Stop-Frame Filming and Discovery of Reactions at the Single-Molecule Level by Transmission Electron Microscopy.

We report an approach, named chemTEM, to follow chemical transformations at the single-molecule level with the electron beam of a transmission electron microscope (TEM) applied as both a tunable source of energy and a sub-angstrom imaging probe. Deposited on graphene, disk-shaped perchlorocoronene molecules are precluded from intermolecular interactions. This allows monomolecular transformations to be studied at the single-molecule level in real time and reveals chlorine elimination and reactive aryne formation as a key initial stage of multistep reactions initiated by the 80 keV e-beam. Under the same conditions, perchlorocoronene confined within a nanotube cavity, where the molecules are situated in very close proximity to each other, enables imaging of intermolecular reactions, starting with the Diels-Alder cycloaddition of a generated aryne, followed by rearrangement of the angular adduct to a planar polyaromatic structure and the formation of a perchlorinated zigzag nanoribbon of graphene as the final product. ChemTEM enables the entire process of polycondensation, including the formation of metastable intermediates, to be captured in a one-shot "movie". A molecule with a similar size and shape but with a different chemical composition, octathio[8]circulene, under the same conditions undergoes another type of polycondensation via thiyl biradical generation and subsequent reaction leading to polythiophene nanoribbons with irregular edges incorporating bridging sulfur atoms. Graphene or carbon nanotubes supporting the individual molecules during chemTEM studies ensure that the elastic interactions of the molecules with the e-beam are the dominant forces that initiate and drive the reactions we image. Our ab initio DFT calculations explicitly incorporating the e-beam in the theoretical model correlate with the chemTEM observations and give a mechanism for direct control not only of the type of the reaction but also of the reaction rate. Selection of the appropriate e-beam energy and control of the dose rate in chemTEM enabled imaging of reactions on a time frame commensurate with TEM image capture rates, revealing atomistic mechanisms of previously unknown processes.

Vibrational Properties of a Two-Dimensional Silica Kagome Lattice.

Kagome lattices are structures possessing fascinating magnetic and vibrational properties, but in spite of a large body of theoretical work, experimental realizations and investigations of their dynamics are scarce. Using a combination of Raman spectroscopy and density functional theory calculations, we study the vibrational properties of two-dimensional silica (2D-SiO2), which has a kagome lattice structure. We identify the signatures of crystalline and amorphous 2D-SiO2 structures in Raman spectra and show that, at finite temperatures, the stability of 2D-SiO2 lattice is strongly influenced by phonon-phonon interaction. Our results not only provide insights into the vibrational properties of 2D-SiO2 and kagome lattices in general but also suggest a quick nondestructive method to detect 2D-SiO2.

Electron beam controlled covalent attachment of small organic molecules to graphene.

The electron beam induced functionalization of graphene through the formation of covalent bonds between free radicals of polyaromatic molecules and C=C bonds of pristine graphene surface has been explored using first principles calculations and high-resolution transmission electron microscopy. We show that the energetically strongest attachment of the radicals occurs along the armchair direction in graphene to carbon atoms residing in different graphene sub-lattices. The radicals tend to assume vertical position on graphene substrate irrespective of direction of the bonding and the initial configuration. The "standing up" molecules, covalently anchored to graphene, exhibit two types of oscillatory motion--bending and twisting--caused by the presence of acoustic phonons in graphene and dispersion attraction to the substrate. The theoretically derived mechanisms are confirmed by near atomic resolution imaging of individual perchlorocoronene (C24Cl12) molecules on graphene. Our results facilitate the understanding of controlled functionalization of graphene employing electron irradiation as well as mechanisms of attachment of impurities via the processing of graphene nanoelectronic devices by electron beam lithography.

Bottom-up formation of robust gold carbide.

A new phenomenon of structural reorganization is discovered and characterized for a gold-carbon system by in-situ atomic-resolution imaging at temperatures up to 1300 K. Here, a graphene sheet serves in three ways, as a quasi transparent substrate for aberration-corrected high-resolution transmission electron microscopy, as an in-situ heater, and as carbon supplier. The sheet has been decorated with gold nanoislands beforehand. During electron irradiation at 80 kV and at elevated temperatures, the accumulation of gold atoms has been observed on defective graphene sites or edges as well as at the facets of gold nanocrystals. Both resulted in clustering, forming unusual crystalline structures. Their lattice parameters and surface termination differ significantly from standard gold nanocrystals. The experimental data, supported by electron energy loss spectroscopy and density-functional theory calculations, suggests that isolated gold and carbon atoms form - under conditions of heat and electron irradiation - a novel type of compound crystal, Au-C in zincblende structure. The novel material is metastable, but surprisingly robust, even under annealing condition.

Defects in bilayer silica and graphene: common trends in diverse hexagonal two-dimensional systems.

By combining first-principles and classical force field calculations with aberration-corrected high-resolution transmission electron microscopy experiments, we study the morphology and energetics of point and extended defects in hexagonal bilayer silica and make comparison to graphene, another two-dimensional (2D) system with hexagonal symmetry. We show that the motifs of isolated point defects in these 2D structures with otherwise very different properties are similar, and include Stone-Wales-type defects formed by structural unit rotations, flower defects and reconstructed double vacancies. The morphology and energetics of extended defects, such as grain boundaries have much in common as well. As both sp(2)-hybridised carbon and bilayer silica can also form amorphous structures, our results indicate that the morphology of imperfect 2D honeycomb lattices is largely governed by the underlying symmetry of the lattice.

Imaging atomic rearrangements in two-dimensional silica glass: watching silica's dance.

Structural rearrangements control a wide range of behavior in amorphous materials, and visualizing these atomic-scale rearrangements is critical for developing and refining models for how glasses bend, break, and melt. It is difficult, however, to directly image atomic motion in disordered solids. We demonstrate that using aberration-corrected transmission electron microscopy, we can excite and image atomic rearrangements in a two-dimensional silica glass-revealing a complex dance of elastic and plastic deformations, phase transitions, and their interplay. We identified the strain associated with individual ring rearrangements, observed the role of vacancies in shear deformation, and quantified fluctuations at a glass/liquid interface. These examples illustrate the wide-ranging and fundamental materials physics that can now be studied at atomic-resolution via transmission electron microscopy of two-dimensional glasses.

A universal scheme to convert aromatic molecular monolayers into functional carbon nanomembranes.

Free-standing nanomembranes with molecular or atomic thickness are currently explored for separation technologies, electronics, and sensing. Their engineering with well-defined structural and functional properties is a challenge for materials research. Here we present a broadly applicable scheme to create mechanically stable carbon nanomembranes (CNMs) with a thickness of ~0.5 to ~3 nm. Monolayers of polyaromatic molecules (oligophenyls, hexaphenylbenzene, and polycyclic aromatic hydrocarbons) were assembled and exposed to electrons that cross-link them into CNMs; subsequent pyrolysis converts the CNMs into graphene sheets. In this transformation the thickness, porosity, and surface functionality of the nanomembranes are determined by the monolayers, and structural and functional features are passed on from the molecules through their monolayers to the CNMs and finally on to the graphene. Our procedure is scalable to large areas and allows the engineering of ultrathin nanomembranes by controlling the composition and structure of precursor molecules and their monolayers.

Functional single-layer graphene sheets from aromatic monolayers.

Self-assembled monolayers of aromatic molecules on copper substrates can be converted into high-quality single-layer graphene using low-energy electron irradiation and subsequent annealing. This two-dimensional solid state transformation is characterized on the atomic scale and the physical and chemical properties of the formed graphene sheets are studied by complementary microscopic and spectroscopic techniques and by electrical transport measurements. As substrates, Cu(111) single crystals and the technologically relevant polycrystalline copper foils are successfully used.

Atomistic description of electron beam damage in nitrogen-doped graphene and single-walled carbon nanotubes.

By combining ab initio simulations with state-of-the-art electron microscopy and electron energy loss spectroscopy, we study the mechanism of electron beam damage in nitrogen-doped graphene and carbon nanotubes. Our results show that the incorporation of nitrogen atoms results in noticeable knock-on damage in these structures already at an acceleration voltage of 80 kV, at which essentially no damage is created in pristine structures at corresponding doses. Contrary to an early estimate predicting rapid destruction via sputtering of the nitrogen atoms, in the case of substitutional doping, damage is initiated by displacement of carbon atoms neighboring the nitrogen dopant, leading to the conversion of substitutional dopant sites into pyridinic ones. Although such events are relatively rare at 80 kV, they become significant at higher voltages typically used in electron energy loss spectroscopy studies. Correspondingly, we measured an energy loss spectrum time series at 100 kV that provides direct evidence for such conversions in nitrogen-doped single-walled carbon nanotubes, in excellent agreement with our theoretical prediction. Besides providing an improved understanding of the irradiation stability of these structures, we show that structural changes cannot be neglected in their characterization employing high-energy electrons.

Accurate measurement of electron beam induced displacement cross sections for single-layer graphene.

We present an accurate measurement and a quantitative analysis of electron-beam-induced displacements of carbon atoms in single-layer graphene. We directly measure the atomic displacement ("knock-on") cross section by counting the lost atoms as a function of the electron-beam energy and applied dose. Further, we separate knock-on damage (originating from the collision of the beam electrons with the nucleus of the target atom) from other radiation damage mechanisms (e.g., ionization damage or chemical etching) by the comparison of ordinary (12C) and heavy (13C) graphene. Our analysis shows that a static lattice approximation is not sufficient to describe knock-on damage in this material, while a very good agreement between calculated and experimental cross sections is obtained if lattice vibrations are taken into account.

Two-dimensional transition metal dichalcogenides under electron irradiation: defect production and doping.

Using first-principles atomistic simulations, we study the response of atomically thin layers of transition metal dichalcogenides (TMDs)--a new class of two-dimensional inorganic materials with unique electronic properties--to electron irradiation. We calculate displacement threshold energies for atoms in 21 different compounds and estimate the corresponding electron energies required to produce defects. For a representative structure of MoS2, we carry out high-resolution transmission electron microscopy experiments and validate our theoretical predictions via observations of vacancy formation under exposure to an 80 keV electron beam. We further show that TMDs can be doped by filling the vacancies created by the electron beam with impurity atoms. Thereby, our results not only shed light on the radiation response of a system with reduced dimensionality, but also suggest new ways for engineering the electronic structure of TMDs.

Atom-by-atom observation of grain boundary migration in graphene.

Grain boundary (GB) migration in polycrystalline solids is a materials science manifestation of survival of the fittest, with adjacent grains competing to add atoms to their outer surfaces at each other's expense. This process is thermodynamically favored when it lowers the total GB area in the sample, thereby reducing the excess free energy contributed by the boundaries. In this picture, a curved boundary is expected to migrate toward its center of curvature with a velocity proportional to the local radius of boundary curvature (R). Investigating the underlying mechanism of boundary migration in a 3D material, however, has been reserved for computer simulation or analytical theory, as capturing the dynamics of individual atoms in the core region of a GB is well beyond the spatial and temporal resolution limits of current characterization techniques. Here, we similarly overcome the conventional experimental limits by investigating a 2D material, polycrystalline graphene, in an aberration-corrected transmission electron microscope, exploiting the energy of the imaging electrons to stimulate individual bond rotations in the GB core region. The resulting morphological changes are followed in situ, atom-by-atom, revealing configurational fluctuations that take on a time-averaged preferential direction only in the presence of significant boundary curvature, as confirmed by Monte Carlo simulations. Remarkably, in the extreme case of a small graphene grain enclosed within a larger one, we follow its shrinkage to the point of complete disappearance.

Direct imaging of a two-dimensional silica glass on graphene.

Large-area graphene substrates provide a promising lab bench for synthesizing, manipulating, and characterizing low-dimensional materials, opening the door to high-resolution analyses of novel structures, such as two-dimensional (2D) glasses, that cannot be exfoliated and may not occur naturally. Here, we report the accidental discovery of a 2D silica glass supported on graphene. The 2D nature of this material enables the first atomic resolution transmission electron microscopy of a glass, producing images that strikingly resemble Zachariasen's original 1932 cartoon models of 2D continuous random network glasses. Atomic-resolution electron spectroscopy identifies the glass as SiO(2) formed from a bilayer of (SiO(4))(2-) tetrahedra and without detectable covalent bonding to the graphene. From these images, we directly obtain ring statistics and pair distribution functions that span short-, medium-, and long-range order. Ab initio calculations indicate that van der Waals interactions with graphene energetically stabilizes the 2D structure with respect to bulk SiO(2). These results demonstrate a new class of 2D glasses that can be applied in layered graphene devices and studied at the atomic scale.

Simulation of bonding effects in HRTEM images of light element materials.

The accuracy of multislice high-resolution transmission electron microscopy (HRTEM) simulation can be improved by calculating the scattering potential using density functional theory (DFT) [1-2]. This approach accounts for the fact that electrons in the specimen are redistributed according to their local chemical environment. This influences the scattering process and alters the absolute and relative contrast in the final image. For light element materials with well defined geometry, such as graphene and hexagonal boron nitride monolayers, the DFT based simulation scheme turned out to be necessary to prevent misinterpretation of weak signals, such as the identification of nitrogen substitutions in a graphene network. Furthermore, this implies that the HRTEM image does not only contain structural information (atom positions and atomic numbers). Instead, information on the electron charge distribution can be gained in addition.In order to produce meaningful results, the new input parameters need to be chosen carefully. Here we present details of the simulation process and discuss the influence of the main parameters on the final result. Furthermore we apply the simulation scheme to three model systems: A single atom boron and a single atom oxygen substitution in graphene and an oxygen adatom on graphene.

Transformations of carbon adsorbates on graphene substrates under extreme heat.

We describe new phenomena of structural reorganization of carbon adsorbates as revealed by in situ atomic-resolution transmission electron microscopy (TEM) performed on specimens at extreme temperatures. In our investigations, a graphene sheet serves as both a quasi-transparent substrate for TEM and as an in situ heater. The melting of gold nanoislands deposited on the substrate surface is used to evaluate the local temperature profile. At annealing temperatures around 1000 K, we observe the transformation of physisorbed hydrocarbon adsorbates into amorphous carbon monolayers and the initiation of crystallization. At temperatures exceeding 2000 K the transformation terminates in the formation of a completely polycrystalline graphene state. The resulting layers are bounded by free edges primarily in the armchair configuration.

Experimental analysis of charge redistribution due to chemical bonding by high-resolution transmission electron microscopy.

The electronic charge density distribution or the electrostatic atomic potential of a solid or molecule contains information not only on the atomic structure, but also on the electronic properties, such as the nature of the chemical bonds or the degree of ionization of atoms. However, the redistribution of charge due to chemical bonding is small compared with the total charge density, and therefore difficult to measure. Here, we demonstrate an experimental analysis of charge redistribution due to chemical bonding by means of high-resolution transmission electron microscopy (HRTEM). We analyse charge transfer on the single-atom level for nitrogen-substitution point defects in graphene, and confirm the ionicity of single-layer hexagonal boron nitride. Our combination of HRTEM experiments and first-principles electronic structure calculations opens a new way to investigate electronic configurations of point defects, other non-periodic arrangements or nanoscale objects that cannot be studied by an electron or X-ray diffraction analysis.

Atomic structure of reduced graphene oxide.

Using high resolution transmission electron microscopy, we identify the specific atomic scale features in chemically derived graphene monolayers that originate from the oxidation-reduction treatment of graphene. The layers are found to comprise defect-free graphene areas with sizes of a few nanometers interspersed with defect areas dominated by clustered pentagons and heptagons. Interestingly, all carbon atoms in these defective areas are bonded to three neighbors maintaining a planar sp(2)-configuration, which makes them undetectable by spectroscopic techniques. Furthermore, we observe that they introduce significant in-plane distortions and strain in the surrounding lattice.