Amber L. Thompson

Jul 172008

Chirality (2008), 20(7), 863-870.    [ doi:10.1002/chir.20561 ]

3 alpha,12 alpha-Dihydroxy-5 beta-cholan-24-oic acid (deoxycholic acid DCA) is able to discriminate between the R- and S-enantiomers of camphorquinone and endo-(+)-3-bromocamphor and select only the S-enantiomers from a racemic mixture. DCA forms novel well ordered 1:l adducts with (1S)-(+)-camphorquinone and (1S)-endo-(-)-3-bromocamphor, both of which have been characterized by single crystal X-ray diffraction (SXRD). When DCA is cocrystallized with (RS)-camphorquinone and (RS)-endo-3-bromocamphor, 1:1 adducts of the S-enantiomers are produced together with crystals of the free racemic guest. In contrast, in the absence of (1S)-(+)-camphorquinone, DCA forms a 2:1 adduct with (1R)-(-)-camphorquinone. In this 2:1 adduct the guest is disordered at ambient temperature and undergoes a phase change in the region 160-130 K similar to that observed for the ferrocene adduct, but with only partial ordering of the guest. The SXRD structure of the low temperature form and the variable temperature C-13 CP/MAS NMR are reported. Cocrystallizing DCA with (1R)-endo-(+)-3-bromocamphor gives the free guest and a glassy solid.

Packing diagram of (deoxycholic acid)2:ferrocene at 100K viewed along the crystallographic a-axis

Packing diagram of (deoxycholic acid)2:ferrocene at 100K viewed along the crystallographic a-axis; hydrogen bonds are represented by dotted lines

May 152008

J. Appl. Cryst. (2008), 41, 491-522.    [ doi:10.1107/S0021889808007279 ]

Most modern small-molecule refinement programs are based on similar algorithms. Details of these methods are scattered through the literature, sometimes in books that are no longer in print and usually in mathematical detail that makes them unattractive to nonprogrammers. This paper aims to discuss these well established algorithms in nonmathematical language, with the intention of enabling crystallographers to use their favourite programs effectively.

Apr 012008

The Annual Meeting of the British Crystallography Association was held in York.  Contributions from Chem. Cryst. included:

Anna Collins, Richard I. Cooper, Andrew R. Cowley, David J. Watkin
2-(1-Hydroxy-2-methyl-propyl)-2,5-dihydro-furan-2-carboxylic acid diisopropylamide:  A study of a phase transition to a pseudosymmetrical Z′=2 structure (Poster)

James Haestier, Mustapha. Sadki, Amber L. Thompson and David J. Watkin
Cell Parameter Standard Uncertainties and their Effect on Crystallographic Data (Poster)

Mustapha Sadki, James Haestier, Amber L. Thompson & David J. Watkin
Computational Infrastructure for Bridging the Gap between Previous and Future Generations of Crystallographers (Poster)

Dec 172006

J. Appl. Cryst. (2006), 39, 842-849.    [ doi:10.1107/S0021889806038489 ]

A sizeable proportion of structures with Z‘ = 2 are thought to exhibit pseudosymmetry, but establishing the extent of the deviation from true symmetry is problematic. By considering both the conformational similarity between the independent molecules and the way in which they are related in space, assessment of the pseudosymmetry of a structure becomes possible. A method of matching two groups of atoms where both these factors are quantified using CRYSTALS [Betteridge, Carruthers, Cooper, Prout & Watkin (2003). J. Appl. Cryst. 36, 1487] is described.

Oct 162005

Nick is Inorganic Nuclear Magnetic Resonance Manager.  Although he comes from The Dark Side, solid state NMR has its uses and he not only works closely with us, but he is also continuing the work he carried out with Keith Prout on deoxycholic acid complexes.  As such he is an honorary member of Chem. Cryst.

Apr 012002

J. Appl. Cryst. (2002), 35, 168-174.    [ doi:10.1107/S0021889802000249 ]

Although non-merohedrally twinned crystal structures can normally be solved without difficulty, problems usually arise during refinement. Careful analysis of poorly fitting data reveals that they belong predominantly to certain distinct zones in which |Fo|2 is systematically larger than |Fc|2. In the computer program ROTAX, a set of data with the largest values of (|Fo2| – |Fc2|)/u(|Fo2|) is identified and their indices transformed by rotations or roto-inversions about possible direct- and reciprocal-lattice directions. Matrices that transform the indices of the poorly fitting data to integers are identified as possible twin laws.

Oct 172000

Acta Cryst. (2000), B56, 747-749.    [ doi:10.1107/S0108768100008466 ]

The reporting of Uequiv and its standard uncertainty has a chequered history. In spite of the recommendation of the IUCr Commission on Journals that authors use the definition of Uequiv of their own choice, possibly without standard uncertainties, there still seems to be some confusion amongst referees and editors about the status of this derived parameter. It is shown that neither of the common definitions are very useful, and that the standard uncertainty computed from the refinement normal matrix is almost worthless. A potential alternative derived parameter is proposed.

Jul 011994

Acta Cryst.  (1994), A50, 411-437.    [ doi:10.1107/S0108767393012784 ]

Each year, many single-crystal structure analyses are reported that show evidence of over- or under-refinement. Often, the refinement strategies have been naive or over-complex and alternative strategies might have been more effective. The many descriptions of crystallographic and numerical techniques suitable for assisting with the control of difficult refinements are distributed widely in the literature and so are not always easily accessible. Without being a review of these procedures (which would require a substantial book), this article attempts to list readily available procedures, together with a brief outline of their backgrounds and examples of their applications to organic and organometallic compounds. The analysis of extended-lattice materials (usually inorganic materials) often raises problems in addition to those covered here. The particular aim of this article is to remind the reader that X-ray structure analysis is a modelling process and that, while standard models may be adequate for most analyses, more care and imagination must be applied to the treatment of difficult cases. Principles of methods are described without detailed mathematical derivations, although sufficient references to the literature are provided to permit careful study. Future requirements for refinement processes are outlined, including the use of new machine architectures, applications of sparse-matrix methods and the development of expert systems.

Electronic reprints

  • Oxford University Research Archive [direct pdf]

Publisher’s copy