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Prebiotic chemical reactivity in solution with quantum accuracy and microsecond sampling using neural network potentials. | LitMetric

Prebiotic chemical reactivity in solution with quantum accuracy and microsecond sampling using neural network potentials.

Proc Natl Acad Sci U S A

CNRS Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Paris Sciences et Lettres University, Université Paris-Cité, 75005 Paris, France.

Published: June 2024

AI Article Synopsis

  • - RNA is seen as a key player in early life development, but making RNA sequences without enzymes is tough due to slow reactions and unclear mechanisms.
  • - The study uses advanced neural network potentials to analyze how phosphoester bonds form in water, revealing that a specific concerted mechanism is the most favorable pathway for this reaction.
  • - Findings indicate that certain phosphate forms, particularly diprotonated phosphate, are less reactive than previously thought, helping to explain some experimental results and offering insights for creating better abiotic catalysts.

Article Abstract

While RNA appears as a good candidate for the first autocatalytic systems preceding the emergence of modern life, the synthesis of RNA oligonucleotides without enzymes remains challenging. Because the uncatalyzed reaction is extremely slow, experimental studies bring limited and indirect information on the reaction mechanism, the nature of which remains debated. Here, we develop neural network potentials (NNPs) to study the phosphoester bond formation in water. While NNPs are becoming routinely applied to nonreactive systems or simple reactions, we demonstrate how they can systematically be trained to explore the reaction phase space for complex reactions involving several proton transfers and exchanges of heavy atoms. We then propagate at moderate computational cost hundreds of nanoseconds of a variety of enhanced sampling simulations with quantum accuracy in explicit solvent conditions. The thermodynamically preferred reaction pathway is a concerted, dissociative mechanism, with the transient formation of a metaphosphate transition state and direct participation of water solvent molecules that facilitate the exchange of protons through the nonbridging phosphate oxygens. Associative-dissociative pathways, characterized by a much tighter pentacoordinated phosphate, are higher in free energy. Our simulations also suggest that diprotonated phosphate, whose reactivity is never directly assessed in the experiments, is significantly less reactive than the monoprotonated species, suggesting that it is probably never the reactive species in normal pH conditions. These observations rationalize unexplained experimental results and the temperature dependence of the reaction rate, and they pave the way for the design of more efficient abiotic catalysts and activating groups.

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Source
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11161780PMC
http://dx.doi.org/10.1073/pnas.2322040121DOI Listing

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