Spontaneous emergence of membrane-forming protoamphiphiles from a lipid–amino acid mixture under wet–dry cycles

Dynamic interplay between peptide synthesis and membrane assembly would have been crucial for the emergence of protocells on the prebiotic Earth. However, the effect of membrane-forming amphiphiles on peptide synthesis, under prebiotically plausible conditions, remains relatively unexplored. Here we discern the effect of a phospholipid on peptide synthesis using a non-activated amino acid, under wet–dry cycles. We report two competing processes simultaneously forming peptides and N-acyl amino acids (NAAs) in a single-pot reaction from a common set of reactants. NAA synthesis occurs via an ester–amide exchange, which is the first demonstration of this phenomenon in a lipid–amino acid system. Furthermore, NAAs self-assemble into vesicles at acidic pH, signifying their ability to form protocellular membranes under acidic geothermal conditions. Our work highlights the importance of exploring the co-evolutionary interactions between membrane assembly and peptide synthesis, having implications for the emergence of hitherto uncharacterized compounds of unknown prebiotic relevance.

Synthesis of lipoamino acids via ester–amide exchange under prebiotically plausible wet-dry cycling conditions that results in vesicles at acidic pH.     

Dissipative self-assembly,competition and inhibition in a self-reproducing protocell model

The bottom-up synthesis of artificial, life-like systems promises to enable the study of emergent properties distinctive to life. Here, we report protocell systems generated from phase-separated building blocks. Vesicle protocells self-reproduce through a phase-transfer mechanism, catalysing their own formation. Dissipative self-assembly by the protocells is achieved when a hydrolysis step to destroy the surfactant is introduced. Competition between micelle and vesicle based replicators for a common feedstock shows that environmental conditions can control what species predominates: under basic conditions vesicles predominate, but in a neutral medium micelles are selected for via a mechanism which inhibits vesicle formation. Finally, the protocells enable orthogonal reactivity by catalysing in situ formation of an amphiphilic organocatalyst, which after incorporation into the vesicle bilayer enantioselectively forms a secondary product.

The bottom-up synthesis of a self-reproducing protocell model enables the study of emergent properties distinctive to life.     

Mechanochemical synthesis of glycine oligomers in a virtual rotational diamond anvil cell

Mechanochemistry of glycine under compression and shear at room temperature is predicted using quantum-based molecular dynamics (QMD) and a simulation design based on rotational diamond anvil cell (RDAC) experiments. Ensembles of high throughput semiempirical density functional tight binding (DFTB) simulations are used to identify chemical trends and bounds for glycine chemistry during rapid shear under compressive loads of up to 15.6 GPa. Significant chemistry is found to occur during compressive shear above 10 GPa. Recovered products consist of small molecules such as water, structural analogs to glycine, heterocyclic molecules, large oligomers, and polypeptides including the simplest polypeptide glycylglycine at up to 4% mass fraction. The population and size of oligomers generally increases with pressure. A number of oligomeric polypeptide precursors and intermediates are also identified that consist of two or three glycine monomers linked together through C–C, C–N, and/or C–O bridges. Even larger oligomers also form that contain peptide C–N bonds and exhibit branched structures. Many of the product molecules exhibit one or more chiral centers. Our simulations demonstrate that athermal mechanical compressive shearing of glycine is a plausible prebiotic route to forming polypeptides.

Compressive shearing forces can induce mechanochemical oligomerization reactions in glycine.     

Construction of coacervate-in-coacervate multi-compartment protocells for spatial organization of enzymatic reactions

Coacervate microdroplets, formed via liquid–liquid phase separation, have been extensively explored as a compartment model for the construction of artificial cells or organelles. In this study, coacervate-in-coacervate multi-compartment protocells were constructed using four polyelectrolytes, in which carboxymethyl-dextran and diethylaminoethyl-dextran were deposited on the surface of as-prepared polydiallyldimethyl ammonium/deoxyribonucleic acid coacervate microdroplets through layer-by-layer assembly. The resulting multi-compartment protocells were composed from two immiscible coacervate phases with distinct physical and chemical properties. Molecule transport experiments indicated that small molecules could diffuse between two coacervate phases and that macromolecular enzymes could be retained. Furthermore, a competitive cascade enzymatic reaction of glucose oxidase/horseradish peroxidase–catalase was performed in the multi-compartment protocells. The different enzyme organization and productions of H₂O₂ led to a distinct polymerization of dopamine. The spatial organization of different enzymes in immiscible coacervate phases, the distinct reaction fluxes between coacervate phases, and the enzymatic cascade network led to distinguishable signal generation and product outputs. The development of this multi-compartment structure could pave the way toward the spatial organization of multi-enzyme cascades and provide new ideas for the design of organelle-containing artificial cells.

A coacervate-in-coacervate micro-architecture is constructed as a multi-compartment protocell model, in which a multi-enzyme cascade is spatially organized for competitive enzymatic reactions.     

Engineering bio-mimicking functional vesicles with multiple compartments for quantifying molecular transport

Controlled design of giant unilamellar vesicles under defined conditions has vast applications in the field of membrane and synthetic biology. Here, we bio-engineer bacterial-membrane mimicking models of controlled size under defined salt conditions over a range of pH. A complex bacterial lipid extract is used for construction of physiologically relevant Gram-negative membrane mimicking vesicles whereas a ternary mixture of charged lipids (DOPG, cardiolipin and lysyl-PG) is used for building Gram-positive bacterial-membrane vesicles. Furthermore, we construct stable multi-compartment biomimicking vesicles using the gel-assisted swelling method. Importantly, we validate the bio-application of the bacterial vesicle models by quantifying diffusion of chemically synthetic amphoteric antibiotics. The transport rate is pH-responsive and depends on the lipid composition, based on which a permeation model is proposed. The permeability properties of antimicrobial peptides reveal pH dependent pore-forming activity in the model vesicles. Finally, we demonstrate the functionality of the vesicles by quantifying the uptake of membrane-impermeable molecules facilitated by embedded pore-forming proteins. We suggest that the bacterial vesicle models developed here can be used to understand fundamental biological processes like the peptide assembly mechanism or bacterial cell division and will have a multitude of applications in the bottom-up assembly of a protocell.

Giant vesicle functional models mimicking a bacterial membrane under physiological conditions are constructed.     

Template effects of vesicles in dynamic covalent chemistry

Vesicle lipid bilayers have been employed as templates to modulate the product distribution in a dynamic covalent library of Michael adducts formed by mixing a Michael acceptor with thiols. In methanol solution, all possible Michael adducts were obtained in similar amounts. Addition of vesicles to the dynamic covalent library led to the formation of a single major product. The equilibrium constants for formation of the Michael adducts are similar for all of the thiols used in this experiment, and the effect of the vesicles on the composition of the library is attributed to the differential partitioning of the library members between the lipid bilayer and the aqueous solution. The results provide a quantitative approach for exploiting dynamic covalent chemistry within lipid bilayers.

Vesicle lipid bilayers have been employed as templates to modulate the product distribution in a dynamic covalent library of Michael adducts formed by mixing a Michael acceptor with thiols.     

Prebiotic access to enantioenriched glyceraldehyde mediated by peptides

A prebiotically plausible route to enantioenriched glyceraldehyde is reported via a kinetic resolution mediated by peptides. The reaction proceeds via a selective reaction between the l-peptide and the l-sugar producing an Amadori rearrangement byproduct and leaving d-glyceraldehyde in excess. Solubility considerations in the synthesis of proline–valine (pro–val) peptides allow nearly enantiopure pro–val to be formed starting from racemic pro and nearly racemic (10%) ee val. (ee = enantiomeric excess = (|d − l|)/(d + l)) Thus enantioenrichment of glyceraldehyde is achieved in a system with minimal initial chiral bias. This work demonstrates synergy between amino acids and sugars in the emergence of biological homochirality.

A prebiotically plausible route to enantioenriched glyceraldehyde is reported via a kinetic resolution mediated by peptides.     

Atomic engineering of single-atom nanozymes for enzyme-like catalysis

Enzyme mimics, especially nanozymes, play a crucial role in replacing natural enzymes for diverse applications related to bioanalysis, therapeutics and other enzyme-like catalysis. Nanozymes are catalytic nanomaterials with enzyme-like properties, which currently face formidable challenges with respect to their intricate structure, properties and mechanism in comparison with enzymes. The latest emergence of single-atom nanozymes (SAzymes) undoubtedly promoted the nanozyme technologies to the atomic level and provided new opportunities to break through their inherent limitations. In this perspective, we discuss key aspects of SAzymes, including the advantages of the single-site structure, and the derived synergetic enhancements of enzyme-like activity, catalytic selectivity and the mechanism, as well as the superiority in biological and catalytic applications, and then highlight challenges that SAzymes face and provide relevant guidelines from our point of view for the rational design and extensive applications of SAzymes, so that SAzyme may achieve its full potential as the next-generation nanozyme.

Single-atom nanozymes with definite active centers, high catalytic activities and enzyme-like selectivities promote the nanozyme research entering a new period of atomic level.     

Preparation and characterization of the enol of acetamide: 1-aminoethenol,a high-energy prebiotic molecule

Amide tautomers, which constitute the higher-energy amide bond linkage, not only are key for a variety of biological but also prebiotic processes. In this work, we present the gas-phase synthesis of 1-aminoethenol, the higher-energy tautomer of acetamide, that has not been spectroscopically identified to date. The title compound was prepared by flash vacuum pyrolysis of malonamic acid and was characterized employing matrix isolation infrared as well as ultraviolet/visible spectroscopy. Coupled-cluster computations at the AE-CCSD(T)/cc-pVTZ level of theory support the spectroscopic assignments. Upon photolysis at λ > 270 nm, the enol rearranges to acetamide as well as ketene and ammonia. As the latter two are even higher in energy, they constitute viable starting materials for formation of the title compound.

Amide tautomers, which constitute the higher-energy amide bond linkage, not only are key for a variety of biological but also prebiotic processes.     

Mechanochemical reactivity inhibited,prohibited and reversed by liquid additives: examples from crystal-form screens

We demonstrate that liquid additives can exert inhibitive or prohibitive effects on the mechanochemical formation of multi-component molecular crystals, and report that certain additives unexpectedly prompt the dismantling of such solids into physical mixtures of their constituents. Computational methods were employed in an attempt to identify possible reasons for these previously unrecognised effects of liquid additives on mechanochemical transformations.

Liquid additives can exert catalytic, inhibitive or prohibitive effects on the mechanochemical formation of multi-component molecular crystals.     

One-pot thiol–amine bioconjugation to maleimides: simultaneous stabilisation and dual functionalisation

Maleimide chemistry is widely used in the site-selective modification of proteins. However, hydrolysis of the resultant thiosuccinimides is required to provide robust stability to the bioconjugates. Herein, we present an alternative approach that affords simultaneous stabilisation and dual functionalisation in a one pot fashion. By consecutive conjugation of a thiol and an amine to dibromomaleimides, we show that aminothiomaleimides can be generated extremely efficiently. Furthermore, the amine serves to deactivate the electrophilicity of the maleimide, precluding further reactivity and hence generating stable conjugates. We have applied this conjugation strategy to peptides and proteins to generate stabilised trifunctional conjugates. We propose that this stabilisation-dual modification strategy could have widespread use in the generation of diverse conjugates.

An alternative approach to maleimide conjugate stabilisation is presented, by the consecutive addition of a thiol and an amine to dibromomaleimides. The amine serves to simultaneously deactivate the maleimide and enable dual functionalisation.     

Leveraging autocatalytic reactions for chemical domain image classification

Autocatalysis is fundamental to many biological processes, and kinetic models of autocatalytic reactions have mathematical forms similar to activation functions used in artificial neural networks. Inspired by these similarities, we use an autocatalytic reaction, the copper-catalyzed azide–alkyne cycloaddition, to perform digital image recognition tasks. Images are encoded in the concentration of a catalyst across an array of liquid samples, and the classification is performed with a sequence of automated fluid transfers. The outputs of the operations are monitored using UV-vis spectroscopy. The growing interest in molecular information storage suggests that methods for computing in chemistry will become increasingly important for querying and manipulating molecular memory.

Kinetic models of autocatalytic reactions have mathematical forms similar to activation functions used in artificial neural networks. Inspired by these similarities, we use a copper-catalyzed reaction to perform digital image recognition tasks.     

Pyrazolone ligation-mediated versatile sequential bioconjugations

Bioconjugation chemistries are critical tools in biotherapeutics discovery. The past efforts have been exclusively focused on two-segment conjugations. However, emerging research directions, such as polypharmacy biotherapeutics, desire multiple-component bioconjugations where more than two pharmacologically related biomolecules can be assembled into a single construct in high efficiency. We present here a set of sequential bioconjugation chemistries centered on a pyrazolone structural motif. It starts with a clickable “pyrazolone ligation” between a hydrazine group and a β-ketoester moiety followed by the conjugation between the newly formed pyrazolone core and an aldehyde-bearing biomolecule through a Knoevenagel reaction forming a Michael addition acceptor that can effectively capture a thiol-bearing biomolecule. When utilized intermolecularly, it quickly assembles four segments together forming a quadruple functional construct. When applied intramolecularly, it offers a set of highly diverse biomolecule scaffolds including stapled peptides and poly-macrocyclic peptides. We envision broad utilities of such sequential ligation chemistries.

A multiple component sequential bioconjugation chemistry establishes upon the joined force of hydrazine, β-keto ester, thiol and aldehyde.     

f-Element silicon and heavy tetrel chemistry

The last three decades have seen a significant increase in the number of reports of f-element carbon chemistry, whilst the f-element chemistry of silicon, germanium, tin, and lead remain underdeveloped in comparison. Here, in this perspective we review complexes that contain chemical bonds between f-elements and silicon or the heavier tetrels since the birth of this field in 1985 to present day, with the intention of inspiring researchers to contribute to its development and explore the opportunities that it presents. For the purposes of this perspective, f-elements include lanthanides, actinides and group 3 metals. We focus on complexes that have been structurally authenticated by single-crystal X-ray diffraction, and horizon-scan for future opportunities and targets in the area.

In this perspective we review the molecular chemistry of f-element silicon and heavy tetrel complexes.     

A happy medium: the synthesis of medicinally important medium-sized rings via ring expansion

Medium-sized rings have much promise in medicinal chemistry, but are difficult to make using direct cyclisation methods. In this minireview, we highlight the value of ring expansion strategies to address this long-standing synthetic challenge. We have drawn on recent progress (post 2013) to highlight the key reaction design features that enable successful ‘normal-to-medium’ ring expansion for the synthesis of these medicinally important molecular frameworks, that are currently under-represented in compound screening collections and marketed drugs in view of their challenging syntheses.

Ring expansion strategies are ideally suited to make synthetically challenging, medium-sized rings with much potential in medicinal chemistry.     

Site-to-site peptide transport on a molecular platform using a small-molecule robotic arm

Peptides attached to a cysteine hydrazide ‘transporter module’ are transported selectively in either direction between two chemically similar sites on a molecular platform, enabled by the discovery of new operating methods for a molecular transporter that functions through ratcheting. Substrate repositioning is achieved using a small-molecule robotic arm controlled by a protonation-mediated rotary switch and attachment/release dynamic covalent chemistry. A polar solvent mixtures were found to favour Z to E isomerization of the doubly-protonated switch, transporting cargo in one direction (arbitrarily defined as ‘forward’) in up to 85% yield, while polar solvent mixtures were unexpectedly found to favour E to Z isomerization enabling transport in the reverse (‘backward’) direction in >98% yield. Transport of the substrates proceeded in a matter of hours (compared to 6 days even for simple cargoes with the original system) without the peptides at any time dissociating from the machine nor exchanging with others in the bulk. Under the new operating conditions, key intermediates of the switch are sufficiently stabilized within the macrocycle formed between switch, arm, substrate and platform that they can be identified and structurally characterized by ¹H NMR. The size of the peptide cargo has no significant effect on the rate or efficiency of transport in either direction. The new operating conditions allow detailed physical organic chemistry of the ratcheted transport mechanism to be uncovered, improve efficiency, and enable the transport of more complex cargoes than was previously possible.

Peptides are transported in either direction between chemically similar sites on a molecular platform, substrate repositioning is achieved using a cysteine hydrazide transporter module and a small-molecule robotic arm controlled by a rotary switch.     

Understanding the reactivity of polycyclic aromatic hydrocarbons and related compounds

This perspective article summarizes recent applications of the combination of the activation strain model of reactivity and the energy decomposition analysis methods to the study of the reactivity of polycyclic aromatic hydrocarbons and related compounds such as cycloparaphenylenes, fullerenes and doped systems. To this end, we have selected representative examples to highlight the usefulness of this relatively novel computational approach to gain quantitative insight into the factors controlling the so far not fully understood reactivity of these species. Issues such as the influence of the size and curvature of the system on the reactivity are covered herein, which is crucial for the rational design of novel compounds with tuneable applications in different fields such as materials science or medicinal chemistry.

This perspective article summarizes recent applications of the combined activation strain model of reactivity and the energy decomposition analysis methods to the study of the reactivity of polycyclic aromatic hydrocarbons and related compounds.     

Recent advances of group 14 dimetallenes and dimetallynes in bond activation and catalysis

Since the first heavy alkene analogues of germanium and tin were isolated in 1976, followed by West''s disilene in 1981, the chemistry of stable group 14 dimetallenes and dimetallynes has advanced immensely. Recent developments in this field veered the focus from the isolation of novel bonding motifs to mimicking transition metals in their ability to activate small molecules and perform catalysis. The potential of these homonuclear multiply bonded compounds has been demonstrated numerous times in the activation of H₂, NH₃, CO₂ and other small molecules. Hereby, the strong relationship between structure and reactivity warrants close attention towards rational ligand design. This minireview provides an overview on recent developments in regard to bond activation with group 14 dimetallenes and dimetallynes with the perspective of potential catalytic applications of these compounds.

This minireview highlights the recent advances in small molecule activation and catalytic applications of homonuclear dimetallenes, dimetallynes and interconnected bismetallylenes of heavier group 14 elements.     

Photoredox catalysis on unactivated substrates with strongly reducing iridium photosensitizers

Photoredox catalysis has emerged as a powerful strategy in synthetic organic chemistry, but substrates that are difficult to reduce either require complex reaction conditions or are not amenable at all to photoredox transformations. In this work, we show that strong bis-cyclometalated iridium photoreductants with electron-rich β-diketiminate (NacNac) ancillary ligands enable high-yielding photoredox transformations of challenging substrates with very simple reaction conditions that require only a single sacrificial reagent. Using blue or green visible-light activation we demonstrate a variety of reactions, which include hydrodehalogenation, cyclization, intramolecular radical addition, and prenylation via radical-mediated pathways, with optimized conditions that only require the photocatalyst and a sacrificial reductant/hydrogen atom donor. Many of these reactions involve organobromide and organochloride substrates which in the past have had limited utility in photoredox catalysis. This work paves the way for the continued expansion of the substrate scope in photoredox catalysis.

Strong bis-cyclometalated iridium photoreductants, in combination with a single sacrificial reductant, enable visible-light-promoted reductive activation of a variety of challenging substrates under simple and general reaction conditions.     

Redesigning donor–acceptor Stenhouse adduct photoswitches through a joint experimental and computational study

Many studies have recently explored a new class of reversible photoswitching compounds named Donor–Acceptor Stenhouse Adducts (DASAs). Upon light irradiation, these systems evolve from a coloured open-chain to a colourless closed-ring form, while the thermal back-reaction occurs at room temperature. In order to fulfill the requirements for different applications, new molecules with specific properties need to be designed. For instance, shifting the activation wavelength towards the red part of the visible spectrum is of relevance to biological applications. By using accurate computational calculations, we have designed new DASAs and predicted some of their photophysical properties. Starting from well-studied donor and acceptor parts, we have shown that small chemical modifications can lead to substantial changes in both photophysical and photoswitching properties of the resulting DASAs. Furthermore, we have also analysed how these substitutions impact the electronic structure of the systems. Finally, some pertinent candidates have been successfully synthesized and their photoswitching properties have been characterized experimentally.

New photoswitch Donor–Acceptor Stenhouse Adducts (DASAs) have been synthesized thanks to accurate computational chemistry predictions. They possess good properties, notably red light activation.