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Phosphorene, a puckered two-dimensional allotrope of phosphorus, has sparked considerable interest in recent years due to its potential especially for optoelectronic applications with its layer-number-dependant direct band gap and strongly bound excitons. However, detailed experimental characterization of its intrinsic defects as well as its defect creation characteristics under electron irradiation are scarce. Here, we report on the creation and stability of a variety of defect configurations under 60 kV electron irradiation in mono- and bilayer phosphorene including the first experimental reports of stable adatom-vacancy-complexes. Displacement cross section measurements in bilayer phosphorene yield a value of 7.7 +- 1.4 barn with an estimated lifetime of adatom-vacancy-complexes of 19.9 +- 0.7 s, while some are stable for up to 68 s under continuous electron irradiation. Surprisingly, ab initio-based simulations indicate that the complexes should readily recombine, even in structures strained by up to 3 %. The presented results will help to improve the understanding of the wide variety of defects in phosphorene, their creation, and their stability, which may enable new pathways for defect engineered phosphorene devices., Comment: 11 pages, 7 figures

Monolayer hexagonal boron nitride (hBN) has recently become the focus of intense research as a material to host quantum emitters. Although it is well known that such emission is associated with point defects, so far no conclusive correlation between the spectra and specific defects has been demonstrated. Here, we prepare atomically clean suspended hBN samples and subject them to low-energy ion irradiation. The samples are characterized before and after irradiation via automated scanning transmission electron microscopy imaging to assess the defect concentrations and distributions. We find an intrinsic defect concentration of ca. 0.03/nm2 (with ca. 55% boron and 8% nitrogen single vacancies, 20% double vacancies and 16% more complex vacancy structures). To be able to differentiate between these and irradiation-induced defects, we create a significantly higher (but still moderate) concentration of defects with the ions (0.30/nm2), and now find ca. 55% boron and 12% nitrogen single vacancies, 14% double vacancies, and 18% more complex vacancy structures. The results demonstrate that already the simplest irradiation provides selectivity for the defect types, and open the way for future experiments to explore changing the selectivity by modifying the irradiation parameters., Comment: 7 pages, 4 figures

Control of water ice formation on surfaces is of key technological and economic importance, but the fundamental understanding of ice nucleation and growth mechanisms and the design of surfaces for controlling water freezing behaviour remain incomplete. Graphene is a two-dimensional (2D) material that has been extensively studied for its peculiar wetting properties with liquid water incl. a heavily debated wetting transparency. Furthermore, graphene is the parent structure of soot particles that are heavily implicated as nuclei in atmospheric ice formation and consequently graphene is often used as a model surface for computational ice nucleation studies. Despite this, to date experimental reports on ice formation on scalable graphene films remain missing. Towards filling this gap, we here report on the water freezing behaviour on scalably grown chemical vapour deposited (CVD) graphene films on application-relevant polycrystalline copper (Cu). We find that as-grown CVD graphene on Cu can be (as we term it) freezing transparent i.e. the graphene presence does not change the freezing temperature curves of liquid water to solid ice on Cu in our measurements. Such freezing transparency has to date not been considered. We also show that chemical functionalization of the graphene films can result in controllable changes to the freezing behaviour to lower/higher temperatures and that also the observed freezing transparency can be lifted via functionalization. Our work thereby introduces the concept of freezing transparency of graphene on a metal support and also introduces scalable CVD graphene/Cu as an ultimately thin platform towards control of ice nucleation behaviour on a technologically highly relevant metal.

Van der Waals atomic solids of noble gases on metals at cryogenic temperatures were the first experimental examples of two-dimensional systems. Recently such structures have also been created on surfaces under encapsulation by graphene, allowing studies at elevated temperatures through scanning tunneling microscopy. However, for this technique, the encapsulation layer often obscures the actual arrangement of the noble gas atoms. Here, we create Kr and Xe clusters in between two suspended graphene layers, and uncover their atomic structure through direct imaging with transmission electron microscopy. We show that small crystals (N<9) arrange as expected based on the simple non-directional van der Waals interaction. Crystals larger than this show some deviations for the outermost atoms, possibly enabled by deformations in the encapsulating graphene lattice. We further discuss the dynamics of the clusters within the graphene sandwich, and show that while all Xe clusters with up to N~100 remain solid, Kr clusters with already N~16 turn occasionally fluid under our experimental conditions with an estimated pressure of ca. 0.3 GPa. This study opens a way for the so-far unexplored frontier of encapsulated two-dimensional van der Waals solids with exciting possibilities for fundamental condensed matter physics research and possible applications in quantum information technology., Comment: 31 pages, 14 figures, including the supplement

Understanding electron irradiation effects is vital not only for reliable transmission electron microscopy characterization, but increasingly also for the controlled manipulation of two-dimensional materials. The displacement cross sections of monolayer hBN are measured using aberration-corrected scanning transmission electron microscopy in near ultra-high vacuum at primary beam energies between 50 and 90 keV. Damage rates below 80 keV are up to three orders of magnitude lower than previously measured at edges under poorer residual vacuum conditions where chemical etching appears to have been dominant. Notably, is possible to create single vacancies in hBN using electron irradiation, with boron almost twice as likely as nitrogen to be ejected below 80 keV. Moreover, any damage at such low energies cannot be explained by elastic knock-on, even when accounting for vibrations of the atoms. A theoretical description is developed to account for lowering of the displacement threshold due to valence ionization resulting from inelastic scattering of probe electrons, modelled using charge-constrained density functional theory molecular dynamics. Although significant reductions are found depending on the constrained charge, quantitative predictions for realistic ionization states are currently not possible. Nonetheless, there is potential for defect-engineering of hBN at the level of single vacancies using electron irradiation., Comment: 38 pages, 15 figures

Electron irradiation-induced damage is often the limiting factor in imaging materials prone to ionization or electronic excitations due to inelastic electron scattering. Quantifying the related processes at the atomic scale has only become possible with the advent of aberration-corrected (scanning) transmission electron microscopes and two-dimensional materials that allow imaging each lattice atom. While it has been shown for graphene that pure knock-on damage arising from elastic scattering is sufficient to describe the observed damage, the situation is more complicated with two-dimensional semiconducting materials such as MoS2. Here, we measure the displacement cross section for sulfur atoms in MoS2 with primary beam energies between 55 and 90 keV, and correlate the results with existing measurements and theoretical models. Our experimental data suggests that the displacement process can occur from the ground state, or with single or multiple excitations, all caused by the same impinging electron. The results bring light to reports in the recent literature, and add necessary experimental data for a comprehensive description of electron irradiation damage in a two-dimensional semiconducting material. Specifically, the results agree with a combined inelastic and elastic damage mechanism at intermediate energies, in addition to a pure elastic mechanism that dominates above 80 keV. When the inelastic contribution is assumed to arise through impact ionization, the associated excitation lifetime is on the order of picoseconds, on par with expected excitation lifetimes in MoS2, whereas it drops to some tens of femtoseconds when direct valence excitation is considered., Comment: 19 pages, 4 figures, 1 table

Some of the materials are more affected by oxidation than others. To elucidate the oxidation-induced degradation mechanisms in transition metal chalcogenides, the chemical effects in single layer MoS$_2$ and MoTe$_2$ were studied in situ in an electron microscope under controlled low-pressure oxygen environments at room temperature.Oxidation is the main cause of degradation of many two-dimensional materials, including transition metal dichalcogenides, under ambient conditions. MoTe$_2$ is found to be reactive to oxygen, leading to significant degradation above a pressure of 1$\times 10^{-7}$ torr. Curiously, the common hydrocarbon contamination found on practically all surfaces accelerates the damage rate significantly, by up to a factor of forty. In contrast to MoTe$_2$, MoS$_2$ is found to be inert under oxygen environment, with all observed structural changes being caused by electron irradiation only, leading to well-defined pores with high proportion of molybdenum nanowire-terminated edges. Using density functional theory calculations, a further atomic-scale mechanism leading to the observed oxygen-related degradation in MoTe$_2$ is proposed and the role of the carbon in the etching is explored. Together, the results provide an important insight into the oxygen-related deterioration of two-dimensional materials under ambient conditions relevant in many fields., Comment: 17 pages, 9 figures and 3 tables

Poor quality interfaces between metal and graphene cause non-linearity and impair the carrier mobility in graphene devices. Here, we use aberration corrected scanning transmission electron microscopy to observe hexagonally close-packed Ti nano-islands grown on atomically clean graphene, and establish a 30{\deg} epitaxial relationship between the lattices. Due to the strong binding of Ti on graphene, at the limit of a monolayer, the Ti lattice constant is mediated by the graphene epitaxy, and compared to bulk Ti, is strained by ca. 3.7% to a value of 0.306(3) nm. The resulting interfacial strain is slightly greater than what has been predicted by density functional theory calculations. Our early growth stage investigations also reveal that, in contrast to widespread assumptions, Ti does not fully wet graphene but grows initially in clusters with a thickness of 1-2 layers. Raman spectroscopy implies charge transfer between the Ti islands and graphene substrate., Comment: 11 pages, 5 figures

Although surface diffusion is critical for many physical and chemical processes, including the epitaxial growth of crystals and heterogeneous catalysis, it is particularly challenging to directly study. Here, we estimate the carbon adatom migration barrier on freestanding monolayer graphene by quantifying its temperature-dependent electron knock-on damage. Due to the fast healing of vacancies by diffusing adatoms, the damage rate decreases with increasing temperature. By analyzing the observed damage rates at 300-1073 K using a model describing our finite scanning probe, we find a barrier of (0.33 \pm 0.03) eV., Comment: 6 pages, 3 figures. Additionally, some supplemental material has been uploaded: 1 PDF, 1 Jupyter Notebook, 1 Python module, 3 data files in tabular form)

Elastic knock-on is the main electron irradiation damage mechanism in metals including graphene. Atomic vibrations influence its cross-section, but only the out-of-plane direction has been considered so far in the literature. Here, we present a full three-dimensional theory of knock-on damage including the effect of temperature and vibrations to describe ejection into arbitrary directions. We thus establish a general quantitative description of electron irradiation effects through elastic scattering. Applying our methodology to in-plane jumps of pyridinic nitrogen atoms, we show their observed rates imply much stronger inelastic effects than in pristine graphene., Comment: 5 pages, 2 figures, 1 table (+ supplement)

Heterostructures composed of two-dimensional (2D) materials are already opening many new possibilities in such fields of technology as electronics and magnonics, but far more could be achieved if the number and diversity of 2D materials is increased. So far, only a few dozen 2D crystals have been extracted from materials that exhibit a layered phase in ambient conditions, omitting entirely the large number of layered materials that may exist in other temperatures and pressures. Here, we demonstrate how these structures can be stabilized in 2D van der Waals stacks under room temperature via growing them directly in graphene encapsulation by using graphene oxide as the template material. Specifically, we produce an ambient stable 2D structure of copper and iodine, a material that normally only occurs in layered form at elevated temperatures between 645 and 675 K. Our results establish a route to the production of more exotic phases of materials that would otherwise be difficult or impossible to stabilize for experiments in ambient., Comment: 15 pages, 6 figures, separate supplementary material included

A boost in the development of flexible and wearable electronics facilitates the design of new materials to be applied as transparent conducting films (TCFs). Although single-walled carbon nanotube (SWCNT) films are the most promising candidates for flexible TCFs, they still do not meet optoelectronic requirements demanded their successful industrial integration. In this study, we proposed and thoroughly investigated a new approach that comprises simultaneous bilateral (outer and inner surfaces) SWCNT doping after their opening by thermal treatment at 400 C under an ambient air atmosphere. Doping by a chloroauric acid (HAuCl$_{4}$) ethanol solution allowed us to achieve the record value of sheet resistance of 31 $\pm$ 4 $\Omega$/sq at a transmittance of 90% in the middle of visible spectra (550 nm). The strong p-doping was examined by open-circuit potential (OCP) measurements and confirmed by ab initio calculations demonstrating a downshift of Fermi level around 1 eV for the case of bilateral doping.

Transmission electron microscopy (TEM) and scanning TEM (STEM) are indispensable tools for materials characterization. However, during a typical (S)TEM experiment, the sample is subject to a number of effects that can change its atomic structure. Of these, perhaps the least discussed are chemical modifications due to the non-ideal vacuum around the sample. With single-layer graphene, we show that even at relatively low pressures typical for many instruments, these processes can have a significant impact on the sample structure. For example, pore growth becomes up to two orders of magnitude faster at a pressure of ca. 10^{-6} mbar as compared to ultra-high vacuum (UHV; 10^{-10} mbar). Even more remarkably,the presence of oxygen at the sample also changes the observed atomic structure: When imaged in UHV, nearly 90% of the identifiable graphene edge configurations have the armchair structure, whereas armchair and zigzag structures are nearly equally likely to occur when the oxygen partial pressure in the column is higher. Our results both bring attention to the role of the often neglected vacuum composition of the microscope column, and show that control over it can allow atomic-scale tailoring of the specimen structure., Comment: 33 pages, including the supplement, 9 figures

Single atoms and few-atom nanoclusters are of high interest in catalysis and plasmonics, but pathways for their fabrication and stable placement remain scarce. We report here the self-assembly of room-temperature-stable single indium (In) atoms and few-atom In clusters (2-6 atoms) that are anchored to substitutional silicon (Si) impurity atoms in suspended monolayer graphene membranes. Using atomically resolved scanning transmission electron microscopy (STEM), we find that the exact atomic arrangements of the In atoms depend strongly on the original coordination of the Si anchors in the graphene lattice: Single In atoms and In clusters with 3-fold symmetry readily form on 3-fold coordinated Si atoms, whereas 4-fold symmetric clusters are found attached to 4-fold coordinated Si atoms. All structures are produced by our fabrication route without the requirement for electron-beam induced materials modification. In turn, when activated by electron beam irradiation in the STEM, we observe in situ the formation, restructuring and translation dynamics of the Si-anchored In structures: Hexagon-centered 4-fold symmetric In clusters can (reversibly) transform into In chains or In dimers, whereas C-centered 3-fold symmetric In clusters can move along the zig-zag direction of the graphene lattice due to the migration of Si atoms during electron-beam irradiation, or transform to Si-anchored single In atoms. Our results provide a novel framework for the controlled self-assembly and heteroatomic anchoring of single atoms and few-atom clusters on graphene.

Important recent advances in transmission electron microscopy instrumentation and capabilities have made it indispensable for atomic-scale materials characterization. At the same time, the availability of two-dimensional materials has provided ideal samples where each atom or vacancy can be resolved. Recent studies have also revealed new possibilities for a different application of focused electron irradiation: the controlled manipulation of structures and even individual atoms. Evaluating the full range of future possibilities for this method requires a precise physical understanding of the interactions of electrons with energies as low as 15 keV now used in (scanning) transmission electron microscopy, becoming feasible due to advances both in experimental techniques and in theoretical models. We summarize the state of current knowledge of the underlying physical processes based on the latest results on two-dimensional materials, with a focus on the physical principles of the electron-matter interaction, rather than the material-specific irradiation-induced defects it causes., Comment: 18 pages, 2 boxes, 2 figures, 1 table

Growth of two-dimensional metals has eluded materials scientists since the discovery of the atomically thin graphene and other covalently bound 2D materials. Here, we report a two-atom-thick hexagonal copper-gold alloy, grown through thermal evaporation on freestanding graphene and hexagonal boron nitride. The structures are imaged at atomic resolution with scanning transmission electron microscopy and further characterized with spectroscopic techniques. Electron irradiation in the microscope provides sufficient energy for a phase transformation of the 2D structure--atoms are released from their lattice sites with the gold atoms eventually forming face-centered cubic nanoclusters on top of 2D regions during observation. The presence of copper in the alloy enhances sticking of gold to the substrate, which has clear implications for creating atomically thin electrodes for applications utilizing 2D materials. Its practically infinite surface-to-bulk ratio also makes the 2D CuAu particularly interesting for catalysis applications., Comment: 24 pages, including 4 figures in main text and 6 in the supplementary information

Porous single layer molybdenum disulfide (MoS$_2$) is a promising material for applications such as DNA sequencing and water desalination. In this work, we introduce irradiation with highly charged ions (HCIs) as a new technique to fabricate well-defined pores in MoS$_2$. Surprisingly, we find a linear increase of the pore creation efficiency over a broad range of potential energies. Comparison to atomistic simulations reveals the critical role of energy deposition from the ion to the material through electronic excitation in the defect creation process, and suggests an enrichment in molybdenum in the vicinity of the pore edges at least for ions with low potential energies. Analysis of the irradiated samples with atomic resolution scanning transmission electron microscopy reveals a clear dependence of the pore size on the potential energy of the projectiles, establishing irradiation with highly charged ions as an effective method to create pores with narrow size distributions and radii between ca. 0.3 and 3 nm., Comment: 22 pages, 4 figures

Graphene and carbon nanotubes (CNTs) share the same atomic structure of hexagonal carbon lattice. Yet, their synthesis differs in many aspects, including the shape and size of the catalyst. Here, we demonstrate a floating-catalyst chemical vapor deposition (FCCVD) technique for substrate-free, single-step growth of CNT-graphene heterostructures (CNT-G-H) using ethylene as a carbon source. The formation of CNT-G-H is directly evidenced by lattice-resolved (scanning) transmission electron microscopy (STEM) and electron diffraction experiments, corroborated by atomic force microscopy (AFM). Our experiments show the relative number density of graphene-nanoflakes can be tuned by optimizing the synthesis conditions. Since in the applied process the formation of the structures take place in gas-suspension, the as-synthesized CNT-G-H films can be deposited on any surface in ambient temperature with an arbitrary thickness. Moreover, this process of CNT-G-H synthesis with strong universality has also been realized in multiple systems of ethylene-based FCCVD with various catalysts and set-ups.

We report the first observation of substitutional silicon atoms in single-layer hexagonal boron nitride (h-BN) using aberration corrected scanning transmission electron microscopy (STEM). The medium angle annular dark field (MAADF) images reveal silicon atoms exclusively filling boron vacancies. This structure is stable enough under electron beam for repeated imaging. Density functional theory (DFT) is used to study the energetics, structure and properties of the experimentally observed structure. The formation energies of all possible charge states of the different silicon substitutions (Si$_\mathrm{B}$, Si$_\mathrm{N}$ and Si$_\mathrm{{BN}}$) are calculated. The results reveal Si$_\mathrm{B}^{+1}$ as the most stable substitutional configuration. In this case, silicon atom elevates by 0.66{\AA} out of the lattice with unoccupied defect levels in the electronic band gap above the Fermi level. The formation energy shows a slightly exothermic process. Our results unequivocally show that heteroatoms can be incorporated into the h-BN lattice opening way for applications ranging from single-atom catalysis to atomically precise magnetic structures.

Transparent and conductive films (TCFs) are of great technological importance. The high transmittance, electrical conductivity and mechanical strength make single-walled carbon nanotubes (SWCNTs) a good candidate for their raw material. Despite the ballistic transport in individual SWCNTs, however, the electrical conductivity of their networks is limited by low efficiency of charge tunneling between the tube elements. Here, we demonstrate that the nanotube network sheet resistance at high optical transmittance is decreased by more than 50% when fabricated on graphene and thus provides a comparable improvement as widely adopted gold chloride ($\mathrm{AuCl_3}$) doping. However, while Raman spectroscopy reveals substantial changes in spectral features of doped nanotubes, no similar effect is observed in presence of graphene. Instead, temperature dependent transport measurements indicate that graphene substrate reduces the tunneling barrier heights while its parallel conductivity contribution is almost negligible. Finally, we show that combining the graphene substrate and $\mathrm{AuCl_3}$ doping, the SWCNT thin films can exhibit sheet resistance as low as 36 $\Omega$/sq. at 90% transmittance., Comment: 21 pages, 6 figures

The recent discovery that impurity atoms in crystals can be manipulated with focused electron irradiation has opened novel perspectives for top-down atomic engineering. These achievements have been enabled by advances in electron optics and microscope stability, but also in the preparation of suitable materials with impurity elements incorporated via ion and electron-beam irradiation or chemical means. Here it is shown that silicon heteroatoms introduced via plasma irradiation into the lattice of single-walled carbon nanotubes (SWCNTs) can be manipulated using a focused 55-60 keV electron probe aimed at neighboring carbon sites. Moving the silicon atom mainly along the longitudinal axis of large 2.7 nm diameter tubes, more than 90 controlled lattice jumps were recorded and the relevant displacement cross sections estimated. Molecular dynamics simulations show that even in 2 nm SWCNTs the threshold energies for out-of-plane dynamics are different than in graphene, and depend on the orientation of the silicon-carbon bond with respect to the electron beam as well as the local bonding of the displaced carbon atom and its neighbors. Atomic-level engineering of SWCNTs where the electron wave functions are more strictly confined than in two-dimensional materials may enable the fabrication of tunable electronic resonators and other devices., Comment: 15 pages, 4 figures

The properties of single-walled carbon nanotubes (SWCNTs) and graphene can be modified by the presence of covalently bound impurities. Although this can be achieved by introducing chemical additives during synthesis, that often hinders growth and leads to limited crystallite size and quality. Here, through the simultaneous formation of vacancies with low-energy argon plasma and the thermal activation of adatom diffusion by laser irradiation, silicon impurities are incorporated into the lattice of both materials. After an exposure of $\sim$1 ion/nm$^{2}$, we find Si substitution densities of 0.15 nm$^{-2}$ in graphene and 0.05 nm$^{-2}$ in nanotubes, as revealed by atomically resolved scanning transmission electron microscopy. In good agreement with predictions of Ar irradiation effects in SWCNTs, we find Si incorporated in both mono- and divacancies, with $\sim$2/3 being of the first type. Controlled inclusion of impurities in the quasi-1D and 2D carbon lattices may prove useful for applications such as gas sensing, and a similar approach might also be used to substitute other elements with migration barriers lower than that of carbon., Comment: 5 Pages, 5 Figures, 1 Table

Transmission electron microscopy (TEM) is carried out in vacuum to minimize the interaction of the imaging electrons with gas molecules while passing through the microscope column. Nevertheless, in typical devices, the pressure remains at 10^-7 mbar or above, providing a large number of gas molecules for the electron beam to crack, which can lead to structural changes in the sample. Here, we describe experiments carried out in a modified scanning TEM (STEM) instrument, based on the Nion UltraSTEM 100. In this instrument, the base pressure at the sample is around 2x10^-10 mbar, and can be varied up to 10^-6 mbar through introduction of gases directly into the objective area while maintaining atomic resolution imaging conditions. We show that air leaked into the microscope column during the experiment is efficient in cleaning graphene samples from contamination, but ineffective in damaging the pristine lattice. Our experiments also show that exposure to O2 and H2O lead to a similar result, oxygen providing an etching effect nearly twice as efficient as water, presumably due to the two O atoms per molecule. H2 and N2 environments have no influence on etching. These results show that the residual gas environment in typical TEM instruments can have a large influence on the observations, and show that chemical etching of carbon-based structures can be effectively carried out with oxygen., Comment: 15 pages, 7 figure

The atomic structure of nanomaterials is often studied using transmission electron microscopy. In addition to image formation, the energetic electrons may also cause damage while impinging on the sample. In a good conductor such as graphene the damage is limited to the knock-on process caused by elastic electron-nucleus collisions. This process is determined by the kinetic energy an atom needs to be sputtered, ie, its displacement threshold energy. This is typically assumed to have a fixed value for all electron impacts on equivalent atoms within a crystal. Here we show using density functional tight-binding simulations that the displacement threshold energy is affected by the thermal perturbation of the atoms from their equilibrium positions. We show that this can be accounted for in the estimation of the displacement cross section by replacing the constant threshold value with a distribution. The improved model better describes previous precision measurements of graphene knock-on damage, and should be considered also for other low-dimensional materials., Comment: 10 pages, 6 figures

We directly visualize the three-dimensional (3D) geometry and dynamics of silicon impurities in graphene as well as their dynamics by aberration-corrected scanning transmission electron microscopy. By acquiring images when the sample is tilted, we show that an asymmetry of the atomic position of the heteroatom in the projection reveals the non-planarity of the structure. From a sequence of images, we further demonstrate that the Si atom switches between up- and down- configurations with respect to the graphene plane, with an asymmetric cross-section. We further analyze the 3D structure and dynamics of a silicon tetramer in graphene. Our results clarify the out-of-plane structure of impurities in graphene by direct experimental observation and open a new route to study their dynamics in three dimensions.

X-ray photoelectron spectroscopy of graphene is important both for its characterization and as a model for other carbon materials. Despite great recent interest, the intrinsic photoemission of its single layer has not been unambiguously measured, nor is the layer-dependence in free-standing multilayers accurately determined. We combine scanning transmission electron microscopy and Raman spectroscopy with synchrotron-based scanning photoelectron microscopy to characterize the same areas of suspended graphene samples down to the atomic level. This allows us to assign spectral signals to regions of precisely known layer number and purity. The core level binding energy of the monolayer is measured at 284.70 eV, thus 0.28 eV higher than that of graphite, with intermediate values found for few layers. This trend is reproduced by density functional theory with or without explicit van der Waals interactions, indicating that intralayer charge rearrangement dominates, but in our model of static screening the magnitudes of the shifts are underestimated by half., Comment: 5 pages, 4 figures, 1 table

We demonstrate insights into the three-dimensional structure of defects in graphene, in particular grain boundaries, obtained via a new approach from two transmission electron microscopy images recorded at different angles. The structure is obtained through an optimization process where both the atomic positions as well as the simulated imaging parameters are iteratively changed until the best possible match to the experimental images is found. We first demonstrate that this method works using an embedded defect in graphene that allows direct comparison to the computationally predicted three-dimensional shape. We then applied the method to a set of grain boundary structures with misorientation angles nearly spanning the whole available range (2.6-29.8{\deg}). The measured height variations at the boundaries reveal a strong correlation with the misorientation angle with lower angles resulting in stronger corrugation and larger kink angles. Our results allow for the first time a direct comparison with theoretical predictions for the corrugation at grain boundaries and we show that the measured kink angles are significantly smaller than the largest predicted ones., Comment: submitted

Electron microscopy is a powerful tool for studying the properties of materials down to their atomic structure. In many cases, the quantitative interpretation of images requires simulations based on atomistic structure models. These typically use the independent atom approximation that neglects bonding effects, which may, however, be measurable and of physical interest. Since all electrons and the nuclear cores contribute to the scattering potential, simulations that go beyond this approximation have relied on computationally highly demanding all-electron calculations. Here, we describe a new method to generate ab initio electrostatic potentials when describing the core electrons by projector functions. Combined with an interface to quantitative image simulations, this implementation enables an easy and fast means to model electron microscopy images. We compare simulated transmission electron microscopy images and diffraction patterns to experimental data, showing an accuracy equivalent to earlier all-electron calculations at a much lower computational cost., Comment: 10 pages, 5 figures, 2 tables

Atomic-level structural changes in materials are important but challenging to study. Here, we demonstrate the dynamics and the possibility of manipulating a phosphorus dopant atom in graphene using scanning transmission electron microscopy (STEM). The mechanisms of various processes are explored and compared with those of other dopant species by first-principles calculations. This work paves the way for designing a more precise and optimized protocol for atomic engineering.

Incorporating heteroatoms into the graphene lattice may be used to tailor its electronic, mechanical and chemical properties. Direct substitutions have thus far been limited to incidental Si impurities and P, N and B dopants introduced using low-energy ion implantation. We present here the heaviest impurity to date, namely $^{74}$Ge$^+$ ions implanted into monolayer graphene. Although sample contamination remains an issue, atomic resolution scanning transmission electron microscopy imaging and quantitative image simulations show that Ge can either directly substitute single atoms, bonding to three carbon neighbors in a buckled out-of-plane configuration, or occupy an in-plane position in a divacancy. First principles molecular dynamics provides further atomistic insight into the implantation process, revealing a strong chemical effect that enables implantation below the graphene displacement threshold energy. Our results show that heavy atoms can be implanted into the graphene lattice, pointing a way towards advanced applications such as single-atom catalysis with graphene as the template., Comment: 20 pages, 5 figures

Studying the atomic structure of intrinsic defects in two-dimensional transition metal dichalcogenides is difficult since they damage quickly under the intense electron irradiation in transmission electron microscopy (TEM). However, this can also lead to insights into the creation of defects and their atom-scale dynamics. We first show that MoTe 2 monolayers without protection indeed quickly degrade during scanning TEM (STEM) imaging, and discuss the observed atomic-level dynamics, including a transformation from the 1H phase into 1T', three-fold rotationally symmetric defects, and the migration of line defects between two 1H grains with a 60{\deg} misorientation. We then analyze the atomic structure of MoTe2 encapsulated between two graphene sheets to mitigate damage, finding the as-prepared material to contain an unexpectedly large concentration of defects. These include similar point defects (or quantum dots, QDs) as those created in the non-encapsulated material, and two different types of line defects (or quantum wires, QWs) that can be transformed from one to the other under electron irradiation. Our density functional theory simulations indicate that the QDs and QWs embedded in MoTe2 introduce new midgap states into the semiconducting material, and may thus be used to control its electronic and optical properties. Finally, the edge of the encapsulated material appears amorphous, possibly due to the pressure caused by the encapsulation., Comment: 33 pages, including 7 figures in manuscript and 9 figures in the supplementary information

The direct manipulation of individual atoms in materials using scanning probe microscopy has been a seminal achievement of nanotechnology. Recent advances in imaging resolution and sample stability have made scanning transmission electron microscopy a promising alternative for single-atom manipulation of covalently bound materials. Pioneering experiments using an atomically focused electron beam have demonstrated the directed movement of silicon atoms over a handful of sites within the graphene lattice. Here, we achieve a much greater degree of control, allowing us to precisely move silicon impurities along an extended path, circulating a single hexagon, or back and forth between the two graphene sublattices. Even with manual operation, our manipulation rate is already comparable to the state-of-the-art in any atomically precise technique. We further explore the influence of electron energy on the manipulation rate, supported by improved theoretical modeling taking into account the vibrations of atoms near the impurities, and implement feedback to detect manipulation events in real time. In addition to atomic-level engineering of its structure and properties, graphene also provides an excellent platform for refining the accuracy of quantitative models and for the development of automated manipulation., Comment: 5 figures, 4 supporting figures

Silicon represents a common intrinsic impurity in graphene, commonly bonding to either three or four carbon neighbors respectively in a single or double carbon vacancy. We investigate the effect of the latter defect (Si-C$_4$) on the structural and electronic properties of graphene using density functional theory (DFT). Calculations based both on molecular models and with periodic boundary conditions have been performed. The two-carbon vacancy was constructed from pyrene (pyrene-2C) which was then expanded to circumpyrene-2C. The structural characterization of these cases revealed that the ground state is slightly non-planar, with the bonding carbons displaced from the plane by up to $\pm$0.2 {\AA}. This non-planar structure was confirmed by embedding the defect into a 10$\times$8 supercell of graphene, resulting in 0.22 eV lower energy than the previously considered planar structure. Natural bond orbital (NBO) analysis showed sp$^3$ hybridization at the silicon atom for the non-planar structure and sp$^2$d hybridization for the planar structure. Atomically resolved electron energy loss spectroscopy (EELS) and corresponding spectrum simulations provide a mixed picture: a flat structure provides a slightly better overall spectrum match, but a small observed pre-peak is only present in the corrugated simulation. Considering the small energy barrier between the two equivalent corrugated conformations, both structures could plausibly exist as a superposition over the experimental timescale of seconds., Comment: 6 figures, 4 tables, supplementary information

Despite decades of research, the ultimate goal of nanotechnology--top-down manipulation of individual atoms--has been directly achieved with only one technique: scanning probe microscopy. In this Review, we demonstrate that scanning transmission electron microscopy (STEM) is emerging as an alternative method for the direct assembly of nanostructures, with possible applications in plasmonics, quantum technologies, and materials science. Atomically precise manipulation with STEM relies on recent advances in instrumentation that have enabled non-destructive atomic-resolution imaging at lower electron energies. While momentum transfer from highly energetic electrons often leads to atom ejection, interesting dynamics can be induced when the transferable kinetic energies are comparable to bond strengths in the material. Operating in this regime, very recent experiments have revealed the potential for single-atom manipulation using the Angstrom-sized electron beam. To truly enable control, however, it is vital to understand the relevant atomic-scale phenomena through accurate dynamical simulations. Although excellent agreement between experiment and theory for the specific case of atomic displacements from graphene has been recently achieved using density functional theory molecular dynamics, in many other cases quantitative accuracy remains a challenge. We provide a comprehensive reanalysis of available experimental data on beam-driven dynamics in light of the state-of-the-art in simulations, and identify important targets for improvement. Overall, the modern electron microscope has great potential to become an atom-scale fabrication platform, especially for covalently bonded 2D nanostructures. We review the developments that have made this possible, argue that graphene is an ideal starting material, and assess the main challenges moving forward., Comment: Perspective article, 12 pages with 4 figures and 1 table

Two-dimensional (2D) materials have considerably expanded the field of materials science in the last decade. Even more recently, various 2D materials have been assembled into vertical van der Waals heterostacks, and it has been proposed to combine them with other low- dimensional structures to create new materials with hybridized properties. Here, we demonstrate the first direct images of a suspended 0D/2D heterostructure incorporating $C_{60}$ molecules between two graphene layers in a buckyball sandwich structure. We find clean and ordered $C_{60}$ islands with thicknesses down to one molecule, shielded by the graphene layers from the microscope vacuum and partially protected from radiation damage during scanning transmission electron microscopy imaging. The sandwich structure serves as a 2D nanoscale reaction chamber allowing the analysis of the structure of the molecules and their dynamics at atomic resolution.

Recent experiments have revealed the possibility of precise electron beam manipulation of silicon impurities in graphene. Motivated by these findings and studies on metal surface quantum corrals, the question arises what kind of embedded Si structures are possible within the hexagonal lattice, and how these are limited by the distortion caused by the preference of Si for $sp^{3}$ hybridization. In this work, we study the geometry and stability of elementary Si patterns in graphene, including lines, hexagons, triangles, circles and squares. Due to the size of the required unit cells, to obtain the relaxed geometries we use an empirical bond-order potential as a starting point for density functional theory. Despite some interesting discrepancies, the classical geometries provide an effective route for the simulation of large structures., Comment: 6 pages, 5 figures

Surface impurities and contamination often seriously degrade the properties of two-dimensional materials such as graphene. To remove contamination, thermal annealing is commonly used. We present a comparative analysis of annealing treatments in air and in vacuum, both ex situ and "pre-situ", where an ultra-high vacuum treatment chamber is directly connected to an aberration-corrected scanning transmission electron microscope. While ex situ treatments do remove contamination, it is challenging to obtain atomically clean surfaces after ambient transfer. However, pre-situ cleaning with radiative or laser heating appears reliable and well suited to clean graphene without undue damage to its structure., Comment: 5 pages, 4 figures

While an increasing number of two-dimensional (2D) materials, including graphene and silicene, have already been realized, others have only been predicted. An interesting example is the two-dimensional form of silicon carbide (2D-SiC). Here, we present an observation of atomically thin and hexagonally bonded nanosized grains of SiC assembling temporarily in graphene oxide pores during an atomic resolution scanning transmission electron microscopy experiment. Even though these small grains do not fully represent the bulk crystal, simulations indicate that their electronic structure already approaches that of 2D-SiC. This is predicted to be flat, but some doubts have remained regarding the preference of Si for sp$^{3}$ hybridization. Exploring a number of corrugated morphologies, we find completely flat 2D-SiC to have the lowest energy. We further compute its phonon dispersion, with a Raman-active transverse optical mode, and estimate the core level binding energies. Finally, we study the chemical reactivity of 2D-SiC, suggesting it is like silicene unstable against molecular absorption or interlayer linking. Nonetheless, it can form stable van der Waals-bonded bilayers with either graphene or hexagonal boron nitride, promising to further enrich the family of two-dimensional materials once bulk synthesis is achieved., Comment: 10 pages, 5 figures, 4 supplementary figures

Molybdenum disulfide (MoS2) is a particularly interesting member of the family of two-dimensional (2D) materials due to its semiconducting and tunable electronic properties. Currently, the most reliable method for obtaining high-quality industrial scale amounts of 2D materials is chemical vapor deposition (CVD), which results in polycrystalline samples. As grain boundaries (GBs) are intrinsic defect lines within CVD-grown 2D materials, their atomic structure is of paramount importance. Here, through atomic-scale analysis of micrometer-long GBs, we show that covalently bound boundaries in 2D MoS2 tend to be decorated by nanopores. Such boundaries occur when differently oriented MoS2 grains merge during growth, whereas the overlap of grains leads to boundaries with bilayer areas. Our results suggest that the nanopore formation is related to stress release in areas with a high concentration of dislocation cores at the grain boundaries, and that the interlayer interaction leads to intrinsic rippling at the overlap regions. This provides insights for the controlled fabrication of large-scale MoS 2 samples with desired structural properties for applications., Comment: 26 pages, including supplementary material

One of the keys behind the success of the modern semiconductor technology has been the ion implantation of silicon, which allows its electronic properties to be tailored. For similar purposes, heteroatoms have been introduced into carbon nanomaterials both during growth and using post-growth methods. However, due to the nature of the samples, it has been challenging to determine whether the heteroatoms have been incorporated into the lattice as intended, with direct observations so far being limited to N and B dopants, and incidental Si impurities. Furthermore, ion implantation of these materials is more challenging due to the requirement of very low ion energies and atomically clean surfaces. Here, we provide the first atomic-resolution imaging and electron energy loss spectroscopy (EELS) evidence of phosphorus atoms incorporated into the graphene lattice by low-energy ion irradiation. The measured P L-edge response of an single-atom EELS spectrum map shows excellent agreement with an ab initio spectrum simulation, conclusively identifying the P in a buckled substitutional configuration. Our results demonstrate the viability of phosphorus as a lattice dopant in $sp^2$-bonded carbon structures and provide its unmistakeable fingerprint for further studies., Comment: 15 pages, 5 figures

The {\AA}ngstr\"om-sized probe of the scanning transmission electron microscope can visualize and collect spectra from single atoms. This can unambiguously resolve the chemical structure of materials, but not their isotopic composition. Here we differentiate between two isotopes of the same element by quantifying how likely the energetic imaging electrons are to eject atoms. First, we measure the displacement probability in graphene grown from either $^{12}$C or $^{13}$C and describe the process using a quantum mechanical model of lattice vibrations coupled with density functional theory simulations. We then test our spatial resolution in a mixed sample by ejecting individual atoms from nanoscale areas spanning an interface region that is far from atomically sharp, mapping the isotope concentration with a precision better than 20%. Although we use a scanning instrument, our method should be applicable to any atomic resolution transmission electron microscope and to other low-dimensional materials., Comment: 35 pages, 6 figures, 1 table

Layered two-dimensional (2D) materials display great potential for a range of applications, particularly in electronics. We report the large-scale synthesis of thin films of platinum diselenide (PtSe2), a thus far scarcely investigated transition metal dichalcogenide. Importantly, the synthesis by thermal assisted conversion is performed at 400 {\deg}C, representing a breakthrough for the direct integration of this novel material with silicon (Si) technology. Besides the thorough characterization of this new 2D material, we demonstrate its promise for applications in high-performance gas sensing with extremely short response and recovery times observed due to the 2D nature of the films. Furthermore, we realized vertically-stacked heterostructures of PtSe2 on Si which act as both photodiodes and photovoltaic cells. Thus this study establishes PtSe2 as a potential candidate for next-generation sensors and (opto-)electronic devices, using fabrication protocols compatible with established Si technologies.

Matter-wave interferometry has become an essential tool in studies on the foundations of quantum physics and for precision measurements. Mechanical gratings have played an important role as coherent beamsplitters for atoms, molecules and clusters since the basic diffraction mechanism is the same for all particles. However, polarizable objects may experience van der Waals shifts when they pass the grating walls and the undesired dephasing may prevent interferometry with massive objects. Here we explore how to minimize this perturbation by reducing the thickness of the diffraction mask to its ultimate physical limit, i.e. the thickness of a single atom. We have fabricated diffraction masks in single-layer and bilayer graphene as well as in 1 nm thin carbonaceous biphenyl membrane. We identify conditions to transform an array of single layer graphene nanoribbons into a grating of carbon nanoscrolls. We show that all these ultra-thin nanomasks can be used for high-contrast quantum diffraction of massive molecules. They can be seen as a nanomechanical answer to the question debated by Bohr and Einstein whether a softly suspended double slit would destroy quantum interference. In agreement with Bohr's reasoning we show that quantum coherence prevails even in the limit of atomically thin gratings., Comment: 10 pages, 7 figures