Dynamic Environmental Conditions Affect the Composition of a Model Prebiotic Reaction Network

Duppen, Peer van; Daines, Elena; Robinson, William E.; Huck, Wilhelm T. S.

doi:10.1021/jacs.3c00908

“…[190] For example, insights into the formose reaction have been recently obtained, and exposure to dynamic conditions such as varying Ca(OH) 2 concentration in time affects system's composition. [191] Such an observation could be consistent with the operation of an underlying ratchet mechanism.…”

Section: Discussionsupporting

confidence: 54%

“…It appears that high‐throughput experimentation, combined with data science and machine learning methods are facilitating the transition of some model systems into what could be considered topics of tractable complexity [190] . For example, insights into the formose reaction have been recently obtained, and exposure to dynamic conditions such as varying Ca(OH) 2 concentration in time affects system's composition [191] . Such an observation could be consistent with the operation of an underlying ratchet mechanism.…”

Section: Discussionmentioning

confidence: 97%

Artificial Molecular Ratchets: Tools Enabling Endergonic Processes

Sangchai,

Al Shehimy,

Penocchio

et al. 2023

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Non‐equilibrium chemical systems underpin multiple domains of contemporary interest, including supramolecular chemistry, molecular machines, systems chemistry, prebiotic chemistry, and energy transduction. Experimental chemists are now pioneering the realization of artificial systems that can harvest energy away from equilibrium. In this tutorial review, we provide an overview of artificial molecular ratchets: the chemical mechanisms enabling energy absorption from the environment. By focusing on the mechanism type – rather than the application domain or energy source – we offer a unifying picture of seemingly disparate phenomena, which we hope will foster progress in this fascinating domain of science.

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“…We will focus on comparing the reactions initiated by C 3 dihydroxyacetone and glyceraldehyde. Both reactions ultimately lead to a similar population of C 6 sugars [35,36] . Nevertheless, there is a striking difference at the beginning of the reaction after adding the initiators (Figure 6).…”

Section: Toward Reconstructing the Topology Of The Networkmentioning

confidence: 93%

“…Accordingly, these ions are detected exclusively as potassium ions (see triangles only in the C6−0C panel in Figure 5b). [47,48] Alternatively, the larger sugars can have a branched structure that could create a favorable oxygen‐rich coordination site for the potassium ion [35,36] …”

Section: Toward Reconstructing the Topology Of The Networkmentioning

confidence: 99%

Direct Analysis of Complex Reaction Mixtures: Formose Reaction

Briš,

Baltussen,

Tripodi

et al. 2023

Angew Chem Int Ed

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0

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Complex reaction mixtures, like those postulated on early Earth, present an analytical challenge because of the number of components, their similarity, and vastly different concentrations. Interpreting the reaction networks is typically based on simplified or partial data, limiting our insight. We present a new approach based on online monitoring of reaction mixtures formed by the formose reaction by ion‐mobility‐separation mass‐spectrometry. Monitoring the reaction mixtures led to large data sets that we analyzed by non‐negative matrix factorization, thereby identifying ion‐signal groups capturing the time evolution of the network. The groups comprised ≈300 major ion signals corresponding to sugar‐calcium complexes formed during the formose reaction. Multivariate analysis of the kinetic profiles of these complexes provided an overview of the interconnected kinetic processes in the solution, highlighting different pathways for sugar growth and the effects of different initiators on the initial kinetics. Reconstructing the network's topology further, we revealed so far unnoticed fast retro‐aldol reaction of ketoses, which significantly affects the initial reaction dynamics. We also detected the onset of sugar‐backbone branching for C6 sugars and cyclization reactions starting for C5 sugars. This top‐down analytical approach opens a new way to analyze complex dynamic mixtures online with unprecedented coverage and time resolution.

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“…Accordingly, these ions are detected exclusively as potassium ions (see triangles only in the C6−0C panel in Figure 5b). [47,48] Alternatively, the larger sugars can have a branched structure that could create a favorable oxygen‐rich coordination site for the potassium ion [35,36] …”

Section: Toward Reconstructing the Topology Of The Networkmentioning

confidence: 99%

Direct Analysis of Complex Reaction Mixtures: Formose Reaction

Briš,

Baltussen,

Tripodi

et al. 2023

Angewandte Chemie

Self Cite

0

View full text Add to dashboard Cite

Complex reaction mixtures, like those postulated on early Earth, present an analytical challenge because of the number of components, their similarity, and vastly different concentrations. Interpreting the reaction networks is typically based on simplified or partial data, limiting our insight. We present a new approach based on online monitoring of reaction mixtures formed by the formose reaction by ion‐mobility‐separation mass‐spectrometry. Monitoring the reaction mixtures led to large data sets that we analyzed by non‐negative matrix factorization, thereby identifying ion‐signal groups capturing the time evolution of the network. The groups comprised ≈300 major ion signals corresponding to sugar‐calcium complexes formed during the formose reaction. Multivariate analysis of the kinetic profiles of these complexes provided an overview of the interconnected kinetic processes in the solution, highlighting different pathways for sugar growth and the effects of different initiators on the initial kinetics. Reconstructing the network's topology further, we revealed so far unnoticed fast retro‐aldol reaction of ketoses, which significantly affects the initial reaction dynamics. We also detected the onset of sugar‐backbone branching for C6 sugars and cyclization reactions starting for C5 sugars. This top‐down analytical approach opens a new way to analyze complex dynamic mixtures online with unprecedented coverage and time resolution.

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Dynamic Environmental Conditions Affect the Composition of a Model Prebiotic Reaction Network

Cited by 19 publications

References 43 publications

Artificial Molecular Ratchets: Tools Enabling Endergonic Processes

Artificial Molecular Ratchets: Tools Enabling Endergonic Processes

Direct Analysis of Complex Reaction Mixtures: Formose Reaction

Direct Analysis of Complex Reaction Mixtures: Formose Reaction

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