Analogies between Synthetic and Biosynthetic Reactions in Which [1,2]-Alkyl Shifts Are Combined with Other Events: Dyotropic, Schmidt, and Carbocation Rearrangements

Concise Total Syntheses of (-)-Crinipellins A and B Enabled by a Controlled Cargill Rearrangement

Herein, we report concise total syntheses of diterpene natural products (-)-crinipellins A and B with a tetraquinane skeleton, three adjacent all-carbon quaternary centers, and multiple oxygenated and labile functional groups. Our synthesis features a convergent Kozikowski β-alkylation to unite two readily available building blocks with all the required carbon atoms, an intramolecular photochemical [2 + 2] cycloaddition to install three challenging and adjacent all-carbon quaternary centers and a 5-6-4-5 tetracyclic skeleton, and a controlled Cargill rearrangement to rearrange the 5-6-4-5 tetracyclic skeleton to the desired tetraquinane skeleton. These strategically enabling transformations allowed us to complete total syntheses of (-)-crinipellins A and B in 12 and 13 steps, respectively. The results of quantum chemical computations revealed that the Bronsted acid-catalyzed Cargill rearrangements likely involve stepwise paths to products and the AlR3-catalyzed Cargill rearrangements likely involve a concerted path with asynchronous alkyl shifting events to form the desired product.

Discovery of a Formal Dyotropic Rearrangement during Acid-Mediated Dioxabicyclo[4.2.1]nonanone Formation

A new reaction mechanism for the construction of dioxabicyclo[4.2.1]nonanone skeletons via a cation cascade has been proposed and examined by DFT and ab initio computations. This mechanism features the following steps: (1) intramolecular Friedel-Crafts-type cyclization with a methyl oxocarbenium cation formed by carboxylate disconnection, (2) electron-rich aromatic ring assisted methoxide loss followed by lactone formation, and (3) stepwise dyotropic rearrangement resulting in skeletal isomerization from a dioxabicyclo[3.2.2]nonanone to the dioxabicyclo[4.2.1]nonanone product observed experimentally. The high regioselectivity and driving force for the overall rearrangement were rationalized, and Lewis and Brønsted acid mediated reactivities were compared.

A concise and stereoselective synthesis of the BCDF tetracyclic ring system of C19-diterpenoid alkaloids

A new synthetic route for the BCDF tetracyclic ring system of C19-diterpenoid alkaloids (C19-DTAs) has been developed. The key step is a Pd-catalyzed transannular alkenylation that installs a functionalized bridged F ring. The overall strategy is concise and stereoselective, and it provides a valuable new tool for the synthesis of C19-DTAs. The synthesis begins with a bridged [3.2.1] ring system, which is converted to a key intermediate through a series of highly regio- and stereoselective processes. The introduction of an allylic side chain with high precision is accomplished, culminating in a Pd-catalyzed transannular alkenylation that installs a functionalized bridged F ring to yield the BCDF tetracyclic analog of C19-DTAs.

Fragmentation and [4 + 3] cycloaddition in sodorifen biosynthesis

Terpenes constitute the largest class of natural products. Their skeletons are formed by terpene cyclases (TCs) from acyclic oligoprenyl diphosphates through sophisticated enzymatic conversions. These enzyme reactions start with substrate ionization through diphosphate abstraction, followed by a cascade reaction via cationic intermediates. Based on isotopic-labelling experiments in combination with a computational study, the cyclization mechanism for sodorifen, a highly methylated sesquiterpene from the soil bacterium Serratia plymuthica, was resolved. A peculiar problem in its biosynthesis lies in the formation of several methyl groups from chain methylene carbons. The underlying mechanism involves a methyltransferase-mediated cyclization and unprecedented ring contraction with carbon extrusion from the chain to form a methyl group. A terpene cyclase subsequently catalyses a fragmentation into two reactive intermediates, followed by hydrogen transfers between them and recombination of the fragments by [4 + 3] cycloaddition. This study solves the intricate mechanistic problem of extra methyl group formation in sodorifen biosynthesis.

Fehér P, Stirling A, Czégény Z, Bényei A, Novák Z. Synthesis of Hydrofluoroolefin‐Based Iodonium Reagent via Dyotropic Rearrangement and Its Utilization in Fluoroalkylation

[1,2]‐shift of atoms in alkyl fragments belongs to the class of dyotropic rearrangements. Various atoms, including halogens can be involved in the migration, however participation of iodine is unprecedented. Herein, we report our experimental and DFT studies on the oxidation triggered dyotropic rearrangement of iodo and chloro functions via butterfly‐type transition state to demonstrate the migrating ability of λ³‐iodane centre. With the exploitation of dyotropic rearrangement we designed and synthesized a novel fluoroalkyl iodonium reagent from industrial feedstock gas HFO‐1234yf. We demonstrated that the hypervalent reagent serves as an excellent fluoroalkylation agent for various amines and nitrogen heterocycles.

Peculiar Reaction Products and Mechanisms Revisited with Machine Learning-Augmented Computational NMR

DU8ML, a fast and accurate machine learning-augmented density functional theory (DFT) method for computing nuclear magnetic resonance (NMR) spectra, proved effective for high-throughput revision of misassigned natural products. In this paper, we disclose another important aspect of its application: correction of unusual reaction mechanisms originally proposed because of incorrect product structures.

Elucidating the selectivity of dyotropic rearrangements of β-lactones: a computational survey

A comprehensive computational study on dyotropic rearrangements of β-lactones has been performed for the first time, which provides a valuable guidance for predicting and controlling the selectivity of the reactions.

ORGANOMETALLIC GAS-PHASE ION CHEMISTRY AND CATALYSIS: INSIGHTS INTO THE USE OF METAL CATALYSTS TO PROMOTE SELECTIVITY IN THE REACTIONS OF CARBOXYLIC ACIDS AND THEIR DERIVATIVES

Carboxylic acids are valuable organic substrates as they are widely available, easy to handle, and exhibit structural and functional variety. While they are used in many standard synthetic protocols, over the past two decades numerous studies have explored new modes of metal-mediated reactivity of carboxylic acids and their derivatives. Mass spectrometry-based studies can provide fundamental mechanistic insights into these new modes of reactivity. Here gas-phase models for the following catalytic transformations of carboxylic acids and their derivatives are reviewed: protodecarboxylation; dehydration; decarbonylation; reaction as coordinated bases in C-H bond activation; remote functionalization and decarboxylative C-C bond coupling. In each case the catalytic problem is defined, insights from gas-phase studies are highlighted, comparisons with condensed-phase systems are made and perspectives are reached. Finally, the potential role for mechanistic studies that integrate both gas- and condensed-phase studies is highlighted by recent studies on the discovery of new catalysts for the selective decomposition of formic acid and the invention of the new extrusion-insertion class of reactions for the synthesis of amides, thioamides, and amidines. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.

Effects of electrostatic drag on the velocity of hydrogen migration - pre- and post-transition state enthalpy/entropy compensation

Ab initio molecular dynamics calculations were used to explore the underlying factors that modulate the velocity of hydrogen migration for 1,2 hydrogen shifts in carbocations in which different groups interact noncovalently with the migrating hydrogen. Our results indicate that stronger electrostatic interactions between the migrating hydrogen and nearby π-systems lead to slower hydrogen migration, an effect tied to entropic contributions from the hydrogen + neighboring group substructures.

Construction of Two-Dimensional Potential Energy Surfaces of Reactions with Post-Transition-State Bifurcations

Reactions with post-transition-state bifurcations (PTSBs) involve initial ambimodal transition-state structures followed by an unstable region leading to two possible products. PTSBs are seen in many organic, organometallic, and biosynthetic reactions, but analyzing the origins of selectivity for these reactions is challenging, in large part due to the complex nature of the potential energy surfaces involved, which precludes analyses based on single intrinsic reaction coordinate (IRC; steepest-descent path in mass-weighted coordinate). While selectivity can be predicted using molecular dynamics simulation, connecting results from such calculations to the topography of potential energy surfaces is difficult. In the present work, a method for generating two-dimensional potential energy surfaces for PTSBs is described. The first dimension starts with the IRC for the first transition-state structure, followed by a modified reaction coordinate that reaches the second transition-state structure, which interconverts the two products of a bifurcating reaction path. The IRC for the second transition-state structure constitutes the second dimension. In addition, a method for mapping trajectories from Born-Oppenheimer molecular dynamics simulations onto these surfaces is described. Both approaches are illustrated with representative examples from the field of organic chemistry. The 2D-PESs for five asymmetric cases tested have clear tilted topography after the first transition-state structure, and the tilted direction correlates well with the selectivity observed from previous dynamic simulation. Instead of selecting reaction coordinates by chemical intuition, our method provides a general means to construct two-dimensional potential energy surfaces for reactions with post-transition-state bifurcations.

Secondary Carbocations in the Biosynthesis of Pupukeanane Sesquiterpenes

The results of quantum chemical calculations on putative biosynthetic carbocation cyclization/rearrangements leading to pupukeanane and related sesquiterpenes indicate that a secondary carbocation proposed as an intermediate is not a minimum on the potential energy surface and instead resides in a region of the potential energy surface associated with a plateau containing multiple exit channels.

Stereospecific Ring Contraction of Bromocycloheptenes through Dyotropic Rearrangements via Nonclassical Carbocation-Anion Pairs

Experimental and theoretical evidence is reported for a rare type I dyotropic rearrangement involving a [1,2]-alkene shift, leading to the regio- and stereospecific ring contraction of bromocycloheptenes. This reaction occurs under mild conditions, with or without a Lewis acid catalyst. DFT calculations show that the reaction proceeds through a nonclassical carbocation–anion pair, which is crucial for the low activation barrier and enantiospecificity. The chiral cyclopropylcarbinyl cation may be a transition state or an intermediate, depending on the reaction conditions.

Theoretical Study on DBU-Catalyzed Insertion of Isatins into Aryl Difluoronitromethyl Ketones: A Case for Predicting Chemoselectivity Using Electrophilic Parr Function

The possible mechanisms of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU)-catalyzed chemoselective insertion of N-methyl isatin into aryl difluoronitromethyl ketone to synthesize 3,3-disubstituted and 2,2-disubstituted oxindoles have been studied in this work. As revealed by calculated results, the reaction occurs via two competing paths, including α and β carbonyl paths, and each path contains five steps, that is, nucleophilic addition of DBU to ketone, C-C bond cleavage affording difluoromethylnitrate anion and phenylcarbonyl-DBU cation, nucleophilic addition of difluoromethylnitrate anion to carbonyl carbon of N-methyl isatin, acyl transfer process, and dissociation of DBU and product. The computational results suggest that nucleophilic additions on different carbonyl carbons of N-methyl isatin via α and β carbonyl paths would lead to different products in the third step, and β carbonyl path associated with the main product 3,3-disubstituted oxindole is more energetically favorable, which is consistent with the experimental observations. Noteworthy, electrophilic Parr function can be successfully applied for exactly predicting the activity of reaction site and reasonably explaining the chemoselectivity. In addition, the distortion/interaction and noncovalent interaction analyses show that much more hydrogen bond interactions should be responsible for the lower energy of the transition state associated with β carbonyl path. The obtained insights would be valuable for the rational design of efficient organocatalysts for this kind of reactions with high selectivities.

From Hydrindane to Decalin: A Mild Transformation through a Dyotropic Ring Expansion

An unexpected ring expansion converting hydrindane cores into decalins has been observed. The process occurs under very mild conditions and with exquisite transfer of chiral information. The ring expansion provides access to decorated decalins with complete stereocontrol. The reaction mechanism is studied in order to gain insight into the underlying causes for the low thermal requirements in this reaction and the nature of the chirality transfer process. Interestingly, both result from an unprecedented dyotropic reaction involving a mesylate group.

Dyotropic rearrangements in natural product total synthesis and biosynthesis

Some recent examples of dyotropic rearrangements involved in complex natural product total synthesis and biosynthesis are highlighted.

Computational study of the threshold energy for the 1,2-interchange of X and R (X, R = halogens, pseudohalogens, and monovalent hydrocarbon groups) on CH2XCH2R

Transition state geometries and threshold energies, E0, were computed for an unusual unimolecular isomerization reaction that exchanges two groups (X, R) on CH2XCH2R. An objective is to determine the most energetically feasible interchanges to guide experimental investigations. The interchanging species included halogens (F, Cl, Br) and pseudohalogens and monovalent hydrocarbons (H, SH, CH3, NH2, OH, OCF3, OCH3, CH=CH2, CH2CH3, CH2OH, C≡CH, CH2CF3, CCl3, CF3) attached to a two carbon backbone. Ground state and transition state geometries were optimized with the B3PW91 level of theory and 6-311+G(2d,p) basis set. The Br–Br interchange had the lowest E0 (141 kJ/mol), and CH3–H had the highest E0 (582 kJ/mol). In general, larger atoms or groups with lone pairs of electrons such as halogens, SH, OH, OCH3, OCF3, and NH2 tend to lower the E0 barrier for interchange, making them the most likely to be experimentally observed.

Dynamic behavior of rearranging carbocations - implications for terpene biosynthesis

This review describes unexpected dynamical behaviors of rearranging carbocations and the modern computational methods used to elucidate these aspects of reaction mechanisms. Unique potential energy surface topologies associated with these rearrangements have been discovered in recent years that are not only of fundamental interest, but also provide insight into the way Nature manipulates chemical space to accomplish specific chemical transformations. Cautions for analyzing both experimental and theoretical data on carbocation rearrangements are included throughout.

Type-I dyotropic rearrangement for 1,2-disubstituted cyclohexanes: substitution effect on activation energy

Migratory aptitude and contribution of specific structural features of synthetically valuable functional groups and halogen atoms in type-I dyotropic rearrangement for both symmetric and unsymmetrical 1,2-disubstituted cyclohexanes are computed.

Mechanistic studies of copper(I)-catalyzed 1,3-halogen migration

An ongoing challenge in modern catalysis is to identify and understand new modes of reactivity promoted by earth-abundant and inexpensive first-row transition metals. Herein, we report a mechanistic study of an unusual copper(I)-catalyzed 1,3-migration of 2-bromostyrenes that reincorporates the bromine activating group into the final product with concomitant borylation of the aryl halide bond. A combination of experimental and computational studies indicated this reaction does not involve any oxidation state changes at copper; rather, migration occurs through a series of formal sigmatropic shifts. Insight provided from these studies will be used to expand the utility of aryl copper species in synthesis and develop new ligands for enantioselective copper-catalyzed halogenation.

How cyclobutanes are assembled in nature--insights from quantum chemistry

Biosynthetic production of cyclobutanes leads to many complex natural products. Recently, theoretical work employing quantum chemical calculations has shed light on many of the details of cyclobutane-formation, in particular, for terpene natural products. Specific insights and general principles derived from these theoretical studies are described herein.

Modulation of inherent dynamical tendencies of the bisabolyl cation via preorganization in epi-isozizaene synthase

The relative importance of preorganization, selective transition state stabilization and inherent reactivity are assessed through quantum chemical and docking calculations for a sesquiterpene synthase (epi-isozizaene synthase, EIZS). Inherent reactivity of the bisabolyl cation, both static and dynamic, appears to determine the pathway to product, although preorganization and selective binding of the final transition state structure in the multi-step carbocation cascade that forms epi-isozizaene appear to play important roles.

Diradical ring closing reactions displaying Woodward–Hoffmann behaviour and torquoselectivity

The applicability of the Woodward–Hoffmann rules seems to expand beyond classical closed shell structures.

In silico study on the mechanism of formation of hydrazine and nitrogen in the reactions of excess hydroxylamine with 2,4-dinitrophenyl diethyl phosphate

Decomposition study of 2,4-dinitrophenyl diethyl phosphate to hydrazine and nitrogen gas with excess of hydroxylamine using quantum chemical calculations.

Biosynthetic consequences of multiple sequential post-transition-state bifurcations

Selectivity in chemical reactions that form complex molecular architectures from simpler precursors is usually rationalized by comparing competing transition-state structures that lead to different possible products. Herein we describe a system for which a single transition-state structure leads to the formation of many isomeric products via pathways that feature multiple sequential bifurcations. The reaction network described connects the pimar-15-en-8-yl cation to miltiradiene, a tricyclic diterpene natural product, and isomers via cyclizations and/or rearrangements. The results suggest that the selectivity of the reaction is controlled by (post-transition-state) dynamic effects, that is, how the carbocation structure changes in response to the distribution of energy in its vibrational modes. The inherent dynamical effects revealed herein (characterized through quasiclassical direct dynamics calculations using density functional theory) have implications not only for the general principles of selectivity prediction in systems with complex potential energy surfaces, but also for the mechanisms of terpene synthase enzymes and their evolution. These findings redefine the challenges faced by nature in controlling the biosynthesis of complex natural products.

Unimolecular isomerization of CH2FCD2Cl via the interchange of Cl and F atoms: assignment of the threshold energy to the 1,2-dyotropic rearrangement

The room-temperature gas-phase recombination of CH2F and CD2Cl radicals was used to prepare CH2FCD2Cl molecules with 91 kcal mol(-1) of vibrational energy. Three unimolecular processes are in competition with collisional deactivation of CH2FCD2Cl; HCl and DF elimination to give CHF═CD2 and CH2═CDCl plus isomerization to give CH2ClCD2F by the interchange of F and Cl atoms. The Cl/F interchange reaction was observed, and the rate constant was assigned from measurement of CHCl═CD2 as a product, which is formed by HF elimination from CH2ClCD2F. These experiments plus previously published results from chemically activated CH2ClCH2F and electronic structure and RRKM calculations for the kinetic-isotope effects permit assignment of the three rate constants for CH2FCD2Cl (and for CH2ClCD2F). The product branching ratio for the interchange reaction versus elimination is 0.24 ± 0.04. Comparison of the experimental rate constant with the RRKM calculated rate constant permitted the assignment of a threshold energy of 62 ± 3 kcal mol(-1) for this type-1 dyotropic rearrangement. On the basis of electronic structure calculations, the nature of the transition state for the rearrangement reaction is discussed. The radical recombination reactions in the chemical system also generate vibrationally excited CD2ClCD2Cl and CH2FCH2F molecules, and the rate constants for DCl and HF elimination were measured in order to confirm that the photolysis of CD2ClI and (CH2F)2CO mixtures was giving reliable data for CH2FCD2Cl.