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Chemical Reactions of Molecules Promoted and SimultaneouslyImaged by the Electron Beam in Transmission Electron MicroscopyPublished as part of the Accounts of Chemical Research special issue Direct Visualization of Chemical and Self-Assembly Processes with Transmission Electron Microscopy.

Stephen T. Skowron, Thomas W. Chamberlain,, Johannes Biskupek, Ute Kaiser, Elena Besley,

and Andrei N. Khlobystov*,,

School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, United KingdomInstitute of Process Research and Development, School of Chemistry, University of Leeds, Leeds LS2 9JT, United KingdomCentral Facility of Electron Microscopy, Electron Microscopy Group of Materials Science, University of Ulm, 89081 Ulm, GermanyNanoscale & Microscale Research Centre, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom

CONSPECTUS: The main objective of this Account is toassess the challenges of transmission electron microscopy(TEM) of molecules, based on over 15 years of our work inthis field, and to outline the opportunities in studying chemicalreactions under the electron beam (e-beam). During TEMimaging of an individual molecule adsorbed on an atomicallythin substrate, such as graphene or a carbon nanotube, the e-beam transfers kinetic energy to atoms of the molecule,displacing them from equilibrium positions. Impact of the e-beam triggers bond dissociation and various chemical reactionswhich can be imaged concurrently with their activation by thee-beam and can be presented as stop-frame movies. Thisexperimental approach, which we term ChemTEM, harnessesenergy transferred from the e-beam to the molecule via direct interactions with the atomic nuclei, enabling accurate predictionsof bond dissociation events and control of the type and rate of chemical reactions. Elemental composition and structure of thereactant molecules as well as the operating conditions of TEM (particularly the energy of the e-beam) determine the productformed in ChemTEM processes, while the e-beam dose rate controls the reaction rate. Because the e-beam of TEM actssimultaneously as a source of energy for the reaction and as an imaging tool monitoring the same reaction, ChemTEM revealsatomic-level chemical information, such as pathways of reactions imaged for individual molecules, step-by-step and in real time;structures of illusive reaction intermediates; and direct comparison of catalytic activity of different transition metals filmed withatomic resolution. Chemical transformations in ChemTEM often lead to previously unforeseen products, demonstrating thepotential of this method to become not only an analytical tool for studying reactions, but also a powerful instrument for discoveryof materials that can be synthesized on preparative scale.


Sub-angstrom resolution was achieved in transmission electronmicroscopy (TEM) at the turn of the century due to significantprogress in aberration correction technology. As a result,structures of molecules can now be imaged with atomicresolution, at least in principle. In practice, however, imaging ofmolecules with atomic resolution is extremely difficult becausethe quality of TEM data is not limited by the resolution of theinstrument but rather by the stability of the molecules under the e-beam. It is not a coincidence that one of the first and moststudied molecules by TEM is the fullerene C60, a highly stablespecies with three strong covalent bonds for each carbon atomand no edges (Figure 1). Early work on TEM imaging of C60and other fullerenes stimulated development of low-voltage

TEM (LV-TEM). In particular, the aberration-corrected TEMdeveloped in the framework of the SALVE project enablesimaging with electron energies in the range between 80 and 20keV (www.salve-project.de1,2).Whenever TEM is applied to the characterization of

molecular materials, atoms of the molecules interact with fastelectrons of the electron beam (e-beam); molecules underTEM investigation always receive energy due to e-beaminteractions with either the electrons of the atoms or theatomic nuclei. Distinction between these two mechanisms of e-beammolecule interactions is crucially important for under-standing the impact of TEM on molecules, and thus it is

Received: February 6, 2017


XXXX American Chemical Society A DOI: 10.1021/acs.accounts.7b00078Acc. Chem. Res. XXXX, XXX, XXXXXX

instructive to assess how these mechanisms depend onexperimental conditions.

E-beamatomic electron interactions are prevalent when alow energy e-beam is used, such as the 0.011 keV e-beam

Figure 1. e-beam dose-series TEM images of C60 fullerenes in carbon nanotubes show a much greater stability of the molecules under the 20 keV (b)than the 80 keV (a) e-beam. (d) Fullerenes inserted into carbon nanotubes (c) C60@SWNT are useful for studying e-beammolecule interactions.

Figure 2. (a) Types of e-beammolecule interactions depend on the energy of the e-beam and the configuration of the sample. (b) E-beaminteraction with the atomic nucleus causes displacement of the atom from its equilibrium position and, if the transferred energy is sufficiently high,dissociation of the chemical bond. (c) Energy to promote a chemical reaction in ChemTEM is supplied by collisions between the individual moleculeand incident electrons, whereas in traditional chemical reactions the activation energy originates from intermolecular collisions. (d) The cross sectiond describes the likelihood of atom displacement from a specific chemical bond (CH, red plot; aromatic CC, green plot; CS, blue plot) as afunction of the e-beam energy.

Accounts of Chemical Research Article

DOI: 10.1021/acs.accounts.7b00078Acc. Chem. Res. XXXX, XXX, XXXXXX


applied for cross-linking organic molecules in self-assembledmonolayers, or when a high energy e-beam interacts with athick molecular material (e.g., thicker than a monolayer), suchas the 3080 keV e-beam in electron beam lithography (EBL)of polymeric films. As the high energy e-beam penetratesdeeper into the material, it undergoes multiple interactions withatoms of the molecules, and the initially fast incident electronsprogressively lose their energy and slow down while generatinga large number of secondary, lower energy electrons, with thelatter being a particularly important process for transformationsof molecules in EBL. These lower energy secondary electronshave a high probability (quantified as a cross section) forinteractions with molecular orbitalseither knocking outfurther valence electrons or undergoing dissociative electronattachment (DEA) with antibonding molecular orbitals, whentheir kinetic energy approaches zero. Therefore, in processessuch as EBL or in TEM experiments with thick molecularsamples, e-beamatomic electron interactions are dominantand the amount of energy transferred from the primary e-beamto the valence electrons of the molecules, ET, is described as

=E b e Eb( ) /(4 )T4

02 2


where e is the charge of an electron, b is the distance betweenthe incident and valence electrons, 0 is the permittivity of freespace, and E is the energy of the primary e-beam. Theseinteractions trigger numerous secondary effects, such as theemission of X-rays or heating of the material, as well as causingCH bond cleavage followed by cross-linking of theneighboring molecules in the polymer film. It is estimatedthat 80% of e-beam damage to organic films (e.g., 100 nmthick PMMA at E = 100 keV) is due to secondary electrons.3

In stark contrast, an isolated molecule or number of discretemolecules, either in vacuum, deposited on a very thin substratesuch as graphene, or in a single-walled carbon nanotube(SWNT), experience very different effects of the e-beam of theTEM. When the material effectively has no bulk volume, theimportance of secondary electrons is limited, which inconjunction with the drastic reduction in the number ofnearest neighbors, limits interactions to the primary electronbeam transferring momentum directly onto atomic nuclei. Theamount of energy transferred, ET, from the e-beam to astationary atom in this case is described as


+ +

= _

Em E E m c

m m c m E


( )2 ( 2 )

( ) 2sin



Tn e


n e2 2



T max2


where mn is the mass of the atom and is the electronscattering angle. In addition, the SWNT and graphenepossessing excellent thermal and electrical conductivitiesef-fectively mitigate heating and ionization. Overall, in contrast toe-beamatomic electron interactions (eq 1), the energytransferred to molecules in e-beamatomic nucleus interactionsis directly proportional to the energy of the e-beam, E (eq 2),which means that the stability of molecules can be improved bydecreasing the energy of the e-beam as demonstrated forfullerenes (Figure 1).2


Whether desired or not, the e-beam interacts with moleculesduring TEM imaging and transfers a fraction of its momentumto atoms, causing the atoms to shift from equilibrium positionswithin the molecule. If the maximum energy that can betransferred from a single electron to an atomic nucleus, ET_max(when = 180), exceeds the threshold energy (Ed) for aparticular chemical reaction, for example a bond dissociation(Figure 2b), the molecule breaks down under