Accumulation of formamide in hydrothermal pores to form prebiotic nucleobases

Deciphering the guanidinium cation: Insights into thermal diffusion

Thermophoresis, or thermodiffusion, is becoming a more popular method for investigating the interactions between proteins and ligands due to its high sensitivity to the interactions between solutes and water. Despite its growing use, the intricate mechanisms behind thermodiffusion remain unclear. This gap in knowledge stems from the complexities of thermodiffusion in solvents that have specific interactions as well as the intricate nature of systems that include many components with both non-ionic and ionic groups. To deepen our understanding, we reduce complexity by conducting systematic studies on aqueous salt solutions. In this work, we focused on how guanidinium salt solutions behave in a temperature gradient, using thermal diffusion forced Rayleigh scattering experiments at temperatures ranging from 15 to 35 °C. We looked at the thermodiffusive behavior of four guanidinium salts (thiocyanate, iodide, chloride, and carbonate) in solutions with concentrations ranging from 1 to 3 mol/kg. The guanidinium cation is disk-shaped and is characterized by flat hydrophobic surfaces and three amine groups, which enable directional hydrogen bonding along the edges. We compare our results to the behavior of salts with spherical cations, such as sodium, potassium, and lithium. Our discussions are framed around how different salts are solvated, specifically in the context of the Hofmeister series, which ranks ions based on their effects on the solvation of proteins.

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.

Direct Synthesis of Formamide from CO2 and H2O with Nickel-Iron Nitride Heterostructures under Mild Hydrothermal Conditions

Formamide can serve as a key building block for the synthesis of organic molecules relevant to premetabolic processes. Natural pathways for its synthesis from CO2 under early earth conditions are lacking. Here, we report the thermocatalytic conversion of CO2 and H2O to formate and formamide over Ni-Fe nitride heterostructures in the absence of synthetic H2 and N2 under mild hydrothermal conditions. While water molecules act as both a solvent and hydrogen source, metal nitrides serve as nitrogen sources to produce formamide in the temperature range of 25-100 °C under 5-50 bar. Longer reaction times promote the C-C bond coupling and formation of acetate and acetamide as additional products. Besides liquid products, methane and ethane are also produced as gas-phase products. Postreaction characterization of Ni-Fe nitride particles reveals structural alteration and provides insights into the potential reaction mechanism. The findings indicate that gaseous CO2 can serve as a carbon source for the formation of C-N bonds in formamide and acetamide over the Ni-Fe nitride heterostructure under simulated hydrothermal vent conditions.

Thermophoresis beyond Local Thermodynamic Equilibrium

We measure the thermophoresis of polysterene beads over a wide range of temperature gradients and find a pronounced nonlinear phoretic characteristic. The transition to the nonlinear behavior is marked by a drastic slowing down of thermophoretic motion and is characterized by a Péclet number of order unity as corroborated for different particle sizes and salt concentrations. The data follow a single master curve covering the entire nonlinear regime for all system parameters upon proper rescaling of the temperature gradients with the Péclet number. For low thermal gradients, the thermal drift velocity follows a theoretical linear model relying on the local-equilibrium assumption, while linear theoretical approaches based on hydrodynamic stresses, ignoring fluctuations, predict significantly slower thermophoretic motion for steeper thermal gradients. Our findings suggest that thermophoresis is fluctuation dominated for small gradients and crosses over to a drift-dominated regime for larger Péclet numbers in striking contrast to electrophoresis.

Prebiotic Synthesis of ATP: A Terrestrial Volcanism-Dependent Pathway

Adenosine triphosphate (ATP) is a multifunctional small molecule, necessary for all modern Earth life, which must be a component of the last universal common ancestor (LUCA). However, the relatively complex structure of ATP causes doubts about its accessibility on prebiotic Earth. In this paper, based on previous studies on the synthesis of ATP components, a plausible prebiotic pathway yielding this key molecule is constructed, which relies on terrestrial volcanism to provide the required materials and suitable conditions.

A heated rock crack captures and polymerizes primordial DNA and RNA

Life is based on informational polymers such as DNA or RNA. For their polymerization, high concentrations of complex monomer building blocks are required. Therefore, the dilution by diffusion poses a major problem before early life could establish a non-equilibrium of compartmentalization. Here, we explored a natural non-equilibrium habitat to polymerize RNA and DNA. A heat flux across thin rock cracks is shown to accumulate and maintain nucleotides. This boosts the polymerization to RNA and DNA inside the crack. Moreover, the polymers remain localized, aiding both the creation of longer polymers and fostering downstream evolutionary steps. In a closed system, we found single nucleotides concentrate 10⁴-fold at the bottom of the crack compared to the top after 24 hours. We detected enhanced polymerization for 2 different activation chemistries: aminoimidazole-activated DNA nucleotides and 2',3'-cyclic RNA nucleotides. The copolymerization of 2',3'-cGMP and 2',3'-cCMP in the thermal pore showed an increased heterogeneity in sequence composition compared to isothermal drying. Finite element models unravelled the combined polymerization and accumulation kinetics and indicated that the escape of the nucleotides from such a crack is negligible over a time span of years. The thermal non-equilibrium habitat establishes a cell-like compartment that actively accumulates nucleotides for polymerization and traps the resulting oligomers. We argue that the setting creates a pre-cellular non-equilibrium steady state for the first steps of molecular evolution.

The Formation of RNA Pre-Polymers in the Presence of Different Prebiotic Mineral Surfaces Studied by Molecular Dynamics Simulations

We used all-atom Molecular Dynamics (MD) computer simulations to study the formation of pre-polymers between the four nucleotides in RNA (AMP, UMP, CMP, GMP) in the presence of different substrates that could have been present in a prebiotic environment. Pre-polymers are C3'-C5' hydrogen-bonded nucleotides that have been suggested to be the precursors of phosphodiester-bonded RNA polymers. We simulated wet-dry cycles by successively removing water molecules from the simulations, from ~60 to 3 water molecules per nucleotide. The nine substrates in this study include three clay minerals, one mica, one phosphate mineral, one silica, and two metal oxides. The substrates differ in their surface charge and ability to form hydrogen bonds with the nucleotides. From the MD simulations, we quantify the interactions between different nucleotides, and between nucleotides and substrates. For comparison, we included graphite as an inert substrate, which is not charged and cannot form hydrogen bonds. We also simulated the dehydration of a nucleotide-only system, which mimics the drying of small droplets. The number of hydrogen bonds between nucleotides and nucleotides and substrates was found to increase significantly when water molecules were removed from the systems. The largest number of C3'-C5' hydrogen bonds between nucleotides occurred in the graphite and nucleotide-only systems. While the surface of the substrates led to an organization and periodic arrangement of the nucleotides, none of the substrates was found to be a catalyst for pre-polymer formation, neither at full hydration, nor when dehydrated. While confinement and dehydration seem to be the main drivers for hydrogen bond formation, substrate interactions reduced the interactions between nucleotides in all cases. Our findings suggest that small supersaturated water droplets that could have been produced by geysers or springs on the primitive Earth may play an important role in non-enzymatic RNA polymerization.

Complementary Experimental Methods to Obtain Thermodynamic Parameters of Protein Ligand Systems

In recent years, thermophoresis has emerged as a promising tool for quantifying biomolecular interactions. The underlying microscopic physical effect is still not understood, but often attributed to changes in the hydration layer once the binding occurs. To gain deeper insight, we investigate whether non-equilibrium coefficients can be related to equilibrium properties. Therefore, we compare thermophoretic data measured by thermal diffusion forced Rayleigh scattering (TDFRS) (which is a non-equilibrium process) with thermodynamic data obtained by isothermal titration calorimetry (ITC) (which is an equilibrium process). As a reference system, we studied the chelation reaction between ethylenediaminetetraacetic acid (EDTA) and calcium chloride (CaCl2) to relate the thermophoretic behavior quantified by the Soret coefficient ST to the Gibb's free energy ΔG determined in the ITC experiment using an expression proposed by Eastman. Finally, we have studied the binding of the protein Bovine Carbonic Anhydrase I (BCA I) to two different benzenesulfonamide derivatives: 4-fluorobenzenesulfonamide (4FBS) and pentafluorobenzenesulfonamide (PFBS). For all three systems, we find that the Gibb's free energies calculated from ST agree with ΔG from the ITC experiment. In addition, we also investigate the influence of fluorescent labeling, which allows measurements in a thermophoretic microfluidic cell. Re-examination of the fluorescently labeled system using ITC showed a strong influence of the dye on the binding behavior.

Soret separation and thermo-osmosis in porous media

When a temperature difference is applied over a porous medium soaked with a fluid mixture, two effects may be observed, a component separation (the Ludwig-Soret effect, thermodiffusion) and a pressure difference due to thermo-osmosis. In this work, we have studied both effects using non-equilibrium thermodynamics and molecular dynamics. We have derived expressions for the two characteristic parameters, the Soret coefficient and the thermo-osmotic coefficient in terms of phenomenological transport coefficients, and we show how they are related. Numerical values for these coefficients were obtained for a two-component fluid in a solid matrix where both fluid and solid are Lennard-Jones/spline particles. We found that both effects depend strongly on the porosity of the medium and weakly on the interactions between the fluid components and the matrix. The Soret coefficient depends strongly on whether the fluid is sampled from inside the porous medium or from bulk phases outside, which must be considered in experimental measurements using packed columns. If we use a methane/decane mixture in bulk as an example, our results for the Soret coefficient give that a temperature difference of 10 K will separate the mixture to about 49.5/50.5 and give no pressure difference. In a reservoir with 30% porosity, the separation will be 49.8/50.2, whereas the pressure difference will be about 15 bar. Thermo-osmotic pressures with this order or magnitude have been observed in frost-heave experiments.

Towards understanding specific ion effects in aqueous media using thermodiffusion

Specific ion effects play an important role in scientific and technological processes. According to Hofmeister, the influence on the hydrogen bond network depends on the ion and leads to a specific order of the ions. Also thermodiffusion the mass transport caused by a temperature gradient is very sensitive to changes of the hydrogen bond network leading to a ranking according to hydrophilicity of the salt. Hence, we investigate various salt solutions in order to compare with the Hofmeister concept. We have studied three different sodium salts in water as a function of temperature (25-45[Formula: see text]C) and concentration (0.5-5 mol kg[Formula: see text]) using Thermal Diffusion Forced Rayleigh Scattering (TDFRS). The three anions studied, carbonate, acetate and thiocyanate, span the entire range of the Hofmeister series from hydrophilic to hydrophobic. We compare the results with the recent measurements of the corresponding potassium salts to see to what extent the cation changes the thermodiffusion of the salt.

Overlapping hydration shells in salt solutions causing non-monotonic Soret coefficients with varying concentration

We develop an intuitive picture that overlapping hydration shells in salt solutions cause non-monotonic Soret coefficients with varying concentration.

In silico all-atom approach to thermodiffusion in dilute aqueous solutions

Thermodiffusion (or thermophoresis) is the phenomenon by which the spatial distributions of constituents of liquid or gas phases become inhomogeneous in response to a temperature gradient. It has been evidenced in a variety of systems and has many practical applications as well as implications in the context of the origins of life. A complete molecular picture of thermophoresis is still missing, and phenomenological approaches are often employed to account for the experimental observations. In particular, the amplitude of the resulting concentration-gradients (quantified by the Soret coefficient) depends on many factors that are not straightforwardly rationalized. All-atom molecular dynamics simulations appear as an exquisite tool to shed light on the molecular origins for this phenomenon in molecular systems, but the practical implementation of thermophoretic settings in silico poses significant challenges. Here, we propose a robust approach to tackle thermophoresis in dilute realistic solutions at the molecular level. We rely on a recent enhanced heat-exchange algorithm to generate temperature-gradients. We carefully assess the convergence of thermophoretic simulations in dilute aqueous solutions. We show that simulations typically need to be propagated on long timescales (hundreds of nanoseconds). We find that the magnitude of the temperature gradient and the box sizes have little effect on the measured Soret coefficients. Practical guidelines are derived from such observations. Provided with this reliable setup, we discuss the results of thermophoretic simulations on several examples of molecular, neutral solutes, which we find in very good agreement with experimental measurements regarding the concentration-, mass-, and temperature-dependence of the Soret coefficient.

Heat flows in rock cracks naturally optimize salt compositions for ribozymes

Catalytic nucleic acids, such as ribozymes, are central to a variety of origin-of-life scenarios. Typically, they require elevated magnesium concentrations for folding and activity, but their function can be inhibited by high concentrations of monovalent salts. Here we show that geologically plausible high-sodium, low-magnesium solutions derived from leaching basalt (rock and remelted glass) inhibit ribozyme catalysis, but that this activity can be rescued by selective magnesium up-concentration by heat flow across rock fissures. In contrast to up-concentration by dehydration or freezing, this system is so far from equilibrium that it can actively alter the Mg:Na salt ratio to an extent that enables key ribozyme activities, such as self-replication and RNA extension, in otherwise challenging solution conditions. The principle demonstrated here is applicable to a broad range of salt concentrations and compositions, and, as such, highly relevant to various origin-of-life scenarios.

Thermophoretic Random Walks and Enhancement of Diffusion

The contribution of the stochastic thermodiffusion to the diffusion enhancement is studied. The thermodiffusion of particles suspended in a liquid may hold place when the spontaneous endo- or exothermal nanoscale events similar to elementary acts of enzymatic reactions occur as the random series in the space and time. In these events, the energy can be emitted or absorbed at nanoscale during few to hundreds of picoseconds. It may cause local spontaneous temperature spikes spreading quickly in the space and decaying with time. The random local temperature spikes create local transient temperature gradients, where thermodiffusion of the molecules and particles holds place as well as the change in the physical properties of the suspending medium due to heating. These thermodiffusion random walks may appear as the enhanced usual Stokes-Einstein diffusion when the energy absorption/generation is high enough. The evaluated relative contribution of the mentioned effect to the molecular mobility is shown to be in agreement with experimental data on enzymatic reactions from the literature.

Theoretical Constraints Imposed by Gradient Detection and Dispersal on Microbial Size in Astrobiological Environments

The capacity to sense gradients efficiently and acquire information about the ambient environment confers many advantages such as facilitating movement toward nutrient sources or away from toxic chemicals. The amplified dispersal evinced by organisms endowed with motility is possibly beneficial in related contexts. Hence, the connections between information acquisition, motility, and microbial size are explored from an explicitly astrobiological standpoint. By using prior theoretical models, the constraints on organism size imposed by gradient detection and motility are elucidated in the form of simple heuristic scaling relations. It is argued that environments such as alkaline hydrothermal vents, which are distinguished by the presence of steep gradients, might be conducive to the existence of "small" microbes (with radii of ≳0.1 μm) in principle, when only the above two factors are considered; other biological functions (e.g., metabolism and genetic exchange) could, however, regulate the lower bound on microbial size and elevate it. The derived expressions are potentially applicable to a diverse array of settings, including those entailing solvents other than water; for example, the lakes and seas of Titan. The article concludes with a brief exposition of how this formalism may be of practical and theoretical value to astrobiology.

A ternary mixture at the border of Soret separation stability

Ternary mixtures with the Soret effect are prone to triple-diffusive convection in a thermal field. The Soret coefficients of the toluene-methanol-cyclohexane mixture, measured in microgravity at a given composition [0.62-0.31-0.07] in mass fractions, showed that the net separation ratio, Ψ, the parameter responsible for the hydrodynamic stability in a gravity field is close to zero. Furthermore, the large cross-diffusion of toluene leads to a curious situation: the Soret coefficient S_T1 is positive while the thermodiffusion coefficient D_T1 is negative. The behavior of this ternary mixture on the border of stability, when Ψ is slightly negative or positive, is examined experimentally and numerically. The mixture is placed in an elongated cell between the differently heated walls. Depending on Ψ and the initial temperature of the liquid (mean temperature, linear profile or cold one), the evolution of concentration patterns are classified by four regimes. We observe the emergence of motionless, metastable, and convective patterns. In the case of Ψ > 0, it was found that cross-diffusion fluxes cause a temporarily unstable density pattern. The initially cold mixture at either Ψ sign shows dissimilar Soret separation in the upper and lower parts of the cell. It leads to the formation of a long-lived inverse density gradient at the upper part of the cell, which finally results in a motionless (Ψ > 0) or convective (Ψ < 0) pattern.

Prebiotic Organic Chemistry of Formamide and the Origin of Life in Planetary Conditions: What We Know and What Is the Future

The goal of prebiotic chemistry is the depiction of molecular evolution events preceding the emergence of life on Earth or elsewhere in the cosmos. Plausible experimental models require geochemical scenarios and robust chemistry. Today we know that the chemical and physical conditions for life to flourish on Earth were at work much earlier than thought, i.e., earlier than 4.4 billion years ago. In recent years, a geochemical model for the first five hundred million years of the history of our planet has been devised that would work as a cradle for life. Serpentinization processes in the Hadean eon affording self-assembled structures and vesicles provides the link between the catalytic properties of the inorganic environment and the impressive chemical potential of formamide to produce complete panels of organic molecules relevant in pre-genetic and pre-metabolic processes. Based on an interdisciplinary approach, we propose basic transformations connecting geochemistry to the chemistry of formamide, and we hint at the possible extension of this perspective to other worlds.

Plausible Emergence of Biochemistry in Enceladus Based on Chemobrionics

Saturn's satellite Enceladus is proposed to have a soda-type subsurface ocean with temperature able to support life and an iron ore-based core. Here, it was demonstrated that ocean chemistry related to Enceladus can support the development of Fe-based hydrothermal vents, one of the places suggested to be the cradle of life. The Fe-based chemical gardens were characterized with Fourier-transform (FT)IR spectroscopy and XRD. The developed chemobrionic structures catalyzed the condensation polymerization of simple organic prebiotic molecules to kerogens. Further, they could passively catalyze the condensation of the prebiotic molecule formamide to larger polymers, suggesting that elementary biochemical precursors could have emerged in Enceladus.

An Unreasonable Universality of the Thermophoretic Velocity

Thermophoresis is the migration of dispersed molecules or particles in an inhomogeneous temperature field. It has been associated with various nonequilibrium phenomena ranging from stratified oil reservoirs to prebiotic evolution and the origin of life. The thermophoretic velocity is difficult to predict and appears almost random. We show that, in the case of strongly asymmetric mixtures with high molecular mass ratios of the solute to the solvent, it unexpectedly assumes a universal value once the trivial influence of the viscosity has been factored out. This asymptotic behavior is surprisingly universal and a general property of many highly asymmetric molecular mixtures ranging from organic molecules in n-alkanes to dilute solutions of high polymers. A quantitative explanation is provided on the basis of the asymmetric limit of the pseudoisotopic Soret effect.

Thermophoresis: The Case of Streptavidin and Biotin

Thermophoretic behavior of a free protein changes upon ligand binding and gives access to information on the binding constants. The Soret effect has also been proven to be a promising tool to gain information on the hydration layer, as the temperature dependence of the thermodiffusion behavior is sensitive to solute–solvent interactions. In this work, we perform systematic thermophoretic measurements of the protein streptavidin (STV) and of the complex STV with biotin (B) using thermal diffusion forced Rayleigh scattering (TDFRS). Our experiments show that the temperature sensitivity of the Soret coefficient is reduced for the complex compared to the free protein. We discuss our data in comparison with recent quasi-elastic neutron scattering (QENS) measurements. As the QENS measurement has been performed in heavy water, we perform additional measurements in water/heavy water mixtures. Finally, we also elucidate the challenges arising from the quantiative thermophoretic study of complex multicomponent systems such as protein solutions.

Chemistry of Abiotic Nucleotide Synthesis

The chemistry of abiotic nucleotide synthesis of RNA and DNA in the context of their prebiotic origins on early earth is a continuing challenge. How did (or how can) the nucleotides form and assemble from the small molecule inventories and under conditions that prevailed on early earth 3.5-4 billion years ago? This review provides a background and up-to-date progress that will allow the reader to judge where the field stands currently and what remains to be achieved. We start with a brief primer on the biological synthesis of nucleotides, followed by an extensive focus on the prebiotic formation of the components of nucleotides-either via the synthesis of ribose and the canonical nucleobases and then joining them together or by building both the conjoined sugar and nucleobase, part-by-part-toward the ultimate goal of forming RNA and DNA by polymerization. The review will emphasize that there are-and will continue to be-many more questions than answers from the synthetic, mechanistic, and analytical perspectives. We wrap up the review with a cautionary note in this context about coming to conclusions as to whether the problem of chemistry of prebiotic nucleotide synthesis has been solved.

Formation of Formamide from HCN + H2O: A Computational Study on the Roles of a Second H2O as a Catalyst, as a Spectator, and as a Reactant

Formamide (NH₂CHO), being the smallest and fundamental building block of life (with a peptide linkage), has recently been able to attract much interests, in the field of astrochemistry, astrophysics, and astrobiology. In this work, using quantum mechanical computations, reactions between HCN and H₂O, leading to the formation of formamide, have been analyzed. For the first time, an alternative and competing reaction channel, which proceeds via a geminal diol intermediate, for the formation of formamide, has been proposed. In this alternative channel, an extra water molecule (second H₂O) was found to be acting as a reactant, in the second step of the reaction path. Effects of second H₂O molecule in the reaction paths, providing catalytic assistance to the reaction or behaving like a spectator (concept is introduced for the first time for this reaction), have also been analyzed. Usefulness of spectator behavior is highlighted for the reactions happening on the rigid water-ice surfaces, where the water-ice may not be getting involved for any catalytic assistance. In light of catalytic assistances provided by the second H₂O, prominent effects in reducing the barrier heights drastically (even for the second step of the reaction, the barrier height was found to be below the reactants), through a hydrogen relay transport mechanism, were observed. In addition to the mechanism studies, interstellar feasibilities of all the reaction channels and their significances are discussed in detail.

Thermophoresis of biological and biocompatible compounds in aqueous solution

With rising popularity of microscale thermophoresis for the characterisation of protein-ligand binding reactions and possible applications in microfluidic devices, there is a growing interest in considering thermodiffusion in the context of life sciences. But although the understanding of thermodiffusion in non-polar mixtures has grown rapidly in recent years, predictions for associated mixtures like aqueous solutions remain challenging. This review aims to give an overview of the literature on thermodiffusion in aqueous systems, show the difficulties in theoretical description that arise from the non-ideal behaviour of water-mixtures, and highlight the relevance of thermodiffusion in a biological context. We find that the thermodiffusion in aqueous systems is dominated by contributions from heat of transfer, hydrogen bond interactions and charge effects. However, the separation of these effects is often difficult, especially in case of biological systems where a systematic exclusion of contributions may not be feasible.

Negative Thermophoretic Force in the Strong Coupling Regime

Negative thermophoresis (a particle moving up the temperature gradient) is a somewhat counterintuitive phenomenon which has thus far eluded a simple thermostatistical description. The purpose of this Letter is to show that a thermodynamic framework based on the formulation of a Hamiltonian of mean force has the descriptive ability to capture this interesting and elusive phenomenon in an unusually elegant and straightforward fashion. We propose a mechanism that describes the advent of a thermophoretic force acting from cold to hot on systems that are strongly coupled to a nonisothermal heat bath. When a system is strongly coupled to the heat bath, the system's eigenenergies E_{j} become effectively temperature dependent. This adjustment of the energy levels allows the system to take heat from the environment, +d⟨E_{j}⟩, and return it as work, -d⟨TdE_{j}/dT⟩. This effect can make the temperature dependence of the effective energy profile nonmonotonic. As a result, particles may experience a force in either direction depending on the temperature.

Thermodiffusion and hydrolysis of 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC)

Presently, microfluidic traps are designed mimicking the environment of hydrothermal pores, where a combination of thermophoresis and convection leads to accumulation so that high concentrations of organic matter can be reached. Such a setup is interesting in the context of the origin of life to observe accumulation and possible further synthesis of small organic molecules or prebiotic molecules such as nucleotides or RNA-fragments, but could also be used to replicate DNA-strands. The addition of coupling agents for the activation of carboxyl or phosphate groups such as 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and EDC-hydrochloride (EDC-HCl) is necessary in order to speed up the process. This work characterizes the thermophoretic properties of EDC and EDC-HCl needed to optimize the design of the traps. At p H 4-6 spontaneous hydrolysis of EDC is observed, which also leads to a neutralisation of the p H. In order to evaluate the thermodiffusion measurements the rate constants were measured at 23 and [Formula: see text] C and the activation energy of the hydrolysis calculated.

Heated gas bubbles enrich, crystallize, dry, phosphorylate and encapsulate prebiotic molecules

Non-equilibrium conditions must have been crucial for the assembly of the first informational polymers of early life, by supporting their formation and continuous enrichment in a long-lasting environment. Here, we explore how gas bubbles in water subjected to a thermal gradient, a likely scenario within crustal mafic rocks on the early Earth, drive a complex, continuous enrichment of prebiotic molecules. RNA precursors, monomers, active ribozymes, oligonucleotides and lipids are shown to (1) cycle between dry and wet states, enabling the central step of RNA phosphorylation, (2) accumulate at the gas-water interface to drastically increase ribozymatic activity, (3) condense into hydrogels, (4) form pure crystals and (5) encapsulate into protecting vesicle aggregates that subsequently undergo fission. These effects occur within less than 30 min. The findings unite, in one location, the physical conditions that were crucial for the chemical emergence of biopolymers. They suggest that heated microbubbles could have hosted the first cycles of molecular evolution.

Direct Prebiotic Pathway to DNA Nucleosides

It is assumed that RNA played a key role in the origin of life, and the transition to more complex but more stable DNA for continuous information storage and replication requires the development of a ribonucleotide reductase to obtain the deoxyribonucleotides from ribonucleotides. This step, as well as an alternative path from abiotic molecules to DNA-based life is completely unknown. Shown here is the formation of deoxyribonucleosides under relevant prebiotic conditions in water in high regio- and stereoselectivity, from all canonical purine and pyrimidine bases, by condensation with acetaldehyde and sugar-forming precursors. Thus, a continuous path to deoxyribonucleosides, starting from simple, prebiotically available molecules has been discovered. Furthermore, the deoxyapionucleosides (DApiNA) were identified as a potential DNA progenitor. The results suggest that the DNA world evolved much earlier than previously assumed.

Prebiotic Syntheses Under Shock in the Water - Formamide - Potassium Bicarbonate - Sodium Hydroxide System

Syntheses under shock in nitrogen bubbled samples of the water - formamide - bicarbonate - sodium hydroxide system at pH 8.63, 9.46 and 10.44 were performed in the stainless steel preservation capsules. The maximum temperature and pressure in the capsules reached 545 K and 12.5 GPa respectively. Using the LC-MS-MS analysis, the 21 synthesis products have been identified, including amines and polyamines, carboxamide, acetamide and urea derivatives, compounds containing aniline, pyrrolidine, pyrrole, imidazole, as well as alcohol groups. It was found that the Fischer-Tropsch-type syntheses with catalysis on the surface of the stainless steel of the conservation capsule associated with the adsorbed hydrogen cyanide reactions and transamidation processes play the main role in the shock syntheses. Formation reactions of all the above-mentioned compounds have been suggested. It was proposed that hydrogen cyanide, ammonia, isocyanic acid, aminonitrile, aminoacetonitrile, as well as adsorbed species H(a), CH(a), CH2(a), CHOH(a), NH2(a) and H2CNH(a) are especially important for the formation of the products. A reduction reaction of adsorbed bicarbonate with hydrogen to formaldehyde has been first postulated. In the studied system also classical reactions take place - Wöhler's synthesis of urea and Butlerov's synthesis of methenamine. It was suggest that material of meteorites may be an effective catalyst in the Fischer-Tropsch-type syntheses at falling of the iron-nickel meteorites in the water - formamide regions on the early Earth. It was concluded that life could have originated due to the impact of meteorites on alkaline water-formamide lakes located near volcanoes on the early Earth.

Correlation between thermophoretic behavior and hydrophilicity for various alcohols⋆

Recent experiments for various amides and sugars showed a clear correlation of the temperature dependence of the Soret coefficient with the hydrophilicity, quantitatively described by the logarithm of the 1-octanol/water partition coefficient log P . This coefficient is a measure for the hydrophilicity/hydrophobicity balance of a solute and is often used to model the transport of a compound in the environment or to screen for potential pharmaceutical compounds. In order to validate whether this concept works also for other water soluble molecules we investigated systematically the thermophoresis of mono- and polyhydric alcohols. As experimental method we use a holographic grating technique called infrared Thermal Diffusion Forced Rayleigh Scattering (IR-TDFRS). Experiments showed that the temperature dependence of the Soret coefficient of polyhydric alcohols also correlates with log P and lies on the same master plot as amides and sugars.

A Universal Geochemical Scenario for Formamide Condensation and Prebiotic Chemistry

The condensation of formamide has been shown to be a robust chemical pathway affording molecules necessary for the origin of life. It has been experimentally demonstrated that condensation reactions of formamide are catalyzed by a number of minerals, including silicates, phosphates, sulfides, zirconia, and borates, and by cosmic dusts and meteorites. However, a critical discussion of the catalytic power of the tested minerals, and the geochemical conditions under which the condensation would occur, is still missing. We show here that mineral self-assembled structures forming under alkaline silica-rich solutions are excellent catalysts for the condensation of formamide with respect to other minerals. We also propose that these structures were likely forming as early as 4.4 billion years ago when the whole earth surface was a reactor, a global scale factory, releasing large amounts of organic compounds. Our experimental results suggest that the conditions required for the synthesis of the molecular bricks from which life self-assembles, rather than being local and bizarre, appears to be universal and geologically rather conventional.

Thermophoresis of a Colloidal Rod: Contributions of Charge and Grafted Polymers

In this study, we investigated the thermodiffusion behavior of a colloidal model system as a function of the Debye length, λ_DH, which is controlled by the ionic strength. Our system consists of an fd-virus grafted with poly(ethylene glycol) (PEG) with a molecular mass of 5000 g mol^-1. The results are compared with recent measurements on a bare fd-virus and with results of PEG. The diffusion coefficients of both viruses are comparable and increase with the increasing Debye length. The thermal diffusion coefficient, D_T, of the bare virus increases strongly with the Debye length, whereas D_T of the grafted fd-virus shows only a very weak increase. The Debye length dependence of both systems can be described with an expression derived for charged rods using the surface charge density and an offset of D_T as adjustable parameters. It turns out that the ratio of the determined surface charges is inverse to the ratio of the surfaces of the two systems, which means that the total charge remains almost constant. The determined offset of the grafted fd-virus describing the chemical contributions is the sum of D_T of PEG and the offset of the bare fd-virus. At high λ_DH, corresponding to the low ionic strength, the S_T values of both colloidal model systems approach each other. This implies a contribution from the polymer layer, which is strong at short λ_DH and fades out for the longer Debye lengths, when the electric double layer reaches further than the polymer chains and therefore dominates interactions with the surrounding water.

A one-pot, water compatible synthesis of pyrimidine nucleobases under plausible prebiotic conditions

A prebiotically plausible one-pot formation pathway of 4-substituted pyrimidine nucleobases in water, starting from cyanoacetylene.

Considering planetary environments in origin of life studies

Early Earth geological conditions would have affected prebiotic chemistry: particularly the lack of atmospheric oxygen, presence of dissolved iron, and increased high-energy radiation. Incorporating planetary conditions into origin-of-life studies can also advance our search for life on other worlds.

Geological and Geochemical Constraints on the Origin and Evolution of Life

The traditional tree of life from molecular biology with last universal common ancestor (LUCA) branching into bacteria and archaea (though fuzzy) is likely formally valid enough to be a basis for discussion of geological processes on the early Earth. Biologists infer likely properties of nodal organisms within the tree and, hence, the environment they inhabited. Geologists both vet tenuous trees and putative origin of life scenarios for geological and ecological reasonability and conversely infer geological information from trees. The latter approach is valuable as geologists have only weakly constrained the time when the Earth became habitable and the later time when life actually existed to the long interval between ∼4.5 and ∼3.85 Ga where no intact surface rocks are known. With regard to vetting, origin and early evolution hypotheses from molecular biology have recently centered on serpentinite settings in marine and alternatively land settings that are exposed to ultraviolet sunlight. The existence of these niches on the Hadean Earth is virtually certain. With regard to inferring geological environment from genomics, nodes on the tree of life can arise from true bottlenecks implied by the marine serpentinite origin scenario and by asteroid impact. Innovation of a very useful trait through a threshold allows the successful organism to quickly become very abundant and later root a large clade. The origin of life itself, that is, the initial Darwinian ancestor, the bacterial and archaeal roots as free-living cellular organisms that independently escaped hydrothermal chimneys above marine serpentinite or alternatively from shallow pore-water environments on land, the Selabacteria root with anoxygenic photosynthesis, and the Terrabacteria root colonizing land are attractive examples that predate the geological record. Conversely, geological reasoning presents likely events for appraisal by biologists. Asteroid impacts may have produced bottlenecks by decimating life. Thermophile roots of bacteria and archaea as well as a thermophile LUCA are attractive.

Chemomimesis and Molecular Darwinism in Action: From Abiotic Generation of Nucleobases to Nucleosides and RNA

Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously emerging in the ensembles of molecules composing prebiotic pools, initiates subsequent evolution of increasingly complex and innovative chemical information. On the conservation side, it is a posteriori observed that numerous biological processes are based on prebiotically promptly made compounds, as proposed by the concept of Chemomimesis. Molecular Darwinian evolution and Chemomimesis are principles acting in balanced cooperation in the frame of Systems Chemistry. The one-pot synthesis of nucleosides in radical chemistry conditions is possibly a telling example of the operation of these principles. Other indications of similar cases of molecular evolution can be found among biogenic processes.

Stability of 2',3' and 3',5' cyclic nucleotides in formamide and in water: a theoretical insight into the factors controlling the accumulation of nucleic acid building blocks in a prebiotic pool

Synthesis of the first RNAs represents one of the cornerstones of the emergence of life. Recent studies demonstrated powerful scenarios of prebiotic synthesis of cyclic nucleotides in aqueous and formamide environments. This raised a question about their thermodynamic stability, a decisive factor determining their accumulation in a prebiotic pool. Here we performed ab initio molecular dynamics simulations at various temperatures in formamide and water to study the relative stabilities of the 2',3' and 3',5' isomers of cyclic nucleotides. The computations show that in an aqueous environment 2',3' cyclic nucleotides are more stable than their 3',5' counterparts at all temperatures up to the boiling point. In contrast, in formamide higher temperatures favor the accumulation of the 3',5' cyclic form, whereas below about 400 K the 2',3' cyclic form becomes more stable. The latter observation is consistent with a formamide-based origin scenario, suggesting that 3',5' cyclic nucleotides accumulated at higher temperatures subsequently allowed oligomerization reactions after fast cooling to lower temperatures. A statistical analysis of the geometrical parameters of the solutes indicates that thermodynamics of cyclic nucleotides in aqueous and formamide environments are dictated by the floppiness of the molecules rather than by the ring strain of the cyclic phosphodiester linkages.

The Prevailing Catalytic Role of Meteorites in Formamide Prebiotic Processes

Meteorites are consensually considered to be involved in the origin of life on this Planet for several functions and at different levels: (i) as providers of impact energy during their passage through the atmosphere; (ii) as agents of geodynamics, intended both as starters of the Earth’s tectonics and as activators of local hydrothermal systems upon their fall; (iii) as sources of organic materials, at varying levels of limited complexity; and (iv) as catalysts. The consensus about the relevance of these functions differs. We focus on the catalytic activities of the various types of meteorites in reactions relevant for prebiotic chemistry. Formamide was selected as the chemical precursor and various sources of energy were analyzed. The results show that all the meteorites and all the different energy sources tested actively afford complex mixtures of biologically-relevant compounds, indicating the robustness of the formamide-based prebiotic chemistry involved. Although in some cases the yields of products are quite small, the diversity of the detected compounds of biochemical significance underlines the prebiotic importance of meteorite-catalyzed condensation of formamide.

Estimating the capacity for production of formamide by radioactive minerals on the prebiotic Earth

Water creates special problems for prebiotic chemistry, as it is thermodynamically favorable for amide and phosphodiester bonds to hydrolyze. The availability of alternative solvents with more favorable properties for the formation of prebiotic molecules on the early Earth may have helped bypass this so-called "water paradox". Formamide (FA) is one such solvent, and can serve as a nucleobase precursor, but it is difficult to envision how FA could have been generated in large quantities or accumulated in terrestrial surface environments. We report here the conversion of aqueous acetonitrile (ACN) via hydrogen cyanide (HCN) as an intermediate into FA by γ-irradiation under conditions mimicking exposure to radioactive minerals. We estimate that a radioactive placer deposit could produce 0.1‒0.8 mol FA km-2 year-1. A uraninite fission zone comparable to the Oklo reactors in Gabon can produce 0.1‒1 mol m-2 year-1, orders of magnitude greater than other scenarios of FA production or delivery for which reaching sizeable concentrations of FA are problematic. Radioactive mineral deposits may be favorable settings for prebiotic compound formation through emergent geologic processes and FA-mediated organic chemistry.

Water-like Behavior of Formamide: Jump Reorientation Probed by Extended Depolarized Light Scattering

Water is a strong self-associated liquid with peculiar properties that crucially depend on H-bonding. As regards its molecular dynamics, only recently has water reorientation been successfully described based on a jump mechanism, which is responsible for the overall H-bonding exchange. Here, using high-resolution broad-band depolarized light scattering, we have investigated the reorientational dynamics of formamide (FA) as a function of concentration from the neat liquid to diluted aqueous solutions. Our main findings indicate that in the diluted regime the water rearrangement can trigger the motion of FA solute molecules, which are forced to reorient at the same rate as water. This highlights an exceptional behavior of FA, which perfectly substitutes water within its network. Besides other fundamental implications connected with the relevance of FA, its water-like behavior provides rare experimental evidence of a solute whose dynamics is completely slaved to the solvent.

Unravelling the hydrophobicity of urea in water using thermodiffusion: implications for protein denaturation

Sensitivity of thermodiffusion to urea–water interactions was studied experimentally and by NEMD simulations, identifying the hydrophobic behaviour of urea.

Anisotropic thermophoresis

Colloidal migration in a temperature gradient is referred to as thermophoresis. In contrast to particles with a spherical shape, we show that elongated colloids may have a thermophoretic response that varies with the colloid orientation. Remarkably, this can translate into a non-vanishing thermophoretic force in the direction perpendicular to the temperature gradient. Opposite to the friction force, the thermophoretic force of a rod oriented with the temperature gradient can be larger or smaller than when oriented perpendicular to it. The precise anisotropic thermophoretic behavior clearly depends on the colloidal rod aspect ratio, and also on its surface details, which provides an interesting tunability to the devices constructed based on this principle. By means of mesoscale hydrodynamic simulations, we characterize this effect for different types of rod-like colloids.