The transcription factor p53 is exquisitely sensitive and selective to a broad variety of cellular environments. Several studies have reported that oxidative stress weakens the p53-DNA binding affinity for certain promoters depending on the oxidation mechanism. Despite this body of work, the precise mechanisms by which the physiologically relevant DNA-p53 tetramer complex senses cellular stresses caused by HO are still unknown. Here, we employed native mass spectrometry (MS) and ion mobility (IM)-MS coupled to chemical labelling and HO-induced oxidation to examine the mechanism of redox regulation of the p53-p21 complex. Our approach has found that two reactive cysteines in p53 protect against HO-induced oxidation by forming reversible sulfenates.

All-solid-state (ASS) batteries are a promising solution to achieve carbon neutrality. ASS lithium-sulfur (Li-S) batteries stand out due to their improved safety, achieved by replacing organic solvents, which are prone to leakage and fire, with solid electrolytes. In addition, these batteries offer the benefits of higher capacity and the absence of rare metals. However, the low electronic conductivity of sulfur poses a major challenge for ASS Li-S batteries. To address this challenge, sulfur is often combined with porous carbon. Despite this standard practice, the local structure of sulfur in these composites remains unclear. Based on small-angle X-ray scattering and pair distribution function analysis, we discovered that sulfur in carbon-sulfur composites formed via melt diffusion is amorphous and primarily comprises S ring-shaped structures. The carbon-sulfur composite demonstrated a high specific capacity of 1625 mAh g (97% of the theoretical specific capacity of sulfur). This remarkable performance is attributed to the extensive contact area between carbon and sulfur, which results in an excellent interface formed through melt diffusion. The insights gained into the local structure of sulfur and the analytical approaches employed enhanced our understanding of electrochemical reactions in ASS Li-S batteries, thereby aiding in the optimization of material design.

Iminophosphoranes with the general formula (RP═NR') have great potential in synthetic chemistry as valuable precursors/intermediates in organic synthesis or as building blocks for various organic compounds. However, the synthetic approaches and conditions to prepare iminophosphoranes are still poorly understood, limiting the utility of this chemistry for organic materials. In this article, a simple and efficient synthesis of previously unattainable poly(arylene iminophosphoranes) is reported. The azide-phosphine Staudinger polycondensation is used, and the reaction conditions are carefully studied, including consideration of light and air, the influence of solvent and temperature, and investigation of the electronic and steric effects of multiazides. The newly defined reaction conditions appear to be highly versatile, allowing the use of both electron-rich and electron-deficient arylazides for reaction with phosphines to synthesize a library of poly(arylene iminophosphorane) networks that exhibit exceptional thermal and oxidative stability. Interestingly, despite the ylidic-form of the iminophosphorane linkage as shown by theoretical calculations, these newly developed poly(arylene-iminophosphorane) networks exhibit semiconducting properties, such as absorption band edges up to 800 nm and optical band gaps in the range of 1.70 to 2.40 eV. Finally, we demonstrate the broad applicability of these polymers by processing them into glassy films, creating foam-like structures and synthesizing metallo-polymer hybrids.

The discovery of fullerene following the synthesis of graphene marked a paradigm shift in chemistry. Here, we report the discovery of biycycloborane, arising from the synthesis of borophane (hydrogen boride). Uniquely, this synthesis method involves a decomposition mechanism rather than traditional atom-by-atom assembly, marking an unique approach to constructing complex borane structures. The mass spectrometry unveiled that the stable molecule has a mass of 178 in atomic mass unit with a stoichiometry of BH. Optical spectra and simulations further evidenced its bicyclic structure, featuring fulvene-like heptagons or octagons. This borane molecule, analogous to cyclic hydrocarbons, adopts a unit configuration with a three-center two-electron (3c-2e) bonding, akin to diborane. The BH molecule has been historically anticipated as a distant descendant of the dodecahedron borane, but it was born from the hydrogen boride sheet with a non-symmorphic symmetry. The discovery of biycycloborane expands the frontiers of boron chemistry, promising advancements in boron-based nanomaterials and beyond.

Various photoactive molecules contain motifs built on aza-aromatic heterocycles, although a detailed understanding of the excited state photophysics and photochemistry in such systems is not fully developed. To help address this issue, the non-adiabatic dynamics operating in azanaphthalenes under hexane solvation was studied following 267 nm excitation using ultrafast transient absorption spectroscopy. Specifically, the species quinoline, isoquinoline, quinazoline, quinoxaline, 1,6-naphthyridine, and 1,8-naphthyridine were investigated, providing a systematic variation in the relative positioning of nitrogen heteroatom centres within a bicyclic aromatic structure. Our results indicate considerable differences in excited state lifetimes, and in the propensity for intersystem crossing vs internal conversion across the molecular series. The overall pattern of behaviour can be explained in terms of potential energy barriers and spin-orbit coupling effects, as demonstrated by extensive quantum chemistry calculations undertaken at the SCS-ADC(2) level of theory. The fact that quantum chemistry calculations can achieve such detailed and nuanced agreement with experimental data across a full set of six molecules exhibiting subtle variations in their composition provides an excellent example of the current state-of-the-art and is indicative of future opportunities for rational design of photoactive molecules.

Generative models have revolutionized de novo drug design, allowing to produce molecules on-demand with desired physicochemical and pharmacological properties. String based molecular representations, such as SMILES (Simplified Molecular Input Line Entry System) and SELFIES (Self-Referencing Embedded Strings), have played a pivotal role in the success of generative approaches, thanks to their capacity to encode atom- and bond- information and ease-of-generation. However, such 'atom-level' string representations could have certain limitations, in terms of capturing information on chirality, and synthetic accessibility of the corresponding designs.In this paper, we present fragSMILES, a novel fragment-based molecular representation in the form of string. fragSMILES encode fragments in a 'chemically-meaningful' way via a novel graph-reduction approach, allowing to obtain an efficient, interpretable, and expressive molecular representation, which also avoids fragment redundancy. fragSMILES contributes to the field of fragment-based representation, by reporting fragments and their 'breaking' bonds independently. Moreover, fragSMILES also embeds information of molecular chirality, thereby overcoming known limitations of existing string notations. When compared with SMILES, SELFIES and t-SMILES for de novo design, the fragSMILES notation showed its promise in generating molecules with desirable biochemical and scaffolds properties.

Validating thermodynamic models is essential in experimental geosciences for exploring increasingly complex systems and developing analytical protocols. However, investigating solid-fluid equilibria in mm-sized experimental capsules poses several challenges, particularly in sulfur-bearing chemical systems. These include maintaining bulk fluid composition and performing quantitative analysis with extremely low amounts of synthesized fluid. We present an innovative methodology for measuring ultra-low amounts of sulfur volatiles (HS and SO) generated during experimental runs at high pressure and temperature conditions of 3 GPa and 700 °C. Using solid sulfides (FeS + FeS) and water as reactants, we performed redox-controlled syntheses employing a piston cylinder apparatus. We demonstrate that ex-situ measurements of these fluids by quadrupole mass spectrometry ensure accurate and precise analysis, confirming predicted thermodynamic compositions. This methodology allows in-depht investigation of sulfide solid-fluid equilibria, shedding light on sulfur volatiles behavior and geochemical cycles under high P-T conditions characteristic of the Earth's interior.

Lactacystin is an irreversible proteasome inhibitor isolated from Streptomyces lactacystinicus. Despite its importance for its biological activity, the biosynthesis of lactacystin remains unknown. In this study, we identified the lactacystin biosynthetic gene cluster by gene disruption and heterologous expression experiments. We also examined the functions of the genes encoding a PKS/NRPS hybrid protein (LctA), NRPS (LctB), ketosynthase-like cyclase (LctC), cytochrome P450 (LctD), MbtH-like protein (LctE), and formyltransferase (LctF) by in vivo and in vitro experiments. In particular, we demonstrated that LctF directly transferred the formyl group of 10-N-formyl tetrahydrofolate to CoA. The formyl group of formyl-CoA was then transferred to ACP1 by LctA_AT1 to form formyl-ACP1. This is the first example of an AT domain recognizing a formyl group. The formyl group is perhaps transferred to methylmalonate tethered on LctA_ACP2 to yield methylmalonyl-semialdehyde-ACP2. Then, it would be condensed with leucine bound to PCP in LctB by the C domain in LctA. Using a mimic compound, we confirmed that LctC catalyzed the formation of the cyclic α,α-disubstituted amino acid structure with concomitant release of the product from PCP. Thus, we figured out the overall biosynthesis of lactacystin including a novel role of a formyl group in a secondary metabolite.

The interplay between attractive London dispersion forces and steric effects due to repulsive forces resulting from the Pauli principle often determines the geometry and stability of nanostructures. Aromatic polyimides (PI) and carbon nanotubes (CNT) were chosen as building blocks as two components in the hetero delocalized electron nanostructures. Two PIs, having the same diamine part and different linkage substituents between two phenyl rings of dianhydride part, one linked with ether bond (C-O-C) (OPI), the other with C-(CF3)2 (FPI), were investigated. Surprisingly, two CNT/PI nanocomposites show distinct failure mode from CNT yielding to CNT pull-out failure. Calculation of the interaction energy and chain conformations of each PI upon CNT was performed by accurate density functional theory (DFT) calculations and molecular dynamic simulation (MDS). OPI chain adopt helically wrapping conformation around CNT with relatively strong interaction energy. FPI chain take the one-side wavelike conformation upon CNT with relatively weak interaction energy.

Aqueous Zn batteries are gaining increasing research attention in the energy storage area due to their intrinsic safety, potentially low cost and environmental friendliness; however, the zinc dendrite formation, zinc corrosion, passivation and the hydrogen evolution reaction induced by water at the anode side, and materials dissolution as well as intrinsic poor reaction kinetics at cathode side in aqueous systems, seriously shorten the cycling life and decrease energy density of batteries and greatly hinder their development. Recent advancements in asymmetric electrolytes with various functions are promising to overcome such challenges for zinc batteries at the same time. It has been proved that the applications of asymmetric electrolytes show significant contributions in the field of zinc-based batteries in suppressing side reactions while maintaining electrochemical performance to satisfy both anode and cathode. Therefore, this perspective summarizes recent advancements in asymmetric electrolytes' design and applications for zinc batteries and outlines opportunities and future challenges, expecting continued research attention in this area.

Superoxide dismutase 1 (SOD1) aggregation is implicated in the development of Amyotrophic Lateral Sclerosis (ALS). Despite knowledge of the role of SOD1 aggregation, the mechanistic understanding remains elusive. Our investigation aimed to unravel the complex steps involved in SOD1 aggregation associated with ALS. Therefore, we probed the aggregation using ThT fluorescence, size-exclusion chromatography, and surface-enhanced Raman spectroscopy (SERS). The removal of metal ions and disulfide bonds resulted in the dimers rapidly first converting to an extended monomers then coming together slowly to form non-native dimers. The rapid onset of oligomerization happens above critical non-native dimer concentration. Structural features of oligomer was obtained through SERS. The kinetic data supported a fragmentation-dominant mechanism for the fibril formation. Quercetin acts as inhibitor by delaying the formation of non-native dimer and soluble oligomers by decreasing the elongation rate. Thus, results provide significant insights into the critical steps in oligomer formation and their structure.

Photoinduced metal-to-ligand (or ligand-to-metal) charge-transfer (CT) states in metal complexes have been extensively studied toward the development of luminescent materials. However, previous studies have mainly focused on CT transitions between d- and π-orbitals. Herein, we report the demonstration of CT emission from 4f- to π-orbitals using a trivalent europium (Eu(III)) complex, supported by both experimental and theoretical analyses. The Eu(III) complex exhibits an eight-coordination structure, comprising three anionic nitrates and two neutral electron-donating ligands containing a carbazole unit. The diffuse reflectance spectrum of the complex displays an absorption band at 440 nm and time-resolved emission analyses reveal a characteristic emission band at 550 nm. Comparative studies employing a trivalent gadolinium (Gd(III)) complex, alongside quantum chemical analyses, confirm that the observed absorption and emission bands are associated with CT transitions between π- and 4f-orbitals. The observation of CT emission based on the 4f-orbital offers novel insights into the field of molecular luminescence science and technology.

Deubiquitinating enzymes (DUBs) are key regulators of cellular homoeostasis, and their dysregulation is associated with several human diseases. The ovarian tumour protease (OTU) family of DUBs are biochemically well-characterised and of therapeutic interest, yet only a few tool compounds exist to study their cellular function and therapeutic potential. Here we present a chemoproteomics fragment screening platform for identifying novel DUB-specific hit matter, that combines activity-based protein profiling with high-throughput chemistry direct-to-biology optimisation to enable rapid elaboration of initial fragment hits against OTU DUBs. Applying these approaches, we identify an enantioselective covalent fragment for OTUD7B, and validate it using chemoproteomics and biochemical DUB activity assays.

Psoralen-conjugated triplex-forming oligonucleotides (Ps-TFOs) have been employed for the photodynamic regulation of gene expression by the photo-cross-linking of psoralen with the target DNA. However, stable triplex formation requires a consecutive purine base sequence in one strand of the target DNA duplexes. The pyrimidine-base interruption in the consecutive purine base sequence drastically decreases the thermodynamic stability of the corresponding triplex, which hampers the TFO application. Here, we propose a design of the Ps-TFO for stable triplex formation with target DNA sequences containing pyrimidine-base interruptions under physiological conditions. This Ps-TFO, named 1'(one)-psoralen-conjugated triplex-forming oligonucleotide (OPTO), incorporates a synthesized nucleoside mimic 1'-psoralen-conjugated deoxyribose to increase the thermodynamic stability of the corresponding triplex by the intercalation of psoralen. The triplex-forming abilities of the OPTO were successfully demonstrated in combination with LNA and 5-methylcytosine, indicating that the use of OPTO will expand the range of the target sequences of TFO for photodynamic gene regulation.

Explainable Artificial Intelligence (XAI) is an emerging field in AI that aims to address the opaque nature of machine learning models. Furthermore, it has been shown that XAI can be used to extract input-output relationships, making them a useful tool in chemistry to understand structure-property relationships. However, one of the main limitations of XAI methods is that they are developed for technically oriented users. We propose the XpertAI framework that integrates XAI methods with large language models (LLMs) accessing scientific literature to generate accessible natural language explanations of raw chemical data automatically. We conducted 5 case studies to evaluate the performance of XpertAI. Our results show that XpertAI combines the strengths of LLMs and XAI tools in generating specific, scientific, and interpretable explanations.

Cyclic lipopeptides (CLPs) produced by the genus Bacillus are amphiphiles composed of hydrophilic amino acid and hydrophobic fatty acid moieties and are biosynthesised by non-ribosomal peptide synthetases (NRPSs). CLPs are produced as a mixture of homologues with different fatty acid moieties, whose length affects CLP activity. Iturin family lipopeptides are a family of CLPs comprising cyclic heptapeptides and β-amino fatty acids and have antimicrobial activity. There is little research on how the length of the fatty acid moiety of iturin family lipopeptides is determined. Here, we demonstrated that the acyl ligase (AL) domain determines the length of the fatty acid moiety in vivo. In addition, enzyme assays revealed how mutations in the substrate-binding pocket of the AL domain affected substrate specificity in vitro. Our findings have implications for the design of fatty acyl moieties for CLP synthesis using NRPS.

Liquid cell transmission electron microscopy (LCTEM) is a powerful technique for investigating crystallisation dynamics with nanometre spatial resolution. However, probing phenomena occurring in liquids while mixing two precursor solutions has proven extremely challenging, requiring sophisticated liquid cell designs. Here, we demonstrate that introducing and withdrawing solvents in sequence makes it possible to maintain optimal imaging conditions while mixing liquids in a commercial liquid cell. We succeeded in visualising a fast nanoscale crystallisation mechanism when an organic molecule of R-BINOL-CN dissolved in chloroform interacts with methanol. The scanning transmission electron microscopy images recorded in real-time during the interaction of the two volatile solvents reveal the formation of chain-like structures of R-BINOL-CN particles, whereas they coalesce to form single large particles when methanol is absent. Our approach of mixing liquids establishes a platform for novel LCTEM studies of a wide range of electron-beam-sensitive materials, including drug molecules, polymers and molecular amphiphiles.

Translation of mRNA into protein is a fundamental process and tightly controlled during development. Several mechanisms acting on the mRNA level regulate when and where an mRNA is expressed. To explore the effects of conditional and transient gene expression in a developing organism, it is vital to experimentally enable abrogation and restoration of translation. We recently developed the FlashCaps technology allowing preparation of translationally muted mRNAs and their controlled activation by light. Here, we validate its functionality in vivo. We demonstrate that translation of FlashCap-eGFP-mRNA can be triggered in zebrafish embryos with spatiotemporal control. The injected FlashCap-mRNA is stable for hours and remains muted. Light-mediated activation up to 24 h post fertilization produces visible amounts of eGFP and can be restricted to distinct parts of the embryo. This methodology extends the toolbox for vertebrate models by enabling researchers to locally activate mRNA translation at different timepoints during development.

Serial macromolecular crystallography has become a powerful method to reveal room temperature structures of biological macromolecules and perform time-resolved studies. ID29, a flagship beamline of the ESRF 4th generation synchrotron, is the first synchrotron beamline in the world capable of delivering high brilliance microsecond X-ray pulses at high repetition rate for the structure determination of biological macromolecules at room temperature. The cardinal combination of microsecond exposure times, innovative beam characteristics and adaptable sample environment provides high quality complete data, even from an exceptionally small amount of crystalline material, enabling what we collectively term serial microsecond crystallography (SµX). After validating the use of different sample delivery methods with various model systems, we applied SµX to an integral membrane receptor, where only a few thousands diffraction images were sufficient to obtain a fully interpretable electron density map for the antagonist istradefylline-bound A receptor conformation, providing access to the antagonist binding mode. SµX, as demonstrated at ID29, will quickly find its broad applicability at upcoming 4th generation synchrotron sources worldwide and opens a new frontier in time-resolved SµX.

The thiol-ene reaction between an alkene and a thiol can be exploited for selective labelling of cysteine residues in protein profiling applications. Here, we explore thiol-ene activation in systems from chemical models to complex cellular milieus, using UV, visible wavelength and redox initiators. Initial studies in chemical models required an oxygen-free environment for efficient coupling and showed very poor activation when using a redox initiator. When thiol-ene activation was performed in protein and cell lysate models, all three initiation methods were successful. Faster thiol-ene reaction was observed as the cysteine and alkene were brought into proximity by a binding event prior to activation, leading to quicker adduct formation in the protein model system than the chemical models. Furthermore, in the protein-protein coupling, none of the activators required an oxygen-free environment. Taken together, these observations demonstrate the broad potential for thiol-ene coupling to be used in protein profiling.