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.

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

Vibrational spectroscopy in the scanning transmission electron microscope (STEM) was introduced two years ago [1, 2], and it has made much progress since. It has opened a new window on the world of materials, in which nothing is quite like it was before. The main vibrational modes occur at energies of 0‐500 meV, and exploring them requires a monochromated STEM‐EELS system with an energy resolution The energy of vibrational modes is given by ΔE = ħ √(k/m) , where k is the force constant of the atomic bond and m the effective mass of the vibrating nucleus. Strongly bonded light atoms give the highest vibrational energies, starting with hydrogen, an element that is nearly invisible in traditional electron microscopy. Fig. 1(a) shows a vibrational spectrum of Ca(OH) 2 [3], in which the peak at 452 meV is due to O‐H stretch, and Fig. 1(b) shows the particle from which the spectrum was recorded. Fig. 1(c) shows how the strength of the vibrational peak varied with the distance from the particle: the signal decayed only gradually outside the particle, and was still 50% strong 35 nm away. Fig. 2 shows an EEL spectrum of guanine compared to an IR spectrum from the same specimen [4]. The agreement between the two types of spectra is very good. EELS has worse energy resolution (~10 meV), but much better spatial resolution than regular IR. As is typical of vibrational spectroscopies, the different peaks can be assigned to different types of bonds and vibration modes (see the inset in Fig. 1). In order to minimize radiation damage, both the OH and guanine spectra were acquired in an “aloof” mode, with the electron beam parked just outside the sample [1, 3‐5]. Aloof spectroscopy makes it possible to select the maximum energy of the beam‐sample interaction, simply by adjusting the beam‐sample distance [4,5]. Its great import to vibrational EELS is that the vibrational signal can be excited even when the interaction energy is limited so that ionization damage of the sample cannot occur. It may even be possible to spatially map the vibrational features of a beam‐sensitive sample by “coarse step (leapfrog) scanning”: scanning with a discrete pixel increment of 10‐100 nm, so that even though the area that the beam traverses in each new position is essentially destroyed, large parts of the sample are not touched by the beam and remain in a pristine state [6].

In this work we demonstrate that a free-standing van der Waals heterostructure, usually regarded as a flat object, can exhibit an intrinsic buckled atomic structure resulting from the interaction between two layers with a small lattice mismatch. We studied a freely suspended membrane of well-aligned graphene on a hexagonal boron nitride (hBN) monolayer by transmission electron microscopy (TEM) and scanning TEM (STEM). We developed a detection method in the STEM that is capable of recording the direction of the scattered electron beam and that is extremely sensitive to the local stacking of atoms. A comparison between experimental data and simulated models shows that the heterostructure effectively bends in the out-of-plane direction, producing an undulated structure having a periodicity that matches the moiré wavelength. We attribute this rippling to the interlayer interaction and also show how this affects the intralayer strain in each layer.

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 damage to most suspended areas. Pre situ annealing of typical dirty graphene samples yields atomically clean areas several hundred nm2 in size.