Practical Applications of Averages and Differences of Friedel Opposites

Dec 072010
 

Acta Cryst. (2011), A67, 21-34.    [ doi:10.1107/S010876731004287X ]

The practical use of the average and difference intensities of Friedel opposites at different stages of structure analysis has been investigated. It is shown how these values may be properly and practically used at the stage of space-group determination. At the stage of least-squares refinement, it is shown that increasing the weight of the difference intensities does not improve their fit to the model. The correct form of the coefficients for a difference electron-density calculation is given. In the process of structure validation, it is further shown that plots of the observed and model difference intensities provide an objective method to evaluate the fit of the data to the model and to reveal insufficiencies in the intensity measurements. As a further tool for the validation of structure determinations, the use of the Patterson functions of the average and difference intensities has been investigated and their clear advantage demonstrated.

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Structure of the Month – December 2010

Dec 012010
 

Presented by:  Dr. Adrian B. Chaplin
Research Leader:  Prof. Andrew S. Weller
Published:  Journal of the American Chemical Society

Making and breaking C–C bonds in the solid state:  The structure of [Ir(BINOR‑S)(PiPr3)][BArF4] over the temperature range 100–250 K reveals a dynamic equilibrium between Ir(III) C–C agostic and Ir(V) bis-alkyl tautomers in the solid-state.  The solid-state dynamic behaviour is shown in the reaction scheme (a), with populations determined using X-ray diffraction (b) and the Van’t Hoff plot for this process (c, R2(fit) = 0.999).The disordered model at 150 K containing (d) Ir(III) and (e) Ir(V). The combined model and thermal ellipsoid plot of the structure refined without cation disorder modelling are also shown (f & g respectively).

Structure of the Month - December 2010

Structure of the Month – December 2010

 

SMTK - A Small-Molecule Toolkit Library for Crystallographic Modelling and Refinement

Nov 272010
 

J. Appl. Cryst. (2011), 44, 52-59.    [ doi:10.1107/S0021889810042470 ]

One of the requirements for the next generation of small-molecule crystallographers is a mathematical programming infrastructure. It should provide a modelling design process, where the model formulation is kept separate from the optimization process to provide gains in reliability, scalability and extensibility, enabling the application of optimization components in general, and refinement-based applications in particular, as applied to crystallographic problems. A research project has been undertaken to design and implement an innovative toolkit library – a small-molecule toolkit (SMTK) – for crystallographic modelling and refinement. This paper provides an overview of SMTK and its object-oriented implementation. As a practical illustration, it also shows the context of use for a set of classes and discusses how the toolkit enables the user rapidly to develop, maintain and explore the full capabilities of crystallography and so create new applications. SMTK reduces the degree of effort required to construct and develop new algorithms and provides users with an easy and efficient means to test ideas, as well as to build large and maintainable models which can readily be adapted to any new situation.

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BCA/PCG Poster Prize

Nov 172010
 

Jeremy Law, a Part II student working with Dr Nick Rees and Dr David Watkin, has won a prize for his poster entitled “Alternative Approaches to Hydrogen Atom Location in the Solid State”. He presented his work to the joint ISIS Crystallography User Group and British Crystallographic Association PCG/SCMP meeting “Current Research in Physical Crystallography”

Teaching Award

Nov 162010
 

Congratulations to Dr David Watkin who received an award under the Oxford Teaching Awards scheme for excellence in teaching as attested by student feedback and with the support of the department. He received a certificate presented by Professor Andrew Hamilton, the Vice-Chancellor of Oxford at Rhodes House.
The Oxford Teaching Awards scheme, co-ordinated by the Oxford University Learning Institute, recognises outstanding contributions award winners have made to teaching and learning at Oxford.

Structure of the Month – November 2010

Nov 012010
 

Presented by:  Nicola K. S. Davis & Dr. Amber L. Thompson
Research Leader:  Prof. Harry L. Anderson
Published:  Journal of the American Chemical Society

Molecules with large planar π-systems show a strong tendancy to aggregate due to π-π interactions. This tetra-anthracene-fused porphyrin forms dimers with the molecules twisted with respect to each other. Bulky aryl groups were necessary for characterisation, but prevent the porphyrins from forming longer stacks in the crystal.  Using long alkyl chains instead could yield systems which form longer π-stacked arrays which may form discotic liquid crystals.  Furthermore, as the porphyrins stack with a near-zero horizontal offset, these have potential as light harvesting arrays since the alignment of the chromophores provides an efficient pathway for holes and electrons along the column.

Structure of the Month - November 2010

Structure of the Month – November 2010

Structure of the Month – September 2010

Sep 012010
 

Presented by:  Dr. Nathan L. Kilah, Matthew D. Wise, Christopher J. Serpell, Nicholas G. White, Dr. Kirsten E. Christensen & Dr. Amber L. Thompson
Research Leader:  Prof. Paul D. Beer
Published:  Journal of the American Chemical Society

This structure represents the first use of solution phase halogen bonding to control and facilitate the anion templated assembly of an interlocked structure.  It  unambiguously confirms the interlocked nature of the system, and the vital role played by halogen bonded anion templation in its assembly.  The crystals were small and diffracted poorly, so data were collected on I19 at Diamond.  Unfortunately, they also suffered severe radiation damage, so data were collected using a single φ scan leading to a paucity of data.  Extensive disorder meant that the final refinement had a data:parameter ratio of 3.6:1 and required 4401 restraints.

Structure of the Month - September 2010

Structure of the Month – September 2010

Structure of the Month – August 2010

Aug 012010
 

Presented by:  Dmitry Kondratiuk, Johannes Sprafke & Dr. Amber L. Thompson.
Research Leader:  Prof. Harry L. Anderson
Published: Journal of the American Chemical Society

Molecules with many strongly coupled π-electrons exhibit unique optical and electronic behaviour because of the way they interact with electric fields, particularly high-frequency optical fields.  The crystals of this material are highly prone to solvent loss as well as giving weak diffraction.  Data were collected on I19 at Diamond and the structure featured on at least four proposals at Diamond and the SRS (Daresbury) before it was finally determined.  Butadiyne linked porphyrin oligomers are generally expected to be rigid, but this structure shows that they are actually quite flexible and can be severely bent to form this highly strained ring.

Structure of the Month - August 2010

Structure of the Month – August 2010

 

CRYSTALS 14.11

Jul 312010
 

CRYSTALS v14.11 is available as a beta-test.

Many small changes in Regularise Replace thanks to a CRYSTALS workshop in Toulouse organised by Carine Duhayon and Laure Vendier.

Cif generator now properly includes esds on refined hydrogen bonds, has incrreased figure-fields for cell parameters, and appends constraint and restraint information as _iucr_ data items at end of cif.

Improved scaling of difference Pattersons – see forthcoming paper by Flack, Sadki, Thompson & Watkin.

Absolute configuration routine (based on PLATON with Ton Spek’s permission) extended to provide more diagnostics and additional data to be re-input as absolute-structure strengthening restraints (see paper by Flack et al. above).

Error tracking for “USE” files has been improved.

Collaboration with Ernesto Mesto (Dipartimento Geomineralogico – Università degli Studi di Bari) uncovered over-sights in the original 1979 code, which lost contributions when a twin component fell onto a centring absence. Difference maps with twinned data now seem to reveal hydrogen atoms very reliably.

ACA Annual Meeting 2010

Jul 292010
 

The ACA was held at the Sheraton Hotel in Chicago, IL.  Contributions from Chem. Cryst. include:

James Haestier, Amber L. Thompson, David J. Watkin, George C. Feast, Jeremy Robertson & Lee Page
Why is P21/n a Standard Non-Standard Space Group? (Poster)

Amber L. Thompson & David J. Watkin
Unpublishable” Data:  Does My R-factor Look Big in This? (Poster)

Amber L. Thompson
Absolute Structure Determination – Interpreting the Flack Parameter  (Presentation)

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