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.
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.
A compact mathematical model of the STEM imaging process including bright field (BF) and dark field (DF) is derived. This description is valid for thin samples, does not rely on the weak phase ...approximation and does not require time-consuming simulation of the scanning process. It is well-known that STEM imaging is a nonlinear technique and therefore cannot be described in terms of a sample-independent linear contrast transfer function (CTF). In this work we derive a nonlinear description showing that a STEM image can in fact be described with two terms. Both terms are cross-correlations between a function that is independent of the sample and a function that depends only on the sample. The latter two can be seen as two different objects. These objects directly correspond to two specific cases: the weak phase approximation (WPA) and annular dark field (ADF) imaging, which are known from the literature. We clarify the need for recognizing and understanding what the object is of any particular STEM technique. The model was validated using simulated STEM images and an excellent agreement as well as a reduction in computation time of 3 orders of magnitude was found.
•A compact mathematical model of BF and DF HR-STEM for thin samples is derived.•This description is nonlinear due to the (well-known) nonlinearity of STEM imaging.•A STEM image is described by two terms, effectively imaging two different objects.•For the first time we combine BF and DF STEM in one formula without using the WPA.•Physical interpretation is obtained without simulation of the STEM scanning process.
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