Conference Agenda

Overview and details of the sessions of this conference. Please select a date or location to show only sessions at that day or location. Please select a single session for detailed view (with abstracts and downloads if available).

Please note that all times are shown in the time zone of the conference. The current conference time is: 18th May 2022, 09:23:01pm CEST

Session Overview
MS-19: Crystal structures of pharmaceutical and organic compounds from electron diffraction
Monday, 16/Aug/2021:
10:20am - 12:45pm

Session Chair: Ute Kolb
Session Chair: Petr Brazda
Location: Terrace 2A
130 2nd floor

Invited: Enrico Mugnaioli (Italy)Brent Nannega (USA)

Session Abstract

Many drugs are provided as microcrystalline compounds. Their uptake in the body, the optimisation of their effectivity, and the minimisation of side effects is guided by properties of crystal packing and inter-particle interactions. As a consequence, 3D electron crystallography has attracted increasing attention in the characterisation of pharmaceutical and organic compounds. This microsymposium aims to discuss possibilities and future directions of 3D electron crystallography.

For all abstracts of the session as prepared for Acta Crystallographica see PDF in Introduction, or individual abstracts below.

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10:20am - 10:25am
ID: 1748 / MS-19: 1

Introduction to session

Ute Kolb, Petr Brázda

10:25am - 10:55am
ID: 1186 / MS-19: 2
Chemical crystallography, crystal structures
Invited lecture to session
MS: Crystal structures of pharmaceutical and organic compounds from electron diffraction
Keywords: MicroED, organic semiconductors, electron diffraction, GIWAXS

Combining MicroED and GIWAXS for determining structure and orientation of organic semiconductor thin films

Brent Nannenga

Arizona State University, Tempe, United States of America

In order to understand the packing and orientation of organic semiconductor thin films, we make use of microcrystal electron diffraction (MicroED) and grazing-incidence wide-angle X-ray scattering (GIWAXS). These complementary techniques provide structural insights to the structure of these thin films and can be used with the same sample preparation methods that are used to create the functional films. This removes the need for time-consuming crystallization experiments that may not directly capture the same semiconductor structure found in the films. We will present the application of these methods on four organic semiconductor samples, some of which represent novel structures determined by MicroED.

10:55am - 11:25am
ID: 927 / MS-19: 3
Chemical crystallography, crystal structures
Invited lecture to session
MS: Crystal structures of pharmaceutical and organic compounds from electron diffraction
Keywords: electron diffraction, small-molecule organics, pharmaceutical compounds, beam damage, nanomaterials

Strategies for structure solution of small-molecule organics by 3D ED using a small beam

Enrico Mugnaioli1, Iryna Andrusenko1, Mauro Gemmi1, Partha P. Das2, Athanassios Galanis2, Stavros Nicolopoulos2

1Center for Nanotechnology Innovation@NEST, Istituto Italiano di Tecnologia, Piazza San Silvestro 12, Pisa 56127, Italy; 2NanoMEGAS SPRL, Rue Émile Claus 49 bte 9, Brussels1050, Belgium

Three-dimensional electron diffraction (3D ED) has matured into a method routinely employed by several worldwide-located laboratories for addressing crystallographic problems, which were considered intractable by X-ray diffraction [1]. The main advantage of ED is the ability to get diffraction data from volumes of few hundreds or even few tens of nanometers. This allows acquiring comprehensive 3D structural information from crystals too small for X-ray single-crystal methods, from coherent domains in pervasively twinned or disordered materials, from isolated domains embedded in inorganic or biological matrices and from minor constituents of powdered polyphasic mixtures.

From the beginning, the main shortcomings of 3D ED appeared connected with the deterioration of the sample induced by TEM vacuum or by beam damage. Moreover, organic crystals are typically affected by mosaicity and bending. In this contribution we will show different experimental protocols for data collection and analysis that can be employed in any experimental set-up, even for low-voltage TEMs. Beam damage is minimised by coupling STEM imaging for sample search and tracking, and a small-size low-intensity parallel electron beam for diffraction data acquisition [2]. The size of the beam is crucial for picking narrow areas of the sample, either when coherent crystal domains are very small or when there is a need for moving to fresh parts of the crystal in order to lessen beam damage effects.

According with the specific sample characteristics, 3D ED data acquisition can be performed in step-wise mode, coupled with beam precession [3], or by continuous rotation [4]. Both approaches strongly benefit by the disposal of a new-generation ultra-fast single-electron detector [5]. Moreover, background noise can be almost completely suppressed with an energy filter that cuts out the inelastic scattering. Structure solution is normally obtained ab-initio by direct methods. Still, global optimisation approaches, like simulated annealing [6], are valuable alternatives when data are affected by low resolution, preferential orientation or experimental errors that compromise the overall intensity reliability (e.g. beam damage, merohedric twinning, diffuse scattering).

We will thus discuss examples of recently published [7, 8] and forthcoming structure characterizations of pharmaceutical compounds, organic charge-transfer co-crystals and polycyclic aromatic hydrocarbons. For each case, specific problematics of the sample will be discussed, together with experimental solutions adopted for achieving structural solution and refinement.

[1] Gemmi, M., Mugnaioli, E., Gorelik, T. E., Kolb, U., Palatinus, L., Boullay, P., Hovmöller, S. & Abrahams, J. P. (2019). ACS Cent. Sci. 5, 1315.

[2] Kolb, U., Gorelik, T., Kübel, C., Otten, M. T. & Hubert, D. (2007). Ultramicroscopy 107, 507.

[3] Lanza, A., Margheritis, E., Mugnaioli, E., Cappello, V., Garau, G. & Gemmi, M. (2019). IUCrJ 6, 178.

[4] Gemmi, M. & Lanza, A. E. (2019). Acta Cryst. B75, 495.

[5] van Genderen, E., Clabbers, M. T. B., Das, P. P., Stewart, A., Nederlof, I., Barentsen, K. C., Portillo, Q., Pannu, N. S., Nicolopoulos, S., Gruene, T. & Abrahams, J. P. (2016). Acta Cryst. A72, 236.

[6] Burla, M. C., Caliandro, R., Carrozzini, B., Cascarano, G. L., Cuocci, C., Giacovazzo, C., Mallamo, M., Mazzone, A. & Polidori, G. (2015). J. Appl. Cryst. 48, 306.

[7] Andrusenko, I., Hamilton, V., Mugnaioli, E., Lanza, A., Hall, C., Potticary, J., Hall, S. R. & Gemmi, M. (2019). Angew. Chem. Int. Ed. 58, 10919.

[8] Das, P. P., Andrusenko, I., Mugnaioli, E., Kaduk, J. A., Nicolopoulos, S., Gemmi, M., Boaz, N. C., Gindhart, A M. & Blaton, T., (2021). Cryst. Growth Des. 21, 2019.

11:25am - 11:45am
ID: 388 / MS-19: 4
Bursary application
MS: Crystal structures of pharmaceutical and organic compounds from electron diffraction
Keywords: 3D electron diffraction, automated acquisition, organic crystals, ab initio crystal structure determination

The crystal structure determination of an organic dye with triclinic symmetry by electron diffraction

Sergi Plana Ruiz1,2, Yasar Krysiak3, Joaquim Portillo Serra4, Edith Alig5, Sònia Estradé1, Francesca Peiró1, Ute Kolb2,6

1LENS, MIND/IN2UB, University of Barcelona, Barcelona, Catalonia; 2Institut für Angewandte Geowissenschaften, Technische Universität Darmstadt, Darmstadt, Germany; 3Fyzikální Ústav, Akademie vĕd České Republiky, Prague, Czech Republic; 4NanoMegas SPRL, Brussels, Belgium; 5Institut für Anorganische Chemie und Analytische Chemie, Goethe-Universität Frankfurt, Frankfurt, Germany; 6Institut für Anorganische Chemie und Analytische Chemie, Johannes Gutenberg-Universität Mainz, Mainz, Germany

3D Electron Diffraction (3D ED) has reached a point where it has become a routine technique for single-crystal diffraction studies at the nanometre scale [1]. Recently, some acquisition softwares have been developed with the aim of automatization and universal application [2]. One of them is the Fast and Automated Diffraction Tomography (Fast-ADT) [3]. This acquisition module is based on two tilt scans of the goniometric stage over the desired tilt range; the first one to monitor the crystal displacement with respect to the tilt angle in order to interpolate the necessary electron beam shifts, and the second one to acquire the diffraction patterns while following the crystal automatically. This procedure allows reliable diffraction acquisitions for crystals down to 20 nm provided that the stage has been aligned for tomography experiments and the holder is kept in good mechanical conditions. Fast-ADT can work in both TEM and STEM mode, but STEM is preferred mainly because of its low dose to acquire scanned images and its clear visualization of tiny or layered crystals in such conditions [4]. Another difference to other 3D ED routines is the use of Nano-Beam Electron Diffraction (NBED) instead of selected area electron diffraction. The combination of Fast-ADT and NBED enables several approaches focused on the optimization of 3D ED experiments, such as the shift of the beam at different positions of the same crystal or different crystals during diffraction pattern acquisitions. This versatility is beneficial as it gives the needed flexibility to study beam sensitive specimens even with post TEM column charged-coupled devices.

As an example, Fast-ADT was used to acquire datasets from disperse red 1 (DRED1) crystals, an organic molecule that was recrystallized in toluene. The dye DRED1 is an azobenzene derivate, which are well known for their photochromatic properties and large optical and electro-optic properties in various polymeric films. The processing of six Fast-ADT datasets­­­­­­­­­­ with eADT [5] revealed a triclinic crystal system with unit-cell parameters of a = 7.72 Å, b = 11.14 Å, c = 19.58 Å, α = 73.8°, β = 83.0°, γ = 70.5° and V = 1523.5 Å3 and indicated four molecules per unit cell. The real space method simulated annealing, implemented in Sir2014 [6], was used to solve the structure and the positions of the azobenzenes were found using both P1 (Z = 4) and P-1 (Z’ = 2). The small difference between structure solutions performed in both space groups was taken as an indication that the crystal structure could be described in the centrosymmetric space group. However, the correct orientation of the flexible side chains was more difficult to retrieve because of their high degree of freedom. For this reason, on one hand, two datasets were merged to obtain a higher number of independent reflections (85%) and, on the other hand, an analytical description of the rocking curves was applied to enable a frame orientation refinement and an improved reflection intensity integration [7]. These processing tools allowed solving the new polymorph of DRED1 ab initio in P-1, directly revealing the 46 non-hydrogen independent atoms from the scattering density map. Finally, the structure model was refined based on X-ray powder diffraction data using the Rietveld method.

- “Topochemical reduction of La2NiO3F2: the first Ni-based Ruddlesden-Popper n = 1 T’-type structure and the impact of reduction on magnetic ordering”, K. Wissel, A. M. Malik, S. Vasala, S. Plana-Ruiz, U. Kolb, P. R. Slater, I. da Silva, L. Alf, J. Rohrer & O. Clemens. Chemistry of Materials (2020).
- “Fast-ADT: a fast and automated electron diffraction tomography setup for structure determination and refinement”, S. Plana-Ruiz, Y. Krysiak, J. Portillo, E. Alig, S. Estradé, F. Peiró & U. Kolb. Ultramicroscopy 211 (2020) 112951.
- “Automated electron diffraction tomography – development and applications”, U. Kolb, Y. Krysiak & S. Plana-Ruiz. Acta Cryst. B75 (2019) 463-474.
- “Structural characterization and ab-initio resolution of natural occurring zaccariniite (RhNiAs) by means of Precession Electron Diffraction”, J. R. Rosell, J. Portillo, T. H. Aiglsperger, S. Plana-Ruiz, P. P. Das, J. M. Gonzalvez, T. Trifonov & J. A. Proenza. Microchemical Journal 148 (2019) 130-140.
- “Quasi-Parallel Precession Diffraction: Alignment method for Scanning Transmission Electron Microscopes”, S. Plana-Ruiz, J. Portillo, S. Estradé, F. Peiró, U. Kolb & S. Nicolopoulos. Ultramicroscopy 193 (2018) 39-51.
- “A high-strength silicide phase in a stainless steel alloy designed for wear-resistant applications” – D. Bowden, Y. Krysiak, L. Palatinus, D. Tsivoulas, S. Plana-Ruiz, E. Sarakinou, U. Kolb, D. Stewart & M. Preuss. Nature Communications 9 (2018) 1374.

11:45am - 12:05pm
ID: 259 / MS-19: 5
Bursary application
MS: Crystal structures of pharmaceutical and organic compounds from electron diffraction
Keywords: aspherical scattering factors, TAAM, electron diffraction, structure refinement

Refinement with multipolar scattering factors

Barbara Gruza, Michał Leszek Chodkiewicz, Paulina Maria Dominiak

Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Poland

Electron diffraction makes it possible to obtain crystal structures at atomic resolutions, for both small and macro-molecules [1-2]. For this purpose, the same as in case of X-ray diffraction, it is necessary to use scattering factors model. After years of experience people learned that Independent Atom Model (IAM) is not the best choice for X-ray diffraction. It is not a surprise that also for electron diffraction it will not give the best results. Different aspherical models, already known for X-ray diffraction, can be implemented for electron diffraction. However, it is necessary to investigate their possibilities and limits, to verify correctness of obtained structures.

We present analysis of refinements of Transferable Aspherical Atom Model (TAAM) with parameters of multipolar model taken from MATTS databank (databank of Multipolar Atom Types from Theory and Statistical clustering) - successor of UBDB databank [3]. We used electron scattering factors implemented in DiSCaMB library[4] and interfaced with Olex2-1.3[5]. Such solution is available through .tsc files [6] and it requires little effort (Fig.1).

Numerous refinements were performed against experimental electron structure factors and theoretical electron structure factors so as to find optimum refinement strategy. We discuss, inter alia, possibility of refinement of atomic displacement parameters, both for hydrogen and non-hydrogen atoms or positions of hydrogen atoms. It is interesting how they change e.g. with resolution cut-off. To confirm that our conclusions could be transferred for different, but still organic structures, we made simulations for several pharmaceutical compounds, such as carbamazepine, paracetamol, 1-methyluracil.

Support of this work by the National Centre of Science (Poland) through grant OPUS No.UMO-2017/27/B/ST4/02721 and PL-Grid through grant ubdb2019 are gratefully acknowledged.

[1] Clabbers, MTB; van Genderen, E; Wan, W; Wiegers, EL; Gruene, T; Abrahamsa, JP. (2017). Acta Cryst. D Struct Biol. 73, 738–748.
[2] Jones, CG; Martynowycz, MW; Hattne, J; Fulton, TJ; Stoltz, BM; Rodriguez, JA; Nelson, HM; Gonen, T. (2018). ACS Cent. Sci. 4(11), 1587−1592.
[3] Jarzembska, KN; Dominiak. PM. (2012). Acta Cryst A, A68, 139–147.
[4] Chodkiewicz, ML; Migacz, S; Rudnicki, W; Makal, A; Kalinowski, JA; Moriarty, NW; Grosse-Kunstleve, RW; Afonine, PV; Adams, PD; Dominiak, PM. (2018). J. Appl. Cryst., 51, 193–199.
[5] Dolomanov, OV; Bourhis, LJ; Gildea, RJ; Howard, JAK; Puschmann, H. J. (2009). Appl. Cryst., 42, 339-341.
[6] Midgley, L., Bourhis, L.J., Dolomanov, O., Peyerimhoff, N., Puschmann, H. (2019).

12:05pm - 12:25pm
ID: 662 / MS-19: 6
Bursary application
MS: Recent advances in electron crystallography techniques, Analysis of the fine structure in electron diffraction data, Application of electron crystallography to functional materials, Crystal structures of pharmaceutical and organic compounds from electron diffraction
Keywords: GIF, energy-filtered 3D electron diffraction, energy-filtered MicroED, STEM HAADF, crystal tracking

Improving data quality for 3D electron diffraction (3DED) by Gatan Image Filter

Taimin Yang, Hongyi Xu, Xiaodong Zou

Stockholm University, Stockholm, Sweden

Electrons interact with matter 106 times stronger than X-rays do, which makes it an ideal radiation source for diffraction and imaging experiments on submicron- and nano-sized crystals. During the last three decades, 3D electron diffraction (3D ED) has been developed into a regular and reliable technique for structure determination, which is complementary to single-crystal X-ray diffraction (SCXD) and single particle analysis. One issue for electron diffraction is inelastic scattering, which brings background in the diffraction patterns. This background is most obvious for electron diffraction patterns from protein crystals, especially at low angles. Even though modern diffraction data software (XDS, DIALS, MOSFLM) has sophisticated background removal algorithms to deal with this, the existence of inelastic scattering will still add errors in the diffraction experiment. The inelastically scattered electrons can be removed by energy filters. Here, we implemented energy-filtered 3D ED using a Gatan Energy Filter (GIF) in both TEM selected area electron diffraction mode and STEM micro/nanoprobe mode. We explained the setup in detail and this implementation can allow researcher to have better accessibility to energy-filtered 3DED experiments because more microscopes are equipped with a GIF than an in-column omega filter. We also proposed a crystal tracking method in STEM mode using live HAADF image stream. This method enables us to collect energy-filtered 3DED datasets in STEM mode with a larger tilt range without foregoing any frames. This can avoid crystal moving out of the beam during the tilting and the tilt range can always reach the maximum tilt range of the microscope (in our case ~150°). We acquired multiple datasets from different crystals and we further processed and refined the structures. We observed that the final R1 will improve 20% to 30% for energy-filtered datasets compared with unfiltered datasets. We also discussed the possible reasons that lead to the improvement.

[1] Dai, H, Y Shen, T Yang, C Lee, D Fu, A Agarwal, T Le, M Tsapatsis, and ... (2020). Finned zeolite catalysts. Nature Materials (4).
[2] Sheng, X, Y Li, T Yang, B Timmer, T Willhammar, O Cheung, L Li, and ... (2020). Hierarchical micro-reactor as electrodes for water splitting by metal rod tipped carbon nanocapsule self-assembly in carbonized wood. Applied Catalysis B: Environmental (11).
[3] Xu, H, H Lebrette, T Yang, V Srinivas, S Hovmöller, M Högbom, and X Zou (2018). A rare lysozyme crystal form solved using highly redundant multiple electron diraction datasets from micron-sized crystals. Structure (10).
[4] Wang, Y, T Yang, H Xu, X Zou, and W Wan (2018). On the quality of the continuous rotation electron diffraction data for accurate atomic structure determination of inorganic compounds. Journal of Applied Crystallography (14).
[5] Seo, S, T Yang, J Shin, D Jo, X Zou, and S Hong (2018). Two aluminophosphate molecular sieves built from pairs of enantiomeric structural building units. Angewandte Chemie (3).

12:25pm - 12:45pm
ID: 815 / MS-19: 7
Chemical crystallography, crystal structures
MS: Crystal chemistry with emerging technology, New trends in pharmaceutical materials, Crystal structures of pharmaceutical and organic compounds from electron diffraction
Posters only: Chemical crystallography, crystal structures (if it does not fit to any specific topics)
Keywords: 3D ED, electron diffraction, nano-crystallography, electron diffractometer

3D electron diffraction: a dedicated device for structural elucidation of nanocrystalline particles

Gustavo Santiso-Quinones, Eric Hovestreydt, Arianna E. Lanza, Gunther Steinfeld

ELDICO Scientific AG, 5234 Villigen, Switzerland

3D Electron Diffraction (3D ED) is a very powerful tool for the structural elucidation of nanocrystalline particles. After its Science nomination for “Breakthrough of the year 2018” [1], 3D ED, using the continuous rotation method [2-3], and well-established crystallographic software, is gaining a lot of attention in all areas of research. In the recent years, many achievements using electron diffraction techniques have been made in the fields of organic and inorganic molecules, polymorphism, geological sciences, natural products, biomolecules, material sciences, energetic materials, batteries, and many others [2-4]. Such experiments are currently done in a (modified) transmission electron microscope, thus requiring customized experimental and data-analysis protocols, which vary depending on each specific instrumental setup. Hence, 3D ED experiments are currently carried out only by specialized staff and require a remarkable investment in terms of time, expertise, knowhow transfer and resources.

A strong need has emerged in the crystallographic community for instrumentation specifically dedicated to 3D ED experiments.

Here we present an electron diffractometer: a new device developed and optimized exclusively for 3D ED which allows a time-effective, automated and standardized experimental workflow along with user-friendly operability. Furthermore, the electron diffractometer is conceived to make use exclusively of well-established crystallographic approaches and to interact seamlessly with readily available crystallographic software. Experimental examples of different kind of materials measured with this device will be showcased.

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