Volume 12 Issue 10, October 2020

Manza B. J. Atkinson talks to Nature Chemistry about his path to become a chemist, and how he applies the scientific method to all aspects of his life — from financial analysis to coaching youth sports teams.

How atoms organize during the earliest stages of nucleation has been a subject of speculation for over a century. Using atomically resolved electron microscopy, the formation and ordering of metal clusters from individual atoms has now been observed in carbon nanotubes that serve as ‘test tubes’.

Electrophilic groups that undergo sulfur-exchange chemistry with protein nucleophiles can serve as the functional basis of chemical proteomic probes. A new addition to this class, sulfuramidimidoyl fluoride (SAF), which can be included in an array of covalent small molecule probes, exhibits a unique reactivity profile with proteins.

After years of speculation on the origins of symmetry-making and -breaking during crystallization, time-resolved in situ scanning probe microscopy and all-atom molecular dynamics simulations have shown that the formation of olanzapine crystals largely occurs by the incorporation of centrosymmetric dimers into growth sites.

The [2+2] photocycloaddition of two double-bond moieties is arguably the most efficient way to form a four-membered ring, but this route is rarely used to construct azetidine rings. Now, the development of an isoxazoline carboxylate cycloaddition partner offers a general approach to synthesize diverse azetidine products.

High-accuracy quantum chemistry methods struggle with a combinatorial explosion of Slater determinants in larger molecular systems, but now a method has been developed that learns electronic wavefunctions with deep neural networks and reaches high accuracy with only a few determinants. The method is applicable to realistic chemical processes such as the automerization of cyclobutadiene.

Although azetidines represent highly desirable building blocks in drug discovery, methods for their efficient and straightforward synthesis remain underdeveloped. Now, it has been shown that highly functionalized azetidines can be prepared via an intermolecular [2+2] photocycloaddition reaction between cyclic oximes and alkenes, in a process enabled by a visible-light-mediated triplet energy transfer.

Latent functional groups—typically unreactive unless activated by protein binding—can provide additional selectivity to covalent drugs. Now, compounds containing the weakly electrophilic sulfuramidimidoyl fluoride group, capable of undergoing sulfur(vi) fluoride exchange, have been used to identify reactive proteins in human cell lysate. This approach has identified a compound that conjugates to and inhibits an important anticancer target.

Crystal symmetry is notoriously uncorrelated to the symmetry of the constituent molecules that make up a crystal. Symmetry breaking is typically thought to occur during nucleation and growth, but a symmetry element of olanzapine crystals—an inversion centre—has now been shown to emerge in centrosymmetric dimers extant in solution prior to crystallization.

Crystal nucleation processes are difficult to probe experimentally because of the spatial and temporal scales involved. Now, the heterogeneous nucleation of three different metals has been observed by electron microscopy with atomic resolution—using single-walled carbon nanotube as test tubes—and, in each case, shown to adopt a two-step nucleation mechanism involving a metastable amorphous precursor.

CD44 is a cell-surface adhesion receptor associated with many biological processes that rely on cellular plasticity. Now, CD44 has been shown to mediate endocytosis of iron-bound hyaluronates. Furthermore, iron catalyses the demethylation of repressive histone marks, thereby unlocking the expression of genes regulating cellular plasticity.

Reversible nanoscale knotting and unknotting of a molecular strand can be used to control the handedness of helical organizations at macroscopic length scales. Dopant knotted and unknotted strands induce supramolecular helical structures of opposite handedness in achiral liquid crystals, and the left- and right-handed forms can be switched in situ.

Quantum machine learning with improved data efficiency and transferability has been achieved using on-the-fly selection of query-dependent training molecules, which are drawn from a ‘dictionary’ of atom-in-molecule-based fragments. The benefits of the resulting models have been demonstrated for important molecular properties and for systems including organic molecules, 2D materials, water clusters, DNA base pairs and ubiquitin.

A selection-based screen has now revealed preferences in small-molecule chemotypes that bind RNA as well as preferences in the RNA motifs that bind small molecules. Analysis of these data enabled the design of a small molecule that selectively binds a non-coding microRNA and upregulates expression of vascular endothelial growth factor A.

Three crystalline complexes comprising a linear [UN₂] moiety that is isoelectronic to the ubiquitous uranyl cation [UO₂]²⁺ have been prepared by reaction of UCl₅ or UBr₅ with liquid ammonia. Quantum chemical calculations showed that the bonding in the [UN₂] moieties is best described with two U≡N triple bonds.

Class II terpene cyclases convert simple linear substrates into complex polycyclic compounds, which typically requires multiple protein domains. Now, a single-domain class II cyclase, a cyanobacterial merosterolic acid synthase, has been identified and characterized. High-resolution X-ray crystal structures provide detailed insights into how a minimalistic enzyme accomplishes this complex cyclization process.