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Prebiotic chemistry

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https://www.readbyqxmd.com/read/29133452/an-intermediate-level-of-abstraction-for-computational-systems-chemistry
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/28945387/giving-rise-to-life-transition-from-prebiotic-chemistry-to-protobiology
#9
Ramanarayanan Krishnamurthy
The challenge of a chemical approach to the origins of life problem involves comprehending the transition from prebiotic chemistry to protobiology. This endeavor demands demonstrating the metamorphosis of a diverse pool of prebiotic building blocks (heterogeneous heterogeneity) into a conglomerate self-assembling system (homogeneous heterogeneity) capable of evolution.
March 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28914790/ancient-living-organisms-escaping-from-or-imprisoned-in-the-vents
#10
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
#11
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...
November 2017: Astrobiology
https://www.readbyqxmd.com/read/28886641/length-and-sequence-relaxation-of-copolymers-under-recombination-reactions
#12
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
#13
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
#14
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
#15
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...
September 5, 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
#16
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
#17
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
#18
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
#19
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
#20
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
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