The reduction of radiation damage in the electron microscope

Direct Imaging of Radiation-Sensitive Organic Polymer-Based Nanocrystals at Sub-Ångström Resolution

Seeing the atomic configuration of single organic nanoparticles at a sub-Å spatial resolution by transmission electron microscopy has been so far prevented by the high sensitivity of soft matter to radiation damage. This difficulty is related to the need to irradiate the particle with a total dose of a few electrons/Å2, not compatible with the electron beam density necessary to search the low-contrast nanoparticle, to control its drift, finely adjust the electron-optical conditions and particle orientation, and finally acquire an effective atomic-resolution image. On the other hand, the capability to study individual pristine nanoparticles, such as proteins, active pharmaceutical ingredients, and polymers, with peculiar sensitivity to the variation in the local structure, defects, and strain, would provide advancements in many fields, including materials science, medicine, biology, and pharmacology. Here, we report the direct sub-ångström-resolution imaging at room temperature of pristine unstained crystalline polymer-based nanoparticles. This result is obtained by combining low-dose in-line electron holography and phase-contrast imaging on state-of-the-art equipment, providing an effective tool for the quantitative sub-ångström imaging of soft matter.

Dose symmetric electron diffraction tomography (DS-EDT): Implementation of a dose-symmetric tomography scheme in 3D electron diffraction

Beam sensitive nanomaterials such as zeolites or metal-organic frameworks (MOF) represent a great challenge for crystallographic structure determination and refinement. The strong electron-matter interaction and the high spatial resolution achievable make electron diffraction the technique of choice for particles of sizes below a micrometer and many different 3-dimensional electron diffraction (3D ED) techniques have been developed in recent years. Nevertheless, beam sensitivity of the samples can lead to the crystal structure being damaged during the data acquisition impeding the determination of its structure. A simple way to reduce beam damage is to lower the dose during the experiment. However, this implies weaker diffraction intensities which can become problematic for the exploitation of the data. In order to obtain complete data sets with strong intensities without damaging the crystals, we developed the dose symmetric electron diffraction tomography (DS-EDT) method, combining the low-dose electron diffraction tomography (LD-EDT) technique with the dose-symmetric tomography scheme known from cryo-EM. In order to reduce the dose on an individual crystal and still obtain enough data for a structure solution and refinement, we partition the dose over several crystals. The individual datasets are then merged in order to achieve the necessary completeness. On two test structures we first show that merging of data from small domains of the reciprocal space is indeed sufficient to obtain reliable data for structure solution and refinement. Second, we show on the beam sensitive manganese formate that high-quality data can be obtained on a few frames while the frames that have suffered from beam damage can still be used to determine the orientation matrix and the unit cell of the crystals. The results from the dynamical refinement on the obtained data show a high accuracy of the atom positions. In this way, DS-EDT can reduce the total dose on an individual crystal by an order of magnitude with respect to the already very dose-efficient LD-EDT.

Effect of self and extrinsic encapsulation on electron resilience of porous 2D polymer nanosheets

Despite the exceptional resolution in aberration-corrected high-resolution transmission electron microscope (AC-HRTEM) images of inorganic two-dimensional (2D) materials, achieving high-resolution imaging of organic 2D materials remains a daunting challenge due to their low electron resilience. Optimizing the critical dose (the electron exposure, the material can accept before it is noticeably damaged) is vital to mitigate this challenge. An understanding of electron resilience in porous crystalline 2D polymers including the effect of sample thickness has not been derived thus far. It is assumed, that additional layers of the sample form a cage around inner layers, which are preventing fragments from escaping into the vacuum and enabling recombination. In the literature this so called caging effect has been reported for perylene and pythalocyanine. In this work we determine the critical dose of a porous, triazine-based 2D polymer as function of the sample thickness. The results show that the caging effect should not be generalized to more sophisticated polymer systems. We argue that pore channels in the framework structure serve as escape routes for free fragments preventing the caging effect and thus showing surprisingly a thickness-independent critical dose. Moreover, we demonstrate that graphene encapsulation prevents fragment escape and results in an increase in the critical electron dose and unit-cell image resolution.

Reactions of polyaromatic molecules in crystals under electron beam of the transmission electron microscope

Reactivity of a series of related molecules under the 80 keV electron beam have been investigated and correlated with their structures and chemical composition. Hydrogenated and halogenated derivatives of hexaazatrinaphthylene, coronene, and phthalocyanine were prepared by sublimation in vacuum to form solventless crystals then deposited onto transmission electron microscopy (TEM) grids. The transformation of the molecules in the microcrystals were triggered by an 80 keV electron beam in the TEM and studied using correlated selected area electron diffraction, conventional bright field imaging, and energy dispersive X-ray spectroscopy. The critical fluence (ē nm^-2) required to cause a disappearance of the diffraction pattern was recorded and used as a measure of the reactivity of the molecules. The same electron flux (10² ē nm^-2 s^-1) was used throughout. Fully halogenated molecules were found to be the most stable and did not change significantly under our experimental conditions, followed by fully hydrogenated molecules with critical fluences of 10⁴ ē nm^-2. Surprisingly, semi-halogenated molecules that contained an equal number of hydrogen and halogen atoms were found to be the least stable, with critical fluences an order of magnitude lower at 10³ ē nm^-2. This is attributed to elimination of H-X (where X = F or Cl), followed by polymerisation of aryne / aryl radicals within the crystal. The critical fluence for the semi-fluorinated hexaazatrinaphthylene is the lowest as the presence of water molecules in its crystal lattice significantly decreased the stability of the organic molecules under the electron beam. Semi-halogenation reduces the beam stability of organic molecules compared to the parent hydrogenated molecule, thus providing the chemical guidance for design of electron beam stable materials. Understanding of molecular reactivity in the electron beam is necessary for advancement of molecular imaging and analysis methods by the TEM, molecular materials processing, and electron beam-driven synthesis of novel materials.

Graphene protection improves the stability of two-dimensional halide perovskites under the electron irradiation

The crystal structure of two-dimensional (2D) organic-inorganic halide perovskites undergoes fast structural collapse under the electron beam irradiation, hindering high-resolution transmission electron microscopy imaging. Graphene protection is an effective solution to mitigate the damage of electron-beam irradiation and has been applied in 2D materials such as MoS₂ . However, the effectivity of graphene protection has not been demonstrated in 2D halide perovskites yet, as traditional wet-transfer of graphene with aqueous solution would cause serious degradation for moisture-sensitive halide perovskites. Here, we verified that graphene protection plays a protection role and developed a method using nonpolar solvent to transfer the graphene layer atop the perovskite nanosheets. With this method, the perovskite nanosheets might be well protected by graphene encapsulation. HIGHLIGHTS: Transfer method of graphene on moisture-sensitive 2D halide perovskites using nonpolar solvents was developed. Graphene substrate is proven to be able to mitigate electron-beam damage to 2D halide perovskites. Encapsulation structure of graphene/halide perovskite/graphene was demonstrated.

The effects of encapsulation on damage to molecules by electron radiation

Encapsulation of materials imaged by high resolution transmission electron microscopy presents a promising route to the reduction of sample degradation, both independently and in combination with other traditional solutions to controlling radiation damage. In bulk crystals, the main effect of encapsulation (or coating) is the elimination of diffusion routes of beam-induced radical species, enhancing recombination rates and acting to limit overall damage. Moving from bulk to low dimensional materials has significant effects on the nature of damage under the electron beam. We consider the major changes in mechanisms of damage of low dimensional materials by separating the effects of dimensional reduction from the effects of encapsulation. An effect of confinement is discussed using a model example of coronene molecules encapsulated inside single walled carbon nanotubes as determined from molecular dynamics simulations calculating the threshold energy required for hydrogen atom dissociation. The same model system is used to estimate the rate at which the nanotube can dissipate excess thermal energy above room temperature by acting as a thermal sink.

Molecular Coatings for Stabilizing Silver and Gold Nanocubes under Electron Beam Irradiation

We study the degradation process of closely spaced silver and gold nanocubes under high-energy electron beam irradiation using transmission electron microscopy (TEM). The high aspect ratio gaps between silver and gold nanocubes degraded in many cases as a result of protrusion and filament formation during electron beam irradiation. We demonstrate that the molecular coating of the nanoparticles can act as a protective barrier to minimize electron-beam-induced damage on passivated gold and silver nanoparticles.

Dose-rate-dependent damage of cerium dioxide in the scanning transmission electron microscope

Beam damage caused by energetic electrons in the transmission electron microscope is a fundamental constraint limiting the collection of artifact-free information. Through understanding the influence of the electron beam, experimental routines may be adjusted to improve the data collection process. Investigations of CeO₂ indicate that there is not a critical dose required for the accumulation of electron beam damage. Instead, measurements using annular dark field scanning transmission electron microscopy and electron energy loss spectroscopy demonstrate that the onset of measurable damage occurs when a critical dose rate is exceeded. The mechanism behind this phenomenon is that oxygen vacancies created by exposure to a 300keV electron beam are actively annihilated as the sample re-oxidizes in the microscope environment. As a result, only when the rate of vacancy creation exceeds the recovery rate will beam damage begin to accumulate. This observation suggests that dose-intensive experiments can be accomplished without disrupting the native structure of the sample when executed using dose rates below the appropriate threshold. Furthermore, the presence of an encapsulating carbonaceous layer inhibits processes that cause beam damage, markedly increasing the dose rate threshold for the accumulation of damage.

High-resolution electron microscopy and spectroscopy of ferritin in biocompatible graphene liquid cells and graphene sandwiches

Atomic and electronic structures of hydrated ferritin are characterized using electron microscopy and spectroscopy through encapsulation in single layer graphene in a biocompatible manner. Graphene's ability to reduce radiation damage levels to hydrogen bond breakage is demonstrated. A reduction of iron valence from 3+ to 2+ is measured at nanometer-resolution in ferritin, showing initial stages of iron release by ferritin.

Cathodoluminescence studies of electron irradiation effects in n-type ZnO

The lifetime of non-equilibrium carriers in n-type unintentionally doped ZnO increases when the sample is exposed to the electron beam of a scanning electron microscope. This is observed by studying the ZnO cathodoluminescence (CL) spectra at different irradiation time durations and temperatures. We found that the decrease in the CL spectra's peak intensity is related to a thermo-activated energy barrier, determined by the calculated activation energy value of 259 ± 30 meV. This energy value comes close to the defect energy level of the zinc interstitial, which is possibly the nature of the energy barrier responsible for this decrease.

Stability due to peripheral halogenation in phthalocyanine complexes

The effect of peripheral halogenation is examined based on analytical transmission electron microscopy and thermal analyses of two chemical family structures, specifically the vanadyl-phthalocyanine family (VOPcX: X = H16, F14.5) and the copper-phthalocyanine family (CuPcX: X = H16, F16, Cl16, Cl8Br8), focusing on the process of molecular changes and crystalline disintegrations. To clarify the molecular transformations, electron energy-loss spectroscopy (EELS) is applied to two fluorinated phthalocyanines (VOPcF14.5 and CuPcF16), by monitoring mass changes as well as energy loss near edge structures (ELNES). The elemental mass of both VOPcF14.5 and CuPcF16 remain constant up to 0.5 C x cm(-2), except in the case of mass reduction attributed to oxygen loss occurring in VOPcF14.5. It is expected that the released oxygen will induce higher radiation damage in VOPcF14.5. Although mass variation is not observed in CuPcF16, it is found from ELNES that the pi resonant system of nitrogen is more radiation sensitive than that of carbon. These results imply that the electron sensitivity in VOPcX is triggered by eliminated oxygen or, thus, an induced larger empty space, whereas the sensitivity of CuPcX is dominated only by a large intermolecular empty space resulting in the following bond alterations. It is also found that the decomposition temperature (Td) measured by thermal analyses and the characteristic dose (D1/e) are exponentially correlated to the "effective molecular occupancy" (Oe) evaluated as a volume function of molecules in unit cells. By measuring Td and/or Oe, we discuss the durability of peripheral halogenation with respect to the radiation damage.

Radiation damage in coronene, rubrene and p-terphenyl, measured for incident electrons of kinetic energy between 100 and 200kev

We have measured the sensitivity of three highly conjugated organic compounds to electron irradiation. Using a 200 keV TEM, loss of crystallinity was determined from quantitative electron-diffraction measurements. Degradation of the molecular ring structure was monitored from fading of the 6 eV pi-excitation peak in the energy-loss spectrum. Measurements at incident energies between 30 keV and 100 eV were made using a scanning electron microscope (SEM), by recording gradual decay of the cathodoluminescence (CL) signal. Expressed in Grays, the energy dose required for CL decay in coronene is a factor of 30 lower than for destruction of crystallinity and a factor of 300 lower than for destruction of the molecular structure. Below 1 keV, the CL-decay cross section shows no evidence of a threshold effect, indicating that the damage involved is caused by valence-electron (rather than K-shell) excitation. Therefore even relatively radiation-resistant organic materials may undergo some form of damage when examined in a low-energy electron microscope or a low-voltage SEM.

Radiation damage in the TEM and SEM

We review the various ways in which an electron beam can adversely affect an organic or inorganic sample during examination in an electron microscope. The effects considered are: heating, electrostatic charging, ionization damage (radiolysis), displacement damage, sputtering and hydrocarbon contamination. In each case, strategies to minimise the damage are identified. In the light of recent experimental evidence, we re-examine two common assumptions: that the amount of radiation damage is proportional to the electron dose and is independent of beam diameter; and that the extent of the damage is proportional to the amount of energy deposited in the specimen.

Imaging of protein molecules--towards atomic resolution

This review discusses some of the recent developments in high resolution imaging of biological molecules. Electron micrographs of unstained biological molecules never show the resolution or contrast that would be predicted. Movements in the specimen caused by radiation damage, and possibly charging of the specimen are the most significant factors in the reduction of image contrast of these radiation-sensitive specimens. Until these limitations are overcome it is unlikely that the structures of biological molecules will be determined to the resolutions to which they are preserved. The causes of contrast loss in images are discussed in a quantitative manner and the use of crystalline paraffin as a model for radiation-sensitive specimens in general is described. Procedures for improving the contrast in images of biological molecules are described, including the new method of spot-scan imaging. Possible future developments, including high resolution imaging of single particles, are discussed.

Methods for specimen thickness determination in electron microscopy. II. Changes in thickness with dose

The electron diffraction patterns of tilted thin crystals were used to determine the unit cell size in the direction normal to the supporting film. The method revealed a considerable dose-dependent thinning or shrinkage. Using a variety of specimens and stains, we found that this amounted to a 50% reduction in volume and could be attributable to two causes. Firstly, the specimen is held to the supporting film so that volume changes can only occur through changes in thickness. Secondly, the decrease in volume is associated with a dose-induced mass loss which is greatly suppressed at liquid nitrogen temperatures.

The "quasi-thermal" mechanism for electron beam damage of n-paraffins

Electron diffraction patterns from epitaxially grown microcrystals of n-hexatriacontane, which are slightly damaged by the electron beam, strongly resemble those from the same material when it is warmed just below the pre-melt hexagonal phase. The identity of these diffraction patterns, which display a marked attenuation of lamellar 001 reflections but much less alteration of the strongest reflections, implies that both processes occur via the induction of chain defects which, in turn, generate chain-end voids in the crystal packing. Such defects, however, need not be identical for the two events. With warming they are probably the gtg-1 kink and the gauche chain conformers identified by infrared spectroscopy. The creation of trans vinylene groups during radiation damage will also increase chain flexibility, and perhaps induce the production of gtg-1 kinks.