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Nickel organic compounds play a crucial role in organic and bioinorganic chemistry, however, their potential role in prebiotic chemistry is not well understood. Here, the authors identify the formation of a nickel bis(dithiolene) from nickel sulfide under an acetylene-containing volcanic hydrothermal experimental environment and reveal its role in the transformation of acetylene to acetaldehyde.

Covalent probes are a powerful tool for investigating small molecule and protein interactions, however, the development of reactive warheads to form covalent probes remains underexplored. Here, the authors develop α-acyloxyenamide electrophiles to covalently bind to lysine residues, and selectively profile the conserved lysine residues of kinase in live cells.

Metal-organic frameworks have demonstrated great promise for application in CO₂ capture, but the enormous breadth of potential building blocks available makes searching the chemical space for the best-performing materials challenging via traditional methods. Here, the authors present a high-throughput computational framework based on a molecular generative diffusion model to accelerate the discovery of MOF structures with high CO₂ capacities and synthesizable linkers.

Collision-induced dissociation tandem mass spectrometry offers to resolve molecular structures through library searches, however, for de novo identifications, one must often rely on in silico-generated spectra as reference. Here, the authors evaluate in silico generated MSⁿ product ion structures by comparison with spectroscopically established structures and find that for 36 randomly selected MS/MS product ions, the vast majority of annotations in three major libraries are incorrect, primarily due to unaccounted for cyclization rearrangements.

Peptides or proteins containing aggregates are pivotal for the integrity of structure and function, however, monitoring the dynamics of such systems remains challenging. Here, the authors investigate the dynamic landscape of peptide-SDS micelles through a synergistic combination of solution-state NMR experiments and molecular dynamics simulations.

Mixed-metal cluster generating reaction solutions contain several species of similar composition and structure that often result in hard-to-separate product mixtures. Here, the authors analyze elemental compositions obtained via high-resolution mass spectrometry with a computational permutative approach and assign individual structures of nickel gallium intermetalloid clusters without the need to isolate pure clusters.

Deep eutectic solvents are promising, sustainable alternatives for diverse applications, including separation, gas capture, electrodeposition, or nanomaterial synthesis, but our fundamental understanding of the nature of these solvents remains limited. Here, the authors report a practical approach for estimating the solid–liquid equilibrium phase diagram of any binary mixture from structural information, using machine learning and quantum chemical techniques.

Molecular dynamics (MD) is a powerful tool for the simulation of proteins and other biomolecules, however, convergence and equilibrium in MD simulations remain underexplored. Here, the authors investigate long MD trajectories of several proteins and reveal that, although full convergence of all properties may not be reached, the most biologically interesting properties do, in fact, reach convergence during multi-microsecond simulation trajectories.

The Guest Editors of Communications Chemistry’s Atomically precise nanochemistry Collection discuss the importance of atomic precision in nanochemistry research, and highlight some of the field’s most pressing challenges.

Controlling excited-state reactivity is a long-standing challenge in photochemistry, as desired pathways may be inaccessible or compete with unwanted channels, which is problematic for applications. Here, the authors show that 2,3,5-trifluorination on the phenolate ring of the green fluorescent protein chromophore leads to both pathway selectivity and doubles the photoisomerization quantum yield.

Enhancing the activity of the oxygen reduction reaction (ORR) is crucial for fuel cell development, but hydrophobic species used to boost ORR activity are often toxic. Here, the authors report that caffeine enhances the specific ORR activity of Pt(111) eleven-fold compared to that without caffeine in a 0.1 M HClO₄ aqueous solution, and find that the enhancement mechanism depends strongly on the surface structures of platinum.

Amines and carboxylic acids are abundant chemical feedstocks, however, the current reaction space of those two building blocks is focused on amide coupling. Here, the authors extensively explore the amine–acid reaction space via systematic reaction enumeration using graph editing and demonstrate its utility in retrosynthetic analysis as well as late-stage diversification.

Molecular fragmentation plays a pivotal role in medicinal chemistry and drug discovery. Here the authors summarize the methodologies for molecular fragmentation and their application in the AI-based fragment-based drug discovery.

Protein tyrosine kinase Src is known to phosphorylate Ras protein on tyrosine32 and 64, and uncouple Ras from the signaling cascade, however, the mechanisms through which phosphorylation modulates these interactions remain poorly understood. Here, the authors quantify the major mono-phosphorylation level on tyrosine64 by ³¹P NMR and mutagenesis, and reveal the key conformational changes of phosphorylated Ras using BeF₃⁻ complexes by X-ray crystallography and ¹⁹F NMR, providing new mechanistic and conformational insights into Ras dynamics regulation.

Single-molecule fluorescent probes can be used for nanoreporting, localization, and now multiplexing, but understanding their stochastic fluctuations in emission intensity is crucial for accurate signal interpretation. Here, the authors elucidate the blinking dynamics of rhodamine, BODIPY, and antraquinone dyes, demonstrate that multiplexing performance improves with photophysical differences, and suggest guidelines for the selection and design of organic fluorophores for single-molecule multiplexing.

Protease inhibitors represent attractive antiviral agents against coronaviruses, however, current inhibitors show restricted efficiency which limits their use. Here, the authors develop covalent reversible peptidyl inhibitors with nitroalkene warheads, showing inhibition against main protease and human Cathepsin L, preventing viral infection in a cellular assay.

Isotope ratios of mollusk shell carbonates are commonly used to reconstruct past environmental conditions, but the shell organic matrix is often overlooked. Here, the authors find the hydrogen and oxygen isotope compositions of the organic matrix of modern Mytilus galloprovincialis shells from sites along a coast-to-upper-estuary environmental gradient reflect environmental variables.

Gangliosides are composed of oligosaccharide chains attached to ceramides and are employed as targeted drugs and diagnostic biomarkers, however, their industrially-relevant synthesis remains challenging. Here, the authors develop a modular chemoenzymatic cascade assembly strategy for the customized and large-scale synthesis of ganglioside analogues with various glycan and ceramide epitopes.

Protein binding plays an important role in the function and design of protein complexes, however, the relationships among protein sequences, structures, and interactions shaped by evolution remain underexplored. Here, the authors use computational simulations to study the binding specificity of a two-component system under protein sequence evolution and reveal that the binding specificity is modulated by both direct intermolecular interactions and long-range epistasis across the binding complex.

Capsid proteins (CPs) of various icosahedral and rod-shaped viruses exhibit structural diversity and tunability as well as application in smart hybrid nanoparticles, however, the potential of CPs of filamentous plant viruses remains underexplored. Here, the authors exploit the structure-based design of CP from potato virus Y to tune the shape, size, RNA encapsidation ability, symmetry, stability, and surface functionalization of nanoparticles.