Mechanism and Enantioselectivity in QUINOX-Catalyzed Asymmetric Allylations of Aromatic Aldehydes: Solvent and Substituent Effects.

Computational investigations were conducted on the QUINOX-catalyzed asymmetric allylation of aromatic aldehydes with allyltrichlorosilanes. Our calculations provide evidence that the catalytic allylation can follow distinct mechanisms, depending on the solvent employed. In toluene and CH2Cl2, the QUINOX-catalyzed allylation predominantly follows an associative pathway, while in CH3CN, a dissociative pathway becomes more favorable. Noncovalent interactions, such as π-stacking effects for the associative mechanism and CH/π interactions for the dissociative mechanism, play a pivotal role in enantiostereodifferentiation in the asymmetric QUINOX-catalyzed reactions of benzaldehyde. Furthermore, the study unveils how different aldehyde substituents exert differing influences on the catalytic allylation reaction. Specifically, the QUINOX-catalyzed allylation of 4-(trifloromethyl)benzaldehyde displays a strong preference for the associative pathway, yielding excellent results in both yield and enantioselectivity. Conversely, 4-methoxybenzaldehyde tends to favor a dissociative mechanism with reduced yields and enantioselectivity. The mechanistic basis for these remarkable substituent effects on the catalytic allylation reaction was also elucidated. In summary, this research enhances our understanding of the QUINOX-catalyzed asymmetric allylation, shedding light on the role of solvents and substituents in the reaction mechanism and enantioselectivity.

Electrostatic Interactions in Asymmetric Organocatalysis.

ConspectusElectrostatic interactions are ubiquitous in catalytic systems and can be decisive in determining the reactivity and stereoselectivity. However, difficulties quantifying the role of electrostatic interactions in transition state (TS) structures have long stymied our ability to fully harness the power of these interactions. Fortunately, advances in affordable computing power, together with new quantum chemistry methods, have increasingly enabled a detailed atomic-level view. Empowered by this more nuanced perspective, synthetic practitioners are now adopting these techniques with growing enthusiasm.In this Account, we narrate our recent results rooted in state-of-the-art quantum chemical computations, describing pivotal roles for electrostatic interactions in the organization of TS structures to direct the reactivity and selectivity in the realm of asymmetric organocatalysis. To provide readers with a fundamental foundation in electrostatics, we first introduce a few guiding principles, beginning with a brief discussion of how electrostatic interactions can be harnessed to tune the strength of noncovalent interactions. We then describe computational approaches to capture these effects followed by examples in which electrostatic effects impact structure and reactivity. We then cover some of our recent computational investigations in three specific branches of asymmetric organocatalysis, beginning with chiral phosphoric acid (CPA) catalysis. We disclose how CPA-catalyzed asymmetric ring openings of meso-epoxides are driven by stabilization of a transient partial positive charge in the SN2-like TS by the chiral electrostatic environment of the catalyst. We also report on substrate-dependent electrostatic effects from our study of CPA-catalyzed intramolecular oxetane desymmetrizations. For nonchelating oxetane substrates, electrostatic interactions with the catalyst confer stereoselectivity, whereas oxetanes with chelating groups adopt a different binding mode that leads to electrostatic effects that erode selectivity. In another example, computations revealed a pivotal role of CH···O and NH···O hydrogen bonding in the CPA-catalyzed asymmetric synthesis of 2,3-dihydroquinazolinones. These interactions control selectivity during the enantiodetermining intramolecular amine addition step, and their strength is modulated by electrostatic effects, allowing us to rationalize the effect of introducing o-substituents. Next, we describe our efforts to understand selectivity in a series of NHC-catalyzed kinetic resolutions, where we discovered that the electrostatic stabilization of key proton(s) is the common driver of selectivity. Finally, we discuss our breakthrough in understanding asymmetric silylium ion-catalyzed Diels-Alder cycloaddition of cinnamate esters to cyclopentadienes. The endo:exo of these transformations is guided by electrostatic interactions that selectively stabilize the endo-transition state.We conclude with a brief overview of the outstanding challenges and potential roles of computational chemistry in enabling the exploitation of electrostatic interactions in asymmetric organocatalysis.

Systematic Study of Heteroarene Stacking Using a Congeneric Set of Molecular Glues for Procaspase-6.

Heteroaromatic stacking interactions are important in drug binding, supramolecular chemistry, and materials science, making protein-ligand model systems of these interactions of considerable interest. Here we studied 30 congeneric ligands that each present a distinct heteroarene for stacking between tyrosine residues at the dimer interface of procaspase-6. Complex X-ray crystal structures of 10 analogs showed that stacking geometries were well conserved, while high-accuracy computations showed that heteroarene stacking energy was well correlated with predicted overall ligand binding energies. Empirically determined KD values in this system thus provide a useful measure of heteroarene stacking with tyrosine. Stacking energies are discussed in the context of torsional strain, the number and positioning of heteroatoms, tautomeric state, and coaxial orientation of heteroarene in the stack. Overall, this study provides an extensive data set of empirical and high-level computed binding energies in a versatile new protein-ligand system amenable to studies of other intermolecular interactions.

Unusual Enantiodivergence in Chiral Brønsted Acid-Catalyzed Asymmetric Allylation with ß-Alkenyl Allylic Boronates.

We report herein a rare example of enantiodivergent aldehyde addition with ß-alkenyl allylic boronates via chiral Brønsted acid catalysis. 2,6-Di-9-anthracenyl-substituted chiral phosphoric acid-catalyzed asymmetric allylation using ß-vinyl substituted allylic boronate gave alcohols with R absolute configuration. The sense of asymmetric induction of the catalyst in these reactions is opposite to those in prior reports. Moreover, in the presence of the same acid catalyst, the reactions with ß-2-propenyl substituted allylic boronate generated homoallylic alcohol products with S absolute configuration. Unusual substrate-catalyst C-H⋅⋅⋅π interactions in the favoured reaction transition state were identified as the origins of observed enantiodivergence through DFT computational studies.

Synthesis, Biological Evaluation, and Computational Analysis of Biaryl Side-Chain Analogs of Solithromycin.

There is an urgent need for new antibiotics to mitigate the existential threat posed by antibiotic resistance. Within the ketolide class, solithromycin has emerged as one of the most promising candidates for further development. Crystallographic studies of bacterial ribosomes and ribosomal subunits complexed with solithromycin have shed light on the nature of molecular interactions (π-stacking and H-bonding) between from the biaryl side-chain of the drug and key residues in the 50S ribosomal subunit. We have designed and synthesized a library of solithromycin analogs to study their structure-activity relationships (SAR) in tandem with new computational studies. The biological activity of each analog was evaluated in terms of ribosomal affinity (Kd determined by fluorescence polarization), as well as minimum inhibitory concentration assays (MICs). Density functional theory (DFT) studies of a simple binding site model identify key H-bonding interactions that modulate the potency of solithromycin analogs.

SEQCROW: A ChimeraX bundle to facilitate quantum chemical applications to complex molecular systems.

We describe a bundle for UCSF ChimeraX called SEQCROW that provides advanced structure editing capabilities and quantum chemistry utilities designed for complex organic and organometallic compounds. SEQCROW includes graphical presets and bond editing tools that facilitate the generation of publication-quality molecular structure figures while also allowing users to build molecular structures quickly and efficiently by mapping new ligands onto existing organometallic complexes as well as adding rings and substituents. Other capabilities include the ability to visualize vibrational modes and simulated IR spectra, to compute and visualize molecular descriptors including percent buried volume, ligand cone angles, and Sterimol parameters, to process thermochemical corrections from quantum mechanical computations, to generate input files for ORCA, Psi4, and Gaussian, and to run and manage computational jobs.

Importance of model size in quantum mechanical studies of DNA intercalation.

The convergence of DFT-computed interaction energies with increasing binding site model size was assessed. The data show that while accurate intercalator interaction energies can be derived from binding site models featuring only the flanking nucleotides for uncharged intercalators that bind parallel to the DNA base pairs, errors remain significant even when including distant nucleotides for intercalators that are charged, exhibit groove-binding tails that engage in noncovalent interactions with distant nucleotides, or that bind perpendicular to the DNA base pairs. Consequently, binding site models that include at least three adjacent nucleotides are required to consistently predict converged binding energies. The computationally inexpensive HF-3c method is shown to provide reliable interaction energies and can be routinely applied to such large models.

Predicting the Strength of Stacking Interactions between Heterocycles and Aromatic Amino Acid Side Chains.

Despite the ubiquity of stacking interactions between heterocycles and aromatic amino acids in biological systems, our ability to predict their strength, even qualitatively, is limited. On the basis of rigorous ab initio data, we developed simple predictive models of the strength of stacking interactions between heterocycles commonly found in biologically active molecules and the amino acid side chains Phe, Tyr, and Trp. These models provide reliable predictions of the stacking ability of a given heterocycle based on readily computed heterocycle descriptors, eliminating the need for quantum chemical computations of stacked dimers. We show that the values of these descriptors, and therefore the strength of stacking interactions with aromatic amino acid side chains, follow predictable trends and can be modulated by changing the number and distribution of heteroatoms within the heterocycle. This provides a simple conceptual means for understanding stacking interactions in protein binding sites and tuning their strength in the context of drug design.

Converting SMILES to Stacking Interaction Energies.

Predicting the strength of stacking interactions involving heterocycles is vital for several fields, including structure-based drug design. While quantum chemical computations can provide accurate stacking interaction energies, these come at a steep computational cost. To address this challenge, we recently developed quantitative predictive models of stacking interactions between druglike heterocycles and the aromatic amino acids Phe, Tyr, and Trp (DOI: 10.1021/jacs.9b00936 ). These models depend on heterocycle descriptors derived from electrostatic potentials (ESPs) computed using density functional theory and provide accurate stacking interactions without the need for expensive computations on stacked dimers. Herein, we show that these ESP-based descriptors can be reliably evaluated directly from the atom connectivity of the heterocycle, providing a means of predicting both the descriptors and the potential for a given heterocycle to engage in stacking interactions without resorting to any quantum chemical computations. This enables the rapid conversion of simple molecular representations (e.g., SMILES) directly into accurate stacking interaction energies using a freely available online tool, thereby providing a way to rank the stacking abilities of large sets of heterocycles.

Understanding the Reactivity and Selectivity of Fluxional Chiral DMAP-Catalyzed Kinetic Resolutions of Axially Chiral Biaryls.

Fluxional chiral DMAP-catalyzed kinetic resolutions of axially chiral biaryls were examined using density functional theory. Computational analyses lead to a revised understanding of this reaction in which the interplay of numerous non-covalent interactions control the conformation and flexibility of the active catalyst, the preferred mechanism, and the stereoselectivity. Notably, while the DMAP catalyst itself is confirmed to be highly fluxional, electrostatically driven π⋅⋅⋅π+ interactions render the active, acylated form of the catalyst highly rigid, explaining its pronounced stereoselectivity.

Tuning Stacking Interactions between Asp-Arg Salt Bridges and Heterocyclic Drug Fragments.

Stacking interactions can play an integral role in the strength and selectivity of protein-drug binding and are of particular interest given the ubiquity and variety of heterocyclic fragments in drugs. In addition to traditional stacking interactions between aromatic rings, stacking interactions involving heterocyclic drug fragments and protein salt bridges have also been observed. These "salt-bridge stacking interactions" can be quite strong but are not well understood. We studied stacked dimers of the acetate···guanidinium ion pair with a diverse set of 63 heterocycles using robust ab initio methods. The computed interaction energies span more than 10 kcal mol-1, indicating the sensitivity of these salt-bridge stacking interactions to heterocycle features. Trends in both the strength and preferred geometry of these interactions can be understood through analyses of the electrostatic potentials and electric fields above the heterocycles. We have developed new heterocycle descriptors that quantify these effects and used them to create robust predictors of the strength of salt-bridge stacking interactions both in the gas phase and a protein-like dielectric environment. These predictive tools, combined with a set of qualitative guidelines, should facilitate the choice of heterocycles that maximize salt-bridge stacking interactions in drug binding sites.

Better Sensing through Stacking: The Role of Non-Covalent Interactions in Guanine-Binding Sensors.

A series of aryl-substituted naphthyridine-based sensors for 9-alkylguanine was analyzed using density functional theory and correlated ab initio methods. First, the 2-acetamido-1,8-naphthyridine backbone of these sensors was examined with rigorous ab initio methods and was shown to exhibit a guanine-binding energy commensurate with that of cytosine. Second, computational analyses of a guanine-specific fluorescent sensor from Fang and co-workers ( Org. Lett. 2016, 18, 1724) resulted in a revised binding model and showed that π-stacking interactions with a pendant pyrenyl group are vital for strong guanine binding. Finally, 24 related guanine sensors with varying aryl groups were studied. Overall, it was found that both the geometry and the point of attachment of the pendant aryl groups significantly impact the guanine-binding affinity. This occurs through both the direct modulation of the π-stacking interactions with guanine and the secondary geometric effects that influence the strength and number of hydrogen bonds between guanine and the ethylenediamine linker connecting the arene to the naphthyridine backbone.

AARON: An Automated Reaction Optimizer for New Catalysts.

We describe an open-source computational toolkit (AARON: An Automated Reaction Optimizer for New catalysts) that automates the quantum mechanical geometry optimization and characterization of the transition state and intermediate structures required to predict the activities and selectivities of asymmetric catalytic reactions. Modern computational quantum chemistry has emerged as a powerful tool for explaining the selectivity and activity of asymmetric catalysts. However, reliably predicting the stereochemical outcome of realistic reactions often requires the geometry optimization of hundreds of transition state and intermediate structures, which is a tedious process. AARON automates these optimizations through an interface with a popular electronic structure package, accelerating quantum chemical workflows to enable the computational screening of potential catalysts. AARON is built using a collection of object-oriented Perl modules (AaronTools) that provide functionality to build and modify molecular and supramolecular structures. The main functionalities of AaronTools are also available as stand-alone command-line scripts. The core features of AaronTools and AARON are explained, and representative applications of AARON to both organocatalyzed and transition-metal-catalyzed reactions are presented.

Anion-π Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids.

Human infection by Mycobacterium tuberculosis (Mtb) continues to be a global epidemic. Computer-aided drug design (CADD) methods are used to accelerate traditional drug discovery efforts. One noncovalent interaction that is being increasingly identified in biological systems but is neglected in CADD is the anion-π interaction. The study reported herein supports the conclusion that anion-π interactions play a central role in directing the binding of phenyl-diketo acid (PDKA) inhibitors to malate synthase (GlcB), an enzyme required for Mycobacterium tuberculosis virulence. Using density functional theory methods (M06-2X/6-31+G(d)), a GlcB active site template was developed for a predictive model through a comparative analysis of PDKA-bound GlcB crystal structures. The active site model includes the PDKA molecule and the protein determinants of the electrostatic, hydrogen-bonding, and anion-π interactions involved in binding. The predictive model accurately determines the Asp 633-PDKA structural position upon binding and precisely predicts the relative binding enthalpies of a series of 2-ortho halide-PDKAs to GlcB. A screening model was also developed to efficiently assess the propensity of each PDKA analog to participate in an anion-π interaction; this method is in good agreement with both the predictive model and the experimental binding enthalpies for the 2-ortho halide-PDKAs. With the screening and predictive models in hand, we have developed an efficient method for computationally screening and evaluating the binding enthalpy of variously substituted PDKA molecules. This study serves to illustrate the contribution of this overlooked interaction to binding affinity and demonstrates the importance of integrating anion-π interactions into structure-based CADD.

Lone-Pair-Induced Topicity Observed in Macrobicyclic Tetra-thia Lactams and Cryptands: Synthesis, Spectral Identification, and Computational Assessment.

The synthesis of a rigid macrobicyclic N,S lactam L1 and a topologically favored in/in N,S cryptand L2 are reported with X-ray structure analysis, dynamic correlation NMR spectroscopy, and computational analysis. Lactam L1 exhibits two distinct rotameric conformations (plus their enantiomeric counterparts) at 25 °C, as confirmed via NMR spectroscopy and computational analysis. Coalescence of the resonances of L1 was observed at 115 °C, allowing for complete nuclei to frequency correlation. Combining computational investigations with experimental data, topological equilibria and relative energies/strain relating to the perturbation of the pore were determined. Due to the increased conformational strain of the N2S2 template, the nitrogen lone pairs in L2 elicit a unique transannular interaction, resulting in a thermodynamically favored in/in nephroidal racemate. The combination of preferred topology, steric relief, and electronic localization of L2 induces a chiral environment imparted through the amine with a computed inversion barrier of 10.3 kcal mol-1.

Stacking Interactions of Heterocyclic Drug Fragments with Protein Amide Backbones.

Stacking interactions can be important enthalpic contributors to drug binding. Among the less well-studied stacking interactions are those occurring between an arene and the π-face of an amide group. Given the ubiquity of heterocycles in drugs, combined with the abundance of amides in the protein backbone, optimizing these noncovalent interactions can provide a potential route to enhanced drug binding. Previously, Diederich et al. (ChemMedChem 2013, 8, 397-404) studied stacked dimers of a model amide with a set of 18 heterocycles, showing that computed interaction energies correlate with the dipole moments of the heterocycles and providing guidelines for the optimization of these interactions. We considered stacked dimers of the same model amide with a larger set of 28 heterocycles common in pharmaceuticals, by using more robust ab initio methods. While the overall trends in these new data corroborate many of the results of Diederich et al., these data provide a more refined view of the nature of amide stacking interactions. We present a robust scoring function for amide stacking interaction energies based on the molecular dipole moment and strength of the electric field above the arene.

Chiral phosphoric acid catalysis: from numbers to insights.

Chiral phosphoric acids (CPAs) have emerged as powerful organocatalysts for asymmetric reactions, and applications of computational quantum chemistry have revealed important insights into the activity and selectivity of these catalysts. In this tutorial review, we provide an overview of computational tools at the disposal of computational organic chemists and demonstrate their application to a wide array of CPA catalysed reactions. Predictive models of the stereochemical outcome of these reactions are discussed along with specific examples of representative reactions and an outlook on remaining challenges in this area.

Torsional Barriers to Rotation and Planarization in Heterocyclic Oligomers of Value in Organic Electronics.

In order to understand the conformational behavior of organic components in organic electronic devices, we have computed the torsional potentials for a library of thiophene-based heterodimers. The accuracy and efficiencies of computational methods for these organic materials were benchmarked for 11 common density functionals with three Pople basis sets against a Focal Point Analysis (FPA) on a model oligothiophene 2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]-thiophene (BTTT) system. This study establishes a set of general trends in regards to conformational preferences, as well as planarization and rotational barriers for a library comprised of common fragments found in organic materials. These gas phase structures are compared to experimental crystal structures to determine the effect of crystal packing on geometry. Finally, we analyze the structure of hole-transporting material DERDTS-TBDT and design a new oligomer likely to be planar in the solid state.

Importance of Electrostatic Effects in the Stereoselectivity of NHC-Catalyzed Kinetic Resolutions.

Three N-heterocyclic carbene (NHC) catalyzed kinetic resolutions (KR) and one dynamic kinetic resolution (DKR) were examined using modern density functional theory methods to identify the origin of catalytic activity and selectivity and the role of cocatalysts in these reactions. The results reveal electrostatic interactions as the common driver of selectivity. Furthermore, in the case of a recently described KR of BINOL-derivatives, a computational examination of the full catalytic cycle reveals that a benzoic acid byproduct changes the turnover limiting transition step, obviating the need for an added cocatalyst. Together, these data provide key insights into the activity and selectivity of NHC-catalyzed kinetic resolutions, and underscore the importance of electrostatic interactions as a driver of selectivity.

Stacked homodimers of substituted contorted hexabenzocoronenes and their complexes with C60 fullerene.

Stacking interactions involving substituted contorted hexabenzocoronene (c-HBC) with C60 were studied at the B97-D3M(BJ)/TZVPP//B97-D/TZV(2d,2p) level of theory. First, we showed that substituent effects in benzeneC60 complexes are uncorrelated with those in the benzene sandwich dimer, underscoring the importance of local, direct interactions in substituent effects in stacking interactions. Second, we showed that c-HBC preferentially forms stacked homodimers over complexes with C60; however, if the bowl depth of c-HBC is increased beyond 1.25 Å, the c-HBCC60 complex becomes preferred over the c-HBC homodimer. Ultimately, we showed that the perfluorination of c-HBC leads to sufficient curvature to allow the c-HBCC60 heterodimers to form preferentially over c-HBC homodimers, suggesting the possibility of the development of c-HBC derivatives that assemble into alternating stacks with C60.