Amber L. Thompson

Aug 302018
 

Chemical Communications 2018, 54, 9849 – 9852 [doi:10.1039/C8CC05430D]

For the collidine analogues of Barluenga’s Reagent (IPy2BF4) reported, a flat cation is necessary for the generation of a modulated phase, in keeping with the “Ratchet Model” theory [Kim et al., Crystal Growth & Design, 2014, 14, 6294]. Attempts to study “diffuse modulation” in Br(Coll)2ClO4 have shown that these non-Bragg features disappear very rapidly on exposure to synchrotron radiation, an effect thought to be caused by the radiation damage disrupting the lattice vibrations that cause the modulation.

 

Radiation Damage

Apr 052018
 

Kiaora Tolmie recieving the CCG Poster PrizeThe 2018 Meeting of the British Crystallographic Association was held at Warwick University where Chem. Cryst. was well represented.  The meeting started with the Young Crystallographers Satellite meeting, during which Lewis Morgan’s oral presentation was so “eggsellent” that he won the Industrial Group Prize for the best talk, and with it, the dubious honour of presenting it again as a plenary in the main meeting.

At the conference dinner Kiaora Tolmie received a CCG CrystEngComm poster prize for her poster on hard-to-crystallize materials, and James Bird was awarded the YCG I’m-a-scientist-get-me-out-of here prize for the poster presenter who most clearly and enthusiastically communicated their results.

Congratulations to all three winners!

 

Lewis Morgan delivering his prize-winning presentation at the BCA Spring Meeting 2018

Lewis Morgan delivering his prize-winning presentation

 

A full list of the presentations from Chem. Cryst.:

George A. Sackman & Richard I. Cooper
Distinguishing Disorder: A Molecular Dynamics Approach (Poster Presentation)

Kiaora L. M. Tolmie & Richard I. Cooper
Structure Determination of Hard-to-Crystallize Materials (Poster Presentation)

Lewis C. F. Morgan, Jack N. Blandy, Claire A. Murray, Kirsten E. Christensen & Amber L. Thompson
Improving Our Understanding of Modulation in Molecular Materials (Poster & Oral Presentation)

James M. Bird & Richard I. Cooper
A Comparison of Molecular Dynamics Techniques for Simulation of Thermal Disorder in Molecular Crystals (Poster Presentation)

Oliver J. A. Bar & Richard I. Cooper
A Study of Phase Transitions in Organic and Metal-organic Inclusion Complexes through Molecular Dynamics Simulation (Poster Presentation)

Richard I. Cooper
CrysPy: CRYSTALS in Python (Poster Presentation)

Amber L. Thompson
When are Bad Data Good Data? (Keynote Oral Presentation)

Nov 012017
 

Tetrahedron Asymmetry 2017, 28(10), 1330-1336 [doi:10.1016/j.tetasy.2017.08.016]

Students of single crystal X-​ray diffraction are often give advice as to how best to collect their data when attempting absolute configuration determination.  These ‘rules’ often have more grounding in gut-​feeling than evidence.  Thus, in an effort to provide advice and evidence that today’s crystallographers can pass onto to tomorrow’s young scientists, we present a systematic study of 1-​deoxy-​L-​arabinitol, a straight chain sugar which crystallizes well in the space group I41.

 

Arabinitol

Oct 052017
 

George is developing machine learning methods for classification and visualisation of experimental data. The first part of his project involves identification of metabolite changes in plants under changing environmental conditions, including the effect of auxinic herbicides. He is also looking at formulation of these herbicides to find ways of increasing their efficiency and reducing environmental impact.

In his spare time George may be found running.

Sep 232016
 

Journal of the American Chemical Society 2016, 138(40), 13314-13325 [doi:10.1021/jacs.6b07501]

Hydrogen bonding with fluoride is a key interaction encountered when analyzing the mode of action of 5′-​fluoro-​5′-​deoxyadenosine synthase, the only known enzyme capable of catalyzing the formation of a C-​F bond from F​. Further understanding of the effect of hydrogen bonding on the structure and reactivity of complexed fluoride is therefore important for catalysis and numerous other applications, such as anion supramol. chem. Herein we disclose a detailed study examg. the structure of 18 novel urea-​fluoride complexes in the solid state, by X-​ray and neutron diffraction, and in soln. phase and explore the reactivity of these complexes as a fluoride source in SN2 chem. Exptl. data show that the structure, coordination strength, and reactivity of the urea-​fluoride complexes are tunable by modifying substituents on the urea receptor. Hammett anal. of aryl groups on the urea indicates that fluoride binding is dependent on σp and σm parameters with stronger binding being obsd. for electron-​deficient urea ligands. For the first time, defined urea-​fluoride complexes are used as fluoride-​binding reagents for the nucleophilic substitution of a model alkyl bromide. The reaction is slower in comparison with known alc.-​fluoride complexes, but SN2 is largely favored over E2, at a ratio surpassing all hydrogen-​bonded complexes documented in the literature for the model alkyl bromide employed. Increased second-​order rate consts. at higher diln. support the hypothesis that the reactive species is a 1:1 urea-​fluoride complex of type [UF]​ (U = urea) resulting from partial dissocn. of the parent compd. [U2F]​​. The dissocn. processes can be quantified through a combination of UV and NMR assays, including DOSY and HOESY analyses that illuminate the complexation state and H-​bonding in soln.

Fluoride–urea complex

Publisher’s copy

Jun 232015
 

Fluoride–alcohol complexChemical Science 2015, 6, 5293-5302
[doi:10.1039/c5sc01812a]

The nucleophilic reactivity of fluoride ion is altered in the presence of hydrogen-bond donors, including alcohols. Relatively little is known about the coordination involved; to rectify this, the X-ray structures of fourteen novel fluoride–alcohol complexes with tetrabutylammonium as the counterion have been determined. The coordination number varies from two to four depending on the steric bulk of the alcohol and is closely linked to trends in reactivity. This diversity in coordination stoichiometry is unprecedented but significant, as it implies differences in the ability of the fluoride-alcohol complexes to dissociate in solution with release of a more active and/or selective fluoride source.

Publisher’s copy

Jan 202014
 

RKV-001Once again, the weather contrived to cause problems, this time with flooding causing closures to both the Botley and the Abingdon Roads.  Despite this, the speakers and organisers and, more importantly cake and lunch (!) all arrived in time even though some of the delegates were unable come (for those who missed it, the program for Red Kite V is available to download).

People who only had a short bus, cycle or walk arrived in good time for the first of the mini-plenary sessions which was presented by Prof. Andrew Weller from Oxford who discussed the preparation of an alkane complex by solid-state hydrogenation.  The session was continued by Jerome Wicker (also Oxford) (who eventually managed to remember his title) and was talking about predicting whether or not materials will crystalise.  This was followed by two more speakers from Oxford, Markus Gerstel talking about radiation damage in protein samples and Joshua Hill discussing framework materials.

After mid morning cake with coffee for those who were quickest and tea for those who weren’t (sorry about that – we will make sure there is more next time!), we started the second session.  This began with our second mini-plenary speaker, Dr. Arwen Pearson from the Research Complex and the Astbury Centre, Leeds, who gave a nice presentation that demonstrated how reactions can be followed in the solid state in proteins.  This was followed by three more speakers from Oxford:  Andrew Jupp talking about novel organophosphorus species, Rémi Tirfoin explaining how important single crystal X-ray diffraction is to organometallic chemists and Andrew Johnston telling us about benzoylmethylecgonine – a simple compound whose structure is more complex that you would think.

Lunch was accompanied by posters and the room was a constant buzz as people mixed munching with science, before the final session began.  The mini-plenary was presented by Prof. Mike Glazer (Oxford) who demonstrated how important it can be to get space groups right and what effect it can have on a phase diagram.  This was followed Dr. Mark Warren (Diamond) explaining how the facilities on the small-molecule beamline I19 can help you follow a reaction.  Next was Dr. Lynne Thomas from the Research Complex and Bath, who showed how you can use a range of techniques to understand the structure of materials as complex as Sitka Spruce (aka aircraft wood).  The final speaker of the day was Dr. Tristan Youngs (ISIS) who explained how complex amorphous systems could be studied using neutrons.  The meeting was brought to a close with the awarding of the obligatory tweeting poster prizes which were given to the nicely alliterating Joe, Jerome and Jamie (Paddison, Wicker and Lawler, respectively);  congratulations to them.

The day finished with a drinks reception giving people who had missed the best posters a chance to talk to the winners.  Once again, everyone seemed to enjoy the day.  We are looking forward to seeing everyone again at the next meeting which will be held on the Harwell site over the summer.

Finally, the organisers would like to thank all the excellent speakers, delightful attendees, esteemed poster judges, kind souls who helped set up the rooms, and especially the John Fell Fund who provided sustenance:  together you made this another fantastic meeting.

Mar 122013
 

The Big Bang Fair is a free educational event open to visiting school groups that happens in March every year moving round the country. It works with partner organisations across business and industry, government and academia to try and give a flavour of the real scale of engineering and science in the UK, aimed at showing young people (primarily aged 7-19) just how many exciting and rewarding opportunities there are out there for them with the right experience and qualifications.

This year the Big Bang Fair is being held in the London, ExCeL Arena, 14th-17th March. Since 2013 is the Bragg centenary, STFC have very kindly funded a stand at this year’s fair, which will be totally dedicated to crystallography. The BCA, Diamond Light Source, ISIS and STFC have worked together to develop the stand designed to tell everyone how great crystallography is through the medium of hands on activities, lasers, and sweets. The fair is expecting 75,000 people (mostly children) through the doors over the course of four days, so Andrew Cairns, Josh Hill, Nick Funnell, Mike Glazer, George Pidgeon, Karim Sutton and Amber Thompson are all going along from Oxford to help out. Here are some photos of the first day.

Lego Beamline

Two crystallographers check the interlocks on the Lego Beamline

You are never too young to learn about packing...

You are never too young to learn about packing…

...especially when there's sweets involved!

…especially when there’s sweets involved!

Teaching physicists chemistry

Teaching physicists chemistry

George demonstrates the Lego Beamline

George demonstrates the Lego Beamline

Smelly molecules

Smelly molecules

Demonstrating Fourier transforms takes concentration

Demonstrating Fourier transforms takes concentration

Growing a crystal, one marble at a time

Growing a crystal, one marble at a time

Protein crystals ar

Protein crystals are beautiful

The Crystallography stand at the Big Bang

The Crystallography stand at the Big Bang

 

The Big Bang Logo

Jan 172013
 

The third Red Kite Meeting was very well attended and comments from attendees indicated that it was very well received.  As well as Richard Cooper chairing the first session, contributions from Chem. Cryst. included posters from Will Brennan, George Pidgeon, Olivia Shehata, Karim Sutton and Jerome Wicker and a presentation from Kirsten Christensen on modulated molecular materials.  The esteemed poster judges picked George’s poster on hydrogen bonding in fluoride complexes as one of two joint prize-winning efforts thanks to the clarity of his presentation.

Pidgeon Catches Kite at RKIII

Pidgeon Catches Kite at RKIII