Revisiting the concept of the (a)synchronicity of diels-alder reactions based on the dynamics of quasiclassical trajectories

Molecular Dynamics Investigations of Dienolate [4 + 2] Reactions

We report quantum mechanics calculations and quasiclassical trajectory simulations of [4 + 2] reactions using three common dienolate substrates: siloxy dienes, Li dienolates, and conjugated Pd enolates. Asynchronous transition structures and unequal bond formation were invariably found, with average time gaps of developing bonds ranging from 26.5 to >251.0 fs. The results display a spectrum of dynamically concerted and stepwise [4 + 2] reactions, offering insights into the origin of the stereochemical outcomes of such reactions.

Elucidating the Racemization Mechanism of Aliphatic and Aromatic Amino Acids by In Silico Tools

The racemization of biomolecules in the active site can reduce the biological activity of drugs, and the mechanism involved in this process is still not fully comprehended. The present study investigates the impact of aromaticity on racemization using advanced theoretical techniques based on density functional theory. Calculations were performed at the ωb97xd/6-311++g(d,p) level of theory. A compelling explanation for the observed aromatic stabilization via resonance is put forward, involving a carbanion intermediate. The analysis, employing Hammett's parameters, convincingly supports the presence of a negative charge within the transition state of aromatic compounds. Moreover, the combined utilization of natural bond orbital (NBO) analysis and intrinsic reaction coordinate (IRC) calculations confirms the pronounced stabilization of electron distribution within the carbanion intermediate. To enhance our understanding of the racemization process, a thorough examination of the evolution of NBO charges and Wiberg bond indices (WBIs) at all points along the IRC profile is performed. This approach offers valuable insights into the synchronicity parameters governing the racemization reactions.

A multiscale ONIOM study of the buckminsterfullerene (C60) Diels-Alder reaction: from model design to reaction path analysis

The hybrid ONIOM (Our own N-layered Integrated molecular Orbital and molecular Mechanics) formalism is employed to investigate the Diels-Alder reaction of the buckminsterfullerene C₆₀. Our computations suggest that the ONIOM2(M06-2X/6-31G(d): SVWN/STO-3G) model, enclosing both the diene and the pyracyclene fragment of C60 in the higher-layer, provides a reasonable trade-off between accuracy and computational cost as it comes to predicting reaction energetics. Moreover, the frontier molecular orbital (FMO) theory and activation strain model (ASM) are jointly relied on to rationalize the effect of -OH and -CN substituents on the activation barrier of this reaction. Finally, reaction paths are scrutinized to get insight into the various forces underpinning the process of cycloadduct formation.

New Insights into the (A)Synchronicity of Diels-Alder Reactions: A Theoretical Study Based on the Reaction Force Analysis and Atomic Resolution of Energy Derivatives

In the present manuscript, we report new insights into the concept of (a)synchronicity in Diels-Alder (DA) reactions in the framework of the reaction force analysis in conjunction with natural population calculations and the atomic resolution of energy derivatives along the intrinsic reaction coordinate (IRC) path. Our findings suggest that the DA reaction transitions from a preferentially concerted mechanism to a stepwise one in a 0.10 Å window of synchronicity indices ranging from 0.90 to 1.00 Å. We have also shown that the relative position of the global minimum of the reaction force constant with respect to the TS is an alternative and quantifiable indicator of the (a)synchronicity in DA reactions. Moreover, the atomic resolution of energy derivatives reveals that the mechanism of the DA reaction involves two inner elementary processes associated with the formation of each of the two C-C bonds. This resolution goes on to indicate that, in asynchronous reactions, the driving and retarding components of the reaction force are mostly due to the fast and slow-forming C-C bonds (elementary processes) respectively, while in synchronous reactions, both elementary processes retard and drive the process concomitantly and equivalently.

Effect of substituents and promoters on the Diels-Alder cycloaddition reaction in the biorenewable synthesis of trimellitic acid

An efficient route to produce oxanorbornene, a precursor for the production of bio-based trimellitic acid (TMLA) via the Diels-Alder (DA) reaction of biomass-derived dienes and dienophiles has been proposed by utilizing density functional theory (DFT) simulations. It has been suggested that DA reaction of dienes such as 5-hydroxymethyl furfural (HMF), 2,5-dimethylfuran (DMF), furan dicarboxylic acid (FDCA) and biomass-derived dienophiles (ethylene derivatives e.g., acrolein, acrylic acid, etc.) leads to the formation of an intermediate product oxanorbornene, a precursor for the production of TMLA. The activation barriers for the DA reaction were correlated to the type of substituent present on the dienes and dienophiles. Among the dienophiles, acrolein was found to be the best candidate showing a low activation energy (<40 kJ mol^-1) for the cycloaddition reaction with dienes DMF, HMF and hydroxy methyl furoic acid (HMFA). The FMO gap and (IP_diene + EA_dienophile)/2 were both suggested to be suitable descriptors for the DA reaction of electron-rich diene and electron-deficient dienophile. Further solvents did not have a significant effect on the activation barrier for DA reaction. In contrast, the presence of a Lewis acid was seen to lower the activation barrier due to the reduction in the FMO gap.

Quantum-chemistry-aided identification, synthesis and experimental validation of model systems for conformationally controlled reaction studies: separation of the conformers of 2,3-dibromobuta-1,3-diene in the gas phase

The Diels-Alder cycloaddition, in which a diene reacts with a dienophile to form a cyclic compound, counts among the most important tools in organic synthesis. Achieving a precise understanding of its mechanistic details on the quantum level requires new experimental and theoretical methods. Here, we present an experimental approach that separates different diene conformers in a molecular beam as a prerequisite for the investigation of their individual cycloaddition reaction kinetics and dynamics under single-collision conditions in the gas phase. A low- and high-level quantum-chemistry-based screening of more than one hundred dienes identified 2,3-dibromobutadiene (DBB) as an optimal candidate for efficient separation of its gauche and s-trans conformers by electrostatic deflection. A preparation method for DBB was developed which enabled the generation of dense molecular beams of this compound. The theoretical predictions of the molecular properties of DBB were validated by the successful separation of the conformers in the molecular beam. A marked difference in photofragment ion yields of the two conformers upon femtosecond-laser pulse ionization was observed, pointing at a pronounced conformer-specific fragmentation dynamics of ionized DBB. Our work sets the stage for a rigorous examination of mechanistic models of cycloaddition reactions under controlled conditions in the gas phase.

Real-Space Approach to the Reaction Force: Understanding the Origin of Synchronicity/Nonsynchronicity in Multibond Chemical Reactions

In this article, we present a complementary analysis based on the reaction force F(ξ)/reaction force constant κ(ξ) and noncovalent interactions (NCI) index to characterize the energetics (kinetic and thermodynamics) and mechanistic pathways of two sets of multibond chemical reactions, namely, two double-proton transfer and two Diels-Alder cycloaddition reactions. This approach offers a very straightforward and useful way to delve into a deeper understanding of this type of process. While F(ξ) allows the partition of the whole pathway into three regions or phases, κ(ξ) describes how orchestrated are the bond-breaking and bond-formation events. In turn, NCI indicates how the inter- and intramolecular bonds evolve. The most innovative aspect is the inclusion of the formation of the reactant complex along the pathway, which, by means of NCI, unveils the early molecular recognition and the comprehension of its role in determining the degree of the synchronicity/nonsynchronicity of one-step processes. This approach should be a useful and alternative tool to characterize the energetics and the mechanism of general chemical reactions.

Effect of the exchange–correlation functional on the synchronicity/nonsynchronicity in bond formation in Diels–Alder reactions: a reaction force constant analysis

The performance of 24 KS-DFT-based methods (GGA, MGGA, HGGA, HMGGA, and DHGGA) was assessed, finding that M11 and M06-2X (HMGGA) predicting reliable TS geometries, energetics, and (a)synchronicities in Diels–Alder reactions.

A novel assessment of the role of the methyl radical and water formation channel in the CH3OH + H reaction

A number of experimental and theoretical papers accounted almost exclusively for two channels in the reaction of atomic hydrogen with methanol: H-abstraction from the methyl (R1) and hydroxyl (R2) functional groups. Recently, several astrochemical studies claimed the importance of another channel for this reaction, which is crucial for kinetic simulations related to the abundance of molecular constituents in planetary atmospheres: methyl radical and water formation (R3 channel). Here, motivated by the lack of and uncertainties about the experimental and theoretical kinetic rate constants for the third channel, we developed first-principles Car-Parrinello molecular dynamics thermalized at two significant temperatures - 300 and 2500 K. Furthermore, the kinetic rate constant of all three channels was calculated using a high-level deformed-transition state theory (d-TST) at a benchmark electronic structure level. d-TST is shown to be suitable for describing the overall rate constant for the CH₃OH + H reaction (an archetype of the moderate tunnelling regime) with the precision required for practical applications. Considering the experimental ratios at 1000 K, k_R1/k_R2 ≈ 0.84 and k_R1/k_R3 ≈ 15-40, we provided a better estimate when compared with previous theoretical work: 7.47 and 637, respectively. The combination of these procedures explicitly demonstrates the role of the third channel in a significant range of temperatures and indicates its importance considering the thermodynamic control to estimate methyl radical and water formation. We expect that these results can help to shed new light on the fundamental kinetic rate equations for the CH₃OH + H reaction.