Friday lecture | 12 March 2021

Upgrading total-scattering electron diffraction at EMAT
an X-ray crystallographer’s journey —

by: Stefano Canossa, Emat



It has been roughly a year since I started using my expertise in X-ray crystallography to approach electron diffraction and try to reach the ideal data quality to conduct total electron scattering analysis. This resulted in a new automated data collection routine available for all EMAT crystallographers, while providing me with suitable total-scattering data on beam-sensitive metal–organic frameworks (MOFs) central to my FWO project. In this presentation I will briefly outline the key differences between single crystal X-ray diffraction and electron diffraction instrumentations, thereby adding an interdisciplinary context to a general overview of my current approach to the acquisition of ED datasets. Finally, I will show some exemplary total-scattering data on the functionalised MOF NO2-MIL-53, which I have been particularly focussing on, and I will highlight the most significant differences between X-ray and electron diffraction patterns obtained from crystals of different sizes.

Friday lecture | 5 March 2021

Exploring single-layer materials and their defects and dynamics in two- and three-dimensions

by: Christoph Hofer, Emat



Identifying the position and chemical identity of each atom in a specimen is the ultimate goal of structural characterization. With the rise of aberration correctors in (scanning) transmission electron microscopy (S/TEM), visualizing interatomic distances and obtaining atomically-resolved chemical maps became routine. However, three-dimensional characterization and chemical analysis of structures susceptible to electron-beam-induced structural changes such as 2D materials is problematic under the high cumulative dose arising from a large number of projections or from the requirement of a high signal-to noise-image.  My talk is organized as follows:

    Firstly, I demonstrate how the Ångström-sized electron probe in STEM allows to distinguish nitrogen (Z=7) and oxygen (Z=8) impurities in graphene allowing to compare nitrogen and oxygen bonding configurations as well as their dynamics. The collected data set allows to create a statistics of all the bonding configurations showing clear differences between the two elements. In addition triple-coordinated oxygen atoms with three carbon neighbors, which so far was only known from a few very exotic compounds, was observed.

    Secondly, I introduce a novel approach to extract the atomic intensities of STEM images in the presence of residual aberrations and noise. The method is based on an optimization process where the simulation of a model is iteratively matched to the experimental STEM image. In order to minimize artifacts arising from a non-perfectly shaped primary beam, the aberration coefficients are included in the optimization process.  The analysis reveals that our method achieves more reliable results compared to the other methods already in the presence of small non-round aberrations, and still allows to extract atomic intensities even if the aberrations are strong.

    Last but not least, I present how to obtain the 3D structure of atomically-thin materials such as graphene directly from only two atomically-resolved experimental images obtained from different tilt angles.  Two prerequisites, which are fulfilled for a single atomic layer 2D material, are required for this to be successful: (1) Each atom has to be visible individually in both projections, and (2) the connectivity matrix can be obtained and shows unambiguously which atom is which in the comparison of the two views. The reconstruction is based on an iterative optimization process where simulated images are matched to the experimental data. This method is used to reveal new insights into the three-dimensional structure and out-of-plane dynamics of defects in graphene, in particular grain boundaries, dopants and mixed-dimensional van-der-Waals heterostructures.

Friday lecture | 19 February 2021

A new deformation mechanism in Olivine, In-situ and Ex-situ TEM studies

by: Ihtasham Ul Haq, Emat


Olivine, (Mg, Fe)2 SiO4 is a silicate mineral having orthorhombic symmetry and is present in the earth’s mantle down to 410 km depth. There is evidence that in the convective mantle, olivine deformation involves dislocation glide and climb. However, due to its low symmetry, this mineral does not possess enough slip systems to satisfy the Von Mises criterion [1,2]. Several recent studies have focused on the possible contribution of grain boundaries (GBs) (sliding, migration) to the deformation of olivine aggregates, but so far, the mechanisms at play are not yet clarified.

To study the deformation mechanisms, deformed olivine samples synthesized from mixed, cold-pressed, and sintered SiO2 and Mg(OH)2 powders, were used for ex-situ TEM investigations. Deformation was carried out using a Paterson press (high-pressure high-temperature deformation apparatus) under a confining pressure of 300±5 MPa, at temperatures between 900-1200 °C, and a constant displacement rate. A detailed HRTEM microstructural investigation revealed the ductile behavior of GBs facilitated by intergranular amorphous layers that accommodate the strain during deformation. For this purpose, we used the PI-95 TEM Pico-indenter holder and the Push-to-Pull (PTP) device (Bruker. Inc) to perform  quantitative in-situ TEM tensile tests. The deformation of the pristine olivine samples which do not have an amorphous layer at the grain boundary by in-situ nanomechanical testing in the TEM provides further opportunity to gain information on the acting mechanisms. To observe this grain boundary mechanism, bi-and tri-crystal nano tensile test olivine samples were prepared from the bulk pristine olivine via FIB. The samples were then mounted on the PTP holder, and used for nano tensile testing. The results show the evidence of stress induced amorphization in the GBs at room temperature in absence of other deformation mechanisms.


[1] R. E. Bernard, W. M. Behr, T. W. Becker, and D. J. Young, “Relationships Between Olivine CPO and Deformation Parameters in Naturally Deformed Rocks and Implications for Mantle Seismic Anisotropy,” Geochemistry, Geophys. Geosystems, vol. 20, no. 7, pp. 3469–3494, 2019, doi: 10.1029/2019GC008289.

[2] M. Thieme, S. Demouchy, D. Mainprice, F. Barou, and P. Cordier, “Stress evolution and associated microstructure during transient creep of olivine at 1000–1200 °C,” Phys. Earth Planet. Inter., vol. 278, no. February, pp. 34–46, 2018, doi: 10.1016/j.pepi.2018.03.002.

Friday lecture | 5 February 2021

Marry 2D crystallization and thin-film polymorphism: case study for PbPc

by: Yansong Hao, Emat


Polymorphism represents the ability of elements or compounds to crystallize into different forms. These crystal forms are named as polymorphs and they normally differ in atomic arrangements or molecular packing. The study of polymorphism becomes very popular as it is closely related to the physical properties of the materials, such as solubility, mechanical properties and electronic properties. Among all types of crystals, polymorphs of organic molecules are abundantly diverse. This is because, within crystals, organic molecules interact often through weak van der Waals interactions. Up to now, controlling crystallization of organic molecules into the desired polymorph or predicting possible polymorphs is still quite challenging. 

Practically, most of the crystallization happens on the substrate, which gives rise to the heterogeneous nucleation. Beyond well-known catalyzing effect, some studies have reported that molecular materials could crystallize into new polymorphic forms only in the vicinity of the substrate and these new forms are called substrate-induced polymorphs (SIPs). Typically, SIPs extend over several molecular layers above the substrate. This makes it different from another conceptually connected research line: self-assembly monolayers (SAMs) of organic molecules. the SAMs of organic molecules have been studied extensively in the last decades. However, the exact connection between the SAMs and SIPs for organic molecules is still unclear. 

The compound of interest for this study is lead phthalocyanine (PbPc). We investigated the SIP of PbPc on highly oriented pyrolytic graphite (HOPG) by combining experiments and multiscale computational-chemistry modelling. Firstly, self-assembled PbPc molecules at solution/HOPG interface were studied by both in-situ scanning tunneling microscope (STM) and atomistic modelling. Next, the SIP of PbPc up to several molecular layers was built on top of the assembly and the modelled SIP agreed well with experimental observations. It is revealed that the SAM acts as a bridging layer between the substrate and the thin-film crystal. Therefore, the crystal structure of SIPs is templated by the SAMs. 

Furthermore, a thin film of PbPc has been prepared by physical vapor deposition and characterized by transmission electron microscopy (TEM). Exit wave reconstruction shows nicely resolved atomic columns in the reconstructed phase, which proves the great capability of TEM in imaging soft organic crystals. Currently, thinner samples are being prepared and a better match between experiments and modelled SIPs is promising.