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True molecular conformation and structure determination of remarkable polycyclic aromatic hydrocarbons
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ECM33 BOOK OF ABSTRACTS
279
MS39 Crystallography at the nanoscale
MS39-03
True molecular conformation and structure determination of remarkable polycyclic aromatic hydrocarbons
I. Andrusenko 1, E. Mugnaioli 2, M. Gemmi 1, W. Schmidt 3
1Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography - Pontedera (Italy),
2Università di Pisa, Dipartimento di Scienze della Terra - Pisa (Italy), 3PAH Research - Igling-Holzhausen
(Germany)
Abstract
The true molecular conformation and the crystal structure of four large (30 – 46 C atoms) polycyclic aromatic
hydrocarbons (PAHs)1,2 were determined by direct methods from 3D electron diffraction (3D ED)3 data, a result
that could not be achieved by single crystal X-ray diffraction (XRD) due to limited crystal size and the thin leaflet
morphology of the samples. Additionally, three of such compounds were isolated as by-products in the synthesis
of similar materials and, therefore, were available only in very limited amount.
The main strength of 3D ED is the ability to perform single crystal diffraction on sub-micrometric areas. Therefore,
this technique can be used for structure determination when crystal size is the limiting factor for single crystal
XRD. Remarkably, this analytical protocol can be performed even on extremely small sample batches, which
cannot be conveniently prepared for conventional powder XRD.
Moreover, the molecular conformation of two compounds could not be determined via classical spectroscopic
methods due to the large size of the molecules and the occurrence of multiple and reciprocally connected
aromatic rings. On the other hand, 3D ED data provided not only ab-initio structure solution, but also the
unbiased determination of the internal molecular conformation. It is noteworthy that ab-initio crystal structure
determination does not require information about the molecular conformation, but only a rough estimation of the
atomic content of the unit cell.
The other two compounds were synthesised more than 50 years ago, but have hitherto remained structurally
unsolved. All molecules have a considerable interest due to their optoelectronic properties, which led to the
creation of a number of functionalised materials based on PAH backbones. Detailed synthetic routes,
spectroscopic analyses and promising properties are also discussed.
References
1. Hall, C. L., Andrusenko, I., Potticary, J., Gao, S., Liu, X., Schmidt, W., Marom, N., Mugnaioli, E., Gemmi, M.
& Hall, S. R. (2021) 3D Electron Diffraction Structure Determination of Terrylene, a Promising Candidate for
Intermolecular Singlet Fission. ChemPhysChem 22(15), 1631-1637.
2. Andrusenko, I., Hall, C. L., Mugnaioli, E., Potticary, J., Schmidt, W., Gao, S., Marom, N., Hall, S. R. & Gemmi,
M. (2022) True Molecular Conformation and Structure Determination by 3D Electron Diffraction of PAH By-
Products Potentially Useful for Electronic Applications, in preparation.
3. Gemmi, M., Mugnaioli, E., Gorelik, T. E., Kolb, U., Palatinus, L., Boullay, P., Hovmöller, S. & Abrahams, J. P.
(2019) 3D Electron Diffraction: The Nanoctystallography Revolution. ACS Cent. Sci. 5, 1315-1329
Automated electron Diffraction Tomography (ADT) – a new technique for structure analysis
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Crystal Structure of New and Highly Complex Organic Molecules Solved by 3D Electron Diffraction
No full text3D electron diffraction allows data collection on nanocrystalline domains, which can be used as kinematical intensities in ab-initio structure solution methods. The development of single electron detectors for diffraction and of fast recording protocols based on continuous rotation of the sample have dramatically reduced the electron dose necessary for collecting a data set with a large coverage. With total doses of less than 1 el/Å2 very beam sensitive samples like organic and macromolecular crystals can now be studied by electron diffraction in nanocrystalline form. Examples of structure solution on known pharmaceutical compounds based on simulated annealing will be presented, as the structure solution attempted in case of low quality 3DED data. Combining STEM imaging with weak beams and the sensitivity of direct electron detectors we will show how it is possible to record high quality 3DED data on organic crystals without the need to work under cryo condition. Standard precession assisted step-wise 3DED data collection allowed the structure solution of metaxalone and of the unknown crystal structure of orthocetamol
Electron diffraction study of polyphasic nanocrystalline M2O-Al2O3-WO3 (M = Na, K) system
No full textOrganic Cocrystals of TCNQ and TCNB Based on an Orthocetamol Backbone Solved by Three-Dimensional Electron Diffraction
No full textWe report the first cocrystals of TCNQ and TCNB based on orthocetamol, a regioisomer of paracetamol. Through a simple solution growth process, cocrystals were produced containing orthocetamol as electron donors with coformers of either 7,7,8,8-tetracyanoquinodimethane (TCNQ) or 1,2,4,5-tetracyanobenzene (TCNB), as electron acceptors. Because of submicron crystalline domains, 3D electron diffraction was employed for structure solution in both systems. This revealed that both systems crystallize in a 1:1 stoichiometry in which orthocetamol forms a backbone allowing for linking of acceptor molecules in a mixed-stack configuration. Orthocetamol-TCNQ adopts an noncentrosymmetric Pc symmetry, and orthocetamol-TCNB a centrosymmetric P-1 symmetry. UV-vis and FT-IR were employed to probe the ability of these cocrystals to create charge transfer (CT) systems, revealing a low degree of charge transfer. Still, the possibility to use orthocetamol backbone as structural scaffold paves the way for an entirely new class of CT materials
Vaterite structure from electron diffraction data – a definitive answer for an old question?
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