The Asymmetry of Organic Aerosol Fission and Prebiotic Chemistry

We examine the prebiotic applicability of our recent analysis of the fission of an atmospheric aerosol particle coated with an organic film. The fission is made possible by the free energy change upon compression of the exterior monolayer film on the parent particle, which overcomes the increase in surface area associated with the production of two spherical daughter particles. Asymmetric division into a larger and a smaller particle becomes possible following surfactant film collapse. The size of the airborne parent particle is determined by the balance between aerodynamics and gravity, while the ratio of the radii of the daughters is determined by the compression characteristics of the amphiphilic molecules comprising the parent film. For an Earth atmosphere of one bar surface pressure, the larger and smaller daughters have the sizes of a single-celled bacterium and of a virus respectively. Chemical differentiation between the daughters is possible.     

Prebiotic Microreactors: A Synthesis of Purines and Dihydroxy Compounds in Aqueous Aerosol

We report the synthesis of purine bases and other heterocycles and the formation of amino acids, hydroxy acids and dihydroxy compounds by the spark activation of an atmosphere of methane, nitrogen and hydrogen, in the presence of an aqueous aerosol. With the aid of the interface air–water, the organic material obtained shows greater amounts and diversity of molecules with biological interest than the products obtained in the absence of an aerosol. Our results support the suggestion that aerosols may have played a significant role in the prebiotic origin of molecular diversity and evolution.     

Prebiotic Synthesis of Methionine and Other Sulfur-Containing Organic Compounds on the Primitive Earth: A Contemporary Reassessment Based on an Unpublished 1958 Stanley Miller Experiment

Original extracts from an unpublished 1958 experiment conducted by the late Stanley L. Miller were recently found and analyzed using modern state-of-the-art analytical methods. The extracts were produced by the action of an electric discharge on a mixture of methane (CH₄), hydrogen sulfide (H₂S), ammonia (NH₃), and carbon dioxide (CO₂). Racemic methionine was formed in significant yields, together with other sulfur-bearing organic compounds. The formation of methionine and other compounds from a model prebiotic atmosphere that contained H₂S suggests that this type of synthesis is robust under reducing conditions, which may have existed either in the global primitive atmosphere or in localized volcanic environments on the early Earth. The presence of a wide array of sulfur-containing organic compounds produced by the decomposition of methionine and cysteine indicates that in addition to abiotic synthetic processes, degradation of organic compounds on the primordial Earth could have been important in diversifying the inventory of molecules of biochemical significance not readily formed from other abiotic reactions, or derived from extraterrestrial delivery.     

A Reassessment of Prebiotic Organic Synthesis in Neutral Planetary Atmospheres

The action of an electric discharge on reduced gas mixtures such as H₂O, CH₄ and NH₃ (or N₂) results in the production of several biologically important organic compounds including amino acids. However, it is now generally held that the early Earth’s atmosphere was likely not reducing, but was dominated by N₂ and CO₂. The synthesis of organic compounds by the action of electric discharges on neutral gas mixtures has been shown to be much less efficient. We show here that contrary to previous reports, significant amounts of amino acids are produced from neutral gas mixtures. The low yields previously reported appear to be the outcome of oxidation of the organic compounds during hydrolytic workup by nitrite and nitrate produced in the reactions. The yield of amino acids is greatly increased when oxidation inhibitors, such as ferrous iron, are added prior to hydrolysis. Organic synthesis from neutral atmospheres may have depended on the oceanic availability of oxidation inhibitors as well as on the nature of the primitive atmosphere itself. The results reported here suggest that endogenous synthesis from neutral atmospheres may be more important than previously thought. Stanley L. Miller died May 20, 2007.     

Stanley L. Miller (1930–2007): Reflections and Remembrances

An appreciation of Stanley L. Miller, the pioneer prebiotic chemist, who died last year.     

The origin of life-a review of facts and speculations

Three popular hypotheses attempt to explain the origin of prebiotic molecules: synthesis in a reducing atmosphere, input in meteorites and synthesis on metal sulfides in deep-sea vents. It is not possible to decide which is correct. It is also unclear whether the RNA world was the first biological world or whether some simpler world preceded it.     

Thermal Wet Decomposition of Prussian Blue: Implications for Prebiotic Chemistry

The complex salt named Prussian Blue, Fe₄[Fe(CN)₆]₃?15 H₂O, can release cyanide at pH>10. From the point of view of the origin of life, this fact is of interest, since the oligomers of HCN, formed in the presence of ammonium or amines, leads to a variety of biomolecules. In this work, for the first time, the thermal wet decomposition of Prussian Blue was studied. To establish the influence of temperature and reaction time on the ability of Prussian Blue to release cyanide and to subsequently generate other compounds, suspensions of Prussian Blue were heated at temperatures from room temperature to 150° at pH 12 in NH₃ environment for several days. The NH₃ wet decomposition of Prussian Blue generated hematite, α‐Fe₂O₃, the soluble complex salt (NH₄)₄[Fe(CN₆)]?1.5 H₂O, and several organic compounds, the nature and yield of which depend on the experimental conditions. Urea, lactic acid, 5,5‐dimethylhydantoin, and several amino acids and carboxylic acids were identified by their trimethylsilyl (TMS) derivatives. HCN, cyanogen (C₂N₂), and formamide (HCONH₂) were detected in the gas phase by GC/MS analysis.     

The evolution of electroreception and bioelectrogenesis in teleost fish: a phylogenetic perspective

According to current phylogenetic theory, both electroreceptors and electric organs evolved multiple times throughout the evolution of teleosts. Two basic types of electroreceptors have been described: ampullary and tuberous electroreceptors. Ampullary‐type electroreceptors appeared once in the common ancestor of the Siluriformes+Gymnotiformes (within the superorder Ostariophysi), and on two other occasions within the superorder Osteoglossomorpha: in the African Mormyriformes and in the African Notopteriformes. Tuberous receptors are assumed to have evolved three times; all within groups that already possessed ampullary receptors. With the exception of a single catfish species, for which studies are still lacking, all fish with tuberous electroreceptors also have an electric organ. Tuberous electroreceptors are found in the two unrelated electrogenic teleost lineages (orders Gymnotiformes and Mormyriformes) and in one non‐electrogenic South American catfish species (order Siluriformes). Electric organs evolved eight times independently among teleosts: five of them among the ostariophysans (once in the gymnotiform ancestor and in four siluriform lineages), once in the common ancestor of Mormyriformes, and in two uranoscopids. With the exception of two uranoscopid genera, for which no electroreceptive capabilities have been discovered so far, all electric organs evolved as an extension of a pre‐existing electroreceptive (ampullary) condition. It is suggested that plesiomorphic electric organ discharges (EODs) possessed a frequency spectrum that fully transgressed the tuning curve of ampullary receptors, i.e. a signal such as a long lasting monophasic pulse. Complex EOD waveforms appeared as a derived condition among electric fish. EODs are under constant evolutionary pressure to develop an ideal compromise between a function that enhances electrolocation and electrocommunication capabilities, and thereby ensures species identity through sexual and behavioural segregation, and minimizes the risk of predation.     

Synthesis of Polycyclic Aromatic Hydrocarbons and Acetylene Polymers in Ice: A Prebiotic Scenario

The recent evidences of presence of subsurface oceans of liquid water and ice on Saturn's moons, and the possible presence and astrobiological importance of polycyclic aromatic hydrocarbons (PAHs) in these environments, provide strong motivation for the exploration of the prebiotic chemistry in ice and to test if PAHs could be experimentally synthesized in ice surfaces under atmospheres containing methane as carbon source. In this work, we present a new design for prebiotic‐chemistry experiments in ice matrix. Using this design, a mixture of products including PAHs, polar aromatic compounds, and hydrophilic acetylene‐based polymers was obtained. We propose that acetylene generation in a methane/nitrogen atmosphere and subsequent polymerization to PAHs and polyynes could be a favored pathway in the presence of water freeze–melt cycles. These results shed light on the processes involved in PAH synthesis in icy environments and on the physical factors that drive the different competing pathways in methane/nitrogen atmospheres.     

The Potential of Photochemical Transition Metal Reactions in Prebiotic Organic Synthesis. I. Observed Conversion of Methanol into Ethylene Glycol as Possible Prototype for Sugar Alcohol Formation

Photochemical processes involving redox reactions between metal ions and organic substrates possess the versatile potential for having harnessed solar energy for prebiotic organic synthesis. The present study in our Laboratory has shown that ultraviolet irradiation of transition metal ions such as of Ni, Co, Fe, Cu and Ti dissolved in primary or secondary alcohols causes photoreduction of the metal ions with the concomitant oxidation of the alcohol to aldehyde or ketone. An observed accompaniment of this novel 'light' reaction has been the known 'dark' pinacol reaction, whereby the carbonyl derivative underwent bimolecular coupling to the diol by the photogenerated reduced transition metal reagent. These tandem 'light-dark' processes possess the potential for the stepwise synthesis of dimeric 1,2-diols from simpler alcohols under conditions that might have prevailed on the prebiotic earth. Experiments reported here have demonstrated that such a tandem 'light-dark' conversion of methanol into ethylene glycol, via formaldehyde, does in fact occur, when nickel(II) acetylacetonate solutions in methanol undergo prolonged irradiation at 185-254 nm. Since ethylene glycol can be considered as the simplest sugar alcohol, these findings may provide novel insight into the prebiotic oligomerization of formaldehyde into higher sugar alcohols or even sugars.     

The chemical origins of life and its early evolution: an introduction

Can we look at contemporary biology and couple this with chemical insight to propose some plausible mechanisms for the origin of life on the planet? In what follows, we examine some promising chemical reactions by which the building blocks for nucleic acids might have been created about a billion years after the Earth formed. This could have led to self-assembling systems that were based on an all-RNA metabolism, where RNA is both catalytic and informational. We consider the breadth of RNA enzymes presently existing in biology, and to what extent these might have covered a wider range of chemistry in the RNA world. Ultimately, the RNA world would probably have given way to protein-based life quite quickly, and the origins of peptidyl transferase activity are discussed below.     

On the asymmetric autocatalysis of aldol reactions: The case of 4‐nitrobenzaldehyde and acetone. A critical appraisal with a focus on theory

Under neutral conditions, spontaneous mirror symmetry breaking has been occasionally reported for aldol reactions starting from achiral reagents and conditions. Chiral induction might be interpreted in terms of autocatalysis exerted by chiral mono‐aldol or bis‐aldol products as source of initial enantiomeric excesses, which may account for such experimental observations. We describe here a thorough Density Functional Theory (DFT) study on this complex and otherwise difficult problem, which provides some insights into this phenomenon. The picture adds further rationale to an in‐depth analysis by Moyano et al, who showed the isolation and characterization of bis‐aldol adducts and their participation in a complex network of reversible steps. However, the lack of enantiodiscrimination (ees vanish rapidly in solution) suggests, according to the present results, a weak association in complexes formed by the catalysts and substrates. The latter would also be consistent with almost flat transition states having similar heights for competitive catalyst‐bound transition structures (actually, we were unable to locate them at the level explored). Overall, neither autocatalysis as once conjectured nor mutual inhibition of enantiomers appears to be operating mechanisms. Asymmetric amplification in early stages harnessing unavoidable enantiomeric imbalances in reaction mixtures of chiral products represents a plausible interpretation.     

Kinetics of Organic Transformations under Mild Aqueous Conditions: Implications for the Origin of Life and its Metabolism

The rates of thermal transformation of organic molecules containing carbon, hydrogen, and oxygen were systematically examined in order to identify the kinetic constraints that governed origin-of-life organic chemistry under mild aqueous conditions. Arrhenius plots of the kinetic data were used to estimate the reaction of half-lifes at 50 degrees C. This survey showed that hydrocarbons and organic substances containing a single oxygenated group were kinetically the most stable; whereas organic substances containing two oxygenated groups in which one group was an alpha- or beta-positioned carbonyl group were the most reactive. Compounds with an alpha- or beta-positioned carbonyl group (aldehyde or ketone) had rates of reaction that were up to 10(24)-times faster than rates of similar molecules lacking the carbonyl group. This survey of organic reactivity, together with estimates of the molecular containment properties of lipid vesicles and liquid spherules, indicates that an origins process in a small domain that used C,H,O-intermediates had to be catalytic and use the most reactive organic molecules to prevent escape of its reaction intermediates.     

The TNA-Family of Nucleic Acid Systems: Properties and Prospects

This report summarizes the content of the author's lecture given at the 9th ISSOL Conference on the 'Origin of Life' in Oaxaca on 2 July 2002*. The report consists of introductory remarks followed by a reproduction of the authentic sequence of slides shown during the lecture. Each slide figure is accompanied with a short commentary on the figure's content. The lecture dealt with the structure and the properties of TNA (alpha-threofuranosyl nucleic acid) and included results of some more recent chemical investigations that had been inspired by the simplicity of TNA's molecular architecture.     

The Sugar Model: Autocatalytic Activity of the Triose–Ammonia Reaction

Reaction of triose sugars with ammonia under anaerobic conditions yielded autocatalytic products. The autocatalytic behavior of the products was examined by measuring the effect of the crude triose–ammonia reaction product on the kinetics of a second identical triose–ammonia reaction. The reaction product showed autocatalytic activity by increasing both the rate of disappearance of triose and the rate of formation of pyruvaldehyde, the product of triose dehydration. This synthetic process is considered a reasonable model of origin-of-life chemistry because it uses plausible prebiotic substrates, and resembles modern biosynthesis by employing the energized carbon groups of sugars to drive the synthesis of autocatalytic molecules.     

Chemical Constraints Governing the Origin of Metabolism: The Thermodynamic Landscape of Carbon Group Transformations under Mild Aqueous Conditions

The thermodynamics of organic chemistry under mildaqueous conditions was examined in order to begin to understand itsinfluence on the structure and operation of metabolism and itsantecedents. Free energies (G) were estimated for four types ofreactions of biochemical importance – carbon-carbon bond cleavage andsynthesis, hydrogen transfer between carbon groups, dehydration ofalcohol groups, and aldo-keto isomerization. The energies werecalculated for mainly aliphatic groups composed of carbon, hydrogen,and oxygen. The energy values showed (1) that generally when carbon-carbon bond cleavage involves groups from different functional groupclasses (i.e., carboxylic acids, carbonyl groups, alcohols, andhydrocarbons), the transfer of the shared electron-pair to the morereduced carbon group is energetically favored over transfer to themore oxidized carbon group, and (2) that the energy of carbon-carbonbond transformation is primarily determined by the functional groupclass of the group that changes oxidation state in the reaction (i.e., the functional group class of the group that donates the sharedelectron-pair during cleavage, or that accepts the incipient sharedelectron-pair during synthesis). In contrast, the energy of hydrogentransfer between carbon groups is determined by the functional groupclass of both the hydrogen-donor group and the hydrogen-acceptorgroup. From these and other observations we concluded that thechemistry involved in the origin of metabolism (and to a lesser degreemodern metabolism) was strongly constrained by (1) the limited redox-based transformation energy of organic substrates that is readilydissipated in a few energetically favorable irreversible reactions;(2) the energy dominance of a few transformation half-reactions thatdetermines whether carbon-carbon bond transformation (cleavage orsynthesis) is energetically favorable (G < –3.5 kcal/mol), reversible(G between ±3.5 kcal/mol), or unfavorable (G > +3.5 kcal/mol);and (3) the dependence of carbon group transformation energy on thefunctional group class (i.e., oxidation state) of participatinggroups that in turn is contingent on prior reactions and precursors inthe synthetic pathway.     

N-Phosphoryl Amino Acids and Biomolecular Origins. Review Paper in Honor of the 50th Anniversary of the Publication of ``A Production of Amino Acids under Possible Primitive Earth Conditions' (Miller, 1953)

The possible role of phosphoryl amino acids for biomolecular origins is briefly reviewed. Peptide formation, ester formation, ester exchange on phosphorus and N to O migration occurred when the N-phosphoryl amino acid was incubated at room temperature. Short nucleotides and peptides were formed when nucleoside was reacted with N-phosphoryl amino acid at room temperature. Serine and threonine residues in their conjugate with different nucleosides (mediated with phosphorus) showed different self-cleavage activities. N-phosphoryl Histine and Ser-His dipeptide could cleave nucleic acids, proteins and esters in neutral medium. Based on a simple model, a pathway of 'co-evolution of protein and nucleic acid' was proposed.     

Chemistry and Dynamics of Dissolved Organic Matter in a Temperate Coniferous Forest on Andic Soils: Effects of Litter Quality

Dissolved organic matter (DOM) plays an important role in transporting carbon and nitrogen from forest floor to mineral soils in temperate forest ecosystems. Thus, the retention of DOM via sorption or microbial assimilation is one of the critical steps for soil organic matter formation in mineral soils. The chemical properties of DOM are assumed to control these processes, yet we lack fundamental information that links litter quality, DOM chemistry, and DOM retention. Here, we studied whether differences in litter quality affect solution chemistry and whether changes in litter inputs affect DOM quality and removal in the field. The effects of litter quality on solution chemistry were evaluated using chemical fractionation methods for laboratory extracts and for soil water collected from a temperate coniferous forest where litter inputs had been altered. In a laboratory extraction, litter type (needle, wood, root) and the degree of decomposition strongly influenced solution chemistry. Root litter produced more than 10 times more water-extractable dissolved organic N (DON) than any other litter type, suggesting that root litter may be most responsible for DON production in this forest ecosystem. The chemical composition of the O-horizon leachate was similar under all field treatments (doubled needle, doubled wood, and normal litter inputs). O-horizon leachate most resembled laboratory extracts of well-decomposed litter (that is, a high proportion of hydrophobic acids), in spite of the significant amount of litter C added to the forest floor and a tendency toward higher mean DOM under doubled-Litter treatments. A lag in DOM production from added litter or microbial modification might have obscured chemical differences in DOM under the different treatments. Net DOM removal in this forest soil was strong; DOM concentration in the water deep in the mineral soil was always low regardless of concentrations in water that entered the mineral soil and of litter input manipulation. High net removal of DOM from O-horizon leachate, in spite of extremely low initial hydrophilic neutral content (labile DOM), coupled with the lack of influence by season or soil depth, suggests that DOM retention in the soil was mostly by abiotic sorption.