Claisen Rearrangements: Insight into Solvent Effects and “on Water” Reactivity from QM/MM Simulations

Assessing the accuracy and efficacy of multiscale computational methods in predicting reaction mechanisms and kinetics of SN2 reactions and Claisen rearrangement

This study investigates the application of quantum mechanical (QM) and multiscale computational methods in understanding the reaction mechanisms and kinetics of SN2 reactions involving methyl iodide with NH2OH and NH2O-, as well as the Claisen rearrangement of 8-(vinyloxy)dec-9-enoate. Our aim is to evaluate the accuracy and effectiveness of these methods in predicting experimental outcomes for these organic reactions. We achieve this by employing QM-only calculations and several hybrids of QM and molecular mechanics (MM) methods, namely QM/MM, QM1/QM2, and QM1/QM2/MM methodologies. For the SN2 reactions, our results demonstrate the importance of explicitly including solvent effects in the calculations to accurately reproduce the transition state geometry and energetics. The multiscale methods, particularly QM/MM and QM1/QM2, show promising performance in predicting activation energies. Moreover, we observe that the size of the MM active region significantly affects the accuracy of calculated activation energies, highlighting the need for careful consideration during the setup of multiscale calculations. In the case of the Claisen rearrangement, both QM-only and multiscale methods successfully reproduce the proposed reaction mechanism. However, the activation free energies calculated using a continuum solvation model, based on single-point calculations of QM-only structures, fail to account for solvent effects. On the other hand, multiscale methods more accurately capture the impact of solvents on activation free energies, with systematic error correction enhancing the accuracy of the results. Furthermore, we introduce a Python code for setting up multiscale calculations with ORCA, which is available on GitHub at https://github.com/iranimehdi/pdbtoORCA .

Catalyst-free selective oxidation of C(sp3)-H bonds in toluene on water

The anisotropic water interfaces provide an environment to drive various chemical reactions not seen in bulk solutions. However, catalytic reactions by the aqueous interfaces are still in their infancy, with the emphasis being on the reaction rate acceleration on water. Here, we report that the oil-water interface activates and oxidizes C(sp3)-H bonds in toluene, yielding benzaldehyde with high selectivity (>99%) and conversion (>99%) under mild, catalyst-free conditions. Collision at the interface between oil-dissolved toluene and hydroxyl radicals spontaneously generated near the water-side interfaces is responsible for the unexpectedly high selectivity. Protrusion of free OH groups from interfacial water destabilizes the transition state of the OH-addition by forming π-hydrogen bonds with toluene, while the H-abstraction remains unchanged to effectively activate C(sp3)-H bonds. Moreover, the exposed free OH groups form hydrogen bonds with the produced benzaldehyde, suppressing it from being overoxidized. Our investigation shows that the oil-water interface has considerable promise for chemoselective redox reactions on water without any catalysts.

Insulator-on-Conductor Fouling Amplifies Aqueous Electrolysis Rates

The chemical industry is a major consumer of fossil fuels. Several chemical reactions of practical value proceed with the gain or loss of electrons, opening a path to integrate renewable electricity into chemical manufacturing. However, most organic molecules have low aqueous solubility, causing green and cheap electricity-driven reactions to suffer from intrinsically low reaction rates in industry's solvent of choice: water. Here, we show that a strategic, partial electrode fouling with hydrophobic insulators (oils and plastics) offsets kinetic limitations caused by poor reactant solubility, opening a new path for the direct integration of renewable electricity into the production of commodity chemicals. Through electrochemiluminescence microscopy, we reveal for the oxidation of organic reactants up to 6-fold reaction rate increase at the "fouled" oil-electrolyte-electrode interface relative to clean electrolyte-electrode areas. Analogously, electrodes partially masked (fouled) with plastic patterns, deposited either photolithographically (photoresists) or manually (inexpensive household glues and sealants), outperform clean electrodes. The effect is not limited to reactants of limited water solubility, and, for example, net gold electrodeposition rates are up to 22% larger at fouled than clean electrodes. In a system involving a surface-active reactant, rate augmentation is driven by the synergy between insulator-confined reactant enrichment and insulator-induced current crowding, whereas only the latter and possibly localized decrease in iR drop near the insulator are relevant in a system composed of non-surface-active species. Our counterintuitive electrode design enhances electrolysis rates despite the diminished area of intimate electrolyte-electrode contact and introduces a new path for upscaling aqueous electrochemical processes.

The emerging chemistry of self-electrified water interfaces

Water is known for dissipating electrostatic charges, but it is also a universal agent of matter electrification, creating charged domains in any material contacting or containing it. This new role of water was discovered during the current century. It is proven in a fast-growing number of publications reporting direct experimental measurements of excess charge and electric potential. It is indirectly verified by its success in explaining surprising phenomena in chemical synthesis, electric power generation, metastability, and phase transition kinetics. Additionally, electrification by water is opening the way for developing green technologies that are fully compatible with the environment and have great potential to contribute to sustainability. Electrification by water shows that polyphasic matter is a charge mosaic, converging with the Maxwell-Wagner-Sillars effect, which was discovered one century ago but is still often ignored. Electrified sites in a real system are niches showing various local electrochemical potentials for the charged species. Thus, the electrified mosaics display variable chemical reactivity and mass transfer patterns. Water contributes to interfacial electrification from its singular structural, electric, mixing, adsorption, and absorption properties. A long list of previously unexpected consequences of interfacial electrification includes: "on-water" reactions of chemicals dispersed in water that defy current chemical wisdom; reactions in electrified water microdroplets that do not occur in bulk water, transforming the droplets in microreactors; and lowered surface tension of water, modifying wetting, spreading, adhesion, cohesion, and other properties of matter. Asymmetric capacitors charged by moisture and water are now promising alternative equipment for simultaneously producing electric power and green hydrogen, requiring only ambient thermal energy. Changing surface tension by interfacial electrification also modifies phase-change kinetics, eliminating metastability that is the root of catastrophic electric discharges and destructive explosions. It also changes crystal habits, producing needles and dendrites that shorten battery life. These recent findings derive from a single factor, water's ability to electrify matter, touching on the most relevant aspects of chemistry. They create tremendous scientific opportunities to understand the matter better, and a new chemistry based on electrified interfaces is now emerging.

Rationalizing and Adapting Water-Accelerated Reactions for Sustainable Flow Organic Processes

Water-accelerated reactions, wherein at least one organic reactant is not soluble in water, are an important class of organic reactions, with a potentially pivotal impact on sustainability of chemical manufacturing processes. However, mechanistic understanding of the factors controlling the acceleration effect has been limited, due to the complex and varied physical and chemical nature of these processes. In this study, a theoretical framework has been established to calculate the rate acceleration of known water-accelerated reactions, giving computational estimations of the change to ΔG^‡ which correlate with experimental data. In-depth study of a Henry reaction between N-methylisatin and nitromethane using our framework led to rationalization of the reaction kinetics, its lack of dependence on mixing, kinetic isotope effect, and different salt effects with NaCl and Na₂SO₄. Based on these findings, a multiphase flow process which includes continuous phase separation and recycling of the aqueous phase was developed, and its superior green metrics (PMI-reaction = 4 and STY = 0.64 kg L^-1 h^-1) were demonstrated. These findings form the essential basis for further in silico discovery and development of water-accelerated reactions for sustainable manufacturing.

Reshuffle Bonds by Ball Milling: A Mechanochemical Protocol for Charge-Accelerated Aza-Claisen Rearrangements

This study presents the development of a mechanochemical protocol for a charge-accelerated aza-Claisen rearrangement. The protocol waives the use of commonly applied transition metals, ligands, or pyrophoric Lewis acids, e.g., AlMe₃. Based on (heterocyclic) tertiary allylamines and acyl chlorides, the desired tertiary amides were prepared in yields ranging from 17% to 84%. Moreover, the same protocol was applied for a Belluš-Claisen-type rearrangement resulting in the synthesis of a 9-membered lactam without further optimization.

Diastereoselective reversible C-C bond exchange of oxindole-thiazolidienediones for dynamic combinatorial chemistry

We herein describe a diastereoselective aldol exchange involving isatins and thiazolidinediones, providing oxindolyl-thiazolidienediones in aqueous media at pH 6. This equilibrium can also be achieved with oxindole exchange as well as cross-exchange within reasonable timescales. These metal and organic catalyst free reversible reactions provide a unique opportunity for the evolution of dynamic combinatorial libraries (DCLs) for target directed dynamic combinatorial chemistry (DCC) and system chemistry.

Capturing Fleeting Intermediates in a Claisen Rearrangement Using Nonequilibrium Droplet Imbibition Reaction Conditions

The Claisen rearrangement of aromatic allyl phenyl ether to 2-allyl phenol is known to be induced by heat, acid, and air-water interfacial (on-water) effects. In this work, we show that the combination of acid and interfacial effects in an "on-droplet" experiment accelerates this reaction even further (by a factor >10×). The reaction acceleration was achieved through a droplet imbibition mass spectrometry (MS) experiment that allows reactants to be deposited on rapidly moving (100 m/s), charged microdroplets while avoiding turbulent mixing. In this case, reactants are concentrated mainly at the surface of the short-lived microdroplets (microseconds), enabling enhanced interfacial effects. By doping n-butylamine in the spray solvent and subsequently exposing the resultant electrosprayed microdroplets to formic acid vapor, the ketone intermediate, 6-allylcyclohexa-2,4-dien-1-one, involved in this Claisen rearrangement was captured and characterized by tandem MS, successfully differentiating it from the corresponding isobaric reactant (allyl phenyl ether) and product (2-allyl phenol). Similar results showing rate acceleration and subsequent capture of the ketone intermediate via an instantaneous reaction with n-butylamine were demonstrated for p-methyl and p-nitro substituted allyl phenyl ether. Density functional theory calculations confirmed that the on-droplet reaction condition, with a high abundance of proton sources, is different from the neutral rearrangement. With a calculated free energy of activation of 5.2 kcal mol^-1 for the protonated reactant, the on-droplet experimental condition provides a unique mechanism for catalyzing the Claisen rearrangement on the microsecond lifetime of the droplets. This experiment marks the first direct capture and detection of a short-lived ketone intermediate in the Claisen rearrangement, a task that is challenged by a thermodynamically favorable tautomerization step to give a more stabilized product (by 20 kcal/mol).

Double proton transfer in hydrated formic acid dimer: Interplay of spatial symmetry and solvent-generated force on reactivity

The double proton transfer (DPT) reaction in the hydrated formic acid dimer (FAD) is investigated at molecular-level detail. For this, a global and reactive machine learned (ML) potential energy surface (PES) is developed to run extensive (more than 100 ns) mixed ML/MM molecular dynamics (MD) simulations in explicit molecular mechanics (MM) solvent at MP2-quality for the solute. Simulations with fixed – as in a conventional empirical force field – and conformationally fluctuating – as available from the ML-based PES – charge models for FAD show a significant impact on the competition between DPT and dissociation of FAD into two formic acid monomers. With increasing temperature the barrier height for DPT in solution changes by about 10% (∼1 kcal mol⁻¹) between 300 K and 600 K. The rate for DPT is largest, ∼1 ns⁻¹, at 350 K and decreases for higher temperatures due to destabilisation and increased probability for dissociation of FAD. The water solvent is found to promote the first proton transfer by exerting a favourable solvent-induced Coulomb force along the O–H⋯O hydrogen bond whereas the second proton transfer is significantly controlled by the O–O separation and other conformational degrees of freedom. Double proton transfer in hydrated FAD is found to involve a subtle interplay and balance between structural and electrostatic factors.

Simulation of double proton transfer in formic acid dimer by reactive ML potential in explicit molecular mechanics water solvent.

Solvation Free Energies in Subsystem Density Functional Theory

For many chemical processes the accurate description of solvent effects are vitally important. Here, we describe a hybrid ansatz for the explicit quantum mechanical description of solute-solvent and solvent-solvent interactions based on subsystem density functional theory and continuum solvation schemes. Since explicit solvent molecules may compromise the scalability of the model and transferability of the predicted solvent effect, we aim to retain both, for different solutes as well as for different solvents. The key for the transferability is the consistent subsystem decomposition of solute and solvent. The key for the scalability is the performance of subsystem DFT for increasing numbers of subsystems. We investigate molecular dynamics and stationary point sampling of solvent configurations and compare the resulting (Gibbs) free energies to experiment and theoretical methods. We can show that with our hybrid model reaction barriers and reaction energies are accurately reproduced compared to experimental data.

Influence of water content on the [2σ+2σ+2π] cycloaddition of dimethyl azodicarboxylate with quadricyclane in mixed methanol-water solvents from QM/MM Monte Carlo simulations

Mixed quantum mechanics/molecular mechanics Monte Carlo (QM/MM/MC) simulations combined with the free energy perturbation (FEP) theory have been performed to investigate the mechanism and solvent effect of the [2σ+2σ+2π] cycloaddition reaction between dimethyl azodicarboxylate and quadricyclanes in the binary mixture solvents of methanol and water by varying the water content from 0 to 100 vol%. The two-dimensional potentials of mean force (2D PMF) calculations demonstrated that the mechanism of the reaction is a collaborative asynchronous procedure. The transition structures do not show large variation among different solvents. The calculated free energies of activation indicated that the QM/MM/MC method reproduced well the tendency of rate enhancement from pure methanol to methanol-water mixtures to "on water" with the water content increasing obtained in the experimental observation. The analyses of the energy pair distribution and radial distribution functions illustrated that hydrogen bonding plays an indispensable role in the stabilization of the transition structures. According to the results in methanol-water mixtures at different volume ratios, it is clear that the site-specific hydrogen bond effects are the central reason which leads to fast rate increases in progressing from a methanol-water volume ratio of 3 : 1 to 1 : 1. This work provides a new insight into the solvent effect for the [2σ+2σ+2π] cycloaddition reaction.

Propensity, free energy contributions and conformation of primary n-alcohols at a water surface

Atmospheric aerosols contain organic molecules that serve as cloud condensation nucleation sites and affect the climate. Several experimental and simulation studies have been dedicated to investigate their surface propensity, but the mechanisms that drive them to the water surface are still not fully understood. In this molecular dynamics (MD) simulation study, primary alcohols are considered as a model system representing polar organic molecules. We find that the surface affinity of n-alcohols increases linearly with the length of the hydrophobic tail. By decomposing the adsorption free energy into enthalpy and entropy contributions, we find that the transition from bulk to surface is entropically driven, compatible with the fact that the hydrophobic effect of small solutes is of entropic origin. The enthalpy of surface adsorption is nearly invariant among different n-alcohols because the loss of solvent-alcohol interactions is balanced by a gain in solvent-solvent interactions. Structural analysis shows that, at the surface, the linear alcohols prefer an orientation with the hydrophobic tail pointing out from the surface, whereas the hydroxyl group remains buried in the water. This general behaviour is likely transferable to other small molecules with similar structures but other functional groups that are present in the atmosphere. Therefore, the present study is a step forward toward a general description of organic molecules in aerosols.

Machine learning of solvent effects on molecular spectra and reactions

Fast and accurate simulation of complex chemical systems in environments such as solutions is a long standing challenge in theoretical chemistry. In recent years, machine learning has extended the boundaries of quantum chemistry by providing highly accurate and efficient surrogate models of electronic structure theory, which previously have been out of reach for conventional approaches. Those models have long been restricted to closed molecular systems without accounting for environmental influences, such as external electric and magnetic fields or solvent effects. Here, we introduce the deep neural network FieldSchNet for modeling the interaction of molecules with arbitrary external fields. FieldSchNet offers access to a wealth of molecular response properties, enabling it to simulate a wide range of molecular spectra, such as infrared, Raman and nuclear magnetic resonance. Beyond that, it is able to describe implicit and explicit molecular environments, operating as a polarizable continuum model for solvation or in a quantum mechanics/molecular mechanics setup. We employ FieldSchNet to study the influence of solvent effects on molecular spectra and a Claisen rearrangement reaction. Based on these results, we use FieldSchNet to design an external environment capable of lowering the activation barrier of the rearrangement reaction significantly, demonstrating promising venues for inverse chemical design.

Molecular reactions at aqueous interfaces

This Review aims to critically analyse the emerging field of chemical reactivity at aqueous interfaces. The subject has evolved rapidly since the discovery of the so-called 'on-water catalysis', alluding to the dramatic acceleration of reactions at the surface of water or at its interface with hydrophobic media. We review critical experimental studies in the fields of atmospheric and synthetic organic chemistry, as well as related research exploring the origins of life, to showcase the importance of this phenomenon. The physico-chemical aspects of these processes, such as the structure, dynamics and thermodynamics of adsorption and solvation processes at aqueous interfaces, are also discussed. We also present the basic theories intended to explain interface catalysis, followed by the results of advanced ab initio molecular-dynamics simulations. Although some topics addressed here have already been the focus of previous reviews, we aim at highlighting their interconnection across diverse disciplines, providing a common perspective that would help us to identify the most fundamental issues still incompletely understood in this fast-moving field.

Effects of solvents on the DACBO-catalyzed vinylogous Henry reaction of isatin with 3,5-dimethyl-4-nitroisoxazole "on-water" and in solution from QM/MM MC simulations

The mechanism of the DABCO-catalyzed vinylogous Henry reaction of isatin with 3,5-dimethyl-4-nitroisoxazole and solvent effects on it have been investigated using density functional theory (DFT) methods and QM/MM Monte Carlo (MC) simulation under "on-water" conditions as well as in methanol and THF solutions. The DFT calculations concluded that Path A, in which DABCO directly catalyzes the reaction of isatin 1a with 3,5-dimethyl-4-nitroisoxazole 2 in water, is the most favorable and the first step, the proton transfer process, is the rate-determining step for the reaction. For the roles of solvents in the reaction, QM/MM MC simulations using free energy perturbation theory and PDDG/PM3 as the QM method have been utilized to predict the free energy profiles. The results indicated that the QM/MM method reproduced well the large rate increases on-water. Solute-solvent energy pair distribution and radial distribution functions were also analyzed and illustrated that hydrogen bonding plays a significant role in stabilizing the transition structures. This work reveals the feasible reaction mechanisms and provides new insight into solvent effects for the DACBO-catalyzed vinylogous Henry reaction.

Polarizable ab initio QM/MM Study of the Reaction Mechanism of N-tert-Butyloxycarbonylation of Aniline in [EMIm][BF₄]

N-t e r t-butoxycarbonylation of amines in solution (water, organic solvents, or ionic liquids) is a common reaction for the preparation of drug molecules. To understand the reaction mechanism and the role of the solvent, quantum mechanical/molecular mechanical simulations using a polarizable multipolar force field with long⁻range electrostatic corrections were used to optimize the minimum energy paths (MEPs) associated with various possible reaction mechanisms employing the nudged elastic band (NEB) and the quadratic string method (QSM). The calculated reaction energies and energy barriers were compared with the corresponding gas-phase and dichloromethane results. Complementary Electron Localization Function (ELF)/NCI analyses provide insights on the critical structures along the MEP. The calculated results suggest the most likely path involves a sequential mechanism with the rate⁻limiting step corresponding to the nucleophilic attack of the aniline, followed by proton transfer and the release of CO 2 without the direct involvement of imidazolium cations as catalysts.

The Transition from Academia: Overcoming the Barrier to a Career in the Drug Discovery Industry

This perspective describes the transition from academic training (specifically graduate school and a postdoctoral fellowship) to a career in the pharmaceutical industry as a computational chemist. My personal journey from childhood to senior scientist is described, along with suggestions and insights into a career in the pharmaceutical industry.

Mechanistic investigation inspired "on water" reaction for hydrobromic acid-catalyzed Friedel-Crafts-type reaction of β-naphthol and formaldehyde

The mechanism of the HBr-catalyzed Friedel-Crafts-type reaction between β-naphthol and HCHO was investigated by DFT to improve this reaction. The HBr-H₂ O co-catalyzed the preferential pathway undergoes the concerted nucleophilic addition and hydrogen shift, stepwise followed by H₂ O elimination and the CC bond formation. The origin of the high catalytic activity of HBr is ascribed to CH···Br^- and OH···Br^- interactions, which suggest that the active species is Br^- . Moreover, water molecules efficiently assist in improving the activity of Br^- . The computational results show that solvent polarity profoundly affects the activation barriers. To our delight, the activation barrier of the rate-determining step for the favored pathway in water is comparable (0.6 kcal/mol difference) with that in acetonitrile. The experimental observation further confirmed our results and demonstrated that the title reaction can be successfully achieved "on water." Therefore, we open a new efficient and green strategy for the synthesis of biphenol derivatives. © 2017 Wiley Periodicals, Inc.

The Role of Water in the Catalyst-Free Aldol Reaction of Water-Insoluble N-Methyl-2,4-thiazolidinedione with N-Methylisatin from QM/MM Monte Carlo Simulations

The role of water in the uncatalyzed aldol reaction of N-methyl-2,4-thiazolidinedione with N-methylisatin is investigated through Monte Carlo statistical mechanics simulations that utilize free energy perturbation theory and the mixed quantum mechanics and molecular mechanics (QM/MM) model with PDDG/PM3 for the QM method in "on-water" and DMSO environments. There are several conceivable orientations between thiazolidinedione and isatin in the process of C-C bond formation. However, the formation of the C-C bond takes place between the re face of isatin and the si face of (E)-enol of the thiazolidinedione to form the preferred anti-type product, which results from enhanced hydrogen-bonding interactions between water molecules and the oxygen atoms undergoing bond breakage and bond formation during the reaction. Novel insights into the effect of water on the aldol reaction are presented herein.

Quantum mechanistic insights on aryl propargyl ether Claisen rearrangement

The mechanism of aryl propargyl ether Claisen rearrangement in gas and solvent phase was investigated using DFT methods. Solvent phase calculations are carried out using N,N-diethylaniline as a solvent in the PCM model. The most favorable pathways involve a [3,3]-sigmatropic reaction followed by proton transfer in the first two steps and then deprotonation or [1,5]-sigmatropic reaction. Finally, cyclization yields benzopyran or benzofuran derivatives. The [3,3]-sigmatropic reaction is the rate-determining step for benzopyran and benzofuran with ΔG(‡) value of 38.4 and 37.9 kcal mol(-1) at M06/6-31+G**//B3LYP/6-31+G* level in gas and solvent phase, respectively. The computed results are in good agreement with the experimental results. Moreover, it is found that the derivatives of aryl propargyl ether proceeded Claisen rearrangement and the rate-determining step may be shifted from the [3,3]-sigmatropic reaction to the tautomerization step. The NBO analysis revealed that substitution of the methyl groups on the aliphatic segment has decreased the stabilization energy E(2) and favors the aryl propargyl ether Claisen rearrangement.

Organic synthesis reactions on-water at the organic–liquid water interface

Organic synthesis on-water has shown surprising successful synthetic methods. This review discusses the array of chemistry, which has been adapted with this methodology.

The reaction mechanism of polyalcohol dehydration in hot pressurized water

The use of high-temperature liquid water (HTW) as a reaction medium is a very promising technology in the field of green chemistry.

Alcohols at the aqueous surface: chain length and isomer effects

Alcohol isomers at the water–vapor interface were studied to determine free energies of adsorption, surface concentrations and enrichment factors.

Surface behavior of amphiphiles in aqueous solution: a comparison between different pentanol isomers

Molecular-level understanding of concentration-dependent changes in the surface structure of different amphiphilic isomers at the water–vapor interface was gained by molecular dynamics (MD) simulation and X-ray photoelectron spectroscopy (XPS).

How does aqueous solubility of organic reactant affect a water-promoted reaction?

It was widely reported that under the "on water" condition, various water-promoted organic reactions can proceed with very high speed. Thus, it is considered that the aqueous solubility of reactant is not an important issue in these reactions. Three types of water-promoted organic reactions were investigated in the current study to distinguish whether the reaction rate of an aqueous reaction was affected by the aqueous solubilities of the reactants. The results showed that, for a Diels-Alder reaction which was fast under the neat conditions, the aqueous solubilities of reactants had little influence on the reaction. However, for the reactions which proceeded slowly under the neat conditions, such as [2σ+2σ+2π] cycloaddition reactions and epoxide aminolysis reactions, the reactants with good aqueous solubilities proceeded fast in water. Poorly aqueous soluble reactants reacted slowly or did not react under the "on water" condition, and an appropriate amount of organic cosolvent was needed to make the reaction become efficient. This evidence suggested that for these two types of reactions, the dissolution of the reactants in water was required.