Behind the Paper

The stuff I couldn't fit in the manuscript

16/04/2020
A Chemically Soldered Polyoxometalate Single-Molecule Transistor

And here I am again, with another paper just published in Angewandte Chemie. This work hasn’t been an emotional rollercoaster like the “hemilabile ligand for molecular electronics” that I described in August last year, but it has been an absolute mammoth of data acquisition and analysis, performed with incredible perseverance and diligence by soon-to-be-Dr. Chuanli Wu.

It all started with a small pot of money I was given in 2018 for the synthesis of some cluster-containing molecular wires. The idea was to use these funds to gain some skills in small, atomically defined cluster preparation and purification (somewhat different from the chemistry I did up to then), and to use these to collect single-cluster conductance data that could underpin my fellowship applications. One of the reviewers for my Future Leaders Fellowship application (alas, unsuccessful) raised doubts on the stability of clusters under an intense electrical field, such as the one that is experienced by a molecular junction, and I wanted to show that these can be extremely resilient species. After the funds were released, I went back to the bench and prepared a few different classes of clusters – from pure metallic materials containing copper, silver or ruthenium, to metal chalcogenides and metal oxides. The latter, perhaps better known as polyoxometalates, interested me for their electrochemical behaviour – some of the larger ones have multiple, well-defined oxidation states, and their cyclic voltammograms (CV) can be oddly fascinating (see here on the right for an example from a Keggin polyoxoanion) as all the different charge states give very well-defined reversible redox processes and therefore many pleasant waves in the CV!

For a cluster to be used efficiently in molecular junctions it needs to be terminated with aurophilic groups, which can form coordination bonds with two nanoelectrodes and close the circuit. This somewhat limits the range of polyoxometalates I could use, as their functionalisation with organic ligands is not exactly straightforward. I started by synthesising a Lindqvist polyoxovanadate (see XRD structure on the left) and I measured its conductance – it proved to be quite poorly conductive, and a bit too close to the noise level of our instruments at the time to be studied in more detail, but it gave me the initial data I needed for my fellowship applications, which I’m sure helped me greatly in securing the Royal Society URF position. That it was so insulating wasn’t surprising – most bulk metal oxides are good insulators, and the Lindqvist anion proved to be no exception. By then, however, I really wanted to find a redox-active cluster that could study at the single-molecule level in an electrochemical environment. A literature search turned up a small polyoxomolybdate, having Anderson-Evans structure, that could be functionalised in an optimal way, with the two organic ligands coordinated to opposite sides of a MnO6 octahedron. The synthesis looked straightforward on paper, but it took me a few weeks before I had a sample pure enough for characterisation and crystal growing – which was good: all useful skills I had to learn if I wanted to work with more of these cluster materials.

Just as I was finishing preparing these compounds, Chuanli, who was visiting our laboratory at the time, had also finished collecting all the data she needed for a project she was working on – the study of the in-situ formation of hydrogen-bonding chains during break-junction experiments (published a few months ago in Nanoscale). Before this work, she had worked quite extensively on the in-situ electrochemistry of NiO, in a project that was very challenging but, alas, resulted only in more questions than answers. Nickel is indeed a weird metal. While partially unsuccessful, she gained a lot of experience in the use of the electrochemical scanning tunnelling microscope, and she decided to take on the challenge of measuring the polyoxometalate single-molecule conductance under electrochemical potential control. The idea here was to probe the charge transport properties of the polyoxometalate in its various electrochemical states. Initial cyclic voltammetry showed us we could both oxidise and reduce the Anderson-Evans cluster from its natural -3 state, to either -2 or -4. And, as usual, our problems started. The polyoxomolybdate wasn’t that soluble in the solvents we regularly use in molecular electronics studies, and the necessity of an ionic environment (an electrolyte) further complicated the issue. Chuanli started screening a few solvents where we knew we could get an electrochemical response – acetonitrile, propylene carbonate, DMF, etc. – but each of them presented an issue in the single-molecule measurements we wanted to perform. They either resulted in too much background noise, dissolved the electrodes coating, prevented formation of junctions or gave an unreliable electrochemical potential (a problem in most non-aqueous electrochemical studies).

At that time, Xiaohang Qiao (a PhD student working with us) was studying the use of deep eutectic mixtures in molecular electronics. These are excellent solvents, they provide an ionic environment ideally suited to electrochemistry, and showed good promise for STM work. So Chuanli and Xiaohang teamed up and started studying the polyoxometalate in a deep eutectic mixture of choline chloride and urea. This started to give us quite good results: the polyoxomolybdate was soluble, we could form junctions in the electrochemical environment (made of 4 electrodes, two Au as source/drain and two Pt as counter/reference as in the figure here), and we could see a difference in the conductance as the potential was made more negative and the polyoxometalate charge state was changed from -3 to -4. Furthermore, the presence of many chloride ions allowed us to use a chloridised silver wire as reference electrode, with excellent stability. Unfortunately, they then had issues at positive potentials: the excess chloride ions that gave us the benefit of a stable reference electrode also caused the Au electrodes to oxidise and dissolve before we could access the -2 state in this setup.

We then remembered that a few years ago our lab published a series of papers in JACS (I helped out on the third in the series) on the use of ionic liquids in single-molecule electronics. They had everything we were looking for: powerful solvents with a wide electrochemical window and a simple Pt wire can be used as reference electrode with excellent stability – thinking back, I don’t really know why we didn’t use these from the beginning.

Ah yes, ionic liquids are quite a nightmare to purify. And expensive. Very expensive.

Ionic liquids tend to pick up water quite quickly – when they’re wet, the electrochemical window narrows down a lot, and we needed all of it, or at least 2.5 V. Also, last year we weren’t exactly swimming in cash. Luckily, we had about 50-75 mL of 1-butyl-3-methylimidazolium trifluoromethanesulfonate in our glove box, leftover from our previous studies – while it sat there for more than 4 years, it couldn’t have gone too bad in an inert, dry atmosphere. We cleaned it up, testing its electrochemistry until it was pure (and it took some time!), and then Chuanli started collecting data. This setup worked like a charm!

As you can read in the paper, using an ionic liquid allowed us to probe conductance over 2.7 V of electrochemical potential, where we could measure the polyoxometalate in all three states (-2, -3 and -4). We found a rather unusual response – as the cluster was oxidised or reduced from its native -3 state, conductance suddenly dropped by one order of magnitude. From our data, it looked like the mechanism of charge transport was phase-coherent tunnelling, and the polyoxometalate in different charge states presented a different barrier to charge tunnelling. While not a novel phenomenon (see examples here, here and here), it was pretty exciting to find out such a behaviour in a polyoxometalate. To further strengthen our claim, we did some modelling, which required quite a lot of data analysis (good thing I had an M.2 NVMe solid state disk with a write speed of ~1.9 GB/s or this would have taken years), and some more experiments, which you can read about in the paper (that is open access and free to read to everyone).

What I think is staggering about this project is the sheer amount of work performed by Chuanli. In the paper, we present data from approximately 100000 (yes, one hundred thousand!) single-molecule devices she fabricated under electrochemical control, and an additional 20000 devices fabricated under source-drain bias modulation. But this is just the tip of the iceberg. There are many “preliminary measurements” in other solvents (the ones that didn’t really worked as we wanted), and from the sheer size of her “POM” folder (sitting on my back-up disk at 11.3 GB zipped at ~20% rate) I estimate at least another 200000 junctions were fabricated for this project. And I’m being conservative!

Anyway, the publishing process was refreshingly quick and straightforward - so this story ends in a quite anticlimatic fashion. We had an initial desk rejection from another journal, but after submitting to Angewandte Chemie we received very good feedback from the reviewers – they asked for a single control experiment which we hadn’t done. We did it, it worked as expected, and we finally got this beast published.

I hope you’ll enjoy reading about our work as much as I enjoyed writing about it – honestly, with experimental data as good as the one Chuanli collected, the paper almost wrote itself.

Many thanks to soon-to-be-Dr. Chuanli Wu for for keeping up with my continuous “MORE DATA!” requests for many months, and to Prof. Richard J. Nichols and Prof. Simon J. Higgins for their help in putting this together.

Edited on 26/05/2020 to correct a few typos. You never proofread enough!

01/08/2019
Hemilabile Ligands as Mechanosensitive Electrode Contacts for Molecular Electronics

So, I'll start this column by writing about this paper here, that we recently published in Angewandte Chemie. As you'll see, this is a nice story with failures, puzzlement and despair, but also great teamwork and sustained effort. It follows a quite oftenly encountered scientific path: we started looking into some compounds to test one particular theory (quantum interference) but instead, we found something completely different (mechanoresistance) but equally exciting, that can also help us to understand some earlier puzzling results we (and other research groups around the world) had obtained. In some ways, it is also a manifestation of Westheimer's Discovery "Why spend a day in the library when you can learn the same thing by working in the laboratory for a month?".

The bulk of this work was performed whilst I was working as a PDRA for Prof. Richard Nichols, and I was training one of Prof. Simon J. Higgins (my PhD supervisor) students in the group, now Dr. Nicolo' Ferri. He picked up a project I left incomplete at the end of my PhD (late 2014-early 2015) as I hadn't been able to synthesise one of the key compounds, a fused bithiophene with a bridging carbonyl function and methyl thioether contact groups for binding to gold electrodes. The target was quite interesting because it had a very narrow bandgap and theory had predicted some odd quantum interference effects from the carbonyl, that would result in unusually high (or unusually low, depending on which theoretician we listened to...) conductance. Following a few recipes for apparently similar compounds I found in the literature just gave a black sticky mess, and after a few disappointing attempts, I started my PDRA working on molecule/semiconductor interfaces and I completely forgot about the whole project. Just to explain what kind of chemist Nicolo' is, he not only willingly accepted this work that gave me only pain and disappointment, but actually managed to synthesise this key compound, grew beautiful (and big) shiny purple crystals, got the SCXRD that confirmed the structure, did some more synthetic work, and performed all the measurements that you can find in the above paper.

Now, for the organikers out there, we initially tried to synthesise this in a quite unpleasant sequence, where all steps involved either something toxic, something smelly or something pyrophoric (well, it's just n-BuLi, but still...)! Starting from cheap-ish 2-bromothiophene he had to do:

  • Old-school Ni-catalysed Kumada coupling to get 2,2'-bithiophene
  • Tetrabromination of 2,2'-bithiophene with elemental Br to give 3,3',5,5'-tetrabromo-2,2'-bithiophene
  • Double selective halogen-lithium exchange and quench with dimethyl disulfide (smell!!!) to give 3,3'-dibromo-5,5'-bis(methylthio)-2,2'-bithiophene
  • Double lithium-halogen exchange with n-BuLi and reaction with an appropriate carbonyl source

So, when Nicolo' tackled this, I had already tried a few carbonyl sources, and I was so desperate I even tried using phosgene at some point(!). Just as a control experiment, Nicolo' tried the published route to the parent compound lacking the two thiomethyl moieties, and it worked perfectly - it was evident that the two -SMe contact groups were messing up the electronic structure of one of the reaction intermediates and prevented efficient ring-closure to a cyclopentadienone. Obviously, it proved impossible to install the two -SMe on the already-made cyclopentadithiophen-4-one - bromination followed by C-S couplings, lithiations, direct -SMe attack using the infamous NaSMe, etc. all failed. This is enough to drive someone mad! Nicolo' decided to go back to the original route we designed (but with commercial 2,2'-bithiophene from Fluorochem as it was cheap enough), and try again the double lithiation of 3,3',5,5'-tetrabromo-2,2'-bithiophene followed by treatment with dimethylcarbamoyl chloride and quench with ammonium chloride. He carefully prepared all the starting materials, and I remember him recrystallising 25g of 3,3',5,5'-tetrabromo-2,2'-bithiophene in a massive round bottom flask I didn't even know was still knocking about in the lab. After a few horrendously unsuccessful attempts, where he varied the reaction conditions to better understand what was going on, he found an obscure Japanese paper (apologies, I can't find the reference now!) discussing other similar ring-closure reactions to cyclopentadienones. In some of the preparations discussed in the paper, the final quench with ammonium chloride (designed to kick out the -N(Me)2 group and give the cyclopentadienone ring) was performed, with no justifying comment or discussion, at -40° C instead of the room temperature reported in all the other recipes we were following. When he tried this, the reaction turned immediately a lovely shade of pink, indicating a low-bandgap material was actually present in the flask, and at the end, after a chromatographic column and careful 2-layers crystal growing, he obtained lovely deep-purple block crystals in 80% yield.

So, all excited about this compound, we did some measurements on its single-molecule charge transport properties. They were an absolute mess. The compound gave conductance values spanning more than two orders of magnitude, making any kind of statistical analysis to determine the most probable conductance quite meaningless. Nicolo' was quite gutted - he spent so much time getting here, making those lovely purple crystals, and now everything turned sour. The results were absolutely horrible.

We started to scour the literature looking for an explanation, and we found out we weren't the first noticing a peculiar behaviour in compounds incorporating terminal thiophenes. Unusually wide conductance histograms were already reported here, and odd effects were found in another paper. However, we weren't completely happy with the explanations given - Simon also pointed out that the thiophene unit could potentially act as additional contact to the electrodes, as it is known it can coordinate, albeit weakly, to transition metals, and reports on the use of thiophenes themselves as contact groups for molecular junctions are aplenty. So the idea we came up with was that the unusually large conductance span was due to an abundance of anchoring places for the electrodes, and therefore the single-molecule junctions weren't as defined as we originally hoped. To test this idea, however, we had to do some serious work on our instruments, to give them more versatility and perform some modulation experiments, where we would vibrate the electrodes to compress and relax the junction with a precision of a few Angstroms, thereby forcing the molecule to adapt different conformations at the electrode interface. Luckily, in late 2016, I visited Prof. Bingqian Xu's laboratory, where they were doing this kind of experiments as part of an ongoing collaboration, and I had more-or-less understood what I had to do to improve our instruments. Armed with an arbitrary waveform generator, a data acquisition board, a wide-bandwidth preamplifier, a dozen BNC cables and a very shallow understanding of how Labview works, I opened our STM, fitted new connections, designed a couple of PCBs (so many thanks to Matt in our electronic workshop!), got them developed, painstakingly soldered some tiny Hirose U-FL connectors (I absolutely hate them!), wired everything, wrote a (very!) crude Labview VI and BAM! We had the instrument we needed. We could drive our system's electrodes with modulations in positions at frequencies up to 10 kHz (higher than that, we would smash our piezo transducers) with sub-Angstrom precision. We tested it for a few weeks, to ensure we weren't damaging the piezos and to check for data consistency with the literature and, when we were finally happy, we did the experiments we wanted. And they worked!

In our experiments, we modulated the position of the electrodes by just 3 Angstroms, and we observed large changes in conductance as the junction was compressed (high G state) or relaxed (low G state). So our idea was almost proven: as the thiophene was brought in proximity to the metallic electrode it interacted with the electrode and increased the electronic coupling, acting like the labile part of a hemilabile ligand. As the junction was relaxed, the electrode-thiophene distance increased and any interaction died out, giving a lower coupling and lower conductance. Nicolo' synthesised a few more compounds, either for control experiments (a biphenylene that didn't show much change in conductance during modulation experiments), or to demonstrate the versatility of our chemical design and to show some degree of chemical control (i.e. he replaced the carbonyl with a gem-dimethylmethylene group which gave even higher conductance modulations), and the brilliant undergraduate student we had in the lab (Maeve McLaughlin) at the time gave a hand with the synthesis. We improved the measurement methods, wrote better software, and kept improving our hardware, as we also wanted to do some very high-frequency modulations to push our instrument to its limits. That wasn't so easy to do as we started to have problems with the data acquisition - it turns out acquiring 24-bit data from 4 channels at 215000 samples per second is quite demanding! However, after some software optimisation, in which I learned A LOT about Labview (and started following DataFlow G on twitter), we were able to obtain the data we presented in the paper, where we drove our junctions at 10 kHz modulations of 3 Angstrom for over 100 ms. Which was pretty cool.

After all this experimental work, we needed a confirmation from theory to show that it was these thiophene-metal interactions that were indeed responsible for the observed behaviour. Our close collaborators in Lancaster, Prof. Colin J. Lambert, Dr. Sara Sangtarash and Dr. Hatef Sadeghi developed the model that explained the observed phenomena. They found that when the junctions with thiomethylthiophene terminal groups are compressed there are indeed increased interactions, as can be seen in the figure here. The interactions result in a stronger contact, more electrically transparent, that leads to a higher conductance. So, FINALLY, everything made sense. Time to write it up as a paper and start the neverending roulette of choosing a journal → formatting the manuscript → submit → peer-review → revise → resubmit → outcome = Y/N? (Y = celebrate; N = back to choosing a journal). The paper was actually rejected on first submission, but it eventually found a very cosy home at Angewandte Chemie.

In brief, and for the fans of tl;dr - we made a hellish small molecule, it didn't do what we wanted it to do, so we tortured it until it behaved and we published the results here.


Many thanks to Dr. Nicolo' Ferri, Prof. Richard J. Nichols and Prof. Simon J. Higgins for their help in putting this together, and for their thorough proofread