Amber L. Thompson

Jan 012011

Presented by:  Nicholas H. Evans & Christopher J. Serpell
Research Leader:  Prof. Paul D. Beer
Published: Angewandte Chemie International Edition

Catenanes and rotaxanes are highly attractive targets for the supramolecular chemist due to their potential uses as molecular machines or as selective hosts for ionic and molecular guests. This molecule was synthesised via chloride anion templation and crystals grown by slow diffusion of diisopropyl ether into a chloroform/catenane solution.  Data were collected on I19 at Diamond.  This first handcuff catenane structure provided proof of the topology, also revealing potential further uses: the degree of slack in the large macrocycle could allow controlled rotation within the handcuff, and the large number of oxygen atoms in the cavity formed by the handcuff linker and large macrocycle could be used to bind cations.

Structure of the Month - January 2011

Structure of the Month - January 2011

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


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

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

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


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)

Jul 012010

There is some really cool chemistry done in Oxford and some even cooler structures.  In order to encourage everyone to take an interest in what other people are doing with our instruments, we have instigated a “Structure of the Month”.  The idea is that users submit a single-crystal structure that they have done (either here or at Diamond/ISIS).  This is done by filling in a form including a short explanation of why it is cool and we will choose the best submission and stick it up in the lab in an obvious place.

The rules are as follows:

In order to keep it current, the structure must have been collected in the previous two months, i.e. the structure for October must have been collected in August or September (or where the work is particularly sensitive, “accepted for publication” in the previous month).

  • The competition is only open to affiliates of Oxford Chemistry
  • We must receive it by email before the end of the previous month, i.e. submissions for October must be received by the end of September.
  • You must include a colour picture.
  • The description must be 100 words or less (we are very strict about this).
  • It must be cool to you, but it can be cool for any reason (see below).
  • The Judges’ decision is final.

You should include a covering comment explaining why it is cool to you.  We will accept most reasons, but examples include:

  • “It’s taken me three years to make it, 200 attempts to crystallise it and 10 days of data collection time, but we got it in the end.”
  • “We crystallised Vac Grease!”
  • “It has an R1 < 1%” (or even “it has an R1 > 35%”).
  • “How on earth did we make that???”
  • “We got an invitation to Stockholm to collect an award because of it…”
  • “I’ve collected 300 datasets and done structures for everyone else in my group, but this was the first one for me.”
  • “It is the first/longest/largest/… example of…”
  • “It’s just a cool molecule”.

If we have no submissions for one month, we will look back over submissions for the previous month and earlier until we find something suitable.

The decision will be based on “coolness”, but we will endeavour to ensure that there is plenty of variety too.  The Judges’ decision is final.  In time, there will be a small trophy that the winner can look after for a month while they are the holder.  For confidentiality reasons, the winning entry will be displayed at the entrance to Chem. Cryst. and will only be reported on the website once it has been published.

Please stick to the template and keep it to a single full page as in the example.  Email submissions to Dr. Amber L. Thompson by the end of the month; late submissions will be entered for the following month.

Jun 152010

Dr David Watkin, an Honorary Member of the BCA, has been awarded the 2010 Fankuchen Award by the American Crystallographic Association. The award recognizes contributions to crystallographic research by one who is known to be an effective teacher of crystallography.

The Award will be presented at the ACA Annual Meeting in New Orleans 2011 at which David will also be delivering a Plenary Lecture.

Apr 152010

Cryst. Rev. (2010), 16(2), 133-144.    [ doi:10.1080/08893110903483238 ]

Recent developments in crystallographic error analysis are described. This report provides an introduction to more-formal work, originally published in Ref. (Haestier, J., J. Appl. Cryst. 2009, 42, 798). Prior to the main discussion, a brief overview of the normal distribution and error-propagation is provided, with some simplified examples to demonstrate the effects of covariance terms on error calculations. A new method is described for absorbing the cell-parameter errors into the variance-covariance matrix of the refined parameters. Problems occur for monoclinic and triclinic cell settings as the crystallographer must ‘choose’ how errors on the cell angles affect the coordinates. The choice has no effect on error-calculations on the internal geometry (bond-lengths, angles and torsion angles) of the structure, but may introduce a bias if the errors are used as weights.

Apr 152010
Susan Huth presents Kirsten Christensen with the Durward Cruickshank Award

Susan Huth presents Kirsten Christensen with the Durward Cruickshank Award

The final dinner of the British Crystallographic Association Spring Meeting in Warwick was interrupted, as always, with the prize winning awards. Amber Thompson was awarded the International Union of Crystallography Prize (a copy of International Tables) for her explanation of the advantages of choosing non-standard space groups. Kirsten Christensen was awarded the Durward Cruickshank prize for a young crystallographer who had made an outstanding contribution to crystallography.



Other contributions include:

N. David Brown, James Haestier, Mustapha Sadki, Amber L. Thompson & David J. Watkin
matchbOx:  Automatic Structure Matching to Facilitate Crystallographic Refinement (YC Presentation)

Kirsten E. Christensen, Christopher J. Serpell, Nicholas E. Evans & Paul D. Beer
Pushing the Boundaries of Small Molecule Crystallography:  The Challenging Structure of a Macrocyclic Anion Sensor (Poster)

Richard I. Cooper, Amber L. Thompson & David J. Watkin
The Hydrogen Challenge:  Where are we Now? (Poster)

Christopher J. Serpell & Paul D. Beer
Refinement of Large Supramolecular Structures (Presentation)

David J. Watkin
Dealing with Difficult Data (Session Chair)