Using 3D printing to automate experiments involving stirring and liquid chromatography

Much to our grievance, we had to cancel an experiment, due to a broken machine.

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With the ever-improving technologies and costs of three-dimensional printing, it is becoming a more and more accessible tool for rapid prototyping and product development. Building on that, we have developed a small device that fits within the sample chamber of a liquid-chromatography system and, using a battery-powered motor, enables continuous stirring of samples. Using the device, it is now possible to automate experiments that require stirring or mixing, thus facilitating time-resolved measurements in a high-throughput manner. We have made the design files and schematics needed to re-produce the device publicly available.

A simplified scheme of the stirring device mechanism. A central motor is rotating a plate with magnets, thus rotating a magnetic field. The rotating magnetic field causes Teflon-coated magnets within the samples to rotate, thus stirring is achieved.

Our lab has been studying a special kind of dynamical combinatorial chemistry – a kind that gives rise to exponential replication through self-assembly under agitation [Science (2010)]. Starting from a dithiol-benzene functionalized building block (“monomer”), a dynamical phase occurs with the appearance of several cyclic oligomers that are dynamically interconverting via reversible disulfide exchange reactions. Eventually, a particular oligomer often exhibits exponential growth and overtakes in the system, in a replication-like process [Science (2010) ; J. Am. Chem. Soc. (2013)]. Importantly, this self-replication is enabled by the ability of the oligomer to self-assemble by stacking to form fibers, in a process that is catalyzed by fibers’ edges [Nat. Commun (2015)]. Under agitation such as stirring, those fibers break and expose more edges in the system therefore promoting the replication process. Given the dynamical nature of the system, an ultra-performance liquid chromatography (UPLC) system is often used for the analysis of the libraries. Laboratory stirring plates are commonly used for triggering the replication and homogenizing the samples.

We reasoned that if we were able to facilitate the stirring of samples inside the chromatography system, we would be able to collect higher amounts and quality of data with less human intervention (and thus minimizing the introduction of experimental error).

When approaching this project, we realized that 3D printing could be instrumental in building and designing prototypes quickly and cheaply, that were at first tested ‘by hand’ by holding or gluing magnets and motors to those prototypes. Once we were somewhat satisfied with the result, the device could mature to provide precise control over stirring speed and visual feedback. Finally, we have confirmed the device’s proper function and stirring both with our chemical system by following its kinetics over several continuous days, and by video analysis.

One of the triggers for developing an automatic device actually came from a canceled experiment due to a broken machine. The plan was for a week-long manual experiment involving day and night shifts together with our lab mates (to whom we are grateful), involving manual placement of the samples in a UPLC for measurements and back in a stirring plate every so often. Given such a demanding experiment, we even managed to eliminate a group meeting (imagine that, no group meeting. Why, in some labs this could be considered as a heresy). Regrettably, the mass-spectrometry malfunctioned just a few days before the beginning of the week-long experiment so the experiment had to be postponed to an unknown date. Given that, we came up with the possibility of building an automated stirring device for continuous stirring while sampling in liquid chromatography systems.

Finally, by sharing the 3D design files (in .STL format) and schematics it is possible to re-produce the device and modify it to the users’ needs. Future modifications can include adjusting the dimensions to fit different chromatography machines, updating the controlling software so that stirring is intermittent, or even extending the capabilities by - for example - adding UV lights for photochemistry investigations, etc.

Using the stirring device for high-throughput data collection. The experiment started with the addition of un-oxidized monomeric building-block, and followed the reaction time course until almost all of the mass resides in the self-replicating hexamer (see full manuscript for more details). All the collected UPLC chromatograms are overlayed to show the kinetics of the system. Inset shows how the amount of hexamer grows over time.

We thank @She_Toot for making the cover image.

Omer Markovitch

Postdoc, University of Groningen

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