Role of Steric Effects on Rates of Hydrogen Atom Transfer Reactions.

The influence of steric effects on the rates of hydrogen atom transfer (HAT) reactions between oxyradicals and alkanes is explored computationally. Quantum chemical density functional theory computations of transition states show that activation barriers and reaction enthalpies are both influenced by bulky substituents on the radical but very little by substituents on the alkane. The activation barriers remain roughly correlated with reaction enthalpies via the Evans-Polanyi relationship even when steric repulsion effects become important, although dispersion effects sometimes stabilize transition states.

Enzymatic Benzofuranoindoline Formation in the Biosynthesis of the Strained Bridgehead Bicyclic Dipeptide (+)-Azonazine A.

We uncovered and reconstituted a concise biosynthetic pathway of the strained dipeptide (+)-azonazine A from marine-derived Aspergillus insulicola. Formation of the hexacyclic benzofuranoindoline ring system from cyclo-(l-Trp-N-methyl-l-Tyr) is catalyzed by a P450 enzyme through an oxidative cyclization. Supplementing the producing strain with various indole-substituted tryptophan derivatives resulted in the generation of a series of azonazine A analogs.

Initiation of fatty acid biosynthesis in Pseudomonas putida KT2440.

Deciphering the mechanisms of bacterial fatty acid biosynthesis is crucial for both the engineering of bacterial hosts to produce fatty acid-derived molecules and the development of new antibiotics. However, gaps in our understanding of the initiation of fatty acid biosynthesis remain. Here, we demonstrate that the industrially relevant microbe Pseudomonas putida KT2440 contains three distinct pathways to initiate fatty acid biosynthesis.

An NmrA-like enzyme-catalysed redox-mediated Diels-Alder cycloaddition with anti-selectivity.

The Diels-Alder cycloaddition is one of the most powerful approaches in organic synthesis and is often used in the synthesis of important pharmaceuticals. Yet, strictly controlling the stereoselectivity of the Diels-Alder reactions is challenging, and great efforts are needed to construct complex molecules with desired chirality via organocatalysis or transition-metal strategies. Nature has evolved different types of enzymes to exquisitely control cyclization stereochemistry; however, most of the reported Diels-Alderases have been shown to only facilitate the energetically favourable diastereoselective cycloadditions.

Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases.

In the biosynthesis of the tryptophan-linked dimeric diketopiperazines (DKPs), cytochromes P450 selectively couple DKP monomers to generate a variety of intricate and isomeric frameworks. To determine the molecular basis for selectivity of these biocatalysts we obtained a high-resolution crystal structure of selective Csp -N bond forming dimerase, AspB. Overlay of the AspB structure onto C-C and C-N bond forming homolog NzeB revealed no significant structural variance to explain their divergent chemoselectivities.

Structural diversification of hapalindole and fischerindole natural products via cascade biocatalysis.

Hapalindoles and related compounds (ambiguines, fischerindoles, welwitindolinones) are a diverse class of indole alkaloid natural products. They are typically isolated from the Stigonemataceae order of cyanobacteria and possess a broad scope of biological activities. Recently the biosynthetic pathway for assembly of these metabolites has been elucidated.

Overcoming Kinetic and Thermodynamic Challenges of Classic Cope Rearrangements.

Systematic evaluation of 1,5-dienes bearing 3,3-electron-withdrawing groups and 4-methylation results in the discovery of a Cope rearrangement for Meldrum's acid-containing substrates that have unexpectedly favorable kinetic and thermodynamic profiles. The protocol is quite general due to a concise and convergent synthesis from abundant starting materials. Furthermore, products with an embedded Meldrum's acid moiety are prepared, which, in turn, can yield complex amides under neutral conditions.

A thermodynamic atlas of carbon redox chemical space.

Redox biochemistry plays a key role in the transduction of chemical energy in living systems. However, the compounds observed in metabolic redox reactions are a minuscule fraction of chemical space. It is not clear whether compounds that ended up being selected as metabolites display specific properties that distinguish them from nonbiological compounds.

Computational Investigation of the Mechanism of Diels-Alderase PyrI4.

We studied the mechanisms of activation and stereoselectivity of a monofunctional Diels-Alderase (PyrI4)-catalyzed intramolecular Diels-Alder reaction that leads to formation of the key spiro-tetramate moiety in the biosynthesis of the pyrroindomycin family of natural products. Key activation effects of PyrI4 include acid catalysis and an induced-fit mechanism that cooperate with the unique "lid" feature of PyrI4 to stabilize the Diels-Alder transition state. PyrI4 enhances the intrinsic Diels-Alder stereoselectivity of the substrate and leads to stereospecific formation of the product.

Mechanism of an Organocatalytic Cope Rearrangement Involving Iminium Intermediates: Elucidating the Role of Catalyst Ring Size.

The mechanism of the organocatalytic Cope rearrangement is elucidated through a combined computational and experimental approach. As reported previously, hydrazides catalyze the Cope rearrangement of 1,5-hexadiene-2-carboxaldehydes via iminium ion formation, and seven- and eight-membered ring catalysts are more active than smaller ring sizes. In the present work, quantum mechanical computations and kinetic isotope effect experiments demonstrate that the Cope rearrangement step, rather than iminium formation, is rate-limiting.

Structure and Function of NzeB, a Versatile C-C and C-N Bond-Forming Diketopiperazine Dimerase.

The dimeric diketopiperazine (DKPs) alkaloids are a diverse family of natural products (NPs) whose unique structural architectures and biological activities have inspired the development of new synthetic methodologies to access these molecules. However, catalyst-controlled methods that enable the selective formation of constitutional and stereoisomeric dimers from a single monomer are lacking. To resolve this long-standing synthetic challenge, we sought to characterize the biosynthetic enzymes that assemble these NPs for application in biocatalytic syntheses.

Computational Investigation into Ligand Effects on Correlated Geared Dynamics in Dirhodium Supramolecular Gears-Insights Beyond the NMR Experimental Window.

The rotational dynamics of dirhodium supramolecular gears, formed with four 9-triptycene carboxylates cyclically arranged around a dirhodium core with variable axial ligands as originally designed by Shionoya , provide an excellent opportunity to evaluate the potential of computational methods and expand our understanding of the factors determining geared dynamics. Rotational dynamic rates in these structures depend on the nature of the axial ligand as shown by simulations over timescales that are not accessible experimentally. Molecular dynamics simulations gave information on the gearing mechanism, and the activation barriers to gearing were calculated using density functional theory.

Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases.

One of the hallmark reactions catalyzed by flavin-dependent enzymes is the incorporation of an oxygen atom derived from dioxygen into organic substrates. For many decades, these flavin monooxygenases were assumed to use exclusively the flavin-C4a-(hydro)peroxide as their oxygen-transferring intermediate. We demonstrate that flavoenzymes may instead employ a flavin-N5-peroxide as a soft α-nucleophile for catalysis, which enables chemistry not accessible to canonical monooxygenases.

Isotopically Directed Symmetry Breaking and Enantioenrichment in Attrition-Enhanced Deracemization.

The evolution of homochirality via attrition-enhanced deracemization (AED) of enantiomorphic solids is carried out using molecules that differ only in the isotopic composition of a phenyl group positioned remote from the chiral center. Enantioenrichment consistently favors the enantiomorph containing a deuterated phenyl group over the protio or C version, and the protio version is consistently favored over the C version. While these isotopic compounds exhibit identical crystal structures and solubilities, the trend in deracemization correlates with melting points.

Fungal indole alkaloid biogenesis through evolution of a bifunctional reductase/Diels-Alderase.

Prenylated indole alkaloids such as the calmodulin-inhibitory malbrancheamides and anthelmintic paraherquamides possess great structural diversity and pharmaceutical utility. Here, we report complete elucidation of the malbrancheamide biosynthetic pathway accomplished through complementary approaches. These include a biomimetic total synthesis to access the natural alkaloid and biosynthetic intermediates in racemic form and in vitro enzymatic reconstitution to provide access to the natural antipode (+)-malbrancheamide.

Exploring the molecular basis for substrate specificity in homologous macrolide biosynthetic cytochromes P450.

Cytochromes P450 (P450s) are nature's catalysts of choice for performing demanding and physiologically vital oxidation reactions. Biochemical characterization of these enzymes over the past decades has provided detailed mechanistic insight and highlighted the diversity of substrates P450s accommodate and the spectrum of oxidative transformations they catalyze. Previously, we discovered that the bacterial P450 MycCI from the mycinamicin biosynthetic pathway in possesses an unusually broad substrate scope, whereas the homologous P450 from tylosin-producing (TylHI) exhibits a high degree of specificity for its native substrate.

Synthesis and Target Identification of a Novel Electrophilic Warhead, 2-Chloromethylquinoline.

Despite its power in identifying highly potent ligands for select protein targets, conventional medicinal chemistry is limited by its low throughput and lack of proteomic selectivity information. We seek to develop a chemoproteomic approach for discovering covalent ligands for protein targets in an unbiased, high-throughput manner. Tripartite probe compounds composed of a heterocyclic core, an electrophilic "warhead", and an alkyne tag have been designed and synthesized for covalently labeling and identifying targets in cells.

Transient [3,3] Cope rearrangement of 3,3-dicyano-1,5-dienes: computational analysis and 2-step synthesis of arylcycloheptanes.

A simple and modular route to arylcycloheptene scaffolds is reported. The two-step route from Knoevenagel adducts and allylic electrophiles is made possible through the design of a Cope rearrangement that utilizes a "traceless" activating group to promote an otherwise thermodynamically unfavorable transformation. Experimentally, the [3,3] rearrangement occurrs transiently at room temperature with a computed barrier of 19.

Controlling, Understanding, and Redirecting the Thermal Rearrangement of 3,3-Dicyano-1,5-enynes.

The thermal [3,3] rearrangement of 3,3-dicyano-1,5-enynes to γ-allenyl alkylidenemalononitriles (the "enyne Cope rearrangement") has largely eluded synthetic value as the desired products, too, are thermally reactive and ultimately yield 6π electrocyclization products. Herein, we describe experimental and computational studies related to the thermal rearrangement of 1,5-enynes, structural features to halt the thermal rearrangement at the allene stage, and a reductive variant for preparing bifunctional allenyl malononitriles. We also describe various ways that the bifunctional building blocks can be manipulated and converted to cyclic and acyclic architectures.

Design of catalysts for site-selective and enantioselective functionalization of non-activated primary C-H bonds.

C-H functionalization represents a promising approach for the synthesis of complex molecules. Instead of relying on modifying the functional groups present in a molecule, the synthetic sequence is achieved by carrying out selective reactions on the C-H bonds, which traditionally would have been considered to be the unreactive components of a molecule. A major challenge is to design catalysts to control both the site- and stereoselectivity of the C-H functionalization.

Enzymatic control of dioxygen binding and functionalization of the flavin cofactor.

The reactions of enzymes and cofactors with gaseous molecules such as dioxygen (O) are challenging to study and remain among the most contentious subjects in biochemistry. To date, it is largely enigmatic how enzymes control and fine-tune their reactions with O, as exemplified by the ubiquitous flavin-dependent enzymes that commonly facilitate redox chemistry such as the oxygenation of organic substrates. Here we employ O-pressurized X-ray crystallography and quantum mechanical calculations to reveal how the precise positioning of O within a flavoenzyme's active site enables the regiospecific formation of a covalent flavin-oxygen adduct and oxygenating species (i.

Structural basis of the Cope rearrangement and cyclization in hapalindole biogenesis.

Hapalindole alkaloids are a structurally diverse class of cyanobacterial natural products defined by their varied polycyclic ring systems and diverse biological activities. These complex metabolites are generated from a common biosynthetic intermediate by the Stig cyclases in three mechanistic steps: a rare Cope rearrangement, 6-exo-trig cyclization, and electrophilic aromatic substitution. Here we report the structure of HpiC1, a Stig cyclase that catalyzes the formation of 12-epi-hapalindole U in vitro.

Compressed Sensing for the Fast Computation of Matrices: Application to Molecular Vibrations.

This article presents a new method to compute matrices from numerical simulations based on the ideas of sparse sampling and compressed sensing. The method is useful for problems where the determination of the entries of a matrix constitutes the computational bottleneck. We apply this new method to an important problem in computational chemistry: the determination of molecular vibrations from electronic structure calculations, where our results show that the overall scaling of the procedure can be improved in some cases.

Compressed Sensing for Multidimensional Spectroscopy Experiments.

Compressed sensing is a processing method that significantly reduces the number of measurements needed to accurately resolve signals in many fields of science and engineering. We develop a two-dimensional variant of compressed sensing for multidimensional spectroscopy and apply it to experimental data. For the model system of atomic rubidium vapor, we find that compressed sensing provides an order-of-magnitude (about 10-fold) improvement in spectral resolution along each dimension, as compared to a conventional discrete Fourier transform, using the same data set.