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Prebiotic chemistry

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https://www.readbyqxmd.com/read/28914790/ancient-living-organisms-escaping-from-or-imprisoned-in-the-vents
#1
REVIEW
J Baz Jackson
We have recently criticised the natural pH gradient hypothesis which purports to explain how the difference in pH between fluid issuing from ancient alkali vents and the more acidic Hadean ocean could have driven molecular machines that catalyse reactions that are useful in prebiotic and autotrophic chemistry. In this article, we temporarily suspend our earlier criticism while we consider difficulties for primitive organisms to have managed their energy supply and to have left the vents and become free-living...
September 15, 2017: Life
https://www.readbyqxmd.com/read/28910143/the-lost-city-hydrothermal-field-a-spectroscopic-and-astrobiological-analogue-for-nili-fossae-mars
#2
Elena S Amador, Joshua L Bandfield, William J Brazelton, Deborah Kelley
Low-temperature serpentinization is a critical process with respect to Earth's habitability and the Solar System. Exothermic serpentinization reactions commonly produce hydrogen as a direct by-product and typically produce short-chained organic compounds indirectly. Here, we present the spectral and mineralogical variability in rocks from the serpentine-driven Lost City Hydrothermal Field on Earth and the olivine-rich region of Nili Fossae on Mars. Near- and thermal-infrared spectral measurements were made from a suite of Lost City rocks at wavelengths similar to those for instruments collecting measurements of the martian surface...
September 14, 2017: Astrobiology
https://www.readbyqxmd.com/read/28886641/length-and-sequence-relaxation-of-copolymers-under-recombination-reactions
#3
Alex Blokhuis, David Lacoste
We describe the kinetics and thermodynamics of copolymers undergoing recombination reactions, which are important for prebiotic chemistry. We use two approaches: the first one, based on chemical rate equations and the mass-action law describes the infinite size limit, while the second one, based on the chemical master equation, describes systems of finite size. We compare the predictions of both approaches for the relaxation of thermodynamic quantities towards equilibrium. We find that for some choice of initial conditions, the entropy of the sequence distribution can be lowered at the expense of increasing the entropy of the length distribution...
September 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28851657/computer-simulation-and-experimental-self-assembly-of-irradiated-glycine-amino-acid-under-magnetic-fields-its-possible-significance-in-prebiotic-chemistry
#4
Alejandro Heredia, María Colín-García, Teresa Pi I Puig, Leticia Alba-Aldave, Adriana Meléndez, Jorge A Cruz-Castañeda, Vladimir A Basiuk, Sergio Ramos-Bernal, Alicia Negrón Mendoza
Ionizing radiation may have played a relevant role in chemical reactions for prebiotic biomolecule formation on ancient Earth. Environmental conditions such as the presence of water and magnetic fields were possibly relevant in the formation of organic compounds such as amino acids. ATR-FTIR, Raman, EPR and X-ray spectroscopies provide valuable information about molecular organization of different glycine polymorphs under static magnetic fields. γ-glycine polymorph formation increases in irradiated samples interacting with static magnetic fields...
August 26, 2017: Bio Systems
https://www.readbyqxmd.com/read/28836818/experimentally-testing-hydrothermal-vent-origin-of-life-on-enceladus-and-other-icy-ocean-worlds
#5
Laura M Barge, Lauren M White
We review various laboratory strategies and methods that can be utilized to simulate prebiotic processes and origin of life in hydrothermal vent systems on icy/ocean worlds. Crucial steps that could be simulated in the laboratory include simulations of water-rock chemistry (e.g., serpentinization) to produce hydrothermal fluids, the types of mineral catalysts and energy gradients produced in vent interfaces where hydrothermal fluids interface with the surrounding seawater, and simulations of biologically relevant chemistry in flow-through gradient systems (i...
September 2017: Astrobiology
https://www.readbyqxmd.com/read/28831002/foldamer-hypothesis-for-the-growth-and-sequence-differentiation-of-prebiotic-polymers
#6
Elizaveta Guseva, Ronald N Zuckermann, Ken A Dill
It is not known how life originated. It is thought that prebiotic processes were able to synthesize short random polymers. However, then, how do short-chain molecules spontaneously grow longer? Also, how would random chains grow more informational and become autocatalytic (i.e., increasing their own concentrations)? We study the folding and binding of random sequences of hydrophobic ([Formula: see text]) and polar ([Formula: see text]) monomers in a computational model. We find that even short hydrophobic polar (HP) chains can collapse into relatively compact structures, exposing hydrophobic surfaces...
August 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28740207/high-energy-radical-chemistry-formation-of-hcn-rich-atmospheres-on-early-earth
#7
Martin Ferus, Petr Kubelík, Antonín Knížek, Adam Pastorek, John Sutherland, Svatopluk Civiš
Recent results in prebiotic chemistry implicate hydrogen cyanide (HCN) as the source of carbon and nitrogen for the synthesis of nucleotide, amino acid and lipid building blocks. HCN can be produced during impact events by reprocessing of carbonaceous and nitrogenous materials from both the impactor and the atmosphere; it can also be produced from these materials by electrical discharge. Here we investigate the effect of high energy events on a range of starting mixtures representative of various atmosphere-impactor volatile combinations...
July 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28727932/laboratory-studies-of-methane-and-its-relationship-to-prebiotic-chemistry
#8
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...
August 2017: Astrobiology
https://www.readbyqxmd.com/read/28723229/the-formation-of-nucleobases-from-the-ultraviolet-photoirradiation-of-purine-in-simple-astrophysical-ice-analogues
#9
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...
August 2017: Astrobiology
https://www.readbyqxmd.com/read/28708927/orotidine-containing-rna-implications-for-the-hierarchical-selection-systems-chemistry-emergence-of-rna
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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...
August 2017: Astrobiology
https://www.readbyqxmd.com/read/28507716/chemistry-in-nanoconfined-water
#17
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
#18
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
#19
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
#20
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
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