Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives

Sharma, Siddhant; Arya, Aayush; Cruz, Romulo; Cleaves, H. James

doi:10.3390/life11111140

Cited by 7 publications

(10 citation statements)

References 183 publications

(182 reference statements)

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“…Moreover, hydrolysis processes during cyanide polymerization can be increased not only by high temperature [ 37 ] but also by high pressure, and together with a variation in the diffusion effects, could be responsible for the decrease in the conversion limit values in the NH 4 CN polymerizations assisted by MWR. Cyanide polymerization is well known to be a very complex chemical system [ 12 , 13 , 14 , 16 , 66 ], but herein, it was clearly supported by statistical methods that the complexity of the system is clearly increasing due to the effect of the MWR. Therefore, if the MWR is adequate to mimic subaerial hydrothermal systems, the plausible prebiotic chemistry in these environments would likely be more intricate than the plausible prebiotic chemistry in the aerial part of the system.…”

Section: Concluding Remarks and Outlooksmentioning

confidence: 70%

Multivariate Analysis Applied to Microwave-Driven Cyanide Polymerization: A Statistical View of a Complex System

et al. 2023

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For the first time, chemometrics was applied to the recently reported microwave-driven cyanide polymerization. Fast, easy, robust, low-cost, and green-solvent processes are characteristic of these types of reactions. These economic and environmental benefits, originally inspired by the constraints imposed by plausible prebiotic synthetic conditions, have taken advantage of the development of a new generation of HCN-derived multifunctional materials. HCN-derived polymers present tunable properties by temperature and reaction time. However, the apparently random behavior observed in the evolution of cyanide polymerizations, assisted by microwave radiation over time at different temperatures, leads us to study this highly complex system using multivariate analytical tools to have a proper view of the system. Two components are sufficient to explain between 84 and 98% of the total variance in the data in all principal component analyses. In addition, two components explain more than 91% of the total variance in the data in the case of principal component analysis for categorical data. These consistent statistical results indicate that microwave-driven polymerization is a more robust process than conventional thermal syntheses but also that plausible prebiotic chemistry in alkaline subaerial environments could be more complex than in the aerial part of these systems, presenting a clear example of the “messy chemistry” approach of interest in the research about the origins of life. In addition, the methodology discussed herein could be useful for the data analysis of extraterrestrial samples and for the design of soft materials, in a feedback view between prebiotic chemistry and materials science.

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Section: Concluding Remarks and Outlooksmentioning

confidence: 70%

Multivariate Analysis Applied to Microwave-Driven Cyanide Polymerization: A Statistical View of a Complex System

et al. 2023

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“…The fifth generation produced 40 512 products—with a cumulative total of 48 401 unique products across all generations. Since this computed model is only an approximation of real chemistry, following 41 we refer to this network as a CRNR. Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Various studies suggesting methods for exploring chemical space, and more particularly in prebiotic chemistry, 41 using CRNRs have been published ( e.g. , ref.…”

Section: Resultsmentioning

confidence: 99%

“…Various studies suggesting methods for exploring chemical space, and more particularly in prebiotic chemistry, 41 using CRNRs have been published (e.g., ref. 73), including a recent report using methods based on scraping chemical databases for reactions known to occur under what the authors considered plausible prebiotic conditions.…”

Section: Detection Of Autocatalytic Motifsmentioning

confidence: 99%

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An open source computational workflow for the discovery of autocatalytic networks in abiotic reactions

et al. 2022

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“…Moreover, it is possible that stepwise complexification depends not only on network topology but also on thermodynamic and kinetic factors, which we did not consider. To evaluate these alternatives, future work will require larger real or rule-based reaction databases [66][67][68] and simulations that can accommodate the stochasticity that will arise when a set of highly diverse chemicals is present, with some chemicals at miniscule concentrations.…”

Section: Future Directionsmentioning

confidence: 99%

The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life

2022

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Prior work on abiogenesis, the emergence of life from non-life, suggests that it requires chemical reaction networks that contain self-amplifying motifs, namely, autocatalytic cores. However, little is known about how the presence of multiple autocatalytic cores might allow for the gradual accretion of complexity on the path to life. To explore this problem, we develop the concept of a seed-dependent autocatalytic system (SDAS), which is a subnetwork that can autocatalytically self-maintain given a flux of food, but cannot be initiated by food alone. Rather, initiation of SDASs requires the transient introduction of chemical “seeds”. We show that, depending on the topological relationship of SDASs in a chemical reaction network, a food-driven system can accrete complexity in a historically contingent manner, governed by rare seeding events. We develop new algorithms for detecting and analyzing SDASs in chemical reaction databases and describe parallels between multi-SDAS networks and biological ecosystems. Applying our algorithms to both an abiotic reaction network and a biochemical one, each driven by a set of simple food chemicals, we detect SDASs that are organized as trophic tiers, of which the higher tier can be seeded by relatively simple chemicals if the lower tier is already activated. This indicates that sequential activation of trophically organized SDASs by seed chemicals that are not much more complex than what already exist could be a mechanism of gradual complexification from relatively simple abiotic reactions to more complex life-like systems. Interestingly, in both reaction networks, higher-tier SDASs include chemicals that might alter emergent features of chemical systems and could serve as early targets of selection. Our analysis provides computational tools for analyzing very large chemical/biochemical reaction networks and suggests new approaches to studying abiogenesis in the lab.

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Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives

Cited by 7 publications

References 183 publications

Multivariate Analysis Applied to Microwave-Driven Cyanide Polymerization: A Statistical View of a Complex System

Multivariate Analysis Applied to Microwave-Driven Cyanide Polymerization: A Statistical View of a Complex System

An open source computational workflow for the discovery of autocatalytic networks in abiotic reactions

The hierarchical organization of autocatalytic reaction networks and its relevance to the origin of life

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