Advanced Periodic DFT and Stochastic Modeling of Prebiotic Ribose to Deoxyribose Conversion on Fe-Doped Montmorillonite: Mechanistic Insights and Side Reaction Analysis(Estimated Calculating Simulation)-(Theoretical Framework)
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2026
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| _version_ | 1866901641426370560 |
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| author | Reza Hashemi |
| author_facet | Reza Hashemi |
| contents | <p>The prebiotic formation of deoxyribose from ribose is a critical step in the RNA-to-DNA transition. We present a combined periodic density functional theory (DFT) and stochastic Gillespie modeling approach to study the selective C2’-deoxygenation of ribose adsorbed on Fe²⁺/Fe³⁺-doped montmorillonite under UV irradiation. Periodic DFT calculations identify the reaction pathway, transition states, and competing side reactions (epimerization, ring-opening, C3’ oxidation), revealing a favored activation barrier of ~28 kcal/mol for deoxyribose formation, while side reactions have higher barriers (35–40 kcal/mol). Stochastic simulations in small compartments show a non-linear threshold behavior (N_R0 ≈ 7–10) for deoxyribose accumulation, quantitatively supporting the environmental synergy factor S_env ≈ 30–50. This integrative study bridges chemical realism and stochastic compartment selection, providing a mechanistic basis for the emergence of DNA precursors in early Earth conditions.</p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18756284 |
| institution | Zenodo |
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| publishDate | 2026 |
| publisher | Zenodo |
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| spellingShingle | Advanced Periodic DFT and Stochastic Modeling of Prebiotic Ribose to Deoxyribose Conversion on Fe-Doped Montmorillonite: Mechanistic Insights and Side Reaction Analysis(Estimated Calculating Simulation)-(Theoretical Framework) Reza Hashemi The prebiotic formation of deoxyribose from ribose,Periodic density functional theory,Stochastic Gillespie modeling,Periodic DFT calculations <p>The prebiotic formation of deoxyribose from ribose is a critical step in the RNA-to-DNA transition. We present a combined periodic density functional theory (DFT) and stochastic Gillespie modeling approach to study the selective C2’-deoxygenation of ribose adsorbed on Fe²⁺/Fe³⁺-doped montmorillonite under UV irradiation. Periodic DFT calculations identify the reaction pathway, transition states, and competing side reactions (epimerization, ring-opening, C3’ oxidation), revealing a favored activation barrier of ~28 kcal/mol for deoxyribose formation, while side reactions have higher barriers (35–40 kcal/mol). Stochastic simulations in small compartments show a non-linear threshold behavior (N_R0 ≈ 7–10) for deoxyribose accumulation, quantitatively supporting the environmental synergy factor S_env ≈ 30–50. This integrative study bridges chemical realism and stochastic compartment selection, providing a mechanistic basis for the emergence of DNA precursors in early Earth conditions.</p> |
| title | Advanced Periodic DFT and Stochastic Modeling of Prebiotic Ribose to Deoxyribose Conversion on Fe-Doped Montmorillonite: Mechanistic Insights and Side Reaction Analysis(Estimated Calculating Simulation)-(Theoretical Framework) |
| topic | The prebiotic formation of deoxyribose from ribose,Periodic density functional theory,Stochastic Gillespie modeling,Periodic DFT calculations |
| url | https://doi.org/10.5281/zenodo.18756284 |