Prebiotic Systems Chemistry: New Perspectives for the Origins of Life

Target-promoted autocatalytic hairpin assembly of bivalent DNAzymes for sensitive and label-free electrochemical metallothionein assay

Metallothionein (MT) has shown to be an important biomarker for environmental monitoring and various diseases, due to its significant binding ability to heavy metal ions. On the basis of such a characteristic and the Hg2+-stabilized DNA duplex (Hg2+-dsDNA) probe, as well as a new autocatalytic hairpin assembly (aCHA)/DNAzyme cascaded signal enhancement strategy, the construction of a highly sensitive and label-free electrochemical MT biosensor is described. Target MT molecules bind Hg2+ in Hg2+-dsDNA to disrupt the duplex structure and to release ssDNA sequences, which trigger subsequent aCHA for efficient production of mimic aCHA triggering strands and many bivalent DNAzymes. The signal hairpins on the electrode are then cyclically cleaved by DNAzyme amplification cascade to liberate plenty G-quadruplex sequences, which bind hemin and yield largely enhanced currents for sensitive assay of MT with a detection limit of 0.217 nM in a label-free approach. Such sensor also shows selective discrimination capability to MT against other interfering proteins and assay of MT in normal serums with dilution has also been verified, indicating its potential for highly sensitive detection of different heavy metal ion binding molecules for various application scenarios.

Protocellular Heme and Iron-Sulfur Clusters

ConspectusCentral to the quest of understanding the emergence of life is to uncover the role of metals, particularly iron, in shaping prebiotic chemistry. Iron, as the most abundant of the accessible transition metals on the prebiotic Earth, played a pivotal role in early biochemical processes and continues to be indispensable to modern biology. Here, we discuss our recent contributions to probing the plausibility of prebiotic complexes with iron, including heme and iron-sulfur clusters, in mediating chemistry beneficial to a protocell. Laboratory experiments and spectroscopic findings suggest plausible pathways, often facilitated by UV light, for the synthesis of heme and iron-sulfur clusters. Once formed, heme displays catalytic, peroxidase-like activity when complexed with amphiphiles. This activity could have been beneficial in two ways. First, heme could have catalytically removed a molecule (H2O2) that could have had degradative effects on a protocell. Second, heme could have helped in the synthesis of the building blocks of life by coupling the reduction of H2O2 with the oxidation of organic substrates. The necessity of amphiphiles to avoid the formation of inactive complexes of heme is telling, as the modern-day electron transport chain possesses heme embedded within a lipid membrane. Conversely, prebiotic iron-sulfur peptides have yet to be reported to partition into lipid membranes, nor have simple iron-sulfur peptides been found to be capable of participating in the synthesis of organic molecules. Instead, iron-sulfur peptides span a wide range of reduction potentials complementary to the reduction potentials of hemes. The reduction potential of iron-sulfur peptides can be tuned by the type of iron-sulfur cluster formed, e.g., [2Fe-2S] versus [4Fe-4S], or by the substitution of ligands to the metal center. Since iron-sulfur clusters easily form upon stochastic encounters between iron ions, hydrosulfide, and small organic molecules possessing a thiolate, including peptides, the likelihood of soluble iron-sulfur clusters seems to be high. What remains challenging to determine is if iron-sulfur peptides participated in early prebiotic chemistry or were recruited later when protocellular membranes evolved that were compatible with the exploitation of electron transfer for the storage of energy as a proton gradient. This problem mirrors in some ways the difficulty in deciphering the origins of metabolism as a whole. Chemistry that resembles some facets of extant metabolism must have transpired on the prebiotic Earth, but there are few clues as to how and when such chemistry was harnessed to support a (proto)cell. Ultimately, unraveling the roles of hemes and iron-sulfur clusters in prebiotic chemistry promises to deepen our understanding of the origins of life on Earth and aids the search for life elsewhere in the universe.

Selective Chiral Interactions between Hydrophilic/Hydrophobic Amino Acids and Growing Gypsum Crystals

In nature, selective interactions between chiral amino acids and crystals are important for the formation of chiral biominerals and provide insight into the mysterious origin of homochirality. Here, we show that chiral amino acids with different hydrophilicities/hydrophobicities exhibit different chiral selectivity preferences in the dynamically growing gypsum [001] steps. Hydrophilic amino acids show a chiral selectivity preference for their d-isomers, whereas hydrophobic amino acids prefer their l-isomers. These differences in chiral recognition can be attributed to the different stereochemical matching between the hydrophilic and hydrophobic amino acids on the [001] steps of growing gypsum. These different chiral selectivities resulting from the amino acid hydrophilicity/hydrophobicity are confirmed by the experimental crystallization investigations from nano regulation on dynamic steps, to microscopic modification of gypsum morphology, and to macroscopic precipitation. Furthermore, as the hydrophilicity of amino acids increases, the disparity in chiral selection rises; conversely, the increase in the hydrophobicity of amino acids results in a decline in chiral selection. These insights improve our understanding of the interaction mechanism between amino acids and crystals and provide insights into the formation process of chiral biominerals and the origin of homochirality in nature.

Chirality and pH Influence the Self-Assembly of Antimicrobial Lipopeptides with Diverse Nanostructures

Chirality plays a crucial role in the self-assembly of biomolecules in nature. Peptides show chirality-dependent conformation and self-assembly. Lipidation of peptides occurs in vivo and has recently been exploited in designed conjugates to drive self-assembly and enhance bioactivity. Here, a library of pH-responsive homochiral and heterochiral lipidated tripeptides has been designed. The designed lipopeptides comprise homochiral C16-YKK or C16-WKK (where all the amino acids are l-isomers), and two heterochiral conjugates C16-Ykk and C16-Wkk (where the two lysines are d-isomers). The self-assembly of all the synthesized lipopeptides in aqueous solution was examined using a combination of spectroscopic methods along with cryogenic-transmission electron microscopy (cryo-TEM) and small-angle X-ray scattering (SAXS). Interestingly, it was observed that at acidic pH all the lipopeptides self-assemble into micelles, whereas at basic pH the homochiral lipopeptides self-assemble into nanofibers, whereas the heterochiral lipopeptides self-assemble into nanotapes and nanotubes. A pH switch was demonstrated using a thioflavin T fluorescence probe of β-sheet structure present in the extended structures at pH 8. We demonstrate that both chirality and pH in lipopeptides influence the self-assembly behavior of the model tripeptides, which also show promising bioactivity. Good cytocompatibility is observed in hemolytic assays and antimicrobial activity against both Gram-negative and Gram-positive bacteria is shown through the determination of minimum inhibition concentration (MIC) and minimum bactericidal concentration (MBC) values and live/dead bacteria staining assay.

Coacervate Formation in Dilute Aqueous Solutions of Inorganic Molecular Clusters with Simple Divalent Countercations

We report a complex coacervate formed by a 2.5 nm-diameter, rigid uranyl peroxide molecular cluster (Li68K12(OH)20)[UO2(O2)OH]60, U6060-) and SrCl2 salt in dilute aqueous solutions, including its location in the phase diagram, composition, rheological features, and critical conditions for phase transitions. In this coacervate, the Sr2+ cations are a major building component, and the coacervate phase covers a substantial region of the phase diagram. This coacervate demonstrates features that differ from traditional coacervates formed by oppositely charged long-chain polyelectrolytes, especially in its formation mechanism, dehydration, enhancement of mechanical strength with increasing ionic strength, and the change of salt partition preference into the coacervate and supernatant phases with ionic strength.

Evolutionary Abilities of Minimalistic Physicochemical Models of Life Processes

The ability of living organisms to persist, grow, evolve and invade environments seemingly challenges physical laws. Emerging Autonomous Systems representing autocatalytic cycles constituted of energized components in a state of Dynamic Kinetic Stability feature some of these properties. These simple theoretical models can grow, can be transferred but need an initiation to emerge and can collapse. Moreover, they can undergo kinetic selection in a way consistent with Darwinian behaviour, though they lack the ability to undergo change. The mere existence of these systems and their open-ended growth potential are proposed to constitute a transmissible factor of a non-coded kind. The onset and selection of epigenetic factors may therefore have preceded that of genetic polymers. Here is addressed the question of how these systems may arise from the diversity exhibited by abiotic organic matter, sometimes associated with intractable mixtures, which may actually be useful in providing initiators. The Darwinian description of evolution may therefore be merged without critical discontinuity within an origin scenario. Accordingly, such a theory would rests solely on physicochemical laws beginning with the potential of emerging autonomous systems to compete and invade the space dimension, and to further develop along other available dimensions including variability and, possibly, cognition.

Kinetics and coexistence of autocatalytic reaction cycles

Biological reproduction rests ultimately on chemical autocatalysis. Autocatalytic chemical cycles are thought to have played an important role in the chemical complexification en route to life. There are two, related issues: what chemical transformations allow such cycles to form, and at what speed they are operating. Here we investigate the latter question for solitary as well as competitive autocatalytic cycles in resource-unlimited batch and resource-limited chemostat systems. The speed of growth tends to decrease with the length of a cycle. Reversibility of the reproductive step results in parabolic growth that is conducive to competitive coexistence. Reversibility of resource uptake also slows down growth. Unilateral help by a cycle of its competitor tends to favour the competitor (in effect a parasite on the helper), rendering coexistence unlikely. We also show that deep learning is able to predict the outcome of competition just from the topology and the kinetic rate constants, provided the training set is large enough. These investigations pave the way for studying autocatalytic cycles with more complicated coupling, such as mutual catalysis.

Protocell Effects on RNA Folding, Function, and Evolution

ConspectusCreating a living system from nonliving matter is a great challenge in chemistry and biophysics. The early history of life can provide inspiration from the idea of the prebiotic "RNA World" established by ribozymes, in which all genetic and catalytic activities were executed by RNA. Such a system could be much simpler than the interdependent central dogma characterizing life today. At the same time, cooperative systems require a mechanism such as cellular compartmentalization in order to survive and evolve. Minimal cells might therefore consist of simple vesicles enclosing a prebiotic RNA metabolism.The internal volume of a vesicle is a distinctive environment due to its closed boundary, which alters diffusion and available volume for macromolecules and changes effective molecular concentrations, among other considerations. These physical effects are mechanistically distinct from chemical interactions, such as electrostatic repulsion, that might also occur between the membrane boundary and encapsulated contents. Both indirect and direct interactions between the membrane and RNA can give rise to nonintuitive, "emergent" behaviors in the model protocell system. We have been examining how encapsulation inside membrane vesicles would affect the folding and activity of entrapped RNA.Using biophysical techniques such as FRET, we characterized ribozyme folding and activity inside vesicles. Encapsulation inside model protocells generally promoted RNA folding, consistent with an excluded volume effect, independently of chemical interactions. This energetic stabilization translated into increased ribozyme activity in two different systems that were studied (hairpin ribozyme and self-aminoacylating RNAs). A particularly intriguing finding was that encapsulation could rescue the activity of mutant ribozymes, suggesting that encapsulation could affect not only folding and activity but also evolution. To study this further, we developed a high-throughput sequencing assay to measure the aminoacylation kinetics of many thousands of ribozyme variants in parallel. The results revealed an unexpected tendency for encapsulation to improve the better ribozyme variants more than worse variants. During evolution, this effect would create a tilted playing field, so to speak, that would give additional fitness gains to already-high-activity variants. According to Fisher's Fundamental Theorem of Natural Selection, the increased variance in fitness should manifest as faster evolutionary adaptation. This prediction was borne out experimentally during in vitro evolution, where we observed that the initially diverse ribozyme population converged more quickly to the most active sequences when they were encapsulated inside vesicles.The studies in this Account have expanded our understanding of emergent protocell behavior, by showing how simply entrapping an RNA inside a vesicle, which could occur spontaneously during vesicle formation, might profoundly affect the evolutionary landscape of the RNA. Because of the exponential dynamics of replication and selection, even small changes to activity and function could lead to major evolutionary consequences. By closely studying the details of minimal yet surprisingly complex protocells, we might one day trace a pathway from encapsulated RNA to a living system.

CO2 Fixation to Prebiotic Intermediates over Heterogeneous Catalysts

ConspectusThe study of the origin of life requires a multifaceted approach to understanding where and how life arose on Earth. One of the most compelling hypotheses is the chemosynthetic origin of life at hydrothermal vents, as this condition has been considered viable for early forms of life. The continuous production of H2 and heat by serpentinization generates reductive conditions at hydrothermal vents, in which CO2 can be used to build large biomolecules. Although this involves surface catalysis and an autocatalytic process, in which solid minerals act as catalysts in the conversion of CO2 to metabolically important organic molecules, the systematic investigation of heterogeneous catalysis to comprehend prebiotic chemistry at hydrothermal vents has not been undertaken.In this Account, we discuss geochemical CO2 fixation to metabolic intermediates by synthetic minerals at hydrothermal vents from the perspective of heterogeneous catalysis. Ni and Fe are the most abundant transition metals at hydrothermal vents and occur in the active site of the enzymes carbon monoxide dehydrogenases/acetyl coenzyme A synthases (CODH/ACS). Synthetic free-standing NiFe alloy nanoparticles can convert CO2 to acetyl coenzyme A pathway intermediates such as formate, acetate, and pyruvate. The same alloy can further convert pyruvate to citramalate, which is essential in the biological citramalate pathway. Thermal treatment of Ni3Fe nanoparticles under NH3, which can occur in hydrothermal vents, results in Ni3FeN/Ni3Fe heterostructures. This catalyst has been demonstrated to produce prebiotic formamide and acetamide from CO2 and H2O using Ni3FeN/Ni3Fe as both substrate and catalyst. In the process of serpentinization, Co can be reduced in the vicinity of olivine, a Mg-Fe silicate mineral. This produces CoFe and CoFe2 with serpentine in nature, representing SiO2-supported CoFe alloys. In mimicking these natural minerals, synthetic SiO2-supported CoFe alloys demonstrate the same liquid products as NiFe alloys, namely, formate, acetate, and pyruvate under mild hydrothermal vent conditions. In contrast to the NiFe system, hydrocarbons up to C6 were detected in the gas phase, which is also present in hydrothermal vents. The addition of alkali and alkaline-earth metals to the catalysts results in enhanced formate concentration, playing a promotional role in CO2 reduction. Finally, Co was loaded onto ordered mesoporous SiO2 after modification with cations to simulate the minerals found in hydrothermal vents. These catalysts were then investigated under diminished H2O concentration, revealing the conversion of CO2 to CO, CH4, methanol, and acetate. Notably, the selectivity to metabolically relevant methanol was enhanced in the presence of cations that could generate and stabilize the methoxy intermediate. Calculation using the machine learning approach revealed the possibility of predicting the selectivity of CO2 fixation when modifying mesoporous SiO2 supports with heterocations. Our research demonstrates that minerals at hydrothermal vents can convert CO2 into metabolites under a variety of prebiotic conditions, potentially paving the way for modern biological CO2 fixation processes.

A primitive cell model involving Vesicles, microtubules and asters

HYPOTHESIS

Simple single-chain amphiphiles (sodium monododecyl phosphate, SDP) and organic small molecules (isopentenol, IPN), both of primitive relevance, are proved to have been the building blocks of protocells on the early Earth. How do SDP-based membrane and coexisting IPN come together in specific ways to produce more complex chemical entities? What kind of cell-like behavior can be endowed with this protocell model? These are important questions in the pre-life chemical origin scenario that have not been answered to date.

EXPERIMENTS

The phase behavior and formation mechanism of the aggregates for SDP/IPN/H2O ternary system were characterized and studied by different electron microscopy, fluorescent probe technology, DLS, IR, ESI-MS, SAXS, etc. The stability (freeze-thaw and wet-dry treatments) and cell-like behavior (chemical signaling communication) were tested via simulating particular scenarios.

FINDINGS

Vesicles, microtubules and asters phases resembling the morphology and structure of modern cells/organelles were obtained. The intermolecular hydrogen bonding is the main driving force for the emergence of the aggregates. The protocell models not only display remarkable stabilities by simulating the primordial Earth's diurnal temperature differences and ocean tides but also are able to exhibit cell-like behavior of chemical signaling transition.

The Role of Hydrogen Bonds in Thermally Responsive Crystallization-Driven Template Autocatalysis

Autocatalysis has been recognized to be involved in the emergence of life and intrinsic to biomolecular replication. Recently, an efficient template autocatalysis driven by solvent-free crystallization has been reported. Herein, we unveil the role of intermolecular hydrogen bonds formed by amides in crystallization-driven template autocatalysis (CDTA), which involves the autocatalytic activity, template selectivity, and thermal responsiveness. We found that the thermal-induced cis-trans isomerization of amides possibly affects the H-bonding-mediated template ability of products for autocatalytic transformation. As a result, CDTA can be reversibly inhibited and activated by tuning the reaction temperatures. Our work sheds light on the significance of noncovalent H-bonding interactions in artificial self-replicators.

New Insights on the Chemical Origin of Life: The Role of Aqueous Polymerization of N-carboxyanhydrides (NCA)

At the origin, the emergence of proteins was based on crucial prebiotic stages in which simple amino acids-based building blocks spontaneously evolved from the prebiotic soup into random proto-polymers called protoproteins. Despite advances in modern peptide synthesis, these prebiotic chemical routes to protoproteins remain puzzling. We discuss in this perspective how polymer science and systems chemistry are reaching a point of convergence in which simple monomers called N-carboxyanhydrides would be able to form such protoproteins via the emergence of a protometabolic cycle involving aqueous polymerization and featuring macromolecular Darwinism behavior.

A Magnesium Binding Site And The Anomeric Effect Regulate The Abiotic Redox Chemistry Of Nicotinamide Nucleotides

Nicotinamide adenine dinucleotide (NAD+) is a redox active molecule that is universally found in biology. Despite the importance and simplicity of this molecule, few reports exist that investigate which molecular features are important for the activity of this ribodinucleotide. By exploiting the nonenzymatic reduction and oxidation of NAD+ by pyruvate and methylene blue, respectively, we were able to identify key molecular features necessary for the intrinsic activity of NAD+ through kinetic analysis. Such features may explain how NAD+ could have been selected early during the emergence of life. Simpler molecules, such as nicotinamide, that lack an anomeric carbon are incapable of accepting electrons from pyruvate. The phosphate moiety inhibits activity in the absence of metal ions but facilitates activity at physiological pH and model prebiotic conditions by recruiting catalytic Mg2+. Reduction proceeds through consecutive single electron transfer events. Of the derivatives tested, including nicotinamide mononucleotide, nicotinamide riboside, 3-(aminocarbonyl)-1-(2,3-dihydroxypropyl)pyridinium, 1-methylnicotinamide, and nicotinamide, only NAD+ and nicotinamide mononucleotide would be capable of efficiently accepting and donating electrons within a nonenzymatic electron transport chain. The data are consistent with early metabolic chemistry exploiting NAD+ or nicotinamide mononucleotide and not simpler molecules.

Multi-Stimuli-Responsive Network of Multicatalytic Reactions using a Single Palladium/Platinum Catalyst

Given her unrivalled proficiency in the synthesis of all molecules of life, nature has been an endless source of inspiration for developing new strategies in organic chemistry and catalysis. However, one feature that remains thus far beyond chemists' grasp is her unique ability to adapt the productivity of metabolic processes in response to triggers that indicate the temporary need for specific metabolites. To demonstrate the remarkable potential of such stimuli-responsive systems, we present a metabolism-inspired network of multicatalytic processes capable of selectively synthesising a range of products from simple starting materials. Specifically, the network is built of four classes of distinct catalytic reactions-cross-couplings, substitutions, additions, and reductions, involving three organic starting materials-terminal alkyne, aryl iodide, and hydrosilane. All starting materials are either introduced sequentially or added to the system at the same time, with no continuous influx of reagents or efflux of products. All processes in the system are catalysed by a multifunctional heteronuclear PdII/PtII complex, whose performance can be controlled by specific additives and external stimuli. The reaction network exhibits a substantial degree of orthogonality between different pathways, enabling the controllable synthesis of ten distinct products with high efficiency and selectivity through simultaneous triggering and suppression mechanisms.

A Fusion-Growth Protocell Model Based on Vesicle Interactions with Pyrite Particles

Protocell models play a pivotal role in the exploration of the origin of life. Vesicles are one type of protocell model that have attracted much attention. Simple single-chain amphiphiles (SACs) and organic small molecules (OSMs) possess primitive relevance and were most likely the building blocks of protocells on the early Earth. OSM@SAC vesicles have been considered to be plausible protocell models. Pyrite (FeS2), a mineral with primitive relevance, is ubiquitous in nature and plays a crucial role in the exploration of the origin of life in the mineral-water interface scenario. "How do protocell models based on OSM@SAC vesicles interact with a mineral-water interface scenario that simulates a primitive Earth environment" remains an unresolved question. Hence, we select primitive relevant sodium monododecyl phosphate (SDP), isopentenol (IPN) and pyrite (FeS2) mineral particles to build a protocell model. The model investigates the basic physical and chemical properties of FeS2 particles and reveals the effects of the size, content and duration of interaction of FeS2 particles on IPN@SDP vesicles. This deepens the understanding of protocell growth mechanisms in scenarios of mineral-water interfaces in primitive Earth environments and provides new information for the exploration of the origin of life.

Natural languages and RNA virus evolution

Information concepts from physics, mathematics and computer science support many areas of research in biology. Their focus is on objective information, which provides correlations and patterns related to objects, processes, marks and signals. In these approaches only the quantitative aspects of the meaning of the information is relevant. In other areas of biology, 'meaningful information', which is subjective in nature, relies on the physiology of the organism's sensory organs and on the interpretation of the perceived signals, which is then translated into action, even if this is only mental (in brained animals). Information is involved, in terms of both amount and quality. Here we contextualize and review the main theories that deal with 'meaningful-information' at a molecular level from different areas of natural language research, namely biosemiotics, code-biology, biocommunication and biohermeneutics. As this information mediates between the organism and its environment, we emphasize how such theories compare with the neo-Darwinian treatment of genetic information, and how they project onto the rapid evolution of RNA viruses.

Proto-neural networks from thermal proteins

Proteinoids are synthetic polymers that have structural similarities to natural proteins, and their formation is achieved through the application of heat to amino acid combinations in a dehydrated environment. The thermal proteins, initially synthesised by Sidney Fox during the 1960s, has the ability to undergo self-assembly, resulting in the formation of microspheres that resemble cells. These microspheres have fascinating biomimetic characteristics. In recent studies, substantial advancements have been made in elucidating the electrical signalling phenomena shown by proteinoids, hence showcasing their promising prospects in the field of neuro-inspired computing. This study demonstrates the advancement of experimental prototypes that employ proteinoids in the construction of fundamental neural network structures. The article provides an overview of significant achievements in proteinoid systems, such as the demonstration of electrical excitability, emulation of synaptic functions, capabilities in pattern recognition, and adaptability of network structures. This study examines the similarities and differences between proteinoid networks and spontaneous neural computation. We examine the persistent challenges associated with deciphering the underlying mechanisms of emergent proteinoid-based intelligence. Additionally, we explore the potential for developing bio-inspired computing systems using synthetic thermal proteins in forthcoming times. The results of this study offer a theoretical foundation for the advancement of adaptive, self-assembling electronic systems that operate using artificial bio-neural principles.

The enol of isobutyric acid

We present the gas-phase synthesis of 2-methyl-prop-1-ene-1,1-diol, an unreported higher energy tautomer of isobutyric acid. The enol was captured in an argon matrix at 3.5 K, characterized spectroscopically and by DFT computations. The enol rearranges likely photochemically to isobutyric acid and dimethylketene. We also identified propene, likely photochemically formed from dimethylketene.

Amino Acid Polymerization on Silica Surfaces

The polymerization of unactivated amino acids (AAs) is an important topic because of its applications in various fields including industrial medicinal chemistry and prebiotic chemistry. Silica as a promoter for this reaction, is of great interest owing to its large abundance and low cost. The amide/peptide bond synthesis on silica has been largely demonstrated but suffers from a lack of knowledge regarding its reaction mechanism, the key parameters, and surface features that influence AA adsorption and reactivity, the selectivity of the reaction product, the role of water in the reaction, etc. The present review addresses these problems by summarizing experimental and modeling results from the literature and attempts to rationalize some apparent divergences in published results. After briefly presenting the main types of silica surface sites and other relevant macroscopic features, we discuss the different deposition procedures of AAs, whose importance is often neglected. We address the possible AA adsorption mechanisms including covalent grafting and H-bonding and show that they are highly dependent on silanol types and density. We then consider how the adsorption mechanisms determine the occurrence and outcome of AA condensation (formation of cyclic dimers or of long linear chains), and outline some recent results that suggest significant polymerization selectivity in systems containing several AAs, as well as the formation of specific elements of secondary structure in the growing polypeptide chains.

Architecture, Function, Regulation, and Evolution of α-Glucans Metabolic Enzymes in Prokaryotes

Bacteria have acquired sophisticated mechanisms for assembling and disassembling polysaccharides of different chemistry. α-d-Glucose homopolysaccharides, so-called α-glucans, are the most widespread polymers in nature being key components of microorganisms. Glycogen functions as an intracellular energy storage while some bacteria also produce extracellular assorted α-glucans. The classical bacterial glycogen metabolic pathway comprises the action of ADP-glucose pyrophosphorylase and glycogen synthase, whereas extracellular α-glucans are mostly related to peripheral enzymes dependent on sucrose. An alternative pathway of glycogen biosynthesis, operating via a maltose 1-phosphate polymerizing enzyme, displays an essential wiring with the trehalose metabolism to interconvert disaccharides into polysaccharides. Furthermore, some bacteria show a connection of intracellular glycogen metabolism with the genesis of extracellular capsular α-glucans, revealing a relationship between the storage and structural function of these compounds. Altogether, the current picture shows that bacteria have evolved an intricate α-glucan metabolism that ultimately relies on the evolution of a specific enzymatic machinery. The structural landscape of these enzymes exposes a limited number of core catalytic folds handling many different chemical reactions. In this Review, we present a rationale to explain how the chemical diversity of α-glucans emerged from these systems, highlighting the underlying structural evolution of the enzymes driving α-glucan bacterial metabolism.

A Surface Hydrothermal Source of Nitriles and Isonitriles

Giant impacts can generate transient hydrogen-rich atmospheres, reducing atmospheric carbon. The reduced carbon will form hazes that rain out onto the surface and can become incorporated into the crust. Once heated, a large fraction of the carbon is converted into graphite. The result is that local regions of the Hadean crust were plausibly saturated with graphite. We explore the consequences of such a crust for a prebiotic surface hydrothermal vent scenario. We model a surface vent fed by nitrogen-rich volcanic gas from high-temperature magmas passing through graphite-saturated crust. We consider this occurring at pressures of 1-1000bar and temperatures of 1500-1700 ∘C. The equilibrium with graphite purifies the leftover gas, resulting in substantial quantities of nitriles (0.1% HCN and 1ppm HC3N) and isonitriles (0.01% HNC) relevant for prebiotic chemistry. We use these results to predict gas-phase concentrations of methyl isocyanide of ∼1 ppm. Methyl isocyanide can participate in the non-enzymatic activation and ligation of the monomeric building blocks of life, and surface or shallow hydrothermal environments provide its only known equilibrium geochemical source.

Generalist versus Specialist Self-Replicators

Darwinian evolution, including the selection of the fittest species under given environmental conditions, is a major milestone in the development of synthetic living systems. In this regard, generalist or specialist behavior (the ability to replicate in a broader or narrower, more specific food environment) are of importance. Here we demonstrate generalist and specialist behavior in dynamic combinatorial libraries composed of a peptide-based and an oligo(ethylene glycol) based building block. Three different sets of macrocyclic replicators could be distinguished based on their supramolecular organization: two prepared from a single building block as well as one prepared from an equimolar mixture of them. Peptide-containing hexamer replicators were found to be generalists, i. e. they could replicate in a broad range of food niches, whereas the octamer peptide-based replicator and hexameric ethyleneoxide-based replicator were proven to be specialists, i. e. they only replicate in very specific food niches that correspond to their composition. However, sequence specificity cannot be demonstrated for either of the generalist replicators. The generalist versus specialist nature of these replicators was linked to their supramolecular organization. Assembly modes that accommodate structurally different building blocks lead to generalist replicators, while assembly modes that are more restrictive yield specialist replicators.

Memfractance of Proteinoids

Proteinoids, or thermal proteins, are amino acid polymers formed at high temperatures by nonbiological processes. The objective of this study is to examine the memfractance characteristics of proteinoids within a supersaturated hydroxyapatite solution. The ionic solution utilized for the current-voltage (I-V) measurements possessed an ionic strength of 0.15 mol/L, a temperature of 37 °C, and a pH value of 7.4. The I-V curves exhibited distinct spikes, which are hypothesized to arise from the capacitive charging and discharging of the proteinoid-hydroxyapatite media. The experimental results demonstrated a positive correlation between the concentration of proteinoids and the observed number of spikes in the I-V curves. This observation provides evidence in favor of the hypothesis that the spikes originate from the proteinoids' capacitive characteristics. The memfractance behavior exemplifies the capacity of proteinoids to retain electrical charge within the hydrated hydroxyapatite media. Additional investigation is required in order to comprehensively identify the memcapacitive phenomena and delve into their implications for models of protocellular membranes. In a nutshell, this study provides empirical support for the existence of capacitive membrane-memfractance mechanisms in ensembles of proteinoids.

Swelling and penetration of fatty acid vesicles under ion-competitive environment

The physicochemical characteristics of fatty acid (FA) vesicles and their ion sensitivity as drug delivery vehicles in an ion-competitive environment have received much attention. Here, we show that in a Na+/K+ competitive ionic environment, FA vesicles undergo a cascade of periodic expansion and selective ion retention in response to osmotic attack. When the Na+/K+ ratio is altered, the expansion and volume of vesicles are affected and the ions in vesicles mix with the hyperosmotic fluid to produce a stable transmembrane potential, consistent with the Donnan effect and iontophoresis theory. Furthermore, osmotic swelling experiments suggest that FA vesicles are more easily maintained in a single Na+ or K+ solution than in a multicomponent ion competition system. As a theoretical basis for the utilization of FA vesicles in multicomponent ionic environments, we developed a core theoretical model to characterize the basic features of the volume fluctuations of FA vesicles in ion-competing environments.

A Prebiotic Precursor to Life's Phosphate Transfer System with an ATP Analog and Histidyl Peptide Organocatalysts

Biochemistry is dependent upon enzyme catalysts accelerating key reactions. At the origin of life, prebiotic chemistry must have incorporated catalytic reactions. While this would have yielded much needed amplification of certain reaction products, it would come at the possible cost of rapidly depleting the high energy molecules that acted as chemical fuels. Biochemistry solves this problem by combining kinetically stable and thermodynamically activated molecules (e.g., ATP) with enzyme catalysts. Here, we demonstrate a prebiotic phosphate transfer system involving an ATP analog (imidazole phosphate) and histidyl peptides, which function as organocatalytic enzyme analogs. We demonstrate that histidyl peptides catalyze phosphorylations via a phosphorylated histidyl intermediate. We integrate these histidyl-catalyzed phosphorylations into a complete prebiotic scenario whereby inorganic phosphate is incorporated into organic compounds though physicochemical wet-dry cycles. Our work demonstrates a plausible system for the catalyzed production of phosphorylated compounds on the early Earth and how organocatalytic peptides, as enzyme precursors, could have played an important role in this.

Interstellar formation of glyceric acid [HOCH2CH(OH)COOH]-The simplest sugar acid

Glyceric acid [HOCH2CH(OH)COOH]-the simplest sugar acid-represents a key molecule in biochemical processes vital for metabolism in living organisms such as glycolysis. Although critically linked to the origins of life and identified in carbonaceous meteorites with abundances comparable to amino acids, the underlying mechanisms of its formation have remained elusive. Here, we report the very first abiotic synthesis of racemic glyceric acid via the barrierless radical-radical reaction of the hydroxycarbonyl radical (HOĊO) with 1,2-dihydroxyethyl (HOĊHCH2OH) radical in low-temperature carbon dioxide (CO2) and ethylene glycol (HOCH2CH2OH) ices. Using isomer-selective vacuum ultraviolet photoionization reflectron time-of-flight mass spectrometry, glyceric acid was identified in the gas phase based on the adiabatic ionization energies and isotopic substitution studies. This work reveals the key reaction pathways for glyceric acid synthesis through nonequilibrium reactions from ubiquitous precursor molecules, advancing our fundamental knowledge of the formation pathways of key biorelevant organics-sugar acids-in deep space.

Transient control of lytic activity via a non-equilibrium chemical reaction system

The development of artificial non-equilibrium chemical reaction systems has recently attracted considerable attention as a new type of biomimetic. However, due to the lack of bioorthogonality, such reaction systems could not be linked to the regulation of any biological phenomena. Here, we have newly designed a non-equilibrium reaction system based on olefin metathesis to produce the Triton X-mimetic non-ionic amphiphile as a kinetic product. Using phospholipid vesicles encapsulating fluorescent dyes and red blood cells as cell models, we demonstrate that the developed chemical reaction system is applicable for transient control of the resulting lytic activity.

Conformational preferences of guanine-containing threose nucleic acid building blocks in B3LYP studies

In this paper, detailed and systematic gas-phase B3LYP conformational studies of four monomers of threose nucleic acid (TNA) with guanine attached at the C1' atom and bearing different substituents (OH, OP(=O)OH2 and OCH3) in the C2' and C3' positions of the α-l-threofuranose moiety are presented. All exocyclic single-bond (χ, ε and γ) rotations, as well as the ν0-ν4 endocyclic torsion angles, were taken into consideration. Three (threoguanosines TG1-TG3) or two (TG4) energy minima were found for the rotation about the χ torsion angle. The syn orientation (the A rotamer family) is strongly privileged in geometries TG1 and TG2, whereas the anti orientation (the C rotamer family) and the syn orientation are observed to be in equilibrium (with populations of 56% and 44%, respectively) for TG3. In the case of TG4, the high-anti orientation (the B rotamer family) turned out to be by far the most favourable, with the contribution exceeding 90% in equilibrium. Such a preference can be attributed to the inability of H-bonding between sugar and nucleobase and possibly because of the steric strains. The low-energy conformers of TG1-TG4 occupy the northeastern (P ∼ 40°) and/or southern (P ∼ 210°) parts of the pseudorotational wheel, which fits the A- and B-type DNA helices quite well. Additionally, in the case of TG4, some relatively stable geometries have the furanoid ring in conformation lying on the northwestern part of the pseudorotational wheel (P ∼ 288°).

Prebiotic Synthesis of Glycolaldehyde and Glyceraldehyde from Formaldehyde: A Computational Study on the Initial Steps of the Formose Reaction

In this work, the initial steps of the mechanism of the Formose reaction (FR) is computationally studied using DFT methods. The FR has been considered to be a relevant process in the prebiotic evolution leading to several types of sugars or carbohydrates. These molecules are some of the basic building blocks of the life. The dimerization of formaldehyde was found to take place via an intramolecular deprotonation reaction, leading to the formation of an intermediate which, after an isomerization, forms a Ca-complex of the cis-enediol tautomer of glycolaldehyde. The aldol reaction of this complex with additional formaldehyde gave glyceraldehyde, the simplest aldotriose. The catalyst Ca(OH)2 plays a dual role in the reaction, acting as a base (in the intramolecular deprotonation) and as Lewis acid (activating the carbonyl group) in the aldol addition.

Prebiotically plausible chemoselective pantetheine synthesis in water

Coenzyme A (CoA) is essential to all life on Earth, and its functional subunit, pantetheine, is important in many origin-of-life scenarios, but how pantetheine emerged on the early Earth remains a mystery. Earlier attempts to selectively synthesize pantetheine failed, leading to suggestions that "simpler" thiols must have preceded pantetheine at the origin of life. In this work, we report high-yielding and selective prebiotic syntheses of pantetheine in water. Chemoselective multicomponent aldol, iminolactone, and aminonitrile reactions delivered spontaneous differentiation of pantoic acid and proteinogenic amino acid syntheses, as well as the dihydroxyl, gem-dimethyl, and β-alanine-amide moieties of pantetheine in dilute water. Our results are consistent with a role for canonical pantetheine at the outset of life on Earth.

The Conformational Contribution to Molecular Complexity and Its Implications for Information Processing in Living Beings and Chemical Artificial Intelligence

This work highlights the relevant contribution of conformational stereoisomers to the complexity and functions of any molecular compound. Conformers have the same molecular and structural formulas but different orientations of the atoms in the three-dimensional space. Moving from one conformer to another is possible without breaking covalent bonds. The interconversion is usually feasible through the thermal energy available in ordinary conditions. The behavior of most biopolymers, such as enzymes, antibodies, RNA, and DNA, is understandable if we consider that each exists as an ensemble of conformers. Each conformational collection confers multi-functionality and adaptability to the single biopolymers. The conformational distribution of any biopolymer has the features of a fuzzy set. Hence, every compound that exists as an ensemble of conformers allows the molecular implementation of a fuzzy set. Since proteins, DNA, and RNA work as fuzzy sets, it is fair to say that life's logic is fuzzy. The power of processing fuzzy logic makes living beings capable of swift decisions in environments dominated by uncertainty and vagueness. These performances can be implemented in chemical robots, which are confined molecular assemblies mimicking unicellular organisms: they are supposed to help humans "colonise" the molecular world to defeat diseases in living beings and fight pollution in the environment.

Direct Analysis of Complex Reaction Mixtures: Formose Reaction

Complex reaction mixtures, like those postulated on early Earth, present an analytical challenge because of the number of components, their similarity, and vastly different concentrations. Interpreting the reaction networks is typically based on simplified or partial data, limiting our insight. We present a new approach based on online monitoring of reaction mixtures formed by the formose reaction by ion-mobility-separation mass-spectrometry. Monitoring the reaction mixtures led to large data sets that we analyzed by non-negative matrix factorization, thereby identifying ion-signal groups capturing the time evolution of the network. The groups comprised ≈300 major ion signals corresponding to sugar-calcium complexes formed during the formose reaction. Multivariate analysis of the kinetic profiles of these complexes provided an overview of the interconnected kinetic processes in the solution, highlighting different pathways for sugar growth and the effects of different initiators on the initial kinetics. Reconstructing the network's topology further, we revealed so far unnoticed fast retro-aldol reaction of ketoses, which significantly affects the initial reaction dynamics. We also detected the onset of sugar-backbone branching for C6  sugars and cyclization reactions starting for C5  sugars. This top-down analytical approach opens a new way to analyze complex dynamic mixtures online with unprecedented coverage and time resolution.

Modifying the Catalytic Activity of Lipopeptide Assemblies with Nucleobases

Biohybrid catalysts that operate in aqueous media are intriguing for systems chemistry. In this paper, we investigate whether control over the self-assembly of biohybrid catalysts can tune their properties. As a model, we use the catalytic activity of functional hybrid molecules consisting of a catalytic H-dPro-Pro-Glu tripeptide, derivatized with fatty acid and nucleobase moieties. This combination of simple biological components merged the catalytic properties of the peptide with the self-assembly of the lipid, and the structural ordering of the nucleobases. The biomolecule hybrids self-assemble in aqueous media into fibrillar assemblies and catalyze the reaction between butanal and nitrostyrene. The interactions between the nucleobases enhanced the order of the supramolecular structures and affected their catalytic activity and stereoselectivity. The results point to the significant control and ordering that nucleobases can provide in the self-assembly of biologically inspired supramolecular catalysts.

Dual-Color Real-Time Chemosensing of a Compartmentalized Reaction Network Involving Enzyme-Induced Membrane Permeation of Peptides

The design of synthetic systems with interrelated reaction sequences that model incipient biological complexity is limited by physicochemical tools that allow the direct monitoring of the individual processes in real-time. To mimic a simple digestion-resorption sequence, the authors have designed compartmentalized liposomal systems that incorporate extra- and intravesicular chemosensing ensembles. The extravesicular reporter pair consists of cucurbit[7]uril and methylene blue to monitor the enzymatic cleavage of short enkephalin-related peptides by thermolysin through a switch-off fluorescence response ("digestion"). Because the substrate is membrane-impermeable, but the dipeptide product is permeable, uptake of the latter into the pre-formed liposomes occurs as a follow-up process. The intravesicular chemosensing ensemble consists of i) cucurbit[8]uril, 2-anilinonaphthalene-6-sulfonic acid, and methyl viologen or ii) cucurbit[7]uril and berberine to monitor the uptake ("resorption") of the enzymatic products through the liposomal membranes by i) a switch-on or ii) a switch-off fluorescence response. The dyes are designed to allow selective optical excitation and read-out of the extra- and intravesicular dyes, which allow for dual-color chemosensing and, therefore, kinetic discrimination of the two sequential reactions.

Cyclophospholipids Enable a Protocellular Life Cycle

There is currently no plausible path for the emergence of a self-replicating protocell, because prevalent formulations of model protocells are built with fatty acid vesicles that cannot withstand the concentrations of Mg2+ needed for the function and replication of nucleic acids. Although prebiotic chelates increase the survivability of fatty acid vesicles, the resulting model protocells are incapable of growth and division. Here, we show that protocells made of mixtures of cyclophospholipids and fatty acids can grow and divide in the presence of Mg2+-citrate. Importantly, these protocells retain encapsulated nucleic acids during growth and division, can acquire nucleotides from their surroundings, and are compatible with the nonenzymatic extension of an RNA oligonucleotide, chemistry needed for the replication of a primitive genome. Our work shows that prebiotically plausible mixtures of lipids form protocells that are active under the conditions necessary for the emergence of Darwinian evolution.

Chirality-Selected Coacervate by Chiral Gemini Surfactant

Chiral surfactants present opportunities to self-assemble into supramolecules with a chiral trait; however, the effects of stereochemistry on the formation of simple coacervates remain unclear. Here, we investigate the chirality-selected phase behavior in mixtures of chiral gemini surfactant 1,4-bis(dodecyl-N,N-dimethylammonium bromide)-2,3-butanediol (12-4(OH)2-12) with an oppositely charged chiral mandelic acid (MA). It demonstrates that altering the chirality of surfactants yields a heightened ability to regulate the phase behavior, leading to the formation of three different network-like structures, i.e., wormlike micelle, coacervate, and hydrogel, in the racemate, enantiomer, and mesomer, respectively. The different aggregate structures arise from the intermolecular and intramolecular hydrogen-bond interactions of the two hydroxyl groups located at stereogenic centers. Intriguingly, although they contain similar microstructures, the solid-like hydrogel and liquid-like wormlike micelle show similar low hydration ability and have no encapsulation capability, whereas only coacervate formed by the enantiomers of 12-4(OH)2-12 displays liquid-like characteristics, strong capacity to sequester diverse solutes, and high affinity for tightly bound water simultaneously. These findings further highlight the unique and advantageous properties of coacervates as a promising model for exploring the biological process and understanding how chirality plays a crucial role in early life scenarios and cell evolution at the molecular level.

Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It

Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.

Selective Encapsulation and Chiral Induction of C60 and C70 Fullerenes by Axially Chiral Porous Aromatic Cages

Chiral induction has been an important topic in chemistry, not only for its relevance in understanding the mysterious phenomenon of spontaneous symmetry breaking in nature but also due to its critical implications in medicine and the chiral industry. The induced chirality of fullerenes by host-guest interactions has been rarely reported, mainly attributed to their chiral resistance from high symmetry and challenges in their accessibility. Herein, we report two new pairs of chiral porous aromatic cages (PAC), R-PAC-2, S-PAC-2 (with Br substituents) and R-PAC-3, S-PAC-3 (with CH3 substituents) enantiomers. PAC-2, rather than PAC-3, achieves fullerene encapsulation and selective binding of C70 over C60 in fullerene carbon soot. More significantly, the occurrence of chiral induction between R-PAC-2, S-PAC-2 and fullerenes is confirmed by single-crystal X-ray diffraction and the intense CD signal within the absorption region of fullerenes. DFT calculations reveal the contribution of electrostatic effects originating from face-to-face arene-fullerene interactions dominate C70 selectivity and elucidate the substituent effect on fullerene encapsulation. The disturbance from the differential interactions between fullerene and surrounding chiral cages on the intrinsic highly symmetric electronic structure of fullerene could be the primary reason accounting for the induced chirality of fullerene.

Optimization and Enhancement of the Peroxidase-like Activity of Hemin in Aqueous Solutions of Sodium Dodecylsulfate

Iron porphyrins play several important roles in present-day living systems and probably already existed in very early life forms. Hemin (= ferric protoporphyrin IX = ferric heme b), for example, is the prosthetic group at the active site of heme peroxidases, catalyzing the oxidation of a number of different types of reducing substrates after hemin is first oxidized by hydrogen peroxide as the oxidizing substrate of the enzyme. The active site of heme peroxidases consists of a hydrophobic pocket in which hemin is embedded noncovalently and kept in place through coordination of the iron atom to a proximal histidine side chain of the protein. It is this partially hydrophobic local environment of the enzyme which determines the efficiency with which the sequential reactions of the oxidizing and reducing substrates proceed at the active site. Free hemin, which has been separated from the protein moiety of heme peroxidases, is known to aggregate in an aqueous solution and exhibits low catalytic activity. Based on previous reports on the use of surfactant micelles to solubilize free hemin in a nonaggregated state, the peroxidase-like activity of hemin in the presence of sodium dodecyl sulfate (SDS) at concentrations below and above the critical concentration for SDS micelle formation (critical micellization concentration (cmc)) was systematically investigated. In most experiments, 3,3',5,5'-tetramethylbenzidine (TMB) was applied as a reducing substrate at pH = 7.2. The presence of SDS clearly had a positive effect on the reaction in terms of initial reaction rate and reaction yield, even at concentrations below the cmc. The highest activity correlated with the cmc value, as demonstrated for reactions at three different HEPES concentrations. The 4-(2-hydroxyethyl)-1-piperazineethanesulfonate salt (HEPES) served as a pH buffer substance and also had an accelerating effect on the reaction. At the cmc, the addition of l-histidine (l-His) resulted in a further concentration-dependent increase in the peroxidase-like activity of hemin until a maximal effect was reached at an optimal l-His concentration, probably corresponding to an ideal mono-l-His ligation to hemin. Some of the results obtained can be understood on the basis of molecular dynamics simulations, which indicated the existence of intermolecular interactions between hemin and HEPES and between hemin and SDS. Preliminary experiments with SDS/dodecanol vesicles at pH = 7.2 showed that in the presence of the vesicles, hemin exhibited similar peroxidase-like activity as in the case of SDS micelles. This supports the hypothesis that micelle- or vesicle-associated ferric or ferrous iron porphyrins may have played a role as primitive catalysts in membranous prebiotic compartment systems before cellular life emerged.

Redox-responsive peptide-based complex coacervates as delivery vehicles with controlled release of proteinous drugs

Proteinous drugs are highly promising therapeutics to treat various diseases. However, they suffer from limited circulation times and severe off-target side effects. Inspired by active membraneless organelles capable of dynamic recruitment and releasing of specific proteins, here, we present the design of coacervates as therapeutic protocells, made from small metabolites (anionic molecules) and simple arginine-rich peptides (cationic motif) through liquid-liquid phase separation. These complex coacervates demonstrate that their assembly and disassembly can be regulated by redox chemistry, which helps to control the release of the therapeutic protein. A model proteinous drugs, tissue plasminogen activator (tPA), can rapidly compartmentalize inside the complex coacervates, and the coacervates formed from peptides conjugated with arginine-glycine-aspartic acid (RGD) motif (a fibrinogen-derived peptide sequence), show selective binding to the thrombus site and thus enhance on-target efficacy of tPA. Furthermore, the burst release of tPA can be controlled by the redox-induced dissolution of the coacervates. Our proof-of-principle complex coacervate system provides insights into the sequestration and release of proteinous drugs from advanced drug delivery systems and represents a step toward the construction of synthetic therapeutic protocells for biomedical applications.

On the Emergence of Autonomous Chemical Systems through Dissipation Kinetics

This work addresses the kinetic requirements for compensating the entropic cost of self-organization and natural selection, thereby revealing a fundamental principle in biology. Metabolic and evolutionary features of life cannot therefore be separated from an origin of life perspective. Growth, self-organization, evolution and dissipation processes need to be metabolically coupled and fueled by low-entropy energy harvested from the environment. The evolutionary process requires a reproduction cycle involving out-of-equilibrium intermediates and kinetic barriers that prevent the reproductive cycle from proceeding in reverse. Model analysis leads to the unexpectedly simple relationship that the system should be fed energy with a potential exceeding a value related to the ratio of the generation time to the transition state lifetime, thereby enabling a process mimicking natural selection to take place. Reproducing life's main features, in particular its Darwinian behavior, therefore requires satisfying constraints that relate to time and energy. Irreversible reaction cycles made only of unstable entities reproduce some of these essential features, thereby offering a physical/chemical basis for the possible emergence of autonomy. Such Emerging Autonomous Systems (EASs) are found to be capable of maintaining and reproducing their kind through the transmission of a stable kinetic state, thereby offering a physical/chemical basis for what could be deemed an epigenetic process.

Aqueous microdroplets promote C-C bond formation and sequences in the reverse tricarboxylic acid cycle

The reverse tricarboxylic acid cycle (rTCA) is a central anabolic network that uses carbon dioxide (CO2) and may have provided complex carbon substrates for life before the advent of RNA or enzymes. However, non-enzymatic promotion of the rTCA cycle, in particular carbon fixation, remains challenging, even with primordial metal catalysis. Here, we report that the fixation of CO2 by reductive carboxylation of succinate and α-ketoglutarate was achieved in aqueous microdroplets under ambient conditions without the use of catalysts. Under identical conditions, the aqueous microdroplets also facilitated the sequences in the rTCA cycle, including reduction, hydration, dehydration and retro-aldol cleavage and linked with the glyoxylate cycle. These reactions of the rTCA cycle were compatible with the aqueous microdroplets, as demonstrated with two-reaction and four-reaction sequences. A higher selectivity giving higher product yields was also observed. Our results suggest that the microdroplets provide an energetically favourable microenvironment and facilitate a non-enzymatic version of the rTCA cycle in prebiotic carbon anabolism.

The protometabolic nature of prebiotic chemistry

The field of prebiotic chemistry has been dedicated over decades to finding abiotic routes towards the molecular components of life. There is nowadays a handful of prebiotically plausible scenarios that enable the laboratory synthesis of most amino acids, fatty acids, simple sugars, nucleotides and core metabolites of extant living organisms. The major bottleneck then seems to be the self-organization of those building blocks into systems that can self-sustain. The purpose of this tutorial review is having a close look, guided by experimental research, into the main synthetic pathways of prebiotic chemistry, suggesting how they could be wired through common intermediates and catalytic cycles, as well as how recursively changing conditions could help them engage in self-organized and dissipative networks/assemblies (i.e., systems that consume chemical or physical energy from their environment to maintain their internal organization in a dynamic steady state out of equilibrium). In the article we also pay attention to the implications of this view for the emergence of homochirality. The revealed connectivity between those prebiotic routes should constitute the basis for a robust research program towards the bottom-up implementation of protometabolic systems, taken as a central part of the origins-of-life problem. In addition, this approach should foster further exploration of control mechanisms to tame the combinatorial explosion that typically occurs in mixtures of various reactive precursors, thus regulating the functional integration of their respective chemistries into self-sustaining protocellular assemblies.

(Photoredox) Organocatalysis in the Emergence of Life: Discovery, Applications, and Molecular Evolution

ConspectusLife as we know it is built on complex and perfectly interlocking processes that have evolved over millions of years through evolutionary optimization processes. The emergence of life from nonliving matter and the evolution of such highly efficient systems therefore constitute an enormous synthetic and systems chemistry challenge. Advances in supramolecular and systems chemistry are opening new perspectives that provide insights into living and self-sustaining reaction networks as precursors for life. However, the ab initio synthesis of such a system requires the possibility of autonomous optimization of catalytic properties and, consequently, of an evolutionary system at the molecular level. In this Account, we present our discovery of the formation of substituted imidazolidine-4-thiones (photoredox) organocatalysts from simple prebiotic building blocks such as aldehydes and ketones under Strecker reaction conditions with ammonia and cyanides in the presence of hydrogen sulfide. The necessary aldehydes are formed from CO2 and hydrogen under prebiotically plausible meteoritic or volcanic iron-particle catalysis in the atmosphere of the early Earth. Remarkably, the investigated imidazolidine-4-thiones undergo spontaneous resolution by conglomerate crystallization, opening a pathway for symmetry breaking, chiral amplification, and enantioselective organocatalysis. These imidazolidine-4-thiones enable α-alkylations of aldehydes and ketones by photoredox organocatalysis. Therefore, these photoredox organocatalysts are able to modify their aldehyde building blocks, which leads in an evolutionary process to mutated second-generation and third-generation catalysts. In our experimental studies, we found that this mutation can occur not only by new formation of the imidazolidine core structure of the catalyst from modified aldehyde building blocks or by continuous supply from a pool of available building blocks but also by a dynamic exchange of the carbonyl moiety in ring position 2 of the imidazolidine moiety. Remarkably, it can be shown that by incorporating aldehyde building blocks from their environment, the imidazolidine-4-thiones are able to change and adapt to altering environmental conditions without undergoing the entire formation process. The selection of the mutated catalysts is then based on the different catalytic activities in the modification of the aldehyde building blocks and on the catalysis of subsequent processes that can lead to the formation of molecular reaction networks as progenitors for cellular processes. We were able to show that these imidazolidine-4-thiones not only enable α-alkylations but also facilitate other important transformations, such as the selective phosphorylation of nucleosides to nucleotides as a key step leading to the oligomerization to RNA and DNA. It can therefore be expected that evolutionary processes have already taken place on a small molecular level and have thus developed chemical tools that change over time, representing a hidden layer on the path to enzymatically catalyzed biochemical processes.

From autocatalysis to survival of the fittest in self-reproducing lipid systems

Studying autocatalysis - in which molecules catalyse their own formation - might help to explain the emergence of chemical systems that exhibit traits normally associated with biology. When coupled to other processes, autocatalysis can lead to complex systems-level behaviour in apparently simple mixtures. Lipids are an important class of chemicals that appear simple in isolation, but collectively show complex supramolecular and mesoscale dynamics. Here we discuss autocatalytic lipids as a source of extraordinary behaviour such as primitive chemical evolution, chemotaxis, temporally controllable materials and even as supramolecular catalysts for continuous synthesis. We survey the literature since the first examples of lipid autocatalysis and highlight state-of-the-art synthetic systems that emulate life, displaying behaviour such as metabolism and homeostasis, with special consideration for generating structural complexity and out-of-equilibrium models of life. Autocatalytic lipid systems have enormous potential for building complexity from simple components, and connections between physical effects and molecular reactivity are only just beginning to be discovered.

Simulation workflows to predict the circular dichroism and circularly polarized luminescence of chiral materials

Chiral materials are attracting considerable interest in various fields in view of their unique properties and optical activity. Indeed, the peculiar features of chiral materials to absorb and emit circularly polarized light enable their use in an extensive range of applications. Motivated by the interest in boosting the development of chiral materials characterized by enhanced chiroptical properties such as circular dichroism (CD) and circular polarized luminescence (CPL), we herein illustrate in this tutorial how theoretical simulations can be used for the predictions and interpretations of chiroptical data and for the identification of chiral geometries. We are focusing on computational frameworks that can be used to investigate the theoretical aspects of chiral materials' photophysical and conformational characteristics. We will then illustrate ab initio methods based on density functional theory (DFT) and its time-dependent extension (TD-DFT) to simulate CD and CPL signals, and we will exemplify a variety of enhanced sampling techniques useful for an adequate sampling of the configurational space for chiral systems.

Kinetic Modeling and Parameter Estimation of a Prebiotic Peptide Reaction Network

Although our understanding of how life emerged on Earth from simple organic precursors is speculative, early precursors likely included amino acids. The polymerization of amino acids into peptides and interactions between peptides are of interest because peptides and proteins participate in complex interaction networks in extant biology. However, peptide reaction networks can be challenging to study because of the potential for multiple species and systems-level interactions between species. We developed and employed a computational network model to describe reactions between amino acids to form di-, tri-, and tetra-peptides. Our experiments were initiated with two of the simplest amino acids, glycine and alanine, mediated by trimetaphosphate-activation and drying to promote peptide bond formation. The parameter estimates for bond formation and hydrolysis reactions in the system were found to be poorly constrained due to a network property known as sloppiness. In a sloppy model, the behavior mostly depends on only a subset of parameter combinations, but there is no straightforward way to determine which parameters should be included or excluded. Despite our inability to determine the exact values of specific kinetic parameters, we could make reasonably accurate predictions of model behavior. In short, our modeling has highlighted challenges and opportunities toward understanding the behaviors of complex prebiotic chemical experiments.

Oscillatory dynamics in a reaction network based on imine hydrolysis

We have built an autocatalytic reaction network, based on the hydrolysis of certain imines, which exhibits bistability in an open system. The positive feedback originates from the interplay of fast acid-base equilibria, leading to hydroxide ion production, and pH-dependent hydrolysis rates. The addition of a first-order removal of the autocatalyst can result in sustained pH oscillations close to physiological conditions. The unit-amplitude pH oscillations are accompanied by the stoichiometric conversion of imine into amine back and forth. A systematic parameter search is carried out to characterize the rich observable dynamics and identify the evolving bifurcations.

The enol of propionic acid

We demonstrate the gas-phase synthesis of prop-1-ene-1,1-diol, the hitherto unreported higher energy tautomer of propionic acid. The enol was trapped in an argon matrix and characterized by IR and UV/Vis spectroscopy in combination with density functional theory computations. Upon photolysis, the enol rearranges to propionic acid and methylketene.

Carbonyl Migration in Uronates Affords a Potential Prebiotic Pathway for Pentose Production

Carbohydrate biosynthesis is fundamental to modern terrestrial biochemistry, but how this collection of metabolic pathways originated remains an open question. Prebiotic sugar synthesis has focused primarily on the formose reaction and Kiliani-Fischer homologation; however, how they can transition to extant biochemical pathways has not been studied. Herein, a nonenzymatic pathway for pentose production with similar chemical transformations as those of the pentose phosphate pathway is demonstrated. Starting from a C6 aldonate, namely, gluconate, nonselective chemical oxidation yields a mixture of 2-oxo-, 4-oxo-, 5-oxo-, and 6-oxo-uronate regioisomers. Regardless at which carbinol the oxidation takes place, carbonyl migration enables β-decarboxylation to yield pentoses. In comparison, the pentose phosphate pathway selectively oxidizes 6-phosphogluconate to afford the 3-oxo-uronate derivative, which undergoes facile subsequent β-decarboxylation and carbonyl migration to afford ribose 5-phosphate. The similarities between these two pathways and the potential implications for prebiotic chemistry and protometabolism are discussed.