It is a special feature of the X-ray crystallography laboratory in Oxford that 'hands-on' crystallography is promoted.  Initially researchers who want to determine their own structures complete a minimal practical health and safety course and are invited to attend crash-courses on crystal structure analysis.  Following tailored one-to-one training in the use of the instrumentation, structure solution/refinement software, preparing files for publication and validation, data can be collected unsupervised, although help is always available in case of difficulties.  Some examples of structures published by The Service are shown left.

In addition to the in-house instrumentation, we also have regular access to the Small Molecule Beamline at the Diamond Light Source, I19 (bottom left) under the Block Allocation System.  As part of The Service, trained users have the opportunity to take their own samples to Diamond to collect data and a team of 4-8 people cover a 24 hr shift once every 1-2 months.

There is always a wide range of Part II and D.Phil. projects available in the Chemical Crystallography Laboratory, from ones in which students prepare their own materials for subsequent analysis through to almost totally theoretical ones developing software and involving little practical work. We collaborate closely with groups from Inorganic and Organic Chemistry, so we can find projects for students interested in almost any kind of chemistry from purely inorganic, through organo-metallic to the products of chiral syntheses.


Absolute Configuration Determination

It is now well established that the different enantiomers of a chiral material can have significantly different physiological properties - for example d and l-limonene. As a consequence of this, drug manufacturers and drug authorisation authorities are increasingly concerned about the absolute configuration of active pharmaceutical ingredients. In appropriate cases, X-ray structure analysis can give very reliable results. Enhancing and controlling this is a fundamental area of research.


Exploiting Synchrotron Radiation

The time allocated on I19 to the Chemical Crystallography Service has really brought the power of synchrotron radiation to our attention.  In addition to a number of collaborative research projects with scientists at Diamond Light Source, we are currently involved in developing the Laue (multi-wavelength) technique for use in small molecule research.


Understanding the Solid State

Despite many years and thousands of pounds spent on research, science still cannot reliably predict whether a material will crystallise, what solvents it will crystallise from and what the final structure will look like.  There are over quarter of a million structures in the Cambridge Structural Database and much can be learnt from these.  Systematic examination of characteristic materials can also give key insight into the process of crystallisation.  Understanding how a material behaves in response to external stimulus (e.g. change in temperature) can also help us to understand how molecules talk to each other.

We are currently recruiting undergraduate research students for the academic year 2011/2.  A range of part II projects for Oxford undergraduate Chemistry students are available in the Chemical Crystallographygroup for the academic year 2012/2013. Email or visit the group in Chemical Crystallography in the CRL basement laboratory for information. An overview of some potential projects is available on the Chem. Cryst. webpages.

In addition, the laboratory generally hosts a number of visiting academics during the summer months (May-October).  If you are interested in carrying out research in the Chemical Crystallography Laboratory, you will need to secure a grant to cover the cost of your accommodation and travel etc..  The group currently has no funding available for new Ph.D. students although we always welcome enquiries from applicants who have their own funding. Overseas Ph.D. candidates are very welcome, but generally need to secure scholarships to fund their studies in Oxford. Information on Graduate Admissions, Studentships and sources of funding can be found in the Oxford University Graduate Prospectus.

Visit the group web pages for more information.

Crystallographic and Structural Studies

CRYSTALS Enhancements: Absolute Structure Determination.
Amber L. Thompson & David J. Watkin, Journal of Applied Crystallography, 44, 1017-1022 (2011).

Chiral Selection in the Formation of Borates from Racemic Binaphthols and Related Diols.
Jevgenij A. Raskatov, John M. Brown
& Amber L. Thompson. CrystEngComm, 13(8) 2923-2929 (2011).

Practical applications of averages and differences of Friedel opposites.
Howard D. Flack, Mustapha
Sadki, Amber L. Thompson & David J. Watkin. Acta Crystallographica, A67, 21-34 (2011).

CRYSTALS Enhancements: Dealing with Hydrogen Atoms in Refinement.
Richard I. Cooper, Amber L. Thompson & David J. Watkin, Journal of Applied Crystallography, 43, 1100-1107 (2010).

An Unusual Methylene Aziridine Refined in P21/c and the Non-standard Setting P21/n.
George C. Feast, James Haestier, Lee W. Page, Jeremy Robertson, Amber L. Thompson & David J. Watkin, Acta Crystallographica, C65, o635o638 (2009).

X-ray Crystallography and Chirality: Understanding the Limitations.
Amber L. Thompson and David J. Watkin, Tetrahedron Asymmetry, 20, 712-717 (2009).

Error Estimates on Bond-length and Angle Corrections from TLS Analysis.
James Haestier, Mustapha Sadki, Amber L. Thompson & David J. Watkin, Journal of Applied Crystallography, 41 531-536, (2008).

The Absolute Configuration of 1-Epialexine Hemihydrate.
Amber L. Thompson, David J. Watkin, Zoltan A. Gal, Laurence Jones, Jackie Hollinshead, Sarah F. Jenkinson, George W. J. Fleet & Robert J. Nash, Acta Crystallographica, C64, o649o651 (2008).


Interesting and Challenging Structures

Belt-Shaped π-Systems: Relating Geometry to Electronic Structure in a Six-Porphyrin Nanoring.
Johannes K. Sprafke, Dmitry V. Kondratuk, Michael Wykes, Amber L. Thompson, Markus Hoffmann, Rokas Drevinskas, Wei-Hsin Chen, Chaw Keong Yong, Joakim Kärnbratt, Joseph E. Bullock, Marc Malfois, Michael R. Wasielewski, Bo Albinsson, Laura M. Herz, Donatas Zigmantas, David Beljonne & Harry L. Anderson, Journal of the American Chemical Association, 133(43), 17262–17273 (2011).

Enhancement of Anion Recognition Exhibited by a Halogen Bonding Rotaxane Host System.
Nathan L. Kilah, Matthew D. Wise, Christopher J. Serpell, Amber L. Thompson, Nicholas White, Kirsten E. Christensen & Paul D. Beer, Journal of the American Chemical Association, 132(34), 11893–11895 (2010).

Bis-Anthracene Fused Porphyrins: Synthesis, Crystal Structure, and Near-IR Absorption.
Nicola K. S. Davis, Amber L. Thompson & Harry L. Anderson, Organic Letters, 12(19), 2124–2127 (2010).

High-Purity Discrete PEG-Oligomer Crystals Allow Structural Insight.
Alister C. French, Amber L. Thompson & Benjamin G. Davis, Angewandte Chemie International Edition, 121, 1274–1278 (2009).

Co-editor for Acta Crystallographica Section C.

Elected Member of Council for the British Crystallographic Association (2011-present).

Organising Committee for the BCA/CCG Intensive School in X-ray Structure Analysis (2003-present).

Secretary of the Computing Commission of the International Union of Crystallography (2010-2011).

Elected Member of Chemical Crystallography Group of the British Crystallographic Association Committee (2007-2010).

Working group for "AMALFI - A Multipurpose Automated Laue μ-Focus Instrument" at Diamond.