Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data

Andersen, Jakob L.; Andersen, T.; Flamm, Christoph; Hanczyc, Martin M.; Merkle, Daniel; Stadler, Peter F.

doi:10.3390/e15104066

Cited by 37 publications

(36 citation statements)

References 43 publications

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“…However, XPS C 1s high resolution spectra of deposited coatings and the components that can be fitted for these spectra (Figure 2a) are consistent with the structural elements that have been proposed for HCN-derived polymers. [32][33][34] The XPS survey spectrum (Figure 2b) also reflects the unusually high N/C (N/C = 0.61 ± 0.02), which is characteristic for these coatings. In comparison, common nitrogenous polymers used in biomedical applications such as polyethyleneimine, poly(L-lysine) and polyallylamine have significantly lower N/C ratios of 0.5, 0.33 and 0.33, respectively.…”

Section: Resultsmentioning

confidence: 99%

Prebiotic-chemistry inspired polymer coatings for biomedical and material science applications

et al. 2015

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In the field of prebiotic chemistry, hydrogen cyanide (HCN)-derived polymers have been studied for many years as a possible source of the precursors that provide the building blocks for proteins as well as nucleic acids, and they have also been associated with the origin of life. The HCN trimer, aminomalononitrile (AMN), polymerizes to give a brown complex nitrogenous polymer. We report the one-step polymerization-deposition of AMN as a simple generic surface-coating method and as an application of prebiotic chemical research to material science. We found that this polymerization, carried out in buffered aqueous solutions, can be used to coat a wide range of organic and inorganic substrate materials. The robust, non-cytotoxic coatings also provide for excellent cell attachment, suggesting potential biomedical applications. Furthermore, the coating chemistry allows for the immobilization of other compounds, including metals, both during coating formation or by performing secondary immobilization reactions.

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Section: Resultsmentioning

confidence: 99%

Prebiotic-chemistry inspired polymer coatings for biomedical and material science applications

et al. 2015

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“…A hypothesis common to nearly all modern origins‐of‐life scenarios is that underlying geophysical processes, by dint of providing an energy source, drove the evolution of complex reaction networks that were fed by simple organic and inorganic feedstocks. The need to make, measure and model complex reaction networks, especially those that give rise to hypothetically relevant prebiological compounds like ribonucleotides and amino acids, is therefore fundamentally important for addressing the chemical mysteries shrouding life's origins. Herein, a chemical reaction network driven by the continuous exposure of gamma rays to solutions containing dilute concentrations of hydrogen cyanide (HCN), as well as ammonium and sodium chloride salts is developed.…”

Section: Introductionmentioning

confidence: 99%

Radiolytic Synthesis of Cyanogen Chloride, Cyanamide and Simple Sugar Precursors

Hongo

Yoda

et al. 2018

ChemistrySelect

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Chemical evolution, from simple molecules to complex systems, is fundamental to modern origins of life research, and complex reaction networks are often supposed to have operated on the early Earth. Herein, a variety of compounds useful particularly for RNA synthesis − namely, cyanogen chloride, cyanamide, and nitrile precursors to simple sugars − are produced in short order by a chemical reaction network starting from hydrogen cyanide and driven by gamma radiolysis. The radiolytic yield of cyanamide was found to be proportional to the concentration of chloride, an often overlooked spectator anion. Aqueous irradiation of hydrogen cyanide in the presence of sodium chloride also affords cyanogen chloride, a possible intermediate in the radiolytic synthesis of cyanamide. Meanwhile, the synthesis of simple sugar precursors is proposed to proceed through a Kiliani‐Fischer homologation mechanism made possible by the reducing power of the solvated electron and hydrogen atom. Such a reaction network has the potential to serve as a model for better understanding and engineering chemical evolution of complex mixtures in the laboratory that could have happened on the early Earth.

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“…This type of computational modelling indeed allows the exploration of large numbers of alternative pathways, some of which are rather unexpected. In a recent investigation into HCN-polymerisation/-hydrolysis chemistry [2], for example, we found several plausible alternatives to Oró's prebiotic adenine synthesis [21]. In the computational re-analysis of Eschenmoser's hypothesis outlined here, we find that autocatalytic pathways can be found abundantly, often involving the same key intermediates.…”

Section: Discussionmentioning

confidence: 63%

In silico Support for Eschenmoser’s Glyoxylate Scenario

Andersen

Flamm

Merkle

et al. 2015

Israel Journal of Chemistry

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1IntroductionTheo rigin of life is among the most fascinating and most interdisciplinary scientific problems.D espite ac entury of research, however, it still presents itself as an enigma.O n the one hand, we still lack both ad etailedu nderstanding of the principles that govern the transition from nonliving matter to livings ystems in general, and ac lear historical scenario of the emergence of life on Earth. See, e.g.,R uiz-Mirazo et al.[1] for arecent review. Ak ey topic of prebioticc hemistry is tof ind synthetic routes to theb iomolecularb uilding blockso fm odern life that are chemicallyp lausible,g iven the environmental conditions one arly Earth. In particular,t hese synthetic routes needt os tart withm aterialt hat wasr easonablya bundant after the formation of the planet. This is an otoriously difficultr esearch problem, fors everal reasons: (1)T he chemical search space is vast;i nf act, it is, by far, too large to enumeratee xhaustively,a nd it cannot be confined to only those compounds that are well-characterised andd escribedi nc urrent chemistry databases.( 2) Thec onstraintsi mposed by our current knowledge of the conditionso ne arly Earth are too vague to exclude large portions of thes earch space.( 3) Thep roblem of findings yntheticr outes to target molecules itself,e venf or af ixed set of chemical reactions,i s av ery difficult combinatorialp roblem.( 4) Experimental verification of potential routes is inherently slow.C onsequently,c onceptual guiding by skilledo rganic chemists is indispensablei nd irecting research towards regions of prebioticc hemical space worthwhile being exploredi n more detail.O nt he other hand, efficient formal,c ompuAbstract:Ac ore topic of research in prebiotic chemistry is the search for plausible synthetic routes that connect the building blocks of modern life, such as sugars, nucleotides, amino acids, and lipidst o" molecular food sources" that were likely to have been abundant on early Earth. In ar ecent contribution, Albert Eschenmoser emphasised the importance of catalytic and autocatalytic cycles in establishing such abiotic synthesis pathways. The accumulation of intermediate productsf urthermore providesa dditional catalysts that allow pathways to change over time. We show here that generative models of chemical spaces based on graph grammars make it possible to studys uch phenomena in as ystematicm anner.I na ddition to reproducing the key steps of Eschenmoser'sh ypothesis paper,w ed iscovered previously unexplored potentially autocatalytic pathways from HCN to glyoxylate. Ac ascadeo fa utocatalytic cycles could efficiently re-route matter,d istributed over the combinatorialc omplex network of HCN hydrolysation chemistry, towards ap otential primordial metabolism. The generative approach also has it intrinsicl imitations:t he unsupervised expansion of the chemical space remains infeasible due to the exponential growth of possible molecules and reactions betweent hem. Here, in particular,t he combinatorial complexity of the HCN polymerisation and hydrolysa...

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Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data

Cited by 37 publications

References 43 publications

Prebiotic-chemistry inspired polymer coatings for biomedical and material science applications

Prebiotic-chemistry inspired polymer coatings for biomedical and material science applications

Radiolytic Synthesis of Cyanogen Chloride, Cyanamide and Simple Sugar Precursors

In silico Support for Eschenmoser’s Glyoxylate Scenario

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