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We measure the two-dimensional elastic modulus $E^\text{2D}$ of atomically clean defect-engineered graphene with a known defect distribution and density in correlated ultra-high vacuum experiments. The vacancies are introduced via low-energy (< 200 eV) Ar ion irradiation and the atomic structure is obtained via semi-autonomous scanning transmission electron microscopy and image analysis. Based on atomic force microscopy nanoindentation measurements, a decrease of $E^\text{2D}$ from 286 to 158 N/m is observed when measuring the same graphene membrane before and after an ion irradiation-induced vacancy density of $1.0\times 10^{13}$ cm$^{-2}$. This decrease is significantly greater than what is predicted by most theoretical studies and in stark contrast to some measurements presented in the literature. With the assistance of atomistic simulations, we show that this softening is mostly due to corrugations caused by local strain at vacancies with two or more missing atoms, while the influence of single vacancies is negligible. We further demonstrate that the opposite effect can be measured when surface contamination is not removed before defect engineering, Comment: 16 pages, 10 figures

Density functional theory with linear combination of atomic orbitals (LCAO) basis sets is useful for studying large atomic systems, especially when it comes to computationally highly demanding time-dependent dynamics. We have implemented the Ehrenfest molecular dynamics (ED) method with the approximate approach of Tomfohr and Sankey within the projector augmented-wave code GPAW. We apply this method to small molecules as well as larger periodic systems, and elucidate its limits, advantages, and disadvantages in comparison to the existing implementation of Ehrenfest dynamics with a real-space grid representation. For modest atomic velocities, LCAO-ED shows satisfactory accuracy at a much reduced computational cost. This method will be particularly useful for modeling ion irradiation processes that require large amounts of vacuum in the simulation cell.

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

We review the GPAW open-source Python package for electronic structure calculations. GPAW is based on the projector-augmented wave method and can solve the self-consistent density functional theory (DFT) equations using three different wave-function representations, namely real-space grids, plane waves, and numerical atomic orbitals. The three representations are complementary and mutually independent and can be connected by transformations via the real-space grid. This multi-basis feature renders GPAW highly versatile and unique among similar codes. By virtue of its modular structure, the GPAW code constitutes an ideal platform for implementation of new features and methodologies. Moreover, it is well integrated with the Atomic Simulation Environment (ASE) providing a flexible and dynamic user interface. In addition to ground-state DFT calculations, GPAW supports many-body GW band structures, optical excitations from the Bethe-Salpeter Equation (BSE), variational calculations of excited states in molecules and solids via direct optimization, and real-time propagation of the Kohn-Sham equations within time-dependent DFT. A range of more advanced methods to describe magnetic excitations and non-collinear magnetism in solids are also now available. In addition, GPAW can calculate non-linear optical tensors of solids, charged crystal point defects, and much more. Recently, support of GPU acceleration has been achieved with minor modifications of the GPAW code thanks to the CuPy library. We end the review with an outlook describing some future plans for GPAW.

Bound states in the continuum (BICs) garnered significant for their potential to create new types of nanophotonic devices. Most prior demonstrations were based on arrays of dielectric resonators, which cannot be miniaturized beyond the diffraction limit, reducing the applicability of BICs for advanced functions. Here, we demonstrate BICs and quasi-BICs based on high-quality factor phonon-polariton resonances in isotopically pure h11BN and how these states can be supported by periodic arrays of nanoresonators with sizes much smaller than the wavelength. We theoretically illustrate how BICs emerge from the band structure of the arrays and verify both numerically and experimentally the presence of these states and enhanced quality factor. Furthermore, we identify and characterize simultaneously quasi-BICs and bright states. Our method can be generalized to create a large number of optical states and to tune their coupling with the environment, paving the way to miniaturized nanophotonic devices with more advanced functions., Comment: 13 pages, 5 figures, early version

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

Charge transfer between atoms is fundamental to chemical bonding but has remained very challenging to detect directly in real space. Atomic-resolution imaging of charge density is not sufficient by itself, as the change in the density due to bonding is very subtle compared to the total local charge density. Sufficiently high sensitivity, precision and accuracy are required, which we demonstrate here for the detection of charge transfer at defects in two-dimensional WS\textsubscript{2} via high-speed electron ptychography and its ability to correct errors due to residual lens aberrations.

Cobalt carbonate hydroxide (CCH) is a pseudocapacitive material with remarkably high capacitance and cycle stability. Previously, it was reported that CCH pseudocapacitive materials are orthorhombic in nature. Recent structural characterization has revealed that they are hexagonal in nature; however, their H positions still remain unclear. In this work, we carried out first-principles simulations to identify the H positions. Through the simulations, we could consider various fundamental deprotonation reactions inside the crystal and computationally evaluate the electromotive forces (EMF) of the deprotonation ($V_\mathrm{dp}$). Compared with the experimental potential window of the reaction ($< 0.6$ V (vs. saturated calomel electrode (SCE))), the computed $V_\mathrm{dp}$ (vs. SCE) value ($3.05$ V) was beyond the potential window, indicating that deprotonation never occurred inside the crystal. This may be attributed to the strongly formed hydrogen-bonds (H-bonds) in the crystal, thereby leading to the structural stabilization. We further investigated the crystal anisotropy in an actual capacitive material by considering the growth mechanism of the CCH crystal. By associating our X-ray diffraction (XRD) peak simulations with experimental structural analysis, we found that the H-bonds formed between CCH $\{(\bar{1}\bar{1}\bar{1}), (2\bar{1}\bar{1}), (2\bar{1}1)\}$ planes (approximately parallel to $ab$-plane) can result in 1-D growth (stacked along with $c$-axis).

The rapid development of metasurfaces - 2D ensembles of engineered nanostructures - is presently fostering a steady drive towards the miniaturization of many optical functionalities and devices to a subwavelength size. The material platforms for optical metasurfaces are rapidly expanding and for the past few years, we are seeing a surge in establishing meta-optical elements from high-index, highly transparent materials with strong nonlinear and electro-optic properties. Crystalline lithium niobate (LN), a prime material of choice in integrated photonics, has shown great promise for future meta-optical components, thanks to its large electro-optical coefficient, second-order nonlinear response and broad transparency window ranging from the visible to the mid-infrared. Recent advances in nanofabrication technology have indeed marked a new milestone in the miniaturization of LN platforms, hence enabling the first demonstrations of LN-based metasurfaces. These seminal works set the first steppingstone towards the realization of ultra-flat monolithic nonlinear light sources with emission ranging from the visible to the infrared, efficient sources of correlated photon pairs, as well as electro-optical devices. Here, we review these recent advances, discussing potential perspectives for applications in light conversion and modulation shaping as well as quantum optics, with a critical eye on the potential setbacks and limitations of this emerging field., Comment: 45 Pages, 6 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)

Doping of the graphene lattice with transition metal atoms resulting in high magnetic anisotropy energy (MAE) is an important goal of materials research owing to its potential application in spintronics. In this article, by using spin-polarized density functional theory including spin-orbit coupling, we examined magnetic properties of graphene with vacancy defects, both bare and nitrogen-decorated, and doped by Cr, Mn and Fe transition metal single atom (TM-SA) and two different TM atoms simultaneously. [...] The computational findings are supplemented by an atomic-resolution characterization of an incidental Mn impurity bonded to four carbon atoms, whose localized spin matches expectations as measured using core-level electron energy-loss spectroscopy. Conducting TM-doped graphene with robust magnetic features offers prospects for the design of graphene-based spintronic devices., Comment: 31 + 61 pages, 5 + 81 figures

We present a quantitatively accurate machine-learning (ML) model for the computational prediction of core-electron binding energies, from which x-ray photoelectron spectroscopy (XPS) spectra can be readily obtained. Our model combines density functional theory (DFT) with $GW$ and uses kernel ridge regression for the ML predictions. We apply the new approach to materials and molecules containing carbon, hydrogen and oxygen, and obtain qualitative and quantitative agreement with experiment, resolving spectral features within 0.1 eV of reference experimental spectra. The method only requires the user to provide a structural model for the material under study to obtain an XPS prediction within seconds. Our new tool is freely available online through the XPS Prediction Server.

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

The precise positioning of dopant atoms within bulk crystal lattices could enable novel applications in areas including solid-state sensing and quantum computation. Established scanning probe techniques are capable tools for the manipulation of surface atoms, but at a disadvantage due to their need to bring a physical tip into contact with the sample. This has prompted interest in electron-beam techniques, followed by the first proof-of-principle experiment of bismuth dopant manipulation in crystalline silicon. Here, we use first principles modeling to discover a novel indirect exchange mechanism that allows electron impacts to non-destructively move dopants with atomic precision within the silicon lattice. However, this mechanism only works for the two heaviest group V donors with split-vacancy configurations, Bi and Sb. We verify our model by directly imaging these configurations for Bi, and by demonstrating that the promising nuclear spin qubit Sb can be manipulated using a focused electron beam., Comment: 23 pages, 4 figures, 1 table

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

Van der Waals materials composed of stacks of individual atomic layers have attracted considerable attention due to their exotic electronic properties that can be altered by, for example, manipulating the twist angle of bilayer materials or the stacking sequence of trilayer materials. To fully understand and control the unique properties of these few-layer materials, a technique that can provide information about their local in-plane structural deformations, twist direction, and out-of-plane structure is needed. In principle, interference in overlap regions of Bragg disks originating from separate layers of a material encodes three-dimensional information about the relative positions of atoms in the corresponding layers. Here, we describe an interferometric four-dimensional scanning transmission electron microscopy technique that utilizes this phenomenon to extract precise structural information from few-layer materials with nm-scale resolution. We demonstrate how this technique enables measurement of local pm-scale in-plane lattice distortions as well as twist direction and average interlayer spacings in bilayer and trilayer graphene, and therefore provides a means to better understand the interplay between electronic properties and precise structural arrangements of few-layer 2D materials.

A continuous CO2 vapor-fed electrochemical cell prototype that performs CO2R with high faradaic efficiency for desired carbon products for up to 72 hours of operation is presented. The cell design facilitates a flow through configuration, capitalizing on gas diffusion electrode (GDE) and membrane electrode architecture (MEA) without requiring a catholyte. We demonstrate stable performance and design adaptability by incorporating various CO2R catalysts and membranes into the cell, investigating lifetime performance and selectivity under established experimental conditions. With an Ag foil and PPO anion exchange membrane, the design achieves an average current density of -30mA/cm2 and FE ~80% for CO obtained over a 12-hour duration. With a Cu-based catalyst, FE ~40% selectivity for ethylene was achieved. The unique geometry and flexibility of the cell provides an adaptive and dynamic GDE electrochemical cell framework, easing future research for novel electro-catalysts on GDE electrodes and MEA/GDE assemblies for enhanced (photo)electrochemical carbon dioxide reduction.

The simulation of transmission electron microscopy (TEM) images or diffraction patterns is often required to interpret their contrast and extract specimen features. This is especially true for high-resolution phase-contrast imaging of materials, but electron scattering simulations based on atomistic models are widely used in materials science and structural biology. Since electron scattering is dominated by the nuclear cores, the scattering potential is typically described by the widely applied independent atom model. This approximation is fast and fairly accurate, especially for scanning TEM (STEM) annular dark-field contrast, but it completely neglects valence bonding and its effect on the transmitting electrons. However, an emerging trend in electron microscopy is to use new instrumentation and methods to extract the maximum amount of information from each electron. This is evident in the increasing popularity of techniques such as 4D-STEM combined with ptychography in materials science, and cryogenic microcrystal electron diffraction in structural biology, where subtle differences in the scattering potential may be both measurable and contain additional insights. Thus, there is increasing interest in electron scattering simulations based on electrostatic potentials obtained from first principles, mainly via density functional theory, which was previously mainly required for holography. In this Review, we discuss the motivation and basis for these developments, survey the pioneering work that has been published thus far, and give our outlook for the future. We argue that a physically better justified $\textit{ab initio}$ description of the scattering potential is both useful and viable for an increasing number of systems, and we expect such simulations to steadily gain in popularity and importance., Comment: 41 pages, 5 figures, 3 tables, 137 references

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.

LiNiO2 has high energy density but easily reacts with moisture in the atmosphere and deteriorates. We performed qualitative and quantitative evaluations of the degraded phase of LiNiO2 and the influence of the structural change on the electrochemical properties of the phase. Li1-xHxNiO2 phase with cation exchange between Li+ and H+ was confirmed by thermogravimetric analysis and Karl Fischer titration measurement. As the H concentration in LiNiO2 increased, the rate capability deteriorated, especially in the low-temperature range and under low state of charge. Experimental and density functional theory (DFT) calculation results suggested that this outcome was due to increased activation energy of Li+ diffusion owing to cation exchange. Rietveld analysis of X-ray diffraction and DFT calculation confirmed that the c lattice parameter and Li-O layer reduced because of the Li+/H+ cation exchange. These results indicate that LiNiO2 modified in the atmosphere has a narrowed Li-O layer, which is the Li diffusion path, and the rate characteristics are degraded., Comment: 8 pages, 11 figures

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

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

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

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

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

We demonstrate here that the gold nanoparticles (AuNPs) obtained in micellar solutions are susceptible to the precursor complex nature and specific counterion effects controlling the reaction kinetics, particles size and shape. The tested approach consisted in reducing the HAuCl4 complex with ascorbic acid or citric acid in dodecyltrimethylammonium (DTA) solutions, at 318 K, in the presence of bromide (Br), methanesulfonate (Ms), trifluoroacetate (TFA) or trifluoromethanesulfonate (Tf) ions. Bromide ions replaced the chloride ions in the precursor gold complex, and no nanoparticle formation could be observed in DTA-Br media, in the absence of seeds. In contrast, scanning electron microscopy images and atomic force microscopy measurements showed that quasi-spherical AuNPs were formed in DTA-Ms and DTA-TFA solutions, while flat disk-like or triangular AuNPs were obtained in DTA-Tf solutions, with no need of adding seeds in all such cases. The results indicated that the reduction of the precursor gold complex takes place at the micellar interface and that the specific counterion effects should be taken into account for controlling nanoparticles formation in micellar media.

In this work, phosphorous-doped single-walled carbon nanotubes have been synthesized by the thermal decomposition of trimethylphosphine using a high-vacuum chemical vapor deposition method. Furthermore, a modified density-gradient-ultracentrifugation process has been applied to carefully purify our doped material. The combined use of Raman and X-ray photoelectron spectroscopy allowed us to provide the first insight into the bonding environment of P incorporated into the carbon lattice, avoiding competing signals arising from synthesis byproducts. This study represents the first step toward the identification of the bonding configuration of P atoms when direct substitution takes place., Comment: 7 pages, 3 figures

X-ray photoelectron spectroscopy (XPS) combined with first principles modeling is a powerful tool for determining the chemical composition and electronic structure of novel materials. Of these, graphene is an especially important model system for understanding the properties of other carbon nanomaterials. Here, we calculate the carbon 1$\textit{s}$ core level binding energy of pristine graphene using two methods based on density functional theory total energy differences: a calculation with an explicit core-hole ($\Delta$KS), and a novel all-electron extension of the delta self-consistent field ($\Delta$SCF) method. We study systematically their convergence and computational workload, and the dependence of the energies on the chosen exchange-correlation functional. The $\mathrm{\Delta}$SCF method is computationally more expensive, but gives consistently higher C 1$\textit{s}$ binding energies. Although there is a significant functional dependence, the binding energy calculated using the PBE functional is found to be remarkably close to what has been measured for graphite., Comment: 5 pages, 3 figures, 2 tables

We have investigated coupling constants in elementary electron-phonon scattering processes on a graphite surface by the combined use of high-resolution electron-energy-loss spectroscopy (HREELS) and very low-energy electron diffraction (VLEED). HREELS is used to measure the modulations of electron transition probabilities from incoming electrons in vacuum to outgoing electrons in vacuum where the transition includes one-phonon scattering processes inside a solid. Determining the electronic band structures of graphite with VLEED, we defined electronic states of the solid surface that electrons entered before and after scattering off phonons. Thus, we observed that the measured electron transition probabilities significantly depended on whether the electrons were in a bulk Bloch state or an evanescent state before scattering off the phonons. This result clearly indicates that the measured electron transition probabilities reflect the strength of the coupling constants in the solid., Comment: 4 pages, 4 figures