Kinetics and Mechanism of Oxirane Formation by Darzens Condensation of Ketones: Quantification of the Electrophilicities of Ketones

Promiscuity Guided Evolution of Decarboxylative Aldolases for Synthesis of Tertiary γ-Hydroxy Amino Acids

Many applications of enzymes benefit from activity on structurally diverse substrates. Here, we sought to engineer the decarboxylative aldolase UstD to perform a challenging C-C bond forming reaction with ketone electrophiles. The parent enzyme had only low levels of activity, portending multiple rounds of directed evolution and a possibility that mutations may inadvertently increase the specificity of the enzyme for a single model screening substrate. We show how to intentionally guide UstD towards generality through multi-generational directed evolution using substrate-multiplexed screening (SUMS). Mutations outside of the active site that impact catalytic function were immediately revealed by shifts in promiscuity, even when the overall activity was lower. By re-targeting these distal residues that couple to the active site with saturation mutagenesis, broadly activating mutations were readily identified. When analyzing active site mutants, SUMS identified both specialist enzymes that would have more limited utility as well as generalist enzymes with complementary activity on diverse substrates. These new UstD enzymes catalyze convergent synthesis of non-canonical amino acids bearing tertiary alcohol side chains. This methodology is easy to implement and enables the rapid and effective evolution of enzymes to catalyze desirable new functions.

Defining the Synthetic Scope of ortho-Quinone Methides by Quantifying their Electrophilicity

A series of aryl-substituted ortho-quinone methides (oQMs) was synthesised and structurally characterised. Kinetic studies of the nucleophilic additions of carbanions (reference nucleophiles) to oQMs were used to determine second-order rate constants k2 for the carbon-carbon bond forming reactions (20 °C, DMSO) at the oQMs' exocyclic π-bond. Analysing the kinetic data by the linear free energy relationship lg k2=sN(N+E) revealed the Mayr electrophilicities E of the oQMs. The electrophilicities E of oQMs correlate linearly with Hammett substituent constants and experimentally determined reduction potentials Ep red as well as with quantum-chemically calculated methyl anion affinities (MAAs), which provides valuable tools for prediciting the reactivity of further types of oQMs. Embedding the oQMs in Mayr's reactivity scales enables to predict novel nucleophilic reaction partners for oQMs and can productively be used to prepare simple Michael adducts as well as 4+2 or 4+1 cyclisation products as demonstrated in this work by several novel reactions with neutral or negatively charged C-, N-, and S-nucleophiles.

Hydrophobic Aerogels and Xerogels based on Trimethoxybenzene-Formaldehyde

Phenolic aerogels based on resorcinol-formaldehyde (RF) are among the best thermally insulating materials. However, the hydrophilicity inherent to the free phenolic moiety of RF gels generally limits their actual range of applications. Prior efforts to render phenolic gels hydrophobic are restricted to post-synthetic functionalizations of hydrophilic gels, processes that are often limited in efficiency, scope, and/or longevity. Here, an acid-mediated conversion of 1,3,5-trimethoxybenzene with formaldehyde is reported, yielding monolithic trimethoxybenzene-formaldehyde (TMBF) aerogels and xerogels with low density (0.11-0.30 g cm-3), high porosity (74-92 %), inner surface areas (SBET) of up to 284 m2 g-1, and thermal conductivity of 34.5-43.9 mW m-1 K-1. For a monolithic xerogel based on TMBF xerogels an unprecedently low thermal conductivity of 34.5 mW m-1 K-1 could be achieved. In addition, all TMBF gels are thermally stable (degradation >280-310 °C) and highly hydrophobic (water contact angles 130°-156°). As such, TMBF serves as a new class of inherently hydrophobic aerogels and xerogels and useful complement to RF materials.

Biocatalytic asymmetric aldol addition into unactivated ketones

Enzymes are renowned for their catalytic efficiency and selectivity, but many classical transformations in organic synthesis have no biocatalytic counterpart. Aldolases are prodigious C-C bond-forming enzymes, but their reactivity has only been extended past activated carbonyl electrophiles in special cases. To probe the mechanistic origins of this limitation, we use a pair of aldolases whose activity is dependent on pyridoxal phosphate. Our results reveal how aldolases are limited by kinetically favourable proton transfer with solvent, which undermines aldol addition into ketones. We show how a transaldolase can circumvent this limitation, enabling efficient addition into unactivated ketones. The resulting products are highly sought non-canonical amino acids with side chains that contain chiral tertiary alcohols. Mechanistic analysis reveals that transaldolase activity is an intrinsic feature of pyridoxal phosphate chemistry and identifies principles for extending aldolase catalysis beyond its previous limits to enable convergent, enantioselective C-C bond formation from simple starting materials.

Electrophile-Arene Affinity: An Energy Scale for Evaluating the Thermodynamics of Electrophilic Dearomatization Reactions

Rational design and development of organic reactions are lofty goals in synthetic chemistry. Quantitative description of the properties of molecules and reactions by physical organic parameters plays an important role in this regard. In this Article, we report an energy scale, namely, electrophile-arene affinity (EAA), for evaluating the thermodynamics of electrophilic dearomatization reactions, a class of important transformations that can rapidly build up molecular complexity and structural diversity by converting planar aromatic compounds into three-dimensional cyclic molecules. The acquisition of EAA data can be readily achieved by theoretically calculating the enthalpy changes (ΔH) of the hypothetical reactions of various (cationic) electrophiles with aromatic systems (taking the 1-methylnaphthalen-2-olate ion as an example in this study). Linear correlations are found between the calculated ΔH values and established physical organic parameters such as the percentage of buried volume %VBur (steric effect), Hammett's σ or Brown's σ+ (electronic effect), and Mayr's E (reaction kinetics). Careful analysis of the ΔH values leads to the rational design of a dearomative alkynylation reaction using alkynyl hypervalent iodonium reagents as the electrophiles.

What defines electrophilicity in carbonyl compounds

The origin of the electrophilicity of a series of cyclohexanones and benzaldehydes is investigated using the activation strain model and quantitative Kohn-Sham molecular orbital (MO) theory. We find that this electrophilicity is mainly determined by the electrostatic attractions between the carbonyl compound and the nucleophile (cyanide) along the entire reaction coordinate. Donor-acceptor frontier molecular orbital interactions, on which the current rationale behind electrophilicity trends is based, appear to have little or no significant influence on the reactivity of these carbonyl compounds.

Electrophilicity index revisited

This review aims to be a comprehensive, authoritative, critical, and accessible review of general interest to the chemistry community; because the electrophilicity index is a very useful global reactivity descriptor defined within a conceptual density functional theory framework. Our group has also introduced electrophilicity based new global and local reactivity descriptors and also new associated electronic structure principles, which are important indicators of structure, stability, bonding, reactivity, interactions, and dynamics in a wide variety of physico-chemical systems and processes. This index along with its local counterpart augmented by the associated electronic structure principles could properly explain molecular vibrations, internal rotations and various types of chemical reactions. The concept of the electrophilicity index has been extended to dynamical processes, excited states, confined environment, spin-dependent and temperature-dependent situations, biological activity, site selectivity, aromaticity, charge removal and acceptance, presence of external perturbation through solvents, external electric and magnetic fields, and so forth. Although electrophilicity and its local variant can adequately interpret the behavior of a wide variety of systems and different physico-chemical processes involving them, their predictive potential remains to be explored. An exhaustive review on all these aspects will set the tone of the future research in that direction.

Quantifying Reductive Amination in Nonenzymatic Amino Acid Synthesis

Amino acid biosynthesis initiates with the reductive amination of α-ketoglutarate with ammonia to produce glutamate. However, the other α-keto acids derived from the glyoxylate and Krebs cycles are converted into amino acids by transamination, rather than by reductive amination. Why is only one amino acid synthesized by reductive amination and not the others? To explore this question, we quantified the inherent reactivities of keto acids in nonenzymatic reduction and reductive amination by using BH3 CN- as a model nucleophile. Biological α-keto acids were found to show pronounced nonenzymatic reactivity differences for the formation of amino acids (α-ketoglutarate Collapse

Key Words

• Amino Acids
• Hydride Transfer
• Kinetics
• Metabolism
• Reductive Amination

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MESH Headings

• Amination
• Ammonia/chemistry
• Ketoglutaric Acids/metabolism
• Amino Acids/chemistry
• Keto Acids
• Glutamic Acid/metabolism
• Amines

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Grants

• HORIZON EUROPE European Research Council
• Volkswagen Foundation
• Deutsche Forschungsgemeinschaft

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Affiliation(s)

Robert J. Mayer Institut de Science et d'Ingénierie Supramoléculaires (ISIS)CNRS UMR 7006Université de Strasbourg8 Allée Gaspard Monge67000StrasbourgFrance
Joseph Moran Institut de Science et d'Ingénierie Supramoléculaires (ISIS)CNRS UMR 7006Université de Strasbourg8 Allée Gaspard Monge67000StrasbourgFrance Institut Universitaire de France (IUF)75005ParisFrance

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Highly Efficient Darzens Reactions Mediated by Phosphazene Bases under Mild Conditions

The highly basic and poorly nucleophilic phosphazene base P1 -t-Bu promotes the Darzens condensation of α-halo esters with aromatic aldehydes affording α,β-epoxy esters in nearly quantitative yields under mild conditions and in short reaction times. The more basic P4 -t-Bu phosphazene was found useful with low reactivity aldehydes. These reactions can be performed in aprotic organic solvents of low polarity, thus minimizing the hydrolysis of α,β-epoxy esters which often accompanies the base-promoted Darzens condensations.

Reliable Functionalization of 5,6-Fused Bicyclic N-Heterocycles Pyrazolopyrimidines and Imidazopyridazines via Zinc and Magnesium Organometallics

DFT-calculations allow prediction of the reactivity of uncommon N-heterocyclic scaffolds of pyrazolo[1,5-a]pyrimidines and imidazo[1,2-b]pyridazines and considerably facilitate their functionalization. The derivatization of these N-heterocycles was realized using Grignard reagents for nucleophilic additions to 5-chloropyrazolo[1,5-a]pyrimidines and TMP2 Zn ⋅ 2 MgCl2  ⋅ 2 LiCl allowed regioselective zincations. In the case of 6-chloroimidazo[1,2-b]pyridazine, bases such as TMP2 Zn ⋅ MgCl2  ⋅ 2 LiCl, in the presence or absence of BF3  ⋅ OEt2 , led to regioselective metalations at positions 3 or 8. Subsequent functionalizations were achieved with TMPMgCl ⋅ LiCl, producing various polysubstituted derivatives (up to penta-substitution). X-ray analysis confirmed the regioselectivity for key functional heterocycles.

Quantum Mechanics and Machine Learning Synergies: Graph Attention Neural Networks to Predict Chemical Reactivity

There is a lack of scalable quantitative measures of reactivity that cover the full range of functional groups in organic chemistry, ranging from highly unreactive C-C bonds to highly reactive naked ions. Measuring reactivity experimentally is costly and time-consuming, and no single method has sufficient dynamic range to cover the astronomical size of chemical reactivity space. In previous quantum chemistry studies, we have introduced Methyl Cation Affinities (MCA*) and Methyl Anion Affinities (MAA*), using a solvation model, as quantitative measures of reactivity for organic functional groups over the broadest range. Although MCA* and MAA* offer good estimates of reactivity parameters, their calculation through Density Functional Theory (DFT) simulations is time-consuming. To circumvent this problem, we first use DFT to calculate MCA* and MAA* for more than 2,400 organic molecules thereby establishing a large data set of chemical reactivity scores. We then design deep learning methods to predict the reactivity of molecular structures and train them using this curated data set in combination with different representations of molecular structures. Using 10-fold cross-validation, we show that graph attention neural networks applied to a relational model of molecular structures produce the most accurate estimates of reactivity, achieving over 91% test accuracy for predicting the MCA* ± 3.0 or MAA* ± 3.0, over 50 orders of magnitude. Finally, we demonstrate the application of these reactivity scores to two tasks: (1) chemical reaction prediction and (2) combinatorial generation of reaction mechanisms. The curated data sets of MCA* and MAA* scores is available through the ChemDB chemoinformatics web portal at cdb.ics.uci.edu under Chemical Reactivities data sets.

Base-Promoted Cascade Reactions for the Synthesis of 3,3-Dialkylated Isoindolin-1-ones and 3-Methyleneisoindolin-1-ones

Cascade reactions of ortho-carbonyl-substituted benzonitriles with ((chloromethyl)sulfonyl)benzenes as pronucleophiles led to new isoindolin-1-ones with a tetrasubstituted C-3 position or to (Z)-3-(sulfonyl-methylene)isoindolin-1-ones. The reactions start from readily available materials, are carried out under mild conditions, and do not require metal catalysis. Promoted only by the cheap and environmentally benign K₂CO₃ as the base, up to six elemental steps can be combined in a single pot. Hence, a sequential one-pot cascade/β-elimination/alkylation furnished useful intermediates for the synthesis of aristolactam natural products. The observed selectivity and the mechanism were investigated by DFT studies.

Recent progress in reactivity study and synthetic application of N-heterocyclic phosphorus hydrides

N-heterocyclic phosphines (NHPs) have recently emerged as a new group of promising catalysts for metal-free reductions, owing to their unique hydridic reactivity. The excellent hydricity of NHPs, which rivals or even exceeds those of many metal-based hydrides, is the result of hyperconjugative interactions between the lone-pair electrons on N atoms and the adjacent σ^*(P–H) orbital. Compared with the conventional protic reactivity of phosphines, this umpolung P–H reactivity leads to hydridic selectivity in NHP-mediated reductions. This reactivity has therefore found many applications in the catalytic reduction of polar unsaturated bonds and in the hydroboration of pyridines. This review summarizes recent progress in studies of the reactivity and synthetic applications of these phosphorus-based hydrides, with the aim of providing practical information to enable exploitation of their synthetically useful chemistry.

Determining Michael Acceptor Reactivity from Kinetic, Mechanistic, and Computational Analysis for the Base-catalyzed Thiol-Michael Reaction

A combined experimental and computational study of the reactivities of seven commonly used Michael acceptors paired with two thiols within the framework of photobase-catalyzed thiol-Michael reactions is reported. The rate coefficients of the propagation (kP), reverse propagation (k-P), chain-transfer (kCT), and overall reaction (koverall) were experimentally determined and compared with the well-accepted electrophilicity parameters of Mayr and Parr, and DFT-calculated energetics. Both Mayr's and Parr's electrophilicity parameters predict the reactivities of these structurally varying vinyl functional groups well, covering a range of overall reaction rate coefficients from 0.5 to 6.2 s-1. To gain insight into the individual steps, the relative energies have been calculated using DFT for each of the stationary points along this step-growth reaction between ethanethiol and the seven alkenes. The free energies of the individual steps reveal the underlying factors that control the reaction barriers for propagation and chain transfer. Both the propagation and chain transfer steps are under kinetic control. These results serve as a useful guide for Michael acceptor selection to design and predict thiol-Michael-based materials with appropriate kinetic and material properties.

Reversible and Stable Hemiaminal Hydrogels from Polyvinylamine and Highly Reactive and Selective Bis(N-acylpiperidone)s

Water-soluble bis(N-acylpiperidone)s with aldehyde-like reactivity are reported to react rapidly with polyvinylamine at room temperature, providing unprecedented clean reaction products. Unlike most amine/ketone reactions that result in arbitrary mixtures of imines, aminals, hemiaminals, or hydrates, in the present study hemiaminals, aminals, or hemiaminal/aminal mixtures are exclusively found. Detailed NMR spectroscopy of solutions, gels, and solids, aided by model reactions, reveals that the hemiaminal/aminal ratio depends on pH, water content, and cross-linking density. Network formation is fully reversible upon changes in pH, with the resulting moduli from rheology spanning almost 3 orders of magnitude. The self-healing ability of the system is probed by rheology as well, demonstrating maintained material properties of fractured and healed samples. The unusually clean, fast, and reversible chemistry highlights bispiperidones as a class of efficient building blocks with unprecedented possibilities in dynamic covalent chemistry.

Enantioselective Desymmetrization of Cyclobutanones: A Speedway to Molecular Complexity

Cyclobutanones hold a privileged role in enantioselective desymmetrization because their inherent ring strain allows for a variety of unusual reactions to occur. Current strategies include α-functionalization, rearrangement, and C-C bond activation to directly convert cyclobutanones into a wide range of enantiomerically enriched compounds, including many biologically significant scaffolds. This Minireview provides an overview of state-of-the-art methods that generate complexity from prochiral cyclobutanones in a single operation.

Methyl Anion Affinities of the Canonical Organic Functional Groups

Calculated methyl anion affinities are known to correlate with experimentally determined Mayr E parameters for individual organic functional group classes but not between neutral and cationic organic electrophiles. We demonstrate that methyl anion affinities calculated with a solvation model (MAA*) give a linear correlation with Mayr E parameters for a broad range of functional groups. Methyl anion affinities (MAA*), plotted on the log scale of Mayr E, provide insights into the full range of electrophilicity of organic functional groups. On the Mayr E scale, the electrophilicity toward the methyl anion spans 180 orders of magnitude.

Synthesis and Organocatalytic Asymmetric Nitro-aldol Initiated Cascade Reactions of 2-Acylbenzonitriles Leading to 3,3-Disubstituted Isoindolinones

In this work, we investigated two strategies for the synthesis of the challenging ketones 2-acylbenzonitriles and we report their use as electrophiles in asymmetric organocatalytic cascade reactions with nitromethane. Promising results were obtained in the presence of chiral bifunctional ammonium salts under phase transfer conditions, which led to novel 3,3-disubstituted isoindolinones in quantitative yields and moderate enantioselectivity.