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On the why's and how's of clay minerals' importance in life's emergence
Abstract
A possibly prominent role for Green Rust minerals in life's emergence is inferred from a comparison of their structural, mechano-dynamic and electrochemical properties and of the layout of bioenergetic, i.e. free energy converting processes in extant organisms. From fundamental thermodynamic considerations, the conversion of environmental free energy into the decrease of entropy that defines life is an indispensable ingredient for life to emerge. A specific scenario for life's emergence mediated by Green Rust minerals in the framework of the alkaline hydrothermal vent hypothesis is proposed.
... These structures would have consisted of redoxactive minerals forming networks of interconnected cavities lined by either inorganic walls or amyloidal membranes (Duval et al., 2020a) within an insulated matrix of other minerals acting as barriers. It has recently been experimentally demonstrated that reduction of CO 2 to formate using H 2 as electron donor does occur in the presence of pH-and redox-gradients corresponding to those of the alkaline hydrothermal vents (Hudson et al., 2020). ...
... It has furthermore been suggested by Duval et al. (2020a) that redox-reactive and structurally flexible green rust fougerite nanocrystals may have formed electron-and anion-transporting pores within the electrostatic and pH-barriers, possibly emulating the function of life's enzymes that generate phosphatetransfer potentials (driving all metabolic reactions of extant life) and hosting catalytic reactions crucial to early metabolism ( Figure 2). ...
... Mineral barriers may have created and maintained steep ionic disequilibria and fougeritecontaining nanoparticles potentially participated in the conversion of environmental redox energy into the chemical disequilibria driving metabolic processes in extant life (Duval et al., 2020a). ...
... These structures would have consisted of redoxactive minerals forming networks of interconnected cavities lined by either inorganic walls or amyloidal membranes (Duval et al., 2020a) within an insulated matrix of other minerals acting as barriers. It has recently been experimentally demonstrated that reduction of CO 2 to formate using H 2 as electron donor does occur in the presence of pH-and redox-gradients corresponding to those of the alkaline hydrothermal vents (Hudson et al., 2020). ...
... It has furthermore been suggested by Duval et al. (2020a) that redox-reactive and structurally flexible green rust fougerite nanocrystals may have formed electron-and anion-transporting pores within the electrostatic and pH-barriers, possibly emulating the function of life's enzymes that generate phosphatetransfer potentials (driving all metabolic reactions of extant life) and hosting catalytic reactions crucial to early metabolism ( Figure 2). ...
... Mineral barriers may have created and maintained steep ionic disequilibria and fougeritecontaining nanoparticles potentially participated in the conversion of environmental redox energy into the chemical disequilibria driving metabolic processes in extant life (Duval et al., 2020a). ...
Fougerite, the natural green rust, first discovered in soils and universally considered as responsible for the blue-green colour of gleys and an indicator of reducing conditions, has been recently considered as a key mineral for life's emergence in the alkaline hydrothermal vents theory. It inherits all of the reactive properties of layered double hydroxides in its hydrated interlayer but also the specific reactivity of mixed Fe(II)-Fe(III) compounds, including redox reactivity with metals and metalloids. Along with its structural and compositional analogy with metallo-enzymes, all these properties have stimulated research on the possible role of fougerite as a membrane, and a catalytic engine, especially where gradients of pH, redox potential and temperature favour mixing of chemically contrasted reactants, such as at hydrothermal systems. Although the presence of fougerite, however difficult to detect, has never been reported at alkaline hydrothermal systems, we have thermodynamically evaluated whether the environmental conditions met in such modern oceanic systems are compatible with the formation of fougerite. Data on fluids from the Lost City hydrothermal field (30°N, Mid Atlantic ridge, Seyfried et al. (2015)) support the reducing nature of this environment, close to the lower limit of stability of water at 90 °C and 80 atm. Calculations show that equilibrium with amakinite, the rare ferrous analogue of brucite, is more likely than equilibrium with brucite. This allows for computing in situ pH values close to 8 and thus mildly alkaline, while pH measured on board on vent fluids at 25 °C is higher than 10. This is in favour of the occurrence of ferrous hydroxide deeper in the root of the hydrothermal system where temperature is higher and pH are lower compared to seafloor vents where the fluids discharge. Secondary oxidation of amakinite, thanks to the recurrent circulation of seawater in the hydrothermal conduits, will necessarily lead to fougerite formation.
To deepen this question, several lines of investigation are finally proposed, including e.g., the stability of fougerite at elevated temperatures and pressures, its reactivity with key elements for life such as C, N, P, Mo, Ni, S etc. and its potential role for free energy conversion and basic functions of metabolism.
... The environmental scarcity of Mo and W may then early on have forced life to devise (organic) alternatives to these metals resulting in quinones and flavins taking over the respective tasks. Alternatively, these aromats may have been produced as side products in disequilibrium-converting processes performed by a specific mineral (see [47,48] and Section 6) and thus may have been woven into the fabric of early metabolic reactions almost from the beginning. In any case, we would like to emphasize that, if quinones and flavins did indeed play pivotal roles already at life's onset, these roles would be dramatically different from those of organic building blocks envisaged by primordial soup scenarios. ...
... The mineral fougerite, however, belongs to an entirely different structural class. These are the layered anionic clays with solvent-accessible interstitial galleries [47,48,[50][51][52][53][54] (Figure 4). They distinguish themselves from solids such as greigite by several properties particularly pertinent to emergence-of-life scenarios: ...
... The above listed properties of GRs are certainly fascinating and potentially important for emergence of life scenarios. However, as we have tried to convey in Sections 1 and 6 as well as in a recent article [48], none of these properties by themselves can rationalize an emergence of life which would be in line with the 2 nd law of thermodynamics. Even the most intricate types of redox catalyses remain "catalyses", that is, they facilitate exergonic reactions rather than driving endergonic ones. ...
... The environmental scarcity of Mo and W may then early on have forced life to devise (organic) alternatives to these metals resulting in quinones and flavins taking over the respective tasks. Alternatively, these aromats may have been produced as side products in disequilibrium-converting processes performed by a specific mineral (see [47,48] and Section 6) and thus may have been woven into the fabric of early metabolic reactions almost from the beginning. In any case, we would like to emphasize that, if quinones and flavins did indeed play pivotal roles already at life's onset, these roles would be dramatically different from those of organic building blocks envisaged by primordial soup scenarios. ...
... The mineral fougerite, however, belongs to an entirely different structural class. These are the layered anionic clays with solvent-accessible interstitial galleries [47,48,[50][51][52][53][54] (Figure 4). They distinguish themselves from solids such as greigite by several properties particularly pertinent to emergence-of-life scenarios: ...
... The above listed properties of GRs are certainly fascinating and potentially important for emergence of life scenarios. However, as we have tried to convey in Sections 1 and 6 as well as in a recent article [48], none of these properties by themselves can rationalize an emergence of life which would be in line with the 2 nd law of thermodynamics. Even the most intricate types of redox catalyses remain "catalyses", that is, they facilitate exergonic reactions rather than driving endergonic ones. ...
Microorganisms are found in almost every conceivable niche of the Earth. They populate every habitable environment, and through their metabolic activity, affect the chemistry and physical properties of their surroundings. They are outstanding chemists and geoengineers, and they did this for billions of years, thus playing an important role in the evolution of the Earth and its atmosphere. Their presence within geologic media has a profound effect on themselves and on the chemical and physical properties of the surrounding environment. Obviously, today spectacular scientific breakthroughs take place between the boundaries of the disciplines of Geology, Paleontology, Chemistry, Physics, and Biology, and new scientific disciplines come up, such as Astrobiology and Geomicrobiology. It is the aim of this chapter to introduce the reader to the fascinating world of microorganisms, and to recognize their important role they have played in the history of the Earth, and still play, in altering our environment. A remarkable number of reactions catalyzed by microbial enzymes have been explored down to the level of protein structure, active site architecture, and specific roles of neighboring amino acid residues. Thus, a lot of once obscure microbiology can be understood nowadays at the atomic level. Notably, numerous geochemical processes observed in the past were discovered through recent years to be catalyzed by microbes, except for those occurring at temperatures beyond 120 °C, the thermal borderline of living organisms. It is the study of microbial interactions with geological media, which advances the exciting field of Geomicrobiology. To speak with microbiologist Bernhard Schink, author of the chapter entitled Microbes: Masters of the Global Element Cycles: “If - after all the great discoveries in chemistry through the last 150 years - chemists may have been tempted to claim “it is all chemistry out there” I tend to oppose: “it is all microbiology - using a highly refined microbial biochemistry”.
... The green rust mineral fougerite is a mixed-valence redox-flexible semi-conducting naturally-occurring anionic clay, dosed with Mg 2+ , Ni 2+ , Mn 2+ , and Co 2+ [146,147]. Fougerite's extensive inner surfaces appear to provide the 'mechanistic' potential to fill the roles of the redox-and pH-converter that enabled life's emergence by driving endergonic-thermodynamically uphill-processes [41,43,62,130,145,[148][149][150][151]. And there was certainly no want for fougerite in the all-enveloping early ocean-the mineral precursor to the diagenetic magnetite comprising the first known banded iron formation outcropping in western Greenland [45,59,60,[152][153][154]. Mimicking this natural process of precipitation and transformation, Konstantinos Simeonidis and his collaborators [155] have generated green rust on a path to nanometric idiomorphic crystals of magnetite-a mineral with potential in catalysis, biotechnology and water remediation, though it is inimical to membrane formation. ...
... Yet to be tested are (i) the presumed potential of green rust situated in the membrane to also act as a proton wire, a proton pyrophosphatase, methane monooxygenase, polymerase and (ii) as an engine of synthesis in the production of aromatic rings (cf. quinones and flavins) [62,65,130,145,150,151,[160][161][162]. ...
... Yet to be tested are i) the presumed potential of green rust situated in the membrane to also act as a proton wire, a proton pyrophosphatase, methane monooxygenase, polymerase and ii) as an engine of synthesis in the production of aromatic rings (cf. quinones and flavins) [62,65,130,145,150,151,[160][161][162]. In the AVT fougerite nano-to micro-crystals comprise the mid and outer portions of an inorganic membrane (see Figure 5) precipitated by-but separating the acidulous ocean from-the alkaline hydrothermal spring waters [145,150,151]. ...
Life cannot emerge on a planet or moon without the appropriate electrochemical disequilibria and the minerals that mediate energy-dissipative processes. Here, it is argued that four minerals, olivine ([Mg>Fe]2SiO4), bridgmanite ([Mg,Fe]SiO3), serpentine ([Mg,Fe,]2-3Si2O5[OH)]4), and pyrrhotite (Fe(1−x)S), are an essential requirement in planetary bodies to produce such disequilibria and, thereby, life. Yet only two minerals, fougerite ([Fe2+6xFe3+6(x−1)O12H2(7−3x)]2+·[(CO2−)·3H2O]2−) and mackinawite (Fe[Ni]S), are vital—comprising precipitate membranes—as initial “free energy” conductors and converters of such disequilibria, i.e., as the initiators of a CO2-reducing metabolism. The fact that wet and rocky bodies in the solar system much smaller than Earth or Venus do not reach the internal pressure (≥23 GPa) requirements in their mantles sufficient for producing bridgmanite and, therefore, are too reduced to stabilize and emit CO2—the staple of life—may explain the apparent absence or negligible concentrations of that gas on these bodies, and thereby serves as a constraint in the search for extraterrestrial life. The astrobiological challenge then is to search for worlds that (i) are large enough to generate internal pressures such as to produce bridgmanite or (ii) boast electron acceptors, including imported CO2, from extraterrestrial sources in their hydrospheres.
... Important though ATP is, clearly ATP synthetase itself is much too complicated to have been available at life's onset. Indeed, the discovery by Baltscheffsky et al. (1966) that inorganic pyrophosphate (PPi), situated in the membrane, can act as 'energy donor' in an Fougerite modeled as a ready-made multifunctional motor enzyme/pump precursor set in the inorganic membrane, wherein it reduces nitrate drawn from the ocean (curved blue arrow to the left) to aminogen or ammonium, or nitrite to NO, N 2 O, and N 2 , vectored from 'left' to 'right' within the hydrate galleries (Hansen et al., 2001;Génin et al., 2005Génin et al., , 2006Trolard et al., 2007Trolard et al., , 2022Trolard and Bourrié, 2012;Gerbois et al., 2014;Russell, 2018;Duval et al., 2019Duval et al., , 2020. At the same time and in theory, methane would be converted to a methyl group by NO (Kampschreur et al., 2011;Nitschke and Russell, 2013). ...
... Barge et al. (2019Barge et al. ( , 2020 show that in the same circumstances, pyruvate can be aminated to alanine and oxalate to glycine. Hydrazine is another speculative product (Duval et al., 2020). Note that an anion-binding pocket forms by the oxidation of the opposed iron molecules as they are confronted with nitrate which is thereby reduced . ...
The demonstration by Ivan Barnes et al. that the serpentinization of fresh Alpine-type ultramafic rocks results in the exhalation of hot alkaline fluids is foundational to the submarine alkaline vent theory (AVT) for life’s emergence to its ‘improbable’ thermodynamic state. In AVT, such alkaline fluids ≤ 150°C, bearing H 2 > CH 4 > HS ⁻ —generated and driven convectively by a serpentinizing exothermic mega-engine operating in the ultramafic crust—exhale into the iron-rich, CO 2 > > > NO 3 ⁻ -bearing Hadean ocean to result in hydrothermal precipitate mounds comprising macromolecular ferroferric-carbonate oxyhydroxide and minor sulfide. As the nanocrystalline minerals fougerite/green rust and mackinawite (FeS), they compose the spontaneously precipitated inorganic membranes that keep the highly contrasting solutions apart, thereby maintaining redox and pH disequilibria. They do so in the form of fine chimneys and chemical gardens. The same disequilibria drive the reduction of CO 2 to HCOO ⁻ or CO, and the oxidation of CH 4 to a methyl group—the two products reacting to form acetate in a sequence antedating the ‘energy-producing’ acetyl coenzyme-A pathway. Fougerite is a 2D-layered mineral in which the hydrous interlayers themselves harbor 2D solutions, in effect constricted to ~ 1D by preferentially directed electron hopping/tunneling, and proton Gröthuss ‘bucket-brigading’ when subject to charge. As a redox-driven nanoengine or peristaltic pump, fougerite forces the ordered reduction of nitrate to ammonium, the amination of pyruvate and oxalate to alanine and glycine, and their condensation to short peptides. In turn, these peptides have the flexibility to sequester the founding inorganic iron oxyhydroxide, sulfide, and pyrophosphate clusters, to produce metal- and phosphate-dosed organic films and cells. As the feed to the hydrothermal mound fails, the only equivalent sustenance on offer to the first autotrophs is the still mildly serpentinizing upper crust beneath. While the conditions here are very much less bountiful, they do offer the similar feed and disequilibria the survivors are accustomed to. Sometime during this transition, a replicating non-ribosomal guidance system is discovered to provide the rules to take on the incrementally changing surroundings. The details of how these replicating apparatuses emerged are the hard problem, but by doing so the progenote archaea and bacteria could begin to colonize what would become the deep biosphere. Indeed, that the anaerobic nitrate-respiring methanotrophic archaea and the deep-branching Acetothermia presently comprise a portion of that microbiome occupying serpentinizing rocks offers circumstantial support for this notion. However, the inescapable, if jarring conclusion is drawn that, absent fougerite/green rust, there would be no structured channelway to life.
... Both cationic clays and anionic clays have been regarded as possible sites for the origins of life. [68,74,[76][77][78][79][80][81][82]. ...
... Examples of anionic clays are Layered Double Hydroxides, such as green rust [82]. Anions commonly found in the interlayers of anionic clays are chloride, nitrate, and carbonate [83]. ...
Intracellular potassium concentrations, [K+], are high in all types of living cells, but the origins of this K+ are unknown. The simplest hypothesis is that life emerged in an environment that was high in K+. One such environment is the spaces between the sheets of the clay mineral mica. The best mica for life’s origins is the black mica, biotite, because it has a high content of Mg++ and because it has iron in various oxidation states. Life also has many of the characteristics of the environment between mica sheets, giving further support for the possibility that mica was the substrate on and within which life emerged. Here, a scenario for life’s origins is presented, in which the necessary processes and components for life arise in niches between mica sheets; vesicle membranes encapsulate these processes and components; the resulting vesicles fuse, forming protocells; and eventually, all of the necessary components and processes are encapsulated within individual cells, some of which survive to seed the early Earth with life. This paper presents three new foci for the hypothesis of life’s origins between mica sheets: (1) that potassium is essential for life’s origins on Earth; (2) that biotite mica has advantages over muscovite mica; and (3) that micaceous clay is a better environment than isolated mica for life’s origins.
... Both cationic clays and anionic clays have been regarded as possible sites for the origins of life. [68,74,[76][77][78][79][80][81][82]. ...
... Examples of anionic clays are Layered Double Hydroxides, such as green rust [82]. Anions commonly found in the interlayers of anionic clays are chloride, nitrate, and carbonate [83]. ...
Intracellular potassium concentrations, [K+], are high in all types of living cells, but the origins of this K+ are unknown. The simplest hypothesis is that life emerged in an environment that was high in K+. One such environment is the spaces between the sheets of the clay mineral, mica. The best mica for life’s origins is the black mica, biotite, because it has a high content of Mg++ and it has iron in various oxidation states. Life also has many of the characteristics of the environment between mica sheets, giving further support for the possibility that mica was the substrate on and within which life emerged.
... One such benefit is the free exchanges of molecules and molecular complexes between mica and the larger diverse environment of the surrounding nonmicaceous clay-and the environment beyond the clay. Research on life's origins in clay is extensive and includes these publications in the last decade (57)(58)(59)(60)(61)(62). ...
Reproducible imaging of DNA by atomic force microscopy was a useful predecessor to Ned Seeman's DNA nano-technology. Many of the products of DNA nanotechnology were imaged in the atomic force microscope. The mica substrate used in this atomic force microscopy research formed the inspiration for the hypothesis that micaceous clay was a likely habitat for the origins of life. Montmorillonite clay has been a successful substrate for the polymerization of amino acids and nucleotides into peptides and DNA oligomers in research on life's origins. Mica and montmorillonite have the same anionic lattice, with a hexagonal spacing of 0.5 nm. Micas are nonswelling clays, with potassium ions (K þ) holding the crystal sheets together, providing a stable environment for the processes and molecular complexes needed for the emergence of living cells. Montmorillonite crystal sheets are held together by smaller sodium ions (Na þ), which results in swelling and shrinking during wet-dry cycles, providing a less stable environment. Also, the cells in all types of living systems have high intracellular K þ concentrations, which makes mica a more likely habitat for the origins of life than montmorillonite. Finally, moving mica sheets provides mechanical energy at the split edges of the sheets in mica ''books.'' This mechanical energy of mica sheets, moving open and shut, in response to fluid flow, may have preceded chemical energy at life's origins, powering early prebiotic processes, such as the formation of covalent bonds, the interactions of molecular complexes, and the budding off of protocells before the molecular mechanism of cell division had developed.
... These findings provide solid evidence that these biocatalysts can be presented before the protein and RNA world, and thereby offer a solution to the "chicken and egg" at life's beginnings [109,110]. All of these inorganic enzyme activities, due to their specialized crystal structure including but not limited to their surface area, do support the metabolism-first hypothesis, not the replicator-first scenario [111,112], and are also to be considered highly important in the context of new theories about the emergence of life [113][114][115]. ...
... These vents are loci for the supply of the gaseous components such as CO 2 , CH 4 , and N 2 which are essential components that form organic molecules and they also supply nutrients such as H 2 , P, Mn, Fe, Ni, Se, Zn, Mo that are useful for the metabolism of microbes (Tunnicliffe and Fowler, 1996;Condie, 2016). Clay minerals act as catalysts in the formation of organic compounds and these compounds are subsequently adsorbed onto the clays (Duval et al., 2020). Hence, the study of hydrothermal and sea water signatures in the carbonaceous phyllites from the present study has been attempted to understand the depositional conditions during the Precambrian time. ...
Carbonaceous shales formed in anoxic, deep marine environment are depocenters of prolific microbial life and rich sources of organic matter. In the present study, geochemical and organic carbon isotopic (δ¹³Corg) signatures of carbonaceous phyllites from Archean Chitradurga, Gadag, Sandur, Shimoga greenstone belts and Proterozoic Cuddapah basin of Dharwar Craton were studied to understand the Precambrian depositional environment by delineating the similarities and differences in the Archean and Proterozoic samples. Both Archean and Proterozoic carbonaceous phyllites are fine grained siliceous in nature with depleted CaO, MgO and alkalies. The REE concentrations in most of the Archean samples are characterized by conspicuous positive Europium anomalies while the Proterozoic counterparts display feebly positive ratios indicating hydrothermal source. The Archean samples possess elevated Chemical Index of Alteration (CIA), Chemical Index of Weathering (CIW), Plagioclase Index of Weathering (PIA) values reflecting extreme weathering conditions while the Proterozoic carbonaceous phyllites are confined to moderate weathering conditions. Cr/Th, La/Sc, Th/Sc and Co/Th indicate mafic provenance and the Cr-Zr relationship suggests deep sea depositional setting for both Archean and Proterozoic carbonaceous phyllites. The Archean carbonaceous phyllites indicate humid to semi-humid paleoclimate conditions while the Proterozoic samples are restricted to humid palaeoclimatic conditions which is evident from Sr/Cu ratios. V/(V + Ni) ratios indicate fluctuating dysoxic to euxinic redox conditions for the Archean samples while the Proterozoic samples display euxinic conditions. The predominantly negative δ¹³Corg values of Chitradurga (−38.5‰ to −14.2‰ VPDB), Gadag (−24.3‰ to −8.06‰ VPDB), Sandur (−24.8‰ to −29.2‰ VPDB), Shimoga (−24.6‰ to −11.8‰ VPDB) and Cuddapah (−30.19 to −13.98‰ VPDB) suggest the role of primitive life forms through biological processes during the deposition of organic matter.
... One such benefit is the free exchanges of molecules and molecular complexes between mica and the larger diverse environment of the surrounding nonmicaceous clay-and the environment beyond the clay. Research on life's origins in clay is extensive and includes these publications in the last decade (57)(58)(59)(60)(61)(62). ...
... The current knowledge about the formation of HCN-derived polymers shows that their features depend on synthesis conditions, including concentration, temperature, presence of oxygen, time of reaction, and raw material [11,46,48,[53][54][55]69,72]. Alkaline hydrothermal systems have been pointed out as very versatile and crucial environments for chemical evolution and, eventually, for origin of life scenarios [38][39][40]45,[90][91][92][93][94][95]. Considering the new perspectives of prebiotic chemistry (that suggest to take into account the dynamism of environments, as well as the interactions among their geochemical variables; [29,46,96]), we tested the role of serpentinite during the polymerization of HCN as a first approximation of a simple simulation of an alkaline hydrothermal system. ...
Hydrogen cyanide, HCN, is considered a fundamental molecule in chemical evolution. The named HCN polymers have been suggested as precursors of important bioorganics. Some novel researches have focused on the role of mineral surfaces in the hydrolysis and/or polymerization of cyanide species, but until now, their role has been unclear. Understanding the role of minerals in chemical evolution processes is crucial because minerals undoubtedly interacted with the organic molecules formed on the early Earth by different process. Therefore, we simulated the probable interactions between HCN and a serpentinite-hosted alkaline hydrothermal system. We studied the effect of serpentinite during the thermolysis of HCN at basic conditions (i.e., HCN 0.15 M, 50 h, 100 °C, pH > 10). The HCN-derived thermal polymer and supernatant formed after treatment were analyzed by several complementary analytical techniques. The results obtained suggest that: I) the mineral surfaces can act as mediators in the mechanisms of organic molecule production such as the polymerization of HCN; II) the thermal and physicochemical properties of the HCN polymer produced are affected by the presence of the mineral surface; and III) serpentinite seems to inhibit the formation of bioorganic molecules compared with the control (without mineral).
... Either way, many of the research challenges for the hypothesized role(s) of fougerite-dosed with various trace elements and anionsare similar. Such research addressing the submarine acid v. alkaline milieu calls for the further employment of tried-and-tested microfluidic and nano-crystallographic techniques [192,201,[202][203][204][205][206][207]224,254,[296][297][298][299][300][301][302]310,[327][328][329][330][331][332][333][334][335][336][337][338]. We enumerate some possible developments from, expectations of, and tests for, the AVT below: ...
The assumption that there was a “water problem” at the emergence of life—that the Hadean Ocean was simply too wet and salty for life to have emerged in it—is here subjected to geological and experimental “reality checks”. The “warm little pond” that would take the place of the submarine alkaline vent theory (AVT), as recently extolled in the journal Nature, flies in the face of decades of geological, microbiological and evolutionary research and reasoning. To the present author, the evidence refuting the warm little pond scheme is overwhelming given the facts that (i) the early Earth was a water world, (ii) its all-enveloping ocean was never less than 4 km deep, (iii) there were no figurative “Icelands” or “Hawaiis”, nor even an “Ontong Java” then because (iv) the solidifying magma ocean beneath was still too mushy to support such salient loadings on the oceanic crust. In place of the supposed warm little pond, we offer a well-protected mineral mound precipitated at a submarine alkaline vent as life’s womb: in place of lipid membranes, we suggest peptides; we replace poisonous cyanide with ammonium and hydrazine; instead of deleterious radiation we have the appropriate life-giving redox and pH disequilibria; and in place of messy chemistry we offer the potential for life’s emergence from the simplest of geochemically available molecules and ions focused at a submarine alkaline vent in the Hadean—specifically within the nano-confined flexible and redox active interlayer walls of the mixed-valent double layer oxyhydroxide mineral, fougerite/green rust comprising much of that mound.
... This suggestion of aquatic habitats on land, as opposed to in the ocean, has been followed up in a number of papers on the location and mechanism of the origin of life (e.g. Follmann & Brownson 2009;Damer & Deamer 2020;Toner & Catling 2020); however, neither a site nor an associated mechanism, can yet explain life's origin (Kitadai & Maruyama 2018;Duval et al. 2020). ...
The earliest branching cyanobacterium, Gloeobacter, exhibits a number of ancestral traits including the lack of thylakoids. It occurs epilithically in microbial mats, both subaerially and submerged in low-salinity habitats. These habitats and the absence of thylakoids are associated with the occurrence of membrane-associated photosynthetic processes in the plasma membrane, possibly limiting the rate of both assembly and reassembly of the oxygen-evolving complex, as well as the photosynthetic rate and in vitro growth rate. These factors interact with the occurrence of Gloeobacter in mats to constrain productivity in nature. Traits found in living Gloeobacter, with the probable time of origin of oxygenic photosynthesis and diversification of cyanobacteria, can be related to the possible role of oxygenic primary productivity and organic carbon burial on land during the early Earth in low-salinity environments around the time of the global oxidation event.
... The magmatic production of Fe/Mg clay minerals evidenced here in a martian meteorite archetypal of the martian crust portends that a possibly significant fraction of the Fe/ Mg clay minerals detected on Mars so far may not be the products of the aqueous alteration of preexisting silicates by (sub)surface water, questioning a priori the past habitability of Mars. Yet the magmatic Fe/Mg clay minerals described here have chemical and physical properties that offer fantastic opportunities for (prebiotic) organic reactions (Russell and Martin, 2004;Duval et al., 2020). In fact, in addition to enabling electron transfer, their high Fe content may promote the synthesis and breakdown of universal metabolic precursors (Stucki, 2006), while their high Mg content may prompt both ribozyme-catalyzed and non-enzymatic RNA copying reactions (Adamala and Szostak, 2013). ...
Mars was habitable in its early history, but the consensus is that it is quite inhospitable today, in particular because its modern climate cannot support stable liquid water at the surface. Here, we report the presence of magmatic Fe/Mg clay minerals within the mesostasis of the martian meteorite NWA 5790, an unaltered 1.3 Ga nakhlite archetypal of the martian crust. These magmatic clay minerals exhibit a vesicular texture that forms a network of microcavities or pockets, which could serve as microreactors and allow molecular crowding, a necessary step for the emergence of life. Because their formation does not depend on climate, such niches for emerging life may have been generated on Mars at many periods throughout its history, regardless of the stability or availability of liquid water at the surface.
Soils are formed from rocks over a period of time by weathering process. Soils are essential for plants for better growth and yield. Soil degradation leads to the loss of soil micro‐ and macronutrients. Nutrient poor soils are unable to produce healthy food which is essential for consumers like human and animals. Over two billion people on this planet suffer from micronutrient deficiencies and various metabolic disorders. Role of 18 nutrients, viz. B, C, Ca, Cl, Cu, Fe, H, K, Mg, Mn, Mo, N, Na, O, P, S, Si, and Zn, which are essential for plant growth and yield and human health, is well established in science. In this chapter, an attempt has been made to highlight the importance of geology and public health, medical geology/geomedicine, environmental medicine, minerals including clays and human health, and georesources and health. Importance of minerals for human and animal health is explained with specific examples. The ancient seers found that drugs of different origin (herbal, metal, or animal) in addition to codes of conduct and dietary regulations are suitable tools to address several diseases. Use of metallic preparations [(Bhasmas = ash and bhasmikarana (=process of preparation of metallic ash which is zero valent)] in healthcare is unique. Bhasmikarana process with mercury, gold, silver, lead, zinc, copper, etc. was frequently used by seers of the Indian tradition to treat different diseases with great certainty of cure. It is generally claimed that these metals are detoxified during the highly complex bhasmikarana process described in Ayurveda especially Rasashastra manuscripts. The Ayurvedic system of medicine has been in practice in India for millennia. Charaka Samhita, one of the scheduled books of Ayurveda, also holds ample references regarding the use of metals for different purposes; selected examples are enumerated in this chapter.
The research on inorganic nanozymes remains very active since the first paper on the “intrinsic peroxidase-like properties of ferromagnetic nanoparticles” was published in Nature Nanotechnology in 2007. However, there is still the question, “What are the inorganic nanozymes?” Inorganic nanomaterials with intrinsic enzyme-like activity were not generated from artificial synthesis processing. The unique architecture of the metal site in inorganic nanomaterials contributes to the specificity and catalytic behavior described by the classic Michaelis-Menten equation, just like an enzyme (protein) or ribozyme (RNA), and as supported by density functional theory calculations. The discovered inorganic nanozymes participate in many key biological catalysis processes, especially related to oxygen. Possibly, they were essential to the emergence of life before RNAs and proteins, and they still play a crucial role in our daily lives, especially from the view of biogeochemistry. These inorganic nanozymes are classified as “inorganic enzymes”, in line with the existing classifications of enzymes (proteins) and ribozymes (RNAs) as biocatalysts. By drawing inspiration from the metal architecture in nanomaterials, scientists can design artificial biocatalysts or functionalized nanozymes that are more stable and specific. It is necessary to pursue research to utilize inorganic nanozymes in current biomedical applications as well as comprehend how they impact our Earth’s environment.
The second law of thermodynamics leaves no doubt that life on planet Earth and its inherent substantial decrease in entropy is fundamentally based on mechanisms converting environmental free energy into the spatial and temporal order of metabolic processes. This argument holds for present life as much as it does for its very beginnings some 4 billion years ago. In this contribution, we try to strip down free energy conversion in extant life (known as “bioenergetics” to the biologists) to its basic principles with the aim to potentially retrodict the nature of the pre‐biotic precursor which drove life into existence. We demonstrate that these basic principles are deeply rooted in aqueous electrochemistry and strongly rely on inorganic redox compounds. The question of life's emergence, generally considered to fall into the realm of organic chemistry, should therefore rather be recognized as an electrochemical problem and its ultimate elucidation will need to strongly implicate the community of electrochemical scientists.
Minerals are widely assumed to protect organic matter (OM) from degradation in the environment, promoting the persistence of carbon in soil and sediments. In this Review, we describe the mechanisms and processes operating at the mineral–organic interface as they relate to OM transformation dynamics. A broad set of interactions occur, with minerals adsorbing organic compounds to their surfaces and/or acting as catalysts for organic reactions. Minerals can serve as redox partners for OM through direct electron transfer or by generating reactive oxygen species, which then oxidize OM. Finally, the compartmentalization of soil and sediment by minerals creates unique microsites that host diverse microbial communities. Acknowledgement of this multiplicity of interactions suggests that the general assumption that the mineral matrix provides a protective function for OM is overly simplistic. Future work must recognize adsorption as a condition for further reactions instead of as a final destination for organic adsorbates, and should consider the spatial and functional complexity that is characteristic of the environments where mineral–OM interactions are observed.
From hydrolysis of phosphate ester to the emergence of life
We here review the extraordinary mineralogical properties of green rusts and their naturally occurring form, fougerite, and discuss the pertinence of these properties within the alkaline hydrothermal vent (AHV) hypothesis for life's emergence. We put forward an extended version of the AHV scenario which enhances the conformity between extant life and its earliest progenitor by extensively making use of fougerite's mechanistic and catalytic particularities.
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.
A mixture of sugar diphosphates is produced in reactions between small aldehyde phosphates catalysed by layered double hydroxide (LDH) clays under plausibly prebiotic conditions. A subset of these, pentose diphosphates, constitute the backbone subunits of nucleic acids capable of base pairing, which is not the case for the other products of these LDH-catalysed reactions. Not only that, but to date no other polymer found capable of base pairing—and therefore information transfer—has a backbone for which its monomer subunits have a plausible prebiotic synthesis, including the ribose-5-phosphate backbone subunit of RNA. Pentose diphosphates comprise the backbone monomers of pentopyranose nucleic acids, some of the strongest base pairing systems so far discovered. We have previously proposed that the first base pairing interactions were between purine nucleobase precursors, and that these were weaker and less specific than standard purine-pyrimidine interactions. We now propose that the inherently stronger pairing of pentopyranose nucleic acids would have compensated for these weaker interactions, and produced an informational polymer capable of undergoing nonenzymatic replication. LDH clays might also have catalysed the synthesis of the purine nucleobase precursors, and the polymerization of pentopyranose nucleotide monomers into oligonucleotides, as well as the formation of the first lipid bilayers.
Korenaga and coworkers presented evidence to suggest that the Earth’s mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense, and relatively stable oceanic crust. In that setting, two distinct and major types of sub-marine hydrothermal vents were active: ~400 °C acidic springs, whose effluents bore vast quantities of iron into the ocean, and ~120 °C, highly alkaline, and reduced vents exhaling from the cooler, serpentinizing crust some distance from the heads of the plumes. When encountering the alkaline effluents, the iron from the plume head vents precipitated out, forming mounds likely surrounded by voluminous exhalative deposits similar to the banded iron formations known from the Archean. These mounds and the surrounding sediments, comprised micro or nano-crysts of the variable valence FeII/FeIII oxyhydroxide known as green rust. The precipitation of green rust, along with subsidiary iron sulfides and minor concentrations of nickel, cobalt, and molybdenum in the environment at the alkaline springs, may have established both the key bio-syntonic disequilibria and the means to properly make use of them—the elements needed to effect the essential inanimate-to-animate transitions that launched life. Specifically, in the submarine alkaline vent model for the emergence of life, it is first suggested that the redox-flexible green rust micro- and nano-crysts spontaneously precipitated to form barriers to the complete mixing of carbonic ocean and alkaline hydrothermal fluids. These barriers created and maintained steep ionic disequilibria. Second, the hydrous interlayers of green rust acted as engines that were powered by those ionic disequilibria and drove essential endergonic reactions. There, aided by sulfides and trace elements acting as catalytic promoters and electron transfer agents, nitrate could be reduced to ammonia and carbon dioxide to formate, while methane may have been oxidized to methyl and formyl groups. Acetate and higher carboxylic acids could then have been produced from these C1 molecules and aminated to amino acids, and thence oligomerized to offer peptide nests to phosphate and iron sulfides, and secreted to form primitive amyloid-bounded structures, leading conceivably to protocells.
Electron bifurcation is here described as a special case of the continuum of electron transfer reactions accessible to two-electron redox compounds with redox cooperativity. We argue that electron bifurcation is foremost an electrochemical phenomenon based on (a) strongly inverted redox potentials of the individual redox transitions, (b) a high endergonicity of the first redox transition, and (c) an escapement-type mechanism rendering completion of the first electron transfer contingent on occurrence of the second one. This mechanism is proposed to govern both the traditional quinone-based and the newly discovered flavin-based versions of electron bifurcation. Conserved and variable aspects of the spatial arrangement of electron transfer partners in flavoenzymes are assayed by comparing the presently available 3D structures. A wide sample of flavoenzymes is analyzed with respect to conserved structural modules and three major structural groups are identified which serve as basic frames for the evolutionary construction of a plethora of flavin-containing redox enzymes. We argue that flavin-based and other types of electron bifurcation are of primordial importance to free energy conversion, the quintessential foundation of life, and discuss a plausible evolutionary ancestry of the mechanism.
Flavin-based electron bifurcation is a newly discovered mechanism, by which a hydride electron pair from NAD(P)H, coenzyme F420H2, H2, or formate is split by flavoproteins into one-electron with a more negative reduction potential and one with a more positive reduction potential than that of the electron pair. Via this mechanism microorganisms generate low- potential electrons for the reduction of ferredoxins (Fd) and flavodoxins (Fld). The first example was described in 2008 when it was found that the butyryl-CoA dehydrogenase-electron-transferring flavoprotein complex (Bcd-EtfAB) of Clostridium kluyveri couples the endergonic reduction of ferredoxin (E0' = -420 mV) with NADH (-320 mV) to the exergonic reduction of crotonyl-CoA to butyryl-CoA (-10 mV) with NADH. The discovery was followed by the finding of an electron-bifurcating Fd- and NAD-dependent [FeFe]-hydrogenase (HydABC) in Thermotoga maritima (2009), Fd-dependent transhydrogenase (NfnAB) in various bacteria and archaea (2010), Fd- and H2-dependent heterodisulfide reductase (MvhADG-HdrABC) in methanogenic archaea (2011), Fd- and NADH-dependent caffeyl-CoA reductase (CarCDE) in Acetobacterium woodii (2013), Fd- and NAD-dependent formate dehydrogenase (HylABC-FdhF2) in Clostridium acidi-urici (2013), Fd- and NADP-dependent [FeFe]-hydrogenase (HytA-E) in Clostridium autoethanogrenum (2013), Fd(?)- and NADH-dependent methylene-tetrahydrofolate reductase (MetFV-HdrABC-MvhD) in Moorella thermoacetica (2014), Fd- and NAD-dependent lactate dehydrogenase (LctBCD) in A. woodii (2015), Fd- and F420H2-dependent heterodisulfide reductase (HdrA2B2C2) in Methanosarcina acetivorans (2017), and Fd- and NADH-dependent ubiquinol reductase (FixABCX) in Azotobacter vinelandii (2017). The electron-bifurcating flavoprotein complexes known to date fall into four groups that have evolved independently, namely those containing EtfAB (CarED, LctCB, FixBA) with bound FAD, a NuoF homolog (HydB, HytB, or HylB) harboring FMN, NfnB with bound FAD, or HdrA harboring FAD. All these flavoproteins are cytoplasmic except for the membrane-associated protein FixABCX. The organisms-in which they have been found-are strictly anaerobic microorganisms except for the aerobe A. vinelandii. The electron-bifurcating complexes are involved in a variety of processes such as butyric acid fermentation, methanogenesis, acetogenesis, anaerobic lactate oxidation, dissimilatory sulfate reduction, anaerobic- dearomatization, nitrogen fixation, and CO2 fixation. They contribute to energy conservation via the energy-converting ferredoxin: NAD⁺ reductase complex Rnf or the energy-converting ferredoxin-dependent hydrogenase complex Ech. This Review describes how this mechanism was discovered.
Phosphorus ester hydrolysis is one of the key chemical processes in biological systems, including signaling, free-energy transaction, protein synthesis, and maintaining the integrity of genetic material. Hydrolysis of this otherwise kinetically stable phosphoester and/or phosphoanhydride bond is induced by enzymes such as purple acid phosphatase. Here, I report that, as in previously reported aged inorganic iron ion solutions, the iron oxide nanoparticles in the solution, which are trapped in a dialysis membrane tube filled with the various iron oxides, significantly promote the hydrolysis of the various phosphate esters, including the inorganic polyphosphates, with enzyme-like kinetics. This observation, along with those of recent studies of iron oxide, vanadium pentoxide, and molybdenum trioxide nanoparticles that behave as mimics of peroxidase, bromoperoxidase, and sulfite oxidase, respectively, indicates that the oxo-metal bond in the oxide nanoparticles is critical for the function of these corresponding natural metalloproteins. These inorganic biocatalysts challenge the traditional concept of replicator-first scenarios and support the metabolism-first hypothesis. As biocatalysts, these inorganic nanoparticles with enzyme-like activity may work in natural terrestrial environments and likely were at work in early Earth environments as well. They may have played an important role in the C, H, O, S, and P metabolic pathway with regard to the emergence and early evolution of life. Key Words: Enzyme-Hydrolysis-Iron oxide-Nanoparticles-Origin of life-Phosphate ester. Astrobiology 18, 294-310.
Some seventy years ago, John Desmond Bernal proposed a role for clays in the origin of life. While much research has since been dedicated to the study of silicate clays, layered double hydroxides, believed to be common on the early Earth, have received only limited attention. Here we examine the role that layered hydroxides could have played in prebiotic peptide formation. We demonstrate how these minerals can concentrate, align and act as adsorption templates for amino acids, and during wetting-drying cycles, promote peptide bond formation. This enables us to propose a testable mechanism for the growth of peptides at layered double hydroxide interfaces in an early Earth environment. Our results provide insights into the potential role of mineral surfaces in mimicking aspects of biochemical reaction pathways.
Far-from-equilibrium thermodynamics underpins the emergence of life, but how has been a long-outstanding puzzle. Best candidate theories based on the maximum entropy production principle could not be unequivocally proven, in part due to complicated physics, unintuitive stochastic thermodynamics, and the existence of alternative theories such as the minimum entropy production principle. Here, we use a simple, analytically solvable, one-dimensional bistable chemical system to demonstrate the validity of the maximum entropy production principle. To generalize to multistable stochastic system, we use the stochastic least-action principle to derive the entropy production and its role in the stability of nonequilibrium steady states. This shows that in a multistable system, all else being equal, the steady state with the highest entropy production is favored, with a number of implications for the evolution of biological, physical, and geological systems.
As many of the methanogens first encountered at hydrothermal vents were thermophilic to hyperthermophilic and comprised one of the lower roots of the evolutionary tree, it has been assumed that methanogenesis was one of the earliest, if not the earliest, pathway to life. It being well known that hydrothermal springs associated with serpentinization also bore abiotic methane, it had been further assumed that emergent biochemistry merely adopted and quickened this supposed serpentinization reaction. Yet, recent hydrothermal experiments simulating serpentinization have failed to generate methane so far, thus casting doubt on this assumption. The idea that the inverse view is worthy of debate, that is, that methanotrophy was the earlier, is stymied by the "fact" that methanotrophy itself has been termed "reverse methanogenesis," so allotting the methanogens the founding pedigree. Thus, attempting to suggest instead that methanogenesis might be termed reverse methanotrophy would require "unlearning"-a challenge to the subconscious! Here we re-examine the "impossibility" of methanotrophy predating methanogenesis as in what we have termed, the "denitrifying methanotrophic acetogenic pathway". Advantages offered by such thinking is that methane would not only be a fuel but also a ready source of reduced carbon to combine with formate or carbon monoxide-available in hydrothermal fluids-to generate acetate, a target molecule of the first autotrophs. And the nitrate/nitrite required for the putative oxidation of methane with activated NO would also be a ready source of fixed nitrogen for amination reactions. Theoretical conditions for such a putative pathway would be met in a hydrothermal green rust-bearing exhalative pile and associated chimneys subject to proton and electron counter gradients. This hypothesis could be put to test in a high-pressure hydrothermal reaction chamber in which a cool carbonate/nitrate/nitrite-bearing early acidulous ocean simulant is juxtaposed across a precipitate membrane to an alkaline solution of hydrogen and methane. Key Words: Green rust-Methanotrophy-Nitrate reduction-Emergence of life. Astrobiology 17, xxx-xxx.
The new mineral mössbauerite (IMA2012−049), Fe 6 ³⁺ O 4 (OH) 8 [CO 3 ]·3H 2 O, is a member of the fougèrite group of the hydrotalcite supergroup. Thus, it has a layered double hydroxide-type structure, in which brucite-like layers [Fe ⁶ ³⁺ O 4 (OH) 8 ] ²⁺ are intercalated with CO 3 ²⁻ anions and water molecules. Mössbauerite is the fully oxidized analogue of fougèrite and trébeurdenite, related to them chemically by the exchange of (Fe ³⁺ O ²⁻ ) with (Fe ²⁺ OH ⁻ ). Mössbauerite, intimately intergrown with trébeurdenite, was discovered in intertidal gleys from Mont Saint-Michel Bay, France, along with quartz, feldspars and clay minerals. Mössbauerite is formed by the oxidation of the other members of the fougèrite group. Like them, it occurs as μm-scale platelets in gleys with restricted access to atmospheric O and decomposes rapidly when exposed to air. Identification and characterization of these minerals has relied on an electrochemical study of synthetic analogues and Mössbauer spectroscopy, which inspired the name of the new mineral.
Unlike fougèrite and trébeurdenite, which are blue-green, pure synthetic mössbauerite is orange in colour. Detailed optical and other physical properties could not be determined because of the small platelet size and instability. The hardness is probably 2−3, by analogy with other members of the supergroup and the density, calculated from unit-cell parameters, is 2.950 g/cm ³ . Synchrotron X-ray data indicate that the natural material is a nanoscale intergrowth of 2 T and 3T polytypes; the latter probably has the 3T 7 stacking sequence. The corresponding maximum possible space group symmetries are P m 1 and P 3 m 1. Unit-cell parameters for the 3 T cell are a = 3.032(7) Å, c = 22.258(4) = 367.420 Å and Z = ½.
Mössbauer spectroscopy at 78 K indicates that two distinct Fe ³⁺ environments exist in a 2:1 ratio. These are interpreted to be ordered within each layer, but without the development of a threedimensional superlattice. Mössbauerite undergoes gradual magnetic ordering at 70−80 K to a ferromagnetic state, below which it splits into three sextets S 1m , S 2m and S 3m , as measured at 15 K, and shows the same intensity ratio ½:⅙:⅓ as the three doublets for fougèrite D 1f , D 2f , D 3f in the paramagnetic state at 78 K. This suggests that there is also short-range coupling of interlayer carbonate anions with respect to the octahedral layers and that the 2D long-range order of carbonates in interlayers remains unchanged.
The present study investigates for the first time the reduction of nitrite by biogenic hydroxycarbonate green rusts, bio-GR(CO3), produced from the bioreduction of ferric oxyhydroxycarbonate (Fohc), a poorly crystalline solid phase, and of lepidocrocite, a well-crystallized Fe(III)-oxyhydroxide mineral. Results show a fast Fe(II) production from Fohc, which leads to the precipitation of bio-GR(CO3) particles that were roughly 2-fold smaller (2.3 ± 0.4 μm) than those obtained from the bioreduction of lepidocrocite (5.0 ± 0.4 μm). The study reveals that both bio-GR(CO3) are capable of reducing nitrite ions into gaseous nitrogen species such as NO, N2O, or N2 without ammonium production at neutral initial pH and that nitrite reduction proceeded to a larger extent with smaller particles than with larger ones. On the basis of the identification of intermediates and end-reaction products using X-ray diffraction and X-ray absorption fine structure (XAFS) spectroscopy at the Fe K-edge, our study shows the formation of hydroxy-nitrite green rust, GR(NO2), a new type of green rust 1, and suggests that the reduction of nitrite by biogenic GR(CO3) involves both external and internal reaction sites and that such a mechanism could explain the higher reactivity of green rust with respect to nitrite, compared to other mineral substrates possessing only external reactive sites.
Abstract This paper presents a reformulation of the submarine alkaline hydrothermal theory for the emergence of life in response to recent experimental findings. The theory views life, like other self-organizing systems in the Universe, as an inevitable outcome of particular disequilibria. In this case, the disequilibria were two: (1) in redox potential, between hydrogen plus methane with the circuit-completing electron acceptors such as nitrite, nitrate, ferric iron, and carbon dioxide, and (2) in pH gradient between an acidulous external ocean and an alkaline hydrothermal fluid. Both CO2 and CH4 were equally the ultimate sources of organic carbon, and the metal sulfides and oxyhydroxides acted as protoenzymatic catalysts. The realization, now 50 years old, that membrane-spanning gradients, rather than organic intermediates, play a vital role in life's operations calls into question the idea of "prebiotic chemistry." It informs our own suggestion that experimentation should look to the kind of nanoengines that must have been the precursors to molecular motors-such as pyrophosphate synthetase and the like driven by these gradients-that make life work. It is these putative free energy or disequilibria converters, presumably constructed from minerals comprising the earliest inorganic membranes, that, as obstacles to vectorial ionic flows, present themselves as the candidates for future experiments. Key Words: Methanotrophy-Origin of life. Astrobiology 14, xxx-xxx. The fixation of inorganic carbon into organic material (autotrophy) is a prerequisite for life and sets the starting point of biological evolution. (Fuchs, 2011 ) Further significant progress with the tightly membrane-bound H(+)-PPase family should lead to an increased insight into basic requirements for the biological transport of protons through membranes and its coupling to phosphorylation. (Baltscheffsky et al., 1999 ).
Green rusts (GRs) are mixed Fe(II)-Fe(III) hydroxides with a high reactivity towards organic and inorganic pollutants. GRs can be produced from ferric reducing or ferrous oxidizing bacterial activities. In this study, we investigated the capability of Klebsiella mobilis to produce iron minerals in the presence of nitrate and ferrous iron. This bacterium is well known to reduce nitrate using an organic carbon source as electron donor, but is unable to enzymatically oxidize Fe(II) species. During incubation, GR formation occurred as a secondary iron mineral precipitating on cell surfaces, resulting from Fe(II) oxidation by nitrite produced via bacterial respiration of nitrate. For the first time, we demonstrate GR formation by indirect microbial oxidation of Fe(II) (i.e. a combination of biotic/abiotic processes). These results therefore suggest that nitrate-reducing bacteria can potentially contribute to the formation of GR in natural environments. In addition, the chemical reduction of nitrite to ammonium by GR is observed, which gradually turns the GR into the end-product goethite. The nitrogen mass-balance clearly demonstrates that the total amount of ammonium produced corresponds to the quantity of bioreduced nitrate. These findings demonstrate how the activity of nitrate-reducing bacteria in ferrous environments may provide a direct link between the biogeochemical cycles of nitrogen and iron.
Layered double hydroxide (LDH) compounds are characterized by structures in which layers with a brucite-like structure carry a net positive charge, usually due to the partial substitution of trivalent octahedrally coordinated cations for divalent cations, giving a general layer formula [( M 1– x ²⁺ M ³⁺ x )(OH) 2 ] x + . This positive charge is balanced by anions which are intercalated between the layers. Intercalated molecular water typically provides hydrogen bonding between the brucite layers. In addition to synthetic compounds, some of which have significant industrial applications, more than 40 mineral species conform to this description. Hydrotalcite, Mg 6 Al 2 (OH) 16 [CO 3 ]·4H 2 O, as the longest-known example, is the archetype of this supergroup of minerals. We review the history, chemistry, crystal structure, polytypic variation and status of all hydrotalcite-supergroup species reported to date. The dominant divalent cations, M ²⁺ , that have been reported in hydrotalcite supergroup minerals are Mg, Ca, Mn, Fe, Ni, Cu and Zn; the dominant trivalent cations, M ³⁺ , are Al, Mn, Fe, Co and Ni. The most common intercalated anions are (CO3) 2– , (SO 4 ) 2– and Cl – ; and OH – , S 2– and [Sb(OH) 6 ]– have also been reported. Some species contain intercalated cationic or neutral complexes such as [Na(H 2 O) 6 ] ⁺ or [MgSO4]0. We define eight groups within the supergroup on the basis of a combination of criteria. These are (1) the hydrotalcite group, with M ²⁺ : M ³⁺ = 3:1 (layer spacing ∼7.8 Å); (2) the quintinite group, with M ²⁺ : M ³⁺ = 2:1 (layer spacing ∼7.8 Å); (3) the fougèrite group, with M ²⁺ = Fe ²⁺ , M ³⁺ = Fe ³⁺ in a range of ratios, and with O2– replacing OH– in the brucite module to maintain charge balance (layer spacing ∼7.8 Å); (4) the woodwardite group, with variable M ²⁺ : M ³⁺ and interlayer [SO4]2 –, leading to an expanded layer spacing of ∼8.9 Å; (5) the cualstibite group, with interlayer [Sb(OH)6]– and a layer spacing of ∼9.7 Å; (6) the glaucocerinite group, with interlayer [SO4]2– as in the woodwardite group, and with additional interlayer H2O molecules that further expand the layer spacing to ∼11 Å; (7) the wermlandite group, with a layer spacing of ∼11 Å, in which cationic complexes occur with anions between the brucite-like layers; and (8) the hydrocalumite group, with M ²⁺ = Ca ²⁺ and M ³⁺ = Al, which contains brucite-like layers in which the Ca:Al ratio is 2:1 and the large cation, Ca ²⁺ , is coordinated to a seventh ligand of 'interlayer' water.
The principal mineral status changes are as follows. (1) The names manasseite, sjögrenite and barbertonite are discredited; these minerals are the 2H polytypes of hydrotalcite, pyroaurite and stichtite, respectively. Cyanophyllite is discredited as it is the 1M polytype of cualstibite. (2) The mineral formerly described as fougèrite has been found to be an intimate intergrowth of two phases with distinct Fe ²⁺ :Fe ³⁺ ratios. The phase with Fe ²⁺ :Fe ³⁺ = 2:1 retains the name fougèrite; that with Fe ²⁺ :Fe ³⁺ = 1:2 is defined as the new species trébeurdenite. (3) The new minerals omsite (IMA2012-025), Ni2Fe ³⁺ (OH) 6 [Sb(OH) 6 ], and mössbauerite (IMA2012-049), Fe ³⁺ 6O 4 (OH) 8 [CO3]·3H 2 O, which are both in the hydrotalcite supergroup are included in the discussion. (4) Jamborite, carrboydite, zincaluminite, motukoreaite, natroglaucocerinite, brugnatellite and muskoxite are identified as questionable species which need further investigation in order to verify their structure and composition. (5) The ranges of compositions currently ascribed to motukoreaite and muskoxite may each represent more than one species. The same applies to the approved species hydrowoodwardite and hydrocalumite. (6) Several unnamed minerals have been reported which are likely to represent additional species within the supergroup.
This report has been approved by the Commission on New Minerals, Nomenclature and Classification (CNMNC) of the International Mineralogical Association, voting proposal 12-B.
We also propose a compact notation for identifying synthetic LDH phases, for use by chemists as a preferred alternative to the current widespread misuse of mineral names.
Because layered Fe(II)Fe(III)-hydroxides (Green rusts, GRs) are anion exchangers, they represent potential orthophosphate sorbents in anoxic soils and sediments. To evaluate this possibility, two types of experiments with synthetic sulphate-interlayered GRs (GRso 4 = Fe2+4Fe3+a(OH)12SO 4 xH20) were studied. First, sorption of phosphate in GRso 4 was followed by reacting suspensions of pure GRso ~ synthesized by oxidation of Fe(II) with an excess of Na2HPO4 (pH 9.3). Second the possible incorporation of phosphate in GR during formation by Fe(II)-induced reductive dissolution of phosphate-containing ferrihydrites was examined in systems containing an excess of Fe(lI) (pH 7). With excess phosphate in solution, GRso ~ initially sorbed phosphate in the interlayer producing a basal layer spacing of 1.04 nm, but only-50% of the interlayer sulphate was exchanged with phosphate. This GR slowly transformed to vivianite within months. In the Fe(II)-rich systems, reaction with synthetic ferrihydrites produced GRso 4 similar to that produced by air oxidation. Reaction of Fe(II) with phosphate-containing ferrihydrites initially produced amorphous greenish phosphate containing precipitates which, after 3-4 h, crystallized to GRso 4 and vivianite. In these solutions, stable phosphate-free GRso 4 can form since precipitation of vi-vianite produced low phosphate activity. Consequently, in both systems GR or amorphous greenish precipitates act as reactive intermediates, but vivianite is the stable end-product limiting phosphate concentration in solution. It is also inferred that Fe(OH) 2 is an unlikely phosphate sorbent in mixed Fe(II)-Fe(III) systems because GR phases are more stable (less soluble) than Fe(OH)2.
Ferric oxyhydroxycarbonate GR(CO32−)*, FeIII6O12H8CO3, is prepared from FeII–III hydroxycarbonate GR(CO32−), FeII4FeIII2(OH)12CO3, by violent oxidation adding H2O2 or by aerial oxidation once dried. Crystals have practically the same aspect and structural features are mainly conserved as testified by X-ray diffraction. Continuous in situ deprotonation of GR(CO32−) by adding the exact amount of H2O2 to reach any value of x={[FeIII]/[Fetotal]} is followed, leading to the general formula FeII6(1−x)FeIII6xO12H2(7−3x)CO3 that can be extended all over the range x∈[0,1] giving also a ferrous GR(CO32−)§. Mössbauer spectra allow us to devise a model of the long range order of anions that remains unchanged over the whole range of composition whereas protonation or deprotonation accompanies the progressive filling of the three sublattices by FeIII ions with periodicity a0×3, if a0 is that of the hexagonal cation pavement. Monitoring the electrode potential Eh during oxidation by H2O2 allowed determining the chemical potential μ○[GR∗(x)] for any value of x leading to two domains approximated by μ○[GR∗(x)]={−618+54x} kJmole−1 in range [(1/3),(2/3)], and μ○[GR∗(x)]={−632+75x} kJmole−1 in range [(2/3),1]. Occurrences of fougerite mineral in the field (IMA 2003-057) limited to x∈[(1/3),(2/3)] are discussed in agreement with their Mössbauer spectra identical to those obtained in this study.
Fougerite is a new iron oxide, a mixed M(II)–M(III) hydroxide, a member of the green rust group. Its structure consists of a brucitic layer of Fe(III)–Fe(II)–Mg(II), where the excess of the positive charge due to Fe3+ is compensated in the interlayer by anions. The limits of composition are structurally and geochemically constrained, and the stabilities of the mineral and green rusts are obtained by a thermodynamic model of a regular solid solution, for different compensating anions and for any allowed composition of the brucitic layer.
Attempts to draft plausible scenarios for the origin of life have in the past mainly built upon palaeogeochemical boundary conditions while, as detailed in a companion article in this issue, frequently neglecting to comply with fundamental thermodynamic laws. Even if demands from both palaeogeochemistry and thermodynamics are respected, then a plethora of strongly differing models are still conceivable. Although we have no guarantee that life at its origin necessarily resembled biology in extant organisms, we consider that the only empirical way to deduce how life may have emerged is by taking the stance of assuming continuity of biology from its inception to the present day. Building upon this conviction, we have assessed extant types of energy and carbon metabolism for their appropriateness to conditions probably pertaining in those settings of the Hadean planet that fulfil the thermodynamic requirements for life to come into being. Wood-Ljungdahl (WL) pathways leading to acetyl CoA formation are excellent candidates for such primordial metabolism. Based on a review of our present understanding of the biochemistry and biophysics of acetogenic, methanogenic and methanotrophic pathways and on a phylogenetic analysis of involved enzymes, we propose that a variant of modern methanotrophy is more likely than traditional WL systems to date back to the origin of life. The proposed model furthermore better fits basic thermodynamic demands and palaeogeochemical conditions suggested by recent results from extant alkaline hydrothermal seeps.
Life is evolutionarily the most complex of the emergent symmetry-breaking, macroscopically organized dynamic structures in the Universe. Members of this cascading series of disequilibria-converting systems, or engines in Cottrell's terminology, become ever more complicated-more chemical and less physical-as each engine extracts, exploits and generates ever lower grades of energy and resources in the service of entropy generation. Each one of these engines emerges spontaneously from order created by a particular mother engine or engines, as the disequilibrated potential daughter is driven beyond a critical point. Exothermic serpentinization of ocean crust is life's mother engine. It drives alkaline hydrothermal convection and thereby the spontaneous production of precipitated submarine hydrothermal mounds. Here, the two chemical disequilibria directly causative in the emergence of life spontaneously arose across the mineral precipitate membranes separating the acidulous, nitrate-bearing CO2-rich, Hadean sea from the alkaline and CH4/H2-rich serpentinization-generated effluents. Essential redox gradients-involving hydrothermal CH4 and H2 as electron donors, CO2 and nitrate, nitrite, and ferric iron from the ambient ocean as acceptors-were imposed which functioned as the original 'carbon-fixing engine'. At the same time, a post-critical-point (milli)voltage pH potential (proton concentration gradient) drove the condensation of orthophosphate to produce a high energy currency: 'the pyrophosphatase engine'.
Significance
Amino acids are formed from simple organic precursors in iron oxyhydroxide mineral systems that contain geochemical gradients. Redox and pH gradients significantly impact reaction pathways: Amino acids only form when the mineral contains both oxidized and reduced iron, and when the surrounding solution is alkaline. This shows that aqueous, partially reducing iron mineral systems (which would have been common in early-Earth seafloor/vent environments) could have facilitated synthesis and concentration of prebiotic organic molecules relevant for the emergence of life. It also suggests that geochemical gradients in vent environments can drive product selectivity for prebiotic chemistry, perhaps leading to more complex organic reaction systems as these molecules continue to diffuse and react under different conditions within the gradients.
Research in origins of life is an intrinsically multi-disciplinary field, aimed at finding answers to the formidably complex problem of understanding the emergence of life from the modern versions of Charles Darwin's celebrated "primordial soup". In the last few years, thanks to the increasing computational power and the development of sophisticated theoretical and numerical methods, several computational chemistry and physics groups have invested this field, providing new microscopic insights on fundamental prebiotic chemistry phenomena possibly occurring in the early Earth and outer space. This review presents the most successful and powerful approaches in computational chemistry, and the main results thus obtained in prebiotic chemistry and origins of life. The aim of this work is both to describe the state-of-the-art in computational prebiotic chemistry, possibly useful both to theorists and experimentalists in origins of life research, and to suggest future directions and new perspectives offered by modern simulation tools.
We argued in Part 1 of this series that because all living systems are extremely far‐from‐equilibrium dynamic confections of matter, they must necessarily be driven to that state by the conversion of chemically specific external disequilibria into specific internal disequilibria. Such conversions require task‐specific macromolecular engines. We here argue that the same is not only true of life at its emergence; it is the enabling cause of that emergence; although here the external driving disequilibria, and the conversion engines needed must have been abiotic. We argue further that the initial step in life's emergence can only create an extremely simple non‐equilibrium “seed” from which all the complexity of life must then develop. We assert that this complexity develops incrementally and progressively, each step tested for value added “in flight.” And we make the case that only the submarine alkaline hydrothermal vent (AHV) model has the potential to satisfy these requirements. The redox‐active ferrous/ferric mineral, green rust—precipitated at the interface of alkaline hydrothermal springs and the carbonic Hadean 4.4 billion years ago—was, we contend, the initial seed of all life. In this case it acts as a precursor nitrate/nitrite reductase, delivering ammonia on‐site as aminator at life's hydrothermal hatchery.
Origin of life models based on “energized assemblages of building blocks” are untenable in principle. This is fundamentally a consequence of the fact that any living system is in a physical state that is extremely far from equilibrium, a condition it must itself build and sustain. This in turn requires that it carries out all of its molecular transformations–obligatorily those that convert, and thereby create, disequilibria–using case‐specific mechanochemical macromolecular machines. Mass‐action solution chemistry is quite unable to do this. We argue in Part 2 of this series that this inherent dependence of life on disequilibria‐converting macromolecular machines is also an obligatory requirement for life at its emergence. Therefore, life must have been launched by the operation of abiotic macromolecular machines driven by abiotic, but specifically “life‐like”, disequilibria, coopted from mineral precipitates that are chemically and physically active. Models grounded in “chemistry‐in‐a‐bag” ideas, however energized, should not be considered.
α-FeOOH (goethite) and γ-FeOOH (lepidocrocite) were found to be the main corrosion products of the steel cathode in the sodium chlorate process; the identification of the phases formed under reducing potentials, along with the study of the electrodes during the re-oxidation, is fundamental to understand their role in this process. In this paper, FeOOH-based electrodes were investigated through in situ and operando X-ray Absorption Spectroscopy (XAS), combined to electrochemical measurements (e.g. voltammetry and chronoamperometry). At sufficiently negative potentials (below -0.4 V vs. RHE ca.) and under hydrogen evolution conditions an unknown iron (II)-containing phase is formed. A comprehensive analysis of the whole XAS spectrum allowed proposing a structure bearing relation with that of green rust (Space Group P3 ̅1m). This phase occurs independently of the nature of the starting electrode (α or γ-FeOOH). During electrochemical re-oxidation, however, the original phase is restored, meaning that the reduced phase brings some memory of the structure of the starting material. Spontaneous re-oxidation in air suppresses the memory effect, producing a mixture of alpha and gamma phase.
The recently realized biochemical phenomenon of energy conservation through electron bifurcation provides biology with an elegant means to maximize utilization of metabolic energy. The mechanism of coordinated coupling of exergonic and endergonic oxidation-reduction reactions by a single enzyme complex has been elucidated through optical and paramagnetic spectroscopic studies revealing unprecedented features. Pairs of electrons are bifurcated over more than 1 volt of electrochemical potential by generating a low-potential, highly energetic, unstable flavin semiquinone and directing electron flow to an iron-sulfur cluster with a highly negative potential to overcome the barrier of the endergonic half reaction. The unprecedented range of thermodynamic driving force that is generated by flavin-based electron bifurcation accounts for unique chemical reactions that are catalyzed by these enzymes.
Virtually every interesting natural phenomenon, not least life itself, entails physical systems being forced to flow thermodynamically up-hill, away from equilibrium rather than towards it. This requires the action of a mechanism, acting as an ëngine”, which lashes the up-hill process to a more powerful one proceeding in its spontaneous, down-hill direction; in this way converting one disequilibrium into another. All organized and dynamic elements of creation, from the galactic to the atomic, can be viewed as powered by, or being the result of, engines of disequilibria conversion; each a link in a great hierarchical cascade of conversions. There is, however, widespread misunderstanding about how disequilibria conversions happen - and indeed about what physically causes them to happen - especially regarding the role of energy and of the physical meaning of free energy. We attempt here to describe and justify what we assert is the correct alternative view of how phenomena are powered in nature, focusing especially on the molecular-level conversion processes (often called “energy conserving“) that power life and that must, then acting in an entirely abiotic context, have driven it first into being.
The activity of microorganisms is a key component of the biogeochemical cycle of Fe in natural systems, where green rusts are often observed as products of microbially driven redox processes. To better define the factors that control green rust formation during microbial Fe(III) reduction, we examined the effects of the presence of an electron shuttle [9,10-anthraquinone-2,6-disulfonate (AQDS)] and phosphate on akaganeite (β-FeOOH) bioreduction by the iron(III)-reducing bacterium (IRB) Shewanella putrefaciens CN32. Framboidal magnetite was the principal secondary mineral formed during akaganeite bioreduction in the absence of phosphate; this is the first time framboidal magnetite has been reported as a product of microbial Fe(III) oxide reduction. Framboidal magnetite was less crystalline when formed in the presence of AQDS than without AQDS and over time was further reduced to chukanovite. Carbonate green rust was the primary secondary mineral observed from akaganeite bioreduction in the presence of phosphate, with and without AQDS; however, siderite was also observed in the presence of AQDS. This first report of green rust as a product of akaganeite bioreduction expands the range of Fe(III) oxides that can be transformed to green rust by IRB, suggesting that the reduction of Fe(III) oxides such as ferrihydrite, lepidocrocite, and akaganeite by IRB is a key process leading to the formation of green rusts in aquatic and terrestrial environments.
IntroductionComputer Simulation TechniquesResultsConclusions and Future WorkAcknowledgmentsReferences
The rates of hydrolysis of 1% solutions of tetramethylammonium tripoly- and pyrophosphates were measured at 30, 60, 90 and 125°, at constant pH values of 1, 4, 7, 10 and 13 in the presence of tetramethylammonium bromide. Tripolyphosphate was also studied in the absence of the electrolyte. In addition sodium tripolyphosphate was hydrolyzed both in the absence and the presence of 0.65 N sodium bromide at several values of pH. and temperature. The hydrolyses follow a first-order law and are catalyzed by acid and not by base Formation of polyphosphato-sodium complexes also increases the rate. The activation energy for the process ranges from 20 to 40 kcal, under various conditions. For non-complexing cations (tetramethylammonium), it increases as the pH. is raised.
Membrane-bound pyrophosphatases (M-PPases) are homodimeric enzymes that couple the generation and utilization of membrane potentials to pyrophosphate (PPi) hydrolysis and synthesis. Since the discovery of the link between PPi use and proton transport in purple, non-sulphur bacteria in the 1960s, M-PPases have been found in all three domains of life and have been shown to have a crucial role in stress tolerance and in plant maturation. The discovery of sodium-pumping and sodium/proton-pumping M-PPases showed that the pumping specificity of these enzymes is not limited to protons, further suggesting that M-PPases are evolutionarily very ancient. The recent structures of two M-PPases, the Vigna radiata H(+)-pumping M-PPase and Thermotoga maritima Na(+)-pumping M-PPase, provide the basis for understanding the functional data. They show that M-PPases have a novel fold and pumping mechanism, different to the other primary pumps. This review discusses the current structural understanding of M-PPases and of ion selection among various M-PPases.
Adsorption isotherms of glycine and its di-, tri- and tetra-peptides from aqueous solution on to sodium, calcium and hydrogen-montmorillonite have been determined at 20°C. The complexes formed have been examined by X-ray diffraction. For the adsorption on calcium montmorillonite, linear isotherms were obtained. The adsorption could, therefore, be treated as a partition between solution and the Stern layer of the adsorbent. Free energies of adsorption were found to increase with increasing molecular weight. When adsorption occurred on hydrogen montmorillonite a proton transfer mechanism led to strong adsorption, but the physical adsorption mechanisms which accounted entirely for the adsorption on sodium and calcium montmorillonite, also operated. Some evidence was obtained that both adsorbate-substrate and adsorbate-adsorbate interactions were involved. The X-ray diffraction results showed that in the moist state, intercalation of the dipolar ions in solution caused an increase in the interlamellar separation beyond the spacing typical of the normally swollen clay in water. The Δ-values for the dried complexes were less than the minimum thicknesses of the adsorbed molecules, but examination of scale models showed that the contractions could be accounted for by " keying " of the adsorbed molecules to the clay surface.
Mössbauer and Raman spectroscopies are used to identify for the first time a green rust as a mineral in a reductomorphic soil from samples extracted in the forest of Fougères (Brittany-France). The Mossbauer spectrum displays two characteristic ferrous and ferric quadrupole doublets, the abundance ratio Fe(II)/Fe(Ill) of which is close to 1. Comparison with synthetic mixed valence Fe(II)Fe(HI) hydroxides supports the conclusion that the most probable formula is Fe2(OH)5, i.e., according to the pyroaurite-like crystal structure [Fe(n1Fe1III)(OH),]+o [OH] -. The microprobe Raman spectrum exhibits two bands at 518 and 427 cm-' as for synthetic green rusts. When exposed to the air, the new mineral goes rapidly from bluish-green to ochrous. The formula is compatible with the values of ionic activity products Q for equilibria between aqueous iron species and minerals obtained from soil waters, which suggests that this new mineral is likely to control the mobility of Fe in the environment.
The transformations ia-x the iron oxide-hydroxide system have been interpreted in a rational crystallochemical manner, some bring characterized as topotactic and some as non-topotacfic. Crystallographic measurements have been made on the more reactive or metastable phases, particularly on the "green rusts." The oxyhydroxides ~-]~eOOFI and ~-FeOOH have been examined more fully, but data on ald the phases have been checked. New data on transformations, such as FeCOa---> FeO and Fe(OH)~-+ FeO are reported.
Certain clay minerals have the ability to catalyze the polymerization of some unsaturated organic compounds (styrene, hydroxyethyl methacrylate) and yet to inhibit polymer formation from other closely related monomers (e.g. methyl methacrylate). This apparently contradictory behaviour of the clay minerals can be rationalized in terms of electron accepting and electron donating sites in the silicate layers. The electron acceptor sites are aluminium at crystal edges and transition metals in the higher valency state in the silicate layers; the electron donor sites are transition metals in the lower valency state. The catalyzed polymerizations involve the conversion of the organic molecule to a reactive intermediate; thus where the clay mineral accepts an electron from the vinyl monomer a radical-cation is formed, where the organic compound gains an electron it forms a radical-anion. Examples of these reactions are discussed. The inhibition of polymerization processes involves the conversion of reactive organic intermediates, such as free radicals, which have been formed by heat or radical initiators, to non-reactive entities. For example, loss of an electron from the free radical gives a carbonium ion; in some cases this will not undergo polymerization. An example of this type is the thermal polymerization of methyl methacrylate. The color reactions on clay minerals are useful in predicting the electron accepting or electron donating behaviour of the clay minerals because they proceed by similar mechanisms to the polymerization reactions. For example, the benzidine blue reaction is a one electron transfer from the organic molecule to the electron accepting sites in the mineral (aluminium edges, transition metals in higher valency state). Masking of the crystal edge with a polyphosphate destroys the electron accepting properties of the crystal edge; this technique can be used to control the reactivity of the mineral and to distinguish between the crystal edge and transition metal sites as electron-acceptor sites in the clay minerals.
Many metalloenzymes that inject and extract reducing equivalents at the beginning and the end of electron transport chains involved in chemiosmosis are suggested, through phylogenetic analysis, to have been present in the Last Universal Common Ancestor (LUCA). Their active centres are affine with the structures of minerals presumed to contribute to precipitate membranes produced on the mixing of hydrothermal solutions with the Hadean Ocean ~4 billion years ago. These mineral precipitates consist of transition element sulfides and oxides such as nickelian mackinawite ([Fe>Ni]2S2), a nickel-bearing greigite (~FeSS[Fe3NiS4]SSFe), violarite (~NiSS[Fe2Ni2S4]SSNi), a molybdenum bearing complex (~MoIV/VI2Fe3S0/2-9) and green rust or fougerite (~[FeIIFeIII(OH)4]+[OH]-). They may be respectively compared with the active centres of Ni-Fe Hydrogenase, Carbon Monoxide Dehydrogenase (CODH), Acetyl Coenzyme-A Synthase (ACS), the Complex Iron-Sulfur Molybdoenzyme (CISM) superfamily and Methane Monooxygenase (MMO). With the look of good catalysts - a suggestion that gathers some support from prebiotic hydrothermal experimentation - and sequestered by short peptides, they could be thought of as the original building blocks of proto-enzyme active centres. This convergence of the makeup of the LUCA-metalloenzymes with mineral structure and composition of hydrothermal precipitates adds credence to the alkaline hydrothermal (chemiosmotic) theory for the emergence of life, specifically to the possibility that the first metabolic pathway - the acetyl CoA pathway - was initially driven from either end, reductively from CO2 to CO and oxidatively and reductively from CH4 through to a methane thiol group, the two entities assembled with the help of a further thiol on a violarite cluster sequestered by peptides. By contrast, the organic coenzymes were entirely a product of the first metabolic pathways. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems.
Montmorillonite catalyzes the oligomerization of activated nucleotides to form RNA. However, the mechanism of the montmorillonite catalysis, used as a model for similar prebiotic chemistry, is still not well understood. We have observed that the extent of catalysis depends not only upon the magnitude of the negative charge on the montmorillonite lattice and the number of cations associated with it, but also on the pH at which the reaction is promoted. The isotherm and catalysis studies have been extended to provide binding information and catalytic outcomes over a wide pH range. The optimal binding occurs in the region of maximal oligomer formation. X-ray diffraction studies revealed changes in layer separations of montmorillonite as reaction occurs. The application of the Scherrer equation to the X-ray diffraction data showed differences in domain size. Modeling of the size of the activated nucleotide monomers and the charge on the montmorillonite surface provided an interpretation of how these factors influence adsorption. This research provides a basis for further understanding of the physical processes in the mechanism of this catalysis.
1. Recent results suggest that the major flux is carried by a monomeric function, not by intermonomer electron flow. 2. The bifurcated reaction at the Q(o)-site involves sequential partial processes, - a rate limiting first electron transfer generating a semiquinone (SQ) intermediate, and a rapid second electron transfer in which the SQ is oxidized by the low potential chain. 3. The rate constant for the first step in a strongly endergonic, proton-first-then-electron mechanism, is given by a Marcus-Brønsted treatment in which a rapid electron transfer is convoluted with a weak occupancy of the proton configuration needed for electron transfer. 4. A rapid second electron transfer pulls the overall reaction over. Mutation of Glu-295 of cyt b shows it to be a key player. 5. In more crippled mutants, electron transfer is severely inhibited and the bell-shaped pH dependence of wildtype is replaced by a dependence on a single pK at ~8.5 favoring electron transfer. Loss of a pK ~6.5 is explained by a change in the rate limiting step from the first to the second electron transfer; the pK ~8.5 may reflect dissociation of QH(.). 6. A rate constant (<10(3) s(-1)) for oxidation of SQ in the distal domain by heme b(L) has been determined, which precludes mechanisms for normal flux in which SQ is constrained there. 7. Glu-295 catalyzes proton exit through H(+) transfer from QH(.), and rotational displacement to delivers the H(+) to exit channel(s). This opens a volume into which Q(.-) can move closer to the heme to speed electron transfer. 8. A kinetic model accounts well for the observations, but leaves open the question of gating mechanisms. For the first step we suggest a molecular "escapement"; for the second a molecular ballet choreographed through coulombic interactions.
Smectites or swelling clays are lamellar minerals made by the stacking of two tetrahedral silica sheets with one octahedral layer inserted of brucite or alumina type. Conductivity measurements and cation diffusion coefficient determination on different smectites, with varying water content, show that the conductivity is mainly protonic and depends on the water content. Structure and micro dynamics of adsorbed water is studied by XRD, IR, QENS, NMR spectroscopies. The protonic conductivity (10−4 S cm−1) exhibited by these minerals is associated with the proton diffusional motion (D=6×10−6 cm2 s−1): its value fits the Einstein relation well with the residence time τ0=10−10 s and the jump length 2.8 Å deduced from high resolution QENS measurements.
FeII–III hydroxycarbonate green rust GR(CO32−), FeII4 FeIII2 (OH)12 CO3·3H2O, is oxidized in aqueous solutions with varying reaction kinetics. Rapid oxidation with either H2O2 or dissolved oxygen under neutral and alkaline conditions leads to the formation of ferric oxyhydroxycarbonate GR(CO32−)∗, FeIII6 O12 H8 CO3·3H2O, via a solid-state reaction. By decreasing the flow of oxygen bubbled in the solution, goethite α-FeOOH forms by dissolution–precipitation mechanism whereas a mixture of non-stoichiometric magnetite Fe(3−x)O4 and goethite is observed for lower oxidation rates. The intermediate FeII–III oxyhydroxycarbonate of formula FeII6(1−x) FeIII6x O12 H2(7−3x) CO3·3H2O, i.e. GR(x)∗ for which x ϵ [1/3, 1], is the synthetic compound that is homologous to the fougerite mineral present in hydromorphic gleysol; in situ oxidation accounts for the variation of ferric molar fraction x = [FeIII]/{[FeII]+[FeIII]} observed in the field as a function of depth and season but limited to the range [1/3, 2/3]. The domain of stability for partially oxidized green rust is observed in the Eh-pH Pourbaix diagrams if thermodynamic properties of GR(x)∗ is compared with those of lepidocrocite, γ-FeOOH, and goethite, α-FeOOH. Electrochemical equilibrium between GR(x)∗ and FeII in solution corresponds to Eh-pH conditions close to those measured in the field. Therefore, the reductive dissolution of GR(x)∗ can explain the relatively large concentration of FeII measured in aqueous medium of hydromorphic soils containing fougerite.