Robert S. Paton

Indolyne and Aryne Distortions and Nucleophilic Regioselectivites

Density functional theory computations reproduce the surprisingly high regioselectivities in nucleophilic additions and cycloadditions to 4,5-indolynes and the low regioselectivities in the reactions of 5,6-indolynes. Transition-state distortion energies control the regioselectivities, activating the 5 and 6 positions over the 4 and 7 positions, leading to high preferences for 5- and 6-substituted products from 4,5- and 6,7-indolynes, respectively. Orbital and electrostatic interactions have only minor effects, producing low regioselectivities in the reactions of 5,6-indolynes. The distortion model predicts high regioselectivities with 6,7-indolynes; these have been verified experimentally. The regioselectivities found with other arynes are explained on the basis of distortion energies that are reflected in reactant geometries.

Indolyne Experimental and Computational Studies: Synthetic Applications and Origins of Selectivities of Nucleophilic Additions

Efficient syntheses of 4,5-, 5,6-, and 6,7-indolyne precursors beginning from commercially available hydroxyindole derivatives are reported. The synthetic routes are versatile and allow access to indolyne precursors that remain unsubstituted on the pyrrole ring. Indolynes can be generated under mild fluoride-mediated conditions, trapped by a variety of nucleophilic reagents, and used to access a number of novel substituted indoles. Nucleophilic addition reactions to indolynes proceed with varying degrees of regioselectivity; distortion energies control regioselectivity and provide a simple model to predict the regioselectivity in the nucleophilic additions to indolynes and other unsymmetrical arynes. This model has led to the design of a substituted 4,5-indolyne that exhibits enhanced nucleophilic regioselectivity.

Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions

We have evaluated the performance of a set of widely used force fields by calculating the geometries and stabilization energies for a large collection of intermolecular complexes. These complexes are representative of a range of chemical and biological systems for which hydrogen bonding, electrostatic, and van der Waals interactions play important roles. Benchmark energies are taken from the high-level ab initio values in the JSCH-2005 and S22 data sets. All of the force fields underestimate stabilization resulting from hydrogen bonding, but the energetics of electrostatic and van der Waals interactions are described more accurately. OPLSAA gave a mean unsigned error of 2 kcal mol(-1) for all 165 complexes studied, and outperforms DFT calculations employing very large basis sets for the S22 complexes. The magnitude of hydrogen bonding interactions are severely underestimated by all of the force fields tested, which contributes significantly to the overall mean error; if complexes which are predominantly bound by hydrogen bonding interactions are discounted, the mean unsigned error of OPLSAA is reduced to 1 kcal mol(-1). For added clarity, web-based interactive displays of the results have been developed which allow comparisons of force field and ab initio geometries to be performed and the structures viewed and rotated in three dimensions.

Diels–Alder Reactivities of Strained and Unstrained Cycloalkenes with Normal and Inverse-Electron-Demand Dienes: Activation Barriers and Distortion/Interaction Analysis

The Diels-Alder reactions of the cycloalkenes, cyclohexene through cyclopropene, with a series of dienes--1,3-dimethoxybutadiene, cyclopentadiene, 3,6-dimethyltetrazine, and 3,6-bis(trifluoromethyl)tetrazine--were studied with quantum mechanical calculations and compared with experimental values when available. The reactivities of cycloalkenes as dienophiles were found by a distortion/interaction analysis to be distortion controlled. The energies required for cycloalkenes to be distorted into the Diels-Alder transition states increase as the ring size of cycloalkenes increases from cyclopropene to cyclohexene, resulting in an increase in activation barriers. The reactivities of the dienes are controlled by both distortion and interaction energies. In normal Diels-Alder reactions with cycloalkenes, the electron-rich 1,3-dimethoxybutadiene exhibits stronger interaction energies than cyclopentadiene, but the high distortion energies required for 1,3-dimethoxybutadiene to achieve transition-state geometries overtake the favorable interaction, resulting in higher activation barriers. In inverse-electron-demand Diels-Alder reactions of 3,6-dimethyltetrazine and 3,6-bis(trifluoromethyl)tetrazine, the reactivities are mainly controlled by interaction energies.

Quantum mechanical calculations suggest that lytic polysaccharide monooxygenases use a copper-oxyl, oxygen-rebound mechanism

Significance Plant cell walls contain significant amounts of the polysaccharides cellulose and hemicellulose, which can be depolymerized by enzymes to sugars and upgraded to renewable fuels and chemicals. Traditionally, enzymes for biomass depolymerization were based on naturally occurring hydrolytic enzymes, until the recent discovery of another natural enzymatic paradigm for carbohydrate deconstruction. Namely, lytic polysaccharide monooxygenases (LPMOs), long thought to be hydrolases or carbohydrate-binding modules, were revealed to be oxidative, copper-containing enzymes. These enzymes are receiving significant attention as they could revolutionize biomass deconstruction to upgradeable intermediates for renewable energy applications. Here, we apply quantum mechanical calculations to elucidate the oxidative reaction mechanism to offer predictions into how LPMOs function. Lytic polysaccharide monooxygenases (LPMOs) exhibit a mononuclear copper-containing active site and use dioxygen and a reducing agent to oxidatively cleave glycosidic linkages in polysaccharides. LPMOs represent a unique paradigm in carbohydrate turnover and exhibit synergy with hydrolytic enzymes in biomass depolymerization. To date, several features of copper binding to LPMOs have been elucidated, but the identity of the reactive oxygen species and the key steps in the oxidative mechanism have not been elucidated. Here, density functional theory calculations are used with an enzyme active site model to identify the reactive oxygen species and compare two hypothesized reaction pathways in LPMOs for hydrogen abstraction and polysaccharide hydroxylation; namely, a mechanism that employs a η1-superoxo intermediate, which abstracts a substrate hydrogen and a hydroperoxo species is responsible for substrate hydroxylation, and a mechanism wherein a copper-oxyl radical abstracts a hydrogen and subsequently hydroxylates the substrate via an oxygen-rebound mechanism. The results predict that oxygen binds end-on (η1) to copper, and that a copper-oxyl–mediated, oxygen-rebound mechanism is energetically preferred. The N-terminal histidine methylation is also examined, which is thought to modify the structure and reactivity of the enzyme. Density functional theory calculations suggest that this posttranslational modification has only a minor effect on the LPMO active site structure or reactivity for the examined steps. Overall, this study suggests the steps in the LPMO mechanism for oxidative cleavage of glycosidic bonds.

Experimental Diels–Alder Reactivities of Cycloalkenones and Cyclic Dienes Explained through Transition‐State Distortion Energies

Quantum chemical calculations are used to investigate the experimentally measured reactivities of cyclic dienes and cycloalkenones in the Diels-Alder reaction. The interaction energies (red) are nearly constant; differences arise in changes in distortion energies of both dienophile (blue) and diene (green; see picture, Ea=activation energy; values in kcal mol-1). Copyright

Gold(I)-catalyzed intermolecular hydroalkoxylation of allenes: a DFT study.

The mechanistic and regiochemical aspects in the Au(I)-catalyzed intermolecular hydroalkoxylation of allenes have been studied computationally. The most favorable pathway is nucleophilic attack of an Au(I)-coordinated allene, which occurs irreversibly. An Au(I)-catalyzed mechanism is proposed that allows the facile interconversion of regioisomeric allylic ether products. The regioisomers are connected via a stabilized diether intermediate with a C-Au sigma-bond, which successfully explains the observed regioselectivity for the thermodynamic product.

A Series of Potent CREBBP Bromodomain Ligands Reveals an Induced-Fit Pocket Stabilized by a Cation–π Interaction

The benzoxazinone and dihydroquinoxalinone fragments were employed as novel acetyl lysine mimics in the development of CREBBP bromodomain ligands. While the benzoxazinone series showed low affinity for the CREBBP bromodomain, expansion of the dihydroquinoxalinone series resulted in the first potent inhibitors of a bromodomain outside the BET family. Structural and computational studies reveal that an internal hydrogen bond stabilizes the protein-bound conformation of the dihydroquinoxalinone series. The side chain of this series binds in an induced-fit pocket forming a cation–π interaction with R1173 of CREBBP. The most potent compound inhibits binding of CREBBP to chromatin in U2OS cells.

Enzymatic catalysis of anti-Baldwin ring closure in polyether biosynthesis

Polycyclic polyether natural products have fascinated chemists and biologists alike owing to their useful biological activity, highly complex structure and intriguing biosynthetic mechanisms. Following the original proposal for the polyepoxide origin of lasalocid and isolasalocid and the experimental determination of the origins of the oxygen and carbon atoms of both lasalocid and monensin, a unified stereochemical model for the biosynthesis of polyether ionophore antibiotics was proposed. The model was based on a cascade of nucleophilic ring closures of postulated polyepoxide substrates generated by stereospecific oxidation of all-trans polyene polyketide intermediates. Shortly thereafter, a related model was proposed for the biogenesis of marine ladder toxins, involving a series of nominally disfavoured anti-Baldwin, endo-tet epoxide-ring-opening reactions. Recently, we identified Lsd19 from the Streptomyces lasaliensis gene cluster as the epoxide hydrolase responsible for the epoxide-opening cyclization of bisepoxyprelasalocid A to form lasalocid A. Here we report the X-ray crystal structure of Lsd19 in complex with its substrate and product analogue to provide the first atomic structure—to our knowledge—of a natural enzyme capable of catalysing the disfavoured epoxide-opening cyclic ether formation. On the basis of our structural and computational studies, we propose a general mechanism for the enzymatic catalysis of polyether natural product biosynthesis.

An Efficient Computational Model to Predict the Synthetic Utility of Heterocyclic Arynes

Think before you act: a computational approach is reported for evaluating the synthetic potential of heterocyclic arynes. Routine and rapid calculations of arene dehydrogenation energies and aryne angle distortion predict the likelihood that a given hetaryne can be generated, as well as the degree of regioselectivity expected in a reaction between a given hetaryne and a nucleophilic trapping agent.