Amber L. Thompson

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)


Dec 202009
A picture of Seizure


A dreary, grey, condemned, 1960s low-rise council flat is an unusual place to find one of the most beautiful pieces of crystallographic art in the UK.  “Seizure” was constructed by transforming the flat into a watertight tank, into which 70,000 litres of hot copper sulphate solution was poured.  After three weeks of patient waiting, and cooling, the mother liquor was removed to reveal a spellbinding, blue, crystal garden. Fortunate visitors to this spectacular exhibit were entranced to behold a magical kingdom of exquisite azure crystals – everyday objects such as light fittings and baths transformed into coruscations of brilliance…



Oct 302009

Inorg. Chim. Acta  (2010), 363(6), 1140-1149.    [ doi:10.1016/j.ica.2009.10.020 ]

Four 2-acetylpyridine 4N-alkyl thiosemicarbazones, and their Ga(III) and In(III) complexes have been prepared and characterised by fluorescence, UV–Vis, IR, 1H and 13C NMR spectroscopy, mass spectrometry and X-ray crystallographic analysis. Comparison of the crystal structures gave an insight into the nature of the complexes formed, demonstrating a preference for [ML2]+ type complexes with gallium and [MLX3] species with indium. Stability studies on two candidates indicated that complex [InL3Cl2MeOH] was stable to chemical degradation for prolonged periods in human serum, giving this complex potential for further biological evaluation.

Electronic reprints

  • Oxford University Research Archive [direct pdf]

Publisher’s copy


Thiosemicarbazone overlay

Overlay of two thiosemicarbazone ligands showing two different conformations.

Oct 072009

The Nobel prize for chemistry has been jointly awarded to Venkatraman Ramakrishnan (MRC Cambridge), Thomas Steitz (Yale) and Ada Yonath (Weizmann Institute, Israel) for their work determining the structure of ribosomes.  The ribosome is an important component of cells that assembles proteins from amino acids.  It is often referred to as “the protein factory”.  This is the second Nobel prize to be awarded for work on ribosomes as Albert Claude, Christian de Duve and George Emil Palade were awarded the Nobel Prize for Medicine, in 1974 for their discovery.


  • Announcement of the 2011 Nobel Prize in Chemistry [video]
  • BBC News Online [Report]


Picture of the structure and shape of the E.coli 70S ribosome.

Structure and shape of the E.coli 70S ribosome.


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)