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 CHCl, the QUINOX-catalyzed allylation predominantly follows an associative pathway, while in CHCN, a dissociative pathway becomes more favorable.

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.

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.

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

We report herein a rare example of enantiodivergent aldehyde addition with β-alkenyl allylic boronates via chiral Brønsted acid catalysis. 2,6-Di-9-anthracenyl-substituted chiral phosphoric acid-catalyzed asymmetric allylation using β-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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

Stacking interactions involving substituted contorted hexabenzocoronene (c-HBC) with C were studied at the B97-D3M(BJ)/TZVPP//B97-D/TZV(2d,2p) level of theory. First, we showed that substituent effects in benzeneC 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 C; however, if the bowl depth of c-HBC is increased beyond 1.

Automated Quantum Mechanical Predictions of Enantioselectivity in a Rhodium-Catalyzed Asymmetric Hydrogenation.

A computational toolkit (AARON: An automated reaction optimizer for new catalysts) is described that automates the density functional theory (DFT) based screening of chiral ligands for transition-metal-catalyzed reactions with well-defined reaction mechanisms but multiple stereocontrolling transition states. This is demonstrated for the Rh-catalyzed asymmetric hydrogenation of (E)-β-aryl-N-acetyl enamides, for which a new C -symmetric phosphorus ligand is designed.

Conformational behavior and stacking interactions of contorted polycyclic aromatics.

We present a systematic computational analysis of the conformations and stacking interactions of a set of 18 saddle-shaped, contorted polycyclic aromatic compounds at the B97-D3M(BJ)/TZV(2d,2p)//B97-D/TZV(2d,2p) level of theory. These doubly-concave systems offer a means of tuning the strength of stacking interactions through variations in molecular curvature, and understanding the intermolecular non-covalent interactions exhibited by these systems will aid the design of contorted polycyclic systems with precisely defined packing in the solid state. Computations reveal wide variations in both the nature of the low-lying conformations and the stacking affinities of these systems.

Ring-Walking of Zerovalent Nickel on Aryl Halides.

While ring-walking is a critical step in transition metal catalyzed cross-coupling reactions, the associated metastable intermediates are often difficult to isolate and characterize. In this work, theoretical structures and energetics for ring-walking and oxidative addition of zerovalent nickel with 1-bromo-2-methylbenzene, 2-bromopyridine, 2-bromo-3-methyl-thiophene, and 2-bromopyrrole were computed at the B3LYP-D3/TZ2P-LANL2TZ(f)-LANL08d level. The mechanisms vary qualitatively with substrate ring size and type-the catalyst weaves along the edges of the benzene and pyridine rings, cuts through the interior of the thiophene ring, and arcs along the bond opposite the nitrogen atom in the pyrrole ring.

Enantioselective Synthesis of Chiral Oxime Ethers: Desymmetrization and Dynamic Kinetic Resolution of Substituted Cyclohexanones.

Axially chiral cyclohexylidene oxime ethers exhibit unique chirality because of the restricted rotation of C=N. The first catalytic enantioselective synthesis of novel axially chiral cyclohexylidene oximes has been developed by catalytic desymmetrization of 4-substituted cyclohexanones with O-arylhydroxylamines and is catalyzed by a chiral BINOL-derived strontium phosphate with excellent yields and good enantioselectivities. In addition, chiral BINOL-derived phosphoric acid catalyzed dynamic kinetic resolution of α-substituted cyclohexanones has been performed and yields versatile intermediates in high yields and enantioselectivities.

Molecular Coplanarity and Self-Assembly Promoted by Intramolecular Hydrogen Bonds.

Active conformational control is realized in a conjugated system using intramolecular hydrogen bonds to achieve tailored molecular, supramolecular, and solid-state properties. The hydrogen bonding functionalities are fused to the backbone and precisely preorganized to enforce a fully coplanar conformation of the π-system, leading to short π-π stacking distances, controllable molecular self-assembly, and solid-state growth of one-dimensional nano-/microfibers. This investigation demonstrates the efficiency and significance of an intramolecular noncovalent approach in promoting conformational control and self-assembly of organic molecules.