Beyond prebiotic chemistry

Summary: How can matter transition from the nonliving to the living state? The answer is essential for understanding the origin of life on Earth and for identifying promising targets in the search for life on other planets. Most studies have focused on the likely chemistry of RNA (1), protein (2), lipid, or metabolic “worlds” (3) and autocatalytic sets (4), including attempts to make life in the lab. But these efforts may be too narrowly focused on the biochemistry of life as we know it today. A radical rethink is necessary, one that explores not just plausible chemical scenarios but also new physical processes and driving forces. Such investigations could lead to a physical understanding not only of the origin of life but also of life itself, as well as to new tools for designing artificial biology

Potential Role of Inorganic Confined Environments in Prebiotic Phosphorylation

A concise outlook on the potential role of confinement in phosphorylation and phosphate condensation pertaining to prebiotic chemistry is presented. Inorganic confinement is a relatively uncharted domain in studies concerning prebiotic chemistry, and even more so in terms of experimentation. However, molecular crowding within confined dimensions is central to the functioning of contemporary biology. There are numerous advantages to confined environments and an attempt to highlight this fact, within this article, has been undertaken, keeping in context the limitations of aqueous phase chemistry in phosphorylation and, to a certain extent, traditional approaches in prebiotic chemistry

Chiral Polymerization in Open Systems From Chiral-Selective Reaction Rates

We investigate the possibility that prebiotic homochirality can be achieved exclusively through chiral-selective reaction rate parameters without any other explicit mechanism for chiral bias. Specifically, we examine an open network of polymerization reactions, where the reaction rates can have chiral-selective values. The reactions are neither autocatalytic nor do they contain explicit enantiomeric cross-inhibition terms. We are thus investigating how rare a set of chiral-selective reaction rates needs to be in order to generate a reasonable amount of chiral bias. We quantify our results adopting a statistical approach: varying both the mean value and the rms dispersion of the relevant reaction rates, we show that moderate to high levels of chiral excess can be achieved with fairly small chiral bias, below 10%. Considering the various unknowns related to prebiotic chemical networks in early Earth and the dependence of reaction rates to environmental properties such as temperature and pressure variations, we argue that homochirality could have been achieved from moderate amounts of chiral selectivity in the reaction rates.Comment: 15 pages, 6 figures, accepted for publication in Origins of Life and Evolution of Biosphere

The Influence of Galactic Cosmic Rays on Ion-Neutral Hydrocarbon Chemistry in the Upper Atmospheres of Free-Floating Exoplanets

Cosmic rays may be linked to the formation of volatiles necessary for prebiotic chemistry. We explore the effect of cosmic rays in a hydrogen-dominated atmosphere, as a proof-of-concept that ion-neutral chemistry may be important for modelling hydrogen-dominated atmospheres. In order to accomplish this, we utilize Monte Carlo cosmic ray transport models with particle energies of $10^6$ eV $< E < 10^{12}$ eV in order to investigate the cosmic ray enhancement of free electrons in substellar atmospheres. Ion-neutral chemistry is then applied to a Drift-Phoenix model of a free-floating giant gas planet. Our results suggest that the activation of ion-neutral chemistry in the upper atmosphere significantly enhances formation rates for various species, and we find that C$_2$H$_2$, C$_2$H$_4$, NH$_3$, C$_6$H$_6$ and possibly C$_{10}$H are enhanced in the upper atmospheres because of cosmic rays. Our results suggest a potential connection between cosmic ray chemistry and the hazes observed in the upper atmospheres of various extrasolar planets. Chemi-ionization reactions are briefly discussed, as they may enhance the degree of ionization in the cloud layer.Comment: 22 pages, 4 figures. Accepted to the International Journal of Astrobiolog

DNA Renaturation at the Water-Phenol Interface

We study DNA adsorption and renaturation in a water-phenol two-phase system, with or without shaking. In very dilute solutions, single-stranded DNA is adsorbed at the interface in a salt-dependent manner. At high salt concentrations the adsorption is irreversible. The adsorption of the single-stranded DNA is specific to phenol and relies on stacking and hydrogen bonding. We establish the interfacial nature of a DNA renaturation at a high salt concentration. In the absence of shaking, this reaction involves an efficient surface diffusion of the single-stranded DNA chains. In the presence of a vigorous shaking, the bimolecular rate of the reaction exceeds the Smoluchowski limit for a three-dimensional diffusion-controlled reaction. DNA renaturation in these conditions is known as the Phenol Emulsion Reassociation Technique or PERT. Our results establish the interfacial nature of PERT. A comparison of this interfacial reaction with other approaches shows that PERT is the most efficient technique and reveals similarities between PERT and the renaturation performed by single-stranded nucleic acid binding proteins. Our results lead to a better understanding of the partitioning of nucleic acids in two-phase systems, and should help design improved extraction procedures for damaged nucleic acids. We present arguments in favor of a role of phenol and water-phenol interface in prebiotic chemistry. The most efficient renaturation reactions (in the presence of condensing agents or with PERT) occur in heterogeneous systems. This reveals the limitations of homogeneous approaches to the biochemistry of nucleic acids. We propose a heterogeneous approach to overcome the limitations of the homogeneous viewpoint