Richard Cooper

Jun 292010

J. Appl. Cryst. (2010), 43, 1100-1107.    [ doi:10.1107/S0021889810025598 ]

Because they scatter X-rays weakly, H atoms are often abused or neglected during structure refinement. The reasons why the H atoms should be included in the refinement and some of the consequences of mistreatment are discussed along with selected real examples demonstrating some of the features for hydrogen treatment that can be found in the software suite CRYSTALS.

Hydrogen addition in CRYSTALS

Hydrogen addition in CRYSTALS

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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.

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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 012009

J. Appl. Cryst. (2009), 42, 798-809.    [ doi:10.1107/S0021889809024376 ]

A new method is presented for handling errors on crystallographic data. In single-crystal diffraction experiments, two variance-covariance matrices are present, one for the cell parameters and the second for the refined parameters (atomic coordinates and anisotropic displacement parameters). These two matrices can be combined so that errors on derived parameters, such as bond distances, bond angles and TLS tensors, may be calculated more simply. The new method works for all space groups but there are limitations on its application to triclinic space groups. The method allows errors to be transformed between space groups.

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May 072009

Tet. Asym. (2009), 20, 712-717.    [ doi:10.1016/j.tetasy.2009.02.025 ]

Advances in hardware and software have made X-ray crystallography even more attractive as the first-option method for structure analysis. For most organic materials containing up to 100 non-hydrogen atoms, getting from the initial visual examination of the sample to producing publication-ready tables and pictures should usually be achievable in a single morning. Improvements in hardware have also increased reliability of the determination of absolute configuration. A recently published new algorithm may extend the range of applicability of the method.

Le Coup de Roi

Le Coup de Roi: making two chiral pieces from an achiral whole

Feb 172009

Bob graduated from St Edmund Hall (Oxford) having completed his Part II year doing copper chemistry with Francis Rossotti. He worked for his D. Phil. (still on copper chemistry) with Keith Prout and Francis, and it was during this work that he became interested in crystallography.

For one of the materials he worked on, aquo(maleato)copper(II), he observed “When the diffraction pattern was indexed, it became apparent that the crystals were unlikely to be orthorhombic, as a strange set of absences were found”. The crystals were twinned. “overlapped reflections were arbitrarily assigned half the measured intensity until a program was written which would include both components in the least squares”. “as there was not sufficient space [memory] it was necessary to rewrite the [AUTOCODE] program in [English Electric Leo Marconi] KDF9 machine language”. AUTOCODE was a symbolic language, rather like a simplified FORTAN. Machine languages are basic to the electronics of the computer, and the programmer has the power and the responsibility of working hands-on with every memory location, even to the extent of synchronising the calculations with the revolutions of the bulk storage devices. So began Bob’s life with computers, and his exceedingly productive partnership with John Rollett.

Immediately after writing his DPhil thesis in 1969, Bob was awarded a fellowship from the Accademia Nazionale dei Lincei in collaboration with the Royal Society which enabled him to work in Rome. There, he set about working with Riccardo Spagna re- implementing the Rollett AUTOCODES in FORTRAN. This program included features such as “riding” and rigid-body constraints, and some of the underlying data-structure can still be found in CAOS (Cerrini S. & Spagna R. (1977) Crystallographic software for a mincomputer, IV Eur. Crystallgr.Meet., Oxford, UK, Abstract A- 212).

On Bob’s return to Oxford he worked with Rollet and Prout, again re-writing the program from scratch but building upon his experiences in Rome. This new program, called CRYSTALS, could handle up to 9 twin components and had a good range of restraints (including facilities now often called SIMU and DELU). Perhaps the most novel feature was “user-defined restraints”, in which the user could define their own equation of restraint as part of the input data, which was then analytically differentiated by CRYSTALS. The equation parser and differentiating engine were all written in beautiful FORTRAN, and are still working, largely unmodified, in the current version of CRYSTALS. Bob’s attitude to programming combined a meticulous attention to detail with a far reaching ability to plan on an expansive scale.

After his Post Doc, Bob started work for Oxford University Computing Service, writing software for data-archiving. However, he continued to work on CRYSTALS whenever he could, and completely re-wrote the underlying data management for a third time when the university upgrade its mainframe to an International Computers Limited (ICL) 2980.

In about 1979 Bob left Oxford to work for Control Data Corporation, implementing meteorology programs on their supercomputers. Apart for a brief period in the 1980’s when he worked with Keith Davies at Chemical Design, Bob has spent most of his career implementing very large FORTRAN program systems, and in recent years modernising massive legacy packages. Weather forecasting may have profited from his work, but there is no doubt that crystallography lost an outstanding programmer when Bob left Oxford.

When not working with computers, Bob was a dependable drinking companion and a formidable Bar Billiards enthusiast. Some of us still remember Bob and George Sheldrick working with other young crystallographers to try to drink the bar dry at ECM 4 in Oxford in 1977. His brilliance as a scientist did not spoil his personality – he as always modest, amiable and good fun.

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 092007

Acta. Cryst. (2007), 63, 303-308. [ doi:10.1107/S0108768106055212 ]

A new polymorph of 2,4-dihydroxybenzoic acid is reported. The structure was characterized by multiple-temperature X-ray diffraction and solid-state DFT computations. The material shows a geometric pattern of hydrogen bonding consistent with cooperativity between the intermolecular carboxylic acid dimer and intramolecular hydrogen bonds. The presence of proton disorder within this hydrogen-bond system, which would support such a cooperative model, was not fully ruled out by the initial X-ray studies. However, solid-state calculations on the three possible end-point tautomers indicate that the dominant crystallographically observed configuration is substantially lower in energy than the other tautomers (by at least 9 kJ mol-1), indicating that no disorder should be expected. It is therefore concluded that no disorder is observed either in the intra- or intermolecular hydrogen bonds of the title compound and that the cooperativity between the hydrogen bonds is not present within the temperature range studied.

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Jan 012006

Francesco obtained his PhD in Rome and since 2004 is Assistant Professor at the Chemical Division of the Department of Pharmaceutical Science of the University of Catania, Italy. He spent some months during 2005 and 2006 in our lab to improve his knowledge of crystallography. His principal area of research is the comparison of experimental X-ray diffraction data with computationally simulated data. The prediction of crystal morphology, polymorphism, atomic displacement parameters (adp), as well as the physico-chemical properties of biologically active compounds are among his interests.