Showing papers on "Transition state published in 2020"

Exploring the Chemistry of Spiroindolenines by Mechanistically-Driven Reaction Development: Asymmetric Pictet–Spengler-type Reactions and Beyond

Abstract: The Pictet-Spengler reaction is a fundamental named reaction in organic chemistry, and it is the most straightforward method for the synthesis of tetrahydro-β-carbolines, a core structure embedded in numerous alkaloids. Spiroindolenines are often proposed as possible intermediates in Pictet-Spengler reactions. However, whether the spiroindolenine species is an intermediate in the mechanism of the asymmetric Pictet-Spengler reaction remains unclear. Questions about the role of the spiroindolenine species regarding the mechanism include the following: Can the spiroindolenine species be formed effectively under Pictet-Spengler conditions? If so, what is its fate? Is the delivery of the enantioenriched tetrahydro-β-carboline product related to the spiroindolenine intermediate? Previous studies regarding these questions have not reached a consensus. Therefore, elucidating these questions will advance the field of synthetic organic chemistry.The first highly enantioselective synthesis of spiroindolenines that have the same molecular scaffold as the proposed key intermediate of the Pictet-Spengler reaction was accomplished by an Ir-catalyzed intramolecular asymmetric allylic substitution reaction of an indol-3-yl allylic carbonate. In this reaction, a piperidine, pyrrolidine, or cyclopentane ring can be introduced in conjunction with the indolenine structure.Spiroindolenines were found to undergo ring-expansive migration reactions when treated with a catalytic amount of an acid, leading to tetrahydro-β-carbolines or related tetrahydrocarbazoles. Comprehensive DFT calculations and Born-Oppenheimer molecular dynamics simulations have provided insight into the mechanism of the migration process. It has been found that the stereochemistry is strongly correlated with the electronic properties of the migratory group along with the acidity of the catalyst. Close interactions between the positively charged migratory group and the electron-rich indole ring favor the stereospecificity of the migration. Furthermore, a continuous mechanistic spectrum of the Pictet-Spengler reactions can be obtained on the basis of two readily accessible energetic parameters that are derived from computed energies for competing transition states relative to a key intermediate species. This theoretical model provides a unified mechanistic understanding of the asymmetric Pictet-Spengler reaction, which has been further supported by rationally designed prototype reactions. Chemically and stereochemically controllable migration can be achieved when multiple potential migratory groups are available.The reactivity of spiroindolenines has also been explored beyond Pictet-Spengler reactions. A one-pot Ir-catalyzed asymmetric allylic dearomatization/stereoconvergent migration allows the facile synthesis of enantioenriched tetrahydro-β-carbolines from racemic starting materials. An unprecedented six- to seven-membered ring-expansive migration can be achieved when a vinyliminium moiety is involved as a highly reactive migratory group. This reaction facilitates the stereoselective synthesis of thermodynamically challenging indole-annulated seven-membered rings. It has also been found that the migration process can be interrupted. The electrophilic migratory group released from the retro-Mannich reaction of a spiroindolenine can be captured by an inter- or intramolecular nucleophile, thus providing new entries into structurally diverse polycyclic indole derivatives.Therefore, the mechanism of the Pictet-Spengler reaction can be probed by manipulating the reactivity of the spiroindolenine species. In turn, the mechanistic insights gained herein will aid in chemical transformations toward various target molecules. This study serves as a vivid example of the positive interplay between experimental and theoretical investigations in synthetic organic chemistry.

Ground state chemistry under vibrational strong coupling: dependence of thermodynamic parameters on the Rabi splitting energy

Abstract: Vibrational strong coupling (VSC) is currently emerging as a tool to control chemical dynamics. Here we study the impact of strong coupling strength, given by the Rabi splitting energy (ħΩR), on the thermodynamic parameters associated with the transition state of the desilylation reaction of the model molecule 1-phenyl-2-trimethylsilylacetylene. Under VSC, the enthalpy and entropy of activation determined from the temperature-dependent kinetic studies varied nonlinearly with the coupling strength. The thermodynamic parameters of the noncavity reaction did not show noticeable variation, ruling out concentration effects other than the enhanced ħΩR for the changes observed under VSC. The difference between the total free energy change under VSC and in noncavity was relatively smaller possibly because the enthalpy and entropy of activation compensate each other. This thermodynamic study gives more insight into the role of collective strong coupling on the transition state that leads to modified dynamics and branching ratios.

Reactants, products, and transition states of elementary chemical reactions based on quantum chemistry.

Abstract: Reaction times, activation energies, branching ratios, yields, and many other quantitative attributes are important for precise organic syntheses and generating detailed reaction mechanisms. Often, it would be useful to be able to classify proposed reactions as fast or slow. However, quantitative chemical reaction data, especially for atom-mapped reactions, are difficult to find in existing databases. Therefore, we used automated potential energy surface exploration to generate 12,000 organic reactions involving H, C, N, and O atoms calculated at the ωB97X-D3/def2-TZVP quantum chemistry level. We report the results of geometry optimizations and frequency calculations for reactants, products, and transition states of all reactions. Additionally, we extracted atom-mapped reaction SMILES, activation energies, and enthalpies of reaction. We believe that this data will accelerate progress in automated methods for organic synthesis and reaction mechanism generation—for example, by enabling the development of novel machine learning models for quantitative reaction prediction. Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.12047193

Structure and solvation of confined water and water-ethanol clusters within microporous Brønsted acids and their effects on ethanol dehydration catalysis.

Abstract: Aqueous-phase reactions within microporous Bronsted acids occur at active centers comprised of water-reactant-clustered hydronium ions, solvated within extended hydrogen-bonded water networks that tend to stabilize reactive intermediates and transition states differently The effects of these diverse clustered and networked structures were disentangled here by measuring turnover rates of gas-phase ethanol dehydration to diethyl ether (DEE) on H-form zeolites as water pressure was increased to the point of intrapore condensation, causing protons to become solvated in larger clusters that subsequently become solvated by extended hydrogen-bonded water networks, according to in situ IR spectra Measured first-order rate constants in ethanol quantify the stability of SN2 transition states that eliminate DEE relative to (C2H5OH)(H+)(H2O)n clusters of increasing molecularity, whose structures were respectively determined using metadynamics and ab initio molecular dynamics simulations At low water pressures (2–10 kPa H2O), rate inhibition by water (−1 reaction order) reflects the need to displace one water by ethanol in the cluster en route to the DEE-formation transition state, which resides at the periphery of water–ethanol clusters At higher water pressures (10–75 kPa H2O), water–ethanol clusters reach their maximum stable size ((C2H5OH)(H+)(H2O)4–5), and water begins to form extended hydrogen-bonded networks; concomitantly, rate inhibition by water (up to −3 reaction order) becomes stronger than expected from the molecularity of the reaction, reflecting the more extensive disruption of hydrogen bonds at DEE-formation transition states that contain an additional solvated non-polar ethyl group compared to the relevant reactant cluster, as described by non-ideal thermodynamic formalisms of reaction rates Microporous voids of different hydrophilic binding site density (Beta; varying H+ and Si–OH density) and different size and shape (Beta, MFI, TON, CHA, AEI, FAU), influence the relative extents to which intermediates and transition states disrupt their confined water networks, which manifest as different kinetic orders of inhibition at high water pressures The confinement of water within sub-nanometer spaces influences the structures and dynamics of the complexes and extended networks formed, and in turn their ability to accommodate the evolution in polarity and hydrogen-bonding capacity as reactive intermediates become transition states in Bronsted acid-catalyzed reactions

Semiautomated Transition State Localization for Organometallic Complexes with Semiempirical Quantum Chemical Methods

Abstract: We present an efficient computational protocol for robust transition state localization that can be routinely applied to complex (organometallic) reactions. The capabilities of the combination of extended tight-binding semiempirical methods (GFNn-xTB) with a state-of-the-art transition state localization algorithm (mGSM) is demonstrated on a modified version of the MOBH35 benchmark set, consisting of 29 organometallic reactions and transition states. Furthermore, for three examples we demonstrate how error-prone the conventional (manual) approach based on chemical intuition can be and how errors are avoided by a semiautomated generation of reaction profiles. The performance of the GFNn-xTB methods is carefully assessed and compared with that of the widely used PM6-D3H4 and PM7 semiempirical methods. The GFNn-xTB methods show much higher success rates of 89.7% (GFN1-xTB) and 86.2% (GFN2-xTB) compared with 72.4% for PM6-D3H4 and 69.0% for PM7. The barrier heights and reaction energies are computed with much better accuracy at reduced computational cost for the GFNn-xTB methods compared with the PMx methods, allowing a semiquantitative assessment of possible reaction pathways already at a semiempirical level. The mean error of GFN2-xTB for the barrier heights (8.2 kcal mol-1) is close to what low-cost density functional approximations provide and substantially smaller than the corresponding error of the competitor methods.

Generating transition states of isomerization reactions with deep learning

Abstract: Lack of quality data and difficulty generating these data hinder quantitative understanding of reaction kinetics. Specifically, conventional methods to generate transition state structures are deficient in speed, accuracy, or scope. We describe a novel method to generate three-dimensional transition state structures for isomerization reactions using reactant and product geometries. Our approach relies on a graph neural network to predict the transition state distance matrix and a least squares optimization to reconstruct the coordinates based on which entries of the distance matrix the model perceives to be important. We feed the structures generated by our algorithm through a rigorous quantum mechanics workflow to ensure the predicted transition state corresponds to the ground truth reactant and product. In both generating viable geometries and predicting accurate transition states, our method achieves excellent results. We envision workflows like this, which combine neural networks and quantum chemistry calculations, will become the preferred methods for computing chemical reactions.

Electrophilic Azides for Materials Synthesis and Chemical Biology.

Abstract: Organic azides are involved in a variety of useful transformations, including nitrene chemistry, reactions with nucleophiles and electrophiles, and cycloadditions. The 1,3-dipolar cycloadditions of azides constitute a major class of highly reliable and versatile reactions, as shown by the development and rapid adoption of click chemistry and bioorthogonal chemistry. Metal-catalyzed azide-alkyne cycloaddition (Cu/RuAAC), the prototypical click reaction, has found wide utility in pharmaceutical, biomedical, and materials sciences. The strain-promoted, or distortion-accelerated, azide-alkyne cycloaddition eliminates the need for a metal catalyst.In the azide-mediated 1,3-dipolar cycloaddition reactions, azides are ambiphilic, i.e., HOMO-LUMO-controlled dipoles where both the HOMO and LUMO interact strongly with the dipolarophile. Azide-alkyne cycloaddition proceeds primarily through the HOMOazide-LUMOdipolarophile interaction, and electron-deficient dipolarophiles react more readily. The inverse-electron-demand reaction, involving the LUMOazide-HOMOdipolarophile interaction, is less common because of the low stability of electron-deficient azides such as acyl, sulfonyl, and phosphoryl azides. Nevertheless, there have been reports since the 1960s showing enhanced reaction kinetics between electron-poor azides and electron-rich dipolarophiles. Our laboratory has developed the use of perfluoroaryl azides (PFAAs), a class of stable electron-deficient azides, as nitrene precursors and for reactions with nucleophiles and electron-rich dipolarophiles. Perfluorination on the aryl ring also facilitates the synthesis of PFAAs and quantitative analysis of the products by 19F NMR spectroscopy.In this Account, we summarize key reactions involving electrophilic azides and applications of these reactions in materials synthesis and chemical biology. These electron-deficient azides exhibit unique reactivity toward nucleophiles and electron-rich or strained dipolarophiles, in some cases leading to new transformations that do not require any catalysts or products that are impossible to obtain from the nonelectrophilic azides. We highlight work from our laboratories on reactions of PFAAs with enamines, enolates, thioacids, and phosphines. In the reactions of PFAAs with enamines or enolates, the triazole or triazoline cycloaddition products undergo further rearrangement to give amidines or amides as the final products at rates of up to 105 times faster than their non-fluorinated anlogues. Computational investigations by the distortion/interaction activation strain model reveal that perfluorination lowers the LUMO of the aryl azide as well as the overall activation energy of the reaction by decreasing the distortion energies of the reactants to reach the transition states. The PFAA-enamine reaction can be carried out in a one-pot fashion using readily available starting materials of aldehyde and amine, making the reaction especially attractive, for example, in the functionalization of nanomaterials and derivatization of antibiotics for the preparation of theranostic nanodrugs. Similar fast kinetics was also observed for the PPAA-mediated Staudinger reaction, which proceeds at 104 times higher rate than the classic Staudinger ligation, giving stable phosphoimines in high yields. The reaction is biorthogonal, allowing cell-surface labeling with minimal background noise.

Accurate Global Potential Energy Surfaces for the H + CH3OH Reaction by Neural Network Fitting with Permutation Invariance

Abstract: The H + CH3OH reaction, which plays an important role in combustion and the interstellar medium, presents a prototypical system with multi channels and tight transition states. However, no globally reliable potential energy surface (PES) has been available to date. Here we develop global analytical PESs for this system using the permutation-invariant polynomial neural network (PIP-NN) and the high-dimensional neural network (HD-NN) methods based on a large number of data points calculated at the level of the explicitly correlated unrestricted coupled cluster single, double, and perturbative triple level with the augmented correlation corrected valence triple-ζ basis set (UCCSD(T)-F12a/AVTZ). We demonstrate that both machine learning PESs are able to accurately describe all dynamically relevant reaction channels. At a collision energy of 20 kcal/mol, quasi-classical trajectory calculations reveal that the dominant channel is the hydrogen abstraction from the methyl site, yielding H2 + CH2OH. The reaction of this major channel takes place mainly via the direct rebound mechanism. Both the vibrational and rotational states of the H2 product are relatively cold, and large portions of the available energy are converted into the product translational motion.

Interplay of water and a supramolecular capsule for catalysis of reductive elimination reaction from gold.

Abstract: Supramolecular assemblies have gained tremendous attention due to their ability to catalyze reactions with the efficiencies of natural enzymes. Using ab initio molecular dynamics, we identify the origin of the catalysis by the supramolecular capsule Ga4L612- on the reductive elimination reaction from gold complexes and assess their similarity to natural enzymes. By comparing the free energies of the reactants and transition states for the catalyzed and uncatalyzed reactions, we determine that an encapsulated water molecule generates electric fields that contributes the most to the reduction in the activation free energy. Although this is unlike the biomimetic scenario of catalysis through direct host-guest interactions, the electric fields from the nanocage also supports the transition state to complete the reductive elimination reaction with greater catalytic efficiency. However it is also shown that the nanocage poorly organizes the interfacial water, which in turn creates electric fields that misalign with the breaking bonds of the substrate, thus identifying new opportunities for catalytic design improvements in nanocage assemblies.

Catalytic resonance theory: parallel reaction pathway control

Abstract: Catalytic enhancement of chemical reactions via heterogeneous materials occurs through stabilization of transition states at designed active sites, but dramatically greater rate acceleration on that same active site can be achieved when the surface intermediates oscillate in binding energy. The applied oscillation amplitude and frequency can accelerate reactions orders of magnitude above the catalytic rates of static systems, provided the active site dynamics are tuned to the natural frequencies of the surface chemistry. In this work, differences in the characteristics of parallel reactions are exploited via selective application of active site dynamics (0 < ΔU < 1.0 eV amplitude, 10−6 < f < 104 Hz frequency) to control the extent of competing reactions occurring on the shared catalytic surface. Simulation of multiple parallel reaction systems with broad range of variation in chemical parameters revealed that parallel chemistries are highly tunable in selectivity between either pure product, even when specific products are not selectively produced under static conditions. Two mechanisms leading to dynamic selectivity control were identified: (i) surface thermodynamic control of one product species under strong binding conditions, or (ii) catalytic resonance of the kinetics of one reaction over the other. These dynamic parallel pathway control strategies applied to a host of simulated chemical conditions indicate significant potential for improving the catalytic performance of many important industrial chemical reactions beyond their existing static performance.

Formic Acid: A Hydrogen-Bonding Cocatalyst for Formate Decomposition

Abstract: Hydrogen bonding accelerates many catalytic reactions by orienting intermediates, stabilizing transition states, and even opening reaction pathways. However, most mechanistic studies regarding the ...

Unusual KIE and dynamics effects in the Fe-catalyzed hetero-Diels-Alder reaction of unactivated aldehydes and dienes

Abstract: Hetero-Diels-Alder (HDA) reaction is an important synthetic method for many natural products. An iron(III) catalyst was developed to catalyze the challenging HDA reaction of unactivated aldehydes and dienes with high selectivity. Here we report extensive density-functional theory (DFT) calculations and molecular dynamics simulations that show effects of iron (including its coordinate mode and/or spin state) on the dynamics of this reaction: considerably enhancing dynamically stepwise process, broadening entrance channel and narrowing exit channel from concerted asynchronous transition states. Also, our combined computational and experimental secondary KIE studies reveal unexpectedly large KIE values for the five-coordinate pathway even with considerable C–C bond forming, due to equilibrium isotope effect from the change in the metal coordination. Moreover, steric and electronic effects are computationally shown to dictate the C=O chemoselectivity for an α,β-unsaturated aldehyde, which is verified experimentally. Our mechanistic study may help design homogeneous, heterogeneous and biological catalysts for this challenging reaction. Recently an iron catalyst was developed to catalyze an oxa-Diels-Alder reaction, whose mechanism is unclear yet. Here the authors combine DFT and molecular dynamics simulations with experimental studies to elucidate the unusual iron effect on kinetic isotope effect and dynamics in this reaction.

Dynamic Features of Transition States for β-Scission Reactions of Alkenes over Acid Zeolites Revealed by AIMD Simulations.

Abstract: Zeolite-catalyzed alkene cracking is key to optimize the size of hydrocarbons. The nature and stability of intermediates and transition states (TS) are, however, still debated. We combine transition path sampling and blue moon ensemble density functional theory simulations to unravel the behavior of C7 alkenes in CHA zeolite. Free energy profiles are determined, linking π-complexes, alkoxides and carbenium ions, for B1 (secondary to tertiary) and B2 (tertiary to secondary) β-scissions. B1 is found to be easier than B2 . The TS for B1 occurs at the breaking of the C-C bond, while for B2 it is the proton transfer from propenium to the zeolite. We highlight the dynamic behaviors of the various intermediates along both pathways, which reduce activation energies with respect to those previously evaluated by static approaches. We finally revisit the ranking of isomerization and cracking rate constants, which are crucial for future kinetic studies.

A DFT and KMC based study on the mechanism of the water gas shift reaction on the Pd(100) surface.

Abstract: We present a combined density functional theory (DFT) and Kinetic Monte Carlo (KMC) study of the water gas shift (WGS) reaction on the Pd(100) surface. We propose a mechanism comprising both the redox and the associative pathways for the WGS within a single framework, which consists of seven core elementary steps, which in turn involve splitting of a water molecule followed by the production of an H-atom and an OH-species on the Pd(100) surface. In the following steps, these intermediates then recombine with each other and with CO leading to the evolution of CO2, and H2. Seven other elementary steps, involving the diffusion and adsorption of the surface intermediate species are also considered for a complete description of the mechanism. The geometrical and electronic properties of each of the reactants, products, and the transition states of the core elementary steps are presented. We also discuss the analysis of Bader charges and spin densities for the reactants, transition states and the products of these elementary steps. Our study indicates that the WGS reaction progresses simultaneously via the direct oxidation and the carboxyl paths on the Pd(100) surface.

Mechanistic study of hydrazine decomposition on Ir(111)

Abstract: Hydrogen transport and storage technology remain one of the critical challenges of the hydrogen economy. Hydrazine (N2H4) is a carbon-free hydrogen carrier which has been widely used as fuel in the field of space exploration. We have combined experiments and computer simulations in order to gain a better understanding of the N2H4 decomposition on Ir catalyst, the most efficient catalyst for hydrazine decomposition up to date. We have identified metallic Ir rather than IrO2 as the active phase for hydrazine decomposition and carried out density functional theory (DFT) calculations to systematically investigate the changes in the electronic structure along with the catalytic decomposition mechanisms. Three catalytic mechanisms to hydrazine decomposition over Ir(111) have been found: (i) intramolecular reaction between hydrazine molecules, (ii) intramolecular reaction between co-adsorbed amino groups, and (iii) hydrazine dehydrogenation assisted by co-adsorbed amino groups. These mechanisms follow five different pathways for which transition states and intermediates have been identified. The results show that hydrazine decomposition on Ir(111) starts preferentially with an initial N-N bond scission followed by hydrazine dehydrogenation assisted by the amino produced, eventually leading to ammonia and nitrogen production. The preference for N-N scission mechanisms was rationalized by analyzing the electronic structure. This analysis showed that upon hydrazine adsorption, the π bond between nitrogen atoms becomes weaker.

Mechanism of the highly effective peptide bond hydrolysis by MOF-808 catalyst under biologically relevant conditions.

Abstract: Efficient and selective hydrolysis of inert peptide bonds is of paramount importance. MOF-808, a metal-organic framework based on Zr6 nodes, can hydrolyze peptide bonds efficiently under biologically relevant conditions. However, the details of the catalyst structure and of the underlying catalytic reaction mechanism are challenging to establish. By means of DFT calculations we first investigate the speciation of the Zr6 nodes and identify the nature of ligands that bind to the Zr6O8H4-x core in aqueous conditions. The core is predicted to strongly prefer a Zr6O8H4 protonation state and to be predominantly decorated by bridging formate ligands, giving Zr6(μ3-O)4(μ3-OH)4(BTC)2(HCOO)6 and Zr6(μ3-O)4(μ3-OH)4(BTC)2(HCOO)5(OH)(H2O) as the most favorable structures at physiological pH. The GlyGly peptide can bind MOF in several different ways, with the preferred structure involving coordination through the terminal carboxylate analogously to the binding mode of formate ligand. The pre-reactive binding mode in which the amide carbonyl oxygen coordinates the metal core lies 7 kcal higher in free energy. The preferred reaction pathway is predicted to have two close-lying transition states, either of which could be the rate-determining step: nucleophilic attack on the amide carbon atom and C-N bond breaking, with calculated relative free energies of 31 and 32 kcal mol-1, respectively. Replacement of formate by water and hydroxide at the Zr6 node is predicted to be possible, but does not appear to play a role in the hydrolysis mechanism.

The Challenge of CO Hydrogenation to Methanol: Fundamental Limitations Imposed by Linear Scaling Relations

Abstract: Recent developments in computational catalysis have allowed the routine reduction of the dimensionality of complex reaction networks to a few descriptors based on linear scaling relations. Despite this convenient benefit, linear scaling relations fundamentally limit the activity and selectivity of a given class of materials towards a given reaction. Here, we show an example by offering a novel description of the fundamental limits on the activity of CO hydrogenation to methanol; a reaction that offers a sustainable route to obtaining value-added chemicals from syngas. First, we show that there is a strong linear correlation between the formation energy of CO* (where * denotes an adsorbed species) and those of the transition states of a number of elementary steps along the methanol synthesis pathway on these surfaces. Using microkinetic modeling, we cast this information into activity volcano plots with the formation energies of a given transition state and CO* as independent descriptors. This analysis reveals the fundamental limits on activity imposed by the aforementioned linear scaling relations, and invites a vigorous search for novel materials that escape these linear scaling relations as a necessary condition for achieving improved activity towards methanol from CO hydrogenation. Specifically, we point out the transition states H–CO* and CH3O–H* as key transition states to be stabilized independently of CO* for improved activity and selectivity towards methanol synthesis.

Thousands of reactants and transition states for competing E2 and S$_\text{N}$2 reactions

Abstract: Reaction barriers are a crucial ingredient for first principles based computational retro-synthesis efforts as well as for comprehensive reactivity assessments throughout chemical compound space. While extensive databases of experimental results exist, modern quantum machine learning applications require atomistic details which can only be obtained from quantum chemistry protocols. For competing E2 and S$_\text{N}$2 reaction channels we report 4'466 transition state and 143'200 reactant complex geometries and energies at respective MP2/6-311G(d) and single point DF-LCCSD/cc-pVTZ level of theory covering the chemical compound space spanned by the substituents NO$_2$, CN, CH$_3$, and NH$_2$ and early halogens (F, Cl, Br) as nucleophiles and leaving groups. Reactants are chosen such that the activation energy of the competing E2 and S$_\text{N}$2 reactions are of comparable magnitude. The correct concerted motion for each of the one-step reactions has been validated for all transition states. We demonstrate how quantum machine learning models can support data set extension, and discuss the distribution of key internal coordinates of the transition states.