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An emergent volume electron microscopy technique called cryogenic serial plasma focused ion beam milling scanning electron microscopy (pFIB/SEM) can decipher complex biological structures by building a three-dimensional picture of biological samples at mesoscale resolution. This is achieved by collecting consecutive SEM images after successive rounds of FIB milling that expose a new surface after each milling step. Due to instrumental limitations, some image processing is necessary before 3D visualization and analysis of the data is possible. SEM images are affected by noise, drift, and charging effects, that can make precise 3D reconstruction of biological features difficult. This article presents Okapi-EM, an open-source napari plugin developed to process and analyze cryogenic serial pFIB/SEM images. Okapi-EM enables automated image registration of slices, evaluation of image quality metrics specific to pFIB-SEM imaging, and mitigation of charging artifacts. Implementation of Okapi-EM within the napari framework ensures that the tools are both user- and developer-friendly, through provision of a graphical user interface and access to Python programming., Competing Interests: M.C.D. is an employee of SPT Labtech. The remaining authors declare that they have no competing interests., (© The Author(s) 2023.)

Serial focussed ion beam scanning electron microscopy (FIB/SEM) enables imaging and assessment of subcellular structures on the mesoscale (10 nm to 10 µm). When applied to vitrified samples, serial FIB/SEM is also a means to target specific structures in cells and tissues while maintaining constituents' hydration shells for in situ structural biology downstream. However, the application of serial FIB/SEM imaging of non-stained cryogenic biological samples is limited due to low contrast, curtaining, and charging artefacts. We address these challenges using a cryogenic plasma FIB/SEM. We evaluated the choice of plasma ion source and imaging regimes to produce high-quality SEM images of a range of different biological samples. Using an automated workflow we produced three-dimensional volumes of bacteria, human cells, and tissue, and calculated estimates for their resolution, typically achieving 20-50 nm. Additionally, a tag-free localisation tool for regions of interest is needed to drive the application of in situ structural biology towards tissue. The combination of serial FIB/SEM with plasma-based ion sources promises a framework for targeting specific features in bulk-frozen samples (>100 µm) to produce lamellae for cryogenic electron tomography., Competing Interests: MD, TG, JS, EH, LP, AP, SK, NY, DF, PL, WB, JP, LW, MB, DC, CS, JN, MG No competing interests declared, RK is an employee of ThermoFisher Scientific, MD is an employee of SPT Labtech, (© 2023, Dumoux et al.)

Conjugated polymers with glycol-based chains, are emerging as a material class with promising applications as organic mixed ionic-electronic conductors, particularly in bioelectronics and thermoelectrics. However, little is still known about their microstructure and the role of the side chains in determining intermolecular interactions and polymer packing. Here, we use the combination of electrospray deposition and scanning tunneling microscopy to determine the microstructure of prototypical glycolated conjugated polymers (pgBTTT and p(g2T-TT)) with submonomer resolution. Molecular dynamics simulations of the same surface-adsorbed polymers exhibit an excellent agreement with the experimental images, allowing us to extend the characterization of the polymers to the atomic scale. Our results prove that, similarly to their alkylated counterparts, glycolated polymers assemble through interdigitation of their side chains, although significant differences are found in their conformation and interaction patterns. A model is proposed that identifies the driving force for the polymer assembly in the tendency of the side chains to adopt the conformation of their free analogues, i.e., polyethylene and polyethylene glycol, for alkyl or ethylene glycol side chains, respectively. For both classes of polymers, it is also demonstrated that the backbone conformation is determined to a higher degree by the interaction between the side chains rather than by the backbone torsional potential energy. The generalization of these findings from two-dimensional (2D) monolayers to three-dimensional thin films is discussed, together with the opportunity to use this type of 2D study to gain so far inaccessible, subnm-scale information on the microstructure of conjugated polymers.

Precise control of the microstructure in organic semiconductors (OSCs) is essential for developing high-performance organic electronic devices. Here, a comprehensive charge transport characterization of two recently reported rigid-rod conjugated polymers that do not contain single bonds in the main chain is reported. It is demonstrated that the molecular design of the polymer makes it possible to achieve an extended linear backbone structure, which can be directly visualized by high-resolution scanning tunneling microscopy (STM). The rigid structure of the polymers allows the formation of thin films with uniaxially aligned polymer chains by using a simple one-step solution-shear/bar coating technique. These aligned films show a high optical anisotropy with a dichroic ratio of up to a factor of 6. Transport measurements performed using top-gate bottom-contact field-effect transistors exhibit a high saturation electron mobility of 0.2 cm 2 V -1 s -1 along the alignment direction, which is more than six times higher than the value reported in the previous work. This work demonstrates that this new class of polymers is able to achieve mobility values comparable to state-of-the-art n-type polymers and identifies an effective processing strategy for this class of rigid-rod polymer system to optimize their charge transport properties., (© 2020 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

A fused donor, thienobenzo[ b ]indacenodithiophene ( TBIDT ), was designed and synthesized using a novel acid-promoted cascade ring closure strategy, and then copolymerized with a benzothiadiazole ( BT ) monomer. The backbone of TBIDT is an expansion of the well-known indacenodithiophene ( IDT ) unit and was expected to enhance the charge carrier mobility by improving backbone planarity and facilitating short contacts between polymer chains. However, the optimized field-effect transistors demonstrated an average saturation hole mobility of 0.9 cm 2 V -1 s -1 , lower than the performance of IDT-BT (∼1.5 cm 2 V -1 s -1 ). Mobilities extracted from time-resolved microwave conductivity measurements were consistent with the trend in hole mobilities in organic field-effect transistor devices. Scanning tunneling microscopy measurements and computational modeling illustrated that TBIDT-BT exhibits a less ordered microstructure in comparison to IDT-BT . This reveals that a regular side-chain packing density, independent of conformational isomers, is critical to avoid local free volume due to irregular packing, which can host trapping impurities. DFT calculations indicated that TBIDT-BT , despite containing a larger, planar unit, showed less stabilization of planar backbone geometries in comparison to IDT-BT . This is due to the reduced electrostatic stabilizing interactions between the peripheral thiophene of the fused core and the BT unit, resulting in a reduction of the barrier to rotation around the single bond. These insights provide a greater understanding of the general structure-property relationships required for semiconducting polymer repeat units to ensure optimal backbone planarization, as illustrated with IDT -type units, guiding the design of novel semiconducting polymers with extended fused backbones for high-performance field-effect transistors.

The solid-state microstructure of a conjugated polymer is the most important parameter determining its properties and performance in (opto)-electronic devices. A huge amount of research has been dedicated to tuning and understanding how the sequence of monomers, the nature and frequency of defects, the exact backbone conformation, and the assembly and crystallinity of conjugated polymers affect their basic photophysics and charge transporting properties. However, because of the lack of reliable high-resolution analytical techniques, all the structure-property relations proposed in the literature are based either on molecular modeling or on indirect experimental data averaged on polydisperse samples. We show that a combination of electrospray vacuum deposition and high-resolution scanning tunneling microscopy allows the imaging of individual conjugated polymers with unprecedented detail, thereby unraveling structural and self-assembly characteristics that have so far been impossible to determine.

The ability to control the transition from a two-dimensional (2D) monolayer to the three-dimensional (3D) molecular structure in the growth of organic layers on surfaces is essential for the production of functional thin films and devices. This has, however, proved to be extremely challenging, starting from the currently limited ability to attain a molecular scale characterization of this transition. Here, through innovative application of low-dose electron diffraction and aberration-corrected transmission electron microscopy (acTEM), combined with scanning tunneling microscopy (STM), we reveal the structural changes occurring as film thickness is increased from monolayer to tens of nanometers for supramolecular assembly of two prototypical benzenecarboxylic acids - terephthalic acid (TPA) and trimesic acid (TMA) - on graphene. The intermolecular hydrogen bonding in these molecules is similar and both form well-ordered monolayers on graphene, but their structural transitions with film thickness are very different. While the structure of TPA thin films varies continuously towards the 3D lattice, TMA retains its planar monolayer structure up to a critical thickness, after which a transition to a polycrystalline film occurs. These distinctive structural evolutions can be rationalized in terms of the topological differences in the 3D crystallography of the two molecules. The templated 2D structure of TPA can smoothly map to its 3D structure through continuous molecular tilting within the unit cell, whilst the 3D structure of TMA is topologically distinct from its 2D form, so that only an abrupt transition is possible. The concept of topological protection of the 2D structure gives a new tool for the molecular design of nanostructured films.