Atomic probe of bond dynamics and reactivity of individual HF and H₂O atoms

August 20, 2020 - A new study of scientists from the Universities of Ulm (Germany), Nottingham (UK), Southampton (UK) and Leeds (UK) enables bond dynamics and reactivity of H₂O and HF to be studied at the single-molecule level. The atomic scale study was conducted at low and very low primary energies of 30 - 80 keV in the SALVE microscope and at 60 keV in the SuperSTEM microscope by entrapping HF and H₂O molecules within fullerene C₆₀ cages in nanotubes.

The carbon nanotube is one of the most robust and effective materials for molecular encapsulation in TEM studies. It can restrict molecular movement and can be used as a tiny test tube [1, 2]. When Fullerenes C₆₀, with a cavity similar to a very small nanotube, are entrapped in bigger nanotubes, (Figure 1), they provide an ideal platform for the entrapment of even isolated atoms.[1 - 5]. A team of scientists has now trapped small volatile molecules like H₂, HF, and H₂O inside C₆₀ in CNT to prevent their rapid molecular movement and to be able to study them at the single molecule level in the TEM. The research helps scientists to better understand the properties of di- or triatomic molecules consisting of light elements. The TEM can also be used to trigger bond dissociation in individual molecules in order to be able to examine chemical bonds and processes at the atomic level.[6, 7] With this approach, the energetics and dynamics of several heteroatomic bonds can be investigated, including CH, CD, CS, CC, Mo-I, and Re-Re at the single-molecule level.[6 - 9]

With the new TEM imaging of the materials, the scientists used 30 keV electron beams (HF @ C₆₀) @ SWNT and (H₂O @ C₆₀) @ SWNT. The ordered chains of fullerene molecules appear as circles within the cylindrical channel of the nanotube very similar to the empty C₆₀ in nanotubes. In contrast to the empty C₆₀ fullerenes, which show no observable damage even at higher electron beam energies such as 40 keV, the endohedral fullerene molecules are noticeably crosslinked and polymerized under the irradiation (Figure 2). However, the crosslinking occurs slowly so that useful insight into the mechanisms by which the electron beam is damaged can be studied. With increasing energy of the electron beam from 30 to 80 keV, the stability of the endohedral fullerenes decreases significantly by a factor of ~ 10 for HF @ C₆₀.

Figure 3. Fingerprinting of F single atoms.

Figure 4. HF dissociation.

Energy Transfer and Bond Dissociation under the Electron Beam
The research also provides an important insight into the state of the caged elements. Figure 3 shows individual F atoms in two intact C₆₀ molecules, while no F signal was detected in polymerized molecules. The diatomic HF and triatomic H₂O molecules are enclosed in HF @ C₆₀ and H₂O @ C₆₀, respectively, so that the F atom and the O atom are positioned in the center of the icosahedral C₆₀ cage, and retains all three degrees of freedom of rotation. The translational freedom is limited by the fullerene cage to ~ 0.2 nm. [3 - 5] Therefore, the enclosed molecules, (HF @ C₆₀) @ SWNT and (H₂O @ C₆₀) @ SWNT, can be described as a free rotator in its original state. A recent theoretical study investigating a hypothetical (HF @ C₆₀) @ SWNT structure concluded that HF molecules in the neighboring HF @ C₆₀ are likely to interact by dipole-dipole coupling on the order of only a few millielectron volts. Overall, the state of the trapped molecules in (HF @ C₆₀) @ SWNT and (H₂O @ C₆₀) @ SWNT is closer to the gas state in terms of rotation and vibration, but closer to a solid crystalline state in terms of translation, so that the lateral positions of individual molecules are severely restricted during TEM imaging. The calculated geometry based on the TEM data of HF @ C₆₀ and H₂O @ C₆₀ indicates that the geometry of the entrapped small molecules is almost identical to that of the gas phase.

The research also provides an important data point for theoretical modeling of Bond Dissociation and atom permeation through C₆₀. After dissociation from the molecule, the kinetic energy of the hydrogen atom is sufficient to continue its movement across the C₆₀ cavity and through the fullerene wall and prevent recombination with HF @ C₆₀ (Video 7). At lower transmitted energies, the penetration barrier depends on the alignment of the H atom momentum with respect to the carbon-carbon bonds of C₆₀, while dissociation with kinetic energies that are insufficient to emit the hydrogen atom from the fullerene cage reforms the original HF or H₂O structure. These results are in agreement with the energy barrier for a hydrogen atom to penetrate through the fullerene wall in the region of 2.6 eV through a hexagon of C₆₀.[10] Therefore, both HF and H₂O are effectively depleted of hydrogen atoms under TEM imaging conditions.

The scientists used the SALVE microscope, which offers the capability of performing atomically resolved HRTEM at very low primary energies down to 20 kV as well as the Nion UltraSTEM microscope at the SuperSTEM lab, which offers the capability of performing atomically resolved EELS analysis at 60 kV. They combined the data with DFT simulations to get insight into the fundamental mechanisms of bond dissociation and reactivity of HF and H₂O.

"The energy barrier for the O atom penetrating through C₆₀ via an epoxide intermediate was found much lower than the barrier for penetration through graphene. These data offer another important building block for the investigation of the permeability of carbon materials," said Ute Kaiser, head of the SALVE microscopy center.

Image and Spectrum Acquisition

HRTEM investigations were performed using a dedicated low-voltage microscope–the sub-Ångström low-voltage electron microscopy (SALVE) instrument based on a Thermo Fischer Themis platform equipped with a dedicated chromatic and spherical (Cc/Cs) aberration corrector developed by CEOS. The SALVE instrument is fully corrected for the fifth-order axial geometric aberrations (including Cs and C5), for the third-order off-axial geometric aberrations, and for the first-order chromatic aberrations (Cc).[11] The TEM was operated at 30 kV or 80 kV. Images with exposure times from 0.2 to 2.0 s were acquired using a CETA 16 camera (using binning 2, resulting in images of size 2048 by 2048 pixels). For all experiments the dose rates were in the order between 1 × 10⁶ and 1 × 10⁷ e^- nm^-2 s^-1.
Additional scanning transmission electron microscopy observations were performed at 60 kV acceleration voltage on a monochromated Nion UltraSTEM 100MC “Hermes” at the SuperSTEM laboratory. This microscope is equipped with a fifth-order probe aberration corrector enabling a probe size of ∼0.09 nm at 60 kV with a convergence semiangle of 31 mrad in the conditions used for these experiments. The monochromator improves the native 350 meV energy resolution of the cold field emitter of this instrument to ∼15 meV in practical experimental conditions (as estimated from the zero-loss-peak, ZLP, full width at half-maximum), with no loss of spatial resolution, enabling the acquisition of molecular vibrational signals. The use of a higher beam energy (60 keV) compared to the HRTEM experiments was necessary to retain both high spatial and energy resolution (at 30 keV in the current configuration of the instrument used, the spatial resolution would not have been sufficient to distinguish the atomic contrast of the object). The beam current with the monochromator slit fully open was ∼80 pA, reduced to ∼5 pA when the slit is closed for high-energy resolution work, also resulting in significantly reduced dose rates (specified within the main text). High-angle annular-dark-field images were recorded using a detector with a semiangular range of 85–195 mrad. Electron energy loss spectra were acquired on a Gatan Enfinium ERS spectrometer, modified with high-stability electronics for improved resolution. The EELS collection semiangle was 36 mrad, with spectra acquired in “dual-EELS” mode, whereby two spectra are recorded quasi simultaneously: one with extremely short exposure time (typically 0.001 s) contains the full zero loss and is used for energy calibration, while the other is optimized for higher signal-to-noise ratio with longer acquisition times (0.15 s for the spectra shown in Figure 3e) with the zero-loss peak shifted off the camera to avoid saturation.

Image Calculations

Resource: Biskupek, J., Skowron, S. T., Stoppiello, C. T., Rance, G. A., Alom, S., Fung, K. L., Whitby, R. J., Levitt, M. H., Ramasse, Q. M., Kaiser, U. A., Besley, E. & Khlobystov, A. N. (2020) Bond Dissociation and Reactivity of HF and H₂O in a Nano Test Tube. ACS Nano, 14, 11178, doi: 10.1021/acsnano.0c02661#.

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Atomic probe of bond dynamics and reactivity of individual HF and H2O atoms

Atomic probe of bond dynamics and reactivity of individual HF and H₂O atoms