Multiscale Treatment for the Molecular Mechanism of a Diels-Alder Reaction in Solution: A QM/MM-MD Study

Enhanced Sampling Simulation Reveals How Solvent Influences Chirogenesis of the Intra-Molecular Diels-Alder Reaction

The timescale involved in chemical reactions is quite often beyond that of normal molecular dynamics simulations. Here, we combine metadynamics with selective integrated tempering sampling to simulate an intra-molecular Diels-Alder reaction in explicit solvents. Based on a one-dimensional collective variable obtained from harmonic linear discriminant analysis, four chiral isomers of products were observed in the simulation. Analyses of reactive trajectories showed that this reaction follows a concerted mechanism in all four solvents. In addition, the hydrogen bond between the reactant and water solvent plays an important role in the water-accelerated reaction mechanism. The dynamics of chirality formation varies significantly with solvents. The chirality of products forms significantly before the transition state, especially in ionic liquid.

2-Methoxyethyl Nitrite as a Reagent for Chemoselective On-Water Nitration

An on-water approach has been developed that allows a nitration of tyrosines and phenols under mild conditions. We envisioned that the assembly of tyrosine/tyrosyl radical couples with interfacial water molecules would realize a biomimetic stacking hydrogen atom transfer (HAT) transition state to facilitate the electron-transfer process. The optimal organic nitrite, 2-methoxyethyl nitrite, resulted in rapid coupling of the tyrosyl radicals with •NO 2 at the oil-water interface to afford the nitrated phenols. Many characteristics found in our on-water strategy are distinct from other complementary systems that include radical nitration. These enticing roles of water in the reaction process introduce new avenues to explore in the design of synthetic organic chemistry systems.

BF3–Catalyzed Diels–Alder Reaction between Butadiene and Methyl Acrylate in Aqueous Solution—An URVA and Local Vibrational Mode Study

In this study we investigate the Diels–Alder reaction between methyl acrylate and butadiene, which is catalyzed by BF3 Lewis acid in explicit water solution, using URVA and Local Mode Analysis as major tools complemented with NBO, electron density and ring puckering analyses. We considered four different starting orientations of methyl acrylate and butadiene, which led to 16 DA reactions in total. In order to isolate the catalytic effects of the BF3 catalyst and those of the water environment and exploring how these effects are synchronized, we systematically compared the non-catalyzed reaction in gas phase and aqueous solution with the catalyzed reaction in gas phase and aqueous solution. Gas phase studies were performed at the B3LYP/6-311+G(2d,p) level of theory and studies in aqueous solution were performed utilizing a QM/MM approach at the B3LYP/6-311+G(2d,p)/AMBER level of theory. The URVA results revealed reaction path curvature profiles with an overall similar pattern for all 16 reactions showing the same sequence of CC single bond formation for all of them. In contrast to the parent DA reaction with symmetric substrates causing a synchronous bond formation process, here, first the new CC single bond on the CH2 side of methyl acrylate is formed followed by the CC bond at the ester side. As for the parent DA reaction, both bond formation events occur after the TS, i.e., they do not contribute to the energy barrier. What determines the barrier is the preparation process for CC bond formation, including the approach diene and dienophile, CC bond length changes and, in particular, rehybridization of the carbon atoms involved in the formation of the cyclohexene ring. This process is modified by both the BF3 catalyst and the water environment, where both work in a hand-in-hand fashion leading to the lowest energy barrier of 9.06 kcal/mol found for the catalyzed reaction R1 in aqueous solution compared to the highest energy barrier of 20.68 kcal/mol found for the non-catalyzed reaction R1 in the gas phase. The major effect of the BF3 catalyst is the increased mutual polarization and the increased charge transfer between methyl acrylate and butadiene, facilitating the approach of diene and dienophile and the pyramidalization of the CC atoms involved in the ring formation, which leads to a lowering of the activation energy. The catalytic effect of water solution is threefold. The polar environment leads also to increased polarization and charge transfer between the reacting species, similar as in the case of the BF3 catalyst, although to a smaller extend. More important is the formation of hydrogen bonds with the reaction complex, which are stronger for the TS than for the reactant, thus stabilizing the TS which leads to a further reduction of the activation energy. As shown by the ring puckering analysis, the third effect of water is space confinement of the reacting partners, conserving the boat form of the six-member ring from the entrance to the exit reaction channel. In summary, URVA combined with LMA has led to a clearer picture on how both BF3 catalyst and aqueous environment in a synchronized effort lower the reaction barrier. These new insights will serve to further fine-tune the DA reaction of methyl acrylate and butadiene and DA reactions in general.

Diels-Alder Reactions in Water Are Determined by Microsolvation

Nanoconfined aqueous environments and the recent advent of accelerated chemistry in microdroplets are increasingly being investigated for catalysis. The mechanisms underlying the enhanced reactivity in alternate solvent environments and whether the enhanced reactivity due to nanoconfinement is a universal phenomenon are not fully understood. Here, we use ab initio molecular dynamics simulations to characterize the free energy of a retro-Diels-Alder reaction in bulk water at very different densities and in water nanoconfined by parallel graphene sheets. We find that the broadly different global solvation environments accelerate the reactions to a similar degree with respect to the gas-phase reaction, with activation free energies that do not differ by more than k_bT from each other. The reason for the same acceleration factor in the extremely different solvation environments is that it is the microsolvation of the dienophile's carbonyl group that governs the transition-state stabilization and mechanism, which is not significantly disrupted by either the lower density in bulk water or the strong nanoconfinement conditions used here. Our results also suggest that significant acceleration of Diels-Alder reactions in microdroplets or on-water conditions cannot arise from local microsolvation when water is present but instead must come from highly altered reaction environments that drastically change the reaction mechanisms.

Design and SAR Analysis of Covalent Inhibitors Driven by Hybrid QM/MM Simulations

Quantum mechanics/molecular mechanics (QM/MM) hybrid technique is emerging as a reliable computational method to investigate and characterize chemical reactions occurring in enzymes. From a drug discovery perspective, a thorough understanding of enzyme catalysis appears pivotal to assist the design of inhibitors able to covalently bind one of the residues belonging to the enzyme catalytic machinery. Thanks to the current advances in computer power, and the availability of more efficient algorithms for QM-based simulations, the use of QM/MM methodology is becoming a viable option in the field of covalent inhibitor design. In the present review, we summarized our experience in the field of QM/MM simulations applied to drug design problems which involved the optimization of agents working on two well-known drug targets, namely fatty acid amide hydrolase (FAAH) and epidermal growth factor receptor (EGFR). In this context, QM/MM simulations gave valuable information in terms of geometry (i.e., of transition states and metastable intermediates) and reaction energetics that allowed to correctly predict inhibitor binding orientation and substituent effect on enzyme inhibition. What is more, enzyme reaction modelling with QM/MM provided insights that were translated into the synthesis of new covalent inhibitor featured by a unique combination of intrinsic reactivity, on-target activity, and selectivity.

Role of Water in the Reaction Mechanism and endo/exo Selectivity of 1,3-Dipolar Cycloadditions Elucidated by Quantum Chemistry and Machine Learning

Asymmetric 1,3-dipolar cycloadditions of azomethine ylides with activated olefins are among the most important and versatile methods for the synthesis of enantioenriched pyrroline and pyrrolidine derivatives. Despite both theoretical and practical importance, the role of water molecules in the reactivity and endo/exo selectivity remains unclear. To explore how water accelerates the reactions and improves the endo/exo selectivity of the cycloadditions of 1,3-dipole phthalazinium-2-dicyanomethanide (1) and two dipolarophiles, an ab initio-quality neural network potential that overcomes the computational bottleneck of explicitly considering water molecules was used. It is demonstrated that not only the nature of both the dipolarophile and the 1,3-dipole, but also the solvent medium, can perturb or even alter the reaction mechanism. An extreme case was found for the reaction of 1,3-dipole 1 with methyl vinyl ketone, in which the reaction mechanism changes from a concerted to a stepwise mode on going from MeCN to H₂ O as solvent, with formation of a zwitterionic intermediate that is a very shallow minimum on the energy surface. Thus, high stereocontrol can still be expected despite the stepwise nature of the mechanism. The results indicate that water can induce global polarization along the reaction coordinate and highlight the role of microsolvation effects and bulk-phase effects in reproducing the experimentally observed aqueous acceleration and enhanced endo/exo selectivity.

Mechanistic Insights into the Reaction of Chlorination of Tryptophan Catalyzed by Tryptophan 7-Halogenase

Tryptophan 7-halogenase catalyzes chlorination of free tryptophan to 7-chlorotryptophan, which is the first step in the antibiotic pyrrolnitrin biosynthesis. Many biologically and pharmaceutically active natural products contain chlorine and thus, an understanding of the mechanism of its introduction into organic molecules is important. Whilst enzyme-catalyzed chlorination is accomplished with ease, it remains a difficult task for the chemists. Therefore, utilizing enzymes in the synthesis of chlorinated organic compounds is important, and providing atomistic mechanistic insights about the reaction mechanism of tryptophan 7-halogenase is vital and timely. In this work, we examined a mechanism for the reaction of tryptophan chlorination, performed by tryptophan 7-halogenase, by calculating potential energy and free energy surfaces using two different Combined Quantum Mechanical/Molecular Mechanical (QM/MM) methods both employing Density Functional Theory (DFT) for the QM region. Both computational strategies agree on the nature of the rate-limiting step and provided close results for the reaction barriers of the two reaction steps. The calculations for both the potential energy and the free energy profiles showed very similar geometric features and hydrogen bonding interactions for the characterized stationary points.

About Underappreciated Yet Active Conformations of Thiourea Organocatalysts

Conformational dynamics can define the function of organocatalysts. While the accepted mechanism of Schreiner's catalyst features a double hydrogen bond to the substrate that only forms with the anti-anti conformation of its central thiourea group, our electronic-structure theory study reveals that binding of the model substrate methyl vinyl ketone prefers syn-anti conformations. We find a new mechanism featuring π stacking interactions and highlight the need for extensive structure searches for flexible molecules, especially when aiming for structure-based design of catalytic activity.