Porphinogen Formation from the Co-Oligomerization of Formaldehyde and Pyrrole: Free Energy Pathways

Kua, Jeremy; Loli, Helen

doi:10.1021/acs.jpca.7b08685

Cited by 5 publications

(32 citation statements)

References 36 publications

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“…A brief summary of the key results are as follows; for full details, see our previous work. 1 When CH 2 O is added to pyrrole, addition to the nitrogen (forming 2 ) is less thermodynamically favorable compared to addition to the carbon. The α-position (forming 3 ) is marginally favored over the β-position (forming 4 ).…”

Section: Resultsmentioning

confidence: 99%

“…Parenthetical values in blue font are the energy barriers under neutral (aqueous) conditions from our previous work. 1…”

Section: Resultsmentioning

confidence: 99%

“…This pathway has already been extensively discussed in our previous work under neutral conditions. 1…”

Section: Resultsmentioning

confidence: 99%

“…These transition states were much easier to optimize, and had one large negative eigenvalue corresponding to the reaction coordinate involving bond breaking/forming and accompanying proton transfer. Whereas these calculated barriers can be compared to our previous work in the absence of acid, 1 they assume the thermodynamic profile of neutral zero-charge species, and cannot be mapped directly on the thermodynamic profile generated for protonated species.…”

Section: Methodsmentioning

confidence: 99%

“…In a previous computational study, we constructed a free-energy map for the co-oligomerization of formaldehyde and pyrrole to form porphyrinogen, 1 as shown in Figure 1. We calculated the thermodynamics and kinetics of various elementary reaction steps in this system under baseline conditions at neutral pH in aqueous solution.…”

Section: Introductionmentioning

confidence: 99%

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Role of Acid in the Co-oligomerization of Formaldehyde and Pyrrole

et al. 2019

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Building on previous work (J. Phys. Chem. A2017,121, 8154–8166) under neutral conditions, we examined the co-oligomerization of CH2O and pyrrole to form porphryinogen under acidic conditions using density functional theory (B3LYP//6-311G**). Thermodynamically, we found that azafulvene intermediates were significantly stabilized under highly acidic conditions. Kinetically, energy barriers were lowered for C–C bond formation, discriminating in favor of reactions that lead to porphyrinogen. However, it was challenging to satisfactorily combine our thermodynamic and kinetic profiles into a unified free-energy profile because of difficulties in optimizing transition states of cationic species involving proton hops. Instead, we used neutral carboxylic acids as a proxy to study how energy barriers changed. By combining data from both neutral and acidic conditions, we estimate a free-energy profile for the initial steps of oligomerization under milder acidic conditions more relevant to prebiotic chemistry.

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Section: Resultsmentioning

confidence: 99%

“…Parenthetical values in blue font are the energy barriers under neutral (aqueous) conditions from our previous work. 1…”

Section: Resultsmentioning

confidence: 99%

“…This pathway has already been extensively discussed in our previous work under neutral conditions. 1…”

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Role of Acid in the Co-oligomerization of Formaldehyde and Pyrrole

et al. 2019

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Early Steps of Glycolonitrile Oligomerization: A Free-Energy Map

Kua

Paradela

2020

J. Phys. Chem. A

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Building on our previous free-energy map (J. Phys. Chem. A 2018, 122, 6769–6779) examining the reactions of monomeric glycolonitrile, we explore the formation of its dimers and trimers in aqueous solution under neutral conditions. While 5-membered rings are kinetically favored, open-chain oligomers with ester or amide linkages are thermodynamically favored. Accessing the 5-membered rings also provides a potential route to glyoxal that bypasses preforming glycolamide, the thermodynamic sink for monomers. However, finding a kinetically accessible route to glycine starting from glycolonitrile in the absence of added ammonia at room temperature proved challenging; the best case involved an intramolecular nucleophilic substitution reaction in a dimer containing neighboring imine and amide groups. Our free-energy map also examines routes to experimentally proposed moieties, explaining why some are observed in low yield or not at all.

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Reactions of Glycolonitrile with Ammonia and Water: A Free Energy Map

Thrush

Kua

2018

J. Phys. Chem. A

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Glycolonitrile, the product of combining CHO and HCN, is an intermediate in the Strecker reaction leading to the synthesis of the amino acid glycine. However, besides glycine, a plethora of other compounds are also generated when CHO and HCN react in the presence of ammonia and water. As a starting point to analyze the possible components of this complex mixture, we have employed density functional theory to construct a free energy map of all two-carbon (C2) species that may be present when glycolonitrile participates in addition or elimination reactions with ammonia and water. By identifying thermodynamic sinks and kinetic barriers, we find that the myriad C2 species can be grouped into three broad regions across the free energy landscape. This allows us to trace possible routes to glycine and other molecules of interest in the reaction mixture. The present map also extends our previous work on one-carbon (C1) species. We had previously found one issue with our computational protocol in the C1 map; however, our present C2 map provides a larger data set that supports using an empirical correction to our original protocol for imidic acid to amide transformations, without increasing the computational cost, while retaining the original protocol for other classes of reactions.

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Porphinogen Formation from the Co-Oligomerization of Formaldehyde and Pyrrole: Free Energy Pathways

Cited by 5 publications

References 36 publications

Role of Acid in the Co-oligomerization of Formaldehyde and Pyrrole

Role of Acid in the Co-oligomerization of Formaldehyde and Pyrrole

Early Steps of Glycolonitrile Oligomerization: A Free-Energy Map

Reactions of Glycolonitrile with Ammonia and Water: A Free Energy Map

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