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Prebiotic chemistry

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https://www.readbyqxmd.com/read/28727932/laboratory-studies-of-methane-and-its-relationship-to-prebiotic-chemistry
#1
Kensei Kobayashi, Wolf D Geppert, Nathalie Carrasco, Nils G Holm, Olivier Mousis, Maria Elisabetta Palumbo, J Hunter Waite, Naoki Watanabe, Lucy M Ziurys
To examine how prebiotic chemical evolution took place on Earth prior to the emergence of life, laboratory experiments have been conducted since the 1950s. Methane has been one of the key molecules in these investigations. In earlier studies, strongly reducing gas mixtures containing methane and ammonia were used to simulate possible reactions in the primitive atmosphere of Earth, producing amino acids and other organic compounds. Since Earth's early atmosphere is now considered to be less reducing, the contribution of extraterrestrial organics to chemical evolution has taken on an important role...
July 20, 2017: Astrobiology
https://www.readbyqxmd.com/read/28723229/the-formation-of-nucleobases-from-the-ultraviolet-photoirradiation-of-purine-in-simple-astrophysical-ice-analogues
#2
Christopher K Materese, Michel Nuevo, Scott A Sandford
Nucleobases are the informational subunits of RNA and DNA and are essential to all known forms of life. The nucleobases can be divided into two groups of molecules: the pyrimidine-based compounds that include uracil, cytosine, and thymine, and the purine-based compounds that include adenine and guanine. Previous work in our laboratory has demonstrated that uracil, cytosine, thymine, and other nonbiological, less common nucleobases can form abiotically from the UV photoirradiation of pyrimidine in simple astrophysical ice analogues containing combinations of H2O, NH3, and CH4...
July 19, 2017: Astrobiology
https://www.readbyqxmd.com/read/28708927/orotidine-containing-rna-implications-for-the-hierarchical-selection-systems-chemistry-emergence-of-rna
#3
Eun-Kyong Kim, Vincent Martin, Ramanarayanan Krishnamurthy
The prebiotic synthesis of canonical nucleobases from HCN is a cornerstone for the RNA world hypothesis. However, their role in the primordial pathways to RNA is still debated. The very same process starting from HCN also gives rise to orotic acid, which (via orotidine) plays a crucial role in extant biology in the de novo synthesis of uridine and cytidine, the informational base-pairs in RNA. However, orotidine itself is absent in RNA. Given the prebiotic and biological relevance of orotic acid vis-à-vis uracil, we investigated orotidine containing RNA oligonucleotides and show that they have severely compromised base-pairing properties...
July 14, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28702783/origins-of-life-research-a-bibliometric-approach
#4
Arsev Umur Aydinoglu, Zehra Taşkın
This study explores the collaborative nature and interdisciplinarity of the origin(s) of life (OoL) research community. Although OoL research is one of the oldest topics in philosophy, religion, and science; to date there has been no review of the field utilizing bibliometric measures. A dataset of 5647 publications that are tagged as OoL, astrobiology, exobiology, and prebiotic chemistry is analyzed. The most prolific authors (Raulin, Ehrenfreund, McKay, Cleaves, Cockell, Lazcano, etc.), most cited scholars and their articles (Miller 1953, Gilbert 1986, Chyba & Sagan 1992, Wȁchtershȁuser 1988, etc...
July 13, 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28652321/nonenzymatic-gluconeogenesis-like-formation-of-fructose-1-6-bisphosphate-in-ice
#5
Christoph B Messner, Paul C Driscoll, Gabriel Piedrafita, Michael F L De Volder, Markus Ralser
The evolutionary origins of metabolism, in particular the emergence of the sugar phosphates that constitute glycolysis, the pentose phosphate pathway, and the RNA and DNA backbone, are largely unknown. In cells, a major source of glucose and the large sugar phosphates is gluconeogenesis. This ancient anabolic pathway (re-)builds carbon bonds as cleaved in glycolysis in an aldol condensation of the unstable catabolites glyceraldehyde 3-phosphate and dihydroxyacetone phosphate, forming the much more stable fructose 1,6-bisphosphate...
July 11, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28640293/collision-cross-section-predictions-using-2-dimensional-molecular-descriptors
#6
M T Soper-Hopper, A S Petrov, J N Howard, S-S Yu, J G Forsythe, M A Grover, F M Fernández
Traditional methods for deriving computationally-generated collision cross sections for comparisons with ion mobility-mass spectrometry data require 3-dimensional energy-minimized structures and are often time consuming, preventing high throughput implementation. Here, we introduce a method to predict ion mobility collision cross sections of lipids and peptide analogs important in prebiotic chemistry and other fields. Using less than 100 2-D molecular descriptors this approach resulted in prediction errors of less than 2%...
July 4, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28614348/organic-compounds-in-fluid-inclusions-of-archean-quartz-analogues-of-prebiotic-chemistry-on-early-earth
#7
Ulrich Schreiber, Christian Mayer, Oliver J Schmitz, Pia Rosendahl, Amela Bronja, Markus Greule, Frank Keppler, Ines Mulder, Tobias Sattler, Heinz F Schöler
The origin of life is still an unsolved mystery in science. Hypothetically, prebiotic chemistry and the formation of protocells may have evolved in the hydrothermal environment of tectonic fault zones in the upper continental crust, an environment where sensitive molecules are protected against degradation induced e.g. by UV radiation. The composition of fluid inclusions in minerals such as quartz crystals which have grown in this environment during the Archean period might provide important information about the first organic molecules formed by hydrothermal synthesis...
2017: PloS One
https://www.readbyqxmd.com/read/28600550/permeability-driven-selection-in-a-semi-empirical-protocell-model-the-roots-of-prebiotic-systems-evolution
#8
Gabriel Piedrafita, Pierre-Alain Monnard, Fabio Mavelli, Kepa Ruiz-Mirazo
The origin-of-life problem has been traditionally conceived as the chemical challenge to find the type of molecule and free-solution reaction dynamics that could have started Darwinian evolution. Different autocatalytic and 'self-replicative' molecular species have been extensively investigated, together with plausible synthetic pathways that might have led, abiotically, to such a minimalist scenario. However, in addition to molecular kinetics or molecular evolutionary dynamics, other physical and chemical constraints (like compartmentalization, differential diffusion, selective transport, osmotic forces, energetic couplings) could have been crucial for the cohesion, functional integration, and intrinsic stability/robustness of intermediate systems between chemistry and biology...
June 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28537771/atmospheric-constraints-on-the-surface-uv-environment-of-mars-at-3-9%C3%A2-ga-relevant-to-prebiotic-chemistry
#9
Sukrit Ranjan, Robin Wordsworth, Dimitar D Sasselov
Recent findings suggest that Mars may have been a clement environment for the emergence of life and may even have compared favorably to Earth in this regard. These findings have revived interest in the hypothesis that prebiotically important molecules or even nascent life may have formed on Mars and been transferred to Earth. UV light plays a key role in prebiotic chemistry. Characterizing the early martian surface UV environment is key to understanding how Mars compares to Earth as a venue for prebiotic chemistry...
May 24, 2017: Astrobiology
https://www.readbyqxmd.com/read/28507716/chemistry-in-nanoconfined-water
#10
Daniel Muñoz-Santiburcio, Dominik Marx
Nanoconfined liquids have extremely different properties from the bulk, which profoundly affects chemical reactions taking place in nanosolvation. Here, we present extensive ab initio simulations of a vast set of chemical reactions within a water lamella that is nanoconfined by mineral surfaces, which might be relevant to prebiotic peptide formation in aqueous environments. Our results disclose a rich interplay of distinct effects, from steric factors typical of reactions occurring in small spaces to a charge-stabilization effect in nanoconfined water at extreme conditions similar to that observed in bulk water when changing from extreme to ambient conditions...
May 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/28474360/anchimeric-assisted-spontaneous-hydrolysis-of-cyanohydrins-under-ambient-conditions-implications-for-cyanide-initiated-selective-transformations
#11
Jayasudhan Reddy Yerabolu, Charles L Liotta, Ramanarayanan Krishnamurthy
Nitrile/cyanide hydrolysis is of importance from the perspective of organic chemistry, especially, prebiotic chemistry. Herein we report that cyanohydrins, generated by the reaction of cyanide with β-keto acids and γ-keto-alcohols, spontaneously hydrolyze under ambient conditions (aqueous medium, RT, and a range of pH). The spontaneous hydrolysis is affected by an intramolecular proton transfer and an intramolecular 5-exo-dig attack, but with a twist. In the case of β-keto acids, the hydrolysis is mediated by the neighboring carboxylic acid group only at pH values less than 7, whereas in the case of γ-keto-alcohols the hydrolysis is mediated by the neighboring hydroxyl group only at pH values greater than 7...
May 4, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28474281/on-the-ability-of-formaldehyde-to-act-as-a-tethering-catalyst-in-water
#12
Mohammad P Jamshidi, Melissa J MacDonald, André M Beauchemin
The low concentration issue is a fundamental challenge when it comes to prebiotic chemistry, as macromolecular systems need to be assembled via intermolecular reactions, and this is inherently difficult in dilute solutions. This is especially true when the reactions are challenging, and reactions that proceeded more rapidly could have dictated chemical evolution. Herein we establish that formaldehyde is capable of catalyzing, via temporary intramolecularity, a challenging reaction in water at low concentrations, thus providing an alternative to other approaches that can either lead to higher concentrations or higher effective molarities...
May 4, 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28467695/non-enzymatic-rna-backbone-proofreading-through-energy-dissipative-recycling
#13
Angelica Mariani, John D Sutherland
Non-enzymatic oligomerization of activated ribonucleotides leads to ribonucleic acids that contain a mixture of 2',5'- and 3',5'-linkages, and overcoming this backbone heterogeneity has long been considered a major limitation to the prebiotic emergence of RNA. Herein, we demonstrate non-enzymatic chemistry that progressively converts 2',5'-linkages into 3',5'-linkages through iterative degradation and repair. The energetic costs of this proofreading are met by the hydrolytic turnover of a phosphate activating agent and an acylating agent...
June 1, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28446711/chemical-roots-of-biological-evolution-the-origins-of-life-as-a-process-of-development-of-autonomous-functional-systems
#14
REVIEW
Kepa Ruiz-Mirazo, Carlos Briones, Andrés de la Escosura
In recent years, an extension of the Darwinian framework is being considered for the study of prebiotic chemical evolution, shifting the attention from homogeneous populations of naked molecular species to populations of heterogeneous, compartmentalized and functionally integrated assemblies of molecules. Several implications of this shift of perspective are analysed in this critical review, both in terms of the individual units, which require an adequate characterization as self-maintaining systems with an internal organization, and also in relation to their collective and long-term evolutionary dynamics, based on competition, collaboration and selection processes among those complex individuals...
April 2017: Open Biology
https://www.readbyqxmd.com/read/28397774/small-and-random-peptides-an-unexplored-reservoir-of-potentially-functional-primitive-organocatalysts-the-case-of-seryl-histidine
#15
REVIEW
Rafal Wieczorek, Katarzyna Adamala, Tecla Gasperi, Fabio Polticelli, Pasquale Stano
Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes, the biocatalysts par excellence, were not available in such an ancient context, and so, instead, small molecule catalysis (organocatalysis) may have occurred. The best candidates for the role of primitive organocatalysts are amino acids and short random peptides, which are believed to have been available in an early period on Earth...
April 9, 2017: Life
https://www.readbyqxmd.com/read/28383486/prebiotic-factors-influencing-the-activity-of-a-ligase-ribozyme
#16
Fabrizio Anella, Christophe Danelon
An RNA-lipid origin of life scenario provides a plausible route for compartmentalized replication of an informational polymer and subsequent division of the container. However, a full narrative to form such RNA protocells implies that catalytic RNA molecules, called ribozymes, can operate in the presence of self-assembled vesicles composed of prebiotically relevant constituents, such as fatty acids. Hereby, we subjected a newly engineered truncated variant of the L1 ligase ribozyme, named tL1, to various environmental conditions that may have prevailed on the early Earth with the objective to find a set of control parameters enabling both tL1-catalyzed ligation and formation of stable myristoleic acid (MA) vesicles...
April 6, 2017: Life
https://www.readbyqxmd.com/read/28378591/semiconductor-photocatalysis-for-chemoselective-radical-coupling-reactions
#17
Horst Kisch
Photocatalysis at semiconductor surfaces is a growing field of general photocatalysis because of its importance for the chemical utilization of solar energy. By analogy with photoelectrochemistry the basic mechanism of semiconductor photocatalysis can be broken down into three steps: photogenerated formation of surface redox centers (electron-hole pairs), interfacial electron transfer from and to substrates (often coupled with proton-transfer), and conversion of primary redox intermediates into the products...
April 5, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28338703/theoretical-investigation-of-proton-collisions-on-prebiotic-candidates-hydrogen-cyanide-polymers
#18
Marie-Christine Bacchus-Montabonel
One of the major concerns in prebiotic chemistry is the formation and destruction routes of prebiotic compounds in space. As detected for a long time, hydrogen cyanide (HCN) has been suggested to be a feedstock molecule at the origin of life driving easy oligomerization, in particular to form adenine. This may focus on its first oligomers because its dimer cyanomethanimine was recently observed in star-forming regions, or its trimer aminomalononitrile. With regard to the assumption of an extra-terrestrial origin of life, the stability of such species under ultraviolet radiation or in ion-collisions is an open question...
March 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28338689/a-prebiotically-plausible-synthesis-of-pyrimidine-%C3%AE-ribonucleosides-and-their-phosphate-derivatives-involving-photoanomerization
#19
Jianfeng Xu, Maria Tsanakopoulou, Christopher J Magnani, Rafał Szabla, Judit E Šponer, Jiří Šponer, Robert W Góra, John D Sutherland
Previous research has identified ribose aminooxazoline as a potential intermediate in the prebiotic synthesis of the pyrimidine nucleotides with remarkable properties. It crystallizes spontaneously from reaction mixtures, with an enhanced enantiomeric excess if initially enantioenriched, which suggests that reservoirs of this compound might have accumulated on the early Earth in an optically pure form. Ribose aminooxazoline can be converted efficiently into α-ribocytidine by way of 2,2'-anhydroribocytidine, although anomerization to β-ribocytidine by ultraviolet irradiation is extremely inefficient...
April 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28323482/constraints-on-the-early-terrestrial-surface-uv-environment-relevant-to-prebiotic-chemistry
#20
Sukrit Ranjan, Dimitar D Sasselov
The UV environment is a key boundary condition to abiogenesis. However, considerable uncertainty exists as to planetary conditions and hence surface UV at abiogenesis. Here, we present two-stream multilayer clear-sky calculations of the UV surface radiance on Earth at 3.9 Ga to constrain the UV surface fluence as a function of albedo, solar zenith angle (SZA), and atmospheric composition. Variation in albedo and latitude (through SZA) can affect maximum photoreaction rates by a factor of >10.4; for the same atmosphere, photoreactions can proceed an order of magnitude faster at the equator of a snowball Earth than at the poles of a warmer world...
March 2017: Astrobiology
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