From interstellar amino acids to prebiotic catalytic peptides: a review

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.

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.

Oxazolone mediated peptide chain extension and homochirality in aqueous microdroplets

Peptide formation from amino acids is thermodynamically unfavorable but a recent study provided evidence that the reaction occurs at the air/solution interfaces of aqueous microdroplets. Here, we show that i) the suggested amino acid complex in microdroplets undergoes dehydration to form oxazolone; ii) addition of water to oxazolone forms the dipeptide; and iii) reaction of oxazolone with other amino acids forms tripeptides. Furthermore, the chirality of the reacting amino acids is preserved in the oxazolone product, and strong chiral selectivity is observed when converting the oxazolone to tripeptide. This last fact ensures that optically impure amino acids will undergo chain extension to generate pure homochiral peptides. Peptide formation in bulk by wet-dry cycling shares a common pathway with the microdroplet reaction, both involving the oxazolone intermediate.

An inorganic mineral-based protocell with prebiotic radiation fitness

Protocell fitness under extreme prebiotic conditions is critical in understanding the origin of life. However, little is known about protocell's survival and fitness under prebiotic radiations. Here we present a radioresistant protocell model based on assembly of two types of coacervate droplets, which are formed through interactions of inorganic polyphosphate (polyP) with divalent metal cation and cationic tripeptide, respectively. Among the coacervate droplets, only the polyP-Mn droplet is radiotolerant and provides strong protection for recruited proteins. The radiosensitive polyP-tripeptide droplet sequestered with both proteins and DNA could be encapsulated inside the polyP-Mn droplet, and form into a compartmentalized protocell. The protocell protects the inner nucleoid-like condensate through efficient reactive oxygen species' scavenging capacity of intracellular nonenzymic antioxidants including Mn-phosphate and Mn-peptide. Our results demonstrate a radioresistant protocell model with redox reaction system in response to ionizing radiation, which might enable the protocell fitness to prebiotic radiation on the primitive Earth preceding the emergence of enzyme-based fitness. This protocell might also provide applications in synthetic biology as bioreactor or drug delivery system.

Building the uracil skeleton in primitive ponds at the origins of life: carbamoylation of aspartic acid

A large set of nucleobases and amino acids is found in meteorites, implying that several chemical reservoirs are present in the solar system. The "geochemical continuity" hypothesis explores how protometabolic paths developed from so-called "bricks" in an enzyme-free prebiotic world and how they affected the origins of life. In the living cell, the second step of synthesizing uridine and cytidine RNA monomers is a carbamoyl transfer from a carbamoyl donor to aspartic acid. Here we compare two enzyme-free scenarios: aqueous and mineral surface scenarios in a thermal range up to 250 °C. Both processes could have happened in ponds under open atmosphere on the primeval Earth. Carbamoylation of aspartic acid with cyanate in aqueous solutions at 25 °C gives high N-carbamoyl aspartic acid yields within 16 h. It is important to stress that, while various molecules could be efficient carbamoylating agents according to thermodynamics, kinetics plays a determining role in selecting prebiotically possible pathways.

On the Evolutionary History of the Twenty Encoded Amino Acids

α-Amino acids are essential molecular constituents of life, twenty of which are privileged because they are encoded by the ribosomal machinery. The question remains open as to why this number and why this 20 in particular, an almost philosophical question that cannot be conclusively resolved. They are closely related to the evolution of the genetic code and whether nucleic acids, amino acids, and peptides appeared simultaneously and were available under prebiotic conditions when the first self-sufficient complex molecular system emerged on Earth. This report focuses on prebiotic and metabolic aspects of amino acids and proteins starting with meteorites, followed by their formation, including peptides, under plausible prebiotic conditions, and the major biosynthetic pathways in the various kingdoms of life. Coenzymes play a key role in the present analysis in that amino acid metabolism is linked to glycolysis and different variants of the tricarboxylic acid cycle (TCA, rTCA, and the incomplete horseshoe version) as well as the biosynthesis of the most important coenzymes. Thus, the report opens additional perspectives and facets on the molecular evolution of primary metabolism.

Gas-phase synthesis of racemic helicenes and their potential role in the enantiomeric enrichment of sugars and amino acids in meteorites

The molecular origins of homochirality on Earth is not understood well, particularly how enantiomerically enriched molecules of astrobiological significance like sugars and amino acids might have been synthesized on icy grains in space preceding their delivery to Earth. Polycyclic aromatic hydrocarbons (PAHs) identified in carbonaceous chondrites could have been processed in molecular clouds by circularly polarized light prior to the depletion of enantiomerically enriched helicenes onto carbonaceous grains resulting in chiral islands. However, the fundamental low temperature reaction mechanisms leading to racemic helicenes are still unknown. Here, by exploiting synchrotron based molecular beam photoionization mass spectrometry combined with electronic structure calculations, we provide compelling testimony on barrierless, low temperature pathways leading to racemates of [5] and [6]helicene. Astrochemical modeling advocates that gas-phase reactions in molecular clouds lead to racemates of helicenes suggesting a pathway for future astronomical observation and providing a fundamental understanding for the origin of homochirality on early Earth.

Computer simulation investigation of the adsorption of acetamide on low density amorphous ice. An astrochemical perspective

The adsorption of acetamide on low density amorphous (LDA) ice is investigated by grand canonical Monte Carlo computer simulations at the temperatures 50, 100, and 200 K, characteristic of certain domains of the interstellar medium (ISM). We found that the relative importance of the acetamide-acetamide H-bonds with respect to the acetamide-water ones increases with decreasing temperature. Thus, with decreasing temperature, the existence of the stable monolayer, characterizing the adsorption at 200 K, is gradually replaced by the occurrence of marked multilayer adsorption, preceding even the saturation of the first layer at 50 K. While isolated acetamide molecules prefer to lay parallel to the ice surface to maximize their H-bonding with the surface water molecules, this orientational preference undergoes a marked change upon saturation of the first layer due to increasing competition of the adsorbed molecules for H-bonds with water and to the possibility of their H-bond formation with each other. As a result, molecules stay preferentially perpendicular to the ice surface in the saturated monolayer. The chemical potential value corresponding to the point of condensation is found to decrease linearly with increasing temperature. We provide, in analogy with the Clausius-Clapeyron equation, a thermodynamic explanation of this behavior and estimate the molar entropy of condensed phase acetamide to be 34.0 J/mol K. For the surface concentration of the saturated monolayer, we obtain the value 9.1 ± 0.8 µmol/m², while the heat of adsorption at infinitely low surface coverage is estimated to be -67.8 ± 3.0 kJ/mol. Our results indicate that the interstellar formation of peptide chains through acetamide molecules, occurring at the surface of LDA ice, might well be a plausible process in the cold (i.e., below 50 K) domains of the ISM; however, it is a rather unlikely scenario in its higher temperature (i.e., 100-200 K) domains.

Experimental identification of aminomethanol (NH2CH2OH)-the key intermediate in the Strecker Synthesis

The Strecker Synthesis of (a)chiral α-amino acids from simple organic compounds, such as ammonia (NH₃), aldehydes (RCHO), and hydrogen cyanide (HCN) has been recognized as a viable route to amino acids on primordial earth. However, preparation and isolation of the simplest hemiaminal intermediate – the aminomethanol (NH₂CH₂OH)– formed in the Strecker Synthesis to even the simplest amino acid glycine (H₂NCH₂COOH) has been elusive. Here, we report the identification of aminomethanol prepared in low-temperature methylamine (CH₃NH₂) – oxygen (O₂) ices upon exposure to energetic electrons. Isomer-selective photoionization time-of-flight mass spectrometry (PI-ReTOF-MS) facilitated the gas phase detection of aminomethanol during the temperature program desorption (TPD) phase of the reaction products. The preparation and observation of the key transient aminomethanol changes our perception of the synthetic pathways to amino acids and the unexpected kinetic stability in extreme environments.

The Strecker synthesis is considered a viable route to amino acids formation on the primordial Earth. Here the authors succeed in observing its elusive intermediate aminomethanol, formed by insertion of an electronically excited oxygen atom in methylamine and stabilized by an icy matrix, using isomer-selective photoionization time-of-flight mass spectrometry during thermal desorption of the ice mixture.

Spatial Information in the Emergence of Life

Information in living systems is part of a complex relationship between the internal organization and functionality of life. In a cell, both genetic-coding sequences and molecular-shape recognition are sources of biological information. For folded polymers, its spatial arrangement contains general references about conditions that shaped them, as imprints, defining the data for spatial (conformational) information. Considering the origin of life problem, prebiotic dynamics of matching and transfer of molecular shapes may emerge as a flow of information in prebiotic assemblages. The property of carrying information in molecular conformations is only displayed at this system organization level. Accordingly, spatial information is a resource for active system responses toward milieu disturbances. Propagation of resilient conformations could be the substrate for structural maintenance through dynamical molecular scaffolding. The above is a basis for adaptive behavior in potentially biogenic systems. Starting from non-structured populations of carrying-information polymers, in the present contribution, we advance toward an entire theoretical framework considering the active role of these polymers to support the emergence of adaptive response in systems that manage conformational information flow. We discuss this scenario as a previous step for the arising of sequential information carried out by genetic polymers.

Water Microdroplets Allow Spontaneously Abiotic Production of Peptides

The chemistry of abiotic synthesis of peptides in the context of their prebiotic origins is a continuing challenge that arises from thermodynamic and kinetic constraints in aqueous media. Here we reported a strategy of microdroplets' mass spectrometry for peptide bonds formed from pure amino acids or a mixture in the presence of phosphoric acids in aqueous microdroplets. In contrast to bulk experiments, the condensation reactions proceed spontaneously under ambient conditions. The microdroplet gave a negative free-energy change (ΔG ∼ -1.1 kcal/mol), and product yields of ∼75% were obtained at the scale of a few milliseconds. Experiments in which nebulization gas pressure and external charge were varied established dependence of peptide production on the droplet size that has a high surface-to-volume ratio. It is concluded that the condensation reactions occurred at or near the air-water interfaces of microdroplets. This aqueous microdroplets approach also provides a route for chemistry synthesis in the prebiotic era.

Conformer-dependent vacuum ultraviolet photodynamics and chiral asymmetries in pure enantiomers of gas phase proline

Proline is a unique amino-acid, with a secondary amine fixed within a pyrrolidine ring providing specific structural properties to proline-rich biopolymers. Gas-phase proline possesses four main H-bond stabilized conformers differing by the ring puckering and carboxylic acid orientation. The latter defines two classes of conformation, whose large ionization energy difference allows a unique conformer-class tagging via electron spectroscopy. Photoelectron circular dichroism (PECD) is an intense chiroptical effect sensitive to molecular structures, hence theorized to be highly conformation-dependent. Here, we present experimental evidence of an intense and striking conformer-specific PECD, measured in the vacuum ultraviolet (VUV) photoionization of proline, as well as a conformer-dependent cation fragmentation behavior. This finding, combined with theoretical modeling, allows a refinement of the conformational landscape and energetic ordering, that proves inaccessible to current molecular electronic structure calculations. Additionally, astrochemical implications regarding a possible link of PECD to the origin of life's homochirality are considered in terms of plausible temperature constraints.

Water-Air Interfaces as Environments to Address the Water Paradox in Prebiotic Chemistry: A Physical Chemistry Perspective

The asymmetric water-air interface provides a dynamic aqueous environment with properties that are often very different than bulk aqueous or gaseous phases and promotes reactions that are thermodynamically, kinetically, or otherwise unfavorable in bulk water. Prebiotic chemistry faces a key challenge: water is necessary for life yet reduces the efficiency of many biomolecular synthesis reactions. This perspective considers water-air interfaces as auspicious reaction environments for abiotic synthesis. We discuss recent evidence that (1) water-air interfaces promote condensation reactions including peptide synthesis, phosphorylation, and oligomerization; (2) photochemistry at water-air interfaces may have been a significant source of prebiotic molecular complexity, given the lack of oxygen and increased availability of near-ultraviolet radiation on early Earth; and (3) water-air interfaces can promote spontaneous reduction and oxidation reactions, potentially providing protometabolic pathways. Life likely began within a relatively short time frame, and water-air interfaces offer promising environments for simultaneous and efficient biomolecule production.

Covalent Linkage and Macrocylization Preserve and Enhance Synergistic Interactions in Catalytic Amyloids

The self-assembly of short peptides into catalytic amyloid-like nanomaterials has proven to be a powerful tool in both understanding the evolution of early proteins and identifying new catalysts for practically useful chemical reactions. Here we demonstrate that both parallel and antiparallel arrangements of β-sheets can accommodate metal ions in catalytically productive coordination environments. Moreover, synergistic relationships, identified in catalytic amyloid mixtures, can be captured in macrocyclic and sheet-loop-sheet species, that offer faster rates of assembly and provide more complex asymmetric arrangements of functional groups, thus paving the way for future designs of amyloid-like catalytic proteins. Our findings show how initial catalytic activity in amyloid assemblies can be propagated and improved in more-complex molecules, providing another link in a complex evolutionary chain between short, potentially abiotically produced peptides and modern-day enzymes.

A Few Experimental Suggestions Using Minerals to Obtain Peptides with a High Concentration of L-Amino Acids and Protein Amino Acids

The peptides/proteins of all living beings on our planet are mostly made up of 19 L-amino acids and glycine, an achiral amino acid. Arising from endogenous and exogenous sources, the seas of the prebiotic Earth could have contained a huge diversity of biomolecules (including amino acids), and precursors of biomolecules. Thus, how were these amino acids selected from the huge number of available amino acids and other molecules? What were the peptides of prebiotic Earth made up of? How were these peptides synthesized? Minerals have been considered for this task, since they can preconcentrate amino acids from dilute solutions, catalyze their polymerization, and even make the chiral selection of them. However, until now, this problem has only been studied in compartmentalized experiments. There are separate experiments showing that minerals preconcentrate amino acids by adsorption or catalyze their polymerization, or separate L-amino acids from D-amino acids. Based on the [GADV]-protein world hypothesis, as well as the relative abundance of amino acids on prebiotic Earth obtained by Zaia, several experiments are suggested. The main goal of these experiments is to show that using minerals it is possible, at least, to obtain peptides whose composition includes a high quantity of L-amino acids and protein amino acids (PAAs). These experiments should be performed using hydrothermal environments and wet/dry cycles. In addition, for hydrothermal environment experiments, it is very important to use one of the suggested artificial seawaters, and for wet/dry environments, it is important to perform the experiments in distilled water and diluted salt solutions. Finally, from these experiments, we suggest that, without an RNA world or even a pre genetic world, a small peptide set could emerge that better resembles modern proteins.

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.

Prebiotic oligomerization and self-assembly of structurally diverse xenobiological monomers

Prebiotic chemists often study how modern biopolymers, e.g., peptides and nucleic acids, could have originated in the primitive environment, though most contemporary biomonomers don't spontaneously oligomerize under mild conditions without activation or catalysis. However, life may not have originated using the same monomeric components that it does presently. There may be numerous non-biological (or "xenobiological") monomer types that were prebiotically abundant and capable of facile oligomerization and self-assembly. Many modern biopolymers degrade abiotically preferentially via processes which produce thermodynamically stable ring structures, e.g. diketopiperazines in the case of proteins and 2', 3'-cyclic nucleotide monophosphates in the case of RNA. This weakness is overcome in modern biological systems by kinetic control, but this need not have been the case for primitive systems. We explored here the oligomerization of a structurally diverse set of prebiotically plausible xenobiological monomers, which can hydrolytically interconvert between cyclic and acyclic forms, alone or in the presence of glycine under moderate temperature drying conditions. These monomers included various lactones, lactams and a thiolactone, which varied markedly in their stability, propensity to oligomerize and apparent modes of initiation, and the oligomeric products of some of these formed self-organized microscopic structures which may be relevant to protocell formation.

Biomimetic synthesis of calcium carbonate under phenylalanine: Control of polymorph and morphology

In biomineralization, organisms have the abilities to produce biominerals with superior properties. One of the most attractive features of biominerals is the presence of the proteins consisting of different contents of amino acids in crystals. In the present work, L-phenylalanine (Phe) was used as an additive for the controllable crystallization of calcium carbonate (CaCO₃). The obtained CaCO₃ crystals were characterized by field emission scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), elemental analysis and high-resolution transmission electron microscopy (HRTEM). The experimental results suggest that single calcite crystals are formed at low Phe concentrations. High concentrations of Phe inhibit the nucleation and growth of calcite, and promote the formation of vaterite crystals with solid or hollow structures. The morphology and crystal form of CaCO₃ are also significantly affected by the flow rate of CO₂. After that, a possible mechanism (competition mechanism) action of Phe in the formation of CaCO₃ is proposed. Finally, the effects of temperature on the formation of vaterite were determined to explore the growth mechanism of hexagonal vaterite. The work of controlling the preparation of CaCO₃ crystals in the presence of Phe will help us to imitate and learn nature, and bring new insights into understanding bionics. Meanwhile, it provides a new method for the synthesis of CaCO₃ biomaterials with different crystal forms and morphologies.

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.

Small Cyclic Peptide for Pyrophosphate Dependent Ligation in Prebiotic Environments

All life on Earth uses one universal biochemistry stemming from one universal common ancestor of all known living organisms. One of the most striking features of this universal biochemistry is its utter dependence on phosphate group transfer between biochemical molecules. Both nucleic acid and peptide biological synthesis relies heavily on phosphate group transfer. Such dependents strongly indicate very early incorporation of phosphate chemistry in the origin of life. Perhaps as early as prebiotic soup stage. We report here on a short cyclic peptide, c(RPDDHR), designed rationally for pyrophosphate interaction, which is able to create a new amide bond dependent on the presence of pyrophosphate. We believe this result to be a first step in the exploration of Phosphate Transfer Catalysts that must have been present and active in prebiotic soup and must have laid down foundations for the universal bioenergetics.

Simultaneous determination of five essential amino acids in plasma of Hyperlipidemic subjects by UPLC-MS/MS

BACKGROUND

Millions of adults have been reported with hyperlipemia in the world. It is still unclear whether the plasma level of essential amino acids (AAs) will be influenced by the hyperlipemia. This study was aimed to investigate the AAs levels and the underlying metabolic relationship in hyperlipidemic subjects.

METHODS

An ultra-high performance liquid chromatography-tandem mass spectrometric (UPLC-MS/MS) method was developed for the determination of phenylalanine (Phe), valine (Val), histidine (His), tryptophan (Trp), and methionine (Met). Plasma samples (100 μL) were precipitated by acetonitrile (300 μL) and analyzed on a BEH C18 (2.1 mm × 100 mm, 1.7 μm) column at 40 °C by gradient elution. The mobile phase composed of 0.1% formic acid and acetonitrile was used with flow rate at 0.2-0.4 ml/0-3 min. Five AAs were determined at positive electrospray ionization (ESI+) at m/z 118.1/72.1 (Val), 150.12/104.02(Met), 156.06/110.05(His), 166.1/120.1(Phe), and 205.2/188.02 (Trp). A total of 75 healthy subjects and 83 hyperlipidemic subjects, who had blood routine test and plasma lipid test were determined by developed UPLC-MS/MS.

RESULTS

It was shown that there was good linearity for Val, Met, His, Phe, and Trp within 1-100 μg/mL. The relative standard deviations of precision and accuracy were all within 15%. The level of Val, Phe, Trp, His, and Met were 35.34 ± 15.64, 22.72 ± 9.13, 17.23 ± 4.94, 16.78 ± 13.64, and 6.24 ± 1.97 μg/mL in healthy subjects, while they were 38.04 ± 16.70, 22.41 ± 8.45, 15.62 ± 5.77, 18.35 ± 14.49, and 6.21 ± 1.97 μg/mL in hyperlipidemic subjects respectively. The Spearman's correlations analysis showed that there were high correlations between Val, Phe, Trp, His, Met and triglyceride in healthy subjects. While, those correlations decreased in hyperlipemia cases.

CONCLUSION

A convenient and sensitive method for simultaneous determination of Val, Phe, Trp, His, and Met in human plasma was developed. There was a high correlation between Val, Phe, Trp, His, Met and triglyceride. Hyperlipemia influences the metabolic balance of His, Phe, Trp, Met and Val.

A minimalistic hydrolase based on co-assembled cyclic dipeptides

The self-assembly of small peptides into larger aggregates is an important process for the fundamental understanding of abiogenesis. In this article we demonstrate that blends of cyclic dipeptides (2,5-diketopiperazines - DKPs) bearing either histidine or cysteine in combination with a lipophilic amino acid form highly stable aggregates in aqueous solution with esterase-like activity. We demonstrate that the catalytic activity is based on an intermolecular cooperative behavior between histidine and cysteine. A high control of the molecular arrangement of the peptide assemblies was gained by C-H-π interactions between Phe and Leu or Val sidechains, resulting in a significant increase in catalytic activity. These interactions were strongly supported by Hartree-Fock calculations and finally confirmed via1H-NMR HRMAS NOE spectroscopy.

Prebiotic Peptides: Molecular Hubs in the Origin of Life

The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.

Prebiotic Peptide Bond Formation Through Amino Acid Phosphorylation. Insights from Quantum Chemical Simulations

Condensation reactions between biomolecular building blocks are the main synthetic channels to build biopolymers. However, under highly diluted prebiotic conditions, condensations are thermodynamically hampered since they release water. Moreover, these reactions are also kinetically hindered as, in the absence of any catalyst, they present high activation energies. In living organisms, in the formation of peptides by condensation of amino acids, this issue is overcome by the participation of adenosine triphosphate (ATP), in which, previous to the condensation, phosphorylation of one of the reactants is carried out to convert it as an activated intermediate. In this work, we present for the first time results based on density functional theory (DFT) calculations on the peptide bond formation between two glycine (Gly) molecules adopting this phosphorylation-based mechanism considering a prebiotic context. Here, ATP has been modeled by a triphosphate (TP) component, and different scenarios have been considered: (i) gas-phase conditions, (ii) in the presence of a Mg²⁺ ion available within the layer of clays, and (iii) in the presence of a Mg²⁺ ion in watery environments. For all of them, the free energy profiles have been fully characterized. Energetics derived from the quantum chemical calculations indicate that none of the processes seem to be feasible in the prebiotic context. In scenarios (i) and (ii), the reactions are inhibited due to unfavorable thermodynamics associated with the formation of high energy intermediates, while in scenario (iii), the reaction is inhibited due to the high free energy barrier associated with the condensation reactions. As a final consideration, the role of clays in this TP-mediated peptide bond formation route is advocated, since the interaction of the phosphorylated intermediate with the internal clay surfaces could well favor the reaction free energies.

Nonequilibrium abundances for the building blocks of life

The difficulty of obtaining appreciable quantities of biologically important molecules in thermodynamic equilibrium has long been identified as an obstacle to life's emergence, and determining the specific nonequilibrium conditions that might have given rise to life is challenging. To address these issues, we investigate how the concentrations of life's building blocks change as a function of the distance from equilibrium on average, in two example settings: (i) the synthesis of heavy amino acids and (ii) their polymerization into peptides. We find that relative concentrations of the heaviest amino acids can be boosted by four orders of magnitude, and concentrations of the longest peptide chains can be increased by hundreds of orders of magnitude. The average nonequilibrium distribution does not depend on the details of how the system was driven from equilibrium, indicating that environments might not have to be fine-tuned to support life.

Cell theory, intrinsically disordered proteins, and the physics of the origin of life

Cell theory, as formulated by Theodor Schwann in 1839, introduced the idea that the cell is the main structural unit of living nature. Later, in solving the problem of cell multiplication, Rudolf Virchow expanded the cell theory with a postulate: all cells only arise from pre-existing cells. But what did the very first cell arise from? This paper proposes extending the Virchow's law by the assumption that between the nonliving protocell and the first living cell the continuity of fundamental physical properties (the principle of invariance of physical properties) is preserved. The protocell is understood here as a cell-shaped physical system on the basis of the self-organized biologically significant prebiotic macromolecules, primarily peptides, having a potential to transform into the living cell. Biophase is considered as the physical basis of the membraneless protocell, the internal environment of which is separated from the external environment due to the phase of adsorbed water. The evidence is given that the first protocells may have been formed on the basis of intrinsically disordered peptides. Data on the similarity of the physical properties of living cells and the following model systems are given: protein and artificial polymer solutions, coacervate droplets, and ion-exchange resin granules. Available data on the similarity of the physical properties of cell models and living cells allow us to rephrase the Virchow's postulate as follows: the physical properties of a living cell could only arise from pre-existing physical properties of the protocell.

The optimal size of protocells from simple entropic considerations

Potential constraints on protocell size are developed from simple entropic considerations. To do that, two new different indexes as measures of their structural and dynamic order were developed and applied to an elemental model of the heterotrophic protocell. According to our results, cell size should be a key factor determining the potential of these primitive systems to evolve and consequently to support life. Our analyses also suggest that the size of the optimal vesicles could be constrained to have radii in the interval [Formula: see text], where the two extreme limits [Formula: see text] and [Formula: see text] represent the states of maximum structural order (largest accumulation of substrate inside the vesicle) and the maximum flux of entropy production, respectively. According to the above criteria, the size of the optimum vesicles falls, approximately, in the same spatial range estimated for biological living cells assuming plausible values for the second-order rate constant involved in the catabolic process. Furthermore, the existence of very small vesicles could be seriously affected by the limited efficiency, far from the theoretical limits, with which these catabolic processes may proceed in a prebiotic system.

One Step up the Ladder of Prebiotic Complexity: Formation of Nonrandom Linear Polypeptides from Binary Systems of Amino Acids on Silica

Evidence for the formation of linear oligopeptides with nonrandom sequences from mixtures of amino acids coadsorbed on silica and submitted to a simple thermal activation is presented. The amino acid couples (glutamic acid+leucine) and (aspartic acid+valine) were deposited on a fumed silica and submitted to a single heating step at moderate temperature. The evolution of the systems was characterized by X-ray diffraction, infrared spectroscopy, thermosgravimetric analysis, HPLC, and electrospray ionization mass spectrometry (ESI-MS). Evidence for the formation of amide bonds was found in all systems studied. While the products of single amino acids activation on silica could be considered as evolutionary dead ends, (glutamic acid+leucine) and, at to some extent, (aspartic acid+valine) gave rise to the high yield formation of linear peptides up to the hexamers. Oligopeptides of such length have not been observed before in surface polymerization scenarios (unless the amino acids had been deposited by chemical vapor deposition, which is not realistic in a prebiotic environment). Furthermore, not all possible amino acid sequences were present in the activation products, which is indicative of polymerization selectivity. These results are promising for origins of life studies because they suggest the emergence of nonrandom biopolymers in a simple prebiotic scenario.

Role of Mineral Surfaces in Prebiotic Chemical Evolution. In Silico Quantum Mechanical Studies

There is a consensus that the interaction of organic molecules with the surfaces of naturally-occurring minerals might have played a crucial role in chemical evolution and complexification in a prebiotic era. The hurdle of an overly diluted primordial soup occurring in the free ocean may have been overcome by the adsorption and concentration of relevant molecules on the surface of abundant minerals at the sea shore. Specific organic⁻mineral interactions could, at the same time, organize adsorbed molecules in well-defined orientations and activate them toward chemical reactions, bringing to an increase in chemical complexity. As experimental approaches cannot easily provide details at atomic resolution, the role of in silico computer simulations may fill that gap by providing structures and reactive energy profiles at the organic⁻mineral interface regions. Accordingly, numerous computational studies devoted to prebiotic chemical evolution induced by organic⁻mineral interactions have been proposed. The present article aims at reviewing recent in silico works, mainly focusing on prebiotic processes occurring on the mineral surfaces of clays, iron sulfides, titanium dioxide, and silica and silicates simulated through quantum mechanical methods based on the density functional theory (DFT). The DFT is the most accurate way in which chemists may address the behavior of the molecular world through large models mimicking chemical complexity. A perspective on possible future scenarios of research using in silico techniques is finally proposed.

Effects of pressure on the structure and lattice dynamics of α-glycine: a combined experimental and theoretical study

This concomitant experimental and theoretical study provides a definitive EOS for α-glycine up to the record pressure of 50 GPa.

Functional Assemblies Emerging in Complex Mixtures of Peptides and Nucleic Acid-Peptide Chimeras

Striking synergy between nucleic acids and proteins is exhibited in living cells. Whether such mutual activity can be performed using simple supramolecular nucleic acid-peptide (NA-pep) architectures remains a mystery. To shed light on this question, we studied the emergence of a primitive synergy in assemblies of short DNA-peptide chimeras. Specifically, we characterized multiple structures forming along gradual mixing trajectory, in which a peptide solution was seeded with increasing amounts of NA-pep chimeras. We report on the systematic change from β-sheet-peptide-based fibrillar architectures into the spherical structures formed by the conjugates. Remarkably, we find that through forming onion-like structures, the conjugates exhibit increased DNA hybridization stability and bind small molecules more efficiently than the peptides or DNA alone. A brief discussion highlights the implications of our findings for the production of new materials and for research on the origin of life.

The Influence of Modularity, Seeding, and Product Inhibition on Peptide Autocatalytic Network Dynamics

Chemical networks often exhibit emergent, systems-level properties that cannot be simply derived from the linear sum of the individual components. The design and analysis of increasingly complex chemical networks thus constitute a major area of research in Systems Chemistry. In particular, much research is focused on the emergence of functional properties in prebiotic chemical networks relevant to the origin and early evolution of life. Here, we apply a formal framework known as RAF theory to study the dynamics of a complex network of mutually catalytic peptides. We investigate in detail the influence of network modularity, initial template seeding, and product inhibition on the network dynamics. We show that these results can be useful for designing new experiments, and further argue how they are relevant to origin of life studies.

In the Beginning was a Mutualism - On the Origin of Translation

The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.

Amyloid and the origin of life: self-replicating catalytic amyloids as prebiotic informational and protometabolic entities

A crucial stage in the origin of life was the emergence of the first molecular entity that was able to replicate, transmit information, and evolve on the early Earth. The amyloid world hypothesis posits that in the pre-RNA era, information processing was based on catalytic amyloids. The self-assembly of short peptides into β-sheet amyloid conformers leads to extraordinary structural stability and novel multifunctionality that cannot be achieved by the corresponding nonaggregated peptides. The new functions include self-replication, catalytic activities, and information transfer. The environmentally sensitive template-assisted replication cycles generate a variety of amyloid polymorphs on which evolutive forces can act, and the fibrillar assemblies can serve as scaffolds for the amyloids themselves and for ribonucleotides proteins and lipids. The role of amyloid in the putative transition process from an amyloid world to an amyloid-RNA-protein world is not limited to scaffolding and protection: the interactions between amyloid, RNA, and protein are both complex and cooperative, and the amyloid assemblages can function as protometabolic entities catalyzing the formation of simple metabolite precursors. The emergence of a pristine amyloid-based in-put sensitive, chiroselective, and error correcting information-processing system, and the evolvement of mutualistic networks were, arguably, of essential importance in the dynamic processes that led to increased complexity, organization, compartmentalization, and, eventually, the origin of life.

Constraining the Prebiotic Cell Size Limits in Extremely Hostile Environments: A Dynamical Perspective

The ability to support a replicator population in an extremely hostile environment is considered in a simple model of a prebiotic cell. We explore from a classical approach how the replicator viability changes as a function of the cell radius. The model includes the interaction between two different species: a substrate that flows from the exterior and a replicator that feeds on the substrate and is readily destroyed in the environment outside the cell. According to our results, replicators in the cell only exist when the radius exceeds some critical value [Formula: see text] being, in general, a function of the substrate concentration, the diffusion constant of the replicator species, and the reproduction rate coefficient. Additionally, the influence of other parameters on the replicator population is also considered. The viability of chemical replicators under such drastic conditions could be crucial in understanding the origin of the first primitive cells and the ulterior development of life on our planet. Key Words: Prebiotic cell-Chemical replicator-Environment-Reproduction rate. Astrobiology 18, 403-411.

Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model

We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol^-1.

Cavitation-Induced Synthesis of Biogenic Molecules on Primordial Earth

Despite decades of research, how life began on Earth remains one of the most challenging scientific conundrums facing modern science. It is agreed that the first step was synthesis of organic compounds essential to obtain amino acids and their polymers. Several possible scenarios that could accomplish this step, using simple inorganic molecules, have been suggested and studied over the years. The present study examines, using atomistic reactive molecular dynamics simulations, the long-standing suggestion that natural cavitation in primordial oceans was a dominant mechanism of organic molecule synthesis. The simulations allow, for the first time, direct observation of the rich and complex sonochemistry occurring inside a collapsing bubble filled with water and dissolved gases of the early atmosphere. The simulation results suggest that dissolved CH₄ is the most efficient carbon source to produce amino acids, while CO and CO₂ lead to amino acid synthesis with lower yields. The efficiency of amino acid synthesis also depends on the nitrogen source used (i.e., N₂, NH₃) and on the presence of HCN. Moreover, cavitation may have contributed to the increase in concentration of NH₃ in primordial oceans and to the production and liberation of molecular O₂ into the early atmosphere. Overall, the picture that emerges from the simulations indicates that collapsing bubbles may have served as natural bioreactors in primordial oceans, producing the basic chemical ingredients required for the beginning of life.

Can an Imidazole Be Formed from an Alanyl-Seryl-Glycine Tripeptide under Possible Prebiotic Conditions?

The five-membered heterocyclic imidazole group, which is an essential component of purines, histidine and many cofactors, has been abiotically synthesized in different model experiments that attempt to simulate the prebiotic environment. The evolutionary significance of imidazoles is highlighted not only by its presence in nucleic acid components and in histidine, but also by experimental reports of its ability to restore the catalytic activity of ribozymes. However, as of today there are no reports of histidine in carbonaceous chondrites, and although the abiotic synthesis of His reported by Shen et al. (1987, 1990a) proceeds via an Amadori rearrangement, like in the biosynthesis of histidine, neither the reactants nor the conditions are truly prebiotic. Based on the autocatalytic biosynthesis of 4-methylidene-imidazole-one (MIO), a cofactor of some members of the amino acid aromatic ammonia-lyases and aminomutases, which occur via the self-condensation of a simple Ala-Ser-Gly motif within the sequence of the enzymes, we propose a possible prebiotic synthesis of an imidazolide.

Computer simulation and experimental self-assembly of irradiated glycine amino acid under magnetic fields: Its possible significance in prebiotic chemistry

Ionizing radiation may have played a relevant role in chemical reactions for prebiotic biomolecule formation on ancient Earth. Environmental conditions such as the presence of water and magnetic fields were possibly relevant in the formation of organic compounds such as amino acids. ATR-FTIR, Raman, EPR and X-ray spectroscopies provide valuable information about molecular organization of different glycine polymorphs under static magnetic fields. γ-glycine polymorph formation increases in irradiated samples interacting with static magnetic fields. The increase in γ-glycine polymorph agrees with the computer simulations. The AM1 semi-empirical simulations show a change in the catalyst behavior and dipole moment values in α and γ-glycine interaction with the static magnetic field. The simulated crystal lattice energy in α-glycine is also affected by the free radicals under the magnetic field, which decreases its stability. Therefore, solid α and γ-glycine containing free radicals under static magnetic fields might have affected the prebiotic scenario on ancient Earth by causing the oligomerization of glycine in prebiotic reactions.

Highly Efficient Fumed Silica Nanoparticles for Peptide Bond Formation: Converting Alanine to Alanine Anhydride

In this work, thermal condensation of alanine adsorbed on fumed silica nanoparticles is investigated using thermal analysis and multiple spectroscopic techniques, including infrared (IR), Raman, and nuclear magnetic resonance (NMR) spectroscopies. Thermal analysis shows that adsorbed alanine can undergo thermal condensation, forming peptide bonds within a short time period and at a lower temperature (∼170 °C) on fumed silica nanoparticle surfaces than that in bulk (∼210 °C). Spectroscopic results further show that alanine is converted to alanine anhydride with a yield of 98.8% during thermal condensation. After comparing peptide formation on solution-derived colloidal silica nanoparticles, it is found that fumed silica nanoparticles show much better efficiency and selectivity than solution-derived colloidal silica nanoparticles for synthesizing alanine anhydride. Furthermore, Raman spectroscopy provides evidence that the high efficiency for fumed silica nanoparticles is likely related to their unique surface features: the intrinsic high population of strained ring structures present at the surface. This work indicates the great potential of fumed silica nanoparticles in synthesizing peptides with high efficiency and selectivity.

Meteorite impacts on ancient oceans opened up multiple NH3 production pathways

A recent series of shock experiments by Nakazawa et al. starting in 2005 (e.g. [Nakazawa et al., Earth Planet. Sci. Lett., 2005, 235, 356]) suggested that meteorite impacts on ancient oceans would have yielded a considerable amount of NH₃ to the early Earth from atmospheric N₂ and oceanic H₂O through reduction by meteoritic iron. To clarify the mechanisms, we imitated the impact events by performing multi-scale shock technique-based ab initio molecular dynamics in the framework of density functional theory in combination with multi-scale shock technique (MSST) simulations. Our previous simulations with impact energies close to that of the experiments revealed picosecond-order rapid NH₃ production during shock compression [Shimamura et al., Sci. Rep., 2016, 6, 38952]. It was also shown that the reduction of N₂ took place with an associative mechanism as seen in the catalysis of nitrogenase enzymes. In this study, we performed an MSST-AIMD simulation to investigate the production by meteorite impacts with higher energies, which are closer to the expected values on the early Earth. It was found that the amount of NH₃ produced further increased. We also found that the increased NH₃ production is due to the emergence of multiple reaction mechanisms at increased impact energies. We elucidated that the reduction of N₂ was not only attributed to the associative mechanism but also to a dissociative mechanism as seen in the Haber-Bosch process and to a mechanism through a hydrazinium ion. The emergence of these multiple production mechanisms capable of providing a large amount of NH₃ would support the suggestions from recent experiments much more strongly than was previously believed, i.e., shock-induced NH₃ production played a key role in the origin of life on Earth.

Meteorite Impact-Induced Rapid NH3 Production on Early Earth: Ab Initio Molecular Dynamics Simulation

NH₃ is an essential molecule as a nitrogen source for prebiotic amino acid syntheses such as the Strecker reaction. Previous shock experiments demonstrated that meteorite impacts on ancient oceans would have provided a considerable amount of NH₃ from atmospheric N₂ and oceanic H₂O through reduction by meteoritic iron. However, specific production mechanisms remain unclear, and impact velocities employed in the experiments were substantially lower than typical impact velocities of meteorites on the early Earth. Here, to investigate the issues from the atomistic viewpoint, we performed multi-scale shock technique-based ab initio molecular dynamics simulations. The results revealed a rapid production of NH₃ within several picoseconds after the shock, indicating that shocks with greater impact velocities would provide further increase in the yield of NH₃. Meanwhile, the picosecond-order production makes one expect that the important nitrogen source precursors of amino acids were obtained immediately after the impact. It was also observed that the reduction of N₂ proceeded according to an associative mechanism, rather than a dissociative mechanism as in the Haber-Bosch process.

The minimotif synthesis hypothesis for the origin of life

Several theories for the origin of life have gained widespread acceptance, led by primordial soup, chemical evolution, metabolism first, and the RNA world. However, while new and existing theories often address a key step, there is less focus on a comprehensive abiogenic continuum leading to the last universal common ancestor. Herein, I present the "minimotif synthesis" hypothesis unifying select origin of life theories with new and revised steps. The hypothesis is based on first principles, on the concept of selection over long time scales, and on a stepwise progression toward complexity. The major steps are the thermodynamically-driven origination of extant molecular specificity emerging from primordial soup leading to the rise of peptide catalysts, and a cyclic feed-forward catalytic diversification of compound and peptides in the primordial soup. This is followed by degenerate, semi-partially conservative peptide replication to pass on catalytic knowledge to progeny protocells. At some point during this progression, the emergence of RNA and selection could drive the separation of catalytic and genetic functions, allowing peptides and proteins to permeate the catalytic space, and RNA to encode higher fidelity information transfer. Translation may have emerged from RNA template driven organization and successive ligation of activated amino acids as a predecessor to translation.

The Activation of Free Dipeptides Promoted by Strong Activating Agents in Water Does not Yield Diketopiperazines

The activation of dipeptides was studied in the perspective of the abiotic formation of oligopeptides of significant length as a requirement for secondary structure formation. The formation of piperazin-2,5-diones (DKP), previously considered as a dead end when activating free dipeptides, was shown in this work to be efficiently suppressed when using strong activating agents (e.g., carbodiimides). This behaviour was explained by the fast formation of a 5(4H)-oxazolone intermediate at a rate that exceeds the time scale of the rotation of the peptide bond from the predominant trans-conformation into the cis-isomer required for DKP formation. No DKP was observed when using strong activating agents whereas phosphate mixed anhydrides or moderately activated esters were observed to predominantly yield DKP. The DKP side-reaction no longer constitutes a drawback for the C-terminus elongation of peptides. These results are considered as additional evidence that pathways involving strong activation are required to drive the emergence of living entities rather than close to equilibrium processes.