Damage-free vibrational spectroscopy of biological materials in the electron microscope

Phonon mode at interface and its impact on interfacial thermal transport

Due to the minimization and integration of micro/nano-devices, the high density of interfaces becomes a significant challenge in various applications. Phonon modes at interface resulting from the mismatch between inhomogeneous functional counterparts are crucial for interfacial thermal transport and overall thermal management of micro/nano-devices, making it a topic of great research interest recently. Here, we comprehensively review the recent advances on the theoretical and experimental investigations of interfacial phonon mode and its impact on interfacial thermal transport. Firstly, we summarize the recent progresses of the theoretical and experimental characterization of interfacial phonon modes at various interfaces, along with the overview of the development of diverse methodologies. Then, the impact of interfacial phonon modes on interfacial thermal transport process are discussed from the normal modal decomposition and inelastic scattering mechanisms. Meanwhile, we examine various factors influencing the interfacial phonon modes and interfacial thermal transport, including temperature, interface roughness, interfacial mass gradient, interfacial disorder, and so on. Finally, an outlook is provided for future studies. This review provides a fundamental understanding of interfacial phonon modes and their impact on interfacial thermal transport, which would be beneficial for the exploration and optimization of thermal management in various micro/nano-devices with high density interfaces.

Footprints of atomic-scale features in plasmonic nanoparticles as revealed by electron energy loss spectroscopy

We present a first-principles theoretical study of the atomistic footprints in the valence electron energy loss spectroscopy (EELS) of nanometer-size metallic particles. Charge density maps of excited plasmons and EEL spectra for specific electron paths through a nanoparticle (Na380 atom cluster) are modeled using ab initio calculations within time-dependent density functional theory. Our findings unveil the atomic-scale sensitivity of EELS within this low-energy spectral range. Whereas localized surface plasmons (LSPs) are particularly sensitive to the atomistic structure of the surface probed by the electron beam, confined bulk plasmons (CBPs) reveal quantum size effects within the nanoparticle's volume. Moreover, we prove that classical local dielectric theories mimicking the atomistic structure of the nanoparticles reproduce the LSP trends observed in quantum calculations, but fall short in describing the CBP behavior observed under different electron trajectories.

μeV electron spectromicroscopy using free-space light

The synergy between free electrons and light has recently been leveraged to reach an impressive degree of simultaneous spatial and spectral resolution, enabling applications in microscopy and quantum optics. However, the required combination of electron optics and light injection into the spectrally narrow modes of arbitrary specimens remains a challenge. Here, we demonstrate microelectronvolt spectral resolution with a sub-nanometer probe of photonic modes with quality factors as high as 10⁴. We rely on mode matching of a tightly focused laser beam to whispering gallery modes to achieve a 10⁸-fold increase in light-electron coupling efficiency. By adapting the shape and size of free-space optical beams to address specific physical questions, our approach allows us to interrogate any type of photonic structure with unprecedented spectral and spatial detail.

Pulsed-beam transmission electron microscopy and radiation damage

We review the use of pulsed electron-beams in transmission electron microscopes (TEMs) for the purpose of mitigating specimen damage. We begin by placing the importance of TEMs with respect to materials characterization into proper context, and we provide a brief overview of established methods for reducing or eliminating the deleterious effects of beam-induced damage. We then introduce the concept of pulsed-beam TEM, and we briefly describe the basic methods and instrument configurations used to create so-called temporally structured electron beams. Following a brief overview of the use of high-dose-rate pulsed-electron beams in cancer radiation therapy, we review historical speculations and more recent compelling but mostly anecdotal findings of a pulsed-beam TEM damage effect. This is followed by an in-depth technical review of recent works seeking to establish cause-and-effect relationships, to conclusively uncover the presence of an effect, and to explore the practicality of the approach. These studies, in particular, provide the most compelling evidence to date that using a pulsed electron beam in the TEM is indeed a viable way to mitigate damage. Throughout, we point out current gaps in understanding, and we conclude with a brief perspective of current needs and future directions.

Single-atom vibrational spectroscopy with chemical-bonding sensitivity

Correlation of lattice vibrational properties with local atomic configurations in materials is essential for elucidating functionalities that involve phonon transport in solids. Recent developments in vibrational spectroscopy in a scanning transmission electron microscope have enabled direct measurements of local phonon modes at defects and interfaces by combining high spatial and energy resolution. However, pushing the ultimate limit of vibrational spectroscopy in a scanning transmission electron microscope to reveal the impact of chemical bonding on local phonon modes requires extreme sensitivity of the experiment at the chemical-bond level. Here we demonstrate that, with improved instrument stability and sensitivity, the specific vibrational signals of the same substitutional impurity and the neighbouring carbon atoms in monolayer graphene with different chemical-bonding configurations are clearly resolved, complementary with density functional theory calculations. The present work opens the door to the direct observation of local phonon modes with chemical-bonding sensitivity, and provides more insights into the defect-induced physics in graphene.

Probing the Boundary between Classical and Quantum Mechanics by Analyzing the Energy Dependence of Single-Electron Scattering Events at the Nanoscale

The relation between the energy-dependent particle and wave descriptions of electron-matter interactions on the nanoscale was analyzed by measuring the delocalization of an evanescent field from energy-filtered amplitude images of sample/vacuum interfaces with a special aberration-corrected electron microscope. The spatial field extension coincided with the energy-dependent self-coherence length of propagating wave packets that obeyed the time-dependent Schrödinger equation, and underwent a Goos-Hänchen shift. The findings support the view that wave packets are created by self-interferences during coherent-inelastic Coulomb interactions with a decoherence phase close to Δφ = 0.5 rad. Due to a strictly reciprocal dependence on energy, the wave packets shrink below atomic dimensions for electron energy losses beyond 1000 eV, and thus appear particle-like. Consequently, our observations inevitably include pulse-like wave propagations that stimulate structural dynamics in nanomaterials at any electron energy loss, which can be exploited to unravel time-dependent structure-function relationships on the nanoscale.

Nanoscale Multimodal Analysis of Sensitive Nanomaterials by Monochromated STEM-EELS in Low-Dose and Cryogenic Conditions

Scanning transmission electron microscopy coupled with electron energy loss spectroscopy (STEM-EELS) provides spatially resolved chemical information down to the atomic scale. However, studying radiation-sensitive specimens such as organic-inorganic composites remains extremely challenging. Here, we analyzed metal-organic framework nanoparticles (nanoMOFs) at low-dose (10 e^-/Ų) and liquid nitrogen temperatures, similar to cryo-TEM conditions usually employed for high-resolution imaging of biological specimens. Our results demonstrate that monochromated STEM-EELS enables damage-free analysis of nanoMOFs, providing in a single experiment, signatures of intact functional groups comparable with infrared, ultraviolet, and X-ray data, with an energy resolution down to 7 meV. The signals have been mapped at the nanoscale (<10 nm) for each of these energy spectral ranges, including the chemical features observed for high energy losses (X-ray range). By controlling beam irradiation and monitoring spectral changes, our work provides insights into the possible pathways of chemical reactions occurring under electron exposure. These results demonstrate the possibilities for characterizing at the nanoscale the chemistry of sensitive systems such as organic and biological materials.

Sub-resolution contrast in neutral helium microscopy through facet scattering for quantitative imaging of nanoscale topographies on macroscopic surfaces

Nanoscale thin film coatings and surface treatments are ubiquitous across industry, science, and engineering; imbuing specific functional or mechanical properties (such as corrosion resistance, lubricity, catalytic activity and electronic behaviour). Non-destructive nanoscale imaging of thin film coatings across large (ca. centimetre) lateral length scales, crucial to a wide range of modern industry, remains a significant technical challenge. By harnessing the unique nature of the helium atom-surface interaction, neutral helium microscopy images these surfaces without altering the sample under investigation. Since the helium atom scatters exclusively from the outermost electronic corrugation of the sample, the technique is completely surface sensitive. Furthermore, with a cross-section that is orders of magnitude larger than that of electrons, neutrons and photons, the probe particle routinely interacts with features down to the scale of surface defects and small adsorbates (including hydrogen). Here, we highlight the capacity of neutral helium microscopy for sub-resolution contrast using an advanced facet scattering model based on nanoscale features. By replicating the observed scattered helium intensities, we demonstrate that sub-resolution contrast arises from the unique surface scattering of the incident probe. Consequently, it is now possible to extract quantitative information from the helium atom image, including localised ångström-scale variations in topography.

Entangling free electrons and optical excitations

The inelastic interaction between flying particles and optical nanocavities gives rise to entangled states in which some excitations of the latter are paired with momentum changes in the former. Specifically, free-electron entanglement with nanocavity modes opens appealing opportunities associated with the strong interaction capabilities of the electrons. However, the achievable degree of entanglement is currently limited by the lack of control over the resulting state mixtures. Here, we propose a scheme to generate pure entanglement between designated optical-cavity excitations and separable free-electron states. We shape the electron wave function profile to select the accessible cavity modes and simultaneously associate them with targeted electron scattering directions. This concept is exemplified through theoretical calculations of free-electron entanglement with degenerate and nondegenerate plasmon modes in silver nanoparticles and atomic vibrations in an inorganic molecule. The generated entanglement can be further propagated through its electron component to extend quantum interactions beyond existing protocols.

Complete Excitation of Discrete Quantum Systems by Single Free Electrons

We reveal a wealth of nonlinear and recoil effects in the interaction between individual low-energy electrons (≲100  eV) and samples comprising a discrete number of states. Adopting a quantum theoretical description of combined free-electron and two-level systems, we find a maximum achievable excitation probability of 100%, which requires specific conditions relating to the coupling strength and the transition symmetry, as we illustrate through calculations for dipolar and quadrupolar modes. Strong recoil effects are observed when the kinetic energy of the probe lies close to the transition threshold, although the associated probability remains independent of the electron wave function even when fully accounting for nonlinear interactions with arbitrarily complex multilevel samples. Our work reveals the potential of free electrons to control localized excitations and delineates the boundaries of such control.

Scanning Electron Thermal Absorbance Microscopy for Light Element Detection and Atomic Number Analysis

Recent developments in nanoscale thermal metrology using electron microscopy have made impressive advancements in measuring either phononic or thermal transport properties of nanoscale samples. However, its potential in material analysis has never been considered. Here we introduce a direct thermal absorbance measurement platform in scanning electron microscope (SEM) and demonstrate that its signal can be utilized for atomic number (Z) analysis at nanoscales. We prove that the measured absorbance of materials is complementary to signals of backscattering electrons but exhibits a much higher collection efficiency and signal-to-noise ratio. Thus, it not only enables successful detections of light elements/compounds under low acceleration voltages of SEM but also allows quantitative Z analyses in agreement with simulations. The direct thermal absorbance measurement platform would become an ideal tool for SEM, especially for thin films, light elements/compounds, or biological samples at nanoscales.

Atomic-scale probing of heterointerface phonon bridges in nitride semiconductor

Interface phonon modes that are generated by several atomic layers at the heterointerface play a major role in the interface thermal conductance for nanoscale high-power devices such as nitride-based high-electron-mobility transistors and light-emitting diodes. Here we measure the local phonon spectra across AlN/Si and AlN/Al interfaces using atomically resolved vibrational electron energy-loss spectroscopy in a scanning transmission electron microscope. At the AlN/Si interface, we observe various interface phonon modes, of which the extended and localized modes act as bridges to connect the bulk AlN modes and bulk Si modes and are expected to boost the phonon transport, thus substantially contributing to interface thermal conductance. In comparison, no such phonon bridge is observed at the AlN/Al interface, for which partially extended modes dominate the interface thermal conductivity. This work provides valuable insights into understanding the interfacial thermal transport in nitride semiconductors and useful guidance for thermal management via interface engineering.

A Novel Monochromator with Offset Cylindrical Lenses and Its Application to a Low-Voltage Scanning Electron Microscope

Low-voltage scanning electron microscopes (LV-SEMs) are widely used in nanoscience. However, image resolution for SEMs is restricted by chromatic aberration due to energy spread of the electron beam at low acceleration voltage. This study introduces a new monochromator (MC) with offset cylindrical lenses (CLs) as one solution for LV-SEMs. The MC optics, with highly excited CLs in offset layouts, has advantageous high performance and simple experimental setup, making it suitable for field emission LV-SEMs. In a preliminary evaluation, our MC reduced the energy spread from 770 to 67 meV. The MC was integrated into a commercial SEM equipped with an out-lens (a conventional objective lens without immersion magnetic or retarding electric fields) and an Everhart–Thornley detector. Comparing SEM images under two conditions with the MC turned on or off, the spatial resolution was improved by 58% at 0.5 and 1 keV. The filtering effect of the MC decreased the probe current with a ratio (i.e., transmittance) of 5.7%, which was consistent with estimations based on measured energy spreads. To the best of our knowledge, this is the first report on an effective MC with higher-energy resolution than 100 meV and the results offer encouraging prospects for LV-SEM technology.

Solid-state separation of hypoxanthine tautomers through a doping strategy

The solid-state separation of hypoxanthine tautomers was realized by a doping strategy. The doping forms of hypoxanthine in HAmG, AG β and AG α are N7-hypoxanthine, and in GM and dehydrated-GM are N9-hypoxanthine.

Toward Compositional Contrast by Cryo-STEM

Electron microscopy (EM) is the most versatile tool for the study of matter at scales ranging from subatomic to visible. The high vacuum environment and the charged irradiation require careful stabilization of many specimens of interest. Biological samples are particularly sensitive due to their composition of light elements suspended in an aqueous medium. Early investigators developed techniques of embedding and staining with heavy metal salts for contrast enhancement. Indeed, the Nobel Prize in 1974 recognized Claude, de Duve, and Palade for establishment of the field of cell biology, largely due to their developments in separation and preservation of cellular components for electron microscopy. A decade later, cryogenic fixation was introduced. Vitrification of the water avoids the need for dehydration and provides an ideal matrix in which the organic macromolecules are suspended; the specimen represents a native state, suddenly frozen in time at temperatures below -150 °C. The low temperature maintains a low vapor pressure for the electron microscope, and the amorphous nature of the medium avoids diffraction contrast from crystalline ice. Such samples are extremely delicate, however, and cryo-EM imaging is a race for information in the face of ongoing damage by electron irradiation. Through this journey, cryo-EM enhanced the resolution scale from membranes to molecules and most recently to atoms. Cryo-EM pioneers, Dubochet, Frank, and Henderson, were awarded the Nobel Prize in 2017 for high resolution structure determination of biological macromolecules.A relatively untapped feature of cryo-EM is its preservation of composition. Nothing is added and nothing removed. Analytical spectroscopies based on electron energy loss or X-ray emission can be applied, but the very small interaction cross sections conflict with the weak exposures required to preserve sample integrity. To what extent can we interpret quantitatively the pixel intensities in images themselves? Conventional cryo-transmission electron microscopy (TEM) is limited in this respect, due to the strong dependence of the contrast transfer on defocus and the absence of contrast at low spatial frequencies.Inspiration comes largely from a different modality for cryo-tomography, using soft X-rays. Contrast depends on the difference in atomic absorption between carbon and oxygen in a region of the spectrum between their core level ionization energies, the so-called water window. Three dimensional (3D) reconstruction provides a map of the local X-ray absorption coefficient. The quantitative contrast enables the visualization of organic materials without stain and measurement of their concentration quantitatively. We asked, what aspects of the quantitative contrast might be transferred to cryo-electron microscopy?Compositional contrast is accessible in scanning transmission EM (STEM) via incoherent elastic scattering, which is sensitive to the atomic number Z. STEM can be regarded as a high energy, low angle diffraction measurement performed pixel by pixel with a weakly convergent beam. When coherent diffraction effects are absent, that is, in amorphous materials, a dark field signal measures quantitatively the flux scattered from the specimen integrated over the detector area. Learning to interpret these signals will open a new dimension in cryo-EM. This Account describes our efforts so far to introduce STEM for cryo-EM and tomography of biological specimens. We conclude with some thoughts on further developments.

Revealing Nanoscale Confinement Effects on Hyperbolic Phonon Polaritons with an Electron Beam

Hyperbolic phonon polaritons (HPhPs) in hexagonal boron nitride (hBN) enable the direct manipulation of mid-infrared light at nanometer scales, many orders of magnitude below the free-space light wavelength. High-resolution monochromated electron energy-loss spectroscopy (EELS) facilitates measurement of excitations with energies extending into the mid-infrared while maintaining nanoscale spatial resolution, making it ideal for detecting HPhPs. The electron beam is a precise source and probe of HPhPs, which allows the observation of nanoscale confinement in HPhP structures and directly extract hBN polariton dispersions for both modes in the bulk of the flake and modes along the edge. The measurements reveal technologically important nontrivial phenomena, such as localized polaritons induced by environmental heterogeneity, enhanced and suppressed excitation due to 2D interference, and strong modification of high-momenta excitations such as edge-confined polaritons by nanoscale heterogeneity on edge boundaries. The work opens exciting prospects for the design of real-world optical mid-infrared devices based on hyperbolic polaritons.

Atomic-scale imaging of CH3NH3PbI3 structure and its decomposition pathway

Understanding the atomic structure and structural instability of organic-inorganic hybrid perovskites is the key to appreciate their remarkable photoelectric properties and understand failure mechanism. Here, using low-dose imaging technique by direct-detection electron-counting camera in a transmission electron microscope, we investigate the atomic structure and decomposition pathway of CH3NH3PbI3 (MAPbI3) at the atomic scale. We successfully image the atomic structure of perovskite in real space under ultra-low electron dose condition, and observe a two-step decomposition process, i.e., initial loss of MA+ followed by the collapse of perovskite structure into 6H-PbI2 with their critical threshold doses also determined. Interestingly, an intermediate phase (MA0.5PbI3) with locally ordered vacancies can robustly exist before perovskite collapses, enlightening strategies for prevention and recovery of perovskite structure during the degradation. Associated with the structure evolution, the bandgap gradually increases from ~1.6 eV to ~2.1 eV. In addition, it is found that C-N bonds can be readily destroyed under irradiation, releasing NH3 and HI and leaving hydrocarbons. These findings enhance our understanding of the photoelectric properties and failure mechanism of MAPbI3, providing potential strategies into material optimization.

Single-particle cryo-EM: alternative schemes to improve dose efficiency

Imaging of biomolecules by ionizing radiation, such as electrons, causes radiation damage which introduces structural and compositional changes of the specimen. The total number of high-energy electrons per surface area that can be used for imaging in cryogenic electron microscopy (cryo-EM) is severely restricted due to radiation damage, resulting in low signal-to-noise ratios (SNR). High resolution details are dampened by the transfer function of the microscope and detector, and are the first to be lost as radiation damage alters the individual molecules which are presumed to be identical during averaging. As a consequence, radiation damage puts a limit on the particle size and sample heterogeneity with which electron microscopy (EM) can deal. Since a transmission EM (TEM) image is formed from the scattering process of the electron by the specimen interaction potential, radiation damage is inevitable. However, we can aim to maximize the information transfer for a given dose and increase the SNR by finding alternatives to the conventional phase-contrast cryo-EM techniques. Here some alternative transmission electron microscopy techniques are reviewed, including phase plate, multi-pass transmission electron microscopy, off-axis holography, ptychography and a quantum sorter. Their prospects for providing more or complementary structural information within the limited lifetime of the sample are discussed.

Automated and Autonomous Experiments in Electron and Scanning Probe Microscopy

Machine learning and artificial intelligence (ML/AI) are rapidly becoming an indispensable part of physics research, with domain applications ranging from theory and materials prediction to high-throughput data analysis. In parallel, the recent successes in applying ML/AI methods for autonomous systems from robotics to self-driving cars to organic and inorganic synthesis are generating enthusiasm for the potential of these techniques to enable automated and autonomous experiments (AE) in imaging. Here, we aim to analyze the major pathways toward AE in imaging methods with sequential image formation mechanisms, focusing on scanning probe microscopy (SPM) and (scanning) transmission electron microscopy ((S)TEM). We argue that automated experiments should necessarily be discussed in a broader context of the general domain knowledge that both informs the experiment and is increased as the result of the experiment. As such, this analysis should explore the human and ML/AI roles prior to and during the experiment and consider the latencies, biases, and prior knowledge of the decision-making process. Similarly, such discussion should include the limitations of the existing imaging systems, including intrinsic latencies, non-idealities, and drifts comprising both correctable and stochastic components. We further pose that the role of the AE in microscopy is not the exclusion of human operators (as is the case for autonomous driving), but rather automation of routine operations such as microscope tuning, etc., prior to the experiment, and conversion of low latency decision making processes on the time scale spanning from image acquisition to human-level high-order experiment planning. Overall, we argue that ML/AI can dramatically alter the (S)TEM and SPM fields; however, this process is likely to be highly nontrivial and initiated by combined human-ML workflows and will bring challenges both from the microscope and ML/AI sides. At the same time, these methods will enable opportunities and paradigms for scientific discovery and nanostructure fabrication.

A Close Look at Molecular Self-Assembly with the Transmission Electron Microscope

Molecular self-assembly is pervasive in the formation of living and synthetic materials. Knowledge gained from research into the principles of molecular self-assembly drives innovation in the biological, chemical, and materials sciences. Self-assembly processes span a wide range of temporal and spatial domains and are often unintuitive and complex. Studying such complex processes requires an arsenal of analytical and computational tools. Within this arsenal, the transmission electron microscope stands out for its unique ability to visualize and quantify self-assembly structures and processes. This review describes the contribution that the transmission electron microscope has made to the field of molecular self-assembly. An emphasis is placed on which TEM methods are applicable to different structures and processes and how TEM can be used in combination with other experimental or computational methods. Finally, we provide an outlook on the current challenges to, and opportunities for, increasing the impact that the transmission electron microscope can have on molecular self-assembly.

Verification of water presence in graphene liquid cells

Graphene liquid cells (GLCs) present the thinnest possible sample enclosures for liquid phase electron microscopy. However, the actual presence of liquid within a GLC is not always guaranteed. Of key importance is to reliably test the presence of the liquid, which is most frequently water or saline. Here, the commonly used methods for verifying the presence of water were evaluated. It is shown that depending on the type of sample, applying a single criterion does not always conclusively verify the presence of water. Testing liquid filling for a specific GLC sample preparation protocol should thus be considered critically. The most reliable method is direct observation of the water exciton peak using electron energy loss spectroscopy (EELS). But if this method cannot be carried out, water filling of the GLC can be verified from a combination of higher contrast in the image, the presence of bubbles, and an oxygen signal in the EEL spectrum, which can be accomplished at a high electron dose in spot mode. Nanoparticle movement does not always occur in a GLC.

Role of Convergence and Collection Angles in the Excitation of Long- and Short-Wavelength Phonons with Vibrational Electron Energy-Loss Spectroscopy

Current generation electron monochromators employed as attachments to scanning transmission electron microscopes (STEM) offer the ability to obtain vibrational information from materials using electron energy-loss spectroscopy (EELS). We show here that in crystals, long- and short-wavelength phonon modes can be probed simultaneously with on-axis vibrational STEM EELS. The long-wavelength phonons are probed via dipole scattering, while the short-wavelength modes are probed via impact scattering of the incident electrons. The localized character of the short-wavelength modes is demonstrated by scanning the electron beam across the edge of a hexagonal boron nitride nanoparticle. It is found that employing convergence angles that encompass multiple Brillouin zone boundaries enhances the short-wavelength phonon contribution to the vibrational energy-loss spectrum much more than that achieved by employing collection angles that encompass multiple Brillouin zone boundaries. Probing short-wavelength phonons at high spatial resolution with on-axis vibrational STEM EELS will help develop a fundamental connection between vibrational excitations and bonding arrangements at atomic-scale heterogeneities in materials.

Theory of Atomic-Scale Vibrational Mapping and Isotope Identification with Electron Beams

Transmission electron microscopy and spectroscopy currently enable the acquisition of spatially resolved spectral information from a specimen by focusing electron beams down to a sub-angstrom spot and then analyzing the energy of the inelastically scattered electrons with few-meV energy resolution. This technique has recently been used to experimentally resolve vibrational modes in 2D materials emerging at mid-infrared frequencies. Here, on the basis of first-principles theory, we demonstrate the possibility of identifying single isotope atom impurities in a nanostructure through the trace that they leave in the spectral and spatial characteristics of the vibrational modes. Specifically, we examine a hexagonal boron nitride molecule as an example of application, in which the presence of a single isotope impurity is revealed through changes in the electron spectra, as well as in the space-, energy-, and momentum-resolved inelastic electron signal. We compare these results with conventional far-field spectroscopy, showing that electron beams offer superior spatial resolution combined with the ability to probe the complete set of vibrational modes, including those that are optically dark. Our study is relevant for the atomic-scale characterization of vibrational modes in materials of interest, including a detailed mapping of isotope distributions.

Variable temperature FTIR spectra of polycrystalline purine nucleobases and estimating strengths of individual hydrogen bonds

In the first part of this work, we report the FTIR spectra of pure NH and isotopically substituted ND (10-15% D and 80-90% D) polycrystalline hypoxanthine, xanthine, adenine and guanine recorded in the 400-4000 cm^-1 range, as a function of temperature (10-300 K). We provide assignments of the stretching and out-of-plane bending amine (NH₂) and imine (NH) bands to the distinct H-bonds present in the crystal, based on the temperature sensitivity and isotopic exchange behavior. Empirical correlations between spectral and thermodynamic or structural parameters enabled us to estimate the energies and lengths of H-bonds in the studied nucleobase crystals and to correlate them with literature data. The empirical H-bonding energies are compared with H-bonding and stacking energies computed for hypoxanthine. In the second part, strategies for using the empirical correlations together with information extracted from quantum mechanical data (in particular from the Bader's quantum theory of atoms in molecules, QTAIM) for the evaluation of hydrogen bonding properties are discussed, and their advantages and drawbacks pointed out. The justification for a cooperative use of quantum-mechanical calculations with empirical spectra-energy correlations is discussed.

Exploring the Spatial Features of Electronic Transitions in Molecular and Biomolecular Systems by Swift Electrons

We devise a new kind of experiment that extends the technology of electron energy loss spectroscopy to probe (supra-)molecular systems: by using an electron beam in a configuration that avoids molecular damage and a very recently introduced electron optics setup for the analysis of the outcoming electrons, one can obtain information on the spatial features of the investigated excitations. Physical insight into the proposed experiment is provided by means of a simple but rigorous model to obtain the transition rate and selection rule. Numerical simulations of DNA G-quadruplexes and other biomolecular systems, based on time dependent density functional theory calculations, point out that the conceived new technique can probe the multipolar components and even the chirality of molecular transitions, superseding the usual optical spectroscopies for those cases that are problematic, such as dipole-forbidden transitions, at a very high spatial resolution.

Protein secondary structure signatures from energy loss spectra recorded in the electron microscope

Infrared spectroscopy is a powerful technique for characterising protein structure. It is now possible to record energy losses corresponding to the infrared region in the electron microscope and to avoid damage by positioning the probe in the region adjacent to the structure being studied. Spectra from bacteriorhodopsin, a protein that is predominately a α helix, and OmpF porin, a protein that is mainly β sheet show significant differences over a spectral range from ∼0.1 to 0.25 eV (∼1000 to 1800 cm^-1 ). Although the energy resolution equivalent to 60 cm^-1 is inferior to Fourier Transform InfraRed Spectroscopy (FTIR) the spectra are very sensitive to molecular orientation. Polar bonds aligned parallel to the specimen grid make particularly strong contributions to the energy loss spectra. Ultra-high-resolution energy loss spectroscopy in the electron microscope can potentially add useful information to imaging and diffraction for determining the secondary structure misfolding believed to be responsible for dementia diseases such as Alzheimer's.

Analysis of complex, beam-sensitive materials by transmission electron microscopy and associated techniques

We review the use of transmission electron microscopy (TEM) and associated techniques for the analysis of beam-sensitive materials and complex, multiphase systems in-situ or close to their native state. We focus on materials prone to damage by radiolysis and explain that this process cannot be eliminated or switched off, requiring TEM analysis to be done within a dose budget to achieve an optimum dose-limited resolution. We highlight the importance of determining the damage sensitivity of a particular system in terms of characteristic changes that occur on irradiation under both an electron fluence and flux by presenting results from a series of molecular crystals. We discuss the choice of electron beam accelerating voltage and detectors for optimizing resolution and outline the different strategies employed for low-dose microscopy in relation to the damage processes in operation. In particular, we discuss the use of scanning TEM (STEM) techniques for maximizing information content from high-resolution imaging and spectroscopy of minerals and molecular crystals. We suggest how this understanding can then be carried forward for in-situ analysis of samples interacting with liquids and gases, provided any electron beam-induced alteration of a specimen is controlled or used to drive a chosen reaction. Finally, we demonstrate that cryo-TEM of nanoparticle samples snap-frozen in vitreous ice can play a significant role in benchmarking dynamic processes at higher resolution. This article is part of a discussion meeting issue 'Dynamic in situ microscopy relating structure and function'.

Properties of Dipole-Mode Vibrational Energy Losses Recorded From a TEM Specimen

The authors discuss the dipole vibrational modes that predominate in the energy-loss spectra of ionic materials below 1 eV, concentrating on thin-film specimens of typical transmission electron microscopy (TEM) thickness. The thickness dependence of the intensity is shown to be a useful guide to the bulk or surface character of vibrational peaks. The lateral and depth resolution of the energy-loss signal is investigated with the aid of finite-element calculations.

Lattice resolution of vibrational modes in the electron microscope

The combination of aberration correction and ultra high energy resolution with monochromators has made it possible to record images showing lattice resolution in phonon modes, both with a displaced collection aperture and more recently with an on -axis collection aperture. In practice the objective aperture has to include Bragg reflections that correspond to the observed lattice image spacings, and the specimen has to be sufficiently thick for adequate phonon scattered intensity. There has been controversy as to whether the images with the on axis detector are really a consequence of lattice resolution in a phonon mode or just a transfer of information from an image that was formed by elastically scattered electrons. We present results of calculations based on a theory that includes the possibility of dynamical electron diffraction for both incident and scattered electrons and the full phonon dispersion relation. We show that Umklapp scattering from the second Brillouin Zone back to the first Brillouin Zone is necessary for lattice resolution with the on axis detector and that it is therefore reasonable to attribute the lattice resolution to the phonon scattering.

Chemical identification through two-dimensional electron energy-loss spectroscopy

We explore a disruptive approach to nanoscale sensing by performing electron energy loss spectroscopy through the use of low-energy ballistic electrons that propagate on a two-dimensional semiconductor. In analogy to free-space electron microscopy, we show that the presence of analyte molecules in the vicinity of the semiconductor produces substantial energy losses in the electrons, which can be resolved by energy-selective electron injection and detection through actively controlled potential gates. The infrared excitation spectra of the molecules are thereby gathered in this electronic device, enabling the identification of chemical species with high sensitivity. Our realistic theoretical calculations demonstrate the superiority of this technique for molecular sensing, capable of performing spectral identification at the zeptomol level within a microscopic all-electrical device.

Tailored Nanoscale Plasmon-Enhanced Vibrational Electron Spectroscopy

Atomic vibrations and phonons are an excellent source of information on nanomaterials that we can access through a variety of methods including Raman scattering, infrared spectroscopy, and electron energy-loss spectroscopy (EELS). In the presence of a plasmon local field, vibrations are strongly modified and, in particular, their dipolar strengths are highly enhanced, thus rendering Raman scattering and infrared spectroscopy extremely sensitive techniques. Here, we experimentally demonstrate that the interaction between a relativistic electron and vibrational modes in nanostructures is fundamentally modified in the presence of plasmons. We finely tune the energy of surface plasmons in metallic nanowires in the vicinity of hexagonal boron nitride, making it possible to monitor and disentangle both strong phonon-plasmon coupling and plasmon-driven phonon enhancement at the nanometer scale. Because of the near-field character of the electron beam-phonon interaction, optically inactive phonon modes are also observed. Besides increasing our understanding of phonon physics, our results hold great potential for investigating sensing mechanisms and chemistry in complex nanomaterials down to the molecular level.

Imaging Beam-Sensitive Materials by Electron Microscopy

Electron microscopy allows the extraction of multidimensional spatiotemporally correlated structural information of diverse materials down to atomic resolution, which is essential for figuring out their structure-property relationships. Unfortunately, the high-energy electrons that carry this important information can cause damage by modulating the structures of the materials. This has become a significant problem concerning the recent boost in materials science applications of a wide range of beam-sensitive materials, including metal-organic frameworks, covalent-organic frameworks, organic-inorganic hybrid materials, 2D materials, and zeolites. To this end, developing electron microscopy techniques that minimize the electron beam damage for the extraction of intrinsic structural information turns out to be a compelling but challenging need. This article provides a comprehensive review on the revolutionary strategies toward the electron microscopic imaging of beam-sensitive materials and associated materials science discoveries, based on the principles of electron-matter interaction and mechanisms of electron beam damage. Finally, perspectives and future trends in this field are put forward.

Functional Group Mapping by Electron Beam Vibrational Spectroscopy from Nanoscale Volumes

Vibrational spectroscopies directly record details of bonding in materials, but spatially resolved methods have been limited to surface techniques for mapping functional groups at the nanoscale. Electron energy loss spectroscopy (EELS) in the scanning transmission electron microscope presents a route to functional group analysis from nanoscale volumes using transmitted subnanometer electron probes. Here, we now use vibrational EELS to map distinct carboxylate and imidazolate linkers in a metal-organic framework (MOF) crystal-glass composite material. Domains <100 nm in size are observed using vibrational EELS, with recorded spatial resolution <15 nm at interfaces in the composite. This nanoscale functional group mapping is confirmed by correlated EELS at core ionization edges as well as X-ray energy dispersive spectroscopy for elemental mapping of the metal centers of the two constituent MOFs. These results present a complete nanoscale analysis of the building blocks of the MOF composite and establish spatially resolved functional group analysis using electron beam spectroscopy for crystalline and amorphous organic and metal-organic solids.

Efficient and Versatile Model for Vibrational STEM-EELS

We introduce a novel method for the simulation of the impact scattering in vibrational scanning transmission electron microscopy electron energy loss spectroscopy simulations. The phonon-loss process is modeled by a combination of molecular dynamics and elastic multislice calculations within a modified frozen phonon approximation. The key idea is thereby to use a so-called δ thermostat in the classical molecular dynamics simulation to generate frequency dependent configurations of the vibrating specimen's atomic structure. The method includes correlated motion of atoms and provides vibrational spectrum images at a cost comparable to standard frozen phonon calculations. We demonstrate good agreement of our method with simulations and experiments for a 15 nm flake of hexagonal boron nitride.

Polarization Selectivity in Vibrational Electron-Energy-Loss Spectroscopy

Orientation-dependent aloof-beam vibrational electron-energy-loss spectroscopy is carried out on uniaxial icosahedral B_{12}P_{2} submicron crystals. We demonstrate that the high sensitivity of the signal to the crystal orientation allows for an unambiguous determination of the symmetry of normal modes occurring at the Brillouin zone center of this anisotropic compound. The experimental results are assessed using first-principles quantum mechanical calculations (density functional theory) of the dielectric response of the specimen. The high spatial resolution inherent to this technique when implemented in the transmission electron microscope thus opens the door to nanoscale orientation-dependent vibrational spectroscopy.

Emerging Electron Microscopy Techniques for Probing Functional Interfaces in Energy Materials

Interfaces play a fundamental role in many areas of chemistry. However, their localized nature requires characterization techniques with high spatial resolution in order to fully understand their structure and properties. State-of-the-art atomic resolution or in situ scanning transmission electron microscopy and electron energy-loss spectroscopy are indispensable tools for characterizing the local structure and chemistry of materials with single-atom resolution, but they are not able to measure many properties that dictate function, such as vibrational modes or charge transfer, and are limited to room-temperature samples containing no liquids. Here, we outline emerging electron microscopy techniques that are allowing these limitations to be overcome and highlight several recent studies that were enabled by these techniques. We then provide a vision for how these techniques can be paired with each other and with in situ methods to deliver new insights into the static and dynamic behavior of functional interfaces.

Unexpected Strong Thermally Induced Phonon Energy Shift for Mapping Local Temperature

Measuring temperature in nanoscale is crucial for the research and development of microelectronic devices. Plasmon resonance has been utilized to map local temperature gradient in metallic materials (Al) due to their large coefficients of thermal expansion. However, most semiconductors (including Si and SiC) possess much smaller coefficients of thermal expansion due to their strong covalent bonding in crystal structure, for which the plasmon-based temperature measurement becomes unreliable. Here, we report an unexpected strong, thermally induced phonon energy shift in SiC by spatially resolved vibrational spectroscopy in transmission electron microscopy with in situ heating, demonstrating that this shift can be applied as a useful tool for measuring nanoscale temperature. When a bulk phonon spectrum is used, the spatial resolution of vibrational spectroscopy can be as high as one nanometer. Molecular dynamics simulations reveal that lattice expansion only contributes a small fraction of phonon energy shift and that vibrant motions away from the bonds are predominate factors. This study gains deeper insight into the understanding of dynamic behaviors of the phonon and provides a new avenue to measure local temperature in nanodevices.

Identification of site-specific isotopic labels by vibrational spectroscopy in the electron microscope

The identification of isotopic labels by conventional macroscopic techniques lacks spatial resolution and requires relatively large quantities of material for measurements. We recorded the vibrational spectra of an α amino acid, l-alanine, with damage-free “aloof” electron energy-loss spectroscopy in a scanning transmission electron microscope to directly resolve carbon-site–specific isotopic labels in real space with nanoscale spatial resolution. An isotopic red shift of 4.8 ± 0.4 milli–electron volts in C–O asymmetric stretching modes was observed for 13C-labeled l-alanine at the carboxylate carbon site, which was confirmed by macroscopic infrared spectroscopy and theoretical calculations. The accurate measurement of this shift opens the door to nondestructive, site-specific, spatially resolved identification of isotopically labeled molecules with the electron microscope.

Vibrational Spectroscopy of Water with High Spatial Resolution

The ability to examine the vibrational spectra of liquids with nanometer spatial resolution will greatly expand the potential to study liquids and liquid interfaces. In fact, the fundamental properties of water, including complexities in its phase diagram, electrochemistry, and bonding due to nanoscale confinement are current research topics. For any liquid, direct investigation of ordered liquid structures, interfacial double layers, and adsorbed species at liquid-solid interfaces are of interest. Here, a novel way of characterizing the vibrational properties of liquid water with high spatial resolution using transmission electron microscopy is reported. By encapsulating water between two sheets of boron nitride, the ability to capture vibrational spectra to quantify the structure of the liquid, its interaction with the liquid-cell surfaces, and the ability to identify isotopes including H2 O and D2 O using electron energy-loss spectroscopy is demonstrated. The electron microscope used here, equipped with a high-energy-resolution monochromator, is able to record vibrational spectra of liquids and molecules and is sensitive to surface and bulk morphological properties both at the nano- and micrometer scales. These results represent an important milestone for liquid and isotope-labeled materials characterization with high spatial resolution, combining nanoscale imaging with vibrational spectroscopy.

Nanoscale Probing of Local Hydrogen Heterogeneity in Disordered Carbon Nitrides with Vibrational Electron Energy-Loss Spectroscopy

In graphitic carbon nitrides, (photo)catalytic functionality is underpinned by the effect that residual hydrogen content, manifesting in amine (N-H _x) defects, has on its optoelectronic properties. Therefore, a detailed understanding of the variation in the local structure of graphitic carbon nitrides is key for understanding structure-activity relationships. Here, we apply aloof-beam vibrational electron energy-loss spectroscopy in the scanning transmission electron microscope (STEM) to locally detect variations in hydrogen content in two different layered carbon nitrides with nanometer resolution. Through low dose rate TEM, we obtain atomically resolved images from crystalline and disordered carbon nitrides. By employing an aloof-beam configuration in a monochromated STEM, radiation damage can be dramatically reduced, yielding vibrational spectra from carbon nitrides to be assessed on 10's of nanometer length scales. We find that in disordered graphitic carbon nitrides the relative amine content can vary locally up to 27%. Cyano (C≡N) defects originating from uncondensed precursor are also revealed by probing small volumes, which cannot be detected by infrared absorption or Raman scattering spectroscopies. The utility of this technique is realized for heterogeneous soft materials, such as disordered graphitic carbon nitrides, in which methods to probe catalytically active sites remain elusive.

Surface-Enhanced Molecular Electron Energy Loss Spectroscopy

Electron energy loss spectroscopy (EELS) in a scanning transmission electron microscope (STEM) is becoming an important technique in spatially resolved spectral characterization of optical and vibrational properties of matter at the nanoscale. EELS has played a significant role in understanding localized polaritonic excitations in nanoantennas and also allows for studying molecular excitations in nanoconfined samples. Here we theoretically describe the interaction of a localized electron beam with molecule-covered polaritonic nanoantennas, and propose the concept of surface-enhanced molecular EELS exploiting the electromagnetic coupling between the nanoantenna and the molecular sample. Particularly, we study plasmonic and infrared phononic antennas covered by molecular layers, exhibiting either an excitonic or vibrational response. We demonstrate that EEL spectra of these molecule-antenna coupled systems exhibit Fano-like or strong coupling features, similar to the ones observed in far-field optical and infrared spectroscopy. EELS offers the advantage to acquire spectral information with nanoscale spatial resolution, and importantly, to control the antenna-molecule coupling on demand. Considering ongoing instrumental developments, EELS in STEM shows the potential to become a powerful tool for fundamental studies of molecules that are naturally or intentionally located on nanostructures supporting localized plasmon or phonon polaritons. Surface-enhanced EELS might also enable STEM-EELS applications such as remote- and thus damage-free-sensing of the excitonic and vibrational response of molecules, quantum dots, or 2D materials.

Exploring the capabilities of monochromated electron energy loss spectroscopy in the infrared regime

Monochromated electron energy loss spectroscopy (EELS) is one of the leading techniques to study materials properties that correspond to low (<5 eV) energy losses (i.e. band-gaps, plasmons, and excitons) with nanoscale spatial resolution. Recently a new generation of monochromators have become available, opening regimes and unlocking excitations that were previously unobservable in the electron microscope. The capabilities of these new instruments are still being explored, and here we study the effect of monochromation on various aspects of EELS analysis in the infrared (<1 eV) regime. We investigate the effect of varying levels of monochromation on energy resolution, zero-loss peak (ZLP) tail reduction, ZLP tail shape, signal-to-noise-ratio, and spatial resolution. From these experiments, the new capabilities of monochromated EELS are shown to be highly promising for the future of localized spectroscopic analysis.