Partial Dislocations in Graphene and Their Atomic Level Migration Dynamics

Role of Bilayer Graphene Microstructure on the Nucleation of WSe2 Overlayers

Over the past few years, graphene grown by chemical vapor deposition (CVD) has gained prominence as a template to grow transition metal dichalcogenide (TMD) overlayers. The resulting two-dimensional (2D) TMD/graphene vertical heterostructures are attractive for optoelectronic and energy applications. However, the effects of the microstructural heterogeneities of graphene grown by CVD on the growth of the TMD overlayers are relatively unknown. Here, we present a detailed investigation of how the stacking order and twist angle of CVD graphene influence the nucleation of WSe₂ triangular crystals. Through the combination of experiments and theory, we correlate the presence of interlayer dislocations in bilayer graphene with how WSe₂ nucleates, in agreement with the observation of a higher nucleation density of WSe₂ on top of Bernal-stacked bilayer graphene versus twisted bilayer graphene. Scanning/transmission electron microscopy (S/TEM) data show that interlayer dislocations are present only in Bernal-stacked bilayer graphene but not in twisted bilayer graphene. Atomistic ReaxFF reactive force field molecular dynamics simulations reveal that strain relaxation promotes the formation of these interlayer dislocations with localized buckling in Bernal-stacked bilayer graphene, whereas the strain becomes distributed in twisted bilayer graphene. Furthermore, these localized buckles in graphene are predicted to serve as thermodynamically favorable sites for binding WSe_x molecules, leading to the higher nucleation density of WSe₂ on Bernal-stacked graphene. Overall, this study explores synthesis-structure correlations in the WSe₂/graphene vertical heterostructure system toward the site-selective synthesis of TMDs by controlling the structural attributes of the graphene substrate.

Retrieving Grain Boundaries in 2D Materials

The coalescence of randomly distributed grains with different crystallographic orientations can result in pervasive grain boundaries (GBs) in 2D materials during their chemical synthesis. GBs not only are the inherent structural imperfection that causes influential impacts on structures and properties of 2D materials, but also have emerged as a platform for exploring unusual physics and functionalities stemming from dramatic changes in local atomic organization and even chemical makeup. Here, recent advances in studying the formation mechanism, atomic structures, and functional properties of GBs in a range of 2D materials are reviewed. By analyzing the growth mechanism and the competition between far-field strain and local chemical energies of dislocation cores, a complete understanding of the rich GB morphologies as well as their dependence on lattice misorientations and chemical compositions is presented. Mechanical, electronic, and chemical properties tied to GBs in different materials are then discussed, towards raising the concept of using GBs as a robust atomic-scale scaffold for realizing tailored functionalities, such as magnetism, luminescence, and catalysis. Finally, the future opportunities in retrieving GBs for making functional devices and the major challenges in the controlled formation of GB structures for designed applications are commented.

Aberration-corrected transmission electron microscopy of a non-graphitizing carbon

Non-graphitizing carbons (NGCs) are an important class of solid carbons which cannot be converted into graphite by high-temperature heat treatment. They include commercially valuable materials such as activated carbon and glassy carbon. These carbons have been intensively studied for decades, but there is still no agreement about their detailed atomic structure, or the reasons for their resistance to graphitization. The first models for graphitizing and NGCs were proposed by Rosalind Franklin in the early 1950s, and while these are broadly correct, they are incomplete. Many alternative models of NGCs have been put forward since Franklin's time, but none has received universal acceptance. Diffraction and spectroscopic techniques can provide important insights into the nature of these carbons, but only direct microscopic imaging can reveal their true atomic structure. Here, we apply aberration-corrected transmission electron microscopy to an activated carbon prepared from waste biomass and present evidence for the presence of pentagonal and heptagonal carbon rings. This provides support for a model of the structure of NGC made up of curved fragments in which non-hexagonal rings are dispersed randomly throughout hexagonal networks.

Exploring order parameters and dynamic processes in disordered systems via variational autoencoders

We suggest and implement an approach for the bottom-up description of systems undergoing large-scale structural changes and chemical transformations from dynamic atomically resolved imaging data, where only partial or uncertain data on atomic positions are available. This approach is predicated on the synergy of two concepts, the parsimony of physical descriptors and general rotational invariance of noncrystalline solids, and is implemented using a rotationally invariant extension of the variational autoencoder applied to semantically segmented atom-resolved data seeking the most effective reduced representation for the system that still contains the maximum amount of original information. This approach allowed us to explore the dynamic evolution of electron beam-induced processes in a silicon-doped graphene system, but it can be also applied for a much broader range of atomic scale and mesoscopic phenomena to introduce the bottom-up order parameters and explore their dynamics with time and in response to external stimuli.

Direct observation and catalytic role of mediator atom in 2D materials

The structural transformations of graphene defects have been extensively researched through aberration-corrected transmission electron microscopy (AC-TEM) and theoretical calculations. For a long time, a core concept in understanding the structural evolution of graphene defects has been the Stone-Thrower-Wales (STW)-type bond rotation. In this study, we show that undercoordinated atoms induce bond formation and breaking, with much lower energy barriers than the STW-type bond rotation. We refer to them as mediator atoms due to their mediating role in the breaking and forming of bonds. Here, we report the direct observation of mediator atoms in graphene defect structures using AC-TEM and annular dark-field scanning TEM (ADF-STEM) and explain their catalytic role by tight-binding molecular dynamics (TBMD) simulations and image simulations based on density functional theory (DFT) calculations. The study of mediator atoms will pave a new way for understanding not only defect transformation but also the growth mechanisms in two-dimensional materials.

Nanocrystalline graphene at high temperatures: insight into nanoscale processes

During high temperature pyrolysis of polymer thin films, nanocrystalline graphene with a high defect density, active edges and various nanostructures is formed. The catalyst-free synthesis is based on the temperature assisted transformation of a polymer precursor. The processing conditions have a strong influence on the final thin film properties. However, the precise elemental processes that govern the polymer pyrolysis at high temperatures are unknown. By means of time resolved in situ transmission electron microscopy investigations we reveal that the reactivity of defects and unsaturated edges plays an integral role in the structural dynamics. Both mobile and stationary structures with varying size, shape and dynamics have been observed. During high temperature experiments, small graphene fragments (nanoflakes) are highly unstable and tend to lose atoms or small groups of atoms, while adjacent larger domains grow by addition of atoms, indicating an Ostwald-like ripening in these 2D materials, besides the mechanism of lateral merging of nanoflakes with edges. These processes are also observed in low-dose experiments with negligible electron beam influence. Based on energy barrier calculations, we propose several inherent temperature-driven mechanisms of atom rearrangement, partially involving catalyzing unsaturated sites. Our results show that the fundamentally different high temperature behavior and stability of nanocrystalline graphene in contrast to pristine graphene is caused by its reactive nature. The detailed analysis of the observed dynamics provides a pioneering overview of the relevant processes during ncg heating.

Anisotropic Fracture Dynamics Due to Local Lattice Distortions

A brittle material under loading fails by the nucleation and propagation of a sharp crack. In monatomic crystals, such as silicon, the lattice geometries front to the crack-tip changes the way of propagation even with the same cleavage surface. In general, however, crystals have multiple kinds of atoms and how the deformation of each atom affects the failure is still elusive. Here, we show that local atomic distortions from the different types of atoms causes a propagation anisotropy in suspended WS₂ monolayers by combining annular dark-field scanning transmission electron microscopy and empirical molecular dynamics that are validated by first-principles calculations. Conventional conditions for brittle failure such as surface energy, elasticity, and crack geometry cannot account for this anisotropy. Further simulations predict the enhancement of the strengths and fracture toughness of the materials by designing void shapes and edge structures.

Nanoscale Behavior and Manipulation of the Phase Transition in Single-Crystal Cu2 Se

Phase transition is a fundamental physical phenomenon that has been widely studied both theoretically and experimentally. According to the Landau theory, the coexistence of high- and low-temperature phases is thermodynamically impossible during a second-order phase transition in a bulk single crystal. Here, the coexistence of two (α and β) phases in wedge-shaped nanosized single-crystal Cu₂ Se over a large temperature range are demonstrated. By considering the surface free-energy difference between the two phases and the shape effect, a thermodynamic model is established, which explicitly explains their coexistence. Intriguingly, it is found that with a precise control of the heating temperature, the phase boundary can be manipulated at atomic level. These discoveries extend the understanding of phase transitions to the nanoscale and shed light on rational manipulation of phase transitions in nanomaterials.

Active Sites in Heterogeneous Catalytic Reaction on Metal and Metal Oxide: Theory and Practice

Active sites play an essential role in heterogeneous catalysis and largely determine the reaction properties. Yet identification and study of the active sites remain challenging owing to their dynamic behaviors during catalysis process and issues with current characterization techniques. This article provides a short review of research progresses in active sites of metal and metal oxide catalysts, which covers the past achievements, current research status, and perspectives in this research field. In particular, the concepts and theories of active sites are introduced. Major experimental and computational approaches that are used in active site study are summarized, with their applications and limitations being discussed. An outlook of future research direction in both experimental and computational catalysis research is provided.

Building Structures Atom by Atom via Electron Beam Manipulation

Building materials from the atom up is the pinnacle of materials fabrication. Until recently the only platform that offered single-atom manipulation was scanning tunneling microscopy. Here controlled manipulation and assembly of a few atom structures are demonstrated by bringing together single atoms using a scanning transmission electron microscope. An atomically focused electron beam is used to introduce Si substitutional defects and defect clusters in graphene with spatial control of a few nanometers and enable controlled motion of Si atoms. The Si substitutional defects are then further manipulated to form dimers, trimers, and more complex structures. The dynamics of a beam-induced atomic-scale chemical process is captured in a time-series of images at atomic resolution. These studies suggest that control of the e-beam-induced local processes offers the next step toward atom-by-atom nanofabrication, providing an enabling tool for the study of atomic-scale chemistry in 2D materials and fabrication of predefined structures and defects with atomic specificity.

Conjugated π electron engineering of generalized stacking fault in graphene and h-BN

Generalized-stacking-fault energy (GSFE) serves as an important metric that prescribes dislocation behaviors in materials. In this paper, utilizing first-principle calculations and chemical bonding analysis, we studied the behaviors of generalized stacking fault in graphene and h-BN. It has been shown that the π bond formation plays a critical role in the existence of metastable stacking fault (MSF) in graphene and h-BN lattice along certain slip directions. Chemical functionalization was then proposed as an effective means to engineer the π bond, and subsequently MSF along dislocation slips within graphene and h-BN. Taking hydrogenation as a representative functionalization method, we demonstrated that, with the preferential adsorption of hydrogen along the slip line, π electrons along the slip would be saturated by adsorbed hydrogen atoms, leading to the moderation or elimination of MSF. Our study elucidates the atomic mechanism of MSF formation in graphene-like materials, and more generally, provides important insights towards predictive tuning of mechanic properties in two-dimensional nanomaterials.

Atomic Structure and Spectroscopy of Single Metal (Cr, V) Substitutional Dopants in Monolayer MoS2

Dopants in two-dimensional dichalcogenides have a significant role in affecting electronic, mechanical, and interfacial properties. Controllable doping is desired for the intentional modification of such properties to enhance performance; however, unwanted defects and impurity dopants also have a detrimental impact, as often found for chemical vapor deposition (CVD) grown films. The reliable identification, and subsequent characterization, of dopants is therefore of significant importance. Here, we show that Cr and V impurity atoms are found in CVD grown MoS₂ monolayer 2D crystals as single atom substitutional dopants in place of Mo. We attribute these impurities to trace elements present in the MoO₃ CVD precursor. Simultaneous annular dark field scanning transmission electron microscopy (ADF-STEM) and electron energy loss spectroscopy (EELS) is used to map the location of metal atom substitutions of Cr and V in MoS₂ monolayers with single atom precision. The Cr and V are stable under electron irradiation at 60 to 80 kV, when incorporated into line defects, and when heated to elevated temperatures. The combined ADF-STEM and EELS differentiates these Cr and V dopants from other similar contrast defect structures, such as 2S self-interstitials at the Mo site, preventing misidentification. Density functional theory calculations reveal that the presence of Cr or V causes changes to the density of states, indicating doping of the MoS₂ material. These transferred impurities could help explain the presence of trapped charges in CVD prepared MoS₂.

In Situ High Temperature Atomic Level Studies of Large Closed Grain Boundary Loops in Graphene

We use an in situ heating holder within an aberration corrected transmission electron microscope (AC-TEM) to study the structure and dynamics of large closed grain boundary (GB) loops in graphene at the atomic level. Temperatures up to 800 °C are used to accelerate dynamic evolution of the defect clusters, increasing bond rotation and atomic addition/loss. Our results show that the large closed GB loops relax under electron beam irradiation into several isolated dislocations far apart from each other. Line defects composed of several adjacent excess-atom clusters can be found during the reconfiguration process. Dislocation ejection from the closed GB loops are seen in real time and are shown to help the reduction in loop size. These results show detailed information about the stability and behavior of large GB loops in 2D materials that have importance in the high temperature processing of these materials.

Direct imaging of rotating molecules anchored on graphene

There has been significant research interest in controlling and imaging molecular dynamics, such as translational and rotational motions, especially at a single molecular level. Here we applied aberration-corrected transmission electron microscopy (ACTEM) to actuate and directly image the rotational motions of molecules anchored on a single-layer-graphene sheet. Nanometer-sized carbonaceous molecules anchored on graphene provide ideal systems for monitoring rotational motions via ACTEM. We observed the preferential registry of longer molecular axis along graphene zigzag or armchair lattice directions due to the stacking-dependent molecule-graphene energy landscape. The calculated cross section from elastic scattering theory was used to experimentally estimate the rotational energy barriers of molecules on graphene. The observed energy barrier was within the range of 1.5-12 meV per atom, which is in good agreement with previous calculation results. We also performed molecular dynamics simulations, which revealed that the edge atoms of the molecule form stably bonds to graphene defects and can serve as a pivot point for rotational dynamics. Our study demonstrates the versatility of ACTEM for the investigation of molecular dynamics and configuration-dependent energetics at a single molecular level.

Electron and phonon properties and gas storage in carbon honeycombs

A new kind of three-dimensional carbon allotrope, termed carbon honeycomb (CHC), has recently been synthesized [PRL 116, 055501 (2016)]. Based on the experimental results, a family of graphene networks has been constructed, and their electronic and phonon properties are studied by various theoretical approaches. All networks are porous metals with two types of electron transport channels along the honeycomb axis and they are isolated from each other: one type of channel originates from the orbital interactions of the carbon zigzag chains and is topologically protected, while the other type of channel is from the straight lines of the carbon atoms that link the zigzag chains and is topologically trivial. The velocity of the electrons can reach ∼10(6) m s(-1). Phonon transport in these allotropes is strongly anisotropic, and the thermal conductivities can be very low when compared with graphite by at least a factor of 15. Our calculations further indicate that these porous carbon networks possess high storage capacity for gaseous atoms and molecules in agreement with the experiments.

Observation and analysis of the Coulter effect through carbon nanotube and graphene nanopores

Carbon nanotubes (CNTs) and graphene are the rolled and flat analogues of graphitic carbon, respectively, with hexagonal crystalline lattices, and show exceptional molecular transport properties. The empirical study of a single isolated nanopore requires, as evidence, the observation of stochastic, telegraphic noise from a blocking molecule commensurate in size with the pore. This standard is used ubiquitously in patch clamp studies of single, isolated biological ion channels and a wide range of inorganic, synthetic nanopores. In this work, we show that observation and study of stochastic fluctuations for carbon nanopores, both CNTs and graphene-based, enable precision characterization of pore properties that is otherwise unattainable. In the case of voltage clamp measurements of long (0.5-1 mm) CNTs between 0.9 and 2.2 nm in diameter, Coulter blocking of cationic species reveals the complex structuring of the fluid phase for confined water in this diameter range. In the case of graphene, we have pioneered the study and the analysis of stochastic fluctuations in gas transport from a pressurized, graphene-covered micro-well compartment that reveal switching between different values of the membrane permeance attributed to chemical rearrangements of individual graphene pores. This analysis remains the only way to study such single isolated graphene nanopores under these realistic transport conditions of pore rearrangements, in keeping with the thesis of this work. In summary, observation and analysis of Coulter blocking or stochastic fluctuations of permeating flux is an invaluable tool to understand graphene and graphitic nanopores including CNTs.