Using state of the art scanning transmission electron microscopy (STEM) it is nowadays possible to directly image single atomic columns at sub-Å resolution. In standard (high angle) annular dark ...field STEM ((HA)ADF-STEM), however, light elements are usually invisible when imaged together with heavier elements in one image. Here we demonstrate the capability of the recently introduced Integrated Differential Phase Contrast STEM (iDPC-STEM) technique to image both light and heavy atoms in a thin sample at sub-Å resolution. We use the technique to resolve both the Gallium and Nitrogen dumbbells in a GaN crystal in Formula: see text orientation, which each have a separation of only 63 pm. Reaching this ultimate resolution even for light elements is possible due to the fact that iDPC-STEM is a direct phase imaging technique that allows fine-tuning the microscope while imaging. Apart from this qualitative imaging result, we also demonstrate a quantitative match of ratios of the measured intensities with theoretical predictions based on simulations.
It has been known since the 1970s that the movement of the center of mass (COM) of a convergent beam electron diffraction (CBED) pattern is linearly related to the (projected) electrical field in the ...sample. We re-derive a contrast transfer function (CTF) for a scanning transmission electron microscopy (STEM) imaging technique based on this movement from the point of view of image formation and continue by performing a two-dimensional integration on the two images based on the two components of the COM movement. The resulting integrated COM (iCOM) STEM technique yields a scalar image that is linear in the phase shift caused by the sample and therefore also in the local (projected) electrostatic potential field of a thin sample. We confirm that the differential phase contrast (DPC) STEM technique using a segmented detector with 4 quadrants (4Q) yields a good approximation for the COM movement. Performing a two-dimensional integration, just as for the COM, we obtain an integrated DPC (iDPC) image which is approximately linear in the phase of the sample. Beside deriving the CTFs of iCOM and iDPC, we clearly point out the objects of the two corresponding imaging techniques, and highlight the differences to objects corresponding to COM-, DPC-, and (HA) ADF-STEM. The theory is validated with simulations and we present first experimental results of the iDPC-STEM technique showing its capability for imaging both light and heavy elements with atomic resolution and a good signal to noise ratio (SNR).
•First DPC-based atomic resolution images of potential and charge density are obtained.•This is enabled by integration and differentiation of 2D DPC signals, respectively.•Integrated DPC (iDPC) based on 4 quadrant imaging is compared to iCOM imaging.•Noise analysis and comparison with standard STEM imaging modes is provided.•iDPC allows direct imaging of light (C, N, O …) and heavy (Ga, Au …) atoms together.
Single-molecule imaging with atomic resolution is a notable method to study various molecular behaviours and interactions1-5. Although low-dose electron microscopy has been proved effective in ...observing small molecules6-13, it has not yet helped us achieve an atomic understanding of the basic physics and chemistry of single molecules in porous materials, such as zeolites14-16. The configurations of small molecules interacting with acid sites determine the wide applications of zeolites in catalysis, adsorption, gas separation and energy storage17-21. Here we report the atomic imaging of single pyridine and thiophene confined in the channel of zeolite ZSM-5 (ref.22). On the basis of integrated differential phase contrast scanning transmission electron microscopy (iDPC-STEM)23-25, we directly observe the adsorption and desorption behaviours of pyridines in ZSM-5 under the in situ atmosphere. The adsorption configuration of single pyridine is atomically resolved and the S atoms in thiophenes are located after comparing imaging results with calculations. The strong interactions between molecules and acid sites can be visually studied in real-space images. This work provides a general strategy to directly observe these molecular structures and interactions in both the static image and the in situ experiment, expanding the applications of electron microscopy to the further study of various single-molecule behaviours with high resolution.
•An undisturbed probe model describing depth-sectioning STEM valid for all STEM techniques is derived under three well-defined conditions.•The model provides closed form expressions for ...depth-sectioning STEM and enables analysis of the 3D resolution.•The range of validity of the undisturbed probe model is tested using multi-slice simulations.•A comparison of depth sectioning using iDPC- and ADF-STEM is made both in simulations and in experiments and the differences are explained.•Practical criteria for deciding whether a sample is thick or thin are proposed.
We derive a model that describes 3D volume imaging in depth-sectioning STEM that is valid for all STEM techniques under three well-defined conditions: linearity, undisturbed probe and elastic scattering. The resulting undisturbed probe model generalizes the widely used idea that the undisturbed probe intensity in three dimensions can be used as the point spread function for depth-sectioning ADF-STEM to all STEM techniques including (A)BF- and iDPC-STEM. The model provides closed expressions for depth-sectioning STEM, which follow directly from the 2D expressions for thin samples, and thereby enables analysis of the 3D resolution. Using the model we explore the consequences of the resulting 3D contrast transfer function (CTF) for the z-resolution at different length scales and illustrate this with experiments. We investigate the validity and limitations of the model using multi-slice simulations showing that it is valid and quantitatively accurate for relatively thick amorphous samples but not for crystalline samples in zone-axis due to channeling. We compare depth-sectioning in iDPC- and ADF-STEM and show that iDPC-STEM can extract information from deeper into the sample, all the way till the bottom of the sample, thereby effectively allowing a thickness measurement. Also the difference in optimal focus conditions between iDPC- and ADF-STEM is explained. Finally, we propose practical criteria for deciding whether a sample is thin or thick.
Abstract
In electron cryomicroscopy (cryo-EM), molecular images of vitrified biological samples are obtained by conventional transmission microscopy (CTEM) using large underfocuses and subsequently ...computationally combined into a high-resolution three-dimensional structure. Here, we apply scanning transmission electron microscopy (STEM) using the integrated differential phase contrast mode also known as iDPC–STEM to two cryo-EM test specimens, keyhole limpet hemocyanin (KLH) and tobacco mosaic virus (TMV). The micrographs show complete contrast transfer to high resolution and enable the cryo-EM structure determination for KLH at 6.5 Å resolution, as well as for TMV at 3.5 Å resolution using single-particle reconstruction methods, which share identical features with maps obtained by CTEM of a previously acquired same-sized TMV data set. These data show that STEM imaging in general, and in particular the iDPC–STEM approach, can be applied to vitrified single-particle specimens to determine near-atomic resolution cryo-EM structures of biological macromolecules.
Single-molecule imaging is challenging but highly beneficial for investigating intermolecular interactions at the molecular level
. Van der Waals interactions at the sub-nanometre scale strongly ...influence various molecular behaviours under confinement conditions
. Inspired by the traditional compass
, here we use a para-xylene molecule as a rotating pointer to detect the host-guest van der Waals interactions in the straight channel of the MFI-type zeolite framework. We use integrated differential phase contrast scanning transmission electron microscopy
to achieve real-space imaging of a single para-xylene molecule in each channel. A good correlation between the orientation of the single-molecule pointer and the atomic structure of the channel is established by combining the results of calculations and imaging studies. The orientations of para-xylene help us to identify changes in the van der Waals interactions, which are related to the channel geometry in both spatial and temporal dimensions. This work not only provides a visible and sensitive means to investigate host-guest van der Waals interactions in porous materials at the molecular level, but also encourages the further study of other single-molecule behaviours using electron microscopy techniques.
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•iDPC-STEM was applied to study biological structures in resin-embedded sections and compared with ABF-STEM and TEM.•With the same dose, iDPC-STEM results in better contrast and ...resolves more biological ultrastructures in molecule resolution.•At the minimal staining condition, iDPC-STEM yields better contrast and much improved SNR with ultrastructural details.•iDPC-STEM has a unique advantage to image thick (up to 600 nm) sections without loss of contrast.
Scanning transmission electron microscopy (STEM) is a powerful imaging technique and has been widely used in current material science research. The attempts of applying STEM (annual dark field (ADF)-STEM or annular bright field (ABF)-STEM) into biological research have been going on for decades while applications have still been limited because of the existing bottlenecks in dose efficiency and non-linearity in contrast. Recently, integrated differential phase contrast (iDPC) STEM technique emerged and achieved a linear phase contrast imaging condition, while resolving signals of light elements next to heavy ones even at low electron dose. This enables successful investigation of beam sensitive materials. Here, we investigate iDPC-STEM advantages in biology, in particular, chemically fixed and resin embedded biological tissues. By comparing results to the conventional TEM, we have found that iDPC-STEM not only shows better contrast but also resolves more structural details at molecular level, including conditions of extremely low dose and minimal heavy-atom staining. We also compare iDPC-STEM with ABF-STEM and found that contrast of iDPC-STEM is even further improved, moderately in lower frequency domains while highly with preserving high frequency biological structural details. For thick sample sections, iDPC-STEM is particularly advantageous. It avoids contrast inversion canceling effects, and by adjusting the depth of focus, fully preserves the contrast of structural details along with the sample. In addition, using depth-sectioning, iDPC-STEM enables resolving in-depth structural variation. Our results suggest that iDPC-STEM have the place and advantages within the future biological research.
A proper amount of excess oxygen plays a significant role in hole‐doped cuprate high‐Tc superconductivity. Here, the dopant oxygen in Bi2Sr2CaCu2O8+δ is directly imaged via integrated differential ...phase contrast combined with state‐of‐the‐art scanning transmission electron microscopy. The location of dopant oxygen is observed to be consistent with the position inferred from local strain analysis of the incommensurate structure. The influence of dopant oxygen on the local atomic lattice and electronic structure is further explored using first‐principle calculations. The dopant oxygen atoms not only aggravate the distortions of the local atomic arrangement but also alter the electronic states by transferring charge from the BiO planes to the CuO2 planes. The underlying mechanism of charge transfer is resolved. The results may also be applicable to other oxygen‐doped cuprates with high‐Tc superconductivity.
A proper amount of excess oxygen plays a significant role in hole‐doped cuprate high‐Tc superconductivity. The dopant oxygen in Bi2Sr2CaCu2O8+δ and the incommensurate atomic structure are directly imaged via integrated differential phase contrast combined with state‐of‐the‐art scanning transmission electron microscopy. The influence of dopant oxygen on the local atomic lattice and electronic structure is further explored using first‐principle calculations.
We study the coherent and semi-coherent Al/α-Al2O3 interfaces using molecular dynamics simulations with a mixed, metallic-ionic atomistic model. For the coherent interfaces, both Al-terminated and ...O-terminated nonstoichiometric interfaces have been studied and their relative stability has been established. To understand the misfit accommodation at the semi-coherent interface, a 1-dimensional (1D) misfit dislocation model and a 2-dimensional (2D) dislocation network model have been studied. For the latter case, our analysis reveals an interface dislocation structure with a network of three sets of parallel dislocations, each with pure-edge character, giving rise to a pattern of coherent and stacking-fault-like regions at the interface. Structural relaxation at elevated temperatures leads to a further change of the dislocation pattern, which can be understood in terms of a competition between the stacking fault energy and the dislocation interaction energy at the interface. Our results are expected to serve as an input for the subsequent dislocation dynamics models to understand and predict the macroscopic mechanical behavior of Al/α-Al2O3 composite heterostructures.
Scanning transmission electron microscopy (STEM) is the most widespread adopted tool for atomic scale characterization of two-dimensional (2D) materials. However, damage free imaging of 2D materials ...with electrons has remained problematic even with powerful low-voltage 60 kV-microscopes. An additional challenge is the observation of light elements in combination with heavy elements, particularly when recording fast dynamical phenomena. Here, we demonstrate that 2D WS
2
suffers from electron radiation damage during 30 kV-STEM imaging, and we capture beam-induced defect dynamics in real-time by atomic electrostatic potential imaging using integrated differential phase contrast (iDPC)-STEM. The fast imaging of atomic electrostatic potentials with iDPC-STEM reveals the presence and motion of single sulfur atoms near defects and edges in WS
2
that are otherwise invisible at the same imaging dose at 30 kV with conventional annular dark-field STEM, and has a vast speed and data processing advantage over electron detector camera based STEM techniques like electron ptychography.
Low-voltage electron microscopy reveals light atoms and their motion in 2D materials using fast atomic electrostatic potential imaging.
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