Stop-Frame Filming of Chemical Reactions

ChemTEM – A New Method to Study Chemistry at the Single-Molecule Level

  • Fig. 1: Entrapment and confinement of molecules in the nanotube controls their positions and dynamic behaviour in ChemTEM.
  • Fig. 2: Energy to promote a chemical reaction in ChemTEM is supplied by collisions between the individual molecule and incident electrons, whereas in traditional chemical reactions the activation energy originates from intermolecular collisions.
  • Fig. 3: Examples of organic (a), organometallic (b) and inorganic (c) reactions imaged by ChemTEM.

One of the biggest challenges of chemistry is that in a given experiment we study reactions of large ensembles of molecules (billions of billions or more) which exist in different states and possess different kinetic energies, colliding with each other in a chaotic motion. Consequently, a reaction observed in the laboratory experiment by ensemble-averaging analytical techniques, such as spectroscopy or diffraction, can only support rather than confirm a proposed mechanism, as the macroscopic measurements are unable to rule out that an alternative atomistic mechanism may exists that also results in the same macroscale observation.

In this context, transmission electron microscopy (TEM) is a unique technique that has sufficient spatial (sub-angstrom) and temporal resolutions [1] to reveal how molecules really react with each other by imaging them in direct space, at the single-molecule level. However, there is a serious drawback – during TEM imaging atoms within the molecules receive energy from fast electrons of the e-beam such that the molecules are affected by the act of observation. The so-called ‘observer effect’ is so exacerbated in TEM that the level of information in TEM images is often limited not by the resolution of the instrument but rather by the lack of stability of the molecules under the e-beam.  Indeed, much effort has been invested in reducing the electron beam energy, such as the SALVE project that is set to develop aberration-corrected imaging with the e-beam down to 20 keV [2].


While in the conventional TEM imaging any changes in the sample due to the e-beam should be avoided at all costs, a new approach termed ChemTEM developed by a multidisciplinary group of researchers harnesses the observer effect to unravel mechanisms of chemical reactions at the single-molecule level [3]. In order to obtain meaningful chemical information from ChemTEM measurements, the experimental conditions should comply with three key principles. First, molecules must be confined within a nanotube (fig. 1). The nanotube suppresses molecular motion, making it commensurate with the timescale of TEM imaging; mitigates inelastic effects (e.g.

ionisation, heating) thus restricting interactions with the e-beam to direct (knock-on) momentum transfer; and controls inter-molecular distances thus precluding or facilitating reactions, as required. Confinement of molecules in single-walled carbon nanotubes (SWNT, diameter 1-2 nm) has already enabled imaging of delicate organic and organometallic compounds in our previous works, with several other studies reporting successful imaging of the alkyl or perflouroakyl groups [4],
polyoxometalates [5], or endohedral metallofullerenes [6] in direct space.

Secondly, it is important to ensure that direct transfer of momentum from a collision of the fast electron with an atom is responsible for the atom to shift from its equilibrium position. If the maximum energy that can be transferred from a single electron, ET_max (when θ = 180°, equation 1), exceeds the threshold energy (Ed) for a particular chemical reaction, for example a bond dissociation (fig. 2), the bond breaks under the e-beam. The likelihood of bond dissociation is determined by the amount of transferred energy ET and the rate of collisions between fast electrons and the atom (controlled by the e-beam dose rate, j). Both parameters are readily controlled by operating conditions of TEM, and can be tuned to promote specific chemical reactions in the ChemTEM.

Equation 1

mn is the mass of the atom, me mass of the electron, E energy of the e-beam, c speed of light and θ is the electron scattering angle.
Finally, stop-frame filming of chemical reactions can be achieved in ChemTEM due to the fact that the reactions are promoted by the e-beam. Thermally activated reactions, where reactant molecules move with a Boltzmann distribution of velocities, are activated through intermolecular collisions that are strongly dependent on the temperature. In contrast, in ChemTEM it is not the intermolecular collisions but collisions of fast electrons with molecules that drive the reactions, such that the amount of transferred energy and the frequency of transfer to the atom fully determine the reaction rate constant in ChemTEM (k), controlled by the dose rate j of the e-beam (equation 2). Timescale of any reaction (t) is inversely proportional to j that can be deliberately tuned to match the image capture rate for stop-frame filming, including temporal evolution of reaction intermediates that are kinetically stabilised in the nanotube [3] – an additional benefit of nanoscale confinement. Therefore, ChemTEM is capable of elucidating exact pathways of the reactions in direct space and real time.

Equation 2

where j is the dose rate of the e-beam, σ is a cross section which is dependent on E and Ed [7].
The concepts of ChemTEM analysis have been applied to continuous, direct imaging of reactions of organic, inorganic and organometallic molecules (fig. 3) which have begun shifting the paradigm of analytical sciences: ChemTEM enables imaging of chemical transformations of individual molecules in real time, and can visualise the entire reaction pathway – from reactants to products, including transient intermediates. The latest examples include a chemical reaction of polycondensation of perchlorocoronene converting small organic molecules to Cl-terminated zigzag nanoribbons via stepwise de-chlorination, Diels-Alder cycloaddition and aromatisation [3]. Under similar conditions a sulphur-containing molecule (octacirculene) transforms into a new type of polymer with an undulated structure. The fact that these new reactions were fortuitously discovered by ChemTEM [3] signals a potential of ChemTEM for becoming not only an indispensable method for elucidating pathways of known chemical reactions, but also a powerful tool for discovery of uncharted chemistry.

[1] A. H. Zewail, J. M. Thomas, “4D Electron Microscopy”, Imperial College Press, London (2010)
[2] Linck, M.; Hartel, P.; Uhlemann, S.; Kahl, F.; Müller, H.; Zach, J.; Haider, M.; Niestadt, M.; Bischoff, M.; Biskupek, J.; Lee, Z.; Lehnert, T.; Börrnert, F.; Rose, H.; Kaiser, U.,: Chromatic Aberration Correction for Atomic Resolution TEM Imaging from 20 to 80 kV, Phys. Rev. Let., 117, 076101 (2016)
[3] T. W. Chamberlain, J. Biskupek, S. T. Skowron, A. V. Markevich, S. Kurasch, O. Reimer, K. E. Walker, G. A. Rance, X. Feng, K. Müllen, A. Turchanin, M. A. Lebedeva, A. G. Majouga, V. G. Nenajdenko, U. Kaiser, E. Besley, A. N. Khlobystov: Stop-Frame Filming and Discovery of Reactions at the Single-Molecule Level by Transmission Electron MicroscopyACS Nano, 11, 2509-2520 (2017)
[4] K. Harano, S. Takenaga, S. Okada, Y. Niimi, N. Yoshikai, H. Isobe, K. Suenaga, H. Kataura, M. Koshino, E. Nakamura: Conformational Analysis of Single Perfluoroalkyl Chains by Single-Molecule Real-Time Transmission Electron Microscopic Imaging, J. Am. Chem. Soc., 136, 466-473 (2014)
[5] J. Sloan, G. Matthewman, C. Dyer-Smith, A. Y. Sung, Z. Zheng, K. Suenaga, A. I. Kirkland, E. Flahaut: Direct Imaging of the Structure, Relaxation, and Sterically Constrained Motion of Encapsulated Tungsten Polyoxometalate Lindqvist Ions within Carbon NanotubesACS Nano, 2, 966-976 (2008)
[6] C. S. Allen, Y. Ito, A. W. Robertson, H. Shinohara, J. H. Warner: Two-Dimensional Coalescence Dynamics of Encapsulated Metallofullerenes in Carbon Nanotubes, ACS Nano, 5, 10084-10089 (2011)
[7] S. T. Skowron, I. V. Lebedeva, A. M. Popov, E. Bichoutskaia: Approaches to modelling irradiation-induced processes in transmission electron microscopyNanoscale, 5, 6677-6692 (2013)


Prof. Dr. Andrei N. Khlobystov
University of Nottingham
Nanoscale & Microscale Research Centre
School of Chemistry
Nottingham, UK

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