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Prebiotic chemistry

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https://www.readbyqxmd.com/read/29328633/size-induced-segregation-in-the-stepwise-microhydration-of-hydantoin-and-its-role-on-proton-induced-charge-transfer
#1
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
https://www.readbyqxmd.com/read/29321594/estimating-the-capacity-for-production-of-formamide-by-radioactive-minerals-on-the-prebiotic-earth
#2
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
https://www.readbyqxmd.com/read/29319888/formation-of-cyanamide-glyoxal-oligomers-in-aqueous-environments-relevant-to-primeval-and-astrochemical-scenarios-a-spectroscopic-and-theoretical-study
#3
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
https://www.readbyqxmd.com/read/29301382/hydrogen-bonds-and-life-in-the-universe
#4
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
https://www.readbyqxmd.com/read/29260254/from-molecules-to-life-quantifying-the-complexity-of-chemical-and-biological-systems-in-the-universe
#5
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
https://www.readbyqxmd.com/read/29259120/modern-diversification-of-the-amino-acid-repertoire-driven-by-oxygen
#6
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
https://www.readbyqxmd.com/read/29237880/j-b-s-haldane-and-the-origin-of-life
#7
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
https://www.readbyqxmd.com/read/29233216/nucleic-acids-function-and-potential-for-abiogenesis
#8
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
https://www.readbyqxmd.com/read/29229963/mineral-surface-chemistry-control-for-origin-of-prebiotic-peptides
#9
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
https://www.readbyqxmd.com/read/29194806/a-direct-prebiotic-synthesis-of-nicotinamide-nucleotide
#10
Hyo-Joong Kim, Steven A Benner
Under the "RNA World" hypothesis, an early episode of natural history on Earth used RNA as the only genetically encoded molecule to catalyze steps in its metabolism catalysis. 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...
November 30, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29168482/uv-light-driven-prebiotic-synthesis-of-iron-sulfur-clusters
#11
Claudia Bonfio, Luca Valer, Simone Scintilla, Sachin Shah, David J Evans, Lin Jin, Jack W Szostak, Dimitar D Sasselov, John D Sutherland, Sheref S Mansy
Iron-sulfur clusters are ancient cofactors that play a fundamental role in metabolism and may have impacted the prebiotic chemistry that led to life. However, it is unclear whether iron-sulfur clusters could have been synthesized on prebiotic Earth. Dissolved iron on early Earth was predominantly in the reduced ferrous state, but ferrous ions alone cannot form polynuclear iron-sulfur clusters. Similarly, free sulfide may not have been readily available. Here we show that UV light drives the synthesis of [2Fe-2S] and [4Fe-4S] clusters through the photooxidation of ferrous ions and the photolysis of organic thiols...
December 2017: Nature Chemistry
https://www.readbyqxmd.com/read/29164768/rewarming-the-primordial-soup-revisitations-and-rediscoveries-in-prebiotic-chemistry
#12
REVIEW
Raffaele Saladino, Judit E Šponer, Jiří Šponer, Ernesto Di Mauro
A short history of primordial soup: In this essay we try to disclose some of the historical connections between the studies that have contributed to our current understanding of the emergence of catalytic RNA molecules and their components from an inanimate matter.
November 22, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/29133452/an-intermediate-level-of-abstraction-for-computational-systems-chemistry
#13
Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
Computational techniques are required for narrowing down the vast space of possibilities to plausible prebiotic scenarios, because precise information on the molecular composition, the dominant reaction chemistry and the conditions for that era are scarce. The exploration of large chemical reaction networks is a central aspect in this endeavour. While quantum chemical methods can accurately predict the structures and reactivities of small molecules, they are not efficient enough to cope with large-scale reaction systems...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29133447/subsumed-complexity-abiogenesis-as-a-by-product-of-complex-energy-transduction
#14
Z R Adam, D Zubarev, M Aono, H James Cleaves
The origins of life bring into stark relief the inadequacy of our current synthesis of thermodynamic, chemical, physical and information theory to predict the conditions under which complex, living states of organic matter can arise. Origins research has traditionally proceeded under an array of implicit or explicit guiding principles in lieu of a universal formalism for abiogenesis. Within the framework of a new guiding principle for prebiotic chemistry called subsumed complexity, organic compounds are viewed as by-products of energy transduction phenomena at different scales (subatomic, atomic, molecular and polymeric) that retain energy in the form of bonds that inhibit energy from reaching the ground state...
December 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/29131221/organocatalysis-using-aldehydes-the-development-and-improvement-of-catalytic-hydroaminations-hydrations-and-hydrolyses
#15
Bin-Jie Li, Claudia Ei-Nachef, André M Beauchemin
Organocatalysis has emerged as a powerful approach to facilitate and accelerate various difficult reactions. This Feature article presents recent developments and improvements using aldehydes as catalysts in difficult Cope-type intermolecular hydroamination, hydration and hydrolysis reactions. Most reactions exploit temporary intramolecularity. In catalytic Cope-type hydroaminations of allylic amines, aldehydes act as tethering catalysts, and allow room temperature reactions and high enantio- or diastereoselectivities if chiral aldehydes or reagents are used...
November 13, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29112424/a-mechanistic-explanation-for-the-regioselectivity-of-nonenzymatic-rna-primer-extension
#16
Constantin Giurgiu, Li Li, Derek K O'Flaherty, Chun Pong Tam, Jack W Szostak
A working model of nonenzymatic RNA primer extension could illuminate how prebiotic chemistry transitioned to biology. All currently known experimental reconstructions of nonenzymatic RNA primer extension yield a mixture of 2'-5' and 3'-5' internucleotide linkages. Although long seen as a major problem, the causes of the poor regioselectivity of the reaction are unknown. We used a combination of different leaving groups, nucleobases, and templating sequences to uncover the factors that yield selective formation of 3'-5' internucleotide linkages...
November 7, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29078402/abiotic-production-of-sugar-phosphates-and-uridine-ribonucleoside-in-aqueous-microdroplets
#17
Inho Nam, Jae Kyoo Lee, Hong Gil Nam, Richard N Zare
Phosphorylation is an essential chemical reaction for life. This reaction generates fundamental cell components, including building blocks for RNA and DNA, phospholipids for cell walls, and adenosine triphosphate (ATP) for energy storage. However, phosphorylation reactions are thermodynamically unfavorable in solution. Consequently, a long-standing question in prebiotic chemistry is how abiotic phosphorylation occurs in biological compounds. We find that the phosphorylation of various sugars to form sugar-1-phosphates can proceed spontaneously in aqueous microdroplets containing a simple mixture of sugars and phosphoric acid...
October 23, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29065330/experimental-conditions-affecting-the-kinetics-of-aqueous-hcn-polymerization-as-revealed-by-uv-vis-spectroscopy
#18
Margarita R Marín-Yaseli, Miguel Moreno, José L de la Fuente, Carlos Briones, Marta Ruiz-Bermejo
HCN polymerization is one of the most important and fascinating reactions in prebiotic chemistry, and interest in HCN polymers in the field of materials science is growing. However, little is known about the kinetics of the HCN polymerization process. In the present study, a first approach to the kinetics of two sets of aqueous HCN polymerizations, from NH4CN and NaCN, at middle temperatures between 4 and 38°C, has been carried out. For each series, the presence of air and salts in the reaction medium has been systematically explored...
October 12, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29058895/metal-ion-and-hydrogen-bond-mediated-interstellar-prebiotic-chemistry-the-first-step-in-the-formose-reaction
#19
Sorakayala Thripati, Raghunath O Ramabhadran
The formose reaction, which offers a feasible chemical pathway for the prebiotic synthesis of sugars, is a well-studied reaction for over two hundred and 50 years. Yet huge knowledge gaps exist even in the very first step of the formose reaction. In this work, we provide a new and otherwise unintuitive reaction pathway for the gas-phase conversion of formaldehyde to glycolaldehyde (the first step in the formose reaction) occurring in the interstellar medium (ISM). Employing electronic structure calculations (CCSD(T) and DFT methods), we exhaustively probe the role of various metal ions and small molecules detected in the ISM to propose a new mechanism wherein metal-oxygen interactions and hydrogen bonds cooperatively facilitate an otherwise implausible chemical reaction...
November 7, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28973920/origin-of-the-rna-world-the-fate-of-nucleobases-in-warm-little-ponds
#20
Ben K D Pearce, Ralph E Pudritz, Dmitry A Semenov, Thomas K Henning
Before the origin of simple cellular life, the building blocks of RNA (nucleotides) had to form and polymerize in favorable environments on early Earth. At this time, meteorites and interplanetary dust particles delivered organics such as nucleobases (the characteristic molecules of nucleotides) to warm little ponds whose wet-dry cycles promoted rapid polymerization. We build a comprehensive numerical model for the evolution of nucleobases in warm little ponds leading to the emergence of the first nucleotides and RNA...
October 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
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