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If you're out for a stroll and reach a hill, the most obvious paths to the other side are over or around. But under the right set of circumstances--such as [...]

A series of computational laboratory experiments aimed at teaching students principles of rational drug design are described and evaluated. These experiments range from an introduction to viewing protein-ligand complexes to optimizing geometries of potential drugs with quantum chemistry and automated docking. Student feedback indicates that such a course increased their appreciation for the roles of chemists in the drug discovery-development process.

Recently, Huang and co‐workers reported a catalytic reaction that utilizes H2 as the sole reductant for a C−C coupling of allyl groups with yields up to 96 %. Here we use computational quantum chemistry to identify several key features of this reaction that provide clarity on how it proceeds. We propose the involvement of a Pd−Pd bound dimer precatalyst, demonstrate the importance of ligand π‐π interactions and counterions, and identify a new, energetically viable, mechanism involving two dimerized, outer‐sphere reductive elimination transition structures that determine both the rate and selectivity. Although we rule out the previously proposed transmetalation step on energetic grounds, we show it to have an unusual aromatic transition structure in which two Pd atoms support rearranging electrons. The prevalence of potential metal‐supported pericyclic reactions in this system suggests that one should consider such processes regularly, but the results of our calculations also indicate that one should do so with caution. [ABSTRACT FROM AUTHOR]

Investigating the reactivity of small nucleophilic scaffolds is a strategic approach for the design of new catalysts aiming at effective detoxification processes of organophosphorus compounds. The drug methimazole (MMZ) is an interesting candidate featuring two non‐equivalent nucleophilic centers. Herein, phosphoryl transfer reactions mediated by MMZ were assessed by means of spectrophotometric kinetic studies, mass spectrometry (MS) analyses, and density functional theory (DFT) calculations using the multi‐electrophilic compound O,O‐diethyl 2,4‐dinitrophenyl phosphate (DEDNPP). MMZ anion acts primarily as an S‐nucleophile, exhibiting a nucleophilic activity comparable to that of certain oximes featuring alpha‐effect. Selective nucleophilic aromatic substitution was observed, consistent with the DFT prediction of a low energy barrier. Overall, the results bring important advances regarding the mechanistic understanding of nucleophilic dephosphorylation reactions, which comprises a strategic tool for neutralizing toxic organophosphates, hence promoting chemical security. [ABSTRACT FROM AUTHOR]

The first assortment of achiral pentafluorosulfanylated cyclobutanes (SF5‐CBs) are now synthetically accessible through strain‐release functionalization of [1.1.0]bicyclobutanes (BCBs) using SF5Cl. Methods for both chloropentafluorosulfanylation and hydropentafluorosulfanylation of sulfone‐based BCBs are detailed herein, as well as proof‐of‐concept that the logic extends to tetrafluoro(aryl)sulfanylation, tetrafluoro(trifluoromethyl)sulfanylation, and three‐component pentafluorosulfanylation reactions. The methods presented enable isolation of both syn and anti isomers of SF5‐CBs, but we also demonstrate that this innate selectivity can be overridden in chloropentafluorosulfanylation; that is, an anti‐stereoselective variant of SF5Cl addition across sulfone‐based BCBs can be achieved by using inexpensive copper salt additives. Considering the SF5 group and CBs have been employed individually as nonclassical bioisosteres, structural aspects of these unique SF5‐CB "hybrid isosteres" were then contextualized using SC‐XRD. From a mechanistic standpoint, chloropentafluorosulfanylation ostensibly proceeds through a curious polarity mismatch addition of electrophilic SF5 radicals to the electrophilic sites of the BCBs. Upon examining carbonyl‐containing BCBs, we also observed rare instances whereby radical addition to the 1‐position of a BCB occurs. The nature of the key C(sp3)−SF5 bond formation step – among other mechanistic features of the methods we disclose – was investigated experimentally and with DFT calculations. Lastly, we demonstrate compatibility of SF5‐CBs with various downstream functionalizations. [ABSTRACT FROM AUTHOR]

In life and in chemistry, not all uphill climbs are created equal. For example, racers come in different sizes; some have built-in advantages that give them a head start. Imagine [...]

Density functional theory was used to elucidate the mechanism and the pericyclicity of chromium‐catalyzed bicyclization reactions that purportedly involve 8‐electron electrocyclization steps. Our computational results indicate that these reactions do indeed proceed via 8‐electron electrocyclization rather than an alternative pathway involving 4‐electron electrocyclization followed by Cope rearrangement. The role of C=[M] groups on the electrocyclization, specifically its pericyclicity, was examined in detail using modern theoretical tools. [ABSTRACT FROM AUTHOR]

When new concepts, models, or theories are introduced in a course, their presentation should be accurate, even if depth is not the goal. In a recent publication in this Journal, the Woodward-Hoffmann rules were invoked in the context of a new laboratory experiment, but the associated description was inaccurate. Here we aim to clarify the theoretical background relevant to the described laboratory experiment, and we describe a new computational experiment that could be used to further illuminate the relevant theoretical concepts. [For a reply to this article, see EJ1159630.]

Herein, we describe our synthetic efforts toward the pupukeanane natural products, in which we have completed the first enantiospecific route to 2‐isocyanoallopupukeanane in 10 steps (formal synthesis), enabled by a key Pd‐mediated cyclization cascade. This subsequently facilitated an unprecedented bio‐inspired "contra‐biosynthetic" rearrangement, providing divergent access to 9‐isocyanopupukeanane in 15 steps (formal synthesis). Computational studies provide insight into the nature of this rearrangement. [ABSTRACT FROM AUTHOR]

Summary: Bioactive triterpenes feature complex fused‐ring structures, primarily shaped by the first‐committed enzyme, 2,3‐oxidosqualene cyclases (OSCs) in plant triterpene biosynthesis. Triterpenes with B,C‐ring‐opened skeletons are extremely rare with unknown formation mechanisms, harbouring unchartered chemistry and biology.Here, through mining the genome of Chenopodium quinoa followed by functional characterization, we identified a stress‐responsive and neofunctionalized OSC capable of generating B,C‐ring‐opened triterpenes, including camelliol A and B and the novel (−)‐quinoxide A as wax components of the specialized epidermal bladder cells, namely the quinoxide synthase (CqQS).Protein structure analysis followed by site‐directed mutagenesis identified key variable amino acid sites underlying functional interconversion between pentacyclic β‐amyrin synthase (CqbAS1) and B,C‐ring‐opened triterpene synthase CqQS. Mutation of one key residue (N612K) in even evolutionarily distant Arabidopsis β‐amyrin synthase could generate quinoxides, indicating a conserved mechanism for B,C‐ring‐opened triterpene formation in plants. Quantum computation combined with docking experiments further suggests that conformations of conserved W613 and F413 of CqQS might be key to selectively stabilizing intermediate carbocations towards B,C‐ring‐opened triterpene formation.Our findings shed light on quinoa triterpene skeletal diversity and mechanisms underlying B,C‐ring‐opened triterpene biosynthesis, opening avenues towards accessing their chemistry and biology and paving the way for quinoa trait engineering and quality improvement. [ABSTRACT FROM AUTHOR]

Nitrogen heterocycles play a vital role in pharmaceuticals and natural products, with the six‐membered aromatic and aliphatic architectures being commonly used. While synthetic methods for aromatic N‐heterocycles are well‐established, the synthesis of their aliphatic functionalized analogues, particularly piperidine derivatives, poses a significant challenge. In that regard, we propose a stepwise dearomative functionalization reaction for the construction of highly decorated piperidine derivatives with diverse functional handles. We also discuss challenges related to site‐selectivity, regio‐ and diastereoselectivity, and provide insights into the reaction mechanism through mechanistic studies and density functional theory computations. [ABSTRACT FROM AUTHOR]

Terpene cyclization, one of the most complex chemical reactions in nature, is generally catalyzed by two classes of terpene cyclases (TCs). Cytochrome P450s that act as unexpected TC‐like enzymes are known but are very rare. In this study, we genome‐mined a cryptic bacterial terpenoid gene cluster, named ari, from the thermophilic actinomycete strain Amycolatopsis arida. By employing a heterologous production system, we isolated and characterized three highly oxidized eunicellane derived diterpenoids, aridacins A−C (1–3), that possess a 6/7/5‐fused tricyclic scaffold. In vivo and in vitro experiments systematically established a noncanonical two‐step biosynthetic pathway for diterpene skeleton formation. First, a class I TC (AriE) cyclizes geranylgeranyl diphosphate (GGPP) into a 6/10‐fused bicyclic cis‐eunicellane skeleton. Next, a cytochrome P450 (AriF) catalyzes cyclization of the eunicellane skeleton into the 6/7/5‐fused tricyclic scaffold through C2−C6 bond formation. Based on the results of quantum chemical computations, hydrogen abstraction followed by electron transfer coupled to barrierless carbocation ring closure is shown to be a viable mechanism for AriF‐mediated cyclization. The biosynthetic logic of skeleton construction in the aridacins is unprecedented, expanding the catalytic capacity and diversity of P450s and setting the stage to investigate the inherent principles of carbocation generation by P450s in the biosynthesis of terpenoids. [ABSTRACT FROM AUTHOR]

A site‐selective C(3)/C(4)‐alkylation of N‐pyridylisoquinolones is achieved by employing C−C bond activation of cyclopropanols under Ru(II)‐catalyzed/Cu(II)‐mediated conditions. The regioisomeric ratios of the products follow directly from the electronic nature of the cyclopropanols and isoquinolones used, with electron‐withdrawing groups yielding predominantly the C(3)‐alkylated products, whereas the electron‐donating groups primarily generate the C(4)‐alkylated isomers. Density functional theory calculations and detailed mechanistic investigations suggest the simultaneous existence of the singlet and triplet pathways for the C(3)‐ and C(4)‐product formation. Further transformations of the products evolve the utility of the methodology thereby yielding scaffolds of synthetic relevance. [ABSTRACT FROM AUTHOR]

Stereoselective Zweifel olefination using boronate complexes carrying two different reactive π‐systems was achieved to synthesize vinyl heteroarenes and conjugated 1,3‐dienes in good yield and up to 100 % stereoselectivity, which remains unexplored until now. Most importantly, we report the unprecedented formation of E vs. Z‐vinyl heteroarenes for different heteroarenes under identical conditions. Density functional theory (DFT) investigations unveil the mechanistic dichotomy between olefin and heteroarene activation followed by 1,2‐migration, leading to E or Z‐vinyl heteroarenes respectively. We also report a previously unknown reversal of stereoselectivity by using 2,3‐Dichloro‐5,6‐dicyano‐1,4‐benzoquinone (DDQ) as an electrophile. The Zweifel olefination using a boronate complex that carries two different olefins was previously unexplored due to significant challenges associated with the site‐selective activation of olefins. We have solved this problem and reported the site‐selective activation of olefins for the stereoselective synthesis of 1,3‐dienes. [ABSTRACT FROM AUTHOR]

We report a detailed experimental and theoretical analysis of through‐space arene activation with halogens, tetrazoles and achiral esters and amides. Contrary to previously assumed direct activation through σ‐complex stabilization, our results suggest that these reactions proceed by a relay mechanism wherein the lone pair‐containing activators form exothermic π‐complexes with electrophilic nitronium ion before transferring it to the probe ring through low barrier transition states. Noncovalent interactions (NCI) plots and Quantum Theory of Atoms in Molecules (QTAIM) analyses depict favorable interactions between the Lewis base (LB) and the nitronium ion in the precomplexes and the transition states, suggesting directing group participation throughout the mechanism. The regioselectivity of substitution also comports with a relay mechanism. In all, these data pave the way for an alternate platform of electrophilic aromatic substitution (EAS) reactions. [ABSTRACT FROM AUTHOR]

The template‐directed C−H insertion of α,β‐unsaturated esters into quinoline was interrogated by using computational quantum chemistry. An energetically viable mechanism for this complex multistep transformation was elucidated, with attention paid throughout to conformational flexibility and alternative ligand binding modes. The selectivity was found to correlate with distortion from a tetrahedral geometry for the carbon atom involved in C−H insertion, a parameter that can be applied to future template design. [ABSTRACT FROM AUTHOR]

The [3s,5s]‐sigmatropic shift is an example of an orbital‐symmetry forbidden pericyclic reaction that is outcompeted by the allowed [3s,3s]‐sigmatropic shift. Density functional theory calculations are used to show that PdII‐complexed systems with strategically placed substituents engaging in key stereoelectronic effects can select for the [3s,5s] process, thereby outcompeting both orbital‐symmetry‐allowed [3s,3s]‐ and [3s,5a]‐shifts. [ABSTRACT FROM AUTHOR]

Many natural products that contain basic nitrogen atoms--for example alkaloids like morphine and quinine--have the potential to treat a broad range of human diseases. However, the presence of a nitrogen atom in a target molecule can complicate its chemical synthesis because of the basicity of nitrogen atoms and their susceptibility to oxidation. Obtaining such compounds by chemical synthesis can be further complicated by the presence of multiple nitrogen atoms, but it can be done by the selective introduction and removal of functional groups that mitigate basicity. Here we use such a strategy to complete the chemical syntheses of citrinalin B and cyclopiamine B. The chemical connections that have been realized as a result of these syntheses, in addition to the isolation of both 17-hydroxycitrinalin B and citrinalin C (which contains abicyclo[2.2.2]diazaoctane structural unit) through carbon-13 feeding studies, support the existence of a common bicyclo[2.2.2]diazaoctane-containing biogenetic precursor to these compounds, as has been proposed previously., The prenylated indole alkaloids are an emerging class of natural products typified by the presence of an indole ring, or derivatives thereof (that is, spirooxindole or pseudoindoxyl), decorated by one [...]

Reported herein is a reactivity of propargyl alcohols as "Three‐Carbon Synthons" in a Rh(III)‐catalyzed C−H functionalization of acetanilides, leading to the synthesis of core structures of isocryptolepine, γ‐carbolines, dihydrochromeno[2,3‐b]indoles, and diindolylmethanes (DIM) derivatives. The transformation involves a rhodium(III)‐catalyzed C−H functionalization and heteroannulation to yield indoles followed by a cascade cyclization with both external and internal nucleophiles to afford diverse products. The role of the hydroxy group, the key function of the silver additive, the origin of the reverse regioselectivity and the rate‐determining step, are rationalized in conformity with the combination of experimental, noncovalent interaction analysis and DFT studies. This protocol is endowed with several salient features, including one‐pot multistep cascade approach, exclusive regioselectivity, good functional group tolerance and synthesis of variety of molecular frameworks. [ABSTRACT FROM AUTHOR]