Free Energy Map for the Co-Oligomerization of Formaldehyde and Ammonia

Nature or number of species in a transition state: the key role of catalytically active molecules in hydrogen transfer stages in atmospheric aldehyde reactions

For the first time, the two factors (the number of sites in the transition state and the nature of the catalytically active species) that affect the energy barriers (Ea and ΔG‡) in atmospheric aldehyde reactions are proposed. The contribution of each factor to the energy barriers of the ammonization and amination stages, dehydration, and intramolecular hydrogen transfer is studied using the example of the acetaldehyde and glyoxal interactions with ammonia in aqueous solution. A regular decrease in energy barriers is observed in a series of 4-, 6-, and 8-membered transition states (TSs) regardless of the nature of the catalytically active species and their numbers. The 8-membered TSs of ammonization, amination, and dehydration reactions are the most efficient catalytic systems. The role of the nature of catalytically active species is secondary and is expressed in different cases through the influence of entropy and different acidity/basicity of catalytically active species and their structures. The regularities for the stage of intramolecular hydrogen transfer stand out from those for the ammonization, amination, and dehydration stages. The intramolecular hydrogen transfer is organized by three atoms in TSs without the participation of catalytically active species, while the 5- and 7-membered TSs are formed with the participation of such species. A proportional decrease in energy barrier with a sequential increase in the number of TS sites (3-, 5-, and 7-) is not observed. A sharp decrease in the barriers occurs only during the formation of the 7-membered TSs, while the 5-membered structures lie above the 3-membered catalytically inactive structures on the potential energy surface (PES) regardless of the nature of the species forming these structures.

The reaction of acetaldehyde, glyoxal, and ammonia to yield 2-methylimidazole: thermodynamic and kinetic analyses of the mechanism

The most thermodynamically and kinetically favorable pathways for the formation of 2-methylimidazole (2MI) in the reaction of glyoxal and acetaldehyde with ammonia in aqueous solution have been determined. The formation of 2MI proceeds through a number of successive intermediates of acyclic and cyclic structures, and the most favorable route (thermodynamically and kinetically) for the formation of the imidazole ring is the condensation of amine intermediates, in contrast to the existing concepts of imine structures. The limiting stage is the stage of cyclization involving the intramolecular attack by the amino group of the precyclic intermediate on the carbon atom bound to the hydroxyl group with the simultaneous release of a water molecule according to the S_N2 mechanism. Further stages of stepwise dehydration lead to the formation of a cyclic diazine, the intramolecular migration of the proton of the tertiary carbon atom to the nitrogen atom of which completes the formation of 2MI. Experimental studies on the effect of the order of mixing of initial reagents on the 2MI yield confirmed the quantum-chemically substantiated favorable pathway for the formation of 2MI during the interaction of amine intermediates, and also revealed that the selectivity of the 2MI formation is achieved by successive mixing of acetaldehyde with ammonia until the formation of hydroxyamine products and their further interaction with glyoxal.

A theoretical insight into the curing mechanism of phthalonitrile resins promoted by aromatic amines

High-temperature phthalonitrile resins have a wide range of applications, and understanding their curing mechanism is of great importance for academic research and engineering applications. However, the actual curing mechanism is still elusive. We presented a density functional theory study on the curing mechanism of phthalonitrile resins promoted by aromatic amines using phthalonitrile and aniline as the model compounds. We found that the rate-determining step is the initial nucleophilic addition of amines with nitrile groups on phthalonitrile to generate an amidine intermediate. The amines play a vital role in the H-transfer promoter throughout the curing reaction. The amidine and isoindoline are the critical intermediates, which can readily react with phthalonitrile through 6-membered transition states. The intramolecular cyclization of amidine intermediates is the vital step in forming isoindoline intermediates, which can be significantly promoted by amines. The proposed curing reaction pathways are kinetically more favorable than the previously reported ones, which can account for the formation of triazine, polyisoindoline, and phthalocyanine and provide a molecular-level understanding of the curing reaction.

Step by Step Strecker Amino Acid Synthesis from Ab Initio Prebiotic Chemistry

The amino acids synthesis from elementary precursors in abiotic conditions is traditionally described according to the Strecker reaction, thoroughly invoked to justify the observation of amino acids in extraterrestrial samples and their emergence in the primordial Earth. To this day, however, a quantitative microscopic description of the mechanism, thermodynamics, and kinetics of the multistep Strecker reaction is still lacking. In the present work we tackle this study by adopting a state-of-the-art ab initio computational approach, combining an efficient scheme of exploration of the relevant chemical networks with a rigorous determination of the underlying free energy and transition states. We determine the step-by-step chemical pathway from "Strecker precursors" to glycine in solution and calculate the corresponding full free energy landscape. Our results agree well with the scarce available experimental data and complete them, thus providing the first end-to-end study of this complex reaction, a crucial bottleneck for the emergence of life.

Early Steps of Glycolonitrile Oligomerization: A Free-Energy Map

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.

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

Building on previous work (J. Phys. Chem. A 2017, 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.

Theoretical analysis of glyoxal condensation with ammonia in aqueous solution

The reactions of glyoxal with ammonia, ammonium salts, and amines cause the formation of the secondary organic aerosol (SOA) components (imidazole and its derivatives) in the atmosphere. The interaction of glyoxal and ammonia in aqueous solution is a primary reaction for these processes, and the explanation of its mechanism will allow developing the methods to control the formation of the SOA components. A detailed mechanism for the formation of key intermediates, namely, ethanediimine, diaminoethanediol, and aminoethanetriol, required for the imidazole ring cyclization, is proposed, and its potential energy surface (PES) has been constructed. This mechanism includes the experimentally identified intermediate compounds and takes into account the conformational and hydration equilibria of glyoxal. The schemes are proposed for further conversion of the key intermediates to the products of condensation between glyoxal and ammonia in the aqueous solution, C-N cyclic oligomers, that were identified. The products are shown to correspond to low positions on the PES in terms of Gibbs free energy, from -30.8 to -68.3 kcal mol-1, which confirms the high probability of their formation. The preferable thermodynamic pathway for formation of the imidazole products does not comprise the conversion of the diimine intermediate with the participation of the proton, but rather the interaction of either the diaminoalcohol with glyoxal monohydrate or two monoamine derivatives between themeselves (aminoethantriol and aminohydroxyacetaldehyde).

Exploring Free Energy Profiles of Uracil and Cytosine Reactions with Formaldehyde

Simple polymers can be potentially formed by the co-oligomerization of pyrimidine nucleobases, uracil and cytosine, with the small molecule formaldehyde. Using density functional calculations, we have constructed a free energy map outlining the thermodynamics and kinetics for (1) the addition of formaldehyde to uracil and cytosine to form hydroxymethylated uracil (HMU) and hydroxymethylated cytosine (HMC), (2) the deamination of cytosine and HMC to uracil and HMU, respectively, and (3) the initial oligomerization of 5-HMU. For the initial formation of monomeric HMU, addition of formaldehyde to the C5 and C6 positions is thermodynamically favored over N1 and N3, but faces higher kinetic barriers, and explains why 5-HMU is the main product observed experimentally. Oligomerization of 5-HMU is thermodynamically favorable although decreasingly so at the tetramer stage. In addition, decreasing concentrations of initial monomer shifts the equilibrium disfavoring oligomer formation.

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

Glycolonitrile, the product of combining CH₂O 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 CH₂O 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.

Nucleophilic Addition of Ketones To Acetylenes and Allenes: A Quantum-Chemical Insight

A CBS-Q//B3 based study has been carried out to elucidate the mechanism of the KOH/DMSO superbase catalyzed ketones nucleophilic addition to alkyl propargyl and alkyl allenyl ethers yielding, along with (Z)-monoadducts, up to 26% of unexpected (E)-diadducts. The impact of different substrates (alkynes versus allenes) on the reaction mechanism has been discussed in detail. Along with the model reaction of acetone addition to propyne and allene, the addition of acetone and acetophenone to methyl propargyl and methyl allenyl ethers is considered. The limiting reaction stage of the starting ketone carbanion addition to propargyl and allenyl systems occurs with activation energies typical for vinylation of ketones. In contrast, the addition of intermediate α-carbanions to the terminal position of methyl allenyl ether is associated with unusually low activation barriers. The results obtained explain the composition of the reaction products and indicate the participation of mainly the allene form in the reaction.

Acetaldehyde-Ammonia Interaction: A DFT Study of Reaction Mechanism and Product Identification

The product of acetaldehyde and ammonia reaction, namely, 2,4,6-trimethyl-1,3,5-hexahydrotriazine trihydrate, was synthesized and identified using a combination of experimental (NMR spectroscopy, IR spectroscopy, melting point determination) and DFT-based theoretical approaches. A reaction mechanism was proposed. The reaction was shown to proceed via the formation of aminoalcohol, imine, and geminal diamine intermediates accompanied by cyclization of these species. The calculation results allowed us to build a potential energy surface of the acetaldehyde and ammonia interaction and determine the most energetically favorable pathway to yield acetaldehyde ammonia trimer. The reaction product was found in an energy minimum (-53.5 kcal/mol).

A DFT kinetic study on 1,3-dipolar cycloaddition reactions in solution

Several popular density functional theory (DFT) methods have been employed to characterize a series of 1,3-dipolar cycloaddition reactions, including the exploration of reaction mechanisms and the calculations of kinetic parameters.