Oct 222009

Acta Cryst. (2009), E65, o2904-o2905.    [ doi:10.1107/S1600536809043827 ]

X-ray crystallographic analysis of the title hydrobromide salt, C10H20N+Br-, of (1R,2S,3R,5R,8aR)-3-hydroxymethyl-5- methyloctahydroindolizine-1,2-diol defines the absolute and relative stereochemistry at the five chiral centres in steviamine, a new class of polyhydroxylated indolizidine alkaloid isolated from Stevia rebaudiana (Asteraceae) leaves.

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Aug 212009

The 25th European Crystallographic Meeting was held in the Harbiye Museum and Cultural Centre in the beautiful city of Istanbul.  It was a very eventful week, and contributions to the conference made by Chem. Cryst. include:

N. David Brown, James Haestier, Mustapha Sadki, Amber L. Thompson & David J. Watkin
A Further Improved Structure Matching Algorithm (Poster)

James Haestier
Handling of Cell Errors and their Effect on Derived Parameters (Poster)

Mustapha Sadki
New Modelling for Disordered Atoms in Free-form Based Hybrid Refinement and Visual Representation

Mustapha Sadki
The Application of Novel Modelling and Refinement Strategies to Crystallography

Amber L. Thompson & David J. Watkin
Absolute Configuration Determination – Is there More Information in the Data? (Poster)

David J. Watkin, Richard I. Cooper & Amber L. Thompson
CRYSTALS:  Refinement and Validation Tools (Poster)

David Watkin
The Future of Small Molecule Software (Session Chair)

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.

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 132004

J. Chem. Inf. Comput. Sci. (2004), 44, 2133-2144. [ doi:10.1021/ci049780b ]

The crystallographically determined bond length, valence angle, and torsion angle information in the Cambridge Structural Database (CSD) has been made accessible by development of a new program (Mogul) for automated retrieval of molecular geometry data from the CSD. The program uses a system of keys to encode the chemical environments of fragments (bonds, valence angles, and acyclic torsions) from CSD structures. Fragments with identical keys are deemed to be chemically identical and are grouped together, and the distribution of the appropriate geometrical parameter (bond length, valence angle, or torsion angle) is computed and stored. Validation experiments indicate that, with rare exceptions, search results afford precise and unbiased estimates of molecular geometrical preferences. Such estimates may be used, for example, to validate the geometries of libraries of modeled molecules or of newly determined crystal structures or to assist structure solution from low-resolution (e.g. powder diffraction) X-ray data.

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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.

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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.

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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.