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Organic cages can possess complex, functionalised cavities that make them promising candidates for synthetic enzyme mimics. Conformationally flexible, chemically robust structures are needed for adaptable guest binding and catalysis, but rapidly exchanging systems are difficult to resolve in solution. Here, we use low-cost calculations and high-throughput crystallisation to identify accessible conformers of a recently reported organic cage by 'locking' them in the solid state. The conformers exhibit varying distances between the internal carboxylic acid groups, suggesting adaptability for binding a wide array of target guest molecules. [ABSTRACT FROM AUTHOR]

Autonomous laboratories can accelerate discoveries in chemical synthesis, but this requires automated measurements coupled with reliable decision-making 1,2 . Most autonomous laboratories involve bespoke automated equipment 3-6 , and reaction outcomes are often assessed using a single, hard-wired characterization technique 7 . Any decision-making algorithms 8 must then operate using this narrow range of characterization data 9,10 . By contrast, manual experiments tend to draw on a wider range of instruments to characterize reaction products, and decisions are rarely taken based on one measurement alone. Here we show that a synthesis laboratory can be integrated into an autonomous laboratory by using mobile robots 11-13 that operate equipment and make decisions in a human-like way. Our modular workflow combines mobile robots, an automated synthesis platform, a liquid chromatography-mass spectrometer and a benchtop nuclear magnetic resonance spectrometer. This allows robots to share existing laboratory equipment with human researchers without monopolizing it or requiring extensive redesign. A heuristic decision-maker processes the orthogonal measurement data, selecting successful reactions to take forward and automatically checking the reproducibility of any screening hits. We exemplify this approach in the three areas of structural diversification chemistry, supramolecular host-guest chemistry and photochemical synthesis. This strategy is particularly suited to exploratory chemistry that can yield multiple potential products, as for supramolecular assemblies, where we also extend the method to an autonomous function assay by evaluating host-guest binding properties., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

77 Se-NMR is used to characterise several chalcogen bonded complexes of derivatives of the organoselenium drug ebselen, exploring a range of electron demand. NMR titration experiments support the intuitive understanding that chalcogen bond donors bearing more electron withdrawing substituents give rise stronger chalcogen bonds. The chemical shift of the selenium nucleus is also shown to move upfield as it participates in a chalcogen bond. Solid-state NMR is used to explore chalcogen bonding in co-crystals. Due to the lack of molecular reorientation on the NMR timescale in the solid state, the shape of the chemical shift tensor can be determined using this technique. A range of co-crystals are shown to have extremely large chemical shift anisotropy, which suggests a strongly anisotropic electron density distribution around the selenium atom. A single crystal NMR experiment was conducted using one of the co-crystals, affording the absolute orientation of the chemical shift tensor within the crystal. This showed that the selenium nucleus is strongly shielded in the direction of the chalcogen bond (due to the approach of the lone pair of the Lewis base), and strongly deshielded in the perpendicular direction. The orientation of the deshielded axis is consistent with the presence of a second σ-hole which is not participating in a chalcogen bond, showing the profound effect of electron density anisotropy on the chemical shift., (© 2024 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

The transformation of two-dimensional (2D) covalent-organic frameworks (COFs) into three-dimensions (3D) is synthetically challenging, and it is typically addressed through interlayer cross-linking of alkene or alkyne bonds. Here, we report the first example of the chemical reconstruction of a 2D COF to a 3D COF with a complete lattice rearrangement facilitated by base-triggered boron hybridization. This chemical reconstruction involves the conversion of trigonal boronate ester linkages to tetrahedral anionic spiroborate linkages. This transformation reticulates the coplanar, closely stacked square cobalt(II) phthalocyanine (PcCo) units into a 3D perpendicular arrangement. As a result, the pore size of COFs expands from 2.45 nm for the initial 2D square lattice ( sql ) to 3.02 nm in the 3D noninterpenetrated network ( nbo ). Mechanistic studies reveal a base-catalyzed boronate ester protodeboronation pathway for the formation of the spiroborate structure.

Soft porous crystals combine flexibility and porosity, allowing them to respond structurally to external physical and chemical environments. However, striking the right balance between flexibility and sufficient rigidity for porosity is challenging, particularly for molecular crystals formed by using weak intermolecular interactions. Here, we report a flexible oxygen-bridged prismatic organic cage molecule, Cage-6-COOH , which has three pillars that exhibit "hinge-like" rotational motion in the solid state. Cage-6-COOH can form a range of hydrogen-bonded organic frameworks (HOFs) where the "hinge" can accommodate a remarkable 67° dihedral angle range between neighboring units. This stems both from flexibility in the noncovalent hydrogen-bonding motifs in the HOFs and the molecular flexibility in the oxygen-linked cage hinge itself. The range of structures for Cage-6-COOH includes two topologically complex interpenetrated HOFs, CageHOF-2α and CageHOF-2β . CageHOF-2α is nonporous, while CageHOF-2β has permanent porosity and a surface area of 458 m 2 g -1 . The flexibility of Cage-6-COOH allows this molecule to rapidly transform from a low-crystallinity solid into the two crystalline interpenetrated HOFs, CageHOF-2α and CageHOF-2β , under mild conditions simply by using acetonitrile or ethanol vapor, respectively. This self-healing behavior was selective, with the CageHOF-2β structure exhibiting structural memory behavior.

Hydrogen-bonded organic frameworks (HOFs) with low densities and high porosities are rare and challenging to design because most molecules have a strong energetic preference for close packing. Crystal structure prediction (CSP) can rank the crystal packings available to an organic molecule based on their relative lattice energies. This has become a powerful tool for the a priori design of porous molecular crystals. Previously, we combined CSP with structure-property predictions to generate energy-structure-function (ESF) maps for a series of triptycene-based molecules with quinoxaline groups. From these ESF maps, triptycene trisquinoxalinedione (TH5) was predicted to form a previously unknown low-energy HOF (TH5-A) with a remarkably low density of 0.374 g cm -3 and three-dimensional (3D) pores. Here, we demonstrate the reliability of those ESF maps by discovering this TH5-A polymorph experimentally. This material has a high accessible surface area of 3,284 m 2  g -1 , as measured by nitrogen adsorption, making it one of the most porous HOFs reported to date., (© 2023 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

Molecular packing controls optoelectronic properties in organic molecular nanomaterials. Here we report a donor-acceptor organic molecule (2,6-bis(4-cyanophenyl)-4-(9-phenyl-9H-carbazol-3-yl)pyridine-3,5-dicarbonitrile) that exhibits two aggregate states in aqueous dispersions: amorphous nanospheres and ordered nanofibres with π-π molecular stacking. The nanofibres promote sacrificial photocatalytic H 2 production (31.85 mmol g -1  h -1 ) while the nanospheres produce hydrogen peroxide (H 2 O 2 ) (3.20 mmol g -1 h -1 in the presence of O 2 ). This is the first example of an organic photocatalyst that can be directed to produce these two different solar fuels simply by changing the molecular packing. These different packings affect energy band levels, the extent of excited state delocalization, the excited state dynamics, charge transfer to O 2 and the light absorption profile. We use a combination of structural and photophysical measurements to understand how this influences photocatalytic selectivity. This illustrates the potential to achieve multiple photocatalytic functionalities with a single organic molecule by engineering nanomorphology and solid-state packing., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)

The crystal structure of the pyridine-substituted benzisoselenazolinone 2-(pyridin-3-yl)-2,3-dihydro-1,2-benzoselenazol-3-one (C 12 H 8 N 2 OSe, 2), related to the antioxidant ebselen [systematic name: 2-phenyl-1,2-benzoselenazol-3(2H)-one, 1], is characterized by strong intermolecular N...Se(-N) chalcogen bonding, where the N...Se distance of 2.3831 (6) Å is well within the sum of the van der Waals radii for N and Se (3.34 Å). This strong interaction results in significant lengthening of the internal N-Se distance, consistent with significant population of the Se-N σ* antibonding orbital. Much weaker intermolecular O...Se chalcogen bonding occurs between the amide-like O atom in 2 and the less polarized C-Se bond in this structure. Charge density analysis of 2 using multipole refinement of high-resolution data allowed the electrostatic surface potential for 2 to be mapped, and clearly reveals the σ-hole at the extension of the Se-N bond as an area of positive electrostatic potential. Topological analysis of the electron-density distribution in 2 was carried out within the Quantum Theory of Atoms in Molecules (QTAIM) framework and revealed bond paths and (3,-1) bond critical points (BCPs) for the N...Se-N moiety consistent with a closed-shell interaction; however, the potential energy term is suggestive of electron sharing. Analysis of the electron localization function (ELF) for the strong N...Se and the weak O...Se chalcogen-bonding interactions in the structure of 2 suggest significant electron sharing in the former interaction, and a largely electrostatic interaction in the latter. Conversion of 2 to its N-methylated derivatives by reaction with methyl iodide [1-methyl-3-(3-oxo-2,3-dihydro-1,2-benzoselenazol-2-yl)pyridin-1-ium iodide, C 13 H 11 N 2 OSe + ·I - ] and methyl tosylate [1-methyl-3-(3-oxo-2,3-dihydro-1,2-benzoselenazol-2-yl)pyridin-1-ium toluenesulfonate trihydrate, C 13 H 11 N 2 OSe + ·C 7 H 7 O 3 S - ·3H 2 O] removes the possibility of N...Se chalcogen bonding and instead structures are obtained where the iodide and tosylate counter-ions fulfill the role of chalcogen-bond acceptors, with a strong I - ...Se interaction in the iodide salt and a weaker p-Tol-SO 3 - ...Se interaction in the tosylate salt., (open access.)

The acyloin natural products are a family of bioactive compounds isolated from fungi and myxobacteria. The total synthesis of 7 members of the acyloin family was achieved via a HWE reaction followed by Mukaiyama-Isayama hydration, using novel Co(II) and Co(III) Schiff base SALPN complexes as catalysts for the key enone hydration step. Furthermore, we have shown that a mild acyloin rearrangement is possible under Mukaiyama hydration conditions, which was crucial in the success of this approach.

The organoselenium compound ebselen has recently been investigated as a treatment for COVID-19; however, efforts to model ebselen in silico have been hampered by the lack of an efficient and accurate method to assess its binding to biological macromolecules. We present here a Generalized Amber Force Field modification which incorporates classical parameters for the selenium atom in ebselen, as well as a positively charged pseudoatom to simulate the σ-hole, a quantum mechanical phenomenon that dominates the chemistry of ebselen. Our approach is justified using an energy decomposition analysis of a number of density functional theory-optimized structures, which shows that the σ-hole interaction is primarily electrostatic in origin. Finally, our model is verified by conducting molecular dynamics simulations on a number of simple complexes, as well as the clinically relevant enzyme SOD1 (superoxide dismutase), which is known to bind to ebselen. Graphical Abstract Ebselen is an organoselenium drug that has shown promise for the treatment of a number of conditions. Computational modelling of drug-target complexes is commonly performed to determine the likely mechanism of action, however this is difficult in the case of ebselen, as an important mode of interaction is not simulated using current techniques. We present here an extension to common methods, which accurately captures this interaction., (© 2022. The Author(s).)

We present the CHAL336 benchmark set-the most comprehensive database for the assessment of chalcogen-bonding (CB) interactions. After careful selection of suitable systems and identification of three high-level reference methods, the set comprises 336 dimers each consisting of up to 49 atoms and covers both σ- and π-hole interactions across four categories: chalcogen-chalcogen, chalcogen-π, chalcogen-halogen, and chalcogen-nitrogen interactions. In a subsequent study of DFT methods, we re-emphasize the need for using proper London dispersion corrections when treating noncovalent interactions. We also point out that the deterioration of results and systematic overestimation of interaction energies for some dispersion-corrected DFT methods does not hint at problems with the chosen dispersion correction but is a consequence of large density-driven errors. We conclude this work by performing the most detailed DFT benchmark study for CB interactions to date. We assess 109 variations of dispersion-corrected and dispersion-uncorrected DFT methods and carry out a detailed analysis of 80 of them. Double-hybrid functionals are the most reliable approaches for CB interactions, and they should be used whenever computationally feasible. The best three double hybrids are SOS0-PBE0-2-D3(BJ), revDSD-PBEP86-D3(BJ), and B2NCPLYP-D3(BJ). The best hybrids in this study are ωB97M-V, PW6B95-D3(0), and PW6B95-D3(BJ). We do not recommend using the popular B3LYP functional nor the MP2 approach, which have both been frequently used to describe CB interactions in the past. We hope to inspire a change in computational protocols surrounding CB interactions that leads away from the commonly used, popular methods to the more robust and accurate ones recommended herein. We would also like to encourage method developers to use our set for the investigation and reduction of density-driven errors in new density functional approximations.

Molecular rotors exhibit fluorescence enhancement in a confined environment and thus have been used extensively in biological imaging. However, many molecular rotors suffer from small Stokes shift and self-aggregation caused quenching. In this work, we have synthesised a series of red emissive molecular rotors based on cationic α-cyanostilbene. Profoundly enhanced aggregation-induced emission (AIE) properties and greatly widened Stokes shifts can be achieved by molecular engineering. With specificity to stain mitochondria, we demonstrate a simple approach to achieve cell uptake and retention upon tuning the pyridinium substituent of the dyes.

An o-nitro-O-aryl oxime was observed to exhibit a short OO contact, which exhibited characteristics consistent with a chalcogen bond. The O-N bond length of the oxime was appreciably longer than the expected value, and NBO calculations indicated the presence of a n(O) → σ(O-N) orbital delocalisation. Topological analysis of the experimental electron density of two analogues shows the presence of a bond path between the two oxygen atoms, with ρ(r) and ∇2ρ(r) values consistent with an electrostatic interaction. Finally, electrostatic potential calculations indicate the presence of a σ-hole, the "smoking gun" indicating a Ch-bond. These results are unusual as oxygen is not typically considered to be a Ch-bond donor, especially in unactivated systems such as oximes.

Methyl pro-amine { N , N ,3-trimethyl-4-[6-(4-methyl-piperazin-1-yl)-1 H ,3' H -[2,5'-bibenzo[ d ]imidazol]-2'-yl]aniline}, C 28 H 35 N 7 O 2 , crystallized as both a dihydrate, C 28 H 31 N 7 ·2H 2 O, and monohydrate, C 28 H 31 N 7 ·H 2 O, form from water in the presence of β-cyclo-dextrin, in the P 2 1 / c and P 2 1 / n space groups, respectively. The two structures adopt different conformations and tautomeric forms as a result of the differing crystal packing as dictated by hydrogen-bonding inter-actions. The dihydrate crystallizes as a three-dimensional hydrogen-bonded network, while the monohydrate crystallizes as a two-dimensional hydrogen-bonded network.