Chemical Reaction Networks from Scratch with Reaction Prediction and Kinetics-Guided Exploration

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 30, 2025

Algorithmic reaction explorations based on transition state searches can now routinely predict relatively short sequences involving small molecules. However, applying these algorithms to deeper chemical network (CRN) exploration still requires the development of more efficient and accurate policies. Here, an algorithm, which we name yet another kinetic strategy (YAKS), is demonstrated that uses microkinetic simulations nascent achieve cost-effective, deep exploration. Key features algorithm are automatic incorporation bimolecular reactions between intermediates, compatibility with short-lived but kinetically important species, rate uncertainty into policy. In validation case studies glucose pyrolysis, rediscovers pathways previously discovered by heuristic policies elucidates new for experimentally obtained products. The resulting CRN first connect all major experimental pyrolysis products glucose. Additional presented investigate role rules, uncertainty, reactions. These show naïve exponential growth estimates vastly overestimate actual number relevant in physical networks. light this, further improvements prediction make it feasible CRNs might soon be predictable some contexts.

Language: Английский

Exploring Chemical Space Using Ab Initio Hyperreactor Dynamics

ACS Central Science, Journal Year: 2024, Volume and Issue: 10(2), P. 302 - 314

Published: Jan. 31, 2024

In recent years, first-principles exploration of chemical reaction space has provided valuable insights into intricate networks. Here, we introduce ab initio hyperreactor dynamics, which enables rapid screening the accessible from a given set initial molecular species, predicting new synthetic routes that can potentially guide subsequent experimental studies. For this purpose, different hyperdynamics derived bias potentials are applied along with pressure-inducing spherical confinement system in dynamics simulations to efficiently enhance reactivity under mild conditions. To showcase advantages and flexibility approach, present systematic study method's parameters on HCN toy model apply it recently introduced for prebiotic formation glycinal acetamide interstellar ices, yields results line findings. addition, show how developed framework complicated transitions like first step nonenzymatic DNA nucleoside synthesis an aqueous environment, where fragmentation problem earlier nanoreactor approaches is avoided.

Language: Английский

Interstellar Formation of Nitrogen Heteroaromatics [Indole, C₈H₇N; Pyrrole, C₄H₅N; Aniline, C₆H₅NH₂]: Key Precursors to Amino Acids and Nucleobases

Journal of the American Chemical Society, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 7, 2024

Nitrogen-substituted polycyclic aromatic hydrocarbons (NPAHs) are not only fundamental building blocks in the prebiotic synthesis of vital biomolecules such as amino acids and nucleobases DNA RNA but also a potential source prominent unidentified 6.2 μm interstellar absorption band. Although NPAHs have been detected meteorites believed to be ubiquitous universe, their formation mechanisms deep space remained largely elusive. Here, we report first bottom-up pathways simplest prototype NPAHs, indole (C8H7N), along with its pyrrole (C4H5N) aniline (C6H5NH2) low-temperature model ices composed acetylene (C2H2) ammonia (NH3). Utilizing isomer-selective techniques resonance-enhanced multiphoton ionization tunable vacuum ultraviolet photoionization reflectron time-of-flight mass spectrometry, indole, pyrrole, were identified gas phase, suggesting that they promising candidates for future astronomical searches star-forming regions. Our laboratory experiments utilizing infrared spectroscopy spectrometry tandem electronic structure calculations reveal critical insights into reaction toward precursors, thus advancing our understanding proteinogenic nucleobases, key classes molecules central Origins Life.

Language: Английский