Reducible oxide chemistry,
structure and functions


    Simple Molecules and the Origin of Life

    The first part of our research deals with the origin of life on Earth`s surface. We address the question, "Is it possible to synthesize simple organic molecules (e.g. amino acids) from inorganic gases such as CO, CO2, N2, NH3, CH4, H2O and H2 using the large laser sparks?"

     The Earth is slightly more than 4.5 billion years old. For the first half billion years or so after its formation, it was impacted by large objects which evaporated the oceans and sterilized the surface [1]. Well-preserved microfossils of organisms that have morphologies similar to those of modern green algae and date back about 3.5 billion years have been found [2],supporting the proposal that life was present 3.8 billion years ago. Life, therefore, originated on Earth or was transported to it, within a window of a few hundred million years, which opened about four billion years ago.

     Three types of ancient Earth proto-atmospheres are considered in the literature. One is a solar-type atmosphere formed by capturing gas from the solar nebula. Another is a transient atmosphere due to impact degassing during accretion. The third is an atmosphere formed by degassing from the late veneer material at the last stage of accretion. Usually, the solar-type atmosphere (or primary atmosphere) is considered to have had a reducing character. In contrast, the atmosphere from degassing (called a secondary atmosphere) would have been oxidizing. The atmospheric oxidation state would then have been modified by reactions between the atmosphere and the early Earth’s hot surface.

     For liquid water to exist on the surface of a planet, the surface environment must satisfy certain conditions: The partial pressure of water vapor at the surface of the planet must exceed the saturation vapor pressure, and the surface temperature must be between the triple point (273.16 K) and the critical point (647.3 K) of water. When the oceans based on liquid water originated, most planetesimals impacted their surface. The numerous impacts evaporated a significant amount of the liquid water. The proto-atmosphere is thought to have contained substantial amounts of CO and H2. After the formation of the proto-oceans, CO possibly reacted with H2O to form CO2 and H2. If the UV flux was at the present level, H2 could have remained in the atmosphere up to 1 billion years. Losses of H2 are likely to have occurred much faster in reality, because the UV fluxes are considered to have been much higher than the present level. CO2 in the proto-atmosphere was dissolved in the protooceans and fixed as carbonates through reaction with Ca2+ and Mg2+ ions. As CO2 was removed from the  atmosphere, the original CO2-rich atmosphere became an N2-rich atmosphere. For more details, see for example Casting’s review article [3]. The uniformity of the biochemistry of all living organisms argues strongly that all modern organisms descend from a last common ancestor. Detailed analysis of protein sequences suggests that this common ancestor had a complexity comparable to that of a simple modern bacterium and lived 3.2-3.8 billion years ago [4]. If we knew the stages by which the  common ancestor evolved from abiotic components present on the primitive Earth, we would have a complete account of the origin of life. In practice, the most ambitious studies of the origin of life address much simpler questions. In this project, we want to mainly discuss only one of them:

 What were the sources of the larger organic molecules that made up

the first self-replicating systems?

     The first step towards answering this question is the elucidation of protein and nucleic acid component synthesis from inorganic sources. The components contain amino acids, nucleic-acid bases, sugars etc. One of the best approaches to solving this problem is simulation of the environment in which life is presumed to have been generated. A typical method is to use an external source to excite gas mixtures that simulate the primitive planetary atmosphere and then analyse the products. Examples of external energy sources for electronic excitation of small inorganic molecules are electrical discharges, high-energy particle or photon beams, and strong laser irradiation, which simulate cosmic rays in outer space, and sunlight as well as lightning discharge in the air. A strongly reducing gas mixture, consisting of methane, ammonia, hydrogen and water vapor, has been thought to well simulate the planetary atmosphere. Miller’s pioneering experiments [5] showed that electrical discharges applied to a strongly reduced gas mixture can generate amino acids and other organic compounds. Recently it has been advocated that the primitive-Earth atmosphere could be better simulated by mildly reducing gas mixtures, consisting of carbon monoxide, carbon dioxide, nitrogen and water, than by strongly reducing ones [3]. It has been found experimentally, however, that organic compounds are difficult to synthesize using electrical discharges or UV irradiation in such mildly reducing gases. Moreover, organic molecules containing nitrogen were not detected at all. Recently, Utsumi et al. [6] have reported experiments in which a mixture of CO2, N2, and H2O vapor at atmospheric pressure have been irradiated by shortwavelength synchrotron radiation to induce chemical reactions resulting in the synthesis of alanine and aspartic acid. Similarly, Takahashi et al. [7], using a synchrotron radiation source, carried out x-ray (1-2 keV) irradiation of a mixture of CO, N2, and H2O. High-pressure liquid chromatography (HPLC) of the hydrolyzed product solution has shown the presence of amino acids. Their optical isomers were generated in almost equal quantities. This implies that the precursors of the amino acids were produced through x-ray induced photolysis of inorganic molecules (amino-acids originating from biological sources exist only as L-type isomers) followed by recombination and polymerization into bioorganic molecules. The difficulty of obtaining amino acids from slightly reducing gases has been explained [6] by the unavailability of a suitable source of radiation. In any case, the radiation source is the most problematic aspect of these experiments. The authors [6,7] used keV-radiation to initiate the reactions in the gas mixtures, although photons with such high energy were relatively rare on the early Earth. However, keV-photons can easily penetrate the Be or Si3N4 windows used to separate the vacuum of the synchrotron radiation sources from the gas mixtures at atmospheric pressure. Moreover, in refs [6,7], the long time used to irradiate the samples is a poor and not very realistic approximation of the initiation of reactions in the Earth’s early atmosphere by impact shocks and lightning. Although Davis et al. [8] first suggested using a aser spark to simulate impact shocks and lightning in planetary atmospheres, it is McKay, Borucki, and Navarro-González [9] who have systematically investigated this approach. In their papers, they also provide a detailed discussion of the advantages of LIDB plasmas over electrical discharges. However, all the research in this area has made use of large numbers of low peak power, low energy (~100 mJ), nanosecond pulses from high-repetition-rate lasers rather than a single, very high peak power, high e nergy pulse. Because of possible differences in the chemical kinetics when starting with some of the reaction products, effects of diffusion to or from unexcited volumes between pulses, and decomposition of products exposed to LIDB plasmas generated by later pulses, the validity of their approach is questionable. This has been discussed in details in refs [10-13]. The above-mentioned shortcomings of previous experiments can be avoided by use of a terawatt laser such as PALS for simulation of the high-energy-density events in the Earth’s early atmosphere.

    PALS (Prague Asterix Laser System) [14] is a single-beam iodine photodissociation laser system providing ≤1-kJ, 400ps pulses at a wavelength of 1.315 μm. The laser beam may be focused into a cell filled with a mixture of molecular gases, the composition of which is inspired by current opinion on the formation and evolution of the Earth’s early atmosphere. The mixture represents a gaseous dielectric in which relatively hot dense plasma is formed by optical breakdown. Although laser-induced dielectric breakdown (LIDB, also called laser  spark) in gases has been studied extensively since 1963, only our group performs this kind of research with a single sub-nanosecond laser pulse with energies of 100 J.

     As opposed to the experiments with high-repetition-rate lasers (see for example [8,9]; a review is given in [11,13]), at the PALS facility we can irradiate a reaction mixture with shorter pulses of much higher energy, i.e. much less focusing of the laser beam is required to reach the LIDB threshold. Thus, the LIDB plasma can be formed in a much larger volume. Such a large-scale LIDB plasma is able to form enough reaction products to be analyzed with our chemical analysis equipment in a single event.

    In this way, high-energy laser pulses make the laboratory simulation of high-energy density events in planetary atmospheres more realistic [10,12]. However, one importrant aspect has remained unnoticed in our previous experiments. In nature, both lightning and hypervelocity impacts do not occur in homogeneous systems. In the first case, dust particles (important to volcanic lightning) and water droplets (rain, fog, clouds) very likely influence the chemistry of energetic events in such an environment whilst in the latter case we should take into account three kinds of condensed phases; the impacting body itself, intrinsic particles in the atmosphere, and the impacted surface, (i.e., rocks, sea water and/or ice on the surfaces of planets or planetary satellites). Although a few experiments have been carried out with plasmas induced by 100-mJ laser pulses in heterogeneous systems of astrobiological importance; see for example refs [15,17,18], up to now, no such an experiment has been realized with a single kJ-ns pulse provided by the high-power laser system.

    Large laser sparks provide a unique way to mimic the chemical effects of high-energy-density events in planetary atmospheres (cometary impact, lightning),  matching the natural energy-density, its spatio-temporal evolution and plasma-volume scaling of such events in a fully-controlled laboratory environment. Laser-induced dielectric breakdown (LIDB) in the molecular gases is achieved with a high-power iodine photo-dissociation laser system PALS (wavelength 1315.2 nm, pulse duration of 400 ps and energy ≤1kJ).

    The analysis of CO2-N2-H2O mixture showed the presence of alanine, glycine, serine, and asparagine. Only alanine was identified among the products formed due to LIDB in the CO2-N2-H2O mixture. These results demonstrate the possibility of the synthesis of small organic compounds, specifically amino acids from these simple inorganic gases and water. The FTIR analysis of the CO2-N2-H2O mixture showed the presence of several hydrocarbons as well.

We continue to test different types of gaseous mixtures.

See also: Thesis of Dr. Babankova, Poster High-power-laser-plasma chemistry and Poster High-power-laser-plasma chemistry II


Photo of the laser spark together with the scheme of the beam collimation. The detail structure of the spark (if shorter exposition time is used) is depicted in the upper white frame.

    Formation of Nucleic Bases from the Formamide Molecule   

    The second part of the research is focused on the origin of nucleic bases. Very interresting molecule is formamide, because it is the simplest prototype of the nucleic base or peptide linkage and it contains all basic elements - hydrogen, carbon, oxygen and nitrogen.

     Origin of Our Environment

In the chemical processes at low temperatures in the dust grains of the molecular cloud, from which the Earth was formed by accretion, only the compounds of C, H, O and N exhibit sufficient mobility and reactivity1. These elements, especially carbon, play a major role in cosmic chemistry2. Many compounds of these elements are considered to be the precursors of biomolecules3 (molecules with a CN group and their polymers, compounds with the amino group, compounds with the carbonyl group and the hydroxyl radical, or nitriles4).

 The main precursors considered are hydrogen cyanide, which condenses to form nucleic bases, polymers of hydrogen cyanide, which in turn form nucleic bases and aminoacids during hydrolysis5  and formaldehyde, which reacts to the formation of sugars6. The interesting precursors of biomolecules are compounds which contain all four macro biomolecules (C, H, O, N). These compounds include formamide, the reactions of which produce both nucleic bases7,8,  and aminoacids9. The formation of biomolecules is initiated by the conditions that could be expected on Earth in the early stages of its development (high temperature and strong UV radiation10). The low volatility of formamide allows it to concentrate in lagoons and react to form biomolecules when exposed to the above-mentioned initiators (as summarized in11).

 The origin of biomolecules and their precursors on Earth can be explained in two ways12,13:

 a) The exogenous synthesis hypothesis, according to which the precursors of biomolecules and the biomolecules themselves are formed in space, in areas of the hot cores of protosolar nebulae around the newly-formed stars14  and are subsequently transported to Earth by the impacts of frigid bodies (comets) or planetesimals, and thus provide material for the formation of life.

 b) The exogenous synthesis hypothesis, according to which the biomolecules were synthesized on Earth from simple compounds (N2, NH3, H2O, H2, CH4, CO2, etc.) by, for example, intensive lightning, UV radiation from the Sun, radioactivity, volcanic processes or transient waves of various origin15,16.

 The existence of primitive life forms is assumed, on the basis of the isotopic composition of the contents of geological samples, to have begun as early as 3.85 billion years ago17  and the oldest confirmed microfossils of bacteria so far come from rocks found in Australia and dating back 3.465 billion years18. In the past, the source of biomolecules was assumed to be the reducing atmosphere composed of simple gases (NH3, CH4, H2O). The isotopic composition of the atmosphere suggests19,20,  that the Earth‘s original gaseous envelope partly or even totally escaped in the early stages, and that the atmosphere was subsequently formed from the volatile substances which were present in rocks and from the impacts of planetesimals and comets21. Traila et al.22  suggests that the primary atmosphere ≈4.5 bil. years ago was not reducing and that the synthesis of biomolecules according to the Urey and Miller model is not a possibility23. Conversely, it probably contained significant quantities of hydrogen and water vapor, which then condensed to form  oceans, and the dominant constituents became CO2, CO (≈10 atm) and N2 (1 atm)24.

Pinto et al.25  showed that the photochemical synthesis of formaldehyde (the parent molecule for the synthesis of sacharides) is possible in such an atmosphere. However, according to Chameides and Walker26, the formation of hydrogen cyanide (the parent molecule for the production of nucleic bases and aminoacids) in an atmosphere rich in CO2 is negligible..

It can be assumed that the atmosphere was not the source of the biomolecules or their precursors. Biomolecules could have been synthesized in the ocean, in which life originated27, e.g.28 around hydrothermal vents. In the work of LaRowe and Regnier it was proved that in such an environment, not only HCN but also complex organic molecules can be formed from simple mixtures of N2, CO, CO2, H2. The synthesis requires higher concentrations of volcanic gases than those known in today's hydrothermal vents. Therefore it is discussed whether the composition was different from the present one and if, in the place of origin, at the calculated optimal temperature of 150oC and optimal pressure of 500 bar, the concentrations of biomolecules could have corresponded to the concentrations in a cellule29. Currently, it is known only that the early ocean, as compared to that of today, was more acid, anoxic, and contained higher concentrations of salts, but the percentage of other substances, such as organic matter, is not accurately known.

 It is assumed that the composition of the oceans and the atmosphere30  was probably influenced by extraterrestrial material31,32,  and the initial conditions could have been favorable from the point of view of the concentrations of simple and more complex organic substances, although these favorable conditions could have had only short-term or local characteristics from the geological point of view. This possibility is still the  subject of extensive discussion. One of the main arguments is that the temperature at the time and place of the Earth´s formation did not allow the incorporation of volatile compounds of the elements (N, C, O, H) into the rock in such a way that they could later be released by volcanic activity and subsequently form the atmosphere, hydrosphere33 or biomolecules. For this reason, it is assumed that the probable exogenous originators of water and other compounds of N, C, O and H were carbonaceous chondrites (which contain up to 22 % water34, about 8% carbonaceous substances35−amongst which are hundreds of ppm amino acids, carbohydrates, etc.36) and comets (which contain about 30 % water in the form of ice37 and 22 % carbonaceous compounds38). According to the data by Chyba et al. , up to 1011 kg/year of organic material could have been brought to the Earth in this way. The frequency of impacts suggests the ratio of the contributions of chondrites to have been 90 % and comets 10 %. If this optimistic estimate is correct, there would have been 0.2 % more available organic compounds than are currently fixed annually by phytoplankton in the seas  (4.5 x 1013 kg/year). Given the volume and level of development of the present biosphere, this number should not be considered to be low. According to the age of the Moon craters, the high frequency period of impacts is assumed to have taken place 3.8 billion years ago . Rises in the frequency of impacts were transient and took place between 4.2−3.8 bil. and 3.24−3.227 bil. years ago .

Given that the impacts of extraterrestrial bodies influenced the composition of the atmosphere and hydrosphere, it is necessary to understand the tranformation processes to which this material was exposed and to answer the questions of whether

 1) the original matter contained only simple volatile substances such as N2, NH3, CH4, HCN, CO, CO2, etc., which, according to the original hyptheses of Urey and Miller , and Oró , provided the material for the synthesis of biomolecules,

2) more complex compounds present in the protoplanetary disc led directly to the synthesis of biomolecules on Earth,

3)  the actual biomolecules present in the space matter were the material for the formation of living matter.

 Simulation of Impacts

Due to the likely influence of impacts on the composition of the primary matter, from which biomolecules were formed, the chemical effects of an extraterrestrial body impact on a planet are an important subject of research (lecture A.−Ch. Levasseur−Regourd , Montpellier 2011).

Although the initial simulations presumed a total destruction of the body by temperature and pressure , later models corrected this view and suggested that the conditions are not necessarily totally destructive if the various geometries of impact  or the pressure-temperature relations of the velocity constants of thermolysis in conjunction with short-term exposure  are considered. It has also been proved that part of a frigid body (a comet) can melt and fall, and disperse in liquid form or disperse after the explosion .

 The simulations of the chemical consequences of an impact are carried out using, for example, projectiles fired at high velocity against the selected target. The primary results of an experiment carried out by Tingle et al. , in which samples of the Murchinson meteorite were used, showed that at high pressures of up to 36 GPa about 70 % of organic matter is degraded (although during the real impact, the pressure can rise as high as 100 GPa, depending on the geometry of the impact). Peterson et al.  added a sample of amino acids to the meteorite material and studied the effect of the impact using the original carbonaceous matrix in order to approximate the actual conditions. At a pressure of 30 GPa, lower losses of 40 − 50 % were found. Systematic experiments have proved that, if the same conditions are kept, the losses are directly proportional to the pressure . However, the surrounding matter can inhibit the effects of the impact. The best characteristics from this point of view were shown by ice and liquids, in which the losses of organic substances reached a maximum of 25 %.

Another approach is mathematical modelling, a laboratory simulation of the plasma resulting from an impact, using laser irradiation , collision of accelerated particles with the target , pyrolysis  or a shock wave . The most recent work concerned with the modelling of plasma chemistry has shown that, depending on the speed of impact, the main products of the destruction of organic compounds in cometary ice are H2 and CO, and that the abundance of organic components typically falls by one or two orders of magnitude.

The highest stability is shown by hydrogen cyanide. This conclusion was confirmed by our own study dealing with the simulation of an impact-generated plasma using a laser spark generated by a high-power Asterix laser. The subject of the study was a sample of liquid formamide, which is considered to be a precursor of nucleic bases. ,  The study showed that the products of the dissociation of formamide are HCN and CO, and simulation using the chemical model proved the thermal instability of other dissociation products (CO2, NH3, HNCO).

Organic compounds can also be formed by the impact. The theoretical simulation of molecular dynamics by Goldman et al.  showed that during the impact, glycine and its complex compounds can be synthesized, and experiments with the effects of plasma and shock waves have also proved the possibility of the synthesis of guanine . In a mixture of simple molecular gases CO2/CO−N2−H2O exposed to the effects of laser plasma and a subsequent shock wave generated using a high-power Asterix laser , we also were able to prove the abiotic synthesis of glycine.

REFERENCES (will be published, text under modification)

    Formation of Nucleic Bases from Formamide

    The term “RNA world” stands for the theory that presumes that RNA played a critical role in the origin of life,1,2 and it hypothesizes that, on Early Earth, RNA functioned as both a carrier of genetic information and an enzyme that catalyzed the synthesis of other RNAs. Although the theory received considerable impetus after catalytic RNAs were discovered,3,4 its plausibility remains controversial, since there are a number of questions to be answered with regard to the prebiotic chemistry of nucleic acids and their components.

    Nucleic acids are polyanions built up by nucleobases, ribose and phosphate groups. Although nature elaborated a pretty sophisticated system for the facile synthesis of these compounds, it is quite challenging to derive them from the so called primordial soup, i.e from the pool of simple compounds that was present about 3.5 billion years ago, when presumably life emerged on Earth. In the frame of the current proposal we would like to contribute to the understanding of this phenomenon using a combined theoretical-experimental approach.

Prebiotic chemistry is an interdisciplinary subject, which encomprises various research areas starting from bio-inorganic and organic chemistry up to geochemistry. Recently quantum chemistry also entered this field due to several advantages of this method. Albeit this method is not able to substitute for the basic synthetic work, it is able to supplement the experiments with a unique insight into the physical chemistry of the studied systems.

Quantum chemical calculations are especially well suited to study chemical systems of prebiotic relevance, since they are able to provide simulatenous picture on the structure, intrinsic stability and electronic properties of the studied systems that is not disturbed by the chemical environment. Thus, this method enables to study such phenomena that might be completely masked by other effects present in complex chemical matrices. In combination with the laser-plasma experiments we will be able to evaluate the relative importance of the prebiotic environment on the outcome of reaction networks responsible for the formation of the first genetic material. In addition, quantum chemical calculations can be used to disclose the mechanism of these reactions. State-of-the-art quantum chemistry is well-matured to provide close to quantitative estimates of reaction free energies as well as activation energies, especially when addressing relative values.

The classical experiment by Oró solved the problem of nucleobase-synthesis using HCN as precursor,6 the synthesis of ribose long remained an unsolved issue. One of the most simple ways to get carbohydrates from the primordial soup is offered by the formose reaction.7 This reaction utilizes formaldehyde and enediolate anions to create carbohydrates. However, this reaction eventually leads to the formation of polymeric aggregates, i.e. it does not stop at ribose, which is the component of the contemporary RNA molecules. In the literature several alternative ways are mentioned to prevent this polymerization step. Springsteen and Joyce suggest that ribose is stabilized via adduct formation with cyanamide.8 Recently, Prieur (Ref. 9) and Benner et al. (Ref. 10) independently suggested that complexation with borate minerals also stabilize aldopentoses. In our recent quantum chemical study11 on the aldopentose-borate complexes, we show that the fortuitous interplay between inter- and intramolecular H-bonding, electrostatic as well as steric interactions present in the hydrated ribose-borate 2:1 complexes may contribute to the fact that, among the four aldopentoses, ribose had the greatest potential to survive in prebiotic conditions and serve as a building unit of the first RNA-architectures.

Saladino and co-workers recently suggested another strategy for the prebiotic synthesis of the building units of nucleic acids. (A complete review of all papers published by this group in this topic can be found in 12.) They show that formamide can give rise to the formation of all five natural nucleobases as well as their nucleosides.13,14

Saladino’s experiments are based on synthetic reactions of hot formamide in the presence of different catalysts ( including cosmic dust analogues, terrestrial olivine, fosferite etc). In this pristine little pond would quickly be enriched by nucleic bases, and if TiO2 was also present, by sugar chains growing onto them. How widespread might have been the photochemistry at the basis of this latter process has not been thoroughly studied, however, it can be confidently assumed that additional catalysts might have also been able carry out similar synthetic processes. In addition, the phosphorylation reaction of the nucleosides is promoted by formamide.15 Thus, basically, formamide can serve as starting material in the synthesis of oligonucleotides.

Eschenmoser’s group uses a very original strategy in the search of the origin of the first genetic material by (for a review see e.g. Ref. 16). Over the years they have synthesized a vast pool of synthetic heterocycles, which can H-bond not only with each other but also with natural nucleobases. These synthetic analogues exhibit very similar steric dimensions as well as H-bonding schemes as their natural counterparts. Thus, they can be considered as the closest relatives of the four nucleic acid bases occurring in the genetic alphabet of the leaving material. The goal of these studies is to answer the question what makes the five naturally occurring nucleobases superior as compared to other base-pair analogues. Similarly, the same group studied numerous backbone variations to see how the chemical structure translates into the evolutionary function of the backbone in nucleic acids.

Despite its advantages, quantum chemical calculations are rather scarce in prebiotic chemistry. Most of these studies concentrate on the synthesis and stabilization of amino acids.17 There are only a few literature examples related to nucleic acids. Glaser et al. studied the reaction network of the cyclization reaction of HCN leading to adenine using ab initio calculations and propose an energetically downhill photolytic pathway for the reaction.18 Jalbout et al have recently investigated the formation of ribose via the formose reaction in gas-phase and found an energetically feasible proton-catalyzed pathway that might be relevant to the interstellar medium.19


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