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# Ribose and related sugars from ultraviolet irradiation of interstellar ice analogs

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## Abstract

Making ribose in interstellar ices Astrobiologists have long speculated on the origin of prebiotic molecules such as amino acids and sugars. Meinert et al. demonstrated that numerous prebiotic molecules can be formed in an interstellar-analog sample containing a mixture of simple ices of water, methanol, and ammonia. They irradiated the sample with ultraviolet light under conditions similar to those expected during the formation of the solar system. This yielded a wide variety of sugars, including ribose—a major constituent of ribonucleic acid (RNA). Science , this issue p. 208

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... The presence of glycolaldehyde in the giant cloud of gas Sagittarius B2 was reported by Hollis and collaborators (2000) and opened the possibility that these molecules could be either formed in early Earth or brought here by a meteorite. Additionally, there is evidence that both ribose and other related sugars could be formed in substantial quantities from photo-processed interstellar ice (mainly composed of H 2 O, CH 3 OH, and NH 3 ) even at room temperature (Meinert et al. 2016). The synthesis of organics in space and their delivery to Earth via interplanetary dust particles, meteorites (Murchinson), and comets is another potentially important source of organics (Lerner and Cooper 2005). ...
... According to the concept of chemical refugia, each of the most important compounds necessary to assemble biological molecules has agglomerated at specific chemical environments in prebiotic Earth. Some of those compounds were: (i) ribose that has been theorized to come from comets being therefore found in their craters (Meinert et al. 2016;Lazcano and Bada 2003); (ii) glyceraldehyde, also coming from comets, became ribose under alkaline conditions through the formose reaction (Hollis et al. 2000). Regarding the (iii) nucleobases, they were also described to be found in meteorites (Burton et al. 2012); although other works propose them to be formed in solutions of water, ice, and urea under ultraviolet irradiation of acetylene in the absence of oxygen (Menor-Salván and Marín-Yaseli 2013); and, most recently, researchers have suggested their spontaneous formation in wet-dry cycles around shallow ponds that become dry and then wet along seasons . ...
... Any scientific experiment sacrifices some degree of realism as we Fig. 1 Examples of prebiotic chemical refugia. Each of the most important compounds necessary to build biological molecules agglomerates at specific chemical environments in prebiotic Earth, such as: ribose, coming from comets and found in their craters (Meinert et al. 2016;Lazcano and Bada 2003); glyceraldehyde, coming from comets, became ribose under alkaline conditions by the formose reaction (Hollis et al. 2000); nucleobases could also come from meteorites (Burton et al. 2012) or they could be formed in solutions of water, ice, and urea under ultraviolet irradiation of acetylene in anoxia (Menor-Salván and Marín-Yaseli 2013), but also in wet-dry cycles around shallow ponds . Phosphates could be produced in carbonate-rich lakes (Toner and Catling 2019). ...
Article
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The origin of life was a cosmic event happened on primitive Earth. A critical problem to better understand the origins of life in Earth is the search for chemical scenarios on which the basic building blocks of biological molecules could be produced. Classic works in pre-biotic chemistry frequently considered early Earth as an homogeneous atmosphere constituted by chemical elements such as methane (CH4), ammonia (NH3), water (H2O), hydrogen (H2) and hydrogen sulfide (H2S). Under that scenario, Stanley Miller was capable to produce amino acids and solved the question about the abiotic origin of proteins. Conversely, the origin of nucleic acids has tricked scientists for decades once nucleotides are complex, though necessary molecules to allow the existence of life. Here we review possible chemical scenarios that allowed not only the formation of nucleotides but also other significant biomolecules. We aim to provide a theoretical solution for the origin of biomolecules at specific sites named “Prebiotic Chemical Refugia.” Prebiotic chemical refugium should therefore be understood as a geographic site in prebiotic Earth on which certain chemical elements were accumulated in higher proportion than expected, facilitating the production of basic building blocks for biomolecules. This higher proportion should not be understood as static, but dynamic; once the physicochemical conditions of our planet changed periodically. These different concentration of elements, together with geochemical and astronomical changes along days, synodic months and years provided somewhat periodic changes in temperature, pressure, electromagnetic fields, and conditions of humidity, among other features. Recent and classic works suggesting most likely prebiotic refugia on which the main building blocks for biological molecules might be accumulated are reviewed and discussed.
... Later, by bombarding with UV photons a mixture of H2O: 13 CH3OH:NH3 (10:3.5:1) they successfully synthesized and detected the RNA monomer building block ribose, along with several related sugars and sugar derivatives, by means of GC×GC-TOFMS (Figure I-8) [93]. More recently, 2-deoxyribose, the monomer building block of DNA, along with other sugars, deoxysugars and deoxysugar derivatives, were discovered in a very primitive interstellar-like ice sample constituted of H2O: 13 CH3OH (2:1) irradiated with UV photons [94]. ...
... Monosaccharides are simple chiral carbohydrates or polyols that are key building blocks for all In the search for the origin of life, monosaccharides are increasingly considered as crucial target molecules in the analysis of meteorites [126][127][128], simulated interstellar ices [91,93,94], and in primordial geochemical settings [213]. Moreover, future space missions in the search for extraterrestrial life will target sugar molecules as biosignatures for extinct or present life on Mars and ...
... Substantial progress has been made in the understanding of the photochemical formation of life's molecular building blocks in interstellar molecular clouds based on the identification of amino acids [68], aldehydes [91], and sugar molecules [93], in simulated interstellar pre-cometary ices. Obtained results were confirmed by in situ data of ESA's cometary Rosetta mission and its COSAC [52], and Ptolemy [334], instruments on board the Philae Lander. ...
Thesis
What caused the emergence of life? Which physico-chemical processes are involved in the selection and organization of the specific molecules that gave birth to the first cells able to take over the primary metabolic tasks like growth and reproduction? Mankind have been fascinated for centuries by these questions and have provided a plethora of scientific or religious theories and hypotheses. Yet, they remain unanswered due to their complexity. The Earth is full of very diverse and complex forms of life but sharing a fundamental and unique property of nature that cannot be ignored when deciphering the origins of life: the homochirality. Essential biological macromolecules such as DNA, RNA, proteins, and phospholipids are made of small chiral units of the same handedness; a curiosity since enantioselective synthesis is not usual without biological input. The origin of this biomolecular asymmetry is still unknown, but it is probably one of the first steps to discover the origins of life. The scientific community proposes the path to homochirality in two stages which are the symmetry breaking or the generation of small enantiomeric excesses, followed by their amplification. This manuscript is essentially focused on the first step.Two processes capable of such symmetry breaking will be discussed here: the interaction of circularly polarized light with organic matter and the interaction between organic matter and mineral matrices. The first chapter summarizes the state of the art on both topics. The second chapter introduces our analytical approach and describes the development of new methods to perform enantioselective analyses of complex mixtures targeting sugars in complex mixtures, a crucial family of chemical compounds for all living systems, by gas chromatography coupled to time-of-flight mass spectrometry. Several methods were tested and compared according to different parameters including sensitivity, enantiomeric resolution, stability, and enantiomeric excess measurements. The third chapter investigates minerals and their capacity to induce a small imbalance between the enantiomers of amino acids, including proteinogenic amino acids. Martian minerals were studied in terms of their adsorption potential as well as the effect of enantioselective adsorption by chiral quartz on the amino acids alanine and leucine. Both axes result in interesting induced enantiomeric excesses and open new perspectives in the field. In the last chapter, we explored the optical activity of key molecules in the gas phase. For this purpose, a temperature- and pressure-controlled gas cell coupled was specifically built. The circular dichroism and anisotropy spectra of seven amino acids and propylene oxide – the first chiral molecule observed in the interstellar medium – were recorded in the gas phase, where any asymmetry is solely determined by the genuine electromagnetic transition moments. The data, complemented by quantum chemical calculation, provide new insights into the original gas phase asymmetric photochemical reactions in interstellar environments for the enantiomeric selection of life’s L-amino acids.
... Glycolic acid (2), glycolaldehyde (HOCH 2 CHO), and ethylene glycol (HOCH 2 CH 2 OH) have all been observed in the soluble organic fraction of carbonaceous chondrites such as the Murchison meteorite (Peltzer & Bada 1978;Peltzer et al. 1984). These are the smallest sugar-related molecules and investigation of their routes of formation may aid in understanding the origin of prebiotic molecules necessary for the origins of life (Braakman et al. 2010;Bossa et al. 2014;Meinert et al. 2016;Zhou et al. 2020). ...
... Numerous synthetic methods have been suggested for the production of glycolic acid (2) in environments relevant to astrochemistry. Bottom-up syntheses based on the irradiation of interstellar ice analogs composed of mixtures of carbon monoxide (CO), carbon dioxide (CO 2 ), water (H 2 O), methanol (CH 3 OH), and ammonia (NH 3 ), or some subset thereof, have repeatedly produced glycolic acid (Agarwal et al. 1985;Briggs et al. 1992;Nuevo et al. 2010;Meinert et al. 2016;Paardekooper et al. 2016). The stability and low vapor pressure of glycolic acid allow for identification through offline gas-chromatography mass spectrometry with which the complex mixture of reaction products were analyzed. ...
Article
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The formation of complex organic molecules by simulated secondary electrons generated in the track of galactic cosmic rays was investigated in interstellar ice analogs composed of methanol and carbon dioxide. The processed ices were subjected to temperature-programmed desorption to mimic the transition of a cold molecular cloud to a warmer star-forming region. Reaction products were detected as they sublime using photoionization reflectron time-of-flight mass spectrometry. By employing isotopic labeling, tunable photoionization and computed adiabatic ionization energies isomers of C 2 H 4 O 3 were investigated. Product molecules carbonic acid monomethyl ester (CH 3 OCOOH) and glycolic acid (HOCH 2 COOH) were identified. The abundance of the reactants detected in analog interstellar ices and the low irradiation dose necessary to form these products indicates that these molecules are exemplary candidates for interstellar detection. Molecules sharing a tautomeric relationship with glycolic acid, dihydroxyacetaldehyde ((OH) 2 CCHO), and the enol ethenetriol (HOCHC(OH) 2 ), were not found to form despite ices being subjected to conditions that have successfully produced tautomerization in other ice analog systems.
... Indeed, silylation is a bimolecular nucleophilic substitution (SN2). Aldoses, ketoses, sugar alcohols, and sugar acids can be identified and resolved using CP-Chirasil-Dex CB coupled to DB-Wax columns (GC×GC) 95 . ...
... Thus, this is a very versatile and convenient derivatization method. However, no enantioseparation was reported using a chiral stationary phase like CP-Chirasil-Dex CB 95 . This major drawback therefore makes this method unsuitable for ee analysis and will not be considered. ...
Thesis
The definition of “life” has not yet reached scientific consensus, but it can be understood as organisms with a life cycle built on cells that can undergo various chemical reactions of metabolism. These organisms are maintained in a state of homeostasis but can grow by cell division, reproduce, evolve, and adapt to their environment. Despite its current abundance on Earth, it must be kept in mind that life appeared at some point, spread and resulted in considerable diversity and complexity. At the molecular level, life emerged on Earth through key chemical building blocks capable of polymerizing and/or self-assembling, generating macromolecules such as DNA, RNA and proteins. These structures have the unique and crucial feature of being made of chiral monomers, and only one enantiomer has been selected to build life. This predominance of an enantiomer over the other is common to all organisms and called homochirality. Abiotically, this particularity is difficult to describe because it implies the selection of one enantiomer over its mirror image that is not generally the case without a biological support: racemic proportions are supposed to be obtained under these conditions. This symmetry breaking event, or the creation of an enantiomeric excess followed by its amplification, is still an ongoing question but is of fundamental importance for the appearance of life. Among the existing hypotheses presented herein, a plausible scenario could be the interaction between circularly polarized light (CPL) with organic matter inducing enantiomeric excesses. Indeed, enantioselective photolysis and/or photosynthesis using chiral light could have occurred on dust particles in the interstellar medium (ISM) and enantiomerically enriched compounds could have been incorporated in meteorites and asteroids that later seeded the early Earth. Therefore, the study of extraterrestrial materials such as meteorites, asteroids and comets become essential to obtain clues about the origin of life. The literature supports the existence of an extraterrestrial source of enantio-enriched building blocks, such as L-amino acids and D-sugars, along with the detection of CPL in the ISM. The means to investigate these excesses are discussed by combining a powerful analytical tool such as comprehensive multidimensional gas chromatography coupled to a time-of-flight mass spectrometer (GC×GC-TOFMS) to analyze complex mixtures and suitable derivatization procedures to improve volatility, detection and enantioseparation of chiral biomolecules. Amino acid derivatization has been studied extensively, whereas sugar derivatization is more challenging due to their cyclization behavior and must be adapted to the purpose of the analysis. To simultaneously investigate amino acids and sugars in extraterrestrial or analogous samples, a methodology for sampling, extraction, purification, and fractionation of these sample has been developed using ion exchange chromatography. Applications of this methodology, or parts of it, on samples such as the synthesis of amino acids starting from hexamethylenetetramine and the synthesis of sugars starting from formaldehyde under conditions simulating meteorite parent body alteration processes are highlighted.
... The formose reaction yields a mixture of both D-and L-isomers of different sugars, including ribose, threose, and erythrose [27]. Similar mixtures of sugars can be obtained by irradiating interstellar ice containing water, methanol, and ammonia [28]. Notably, the amino acids from the spark discharge experiments were obtained as racemic mixtures as well [8,29]. ...
Article
Full-text available
It is not a stretch to say that the search for extraterrestrial life is possibly the biggest of the cosmic endeavors that humankind has embarked upon. With the continued discovery of several Earth-like exoplanets, the hope of detecting potential biosignatures is multiplying amongst researchers in the astrobiology community. However, to be able to discern these signatures as being truly of biological origin, we also need to consider their probable abiotic origin. The field of prebiotic chemistry, which is aimed at understanding enzyme-free chemical syntheses of biologically relevant molecules, could particularly aid in this regard. Specifically, certain peculiar characteristics of prebiotically pertinent messy chemical reactions, including diverse and racemic product yields and lower synthesis efficiencies, can be utilized in analyzing whether a perceived ‘signature of life’ could possibly have chemical origins. The knowledge gathered from understanding the transition from chemistry to biology during the origin of life could be used for creating a library of abiotically synthesized biologically relevant organic molecules. This can then be employed in designing, standardizing, and testing mission-specific instruments/analysis systems, while also enabling the effective targeting of exoplanets with potentially ‘ongoing’ molecular evolutionary processes for robust detection of life in future explorative endeavors.
... Synthesis of numerous necessary small building blocks of life has been demonstrated under varying levels of primordial plausibility 17 . As varying amounts of comparable chemical entities were also discovered in extraterrestrial materials such as meteorites or real samples from asteroid sample return missions [18][19][20][21] , the aim of this paper was a demonstration of a potentially universal, auto-regulatory, up-scalable synthesis of aldehydes explaining the occurrence of aldehydes under both Early Earth and extraterrestrial conditions. ...
Article
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Many essential building blocks of life, including amino acids, sugars, and nucleosides, require aldehydes for prebiotic synthesis. Pathways for their formation under early earth conditions are therefore of great importance. We investigated the formation of aldehydes by an experimental simulation of primordial early earth conditions, in line with the metal-sulfur world theory in an acetylene-containing atmosphere. We describe a pH-driven, intrinsically autoregulatory environment that concentrates acetaldehyde and other higher molecular weight aldehydes. We demonstrate that acetaldehyde is rapidly formed from acetylene over a nickel sulfide catalyst in an aqueous solution, followed by sequential reactions progressively increasing the molecular diversity and complexity of the reaction mixture. Interestingly, through inherent pH changes, the evolution of this complex matrix leads to auto-stabilization of de novo synthesized aldehydes and alters the subsequent synthesis of relevant biomolecules rather than yielding uncontrolled polymerization products. Our results emphasize the impact of progressively generated compounds on the overall reaction conditions and strengthen the role of acetylene in forming essential building blocks that are fundamental for the emergence of terrestrial life.
... The product from the reactions will be probed with MIR spectroscopy via their MIR fingerprints. This setup is similar to [4][5][6][7], which are astrochemistry laboratories to study the complex molecules in molecular cloud conditions. Although, each of these laboratories has unique variations of the setup for conditions such as varying VUV intensity, multi-stage gas, and atomic sources. ...
... Widespread synthesis of complex organics (amino acids, nucleobases, sugars) occurred early in the history of the solar nebula due to radiation processing of ices (Ciesla and Sandford 2012;Nuevo et al. 2012;Nuevo et al. 2009;Meinert et al. 2016), which is likely to occur throughout the universe. These building blocks of "life as we know it" are believed to have been delivered to all potentially habitable zones in the Solar System by comet and meteorite impacts (Schmitt-Kopplin et al. 2010;Engel and Macko 1997;Cooper et al. 2011;Martins et al. 2008;Callahan et al. 2011). ...
Preprint
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Growing evidence of the potential habitability of Ocean Worlds across our Solar System is motivating the advancement of technologies capable of detecting life as we know it – sharing a common ancestry or common physicochemical origin to life on Earth – or don’t know it, representing a distinct genesis event of life quite different than our one known example. Here, we propose the Electronic Life-detection Instrument for Enceladus/Europa (ELIE), a solid-state single-molecule instrument payload that aims to search for life based on the detection of amino acids and informational polymers (IPs) at the parts per billion to trillion level. As a first proof-of- principle in a laboratory environment, we demonstrate single-molecule detection of the amino acid L-proline at a 10 µM concentration in a compact system. Based on ELIE’s solid-state quantum electronic tunneling sensing mechanism, we further propose the quantum property of the HOMO–LUMO gap (energy difference between a molecule’s highest energy occupied molecular orbital and lowest energy unoccupied molecular orbital) as a novel approach to measure amino acid complexity. Finally, we assess the potential of ELIE to discriminate between abiotically and biotically derived (-amino acids in order to reduce false positive risk for life detection. Nanogap technology can also be applied to the detection of nucleobases and short sequences of IPs such as, but not limited to, RNA and DNA. Future missions may utilize ELIE to target preserved biosignatures on the surface of Mars, extant life in its deep subsurface, or life or its biosignatures in the plume, surface, or subsurface of ice moons such as Enceladus or Europa. One Sentence Summary A solid-state nanogap can determine the abundance distribution of amino acids, detect nucleic acids, and shows potential for detecting life as we know it and life as we don’t.
... Organic compounds, which are critical for life as we know it, such as ribose, amino acids, and nucleobases, have been detected in meteorites and comets (Cronin & Chang 1993;Elsila et al. 2009;Cobb & Pudritz 2014;Altwegg et al. 2016) and synthesized in laboratory experiments simulating the evolution of icy dust grains in the interstellar medium (ISM; Bernstein et al. 2002;Muñoz Caro et al. 2002;Nuevo et al. 2006;Elsila et al. 2007;Nuevo et al. 2012;Meinert et al. 2016;Oba et al. 2016;Krasnokutski et al. 2020) and circumstellar disks around young stars (Potapov et al. 2022). Moreover, meteorites, comets, and IDPs contain refractory organic compounds (Cooper et al. 2001;Matrajt et al. 2004;Keller et al. 2006;Rotundi et al. 2008;Dartois et al. 2013;Rotundi et al. 2014;Goesmann et al. 2015;Dartois et al. 2018;Dionnet et al. 2018). ...
Article
Full-text available
The origin of organic compounds detected in meteorites and comets, some of which could have served as precursors of life on Earth, remains an open question. The aim of the present study is to make one more step in revealing the nature and composition of organic materials of extraterrestrial particles by comparing infrared spectra of laboratory-made refractory organic residues to spectra of cometary particles returned by the Stardust mission, interplanetary dust particles, and meteorites. Our results reinforce the idea of a pathway for the formation of refractory organics through energetic and thermal processing of molecular ices in the solar nebula. There is also the possibility that some of the organic material had formed already in the parental molecular cloud before it entered the solar nebula. The majority of the IR “organic” bands of the studied extraterrestrial particles can be reproduced in the spectra of the laboratory organic residues. We confirm the detection of water, nitriles, hydrocarbons, and carbonates in extraterrestrial particles and link it to the formation location of the particles in the outer regions of the solar nebula. To clarify the genesis of the species, high-sensitivity observations in combination with laboratory measurements like those presented in this paper are needed. Thus, this study presents one more piece of the puzzle of the origin of water and organic compounds on Earth and motivation for future collaborative laboratory and observational projects.
... Since this classic experiment, several research groups around the world have focused their studies on the search for the right chemical conditions that allowed the synthesis of other relevant biomolecules under primitive conditions. Thus, we currently have demonstrations for the abiotic synthesis of riboses (Meinert et al., 2016;Lazcano and Bada, 2003), nucleotidic bases (Burton et al., 2012;Menor-Salván and Marín-Yaseli, 2013), small peptides (Levy et al., 2000;Johnson et al., 2008), carbohydrates (Hollis et al., 2000), lipids (Lopez and Fiore, 2019;Damer and Deamer, 2015;Pasek and Lauretta, 2008), and other compounds that constitute the contemporary biological systems (Orgel, 2004;Becker et al., 2018). Even if the precise conditions to produce nucleotides, lipids and carbohydrates are still under debate, most researchers agree that there were indeed conditions that favored the production of those basic bricks for biological macromolecules in early Earth. ...
Article
The occurrence of organized chemical transformations defined as metabolism is one of the most important characteristics of life. Surprisingly though, there is not a consensus about how those transformations were originated in the origin of life. RNA world advocates suggest that biochemical pathways started with ribozymes that were further substituted by enzymes. However, most of the biosynthetic routes of ribozymes described do not overlap with the enzymatic routes, and there is not a clear theory about how this transition happened. An important step to solve this dilemma has been elucidated in the last decade when researchers found that some complex routes of chemical transformations, such as the glycolytic and the citric acid pathways, already existed in prebiotic Earth due to physicochemical forces alone. Defined here as protobiotic pathways, we propose that those metabolic exchanges working without the aiding of any biological catalysts were the ones that guided the origin of metabolism. Under this scenario, some quasi-randomly encoded peptides at the origins of translation systems would be capable to bind metabolites in protobiotic routes. When those bounds facilitated or accelerated the conversion of metabolites along the protobiotic path and the products were beneficial, then natural molecular selection acted to preserve the system. Thus, we propose that the origin of metabolism happened when peptides started to bind metabolites in protobiotic routes without disturbing (and possibly aiding) their chemical transformation paths. This should have been the entry point to the metabolic labyrinth, the key step that allowed peptides to come into the path of chemical transformations and further evolve into the enzymes that coordinate nowadays the biochemical pathways.
... It is well established from several laboratory experiments that ribose can be formed only in modest quantities during different types of formose reactions and that it quickly caramelizes to an insoluble tar [29]. More recent investigations have proved the possibility to conduct a whole formose reaction up to ribose and ribose-related compounds under UV radiation [84]. Due to the brief lifetime of ribose observed in some experiments, other "XNA theories", involving simpler RNA precursors formed by either a threose or a peptide backbone capable of storing and transcribing genetic information but holding a simpler and more stable moiety, have been proposed [85][86][87][88]. ...
Article
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The search for the chemical origins of life represents a long-standing and continuously debated enigma. Despite its exceptional complexity, in the last decades the field has experienced a revival, also owing to the exponential growth of the computing power allowing for efficiently simulating the behavior of matter—including its quantum nature—under disparate conditions found, e.g., on the primordial Earth and on Earth-like planetary systems (i.e., exoplanets). In this minireview, we focus on some advanced computational methods capable of efficiently solving the Schro¨dinger equation at different levels of approximation (i.e., density functional theory)—such as ab initio molecular dynamics—and which are capable to realistically simulate the behavior of matter under the action of energy sources available in prebiotic contexts. In addition, recently developed metadynamics methods coupled with first-principles simulations are here reviewed and exploited to answer to old enigmas and to propose novel scenarios in the exponentially growing research field embedding the study of the chemical origins of life.
... The formose reaction is feasible under a plethora of prebiotic scenarios, including hydrothermal (both subaerial (Deamer & Weber, 2010) and submarine (Omran, 2020)) systems, the interstellar medium (Meinert et al., 2016), and small exogenous rocky bodies (i.e. asteroids and comets (Pallmann et al., 2018;Furukawa et al., 2019;Haas et al., 2020). ...
Article
The formose reaction has been a leading hypothesis for the prebiotic synthesis of sugars such as ribose for many decades but tends to produce complex mixtures of sugars and often tars. Channeling the formose reaction towards the synthesis of biologically useful sugars such as ribose has been a holy grail of origins-of-life research. Here, we tested the hypothesis that a simple, prebiotically plausible phosphorylating agent, acetyl phosphate, could direct the formose reaction towards ribose through phosphorylation of intermediates in a manner resembling gluconeogenesis and the pentose phosphate pathway. We did indeed find that addition of acetyl phosphate to a developing formose reaction stabilized pentoses, including ribose, such that after 5 h of reaction about 10-fold more ribose remained compared with control runs. But mechanistic analyses using liquid chromatography-mass spectrometry showed that, far from being directed towards ribose by phosphorylation, the formose reaction was halted by the precipitation of Ca2+ ions as phosphate minerals such as apatite and hydroxyapatite. Adding orthophosphate had the same effect. Phosphorylated sugars were only detected below the limit of quantification when adding acetyl phosphate. Nonetheless, our findings are not strictly negative. The sensitivity of the formose reaction to geochemically reasonable conditions, combined with the apparent stability of ribose under these conditions, serves as a valuable constraint on possible pathways of sugar synthesis at the origin of life.
... In order to detect sugar derivatives, photoprocessing of an interstellar ice analog composed of H 2 O, CH 3 OH and NH 3 (10:3.5:1 molar ratio) was performed at 78 K and 10 -7 mbar (Meinert et al. 2016). Potential carbon contamination during manipulation was excluded by using 13 C-labeled methanol. ...
Article
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By paraphrasing one of Kipling’s most amazing short stories (How the Leopard Got His Spots), this article could be entitled “How Sugars Became Homochiral”. Obviously, we have no answer to this still unsolved mystery, and this perspective simply brings recent models, experiments and hypotheses into the homochiral homogeneity of sugars on earth. We shall revisit the past and current understanding of sugar chirality in the context of prebiotic chemistry, with attention to recent developments and insights. Different scenarios and pathways will be discussed, from the widely known formose-type processes to less familiar ones, often viewed as unorthodox chemical routes. In particular, problems associated with the spontaneous generation of enantiomeric imbalances and the transfer of chirality will be tackled. As carbohydrates are essential components of all cellular systems, astrochemical and terrestrial observations suggest that saccharides originated from environmentally available feedstocks. Such substances would have been capable of sustaining autotrophic and heterotrophic mechanisms integrating nutrients, metabolism and the genome after compartmentalization. Recent findings likewise indicate that sugars’ enantiomeric bias may have emerged by a transfer of chirality mechanisms, rather than by deracemization of sugar backbones, yet providing an evolutionary advantage that fueled the cellular machinery.
... have become of increasing interest after the findings of plausible physical and chemical pathways for the formation of relevant organic matter as for instance in meteorites or comets (de Marcellus et al. 2015;Meinert et al. 2016;Cooper et al. 2018;Furukawa et al. 2019;Osinski et al. 2020;Glavin et al. 2020). As an Occam's razor assumption, the precursor (A) in our model system is considered as an achiral compound. ...
Article
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To explore abiotic theories related to the origin of biomolecular homochirality, we analyze two entirely reversible kinetic models composed of an enantioselective autocatalysis with limited stereoselectivity that is coupled to an enantiomeric mutual inhibition (Frank-like models). The two models differ in their autocatalytic steps in respect to the formation of monomer species in one model and of dimer species in the other. While fully reversible and running in a closed system, spontaneous mirror symmetry breaking (SMSB) gives rise to transient chiral excursions, even when starting from a strictly achiral situation. Before the SMSB, the two models differ in the main dissipative processes. At the SMSB, the entropy production rate reaches its maximum in both models. Here it is the enantioselective autocatalysis with retention of the winner enantiomer that dominates. During the terminal phase, the enantioselective autocatalysis with inversion prevails, while the entropy production rate vanishes, thus fulfilling the conditions of microscopic reversibility. SMSB does not occur if the autocatalytic rate constant is too strong or too weak. However, when the autocatalysis is relatively weak, the temporary chiral excursions last for long periods of time and could be the starting point of a cascade of asymmetric reactions. The realism of such Frank-like models is discussed from the viewpoint of their relevance to prebiotic chemistry.
... Prebiotic sugar synthesis would likely occur in a completely different setting from pyrimidine synthesis, as the synthesis of sugars from highly reactive aldehydes would be incompatible with a setting enriched in urea. Assuming that the problem of prebiotic sugar availability is provided by its synthesis in alternative or extraterrestrial icy environments, [31,32] the formation of nucleosides from pyrimidines in a plausible prebiotic environment would require a strict timing in the formylation and sugar concentration for ribosylation, together with pH control, to divert the preferential formation of pteridines to nucleosides. An efficient nucleoside formation through Traube synthesis would require the incorporation of a high relative amount of sugar exactly between the formylation and the ring closure to form the free nucleobase. ...
Article
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The prebiotic origins of biopolymers and metabolic co‐factors are key questions in Origins of Life studies. In a simple warm little pond model, utilizing a drying phase to produce a urea‐enriched solution, we present a prebiotic synthetic path for the simultaneous formation of neopterins and tetrahydroneopterins, along with purine nucleosides. We show that the formation of neopterins from pyrimidine precursors, in the presence of ribose, and in a formylating environment consisting of a urea, ammonium formate, water (UAFW) is robust, while the simultaneous formation of guanosine requires a significantly higher ribose concentration. Furthermore, these reactions provide a redox pair of tetrahydropterin‐pterin. This model suggests a prebiotic link in the origin of purine nucleosides and pterin cofactors, which provides a possible deep prebiotic temporal connection for the emergence of nucleic acids and metabolic cofactors
... In addition, at ICN we applied multidimensional gas chromatography for the identification of ribose in laboratorysimulated cometary ice. [14] ICN's aroma and perfume research axis investigated the molecular mechanisms of odor perception. It has shown that these mechanisms are controlled by amino acid motifs conserved among all the olfactory receptors of all mammals. ...
Article
The cover picture shows the Institut de Chimie de Nice (ICN), the chemistry research laboratory of the Université Côte d'Azur and the CNRS, which is located in the Parc Valrose in Nice, France. One‐hundred chemists work at the ICN, and are organized in four research teams: aroma, biomedical, radio‐, and material chemistry. This Editorial summarizes the history and current research interests of the ICN. The ICN celebrates its tenth anniversary in 2022, and more details found in the ICN Special Collection organized for this occasion. The image shows the architect's impression of the ICN building after renovation in 2023. Image credit: Cabinet d'architecture Kardham and Fabien Fontaine‐Vive.
... [135,136]), leading to glycine formation. The first pathway was also tested experimentally by adding C atoms to ice clusters containing H 2 , NH 3 , and CO 2 molecules [61]. However, it is worth mentioning that these C-addition-based reactions (both C + H 2 and C + NH 3 ) as well as the subsequent reactivity, although aimed at occurring on the grain surfaces, were simulated in their absence, namely, under gas-phase conditions. ...
Article
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Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. However, they are spread in the literature and difficult to harmonize in a consistent way due to different computational chemistry methodologies and model systems. This review aims to collect the work done so far to characterize, at a quantum mechanical level, the chemical life of Gly, i.e., from its synthesis in the interstellar medium up to its polymerization on Earth.
... Bennett & Kaiser 2007;Woods et al. 2012Woods et al. , 2013Butscher et al. 2015;Fedoseev et al. 2015;Coutens et al. 2018;Skouteris et al. 2018;Rivilla et al. 2019a). While glyceraldehyde has been discovered in meteoritic samples (Cooper et al. 2001;Pizzarello et al. 2012;Furukawa et al. 2019), and in laboratory experiments of interstellar ice analogues (Meinert et al. 2016;de Marcellus et al. 2015;Fedoseev et al. 2017), its interstellar detection is elusive despite observational searches (e.g. Jiménez-Serra et al. 2020). ...
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We present the first detection of ( Z )-1,2-ethenediol, (CHOH) 2 , the enol form of glycolaldehyde, in the interstellar medium toward the G+0.693−0.027 molecular cloud located in the Galactic Center. We have derived a column density of (1.8 ± 0.1) × 10 ¹³ cm ⁻² , which translates into a molecular abundance with respect to molecular hydrogen of 1.3 × 10 ⁻¹⁰ . The abundance ratio between glycolaldehyde and ( Z )-1,2-ethenediol is ∼5.2. We discuss several viable formation routes through chemical reactions from precursors such as HCO, H 2 CO, CHOH, or CH 2 CHOH. We also propose that this species might be an important precursor in the formation of glyceraldehyde (HOCH 2 CHOHCHO) in the interstellar medium through combination with the hydroxymethylene (CHOH) radical.
... Bennett & Kaiser 2007;Woods et al. 2012Woods et al. , 2013Butscher et al. 2015;Fedoseev et al. 2015;Coutens et al. 2018;Skouteris et al. 2018;Rivilla et al. 2019a). While glyceraldehyde has been discovered in meteoritic samples (Cooper et al. 2001;Pizzarello et al. 2012;Furukawa et al. 2019), and in laboratory experiments of interstellar ice analogues (Meinert et al. 2016;de Marcellus et al. 2015;Fedoseev et al. 2017), its interstellar detection is elusive despite observational searches (e.g. Jiménez-Serra et al. 2020). ...
Preprint
We present the first detection of ($Z$)-1,2-ethenediol, (CHOH)$_2$, the enol form of glycolaldehyde, in the interstellar medium towards the G+0.693-0.027 molecular cloud located in the Galactic Center. We have derived a column density of (1.8$\pm$0.1)$\times$10$^{13}$ cm$^{-2}$, which translates into a molecular abundance with respect to molecular hydrogen of 1.3$\times$10$^{-10}$. The abundance ratio between glycolaldehyde and ($Z$)-1,2-ethenediol is $\sim$5.2. We discuss several viable formation routes through chemical reactions from precursors such as HCO, H$_2$CO, HCOH or CH$_2$CHOH. We also propose that this species might be an important precursor in the formation of glyceraldehyde (HOCH$_2$CHOHCHO) in the interstellar medium through combination with the hydroxymethylene (CHOH) radical.
... In addition, at ICN we applied multidimensional gas chromatography for the identification of ribose in laboratorysimulated cometary ice. [14] ICN's aroma and perfume research axis investigated the molecular mechanisms of odor perception. It has shown that these mechanisms are controlled by amino acid motifs conserved among all the olfactory receptors of all mammals. ...
Article
The ‘Institut de Chimie de Nice’ (ICN), founded in 2012, celebrates its 10th anniversary in 2022. Today, the ICN is part of the University Côte d'Azur (UCA), one out of nine excellence universities in France. ICN is also affiliated to the CNRS. We use the institute's anniversary to reflect on the origins and the successful evolution of research in chemical sciences in Nice, France. We outline research topics and their development towards modern chemistry in Nice that are characterized by innovation and territorial anchoring. At present, four research axes, namely aroma and perfume chemistry, medicinal chemistry, radiochemistry, and material chemistry structure the institute. ICN has created five start‐up companies and includes a technological platform. The ICN is central part of the university and contributes to the advancement in chemical sciences as evidenced by both fundamental research and active contributions to local partnerships. The Institut de Chimie de Nice (ICN) – chemistry research laboratory of the Université Côte d'Azur and the CNRS (UMR 7272) – is directed by Prof. Dr. Uwe J. Meierhenrich and located in Nice, Côte d'Azur, France, in Parc Valrose. ICN is organized in four research teams: aroma, biomedical, radio‐, and material chemistry. This modern institute celebrates its 10th anniversary in 2022, and this Guest Editorial outlines the history of chemistry in Nice and presents the ICN.
... Astrophysical ices are widespread in cold space environments and are the likely nurseries of large organic molecules from their surface or bulk reactions, mostly triggered by ionizing radiation such as cosmic rays (CRs), ultraviolet (UV), and soft X-rays (e.g., Munoz-Caro et al. 2002;Meinert et al. 2016), or via atom additions (e.g., Qasim et al. 2019;Chuang et al. 2020;Ioppolo et al. 2021). Astronomical observations in the infrared (IR) have provided plenty of information about the chemical composition of such ices in different regions including the dense interstellar medium (ISM) and protostellar environments, as well as from other colder regions such as surfaces of frozen moons and comets (e.g., Ehrenfreund & Charnley 2000;Fraser et al. 2002;van Dishoeck 2014;Boogert et al. 2015;Tielens 2013;Kwok 2016). ...
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Astrophysical ices are being exposed to ionizing radiation in space environments, which trigger new reactions and desorption processes. In the lab, such processing by radiation has revealed the appearance of several new species and complements the study of the chemical evolution of icy astrophysical scenarios. Here, we develop a computational methodology that helps to clarify the chemical evolution of ices investigated experimentally under photolysis/radiolysis processes until reaching chemical equilibrium (CE). Briefly, the code (named PROCODA) solves a system of coupled differential equations and describes the evolution of the molecular abundances with the irradiation time for ices under processing by radiation. Two experimental ice samples containing pure CO 2 and irradiated by two ionizing agents (cosmic rays and ultraviolet photons) were considered prototype systems. Here, we considered 11 different chemical species within the ice (four observed: CO 2 , CO, O 3 , and CO 3 ; seven nonobserved or unknown: O, O 2 , C, C2, C 2 O, C 2 O 2 , and C 2 O 3 ), 100 reaction routes (e.g., direct dissociation reactions, bimolecular and termolecular reactions) and radiation-induced desorption processes. The best-fit models provide the reaction rates, several desorption parameters, as well as the characterization of the CE phase. At CE, the percentage of nonobserved species in the UV model was almost triple the one calculated in the CR model (which also includes a lot of O and C atoms). The determined values can be employed in future astrochemical models to map chemical evolution embedded species in astrophysical regions under the presence of an ionizing radiation field.
... I searched for all chemical formulae that could correspond to molecules of prebiotic interest in radical form M •+ or M •-, or in (de)protonated form [M+H] + or [M-H] -. Due to their detection in extraterrestrial objects (e.g., meteorites, comets) or laboratoryanalogues (e.g., aerosols, interstellar ices), I considered the following types of molecules: nucleobases and derivatives (e.g.,Martins et al., 2008;Callahan et al., 2011;Burton, Stern, et al., 2012;Hörst et al., 2012;Sebree et al., 2018;Kawai et al., 2019;Oba et al., 2019;Moran et al., 2020), proteinogenic and non-proteinogenic amino acids (e.g.,Neish, Somogyi and Smith, 2010;Burton, Elsila, et al., 2012;Burton, Stern, et al., 2012;Evans et al., 2012;Hörst et al., 2012;Sebree et al., 2018;Moran et al., 2020), monosaccharides (e.g.,Meinert et al., 2016;Cooper, Rios and Nuevo, 2018;Furukawa et al., 2019;Moran et al., 2020), fatty acids (e.g., ...
Thesis
On July 14th, 2015, NASA’s New Horizons spacecraft flew by Pluto, revealing a complex atmosphere and surface seen nowhere else in the Solar System. Pluto’s surface ices are composed of molecular nitrogen N2, methane CH4, and carbon monoxide CO. During Pluto’s elliptical orbit, these ices undergo a sublimation/condensation cycle resulting in a tenuous atmosphere (~11 µbar at the surface). This atmosphere is mostly composed of N2 and CH4, with ~500 ppm of CO. Subjected to extreme ultraviolet radiation and Lyman-α photons, it is the place of photochemical aerosol production, aerosols being solid particles in suspension in the atmosphere. The exact processes of formation of these aerosols are however not well constrained yet. These solid particles, whose chemical composition and optical properties are unknown, are observed up to more than 350 km of altitude in the atmosphere of Pluto. Numerical models have shown that the presence of these aerosols in the atmosphere could have an impact on the atmospheric chemistry and climate of Pluto. Moreover, it has been suggested that these aerosols sediment and constitute a source of organic matter on the surface of Pluto.During my Ph.D., I used an experimental approach to study the aerosols of Pluto, from their formation in the upper atmosphere to their evolution on the surface, through their interactions with the atmosphere. The formation of Pluto’s aerosols by photochemistry and their chemical composition are the subjects of the first and second part of this Ph.D. thesis (Chapter III and Chapter IV). The interaction of Pluto’s aerosols with solar radiation and the contribution of photochemical aerosols as a coloring agent on the surface of Pluto are the subjects of the third and fourth part of this Ph.D. thesis (Chapter V and Chapter VI).The experimental setup PAMPRE (Production of Aerosols in Microgravity by REactive Plasma), located at LATMOS, has been used to simulate the atmospheric chemistry of Pluto and to synthesize analogues of photochemical aerosols, usually called "tholins". Experiments have also been performed at GANIL, using the IGLIAS (Irradiation of astrophysical ices) experimental setup. By irradiating tholins with heavy ions, the objective was to simulate the ageing of organic matter on the surface of Pluto due to the charged particles constituting the galactic cosmic rays.Thanks to the physicochemical analyses carried out to characterize the chemical composition of Pluto-simulated atmosphere as well as that of the synthesized aerosol analogues, I was able to conclude to the importance of N2 and CO reactivity in the atmospheric chemistry of Pluto. The nitrogen constituting the molecules produced in the gas phase and ultimately incorporated in the solid particles is included not only in the form of terminal functional groups (amine, nitrile, isocyanide), but also in the form of nitrogen heterocycles (triazine, pyrazole, pyrazine, pyrrole). Regarding oxygen, only terminal oxygenated chemical functions (alcohol, carboxylic acid, carbonyl) were detected. These nitrogenous and/or oxygenated organic molecules are responsible for a strong absorption in the ultraviolet spectral range by Pluto aerosol analogues and a more moderate absorption in the visible and near-infrared. These results are consistent with spectral observations of Pluto’s surface and atmosphere by instruments onboard New Horizons. Finally, thanks to the experiments of irradiation of Pluto aerosol analogues by heavy ions, I was able to conclude that the surface of Pluto is processed by galactic cosmic ray irradiation, probably explaining the characteristic featureless spectra of the Cthulhu region.
... al. (2009) ha demostrado que la fotólisis de capas sólidas de CH3OH dio como resultado la formación de varios COM como dimetiléter (CH3OCH3) y formiato de metilo (HCOOCH3). Además, la formación de Moléculas astrobiológicamente importantes como los aminoácidos y azúcares se ha comprobado en numerosos experimentos de laboratorio en los que mezclas de hielo contienen H2O y NH3 junto con el CH3OH (Bernstein et al., 2002;Muñoz Caro et al., 2002;De Marcellus et al., 2015;Meinert et al., 2016). ...
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El autor otorga al INAOE el permiso de reproducir y distribuir copias de esta tesis en su totalidad o en partes mencionando la fuente. Astrobiología en el sistema solar: Predicciones sobre el contenido molecular en el ambiente de Encélado para el GTM
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1,2-Ethenediols are deemed key intermediates in prebiotic and interstellar syntheses of carbohydrates. Here we present the gas-phase synthesis of these enediols, the high-energy tautomers of glycolaldehyde, trapped in cryogenic argon...
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With the discovery of thousands of extrasolar planetary systems it becomes more and more evident that a large variety of planetary system architectures, including very different types of planets, have been realized in nature. Our solar system is just one among many. We do not know yet whether the evolution of the planets and moons in the solar system is typical for such objects in similar environments, or not. This includes in particular the capability to develop habitable surface conditions, or even life. Planets orbiting host stars different to our Sun can experience very different environmental conditions such as stellar spectral energy distributions and harsh cosmic rays impacting the orbiting planets. The dynamical evolution of planetary systems depends on the formation processes and interactions with the protoplanetary disk as well as migration processes. Looking at extrasolar planets in the sky today, we see systems in different astrophysical environments, at different ages and with different evolutionary histories. As outlined above, the number of processes shaping the characteristics of planets is large. Yet, for extrasolar planets the number of observables is small. Observational constraints are usually limited to orbital parameters, planetary masses, radii, and some of the atmospheric constituents. In fortunate cases additional constraints like magnetic fields and Love numbers will become accessible in the future. Additional constraints are given by the host star characteristics (metallicity, composition, age, temperature, etc.), but the link between stellar properties and planetary characteristics is complex and not fully understood yet. In view of this limited achievable data set, it becomes vital to better understand how we can learn from our detailed knowledge of the bodies in the solar system to better understand the planets and moons in extrasolar systems. Vice versa, extrasolar systems show us the possible variety of planetary systems, which helps us in particular to better understand planet formation processes. Furthermore, with the increasing number of terrestrial planets found orbiting in the habitable zone of their hosts, the number of potential targets to search for life significantly increases. Finding clear evidence for life will, however, require a very good understanding of the biogenic processes on planets, their interaction with the atmosphere, and a careful study of nonbiogenetic processes to avoid false alarms. So far, we know life only in our solar system, on Earth. It is therefore crucial to bring together the knowledge we have from both the detailed solar system view and the statistical view of a large number of extrasolar planets. After a brief review of the missions planned to study solar system and extrasolar planets in the future, our knowledge of planets and planetary systems is reviewed and prospects for synergies of solar system and exoplanet research discussed. The discussion includes planet formation processes as well as the geophysical evolution of planets and moons. Particular emphasis is given to the understanding of habitats and search for biosignatures in extrasolar planets and lessons learned from the Earth. Future large telescope facilities will allow us to search for biosignatures outside the solar system, enhancing the prospects to answer the long-standing question whether life has developed elsewhere in our galaxy, at least within our neighborhood. The contents presented in this chapter draw heavily on the presentations, discussions, and final report of the forum “Solar System/Exoplanet Science Synergies in a multi-decadal Perspective” jointly organized by the Europlanet Research Infrastructure and the International Space Science Institute in Bern, Switzerland, on February 19 and 20, 2019.
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Context. Cosmic rays and solar energetic particles induce changes in the composition of compounds frozen onto dust grains in the interstellar medium (ISM), in comets, and on the surfaces of atmosphere-less small bodies in the outer Solar System. This induces the destruction of pristine compounds and triggers the formation of various species, including the precursors of complex organics. Aims. We investigate the role of energetic ions in the formation of formaldehyde (H 2 CO) and acetaldehyde (CH 3 CHO), which are observed in the ISM and in comets, and which are thought to be the precursors of more complex compounds such as hexamethylenete-tramine (HMT), which is found in carbonaceous chondrites and in laboratory samples produced after the irradiation and warm-up of astrophysical ices. Methods. We performed ion irradiation of water, methanol, and ammonia mixtures at 14–18 K. We bombarded frozen films with 40–200 keV H ⁺ that simulate solar energetic particles and low-energy cosmic rays. Samples were analysed by infrared transmission spectroscopy. Results. Among other molecules, we observe the formation of H 2 CO and CH 3 CHO, and we find that their abundance depends on the dose and on the stoichiometry of the mixtures. We find that the H 2 CO abundance reaches the highest value after a dose of 10 eV/16u and then it decreases as the dose increases. Conclusions. The data suggest that surfaces exposed to high doses are depleted in H 2 CO. This explains why the amount of HMT in organic residues and that formed after irradiation of ices depends on the dose deposited in the ice. Because the H 2 CO abundance decreases at doses higher than 10 eV/16u, a lower quantity of H 2 CO is available to form HMT during the subsequent warm-up. The H 2 CO abundances caused by ion bombardment are insufficient to explain the ISM abundances, but ion bombardment can account for the abundance of CH 3 CHO towards the ISM and comets.
Thesis
La synapse immunologique est une structure qui se forme à l’interface entre un lymphocyte T et une cellule présentatrice d’antigène lors de la reconnaissant d’un antigène étranger spécifique. Cette plate‑forme est actuellement considérée comme le lieu d’où est déclenchée la cascade de signalisation moléculaire conduisant à l’activation lymphocytaire. Les travaux présentés dans ce manuscrit décrivent un autre pôle de signalisation localisé sur le lymphocyte T, à l’opposé de la zone de contact. Ce pôle a été nommé antisynapse. On peut détecter cette structure dans la première minute avant le contact, avant l’apparition de la synapse immunologique. Elle contient les composants classiquement décrit à la synapse immunologique. Sa formation est indépendante de la reconnaissance d’antigène et déclenchée par l’adhésion entre les cellules. Plusieurs fonctions potentielles sont étudiés, l’antisynapse agit notamment comme un réservoir de molécules qui sont transférées à la synapse immune de manière dépendante des microtubules. L’antisynapse peut également être considérée comment une pre-synapse déclenchée avant la reconnaissance d’antigène.
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The prebiotic origins of ribose, nucleosides, and eventually RNA are enduring questions whose answers are central to the RNA World hypothesis. The abiotic synthesis of sugars was first demonstrated over a century ago, but no known prebiotic reaction produces ribose (an aldose sugar) selectively and in good yield. In contrast, ribulose and fructose (ketose sugars) and other monosaccharides are formed in high yield by several robust abiotic reactions. We report here that ketose sugars—both ketopentoses and ketohexoes—serve as precursors for the formation of ribosides and other aldosides, as demonstrated by glycoside‐forming reactions involving barbituric acid, a plausibly prebiotic nucleobase. Moreover, we discovered a one‐pot reaction of glyceraldehyde and barbituric acid that under mild conditions, and without special minerals or other catalysts, results in the formation of glycosides. These results reveal that an exclusive or high‐yielding generation of free ribose was not required for its incorporation into processes that provided the foundations for life.
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Context. High-quality vibrational spectra of solid-phase molecules in ice mixtures and for temperatures of astrophysical relevance are needed to interpret infrared observations toward protostars and background stars. Such data are collected worldwide by several laboratory groups in support of existing and upcoming astronomical observations. Over the last 25 yr, the Laboratory for Astrophysics at Leiden Observatory has provided more than 1100 (high-resolution) spectra of diverse ice samples. Aims. In time with the recent launch of the James Webb Space Telescope, we have fully upgraded the Leiden Ice Database for Astrochemistry (LIDA) adding recently measured spectra. The goal of this paper is to describe what options exist regarding accessing and working with a large collection of infrared (IR) spectra, and the ultraviolet-visible (UV/vis) to the mid-infrared refractive index of H 2 O ice. This also includes astronomy-oriented online tools to support the interpretation of IR ice observations. Methods. This ice database is based on open-source Python software, such as Flask and Bokeh , used to generate the web pages and graph visualization, respectively. Structured Query Language (SQL) is used for searching ice analogs within the database and Jmol allows for three-dimensional molecule visualization. The database provides the vibrational modes of molecules known and expected to exist as ice in space. These modes are characterized using density functional theory with the orca software. The IR data in the database are recorded via transmission spectroscopy of ice films condensed on cryogenic substrates. The real UV/vis refractive indices of H 2 O ice are derived from interference fringes created from the simultaneous use of a monochromatic HeNe laser beam and a broadband Xe-arc lamp, whereas the real and imaginary mid-IR values are theoretically calculated. LIDA not only provides information on fundamental ice properties, but it also offers online tools. The first tool, SPECFY, is directly linked to the data in the database to create a synthetic spectrum of ices towards protostars. The second tool allows the uploading of external files and the calculation of mid-infrared refractive index values. Results. LIDA provides an open-access and user-friendly platform to search, download, and visualize experimental data of astrophysically relevant molecules in the solid phase. It also provides the means to support astronomical observations; in particular, those that will be obtained with the James Webb Space Telescope. As an example, we analysed the Infrared Space Observatory spectrum of the protostar AFGL 989 using the resources available in LIDA and derived the column densities of H 2 O, CO and CO 2 ices.
Article
The molecular origins of homochirality on Earth is not understood well, particularly how enantiomerically enriched molecules of astrobiological significance like sugars and amino acids might have been synthesized on icy grains in space preceding their delivery to Earth. Polycyclic aromatic hydrocarbons (PAHs) identified in carbonaceous chondrites could have been processed in molecular clouds by circularly polarized light prior to the depletion of enantiomerically enriched helicenes onto carbonaceous grains resulting in chiral islands. However, the fundamental low temperature reaction mechanisms leading to racemic helicenes are still unknown. Here, by exploiting synchrotron based molecular beam photoionization mass spectrometry combined with electronic structure calculations, we provide compelling testimony on barrierless, low temperature pathways leading to racemates of [5] and [6]helicene. Astrochemical modeling advocates that gas-phase reactions in molecular clouds lead to racemates of helicenes suggesting a pathway for future astronomical observation and providing a fundamental understanding for the origin of homochirality on early Earth.
Article
Ribose plays an important role in the process of life. Excessive ribose in the human cerebrospinal fluid or urine can be used as an early diagnostic marker of leukoencephalopathy. Fluorinated phenylboronic acid combined with 19F NMR spectroscopy was a powerful method for molecular recognition. However, phenylboronic acid-based sensors for selective detection of ribose are rarely reported in the literature. In this study, the rapid and highly selective recognition of ribose was studied by 19F NMR and 2-fluorophenylboric acid. It was found that 2-fluoro-phenylboric acid was an appropriate 19F NMR-based sensor molecule for the determination of ribose under physiological conditions with high selectivity and robust anti-interference ability. When 2-fluorophenylboric acid was used for the detection of ribose in human urine without any sample pretreatment, a limit of detection of 78 μM was obtained at room temperature under given 19F NMR experimental conditions (400 MHz, 512 scans, ca. 12 min), which can well meet the needs of practical application.
Article
Silicon monoxide (SiO) is classified as a key precursor and fundamental molecular building block to interstellar silicate nanoparticles, which play an essential role in the synthesis of molecular building blocks connected to the Origins of Life. In the cold interstellar medium, silicon monoxide is of critical importance in initiating a series of elementary chemical reactions leading to larger silicon oxides and eventually to silicates. To date, the fundamental formation mechanisms and chemical dynamics leading to gas phase silicon monoxide have remained largely elusive. Here, through a concerted effort between crossed molecular beam experiments and electronic structure calculations, it is revealed that instead of forming highly-stable silicon dioxide (SiO2), silicon monoxide can be formed via a barrierless, exoergic, single-collision event between ground state molecular oxygen and atomic silicon involving non-adiabatic reaction dynamics through various intersystem crossings. Our research affords persuasive evidence for a likely source of highly rovibrationally excited silicon monoxide in cold molecular clouds thus initiating the complex chain of exoergic reactions leading ultimately to a population of silicates at low temperatures in our Galaxy.
Chapter
Prebiotic chemistry has dominated the origins of life (OoL) field to such an extent that often these terms have been used interchangeably. While prebiotic chemistry has benefited from cross-seeding with other disciplines (e.g., biochemistry, biophysics, computational sciences, geosciences), the OoL problem is still primarily a chemical one. The range of possible non-enzymatic pathways provisioning important biomolecules is becoming clearer, and the problem can now be cast in terms of understanding how the constructive interplay between such pathways is underlying the mechanisms controlling their self-organization into systems. Those systems must be capable of producing their constituent parts and reproducing as a result, with a degree of maintaining and transferring their information content. This chapter provides a concise historical overview of the research field, presents a comprehensive panorama of the possible synthesis pathways for each biomolecular domain, discusses the homochirality conundrum, argues a case for experimentation using non-classical materials, and models, and finally considers current and future trends.
Article
The proposed hypothesis of ‘Advanced Panspermia Origin of Life’ addresses the two critical areas of advanced complex life of Cambrian explosion and the development of even more complex and intricate Human Brain on earth. The hypothesis explains the plausible mechanism of connecting the inorganic chemistry available to us in the universe and that life arose from it as an emergent property of matter. While ‘Origin of Life’ is critical to ‘Evolution’ itself, the mechanism of transformation of protocells into living cells in origin with information encoded DNA is even more critical to both ‘Origin’ and ‘Evolution’. This compels one to turn to religion (Not ‘God of the Gaps’) that stands on solid foundation of science which describes the present hypothesis as the study based on the interaction of electromagnetism with matter. Proto cells are plausibly transformed into ‘living cells’ with the manifestation of soul/spirit (vibration) with specific frequency of each of the species.
Article
‘Origin of Life’ is critical to Evolution of heritable change of organisms over multiple generations. The process of encoding information in DNA in the ‘Panspermia Origin of Life’ and decoding the same in ‘Evolution’ ought not to be different for the proposed process to be true. In the present study, it is observed that the process of decoding information in DNA in ‘Evolution’ is just the reverse process of encoding DNA in ‘Panspermia Origin of Life’ that works on the principle of electromagnetism with its usual frequencies, oscillations, energies and resonances. Incidentally, the present hypothesis provides a more viable and reasonable theory of evolution of heritable organisms over multiple generations, in contradistinction to Darwin’s Theory of Evolution and Natural Selection.
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The single chirality of biological molecules in terrestrial biology raises more questions than certitudes about its origin. The emergence of biological homochirality (BH) and its connection with the appearance of life have elicited a large number of theories related to the generation, amplification and preservation of a chiral bias in molecules of life under prebiotically relevant conditions. However, a global scenario is still lacking. Here, the possibility of inducing a significant chiral bias "from scratch", i.e. in the absence of pre-existing enantiomerically-enriched chemical species, will be considered first. It includes phenomena that are inherent to the nature of matter itself, such as the infinitesimal energy difference between enantiomers as a result of violation of parity in certain fundamental interactions, and physicochemical processes related to interactions between chiral organic molecules and physical fields, polarized particles, polarized spins and chiral surfaces. The spontaneous emergence of chirality in the absence of detectable chiral physical and chemical sources has recently undergone significant advances thanks to the deracemization of conglomerates through Viedma ripening and asymmetric auto-catalysis with the Soai reaction. All these phenomena are commonly discussed as plausible sources of asymmetry under prebiotic conditions and are potentially accountable for the primeval chiral bias in molecules of life. Then, several scenarios will be discussed that are aimed to reflect the different debates about the emergence of BH: extra-terrestrial or terrestrial origin (where?), nature of the mechanisms leading to the propagation and enhancement of the primeval chiral bias (how?) and temporal sequence between chemical homochirality, BH and life emergence (when?). Intense and ongoing theories regarding the emergence of optically pure molecules at different moments of the evolution process towards life, i.e. at the levels of building blocks of Life, of the instructed or functional polymers, or even later at the stage of more elaborated chemical systems, will be critically discussed. The underlying principles and the experimental evidence will be commented for each scenario with particular attention on those leading to the induction and enhancement of enantiomeric excesses in proteinogenic amino acids, natural sugars, and their intermediates or derivatives. The aim of this review is to propose an updated and timely synopsis in order to stimulate new efforts in this interdisciplinary field.
Article
Context. While synthesis of organic molecules in molecular clouds or protoplanetary disks is complex, observations of interstellar grains, analyses of carbonaceous chondrites, and UV photochemistry experiments are rapidly developing and are providing constraints on and clues to the complex organic molecule synthesis in space. This motivates us to construct a theoretical synthesis model. Aims. We developed a new code to simulate global reaction sequences of organic molecules and apply it to sugar synthesis by intermittent UV irradiation on the surface of icy particles in a protoplanetary disk. Here we show the first results of our new simulation. Methods. We applied a Monte Carlo method to select reaction sequences from all possible reactions, using the graph-theoretic matrix model for chemical reactions and modeling reactions on the icy particles during UV irradiation. Results. We obtain results consistent with the organic molecules in carbonaceous chondrites and obtained by experiments, albeit through a different pathway from the conventional formose reactions previously suggested. During UV irradiation, loosely bonded O-rich large molecules are continuously created and destroyed. After UV irradiation is turned off, the ribose abundance rapidly increases through the decomposition of the large molecules via breakage of O−O bonds and replacements of C−OH by C−H to reach O/C = 1 for sugars. The sugar abundance is regulated mostly by the total atomic ratio H/O of starting materials, but not by their specific molecular forms. Deoxyribose is simultaneously synthesized, and most of the molecules end up in complexes with C-rich molecules.
Article
Glycolaldehyde, a C2 compound, is the simplest sugar molecule, but whether it inherently exists in plants remains bewildered due to its complicated existence form in aqueous solution. By combination of...
Article
Rationale: Sugars are key molecules of life but challenging to detect via Electrospray ionization mass spectrometry (ESI-MS). Unfortunately, sugars are challenging analytes for mass spectrometric methods due to their high gas-phase deprotonation energies and low gas-phase proton affinities which make them difficult to be ionized in high abundance for MS detection. Methods: Hydrogen bond interactions in H2 PO4 ̅ - Saccharide anionic systems both experimentally (via Electrospray Fourier transform ion cyclotron resonance mass spectrometry, ESI-FT-ICR-MS) and computationally by several sophisticated density-functional theoretical (DFT and DFT-D3) methods. Results: H2 PO4 ̅ dopant boosts the detection of sugars up to 51-times in case of sucrose and up to 263-times for glucose (at 0.1 ppm concentration level). H2 PO4 ̅ binds toward sugar molecules with noticeably more hydrogen bonds than the established dopant chloride Cl ̅ does, with increasing binding energies in the order: Monosaccharides < Trisaccharides < Disaccharides. Analysis of a complex oak plant sample revealed that NH4 H2 PO4 specifically labeled a diverse set of sugar-type plant metabolites in form of [M+H2 PO4 ] ̅ complexes. Conclusions: We reveal the mechanism of interaction of H2 PO4 ̅ with different sugars and glycosylated organic compounds, which significantly enhances their ionization in mass spectrometry. A computational and experimental investigation is presented. A strong correlation between MS signal intensities of detected [M+H2 PO4 ] ̅ anions of different saccharides and their calculated dissociation enthalpies was revealed. Thus, the variation of MS signal intensities can be very well described to a large extent by variation of calculated saccharides affinities toward H2 PO4 ̅ dopant anion, showing that DFT-D3 can very well describe experimental FT-ICR-MS observations.
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Life on Earth employs chiral amino acids in stereochemical l-form, but the cause of molecular symmetry breaking remains unknown. Chiroptical properties of amino acids – expressed in circular dichroism (CD) – have been previously investigated in solid and solution phase. However, both environments distort the intrinsic charge distribution associated with CD transitions. Here we report on CD and anisotropy spectra of amino acids recorded in the gas phase, where any asymmetry is solely determined by the genuine electromagnetic transition moments. Using a pressure- and temperature-controlled gas cell coupled to a synchrotron radiation CD spectropolarimeter, we found CD active transitions and anisotropies in the 130–280 nm range, which are rationalized by ab initio calculation. As gas phase glycine was found in a cometary coma, our data may provide insights into gas phase asymmetric photochemical reactions in the life cycle of interstellar gas and dust, at the origin of the enantiomeric selection of life’s l-amino acids.
Chapter
A fascinating question of abiogenesis is how simple organic molecules have developed into complex biological systems that are capable of being altered by evolutionary mechanisms. The fundamental question is what complexity is required to trigger evolution at the molecular level, i.e. molecules undergo their synthesis, selection and mutation leading to selectivity and replication. This question is closely linked to processes that lead to spontaneous symmetry breaking (chirogenesis) and ultimately to homochirality. This chapter focuses on mechanisms that lead to evolutionary systems at the level of organic molecules and open the possibility of chirogenesis. On the one hand, this is shown by the emergence of prebiotic organocatalysts and, on the other hand, a mechanism is discussed that leads naturally to the preferential formation of (deoxy)ribonucleosides and nucleotides. This creates the basis for self-sustaining and information-storing structures that can undergo dynamic alterations.
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ABSTRACT Context. Formaldehyde is a potential biogenic precursor involved in prebiotic chemical evolution. The cold conditions of the inter�stellar medium (ISM) allow H2CO to be reactive, playing a significant role as a chemical intermediate in formation pathways leading to interstellar complex organic molecules. However, gas-phase molecular formation mechanisms in cold regions of the ISM are poorly understood. Aims. We computationally determine the most favored gas-phase molecular formation mechanisms at local thermodynamic equillibrium conditions that can produce the detected amounts of H2CO in diffuse molecular clouds (DMCs), in dark, cold, and dense molecular clouds (DCDMCs), and in three regions of circumstellar envelopes of low-mass protostars (CELMPs). Methods. The potential energy surfaces, thermodynamic functions, and single-point energies for transition states were calculated at the CCSD(T)-F12/cc-pVTZ-F12 and MP2/aug-cc-pVDZ levels of theory and basis sets. Molecular thermodynamics and related partition functions were obtained by applying the Maxwell-Boltzmann quantum statistics theory from energies computed at CCSD(T)-F12/cc-pVTZ F12 with corrections for zero-point energy. A literature review on detected abundances of reactants helped us to propose the most favorable formation routes. Results. The most probable reactions that produce H2CO in cold astrophysical regions are: 1CH2 + ·3O2 → 1H2CO + O·(3P) in DMCs, ·3CH2 + ·3O2 → 1H2CO + ·O(3P) in DCDMCs, and ·CH3 + ·O(3P) → 1H2CO + ·H in region III, ·CH3 +·O(1D) → 1H2CO + ·H in region II, and 1CH2 + ·3O2 → 1H2CO + ·O(3P) in region I belonging to CELMPs. Conclusions. Quantum chemical calculations suggest that the principal carbonaceous precursors of H2CO in cold regions for the gas-phase are CH2(a1A1), and ·CH2(X3B1) combined with ·O2( 3 Σ g) and ·CH3(2A”) + ·O(3P) / O(1D). Reactions based on more complex reagents yield less effective thermodynamics in the gas-phase H2CO molecular formation.
Thesis
Présentes depuis la formation du Système Solaire, les comètes suscitent un intérêt particulier. Elles ont pu apporter sur la Terre primitive des composés organiques, et ainsi favoriser l’apparition de la vie. Des observations depuis la Terre et des missions spatiales ont permis de mesurer la composition de ces petits corps, et en particulier celle de son atmosphère. Un grand nombre des molécules observées dans l’environnement cométaire provient directement de la sublimation des glaces du noyau, mais la distribution de certaines d’entre elles est plus complexe.Ce travail de thèse entre dans le cadre de l’étude des sources distribuées dans les comètes. Deux molécules ont été étudiées au cours de cette thèse. D’une part, le formaldéhyde qui présente un comportement atypique dans la plupart des comètes dans lesquelles il a été détecté. Le cas de six comètes est discuté : C/2001 Q4 (NEAT), C/2004 Q2 (Machholz), 8P/Tuttle, C/1996 B2 (Hyakutake), C/2012 S1 (ISON) et C/2012 F6 (Lemmon). D’autre part la glycine, pour laquelle un profil de densité en fonction de la distance au noyau a été mesuré dans la comète 67P/Churyumov-Gerasimenko lors de la mission Rosetta. Ce profil de densité présente un comportement particulier.Afin d’interpréter ces observations, j’ai développé un modèle numérique appliqué dans un premier temps à la production de formaldéhyde dans les atmosphères cométaires, puis étendu au cas de la glycine. Deux cas ont été considérés pour l’étude du formaldéhyde : a. celui-ci est formé à partir de sublimation des glaces du noyau, b. celui-ci est produit à partir d’une source distribuée impliquant la dégradation thermique et photochimique du polyoxyméthylène présent sur les particules éjectées du noyau. Concernant la glycine, trois cas ont été pris en compte : a. celle-ci est émise directement et uniquement à partir de la sublimation des glaces du noyau, b. celle-ci est produite à partir de la sublimation de glycine solide présente sur les particules de poussière éjectées du noyau, c. celle-ci serait incluse dans la matrice de glace d’eau présente sur les particules de poussière éjectées du noyau et serait émise en phase gazeuse en même temps que la glace d’eau sublimerait. Ces deux derniers cas s’apparentent à une source distribuée.Une source unique à partir du noyau n’explique pas les profils de densité mesurés de formaldéhyde dans les comètes C/2001 Q4 (NEAT), C/2004 Q2 (Machholz), 8P/Tuttle, C/1996 B2 (Hyakutake), C/2012 S1 (ISON) et C/2012 F6 (Lemmon). Ce cas ne permet pas non plus d’expliquer les observations de glycine faites dans la comète 67P/Churyumov-Gerasimenko. La meilleure hypothèse concernant le formaldéhyde correspond donc, d’une part, à une faible production à partir du noyau, soit entre 0 et 0,2% par rapport à la production de gaz total. Et d’autre part à une majorité de formaldéhyde provenant d’une source distribuée à partir de la dégradation de son polymère, le polyoxyméthylène pour des quantités qui varient, d’une comète à l’autre, entre 0,25 et 2,7 % de polyoxyméthylène en masse dans les particules. En ce qui concerne la glycine, les observations peuvent être ajustées si l’on considère la sublimation de glace d’eau à partir des particules de poussière dans l’atmosphère avec une abondance de glycine d’environ 170 ppb en masse au sein de la glace d’eau
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The presence of numerous complex organic molecules (COMs; defined as those containing six or more atoms) around protostars shows that star formation is accompanied by an increase of molecular complexity. These COMs may be part of the material from which planetesimals and, ultimately, planets formed. Comets represent some of the oldest and most primitive material in the solar system, including ices, and are thus our best window into the volatile composition of the solar protoplanetary disk. Molecules identified to be present in cometary ices include water, simple hydrocarbons, oxygen, sulfur, and nitrogen-bearing species, as well as a few COMs, such as ethylene glycol and glycine. We report the detection of 21 molecules in comet C/2014 Q2 (Lovejoy), including the first identification of ethyl alcohol (ethanol, C2H5OH) and the simplest monosaccharide sugar glycolaldehyde (CH2OHCHO) in a comet. The abundances of ethanol and glycolaldehyde, respectively 5 and 0.8% relative to methanol (0.12 and 0.02% relative to water), are somewhat higher than the values measured in solar- type protostars. Overall, the high abundance of COMs in cometary ices supports the formation through grain-surface reactions in the solar system protoplanetary disk.
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Comets harbor the most pristine material in our solar system in the form of ice, dust, silicates, and refractory organic material with some interstellar heritage. The evolved gas analyzer Cometary Sampling and Composition (COSAC) experiment aboard Rosetta's Philae lander was designed for in situ analysis of organic molecules on comet 67P/Churyumov-Gerasimenko. Twenty-five minutes after Philae's initial comet touchdown, the COSAC mass spectrometer took a spectrum in sniffing mode, which displayed a suite of 16 organic compounds, including many nitrogen-bearing species but no sulfur-bearing species, and four compounds-methyl isocyanate, acetone, propionaldehyde, and acetamide-that had not previously been reported in comets. Copyright © 2015, American Association for the Advancement of Science.
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Significance In molecular clouds out of which stars and planetary systems form, simple solid-state molecules made in large part of H 2 O, CO, CO 2 , CH 3 OH, and NH 3 are abundantly present. In these environments, energetic and thermal processes on these ices, which can be simulated in the laboratory, lead to complex organic matter. Possibly at the origin of the organic matter in our Solar System and incorporated into planetesimals, this material may be considered as a potential source for prebiotic chemistry on telluric planets, following a process that may be quite universal. The composition of these laboratory-evolved ices includes potentially prebiotic species such as amino acids and, as presented in this paper, aldehydes and sugars.
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Divided into two parts, the first four chapters of Comets and their Origin refer to comets and their formation in general, describing cometary missions, comet remote observations, astrochemistry, artificial comets, and the chirality phenomenon. The second part covers the cometary Rosetta mission, its launch, journey, scientific objectives, and instrumentations, as well as the landing scenario on a cometary nucleus. Along the way, the author presents general questions concerning the origin of terrestrial water and the molecular beginnings of life on Earth, as well as how the instruments used on a space mission like Rosetta can help answer them. The text concludes with a chapter on what scientists expect from the Rosetta mission and how its data will influence our life on Earth. As a result, the author elucidates highly topical and fascinating knowledge to scientists and students of various scientific backgrounds, allowing them to work with Rosetta‘s data.
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The discovery of meteoritic amino acids with enantiomeric excesses of the L-form (ee L) has suggested that extraterrestrial organic materials may have contributed to prebiotic chemistry and directed the initial occurrence of the ee L that further led to homochirality of amino acids on Earth. A proposed mechanism for the origin of ee L in meteorites involves an asymmetric photochemistry of extraterrestrial ices by UV circularly polarized light (CPL). We have performed the asymmetric synthesis of amino acids on achiral extraterrestrial ice analogs by VUV CPL, investigating the chiral asymmetry transfer at two different evolutionary stages at which the analogs were irradiated (regular ices and/or organic residues) and at two different photon energies (6.6 and 10.2 eV). We identify 16 distinct amino acids and precisely measure the L-enantiomeric excesses using the enantioselective GC × GC-TOFMS technique in five of them: α-alanine, 2,3-diaminopropionic acid, 2-aminobutyric acid, valine, and norvaline, with values ranging from ee L = –0.20% ± 0.14% to ee L = –2.54% ± 0.28%. The sign of the induced ee L depends on the helicity and the energy of CPL, but not on the evolutionary stage of the samples, and is the same for all five considered amino acids. Our results support an astrophysical scenario in which the solar system was formed in a high-mass star-forming region where icy grains were irradiated during the protoplanetary phase by an external source of CPL of a given helicity and a dominant energy, inducing a stereo-specific photochemistry.
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Light work: UV irradiation of a system formed by adding copper(I) cyanide to an aqueous solution of glycolonitrile, sodium phosphate, and hydrogen sulfide efficiently generates aldehyde precursors to the building blocks of RNA and proteins.
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This study presents a liquid chromatography-ultraviolet (LC-UV) method for the accurate analysis of formose reaction products with regard to sum parameters. Limitations encountered in gas chromatography (e.g., thermal stability of analytes) were overcome. First, alditols are O-benzoylated and subjected to reversed-phase chromatography. They are then detected by UV and by electrospray ionization-mass spectrometry (ESI-MS) for validation purposes. Compared with standard 2,4-dinitrophenylhydrazine labeling, the accuracy of results from LC-UV is dramatically improved due to enhanced chromatographic resolution and validation by ESI-MS. For the first time ever, LC-UV may be used to accurately quantify 2-hydroxymethylglycerol, a branched chain alditol, D,L-glyceraldehyde, D,L-galactose, which represents the group of D,L-iditol/galactose/glucose/mannose and D,L-erythrose in formose reaction products.
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Interstellar glycolaldehyde (CH2OHCHO) has been detected in emission toward the Galactic center source Sagittarius B2(N) by means of millimeter-wave rotational transitions. Glycolaldehyde is an important biomarker since it is structurally the simplest member of the monosaccharide sugars that heretofore have gone undetected in interstellar clouds. There is no consensus as to how any such large complex molecules are formed in the interstellar clouds. It may be that the typical environment of dense interstellar clouds is favorable to glycolaldehyde synthesis by means of the polymerization of formaldehyde (H2CO) molecules either on grain surfaces or in the gas phase. Alternatively, we speculate that glycolaldehyde and other complex molecules may undergo assembly from functional molecular groups on grain surfaces. Utilizing common chemical precursors, a chance process could account for the high degree of isomerism observed in complex interstellar molecules (e.g., methyl formate, acetic acid, and glycolaldehyde). This work suggests that the phenomenon of isomerism be investigated further as a means of potentially constraining interstellar chemistry routes for those individual sources where the condition of good source-beam coupling can be achieved.
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Complex organic compounds, including many important to life on Earth, are commonly found in meteoritic and cometary samples, though their origins remain a mystery. We examined whether such molecules could be produced within the solar nebula by tracking the dynamical evolution of ice grains in the nebula and recording the environments to which they were exposed. We found that icy grains originating in the outer disk, where temperatures were less than 30 kelvin, experienced ultraviolet irradiation exposures and thermal warming similar to that which has been shown to produce complex organics in laboratory experiments. These results imply that organic compounds are natural by-products of protoplanetary disk evolution and should be important ingredients in the formation of all planetary systems, including our own.
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The much-studied Murchison meteorite is generally used as the standard reference for organic compounds in extraterrestrial material. Amino acids and other organic compounds important in contemporary biochemistry are thought to have been delivered to the early Earth by asteroids and comets, where they may have played a role in the origin of life. Polyhydroxylated compounds (polyols) such as sugars, sugar alcohols and sugar acids are vital to all known lifeforms-they are components of nucleic acids (RNA, DNA), cell membranes and also act as energy sources. But there has hitherto been no conclusive evidence for the existence of polyols in meteorites, leaving a gap in our understanding of the origins of biologically important organic compounds on Earth. Here we report that a variety of polyols are present in, and indigenous to, the Murchison and Murray meteorites in amounts comparable to amino acids. Analyses of water extracts indicate that extraterrestrial processes including photolysis and formaldehyde chemistry could account for the observed compounds. We conclude from this that polyols were present on the early Earth and therefore at least available for incorporation into the first forms of life.
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Glycerol nucleic acid (GNA) is an interesting alternative base-pairing system based on an acyclic, glycerol-phosphate backbone repeat unit. The question of whether DNA polymerases can catalyze efficient template-dependent synthesis using GNA as the template is of particular interest because GNA is unable to form a stable duplex with DNA. In the present study, we screened a variety of DNA polymerases for GNA-dependent DNA synthesis. We find that Bst DNA polymerase can catalyze full-length DNA synthesis on a dodecamer GNA template. The efficiency of DNA synthesis is increased by replacing adenine with diaminopurine in both the GNA template and the DNA monomers and by the presence of manganese ions. We suggest that the BstDNA polymerase maintains a short, transient region of base-pairing between the DNA product strand and the GNA template, but that stable duplex formation between product and template strands is not required for template-dependent polymerization. • information transfer • polymerase
Book
This volume contains the lectures presented at the second course of the International School of Space Chemistry held in Erice (Sicily) from October 20 - 30 1991 at the "E. Majorana Centre for Scientific Culture". The course was attended by 58 participants from 13 countries. The Chemistry of Life's Origins is well recognized as one of the most critical subjects of modem chemistry. Much progress has been made since the amazingly perceptive contributions by Oparin some 70 years ago when he first outlined a possible series of steps starting from simple molecules to basic building blocks and ultimate assembly into simple organisms capable of replicating, catalysis and evolution to higher organisms. The pioneering experiments of Stanley Miller demonstrated already forty years ago how easy it could have been to form the amino acids which are critical to living organisms. However we have since learned and are still learning a great deal more about the primitive conditions on earth which has led us to a rethinking of where and how the condition for prebiotic chemical processes occurred. We have also learned a great deal more about the molecular basis for life. For instance, the existence of DNA was just discovered forty years ago.
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Divided into two parts, the first four chapters of Comets and their Origin refer to comets and their formation in general, describing cometary missions, comet remote observations, astrochemistry, artificial comets, and the chirality phenomenon. The second part covers the cometary ROSETTA mission, its launch, journey, scientific objectives, and instrumentations, as well as the landing scenario on a cometary nucleus. Along the way, the author presents general questions concerning the origin of terrestrial water and the molecular beginnings of life on Earth, as well as how the instruments used on a space mission like ROSETTA can help answer them. The text concludes with a chapter on what scientists expect from the ROSETTA mission and how its data will influence our life on Earth. As a result, the author elucidates highly topical and fascinating knowledge to scientists and students of various scientific backgrounds, allowing them to work with ROSETTA's data.
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The surface and subsurface of comets preserve material from the formation of the solar system. The properties of cometary material thus provide insight into the physical and chemical conditions during their formation. We present mass spectra taken by the Ptolemy instrument 20 minutes after the initial touchdown of the Philae lander on the surface of comet 67P/Churyumov-Gerasimenko. Regular mass distributions indicate the presence of a sequence of compounds with additional -CH2- and -O- groups (mass/charge ratios 14 and 16, respectively). Similarities with the detected coma species of comet Halley suggest the presence of a radiation-induced polymer at the surface. Ptolemy measurements also indicate an apparent absence of aromatic compounds such as benzene, a lack of sulfur-bearing species, and very low concentrations of nitrogenous material. Copyright © 2015, American Association for the Advancement of Science.
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This chapter describes that mass spectrometry (m.s.) has become an important and versatile technique in carbohydrate chemistry. The chapter deals with m.s. as a tool in the structural analysis of naturally occurring carbohydrates. The mass spectra of permethylated methyl glycosides show ions derived from a number of specific degradation pathways. These fragmentations have been carefully studied in the chapter, by using deuterium-labelling techniques. Direct derivatization of reducing sugars by permethylation, peracetylation, or per( trimethylsilyl )ation gives a mixture of glycosides. These derivatives are suitable for g.1.c. analysis, although, for complex mixtures of sugars, the multiplicity of peaks caused by the derivatization may complicate elucidation of the results. The partially methylated sugars are separated and converted into the methyl glycosides, and these are methylated with trideuteriomethyl iodide. The substitution pattern of the trideuteriomethyl groups can be determined by m.s., and the nature of the sugar ascertained by g.1.c. (by comparison with the permethylated compound used as the reference sample).
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Under UV irradiation in the presence of an inorganic base, aqueous formaldehyde was found to give pentaerythritol and 2-hydroxymethylglycerol as the main products, accompanied by the concomitant formation of a mixture of sugars and sugar alcohols. The results indicate that this photochemical formose reaction is considerably different in product distribution from the thermal formose reaction using the Ca(OH)2 catalyst. The detailed examination of the photochemical formose reaction was carried out in the presence of Na2CO3, and a possible scheme for the formation of pentaerythritol and 2-hydroxymethylglycerol is proposed.
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Trimethylsilyl ethers of alditols with 3, 4, 5 and 6 C atoms were investigated. The mass spectra are unusually clearly correlated with the structures. The predominant fragmentations are cleavages in the carbon chain and rearrangement loss of trimethylsilanol. The spectra are closely related to those of the methyl ethers. A spectrum unambiguously identifies a compound as an alditol and permits the determination of its molecular weight.
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The four components of each aldopentose were separated as O-trimethylsilyl ethers on several packed and capillary columns. In order to establish which characteristics affect the retention and to achieve a better understanding of the chromatographic behaviour of these compounds, a mathematical approach was applied which tries to relate structural characteristics with retention indices on several stationary phases.
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Motivated by detections of glycolaldehyde and ethylene glycol in the interstellar medium and, for ethylene glycol, in comet Hale-Bopp, we report the low-temperature mid-IR spectra of these two molecules, including selected band strengths and positions. Each molecule has also been irradiated with 0.8MeV protons to simulate cosmic-ray exposure, to measure each molecule’s radiation lifetime, and to determine radiation chemical products. Evidence is presented that glycolaldehyde is readily formed from irradiated ethylene glycol ices, both in the presence and absence of H2O ice.
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The chemical and morphological structure of comets is based on a fluffy aggregate of interstellar dust with an average porosity of P = 0.8. Observations of the volatile and dust (refractory) components of comets are seen to provide evidence of the preservation of a major fraction of the interstellar dust composition in periodic comets even after 4.5 billion years in the Oort cloud. The effects of thermal evolution do not appear to introduce any gross chemical modification. The fluffy character of the nucleus in combination with the submicron units of its structure indicate a possible mechanism for delivery of a substantial fraction of the prebiotic interstellar dust molecules by nucleus fragmentation and ablation so long as comet impacts were cushioned by a dense atmosphere on the early earth.
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Interstellar ices were simulated by condensing and UV irradiating molecules such as H2O, CH3OH, and NH3 at 80 K. Multidimensional gas chromatography analyses allowed for the identification of 26 amino and diamino acids (see graph). The results support the suggestion that potentially prebiotic molecules originating from the photochemistry of interstellar ices could have been incorporated in cometary dust and delivered to the early Earth.
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The mass spectra of the trimethylsilyl ethers of α-D-glucose and its 1,2,3,4,5,6,6-d 7, 1-d, and 6,6-d 2 analogs, of methyl α-D-glucopyranoside, of ethyl β-D-galactofuranoside, and of methyl 3-acetamido-3-deoxy-α-D-glucopyranoside and its NHCOCD 3 analog are presented. The fragmentations of these derivatives are discussed in detail, using deuterium-labeling and exact-mass data from high-resolution measurements to support the interpretations. The mass spectra of these model compounds are used in the identification of minor components formed in the trimethylsilylation of equilibrium mixtures of D-galactose, D-glucose and three of its deuterated analogs, 3-O-methyl-D-glucose, and 2-acetamido-2-deoxy-D-galactose. The same approach was used to determine the products from glycosidation of D-galactose and D-glucose. The mass spectra of these minor components were obtained from a coupled gas chromatograph-mass spectrometer. Furanose and furanoside structures can be assigned to the minor components.
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The separation and estimation of carbohydrates and related polyhydroxy compounds by gas-liquid chromatography of trimethylsilyl (TMS) derivatives is described. The formation of the TMS derivative, in pyridine containing hexamethyldisilazane and trimethylchlprosilane, occurs very rapidly at room temperature so that analyses can be made within a few minutes. Comparative studies of the reaction product of methyl a-glucopyranoside and authentic methyl (tetra-O-trimethylsilyl )-α-glucOpyranoside indicate that silylation of all free hydroxyl groups occurs and that the yield of TMS derivative is virtually quantitative. Conditions are described for chromatography of a wide variety of carbohydrates from C 2 (glycolaldehyde) to C 24 (stachyose) and related substances such as glycosides, deoxysugars, inositols, hexosamines, and N-acetylneuraminic acid. Most of the studies have been made with a silicone column (SE-52) and a polyester column (polyethylene glycolsuccinate) but separations of the TMS derivatives are possible on other polar and non-polar columns. Iso-thermal conditions are usually employed for separations within a narrow range of molecular weight; separations of more complex mixtures, with components of widely differing molecular weights, may be made by linear temperature-programmed analysis. Excellent separations are generally observed with anomeric pairs as well as configurational isomers within a given class such as pentoses, hexoses, disaccharides, etc. The identity of an unknown sugar may be determined by multiple analyses on a number of liquid phases or, alternatively, by analyses of the parent sugar and various derivatives such as methyl glycoside, alcohol, lactone, oxime, and acetal. In all such cases TMS derivatives are prepared prior to gas chromatography. Comparisons are reported for the compositions of aqueous equilibrium solutions of aldoses, by gas Chromatographic analysis, with those reported by measurements of optical rotation and bromine oxidation. Ih several cases unexpected retention times are interpreted in terms of conformational differences of the sugars.
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The introduction and development of comprehensive two-dimensional gas chromatography offers greatly enhanced resolution and identification of organic analytes in complex mixtures compared to any one-dimensional separation technique. Initially promoted by the need to resolve highly complex petroleum samples, the technique's enormous separation power and enhanced ability to gather information has rapidly attracted the attention of analysts from all scientific fields. In this Minireview, we highlight the fundamental theory, recent advances, and future trends in the instrumentation and application of comprehensive two-dimensional column separation.
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Glycolaldehyde (HCOCH2OH) is the simplest sugar and an important intermediate in the path toward forming more complex biologically relevant molecules. In this paper we present the first detection of 13 transitions of glycolaldehyde around a solar-type young star, through Atacama Large Millimeter Array (ALMA) observations of the Class 0 protostellar binary IRAS 16293-2422 at 220 GHz (6 transitions) and 690 GHz (7 transitions). The glycolaldehyde lines have their origin in warm (200-300 K) gas close to the individual components of the binary. Glycolaldehyde co-exists with its isomer, methyl formate (HCOOCH3), which is a factor 10-15 more abundant toward the two sources. The data also show a tentative detection of ethylene glycol, the reduced alcohol of glycolaldehyde. In the 690 GHz data, the seven transitions predicted to have the highest optical depths based on modeling of the 220 GHz lines all show red-shifted absorption profiles toward one of the components in the binary (IRAS16293B) indicative of infall and emission at the systemic velocity offset from this by about 0.2" (25 AU). We discuss the constraints on the chemical formation of glycolaldehyde and other organic species - in particular, in the context of laboratory experiments of photochemistry of methanol-containing ices. The relative abundances appear to be consistent with UV photochemistry of a CH3OH-CO mixed ice that has undergone mild heating. The order of magnitude increase in line density in these early ALMA data illustrate its huge potential to reveal the full chemical complexity associated with the formation of solar system analogs.
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Equilibrium tautomers of aldopentoses (arabinose, ribose, xylose and lyxose) and aldohexones (allose, altrose, gulose, idose and talose) have been analyzed as their trimethyl-silyl ethers by capillary GC. Pentoses were separated on SE-54 and hexoses on OV-225. The four components of the tautomer equilibrium mixture have been identified using GC/MS and NMR data.
Article
Open-chain trimethylsilyl derivatives of aldonic and deoxyaldonic acids, which can be prepared from salts of the acids, are well suited for structure determination by mass spectrometry. The study is focussed on aldonic and unbranched monodeoxyaldonic acids, but several dideoxyaldonic and branched deoxyaldonic acids are included. Spectra of the derivatives of glycolic, lactic and hydracrylic acids are discussed.The structural isomers exhibit interpretable differences, whereas the spectra of the diastereomers are similar. The molecular weight and the number of OH groups can be deduced from the spectra, as well as the position of the “deoxy group” in unbranched deoxyaldonic acids. The most prominent fragmentations are α-cleavages of the carbon chain, frequently followed by rearrangement loss of trimethylsilanol. A structurally significant McLafferty-type rearrangement of a trimethylsilyl group is described. Several types of ions decompose by expulsion of small molecules such as CO, CH2O and CO2.
Article
Irradiation of interstellar/circumstellar ice analogs by ultraviolet (UV) light followed by warm up in the laboratory leads to the formation of complex organic molecules, stable at room temperature. Hydrolysis of the room temperature residue releases amino acids, the building blocks of proteins. These amino acids exist in two different forms (l and d), but proteins encountered in living beings consist exclusively of l enantiomers. The origin of this property, called homochirality, is still unknown. Amino acids can be detected and quantified by chemical techniques such as chiral gas chromatography coupled with mass spectrometry (GC-MS). Enantiomers of chiral organics are also known to interact selectively with circularly polarized light (CPL), leading to a selective production or destruction of the final compounds. This paper describes how we settled an experiment where amino acids are formed by irradiation of interstellar/circumstellar ice analogs with ultraviolet (UV) CPL, produced by a synchrotron radiation beamline, which allowed us to quantify the effect of such polarized light on the production of amino acids. These results can be compared to the enantiomeric excesses measured in primitive meteorites such as Murchison.
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Summary Fragmentation patterns and quantitation possibilities of gas chromatography-mass spectrometry (GC-MS) with Ion Trap Detection (ITD) are reported for the trimethylsilyl (TMS) derivatives of selected aliphatic and aromatic/cyclohexanoic, mono-, di- and polyhydroxy/methoxy carboxylic acids,o-phosphoric acid, proline and 5-hydroxymethylfurfurol (HMF)— (common in natural matrices, such as fruits, honey etc.). In order to maintain stability of derivatives, their stock solutions were diluted with hexamethyldisilazane. Quantitation was carried out simultaneously on the basis both of the total ion current (TIC) and selective fragment ion (SFI) values. Data obtained proved that (i) the fragmentation of different TMS acids provided very informative, utilizable characteristics, that were also suitable for quantitation; (ii) the type of fragments do not differ in their m/z values compared to those obtained in the Mass Spectral Database; (iii) the advantages of ITD due to its ‘soft’ fragmentation feature resulted in higher abundance of characteristic ions $$[M]^{_ \cdot ^ + }$$ , ([M−CH3]+, [M+1]+, [M+TMS]+, [M+2TMS]+) compared to the non characteristic reagent ones (at m/z=73,147). Determination of oxalic, glycolic, pyruvic, levulinic, succinic, malic, pimelic, tartaric, citric, palmitic, oleic, stearic, arachidic, shikimic, quinic, chlorogenic acids, as well as those ofo-phosphoric acid, HMF and proline have been carried out in the concentration range of 1–20 ng of compounds. Reproducibility on the basis of TIC and SFI values, in the order listed, proved to be 0.8–8.6% and 1.3–16.0% (relative standard deviation percentages).
Article
The pre-RNA world hypothesis postulates that RNA was preceded in the evolution of life by a simpler genetic material, but it is not known if such systems can fold into structures capable of eliciting a desired function. Presumably, whatever chemistry gave rise to RNA would have produced other RNA analogues, some of which may have preceded or competed directly with RNA. Threose nucleic acid (TNA), a potentially natural derivative of RNA, has received considerable interest as a possible RNA progenitor due to its chemical simplicity and ability to exchange genetic information with itself and RNA. Here, we have applied Darwinian evolution methods to evolve, in vitro, a TNA receptor that binds to an arbitrary target with high affinity and specificity. This demonstration shows that TNA has the ability to fold into tertiary structures with sophisticated chemical functions, which provides evidence that TNA could have served as an ancestral genetic system during an early stage of life.
Article
One of the central goals of multi-wavelength galaxy cluster cosmology is to unite all cluster observables to form a consistent understanding of cluster mass. Here, we study the impact of systematic effects from optical cluster catalogs on stacked SZ signals. We show that the optically predicted Y-decrement can vary by as much as 50% based on the current 2 sigma systematic uncertainties in the observed mass-richness relationship. Mis-centering and impurities will suppress the SZ signal compared to expectations for a clean and perfectly centered optical sample, but to a lesser degree. We show that the level of these variations and suppression is dependent on the amount of systematics in the optical cluster catalogs. We also study X-ray luminosity-dependent sub-sampling of the optical catalog and find that it creates Malmquist bias increasing the observed Y-decrement of the stacked signal. We show that the current Planck measurements of the Y-decrement around SDSS optical clusters and their X-ray counterparts are consistent with expectations after accounting for the 1 sigma optical systematic uncertainties using the Johnston mass richness relation.
Article
MassBank is the first public repository of mass spectra of small chemical compounds for life sciences (<3000 Da). The database contains 605 electron-ionization mass spectrometry (EI-MS), 137 fast atom bombardment MS and 9276 electrospray ionization (ESI)-MS(n) data of 2337 authentic compounds of metabolites, 11 545 EI-MS and 834 other-MS data of 10,286 volatile natural and synthetic compounds, and 3045 ESI-MS(2) data of 679 synthetic drugs contributed by 16 research groups (January 2010). ESI-MS(2) data were analyzed under nonstandardized, independent experimental conditions. MassBank is a distributed database. Each research group provides data from its own MassBank data servers distributed on the Internet. MassBank users can access either all of the MassBank data or a subset of the data by specifying one or more experimental conditions. In a spectral search to retrieve mass spectra similar to a query mass spectrum, the similarity score is calculated by a weighted cosine correlation in which weighting exponents on peak intensity and the mass-to-charge ratio are optimized to the ESI-MS(2) data. MassBank also provides a merged spectrum for each compound prepared by merging the analyzed ESI-MS(2) data on an identical compound under different collision-induced dissociation conditions. Data merging has significantly improved the precision of the identification of a chemical compound by 21-23% at a similarity score of 0.6. Thus, MassBank is useful for the identification of chemical compounds and the publication of experimental data.
Article
We simulate experimentally the physical conditions present in dense clouds by means of a high vacuum experimental setup at low temperature $T$ $\approx$ 12 K. The accretion and photoprocessing of ices on grain surfaces is simulated in the following way: an ice layer with composition analogous to that of interstellar ices is deposited on a substrate window, while being irradiated by ultraviolet (UV) photons. Subsequently the sample is slowly warmed up to room temperature; a residue remains containing the most refractory products of photo- and thermal processing. In this paper we report on the Fourier transform-infrared (FT-IR) spectroscopy of the refractory organic material formed under a wide variety of initial conditions (ice composition, UV spectrum, UV dose and sample temperature). The refractory products obtained in these experiments are identified and the corresponding efficiencies of formation are given. The first evidence for carboxylic acid salts as part of the refractory products is shown. The features in the IR spectrum of the refractory material are attributed to hexamethylenetetramine (HMT, [ (CH$_2$)$_6$N$_4$] ), ammonium salts of carboxylic acids [ (R–COO$^-$)(NH$^+_4$)] , amides [ H$_2$NC(=O)–R] , esters [ R–C(=O)–O–R$'$] and species related to polyoxymethylene (POM, [ (–CH$_2$O–)$_n$] ). Furthermore, evidence is presented for the formation of HMT at room temperature, and the important role of H$_2$O ice as a catalyst for the formation of complex organic molecules. These species might also be present in the interstellar medium (ISM) and form part of comets. Ongoing and future cometary missions, such as Stardust and Rosetta, will allow a comparison with the laboratory results, providing new insight into the physico-chemical conditions present during the formation of our solar system.
Article
The general features of the genetic code are described. It is considered that originally only a few amino acids were coded, but that most of the possible codons were fairly soon brought into use. In subsequent steps additional amino acids were substituted when they were able to confer a selective advantage, until eventually the code became frozen in its present form.
Article
It is argued that the evolution of the genetic apparatus must have required the abiotic formation of macromolecules capable of residue-by-residue replication. This suggests that polynucleotides were present even in the most primitive ancestors of contemporary organisms. Models which explain the evolution of the association between polynucleotide and polypeptide sequences are discussed.
Article
The interstellar grains are currently considered to be the basic building blocks of comets and, possibly, meteorites. To test this theory, a simulation of the organic layer accreted onto interstellar dust particles was prepared by slow deposition of a CO:NH3:H2O gas mixture on an Al block at 10 K, with concomitant irradiation with vacuum UV. The results of the HPLC and IR analyses of the nonvolatile residue formed by photolysis at 10 K are compared with those observed at 77 K and 298 K. Some of the compounds that may be present on the surfaces of interstellar dust particles have been identified, and some specific predictions concerning the types of molecular species present in comets could be drawn. The results also suggest that photochemical reactions may have been important for the formation of meteorite components. The implication of the findings to the questions of the source of organic matter on earth and the origin of life are discussed.