Environmental conditions drive self-organisation of reaction pathways in a prebiotic reaction network

Abstract The evolution of life from the prebiotic environment required a gradual process of chemical evolution towards greater molecular complexity. Elaborate prebiotically-relevant synthetic routes to the building blocks of life have been established. However, it is still unclear how functional chemical systems evolved with direction using only the interaction between inherent molecular chemical reactivity and the abiotic environment. Here, we demonstrate how complex systems of chemical reactions exhibit well-defined self-organisation in response to varying environmental conditions. This self-organisation allows the compositional complexity of the reaction products to be controlled as a function of factors such as feedstock and catalyst availability. We observe how Breslow’s cycle contributes to the reaction composition by feeding C2 building blocks into the network, alongside reaction pathways dominated by formaldehyde-driven chain growth. The emergence of organised systems of chemical reactions in response to changes in the environment offers a potential mechanism for a chemical evolution process that bridges the gap between prebiotic chemical building blocks and the origin of life.

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Wet-Dry Cycling Delays the Gelation of Hyperbranched Polyesters: Implications to the Origin of Life

Life ◽

10.3390/life9030056 ◽

2019 ◽

Vol 9 (3) ◽

pp. 56 ◽

Cited By ~ 2

Author(s):

Irena Mamajanov

Keyword(s):

Chemical Evolution ◽

Environmental Conditions ◽

Environmental Control ◽

Continuous Heating ◽

Partial Hydrolysis ◽

Chain Growth ◽

Chemical Systems ◽

Hyperbranched Polyesters ◽

Controlled Systems ◽

Dew Formation

In extant biology, biopolymers perform multiple crucial functions. The biopolymers are synthesized by enzyme-controlled biosystems that would not have been available at the earliest stages of chemical evolution and consist of correctly sequenced and/or linked monomers. Some of the abiotic “messy” polymers approximate some functions of biopolymers. Condensation polymers are an attractive search target for abiotic functional polymers since principal polymers of life are produced by condensation and since condensation allows for the accurate construction of high polymers. Herein the formation of hyperbranched polyesters that have been previously used in the construction of enzyme-like catalytic complexes is explored. The experimental setup compares between the branched polyesters prepared under mild continuous heating and the wet-dry cycling associated with environmental conditions, such as dew formation or tidal activities. The results reveal that periodic wetting during which partial hydrolysis of the polyester occurs, helps to control the chain growth and delays the gel transition, a mechanism contributing to the tar formation. Moreover, the NMR and mass spec analyses indicate that continuously dried samples contain higher quantities of crosslinked and macrocyclic products, whereas cycled systems are enriched in branched structures. Ostensibly, environmental conditions have the ability to exert a rudimentary pressure to selectively enrich the polyesterification products in polymers of different structures and properties. At the early stages of chemical evolution, in the absence of biological machinery, this example of environmental control could have been for selectivity in chemical systems. As expected in marginally controlled systems, the identification of each component of the heterogeneous system has proved challenging, but it is not crucial for drawing the conclusions.

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Polyesters as a Model System for Building Primitive Biologies from Non-Biological Prebiotic Chemistry

Life ◽

10.3390/life10010006 ◽

2020 ◽

Vol 10 (1) ◽

pp. 6 ◽

Cited By ~ 4

Author(s):

Chandru ◽

Mamajanov ◽

Cleaves ◽

Jia

Keyword(s):

Chemical Evolution ◽

Hot Springs ◽

Prebiotic Chemistry ◽

Chemical Reactivity ◽

Structural Diversity ◽

Building Blocks ◽

Chemical Diversity ◽

Prebiotic Chemical ◽

Small Set ◽

Prebiotic Earth

A variety of organic chemicals were likely available on prebiotic Earth. These derived from diverse processes including atmospheric and geochemical synthesis and extraterrestrial input, and were delivered to environments including oceans, lakes, and subaerial hot springs. Prebiotic chemistry generates both molecules used by modern organisms, such as proteinaceous amino acids, as well as many molecule types not used in biochemistry. As prebiotic chemical diversity was likely high, and the core of biochemistry uses a rather small set of common building blocks, the majority of prebiotically available organic compounds may not have been those used in modern biochemistry. Chemical evolution was unlikely to have been able to discriminate which molecules would eventually be used in biology, and instead, interactions among compounds were governed simply by abundance and chemical reactivity. Previous work has shown that likely prebiotically available α-hydroxy acids can combinatorially polymerize into polyesters that self-assemble to create new phases which are able to compartmentalize other molecule types. The unexpectedly rich complexity of hydroxy acid chemistry and the likely enormous structural diversity of prebiotic organic chemistry suggests chemical evolution could have been heavily influenced by molecules not used in contemporary biochemistry, and that there is a considerable amount of prebiotic chemistry which remains unexplored.

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Synthesis, Characterization and Evaluation of Peptide Nanostructures for Biomedical Applications

Molecules ◽

10.3390/molecules26154587 ◽

2021 ◽

Vol 26 (15) ◽

pp. 4587

Author(s):

Fanny d’Orlyé ◽

Laura Trapiella-Alfonso ◽

Camille Lescot ◽

Marie Pinvidic ◽

Bich-Thuy Doan ◽

...

Keyword(s):

Amino Acids ◽

Biomedical Applications ◽

Chemical Reactivity ◽

Physical Stability ◽

Chemical Properties ◽

Building Blocks ◽

Imaging Probes ◽

Therapeutic Molecules

There is a challenging need for the development of new alternative nanostructures that can allow the coupling and/or encapsulation of therapeutic/diagnostic molecules while reducing their toxicity and improving their circulation and in-vivo targeting. Among the new materials using natural building blocks, peptides have attracted significant interest because of their simple structure, relative chemical and physical stability, diversity of sequences and forms, their easy functionalization with (bio)molecules and the possibility of synthesizing them in large quantities. A number of them have the ability to self-assemble into nanotubes, -spheres, -vesicles or -rods under mild conditions, which opens up new applications in biology and nanomedicine due to their intrinsic biocompatibility and biodegradability as well as their surface chemical reactivity via amino- and carboxyl groups. In order to obtain nanostructures suitable for biomedical applications, the structure, size, shape and surface chemistry of these nanoplatforms must be optimized. These properties depend directly on the nature and sequence of the amino acids that constitute them. It is therefore essential to control the order in which the amino acids are introduced during the synthesis of short peptide chains and to evaluate their in-vitro and in-vivo physico-chemical properties before testing them for biomedical applications. This review therefore focuses on the synthesis, functionalization and characterization of peptide sequences that can self-assemble to form nanostructures. The synthesis in batch or with new continuous flow and microflow techniques will be described and compared in terms of amino acids sequence, purification processes, functionalization or encapsulation of targeting ligands, imaging probes as well as therapeutic molecules. Their chemical and biological characterization will be presented to evaluate their purity, toxicity, biocompatibility and biodistribution, and some therapeutic properties in vitro and in vivo. Finally, their main applications in the biomedical field will be presented so as to highlight their importance and advantages over classical nanostructures.

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Epitaxy and Chemical Reactions During Thin Film Formation from Low Energy Ions New Kinetic Pathways, New Phases and New Properties

MRS Proceedings ◽

10.1557/proc-236-287 ◽

1991 ◽

Vol 236 ◽

Cited By ~ 1

Author(s):

Nicole Herbots ◽

O.C. Hellman ◽

O. Vancauwenberghe

Keyword(s):

Thin Film ◽

Chemical Reactions ◽

Degrees Of Freedom ◽

Film Growth ◽

Film Formation ◽

Chemical Reactivity ◽

Ion Beam ◽

Low Energy ◽

Low Energy Ions ◽

Beam Deposition

AbstractThree important effects of low energy direct Ion Beam Deposition (IBD) are the athermal incorporation of material into a substrate, the enhancement of atomic mobility in the subsurface, and the modification of growth kinetics it creates. All lead to a significant lowering of the temperature necessary to induce epitaxial growth and chemical reactions. The fundamental understanding and new applications of low temperature kinetics induced by low energy ions in thin film growth and surface processing of semiconductors are reviewed. It is shown that the mechanism of IBD growth can be understood and computed quantitatively using a simple model including ion induced defect generation and sputtering, elastic recombination, thermal diffusion, chemical reactivity, and desorption The energy, temperature and dose dependence of growth rate, epitaxy, and chemical reaction during IBD is found to be controlled by the net recombination rate of interstitials at the surface in the case of epitaxy and unreacted films, and by the balance between ion beam decomposition and phase formation induced by ion beam generated defects in the case of compound thin films. Recent systematic experiments on the formation of oxides and nitrides on Si, Ge/Si(100), heteroepitaxial SixGe1−x/Si(100) and GaAs(100) illustrate applications of this mechanism using IBD in the form of Ion Beam Nitridation (IBN), Ion Beam Oxidation (IBO) and Combined Ion and Molecular beam Deposition (CIMD). It is shown that these techniques enable (1) the formation of conventional phases in conditions never used before, (2) the control and creation of properties via new degrees of freedom such as ion energy and lowered substrate temperatures, and (3) the formation of new metastable heterostructures that cannot be grown by pure thermal means.

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A Molecular Artisans Guide to Supramolecular Coordination Complexes and Metal Organic Frameworks

Journal of Molecular and Engineering Materials ◽

10.1142/s2251237315400043 ◽

2015 ◽

Vol 03 (01n02) ◽

pp. 1540004 ◽

Cited By ~ 2

Author(s):

Xialu Wu ◽

David J. Young ◽

T. S. Andy Hor

Keyword(s):

Chemical Reactivity ◽

Metal Organic Frameworks ◽

Building Blocks ◽

Coordination Complexes ◽

Large Molecules ◽

Molecular Building Blocks ◽

Supramolecular Coordination ◽

Metal Organic ◽

Molecular Synthesis ◽

And Function

As molecular synthesis advances, we are beginning to learn control of not only the chemical reactivity (and function) of molecules, but also of their interactions with other molecules. It is this basic idea that has led to the current explosion of supramolecular science and engineering. Parallel to this development, chemists have been actively pursuing the design of very large molecules using basic molecular building blocks. Herein, we review the general development of supramolecular chemistry and particularly of two new branches: supramolecular coordination complexes (SCCs) and metal organic frameworks (MOFs). These two fields are discussed in detail with typical examples to illustrate what is now possible and what challenges lie ahead for tomorrow's molecular artisans.

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Chemically Selective Reactions in Confined Spaces in Hybrid Aerogels

MRS Proceedings ◽

10.1557/proc-0899-n06-06 ◽

2005 ◽

Vol 899 ◽

Author(s):

Xipeng Liu ◽

Chunhua Yao ◽

William M Risen

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Metal Ions ◽

Chemical Reactions ◽

Reaction Products ◽

Spatial Confinement ◽

Confined Spaces ◽

Hybrid Silica ◽

Hybrid Aerogels ◽

Chemically Selective

AbstractBy employing novel hybrid silica/functional polymer aerogels, control of the course of chemical reactions between reactants confined inside of the aerogels with reactants whose access to the confinement domain is controlled by diffusion has been explored. Thus, monolithic silica/biopolymer hybrid aerogels have been synthesized with coordinated metal ions that can react with amino acids, such as L-cysteine, that are provided externally in a surrounding solution. Metal ions, such as Au(III), that can react in solution with the amino acid to produce one set of products under a given set of stoichiometric or concentration conditions, and a different set of products under a second set of conditions, were selected for incorporation into the aerogel. It was discovered that the course of the reaction can be changed by spatial confinement of the reaction domain in the aerogel. For example, in the case of Au(III) and L-cysteine, the Au(III) ions are confined in nanoscale domains, and when they are reacted with the amino acid, the nature of the reaction products is controlled by diffusion of the L-cysteine into the domains. Exploration of these and related phenomena will be presented.

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The formation of the building blocks of peptides on interstellar dust grains

Proceedings of the International Astronomical Union ◽

10.1017/s1743921320000010 ◽

2019 ◽

Vol 15 (S350) ◽

pp. 216-219

Author(s):

N. F. W. Ligterink ◽

J. Terwisscha van Scheltinga ◽

V. Kofman ◽

V. Taquet ◽

S. Cazaux ◽

...

Keyword(s):

Interstellar Dust ◽

Reaction Network ◽

Building Blocks ◽

Dust Grains ◽

Reaction Products ◽

Experimental Conditions ◽

Interstellar Dust Grains ◽

Temperature Programmed ◽

Life On Earth ◽

Emergence Of Life

AbstractThe emergence of life on Earth may have its origin in organic molecules formed in the interstellar medium. Molecules with amide and isocyanate groups resemble structures found in peptides and nucleobases and are necessary for their formation. Their formation is expected to take place in the solid state, on icy dust grains, and is studied here by far-UV irradiating a CH4:HNCO mixture at 20 K in the laboratory. Reaction products are detected by means of infrared spectroscopy and temperature programmed desorption - mass spectrometry. Various simple amides and isocyanates are formed, showing the importance of ice chemistry for their interstellar formation. Constrained by experimental conditions, a reaction network is derived, showing possible formation pathways of these species under interstellar conditions.

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REACTIVE ACCELERATED CLUSTER EROSION (RACE)

Surface Review and Letters ◽

10.1142/s0218625x96001613 ◽

1996 ◽

Vol 03 (01) ◽

pp. 897-900 ◽

Cited By ~ 6

Author(s):

JÜRGEN GSPANN

Keyword(s):

Kinetic Energy ◽

Chemical Reactions ◽

Target Material ◽

Surface Erosion ◽

Reaction Products ◽

Surface Structuring

Beams of ionized clusters of some thousand atoms are accelerated to about 100-keV kinetic energy to be used for area selective surface erosion. Mask projective cluster-impact lithography allows surface structuring in the submicron regime. Chemical reactions between the cluster and the target material may provide volatile reaction products facilitating ejecta removal. The reactive accelerated cluster erosion (RACE) process is applied to metals like copper and gold, to semiconductors such as silicon, and to insulators like glass, quartz, or sapphire, giving very smooth eroded surface and steep sidewalls.

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Haematite–water system on Mars and its possible role in chemical evolution

International Journal of Astrobiology ◽

10.1017/s1473550407003825 ◽

2007 ◽

Vol 6 (4) ◽

pp. 267-271 ◽

Cited By ~ 14

Author(s):

Avnish Kumar Arora ◽

Varsha Tomar ◽

Aarti ◽

K.T. Venkateswararao ◽

Kamaluddin

Keyword(s):

Chemical Evolution ◽

Water System ◽

American Chemical Society ◽

Building Blocks ◽

Chemical Society ◽

Geological Evidence ◽

Water On Mars ◽

Western Regional ◽

Living Organisms ◽

Aqueous Conditions

AbstractRecent findings on the presence of water on Mars (Baker, V.R. (2006). Geomorphological evidence for water on Mars. Elements2(3), 139–143; DeJong, E. (2006). Geological evidence of the presence of water on Mars. Abstracts from the 40th Western Regional Meeting of the American Chemical Society, Anaheim, CA, January, 2006, pp. 22–25. American Chemical Society, Washington, DC; McSween, H.Y. Jr. (2006). Water on Mars. Elements2(3), 135–137; Mitrofanov, I.G. (2005). Water explorations on Mars. Priroda9, 34–43) strongly suggest that there existed a period of chemical evolution eventually leading to life processes on primitive Mars (Kanavarioti, A. & Maneinelli, R.L. (1990). Could organic matter have been preserved on Mars for 3.5 billion years. Icarus84, 196–202). Owing to the adverse conditions, it is quite likely that the process of chemical evolution would have been suppressed and any living organisms that formed would have become extinct over time on Mars. The presence of water as a necessity for the survival of living organisms and the presence of grey haematite, originated under aqueous conditions, have led us to investigate the possible role of haematite in the chemical evolution on Mars. Our observations suggest that iron oxide hydroxide (FeOOH), a precursor of haematite, has a much higher binding affinity towards ribose nucleotides (the building blocks of RNA) than the haematite itself. This would mean that during the process of haematite formation, especially through the probable process of Fe3+ hydrolysis by aqueous ammonia, the precursors of haematite might have played a significant role in the processes leading to chemical evolution and the possible origin of life on Mars.

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Gasification Pathways and Reaction Mechanisms of Primary Alcohols in Supercritical Water

10.26434/chemrxiv.10062515 ◽

2019 ◽

Author(s):

Brian Pinkard ◽

John Kramlich ◽

Igor V. Novosselov

Keyword(s):

Free Radical ◽

Supercritical Water ◽

Reaction Mechanisms ◽

Radical Reaction ◽

Water Environment ◽

Waste To Energy ◽

Reaction Pathways ◽

Free Radical Reaction ◽

Reaction Products ◽

Primary Alcohols

<div> <p></p><p>Supercritical water gasification is a promising waste-to-energy technology with the ability to convert aqueous and/or heterogeneous organic feedstocks to high-value gaseous products. Reaction behavior of complex molecules in supercritical water can be inferred through knowledge of the reaction pathways of model compounds in supercritical water. In this study methanol, ethanol, and isopropyl alcohol are gasified in a continuous supercritical water reactor at temperatures between 500 and 560 °C, and for residence times between 3 and 8 s. <i>In situ</i> Raman spectroscopy is used to rapidly identify and quantify reaction products. The results suggest the dominance of chain-branching, free radical reaction mechanisms that are responsible for decomposing primary alcohols in the supercritical water environment. The presence of a catalytic surface is proposed to be highly significant for initiating radical reactions. Global reaction pathways are proposed, and mechanisms for free radical reaction initiation, propagation, and termination are discussed in light of these and previously published experimental results.</p><br><p></p></div>

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