CASE 2015 on the Cover of Supramolecular Chemistry

It was great to read a comprehensive write-up of CASE2015 in Supramolecular Chemistry ( I designed the website for this conference and helped out with logistics. Many of the photos that appear in the article were taken by me – great that they can be used to show the community how productive a few days it was.


Gunnlaugsson Group, Trinity College Dublin

img_7678 This month’s cover of Supramolecular Chemistry

This month’s issue of the Taylor & Francis journal Supramolecular Chemistry features a review on CASE 2015 by Robert Elmes, with a picture from the conference on the cover. CASE 2015  (Catalysis and Sensing for our Environment) was part-hosted in Trinity College Dublin, and organised by Thorri, along with Aisling Hume (TCD), Donal O’Shea (RCSI), and Robert Elmes (Maynooth).

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It was great news today to hear the 2016 Nobel Prize in Chemistry was awarded to some pioneers in the field of supramolecular chemistry: Jean-Pierre Sauvage, J Fraser Stoddart and Bernard Feringa. During my PhD studies, I read the work of Sauvage and Stoddart a lot for inspiration; they are constantly producinSauvage's article in Tetrahedron Letters 1983g beautiful and elegant structures from discrete molecular units interacting in controlled ways. While most of my PhD ended up focussing on lanthanide-directed self assembly and luminescent compounds, I was always chasing the goal of interlocked structures and remember being fascinated by Sauvage’s early results describing the first metal-directed catenanes (Tetrahedron Letters 1983), mechanically interlocked rings with no chemical bonds between the two molecular components. This article laid the groundwork for the tiny molecular machines for which the trio were given the prestigious award today. Stoddart’s contributions to controlling rotaxane movement and Feringa’s publication of the first ‘molecular motor’ were remarkable breakthroughs, but the elegance of interlocked systems has fascinated me since I first saw them and I was delighted to finally publish some of my own work on catenanes in Angewandte Chemie this year, contributing in a small way to the ever-expanding supramolecular field.

To end this post, I’ll add a quote from my PhD supervisor Prof Thorri Gunnlaugsson (Trinity College Dublin) talking today about Sir JF Stoddart, a man he greatly admires and who received an honorary doctorate from Trinity a few years ago:

Speaking about the significance of the work that led to him sharing the 2016 Nobel Prize, Professor of Chemistry at Trinity, Thorri Gunnlaugsson, said: This is truly a fantastic day for chemists and specially for those of us who are involved in the development of supramolecular and nano-chemistry. The development of molecules that are functional and can carry out actions such as programmed operations, and can mimic macroscopic function on the nanoscale, such as that of machines, has been at the heart of this area of chemistry.”

“Today’s announcement of the Nobel Prize in Chemistry being awarded to Professors Stoddart, Sauvage and Feringa, for their development of molecular machines, acknowledges the major scientific achievement made to date in this important field.”



80 Days featured on

Irish “news source for the bemused” has given a plug to our podcast 80 Days, which – I think – means we’ve definitely made it! I’m a big fan of Broadsheet’s mixture of hard-hitting corruption exposés, parish bulletin-board style notices about lost bikes and things involving Irish people all over the world. It makes for the ideal combination of news and humour for my generation.

Their article focusses on the fact that Luke, Mark and I are all Irish men abroad, using this medium to explore the world and maintain connections around it. I think (and hope) our project will resonate with a lot of people. You can read it by clicking on this link.


S1E06: Liberia

This is probably the darkest history we’ve researched while doing “80 Days”, including civil war, cannibalism and the Ebola epidemic, but still makes for a fascinating listen in spite of that.

80 Days

Audio: S1E06 Liberia

This week in 80 Days, we looked at Liberia, a small country on the west coast of Africa. Founded by freed American and Caribbean slaves, Liberia is Africa’s oldest republic and takes its name from the the Latin phrase meaning “Land of the Free.” Unfortunately, the country is best known for a long and bloody civil war that look place in the 1990s and 2000s, and more recently for the Ebola epidemic of 2014. The lush, rainforested country is just 700 kilometres or 430 miles north of the equator, and is bordered by Sierra Leone to its west, Guinea to its north and Ivory Coast (Côte d’Ivoire) to its east. Today, the country is home to around 4.5 million inhabitants, although most are native Africans rather than the descendants of freed slaves. It maintains strong ties to America, and even has…

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S1E01: Namibia

S1E01: Namibia

The first episode of my new podcast with Luke and Mark. A particular highlight of researching Namibia for me was the role the Garda Síochána played in helping the transition to democracy.

80 Days

Audio: S1E01 Namibia
In this week’s first episode of 80 Days, we are talking about Namibia, a large African nation, sharing its southern border with South Africa and with an Atlantic coastline of almost 1,000 miles, known as the ‘Skeleton Coast’. Major features include the Namib Desert, considered to be the oldest desert in the world and the famous Fish River Canyon. The country is roughly similar in size to Pakistan bigger than France or Germany and one of the driest places on earth. Its history includes colonisation by Germany and South Africa, with independence coming in the 1990s. Today it is a stable and developing young democracy. Your hosts are Luke Kelly@thelukejkelly, Mark Boyle@markboyle86 and Joe Byrne@anbeirneach, in Hong Kong, the UK and Ireland, respectively. (Music by Thomas O’Boyle)

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Namibia’s history spans over many many centuries and is defined by the movement of…

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Monosaccharide azides – challenges

I am not a carbohydrate chemist by training. I remember as an undergrad being very intimidated by the chair conformations, Fischer projections and the seemingly endless chiral centres, so I filed that knowledge away as “unlikely to use” and focussed on supramolecular chemistry. In recent times however, I couldn’t help but be drawn back to looking at these natural sources of chirality, particularly as a next direction to turn after my investigations to amino-acid derived triazolyl(pyridine) ligands. Sugars seemed a way to get chirality and solubility all in one go with the potential for biological interactions as a bonus.

oac-n3 sugar scheme

So, I began researching how to make various monosaccharide azides of the above form in a selective way, so that I could very the stereochemical properties at will when making families of compounds. It required a lot of searching to find everything I need, so I will present it here for anyone else who might be interested in making (in particular) tetra-acetylated glucose, galactose and mannose with an azide in the anomeric position, either α or β.

For glucose and galactose, buried in the German-language pages of a paper by Paulsen et al. from 1974 is a Lewis acid catalysed reaction, which selectively gives the β-azide derivative directly from reacting the penta-acetylated sugar (with mixed anomeric configuration) with tin(IV) chloride and trimethylsilyl-azide. This reaction has some nasty components and leaves you with a lot of tin-contaminated water to dispose of. I was delighted, therefore to find that the reaction can also be carried out rather straightforwardly from the commercially-available α-bromo tetra-acetylated compounds (for glucose and galactose) by simply heating overnight with sodium azide in a water-acetone mixture, a methodology that comes from that oft-overlooked source: Journal of Chemical Education (Norris and co-workers, 2012).

With mannose, things are a little trickier! It differs from glucose and galactose, by having the C-2 hydroxyl group in the axial position, and since this is adjacent to the reactive anomeric position, this will influence the outcome. Using tin(IV) chloride, as above, for instance, will yield the α-azide. This is a result of the reaction, as above, favour a 1,2-trans geometry. For the purposes of my research, however, I was really interested in using the β-azide to make a compound which differed from the glucose derivative in only one position. After a lot of hunting, I stumbled upon a two-step reaction in an article by Prof Paul Murphy from NUI Galway (Chem. Eur. J. 2013), which had originated with an early study from University of California. This approach generated an α-glycosyl-iodide in situ and reaction with tetrabutylammonium azide gave the desired β-azide product in good yields. Importantly, this gives β-azides in all cases and allowed me access to the building blocks I need to pursue my current project.

“Captured and put in chains” – new article in Angewandte Chemie

“Captured and put in chains” – new article in Angewandte Chemie

I recently finished working in Trinity College Dublin after five and a half productive years. My final project was completed in the weeks before I left and submitted to the prestigious journal Angewandte Chemie on the 1st April, the day I started in my new position at Universität Bern.

This article has just come out, and I’m rather proud of it, and happy that it is a fitting ending to my time in Dublin. My original goal in Thorri Gunnlaugsson’s research groupwas to form interlocked molecules, such as “catenanes”, but this challenging goal kept moving further down the queue as we discovered new and interesting ways to exploit the “btp” motif (which has been the topic of all my research to date). But finally, and somewhat unexpectedly, we achieved this goal.

Creating these new structures built upon interesting behaviour we reported in our Chemistry – A European Journal article early this year – where we saw that btp molecules could interact with each other, forming pairs through weak hydrogen bonding. We wondered if this could be used to pre-organise molecules together in such a way that they could be ‘clipped’ together into interlocked rings (by “RCM”, as outlined in the Scheme above). This approach has occasionally been reported before for amides,but not for molecules like the ones we describe.

A representation of the formation of catenanes from btp ligands

In fact, this reaction was more successful than expected – and in the first case I tried, we were surprised to find the majority product (50% yield) was the interlocked “catenane”, with independent non-interlocked rings also observed. We were able to fully identify and characterise these molecules using X-ray crystallographic analysis, giving the clear pictures below (thanks to Dr Salvador Blasco).

These were nice structures, but I wanted them to do something more than look pretty! Discussions with my friend Anna Aletti opened up the idea that the cavity in the middle of the structures might be a perfect fit for some negatively charged ion guest, such as chloride, nitrate or sulfate – none of these ions did very much, but phosphate (the tetrahedral H2PO4- ion), on the other hand, caused changes in the “catenane” host, indicating specific interactions between these two molecules. This was exciting. It makes these the first catenanes in the literature to have such interactions with tetrahedral anions.

The catenane acts as a selective host for phosphate, as can be seen from changes in the NMR spectrum

Detailed analysis of the formation of these interesting compounds, as well as their adducts with phosphate was important to strengthening these results and making sure we understood what we were seeing. Working closely with Dr Gary Hessman, Technical Officer at TCD, allowed further insight into the systems and their composition.

If any of this sounds interesting, then you should read the article ( or at least look at the pictures! One fun advantage of publishing in Angewandte Chemie is that they translate your abstract into German (which I am currently learning), which means I now know the useful everyday term “Triazolylwasserstoffbrüken“, which – of course – means “triazolyl hydrogen-bonding interactions”. I now use that in the pubs of Bern almost daily!