Hydrogen-Bond-Enabled Dynamic Kinetic Resolution of Axially Chiral Amides Mediated by a Chiral Counterion

Non-biaryl atropisomers are valuable in medicine, materials, and catalysis, but their enantioselective synthesis remains a challenge. Herein, a counterion-mediated O-alkylation method for the generation of atropisomeric amides with an er up to 99:1 is outlined. This dynamic kinetic resolution is enabled by the observation that the rate of racemization of atropisomeric naphthamides is significantly increased by the presence of an intramolecular O-H⋅⋅⋅NCO hydrogen bond. Upon O-alkylation of the H-bond donor, the barrier to rotation is significantly increased. Quantum calculations demonstrate that the intramolecular H-bond reduces the rotational barrier about the aryl-amide bond, stabilizing the planar transition state for racemization by approximately 40 kJ mol-1 , thereby facilitating the observed dynamic kinetic resolution.

Non-Hydrolytic β-Lactam Antibiotic Fragmentation by l,d-Transpeptidases and Serine β-Lactamase Cysteine Variants

Enzymes often use nucleophilic serine, threonine, and cysteine residues to achieve the same type of reaction; the underlying reasons for this are not understood. While bacterial d,d-transpeptidases (penicillin-binding proteins) employ a nucleophilic serine, l,d-transpeptidases use a nucleophilic cysteine. The covalent complexes formed by l,d-transpeptidases with some β-lactam antibiotics undergo non-hydrolytic fragmentation. This is not usually observed for penicillin-binding proteins, or for the related serine β-lactamases. Replacement of the nucleophilic serine of serine β-lactamases with cysteine yields enzymes which fragment β-lactams via a similar mechanism as the l,d-transpeptidases, implying the different reaction outcomes are principally due to the formation of thioester versus ester intermediates. The results highlight fundamental differences in the reactivity of nucleophilic serine and cysteine enzymes, and imply new possibilities for the inhibition of nucleophilic enzymes.

Hydrogen-Bond-Dependent Conformational Switching: A Computational Challenge from Experimental Thermochemistry

We have compiled an experimental data set (SWITCH10) of equilibrium constants for a series of hydrogen-bond-dependent conformational switches. These organic molecules possess common functionalities and are representative in terms of size and composition of systems routinely studied computationally. They exist as two well-defined conformations which serve as a useful tool to benchmark computational estimates of experimental Gibbs energy differences. We examine the performance of HF theory and a variety of density functionals (B3LYP, B3LYP-D3, CAM-B3LYP, ωB97X-D, M06-2X) against these experimental benchmarks. Surprisingly, despite a strong similarity between the two switch conformations, the average errors (0.4-1.7 kcal·mol^-1) obtained across the data set for all methods are larger than obtained with HF calculations. B3LYP was found to outperform implicitly and explicitly dispersion-corrected functionals, with an average error smaller by 1 kcal·mol^-1. Unsystematic errors in the optimized structures were found to contribute to the relatively poor performance obtained, while quasi-rigid rotor harmonic oscillator thermal contributions are important in improving the accuracy of computed Gibbs energy differences. These results emphasize the challenge of quantitative accuracy in computing solution-phase thermochemistry for flexible systems and caution against the often used (but unstated) assumption of favorable error cancellation in comparing conformers or stereoisomers.

Frontier molecular orbital effects control the hole-catalyzed racemization of atropisomeric biaryls

Biaryl atropisomerization is dramatically accelerated by the removal of an electron. The planar transition state is preferentially stabilized from depopulation of the highest occupied molecular orbital.

Atropisomeric biaryl systems are privileged architectures used in asymmetric synthesis and pharmaceutical structures. We report that by simply removing a single-electron, the resistance of biaryls towards racemization is reduced dramatically. Even though the steric properties are unaltered, biaryl oxidation changes atropisomerization into a two step mechanism with considerably smaller activation barriers than closed-shell biaryls. The effect is general for a series of biaryls and helicenes studied and results from the dependence of frontier molecular orbital energies on biaryl conformation.

Catalytic Enantio- and Diastereoselective Mannich Addition of TosMIC to Ketimines

Chiral amines bearing a stereocenter in the α position are ubiquitous compounds with many applications in the pharmaceutical and agrochemical sectors, as well as in catalysis. Catalytic asymmetric Mannich additions represent a valuable method to access such compounds in enantioenriched form. This work reports the first enantio- and diastereoselective addition of commercially available p-toluenesulfonylmethyl isocyanide (TosMIC) to ketimines, affording 2-imidazolines bearing two contiguous stereocenters, one of which is fully-substituted, with high yields and excellent stereocontrol. The reaction, catalyzed by silver oxide and a dihydroquinine-derived N,P-ligand, is broad in scope, operationally simple, and scalable. Derivatization of the products provides enantioenriched vicinal diamines, precursors to NHC ligands and sp³ -rich heterocyclic scaffolds. Computations are used to understand catalysis and rationalize stereoselectivity.

Stereospecific 1,3-H Transfer of Indenols Proceeds via Persistent Ion-Pairs Anchored by NH···π Interactions

The base-catalyzed rearrangement of arylindenols is a rare example of a suprafacial [1,3]-hydrogen atom transfer. The mechanism has been proposed to proceed via sequential [1,5]-sigmatropic shifts, which occur in a selective sense and avoid an achiral intermediate. A computational analysis using quantum chemistry casts serious doubt on these suggestions: These pathways have enormous activation barriers, and in constrast to what is observed experimentally, they overwhelmingly favor a racemic product. Instead we propose that a suprafacial [1,3]-prototopic shift occurs in a two-step deprotonation/reprotonation sequence. This mechanism is favored by 15 kcal mol^-1 over that previously proposed. Most importantly, this is also consistent with stereospecificity since reprotonation occurs rapidly on the same π-face. We have used explicitly solvated molecular dynamics studies to study the persistence and condensed-phase dynamics of the intermediate ion-pair formed in this reaction. Chirality transfer is the result of a particularly resilient contact ion-pair, held together by electrostatic attraction and a critical NH···π interaction which ensures that this species has an appreciable lifetime even in polar solvents such as DMSO and MeOH.

Bifunctional iminophosphorane catalysed enantioselective sulfa-Michael addition of alkyl thiols to alkenyl benzimidazoles

The first enantioselective sulfa-Michael addition of alkyl thiols to alkenyl benzimidazoles, enabled by a bifunctional iminophosphorane (BIMP) organocatalyst, is described. The iminophosphorane moiety of the catalyst provides the required basicity to deprotonate the thiol nucleophile while the chiral scaffold and H-bond donor control facial selectivity. The reaction is broad in scope with respect to the thiol and benzimidazole reaction partners with the reaction proceeding in up to 98% yield and 96 : 4 er.

Selectivity in Transition Metal-catalyzed Cyclizations: Insights from Experiment and Theory

Transition metal-catalyzed cycloisomerization reactions offer a powerful tool for the synthesis of complex cyclic organic molecules from acyclic precursors. In addition to ring formation, these processes can result in the generation of new stereocentres at the site of ring formation; understanding the origins of stereoselectivity enables the use of cycloisomerization chemistry in synthesis, and promotes the design of new reactions. In this article, some recent developments from our groups in regio- and stereoselective cycloisomerization reactions are discussed. Alongside experimental observations, crucial to developing a robust understanding of selectivity has been the use of computation to explore theoretical reaction pathways, which provides an exceptional level of insight into selectivity. In its most valuable form, this correlation between experiment and theory enables the design of improved catalyst systems exhibiting both enhanced reactivity, and selectivity.

Asymmetric nucleophilic fluorination under hydrogen bonding phase-transfer catalysis

Common anionic nucleophiles such as those derived from inorganic salts have not been used for enantioselective catalysis because of their insolubility. Here, we report that merging hydrogen bonding and phase-transfer catalysis provides an effective mode of activation for nucleophiles that are insoluble in organic solvents. This catalytic manifold relies on hydrogen bonding complexation to render nucleophiles soluble and reactive, while simultaneously inducing asymmetry in the ensuing transformation. We demonstrate the concept using a chiral bis-urea catalyst to form a tridentate hydrogen bonding complex with fluoride from its cesium salt, thereby enabling highly efficient enantioselective ring opening of episulfonium ion. This fluorination method is synthetically valuable considering the scarcity of alternative protocols and points the way to wider application of the catalytic approach with diverse anionic nucleophiles.

Formation of quaternary centres by copper catalysed asymmetric conjugate addition to β-substituted cyclopentenones with the aid of a quantitative structure-selectivity relationship

A new asymmetric conjugate addition method was developed for β-substituted cyclopentenones to form quaternary centres using alkylzirconocene nucleophiles giving up to 97% yield and 92% ee.

A new asymmetric conjugate addition method was developed for β-substituted cyclopentenones to form quaternary centres using alkylzirconocene nucleophiles giving up to 97% yield and 92% ee. Key to the reaction's success was the design of suitable phosphoramidite ligands which was aided by a linear quantitative structure–selectivity relationship (QSSR). QSSR models were created from the ligand screening data (a total of 36 ligands) which revealed important electronic and steric requirements and led to the synthesis of more enantioselective ligands. DFT calculations of competing transition structures enable the interpretation of the electronic and steric terms present in the QSSR models.

Cation-π interactions in protein-ligand binding: theory and data-mining reveal different roles for lysine and arginine

The interactions of neutral aromatic ligands with cationic arginine, histidine and lysine amino acid residues have been studied with ab initio calculations, symmetry adapted perturbation theory (SAPT), and a systematic meta-analysis of X-ray structures.

We have studied the cation–π interactions of neutral aromatic ligands with the cationic amino acid residues arginine, histidine and lysine using ab initio calculations, symmetry adapted perturbation theory (SAPT), and a systematic meta-analysis of all available Protein Data Bank (PDB) X-ray structures. Quantum chemical potential energy surfaces (PES) for these interactions were obtained at the DLPNO-CCSD(T) level of theory and compared against the empirical distribution of 2012 unique protein–ligand cation–π interactions found in X-ray crystal structures. We created a workflow to extract these structures from the PDB, filtering by interaction type and residue pK_a. The gas phase cation–π interaction of lysine is the strongest by more than 10 kcal mol^–1, but the empirical distribution of 582 X-ray structures lies away from the minimum on the interaction PES. In contrast, 1381 structures involving arginine match the underlying calculated PES with good agreement. SAPT analysis revealed that underlying differences in the balance of electrostatic and dispersion contributions are responsible for this behavior in the context of the protein environment. The lysine–arene interaction, dominated by electrostatics, is greatly weakened by a surrounding dielectric medium and causes it to become essentially negligible in strength and without a well-defined equilibrium separation. The arginine–arene interaction involves a near equal mix of dispersion and electrostatic attraction, which is weakened to a much smaller degree by the surrounding medium. Our results account for the paucity of cation–π interactions involving lysine, even though this is a more common residue than arginine. Aromatic ligands are most likely to interact with cationic arginine residues as this interaction is stronger than for lysine in higher polarity surroundings.

Computing organic stereoselectivity - from concepts to quantitative calculations and predictions

Advances in theory and processing power have established computation as a valuable interpretative and predictive tool in the discovery of new asymmetric catalysts. This tutorial review outlines the theory and practice of modeling stereoselective reactions. Recent examples illustrate how an understanding of the fundamental principles and the application of state-of-the-art computational methods may be used to gain mechanistic insight into organic and organometallic reactions. We highlight the emerging potential of this computational tool-box in providing meaningful predictions for the rational design of asymmetric catalysts. We present an accessible account of the field to encourage future synergy between computation and experiment.

A New Mechanism for β-Lactamases: Class D Enzymes Degrade 1β-Methyl Carbapenems through Lactone Formation

β‐Lactamases threaten the clinical use of carbapenems, which are considered antibiotics of last resort. The classical mechanism of serine carbapenemase catalysis proceeds through hydrolysis of an acyl‐enzyme intermediate. We show that class D β‐lactamases also degrade clinically used 1β‐methyl‐substituted carbapenems through the unprecedented formation of a carbapenem‐derived β‐lactone. β‐Lactone formation results from nucleophilic attack of the carbapenem hydroxyethyl side chain on the ester carbonyl of the acyl‐enzyme intermediate. The carbapenem‐derived lactone products inhibit both serine β‐lactamases (particularly class D) and metallo‐β‐lactamases. These results define a new mechanism for the class D carbapenemases, in which a hydrolytic water molecule is not required.