Behind the Paper

The stuff I couldn't fit in the manuscript

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