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To make modern data management and analysis that is committed to FAIR principles and improved reproducibility a reality, Flanders BioImaging in a team effort with the Flemish supercomputing center (Vlaams Supercomputer Centrum, VSC) and KU Leuven’s central IT infrastructure, is exploring new models for data management, metadata handling, and image analysis., Grant FWO: Flanders BioImaging Leading Imaging Application Integrated Service & Enablement (FBI-LIAISE) 2023-2026

Despite the central role of aromaticity in the chemistry of expanded porphyrins, the evaluation of aromaticity remains difficult for these extended macrocycles. The presence of multiple conjugation pathways and different planar and nonplanar π-conjugation topologies makes the quantification of global and local aromaticity even more challenging. In neutral expanded porphyrins, the predominance of the aromatic conjugation pathway passing through the imine-type nitrogens and circumventing the amino NH groups is established. However, for charged macrocycles, the question about the main conjugation circuit remains open. Accordingly, different conjugation pathways in a set of neutral, anionic, and cationic expanded porphyrins were investigated by means of several aromaticity indices rooted in the structural, magnetic, and electronic criteria. Overall, our results reveal the predominance of the conjugation pathway that passes through all nitrogen atoms to describe the aromaticity of deprotonated expanded porphyrins, while the outer pathway through the perimeter carbon atoms becomes the most aromatic in protonated macrocycles. In nonplanar and charged macrocycles, a discrepancy between electronic and magnetic descriptors is observed. Nevertheless, our work demonstrates AVmin remains the best tool to determine the main conjugation pathway of expanded porphyrins. M.A. and I.C.R. wish to acknowledge the VUB for a Strategic Research Program awarded to ALGC. The resources and services used in this work were provided by the Flemish Supercomputer Center (VSC), funded by the Research Foundation - Flanders (FWO), and the Flemish Government. I.C.R. acknowledges co-funding from the European Union′s Horizon 2020 research and innovation Maria Skłodowska-Curie Actions, under grant agreement number 945380. It has been also supported by grants from the Spanish government MICINN (PGC2018-098212-B-C21, PID2019-104772GB, PID2019-105488GB-I00, and PCI2019-103657), Diputación Foral de Gipuzkoa (2019-CIEN-000092-01), Gobierno Vasco (IT1346-19, IT1254-19, and PIBA19-0004), and the DIPC (DIPC_INV_003132). Open Access funding provided by University of Basque Country.

Summary report about a workshop on research data management and data deposition for biological images. This workshop took place on 23/06/2022 and was organized by VIB and Flanders Bioimaging consortium in collaboration with Elixir Belgium and Flemish Supercomputer Center. https://training.vib.be/all-trainings/workshop-data-management-and-data-deposition-biological-images, {"references":["Woller, Tatiana, Botzki, Alexander and Munck, Sebastian (2022, October), Workshop on data management and data deposition for biological images"]}

Expanded porphyrins are currently recognized as the ideal test bed to explore the correlation between molecular properties and (anti)aromaticity since they can adopt different π-conjugation topologies and change easily the number of π-electrons along the conjugation pathway. From recent studies, aromaticity indeed emerges as the guiding concept to rationalize the spectroscopic features and the two-photon absorption cross sections in expanded porphyrins. However, from the theoretical point of view, the complex structure-property relationship between aromaticity, π-conjugation topology, and photophysical properties is not fully understood yet. To unravel such structure-property relationships, we focused on octaphyrin(1.1.1.1.1.1.1.1) macrocycles since they are flexible enough to provide twisted-Hückel, Möbius, and Hückel untwisted topologies with distinct aromaticity character. In this work, the (anti)aromaticity of the different states was first quantified using different aromaticity criteria. Second, the fingerprints of aromaticity on UV/vis spectra were elucidated. Importantly, we found that the absorption spectra of certain antiaromatic Hückel structures are characterized by more intense absorption bands than its aromatic homologues, contrary to the general statement that antiaromatic expanded porphyrins exhibit significantly attenuated absorption bands compared to aromatic ones. Finally, the role of aromaticity and π-conjugation topology on linear and nonlinear optical properties was scrutinized and our results pinpoint the importance of molecular topology and symmetry on the first and second hyperpolarizabilities. Overall, we demonstrate that expanded porphyrins upon topology interconversions can act as efficient nonlinear optical switches. ©

Non-covalent interactions involving aromatic rings play a central role in many areas of modern chemistry. In medicinal and bioorganic chemistry, the intermolecular interactions between the aromatic side chains of amino acids, such as phenylalanine and tyrosine, are of great interest. To enhance the affinity between such aromatic side chains, halogenation is a promising modification strategy. In the current work, the nature and strength of halogenated p-p stacked phenylalanine (Phe) dimers have been investigated using density functional theory, energy decomposition analyses and the non-covalent interaction (NCI) method. Our analysis shows that increasing the degree of halogenation enhances the strength of the stacking interactions and, moreover, the heavier halides (Cl, Br and I) lead to stronger interactions compared to the lighter F. This effect was traced back to local secondary interactions of the halide with the aliphatic C-H bonds of the phenylalanine side chain. Based on the computational findings, a set of peptide hydrogelators was synthesized, and the resulting hydrogel properties were further investigated via dynamic rheometry. Experimental observations can be correlated to the trends found in the theoretical analysis, suggesting that local interactions indeed play a noticeable role in enhancing peptide-based hydrogel strength. This journal is

Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. Taking into account its size and huge conformational flexibility, DFT remains the workhorse for modeling such extended macrocycles. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, p···p stacking, steric effects, ring strain and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wavefunction methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a pronouncedly stronger degree of static correlation than the Hückel and figure-eight structures, and as a result the relative energies of singly-twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between MP2/cc-pVDZ and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol-1 with the CCSD(T) relative energies. Regarding DFT methods, only M06-2X provides relative errors close to chemical accuracy with a RMSD of 1.2 kcal mol-1. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended p-systems, the errors drop down to 2 kcal mol-1 for the revised revDSD-PBEP86-NL, again showing that same-spin MP2-like correlation has a detrimental impact on performance like the SOS-MP2 results.

Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. DFT remains the workhorse for modeling such extended macrocycles, when taking into account their size and huge conformational flexibility. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, π···π stacking, steric effects, ring strain, and electron delocalization. As a consequence, the selection of an exchange–correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wave function methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a stronger degree of static correlation than the Hückel and twisted-Hückel structures, and as a result the relative energies of singly twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between the extrapolated MP2/CBS energies estimated from cc-pV{T,Q}Z, diffuse-augmented heavy-aug-cc-pV{T,Q}Z and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol–1 with the CCSD(T) relative energies. Regarding DFT methods, the range-separated double hybrids, such as ωB97M(2) and B2GP-PLYP, outperform other functionals with RMSDs of 0.6 and 0.8 kcal mol–1, respectively. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended π-systems, the errors drop down to 1.9 kcal mol–1 for the revised revDOD-PBEP86-NL, which eliminates the same-spin correlation energy. Minnesota meta-GGA functionals with high fractions of exact exchange (M06-2X and M08-HX) also perform reasonably well, outperforming more robust and significantly less empirically parametrized functionals like SCAN0-D3.

The importance of axially chiral biaryls has risen steeply in the recent decades. This structural motif proved to be successful in catalytic asymmetric synthesis and the configuration of the biaryl axis is decisive for the biological activity. A new approach for the atroposelective synthesis of biaryls would be through a cycloaddition between an enantiopure phenyl-substituted thiophene S-oxide and an alkyne. Importantly, the chiral center of the thiophene S-oxide needs to be stable enough to avoid pyramidal inversion during the cycloaddition. Considering that the racemization of thiophene monoxides has been scarcely investigated so far, we perform a thorough quantum chemical study on the inversion barriers of a large number of chiral thiophene S-oxide derivatives. Our main goal is to identify substitution patterns leading to stable atropisomers at room temperature. Appealingly, the role of stereoelectronic effects and the position of the substituents as well as the importance of aromaticity on the pyramidal inversion barrier are elucidated for the first time.

International audience; The role of aromaticity in porphyrinoids is a current subject of debate due to the intricate structure of these macrocycles, which in some cases adopt Hückel, Möbius and even figure-eight conformers. One of the main challenges in these large π-conjugated structures is identifying the most conjugated pathway because, among aromaticity descriptors, there are very few that can be applied coherently to this variety of conformers. In this paper, we have investigated the conjugated pathways in nine porphyrinoid compounds using several aromaticity descriptors, including BLA, BOA, FLU and HOMA, as well as the recently introduced AV1245 and AVmin indices. All the indices agree on the general features of these compounds, such as the fulfillment of Hückel's rule or which compounds should be more or less aromatic from the series. However, our results evince the difficulty in finding the most aromatic pathway in the macrocycle for large porphyrinoids. In fact, only AVmin is capable of recognizing the annulene pathway as the most aromatic one in the nine studied structures. Finally, we study the effect of the exchange in DFT functionals on the description of the aromaticity of the porphyrinoids. The amount of exact exchange quantitatively changes the picture for most aromaticity descriptors, AVmin being the only exception that shows the same qualitative results in all cases.

International audience; Describing non-covalent interactions (NCIs) has shown to be of paramount importance in many areas of theoretical chemistry and related disciplines, such as biochemistry and material science. However, non-covalent interactions are subtle effects, very difficult to reproduce from most common computational approaches. Electron density studies have shown to provide a good semiquantitative visual approach to such interactions, which are much less prone to method dependency. But to which extent? This is the question addressed in this contribution. The NCI approach based on the reduced density gradient is given the third degree so as to provide the user with a benchmark on how it is affected by the computational method and the basis set of choice. We have assessed the dependence of the NCI results on the geometry. This last question is addressed in detail to dissect how, why and when the NCI method can be used to understand dispersion interactions. Along various examples, we will show that the NCI index is very little dependent on the method and basis set used in the calculation of the electron density as long as the geometry is kept fixed. Indeed, the biggest variations in NCI come from changes in the geometry. Thus, methods which provide descriptions of a given interaction type of different accuracies will yield different electron density organizations. This gives no qualitative variations in the NCI 3D picture. But it is reflected in quantitative NCI measures even in very subtle cases. Moreover, in the case of a failure of the calculation method, NCI can also reveal the sources of its error. NCI volumes are able to locate the energetic ordering in various conformational situations, but always in a relative manner. Absolute values should not be used in comparisons, nor between compounds that do not belong to the same family.

International audience; In recent years, expanded porphyrins have emerged as a promising class of π-conjugated molecules that display unique electronic, optical and conformational properties. Several expanded porphyrins can switch between planar and twisted conformations, which have different photophysical properties. Such a change of topology involves a Hückel–Möbius aromaticity switch in a single molecule and it can be induced by solvent, pH and metallation. These features make expanded porphyrins suitable for the development of a novel type of molecular switches for molecular electronic devices. Octaphyrins consisting of eight pyrrole rings, exhibit twisted-Hückel, Möbius and Hückel π-conjugation topologies depending on the oxidation and protonation state, with distinct electronic structures and aromaticity. Our working hypothesis is that a significant change in the conductance of expanded porphyrins will be observed after the topology switching. Despite the potential of Hückel–Möbius systems as conductance switches, the relationship between the conductance and the molecular topology is not yet understood. We have explored the performance of local descriptors of conductivity in simple molecules, as well as the relationship with conductance. Since these indexes provide a qualitative measure of delocalization and conductance in the probe molecules, we have carried out a local analysis of electrical conductance changes as a function of the π-conjugation in two examples. In one of them, the locality of the electronic changes ensures the ability of these indexes to describe the conductance as local. Moreover, it enables to identify which conformational switch would be more efficient from an electronic device perspective. However, we also show that it is not always possible to reduce conductance changes to one bond, and in those molecules where a deep rearrangement occurs far from the structural perturbation, local measures show a limited efficiency. This is a first step for the description of the connection between the molecular structure and conductance in molecular switches.

With their versatile molecular topology and aromaticity, porphyrinoid systems combine remarkable chemistry with interesting photophysical properties and nonlinear optical properties. Hence, the field of application of porphyrinoids is very broad ranging from near-infrared dyes to opto-electronic materials. From previous experimental studies, aromaticity emerges as an important concept in determining the photophysical properties and two-photon absorption cross sections of porphyrinoids. Despite a considerable number of studies on porphyrinoids, few investigate the relationship between aromaticity, UV/vis absorption spectra and nonlinear properties. To assess such structure-property relationships, we performed a computational study focusing on a series of H&uuml, ckel porphyrinoids to: (i) assess their (anti)aromatic character, (ii) determine the fingerprints of aromaticity on the UV/vis spectra, (iii) evaluate the role of aromaticity on the NLO properties. Using an extensive set of aromaticity descriptors based on energetic, magnetic, structural, reactivity and electronic criteria, the aromaticity of [4n+2] &pi, electron porphyrinoids was evidenced as was the antiaromaticity for [4n] &pi, electron systems. In agreement with previous studies, the absorption spectra of aromatic systems display more intense B and Q bands in comparison to their antiaromatic homologues. The nature of these absorption bands was analyzed in detail in terms of polarization, intensity, splitting and composition. Finally, quantities such as the average polarizability and its anisotropy were found to be larger in aromatic systems, whereas first and second hyperpolarizability are influenced by the interplay between aromaticity, planarity and molecular symmetry. To conclude, aromaticity dictates the photophysical properties in porphyrinoids, whereas it is not the only factor determining the magnitude of NLO properties.

Noncovalent interactions involving aromatic rings, such as π-stacking and CH/π interactions, are central to many areas of modern chemistry. However, recent studies proved that aromaticity is not required for stacking interactions, since similar interaction energies were computed for several aromatic and aliphatic dimers. Herein, the nature and origin of π/π, σ/σ, and σ/π dispersion interactions has been investigated by using dispersion-corrected density functional theory, energy decomposition analysis, and the recently developed noncovalent interaction (NCI) method. Our analysis shows that π/π and σ/σ stacking interactions are equally important for the benzene and cyclohexane dimers, explaining why both compounds have similar boiling points. Also, similar dispersion forces are found in the benzene⋅⋅⋅methane and cyclohexane⋅⋅⋅methane complexes. However, for systems larger than naphthalene, there are enhanced stacking interactions in the aromatic dimers adopting a parallel-displaced configuration compared to the analogous saturated systems. Although dispersion plays a decisive role in stabilizing all the complexes, the origin of the π/π, σ/σ, and σ/π interactions is different. The NCI method reveals that the dispersion interactions between the hydrogen atoms are responsible for the surprisingly strong aliphatic interactions. Moreover, whereas σ/σ and σ/π interactions are local, the π/π stacking are inherently delocalized, which give rise to a non-additive effect. These new types of dispersion interactions between saturated groups can be exploited in the rational design of novel carbon materials.

The performance of density functionals and wavefunction methods for describing the thermodynamics and kinetics of hydride reductions of 2-substituted cyclohexanones has been evaluated for the first time. A variety of exchange correlation functionals ranging from generalized gradient approximations to double hybrids have been tested and their performance to describe the facial selectivity of hydride reductions of cyclohexanones has been carefully assessed relative to the CCSD(T) method. Among the tested methods, an approach in which single-point energy calculations using the double hybrid B2PLYP-D3 functional on ωB97X-D optimized geometries provides the most accurate transition state energies for these kinetically-controlled reactions. Moreover, the role of torsional strain, temperature, solvation, noncovalent interactions on the stereoselectivity of these reductions was elucidated. Our results indicate a prominent role of the substituent on the cis/trans ratios driven by the delicate interplay between torsional strain and dispersion interactions. ispartof: Chemistryopen vol:8 issue:6 pages:788-806 ispartof: location:Germany status: Published online