Research Guides

Department of Chemistry University of Oxford

Dr D.J. Watkin

The Chemical Crystallography Laboratory

We are one of the UK's leading high resolution X-ray crystallography groups. The laboratory is equipped with two state-of-the-art Agilent dual microsource Kccd area detector diffractometers and two Nonius single wavelength Kccd 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 Data Base is installed on selected PCs.

The Laboratory houses the Single Crystal X-ray Analytical Service, run by Dr Amber Thompson.  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.

Research Facilities

A special feature of the X-ray crystallography laboratory in Oxford is its promotion of 'hands-on' crystallography, and its interaction with other research groups. Students from any research group are invited to attend crash-courses on crystal structure analysis and the hands-on use of diffractometers, the general use of interactive computers and crystallographic data base searching. Students based in the laboratory also have the opportunity to learn computer programming. No previous experience with computers is necessary.

There is always a wide range of Part II and D.Phil. projects available, 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 that 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.


Principal Research Projects:

1. The development of software for automated structure analysis and structure evaluation. The new generation of area detector diffractometers have enormous data collection capabilities. To take advantage of this, it is necessary to make the data processing software useable by preparative chemists. The main thrust of our work is towards the development of a knowledge-based X-ray structure analysis system. It includes work on pattern recognition for the identification of molecular fragments, evaluation of numerical techniques, formalisation of 'rules of thumb', and design of 'criteria for correctness'. A new structure analysis program is under development to enable chemists to use their chemical training to interact with the mathematics of structure analysis. Students contributing to this project acquire skills in program design and development, as well as learning how to configure and maintain a personal computer.

2. Investigations are under way to attempt to understand crystallisation and crystal growth of molecular crystals from solutions. Tightening controls in the pharmaceutical industry now require detailed characterisation of all products, including X-ray crystal structure determinations. In addition, the bulk processing of materials and their bio-availability is strongly dependent upon their crystalline form. Current work involves systematic studies of the crystallisation of series of closely related organic materials showing polymorphism.

3. Investigations aimed at trying to understand why many materials form crystals in which the basic crystalline building block, the asymmetric unit, is composed of several independent molecules. The number of Z'>1 crystals found each year is increasing, possibly because of the growing use of area detector diffractometers. Such materials frequently present difficulties in data acquisition and processing.

4. Ab-initio crystal structure prediction has made great advances recently, but often leads to many equi-energetic potential structures. As an alternative to trying to improve the energy calculations, we are searching the Cambridge Crystallographic Database for recurrent structural motifs to be used as discriminators in the final stages of structure prediction.

Computer software

 Version 14 of the CRYSTALS program is available for free download from the Chem Cryst website.

CRYSTALS 12.11, Watkin, D.J. Prout, C.K., Carruthers, J.R., Betteridge, P.W., Cooper, R.I., (2003), Chemical Crystallography Laboratory, University of Oxford, Oxford.

Recent Publications from the Chemical Crystallography Laboratory:

SMTK - The Small Molecule Toolkit Library for Crystallographic Modelling and Refinement. Mustapha Sadki and David Watkin. J. Appl. Cryst., in press

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

Chemical Crystallography – Science, Technology or a Black Art.
David J. Watkin, Crystallography Reviews, 16: 3, 197 — 230, 2010

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).

Crystal Structure Analysis Principles and Practice.  Second Edition .
Edited by William Clegg, Alexander J Blake, Jacqueline M Cole, John S O Evans, Peter Main, Simon Parsons, and David J Watkin.  Oxford University Press, 2009

An Unusual Methylene Aziridine Refined in P21/c and the Nonstandard Setting P21/n.
George C. Feast, James Haestier, Lee W. Page, Jeremy Robertson, Amber L. Thompson & David J. Watkin, Acta
Crystallographica, C65, o635–o638 (2009).

X-ray crystallography and chirality: understanding the limitations. A.L. Thompson, and D.J. Watkin, Tet: Asymm., 20, 712-717, 2009.

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).

Error estimates on bond-length and angle corrections from TLS analysis. J. Haestier, M. Sadki, A.L. Thompson, and D. Watkin, J. Appl. Cryst., 41 531-536, 2008.

Structure refinement: some background theory and practical strategies. D. Watkin, J. Appl. Cryst., 41, 491-522, 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, o649–o651 (2008).

The concomitant crystallization of two polymorphs of 1-deoxy-alpha-D-tagatose. N.A. Jones, S.F. Jenkinson, R. Soengas, K. Izumori, G.W.J. Fleet, and D.J. Watkin, Acta Cryst., C63, O7-O10, 2007.

Recent Lectures by Members of Chemical Crystallography Laboratory:

Dr D.J. Watkin. 2005. 20th Congress of the International Union of Crystallography, Florence.
Dr D.J. Watkin. 2007 24th European Crystallographic Meeting, Marrakech.
Dr D.J.Watkin. 2009. British Crystallographic Association Lonsdale Lecture.
Dr M. Sadki, 2009. British Crystallographic Association Annual Meeting.
Dr M. Sadki, 2009. 25th European Crystallographic Meeting, Istanbul.
Dr D.J. Watkin. 2009. Oxford University Science Society.
Dr A.L. Thompson. 2010. Annual Meeting of the American Crystallographic Association, Chicago.
Dr D.J. Watkin. 2010. Chemistry Out-reach Schools 6-form Lecture
Mr N.D. Brown. 2010 British Crystallographic Association Annual Meeting.
Dr D.J. Watkin. 2010. RSC Advances in Structure Elucidation, Hinckley.

Recent Teaching:

2005. British Crystallographic Association Intensive Course.
2005. International Union of Crystallography Computing School, Siena, Italy.
2006. IUCr Teaching Commission.  Intensive Course in Basic Crystallography, Siena, Italy 
2006. École Thématique du CNRS. "Analyse structurale par diffraction des rayons X, cristallographie sous perturbation". Pont a Mousson, France
2007. British Crystallographic Association Intensive Course.
2008. SCANZ Intensive Course in X-ray Structure Determination, Monash University, Australia.
2008. International Union of Crystallography Computing Commission School in Crystallographic Computing, Kyoto, Japan
2008. Spanish Master Class in Crystallography, University of Zaragoza.
2009. Masters In Crystallography and Crystallization at the Universidad Internacional Menéndez Pelayo, Spain.
2009. 4ème École Thématique. Analyse Structurale par Diffraction des Rayons X sur Monocristal et Applications à la Cristallographie sous Contraintes. Pont a Mousson, France
2009. British Crystallographic Association Intensive Course.