Nov 182009

Acta Cryst. (2009), C65, o635-o638.    [ doi:10.1107/S0108270109046952 ]

The unusual methylene aziridine 6-tert-butyl-3-oxa-2-thia-1-azabicyclo[5.1.0]oct-6-ene 2,2-dioxide, C9H15NO3S, was found to crystallize with two molecules in the asymmetric unit. The structure was solved in both the approximately orthogonal and the oblique settings of space group No. 14, viz. P21/n and P21/c, respectively. A comparison of these results clearly displayed an increase in the correlation between coordinates in the ac plane for the oblique cell. The increase in the corresponding covariances makes a significant contribution to the standard uncertainties of derived parameters, e.g. bond lengths. Since there is yet no CIF definition for the full variance-covariance matrix, there are clear advantages to reporting the structure in the nonstandard space-group setting.

Publisher’s copy: IUCr

Apr 012009
David Watkin gives the Lonsdale Lecture

David Watkin gives the Lonsdale Lecture

Every two years, the Young Crystallographers Group of the British Crystallographic Association nominate a speaker to give the prestigious Kathleen Lonsdale Lecture. Traditionally, they invite well respected scientist who has a good rapport with students. This year the Lonsdale Lecturer was David Watkin who is well known within the community, principally as a result of his involvement with the highly respected refinement software CRYSTALS, developed in Oxford and through the BCA biannual teaching school which he co-founded twenty-five years ago.

Dec 152008

Acta Cryst. (2008), C64, o649-o652.    [ doi:10.1107/S0108270108037086 ]

The absolute and relative configurations of 1-epialexine are established by X-ray crystallographic analysis, giving (1S,2R,3R,7S,7aS)-1,2,7-trihydroxy-3-(hydroxymethyl)pyrrolizidine. The compound crystallizes as the hemihydrate C8H15NO4·0.5H2O, with hydrogen bonds holding the water molecule in a hydrophilic pocket between epialexine bilayers. In addition, a comparison was made between results obtained from examination of the Bijvoet pairs from data sets collected using molybdenum and copper radiation.

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 082008

J. Appl. Cryst. (2008), 41, 531-536.    [ doi:10.1107/S0021889808005463 ]

Librational motion within a crystal structure distorts the measured bond distances and angles from their physical values. TLS analysis of a rigid molecule or a rigid part of a molecule allows the calculation of bond-length and angle corrections. Until now, no estimate of the error on these corrections has been available. A method is presented for propagating the errors on the anisotropic displacement parameters (ADPs) to the bond-length and angle corrections which are a function of the libration tensor. The numerical significance of approximations made during the calculation is discussed.

Publisher copy: IUCr

Apr 222004

J. Appl. Cryst. (2004), 37, 545-550.    [ doi:10.1107/S0021889804009847 ]

A Cp* fragment consisting of partial atoms embedded in annuliThe program CRYSTALS [Betteridge, Carruthers, Cooper, Prout & Watkin (2003). J. Appl. Cryst. 36, 1487] has been extended to include an option for the refinement of a continuous electron density distribution lying along a line, a ring or on the surface of a sphere. These additional non-atomic electron distributions can be refined in any combination with traditional anisotropically distributed spherical atoms, including the refinement of `partial’ atoms overlapping with the special electron distributions.

Electronic reprints

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Dec 012003

J. Appl. Cryst. (2003), 36, 1487.    [ doi:10.1107/S0021889803021800 ]

CRYSTALS version 12 contains a modern crystallographic user interface, and novel strategies that incorporate chemical knowledge and crystallographic guidance into the crystal structure analysis software.

Electronic reprints

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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]

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