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Prebiotic chemistry

Christina Schneider, Sidney Becker, Hidenori Okamura, Antony Crisp, Tynchtyk Amatov, Michael Stadlmeier, Thomas Carell
The RNA world hypothesis assumes that life on earth started with small RNA molecules that catalyzed their own formation. Vital to this hypothesis is the need for prebiotic routes towards RNA. Contemporary RNA, however, is not only constructed from the four canonical nucleobases (A, C, G and U), but it contains in addition many chemically modified (non-canonical) bases. A yet open question is if these non-canonical bases were formed in parallel to the canonical bases (chemical origin), or whether they were created later, when life demanded higher functional diversity (biological origin)...
March 13, 2018: Angewandte Chemie
Brooke Anderson, Ramanarayanan Krishnamurthy
Pyrophosphate linkages are important in extant biology and are hypothesized to have played a role in prebiotic chemistry and in the origination of oligonucleotides. Inspired by the possible role of pyrophosphate as backbones of primordial oligomers, we synthesized DNA oligomers with varying amounts of pyrophosphate inserts (ppDNA) and investigated their base-pairing properties. As expected, with increasing amounts of pyrophosphate inserts in the backbone the thermal stability of ppDNA-DNA duplexes was compromised...
March 12, 2018: Chemistry: a European Journal
Avinash Vicholous Dass, Maguy Jaber, André Brack, Frédéric Foucher, Terence P Kee, Thomas Georgelin, Frances Westall
A concise outlook on the potential role of confinement in phosphorylation and phosphate condensation pertaining to prebiotic chemistry is presented. Inorganic confinement is a relatively uncharted domain in studies concerning prebiotic chemistry, and even more so in terms of experimentation. However, molecular crowding within confined dimensions is central to the functioning of contemporary biology. There are numerous advantages to confined environments and an attempt to highlight this fact, within this article, has been undertaken, keeping in context the limitations of aqueous phase chemistry in phosphorylation and, to a certain extent, traditional approaches in prebiotic chemistry...
March 5, 2018: Life
Raffaele Saladino, Lorenzo Botta, Ernesto Di Mauro
Meteorites are consensually considered to be involved in the origin of life on this Planet for several functions and at different levels: (i) as providers of impact energy during their passage through the atmosphere; (ii) as agents of geodynamics, intended both as starters of the Earth's tectonics and as activators of local hydrothermal systems upon their fall; (iii) as sources of organic materials, at varying levels of limited complexity; and (iv) as catalysts. The consensus about the relevance of these functions differs...
February 22, 2018: Life
Sandra L Blair, Nga L Ng, Stephen C Zambrzycki, Anyin Li, Facundo M Fernández
In this communication, we report on the real-time analysis of organic aerosol particles by Vacuum-assisted Plasma Ionization-Mass Spectrometry (Aero-VaPI-MS) using a home-built VaPI ion source coupled to a Synapt G2-S HDMS ion mobility-mass spectrometry (IM-MS) system. Standards of organic molecules of interest in prebiotic chemistry were used to generate aerosols. Monocaprin and decanoic acid aerosol particles were successfully detected in both the positive and negative ion modes, respectively. A complex aerosol mixture of different sizes of polymers of L-malic acid was also examined through ion mobility (IM) separations, resulting in the detection of polymers of up to eight monomeric units...
February 5, 2018: Journal of the American Society for Mass Spectrometry
Saúl A Villafañe-Barajas, João Paulo T Baú, María Colín-García, Alicia Negrón-Mendoza, Alejandro Heredia-Barbero, Teresa Pi-Puig, Dimas A M Zaia
Any proposed model of Earth's primitive environments requires a combination of geochemical variables. Many experiments are prepared in aqueous solutions and in the presence of minerals. However, most sorption experiments are performed in distilled water, and just a few in seawater analogues, mostly inconsistent with a representative primitive ocean model. Therefore, it is necessary to perform experiments that consider the composition and concentration of dissolved salts in the early ocean to understand how these variables could have affected the absorption of organic molecules into minerals...
February 1, 2018: Origins of Life and Evolution of the Biosphere
Surajit Nandi, Debankur Bhattacharyya, Anakuthil Anoop
The HCN oligomerization is considered to be one of the important pathways in the chemical evolution. Nucleobases, aminoacids and many other complex organic molecules can be evolved through this pathway. We report an explorative study based on automated reaction search method that avoid the cognitive bias in searching the chemical reaction space. We have discussed the chemical space of HCN dimer elaborately, and the important trimers and tetramers are discussed briefly. A component wise molecular fingerprint based methodology is proposed for identifying molecular similarity...
January 25, 2018: Chemistry: a European Journal
Clémentine Gibard, Subhendu Bhowmik, Megha Karki, Eun-Kyong Kim, Ramanarayanan Krishnamurthy
Prebiotic phosphorylation of (pre)biological substrates under aqueous conditions is a critical step in the origins of life. Previous investigations have had limited success and/or require unique environments that are incompatible with subsequent generation of the corresponding oligomers or higher-order structures. Here, we demonstrate that diamidophosphate (DAP)-a plausible prebiotic agent produced from trimetaphosphate-efficiently (amido)phosphorylates a wide variety of (pre)biological building blocks (nucleosides/tides, amino acids and lipid precursors) under aqueous (solution/paste) conditions, without the need for a condensing agent...
February 2018: Nature Chemistry
Vanessa Riffet, Gilles Frison, Guy Bouchoux
The two first steps of the Strecker synthesis of glycine, namely (a) addition of ammonia to formaldehyde to give aminomethanol and (b) its dehydration leading to methaneimine, is studied using high level quantum chemistry computations (G3B3). Water solvation is modeled by considering the effect of adding a discrete number of active or passive molecules of water (up to four) and by immersing the identified water-solute complexes in a conductor-like polarizable continuum solvent model. Activation of the reactants by protonation is also examined...
January 22, 2018: Journal of Physical Chemistry. A
Queenie H S Chan, Michael E Zolensky, Yoko Kebukawa, Marc Fries, Motoo Ito, Andrew Steele, Zia Rahman, Aiko Nakato, A L David Kilcoyne, Hiroki Suga, Yoshio Takahashi, Yasuo Takeichi, Kazuhiko Mase
Direct evidence of complex prebiotic chemistry from a water-rich world in the outer solar system is provided by the 4.5-billion-year-old halite crystals hosted in the Zag and Monahans (1998) meteorites. This study offers the first comprehensive organic analysis of the soluble and insoluble organic compounds found in the millimeter-sized halite crystals containing brine inclusions and sheds light on the nature and activity of aqueous fluids on a primitive parent body. Associated with these trapped brines are organic compounds exhibiting wide chemical variations representing organic precursors, intermediates, and reaction products that make up life's precursor molecules such as amino acids...
January 2018: Science Advances
Florent Calvo, Marie-Christine Bacchus-Montabonel
Recent photochemistry experiments provided evidence for the formation of hydantoin by irradiation of interstellar ice analogues. The significance of these results and the importance of hydantoin in prebiotic chemistry and polypeptide synthesis motivate the present theoretical investigation, in which we analyzed the effects of stepwise hydration on the structures, electronic and thermodynamical properties of microhydrated hydantoin using a variety of computational approaches. We generally find microhydration to proceed around the hydantoin heterocycle until 5 water molecules are reached, at which stage hydration becomes segregated with a water cluster forming aside the heterocycle...
January 12, 2018: Journal of Physical Chemistry. A
Zachary R Adam, Yayoi Hongo, H James Cleaves, Ruiqin Yi, Albert C Fahrenbach, Isao Yoda, Masashi Aono
Water creates special problems for prebiotic chemistry, as it is thermodynamically favorable for amide and phosphodiester bonds to hydrolyze. The availability of alternative solvents with more favorable properties for the formation of prebiotic molecules on the early Earth may have helped bypass this so-called "water paradox". Formamide (FA) is one such solvent, and can serve as a nucleobase precursor, but it is difficult to envision how FA could have been generated in large quantities or accumulated in terrestrial surface environments...
January 10, 2018: Scientific Reports
Nieves Lavado, Juan García de la Concepción, Reyes Babiano, Pedro Cintas
The condensation of cyanamide and glyoxal, two well-known prebiotic monomers, in aqueous phase has been investigated in great detail, demonstrating the formation of oligomeric species of varied structure, though consistent with generalizable patterns. This chemistry involving structurally simple substances also illustrates the ability of building molecular complexity under prebiotically plausible conditions, not only on Earth but also on extraterrestrial scenarios. We show that cyanamide-glyoxal reactions in water lead to mixtures comprising both acyclic and cyclic fragments, largely based on fused five- and six-membered rings, which can be predicted by computation...
January 10, 2018: Chemistry: a European Journal
Giovanni Vladilo, Ali Hassanali
The scientific community is allocating more and more resources to space missions and astronomical observations dedicated to the search for life beyond Earth. This experimental endeavor needs to be backed by a theoretical framework aimed at defining universal criteria for the existence of life. With this aim in mind, we have explored which chemical and physical properties should be expected for life possibly different from the terrestrial one, but similarly sustained by genetic and catalytic molecules. We show that functional molecules performing genetic and catalytic tasks must feature a hierarchy of chemical interactions operating in distinct energy bands...
January 3, 2018: Life
Thomas Böttcher
Life is a complex phenomenon and much research has been devoted to both understanding its origins from prebiotic chemistry and discovering life beyond Earth. Yet, it has remained elusive how to quantify this complexity and how to compare chemical and biological units on one common scale. Here, a mathematical description of molecular complexity was applied allowing to quantitatively assess complexity of chemical structures. This in combination with the orthogonal measure of information complexity resulted in a two-dimensional complexity space ranging over the entire spectrum from molecules to organisms...
December 19, 2017: Journal of Molecular Evolution
Matthias Granold, Parvana Hajieva, Monica Ioana Toşa, Florin-Dan Irimie, Bernd Moosmann
All extant life employs the same 20 amino acids for protein biosynthesis. Studies on the number of amino acids necessary to produce a foldable and catalytically active polypeptide have shown that a basis set of 7-13 amino acids is sufficient to build major structural elements of modern proteins. Hence, the reasons for the evolutionary selection of the current 20 amino acids out of a much larger available pool have remained elusive. Here, we have analyzed the quantum chemistry of all proteinogenic and various prebiotic amino acids...
December 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
Stéphane Tirard
In 1929 the British biologist John Burdon Sanderson Haldane published a hypothesis on the origin of life on earth, which was one of the most emblematic of the interwar period. It was a scenario describing the progressive evolution of matter on the primitive earth and the emergence of life. Firstly, this paper presents the main ideas put forward by Haldane in this famous text. The second part makes comparisons between Haldane and Alexander Ivanovitch Oparin's ideas regarding the origins of life (1924). These two theories, apparently very similar, presented distinct conclusions...
November 2017: Journal of Genetics
Falk Wachowius, James Attwater, Philipp Holliger
The emergence of functional cooperation between the three main classes of biomolecules - nucleic acids, peptides and lipids - defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i...
January 2017: Quarterly Reviews of Biophysics
Valentina Erastova, Matteo T Degiacomi, Donald G Fraser, H Chris Greenwell
Some seventy years ago, John Desmond Bernal proposed a role for clays in the origin of life. While much research has since been dedicated to the study of silicate clays, layered double hydroxides, believed to be common on the early Earth, have received only limited attention. Here we examine the role that layered hydroxides could have played in prebiotic peptide formation. We demonstrate how these minerals can concentrate, align and act as adsorption templates for amino acids, and during wetting-drying cycles, promote peptide bond formation...
December 11, 2017: Nature Communications
Hyo-Joong Kim, Steven A Benner
The "RNA World" hypothesis proposes an early episode of the natural history of Earth, where RNA was used as the only genetically encoded molecule to catalyze steps in its metabolism. This, according to the hypothesis, included RNA catalysts that used RNA cofactors. However, the RNA World hypothesis places special demands on prebiotic chemistry, which must now deliver not only four ribonucleosides, but also must deliver the "functional" portion of these RNA cofactors. While some (e.g., methionine) present no particular challenges, nicotinamide ribose is special...
January 12, 2018: Chemistry: a European Journal
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