Unraveling the mechanism of epoxide formation from sulfur ylides and aldehydes

Application of Enantioselective Sulfur Ylide Epoxidation to a Short Asymmetric Synthesis of Bedaquiline, a Potent Anti-Tuberculosis Drug

A highly selective asymmetric synthesis of a potent anti-TB drug (-)-bedaquiline is accomplished using sulfur ylide asymmetric epoxidation, employing (+)-isothiocineole as an inexpensive and readily available chiral sulfide. Excellent enantioselectivity (er 96:4) and diastereoselectivity (dr 90:10) were obtained for the construction of the key diaryl epoxide, which was subsequently subjected to a highly regioselective ring opening (96:4). The synthesis was completed in nine steps starting from commercially available aldehyde in 8% overall yield.

Concise Synthesis of Tunicamycin V and Discovery of a Cytostatic DPAGT1 Inhibitor

A short total synthesis of tunicamycin V (1), a non-selective phosphotransferase inhibitor, is achieved via a Büchner-Curtius-Schlotterbeck type reaction. Tunicamycin V can be synthesized in 15 chemical steps from D-galactal with 21 % overall yield. The established synthetic scheme is operationally very simple and flexible to introduce building blocks of interest. The inhibitory activity of one of the designed analogues 28 against human dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 (DPAGT1) is 12.5 times greater than 1. While tunicamycins are cytotoxic molecules with a low selectivity, the novel analogue 28 displays selective cytostatic activity against breast cancer cell lines including a triple-negative breast cancer.

Asymmetric Synthesis of Bicyclic Pyrazolidinones through Alkaloid-Catalyzed [3+2]-Cycloadditions of Ketenes and Azomethine Imines

A versatile asymmetric synthesis of bicyclic pyrazolidinones through alkaloid-catalyzed formal [3+2]- and [3+2+2]-cycloadditions of ketenes with azomethine imines is described. The methodology was found to be tolerant of ketene and a variety of monosubstituted ketenes (R=alkyl, OAc). The products were formed in good to excellent yields (71-99 % for 24 examples, 39 examples in all), with good to excellent diastereoselectivity in many cases (dr 3 : 1 to 27 : 1 for 22 examples), and with excellent enantioselectivity for most examples (≥93 % ee for 34 products). In the case of most disubstituted ketenes, the reaction proceeded through a [3+2+2]-cycloaddition to form structurally interesting bicyclic pyrazolo-oxadiazepinediones with moderate diastereoselectivity (dr up to 3.7 : 1) and as racemic mixtures (3 examples). The method represents the first unambiguous example of an enantioselective reaction between ketenes and a 1,3-dipole.

Feeding sequence-regulated divergent (4 + 1 + 1’) annulations of α-bromo carbonyls and 1-azadienes via computational calculations-based mechanism elucidation

By investigating the mechanism of our previously reported (4 + 1 + 1) annulations of α-bromo carbonyls and 1-azadienes via density functional theory (DFT) calculations, the formation of a carbon...

Diastereoselective synthesis of spiro-cyclopropanyl-cyclohexadienones via direct sulfide-catalyzed [2 + 1] annulation of para-quinone methides with bromides

A sulfide-catalyzed [2 + 1] annulation of para-quinone methides with diverse bromides was disclosed to access appealing spiro-cyclopropanyl-cyclohexadienones with high diastereoselectivity.

Sulfoxonium ylides: simple compounds with chameleonic reactivity

Sulfoxonium ylides, manageable compounds with an appealing safety profile, adapt to reaction partners like chameleons to their environment, resulting in a variety of useful, and sometimes surprising and unique, reactions.

Synthesis of γ-Lactones Utilizing Ketoacids and Trimethylsulfoxonium Iodide

The Johnson-Corey-Chaykovsky epoxidation is one of the oldest methods for the synthesis of terminal epoxides from carbonyl compounds. Herein we present a simplified extension of the Johnson-Corey-Chaykovsky epoxidation, where ketoacids are employed as the substrates and commercially available trimethylsulfoxonium iodide is employed as the carbon-atom homologating reagent. A variety of lactones are produced in a single step in synthetically useful yields.

ChemEngine: harvesting 3D chemical structures of supplementary data from PDF files

Digital access to chemical journals resulted in a vast array of molecular information that is now available in the supplementary material files in PDF format. However, extracting this molecular information, generally from a PDF document format is a daunting task. Here we present an approach to harvest 3D molecular data from the supporting information of scientific research articles that are normally available from publisher's resources. In order to demonstrate the feasibility of extracting truly computable molecules from PDF file formats in a fast and efficient manner, we have developed a Java based application, namely ChemEngine. This program recognizes textual patterns from the supplementary data and generates standard molecular structure data (bond matrix, atomic coordinates) that can be subjected to a multitude of computational processes automatically. The methodology has been demonstrated via several case studies on different formats of coordinates data stored in supplementary information files, wherein ChemEngine selectively harvested the atomic coordinates and interpreted them as molecules with high accuracy. The reusability of extracted molecular coordinate data was demonstrated by computing Single Point Energies that were in close agreement with the original computed data provided with the articles. It is envisaged that the methodology will enable large scale conversion of molecular information from supplementary files available in the PDF format into a collection of ready- to- compute molecular data to create an automated workflow for advanced computational processes. Software along with source codes and instructions available at https://sourceforge.net/projects/chemengine/files/?source=navbar.Graphical abstract.

Alkaloid-Catalyzed Enantioselective [3 + 2] Cycloaddition of Ketenes and Azomethine Imines

A new asymmetric synthesis of bicyclic pyrazolidinones through an alkaloid-catalyzed formal [3 + 2] cycloaddition of in situ generated ketenes and azomethine imines is described. The products were formed in good to excellent yields (52-99% for 17 examples), with good to excellent diastereoselectivity (dr 5:1 to 27:1 for 11 examples), and with excellent enantioselectivity in all cases (≥96% ee). This method represents the first unambiguous example of an enantioselective reaction between ketenes and a 1,3-dipole.

Diastereoselective Johnson-Corey-Chaykovsky trifluoroethylidenation

(2,2,2-Trifluoroethyl)diphenylsulfonium triflate was found to be an efficient ylide reagent for the Johnson-Corey-Chaykovsky reaction to afford trifluoromethyl epoxides, cyclopropanes and aziridines. Interestingly, excellent but different diastereoselectivity was observed for these transformations. Both trifluoromethyl epoxides and cyclopropanes were obtained with trans-selectivity, whereas aziridines were obtained with cis-selectivity.

Muraymycin nucleoside-peptide antibiotics: uridine-derived natural products as lead structures for the development of novel antibacterial agents

Muraymycins are a promising class of antimicrobial natural products. These uridine-derived nucleoside-peptide antibiotics inhibit the bacterial membrane protein translocase I (MraY), a key enzyme in the intracellular part of peptidoglycan biosynthesis. This review describes the structures of naturally occurring muraymycins, their mode of action, synthetic access to muraymycins and their analogues, some structure-activity relationship (SAR) studies and first insights into muraymycin biosynthesis. It therefore provides an overview on the current state of research, as well as an outlook on possible future developments in this field.

Homologation of boronic esters with organolithium compounds: a computational assessment of mechanism

Ab initio calculations are reported for the reaction of methyl boronic ester with organolithium reagents with α-leaving groups. The best calculations rely on density functional theory prediction of structures and coupled-cluster theory calculation of accurate potential energies. The results provide strong confirmation of the feasibility of a two-step mechanism with rapid initial formation of a boron-ate complex followed by slower migration of methyl from boron to carbon with loss of the leaving group. The calculated free energy of activation is consistent with observed kinetic behavior, and the calculations provide a framework for exploring substituent and other effects on reactivity. Obtaining reasonable agreement with experiment in this way is not trivial and requires careful treatment of level of theory (density functional theory calculations tend to yield inaccurate results), of conformational complexity, especially for the ate complexes, and of the nature of the microscopic model of reactants and solvent. The methodological challenges and possible pitfalls, many of which are relevant more broadly to computational modeling of organic reaction mechanisms, are discussed in detail.

Asymmetric organocatalytic epoxidations: reactions, scope, mechanisms, and applications

Chiral epoxides serve as versatile building blocks in the synthesis of complex organic frameworks. The high strain imposed by the three-membered ring system makes epoxides prone to a variety of nucleophilic ring-opening reactions. Since the development of the Sharpless epoxidation, there have been many important contributions and advances in this area. With the rapid development of the field of asymmetric organocatalysis, a wide range of organocatalysts is now able to catalyze the epoxidation of broad class of unsaturated carbonyl compounds. In this Minireview, recent progress in the development of organocatalytic asymmetric epoxidation methods, the proposed mechanisms of these reactions and their applications as intermediates is reported.

Practical and highly selective sulfur ylide-mediated asymmetric epoxidations and aziridinations using a cheap and readily available chiral sulfide: extensive studies to map out scope, limitations, and rationalization of diastereo- and enantioselectivities

The chiral sulfide, isothiocineole, has been synthesized in one step from elemental sulfur, γ-terpinene, and limonene in 61% yield. A mechanism involving radical intermediates for this reaction is proposed based on experimental evidence. The application of isothiocineole to the asymmetric epoxidation of aldehydes and the aziridination of imines is described. Excellent enantioselectivities and diastereoselectivities have been obtained over a wide range of aromatic, aliphatic, and α,β-unsaturated aldehydes using simple protocols. In aziridinations, excellent enantioselectivities and good diastereoselectivities were obtained for a wide range of imines. Mechanistic models have been put forward to rationalize the high selectivities observed, which should enable the sulfide to be used with confidence in synthesis. In epoxidations, the degree of reversibility in betaine formation dominates both the diastereoselectivity and the enantioselectivity. Appropriate tuning of reaction conditions based on understanding the reaction mechanism enables high selectivities to be obtained in most cases. In aziridinations, betaine formation is nonreversible with semistabilized ylides and diastereoselectivities are determined in the betaine forming step and are more variable as a result.

Enantioselective synthesis of (thiolan-2-yl)diphenylmethanol and its application in asymmetric, catalytic sulfur ylide-mediated epoxidation

This work describes an expeditious and efficient preparation of enantiopure (thiolan-2-yl)diphenylmethanol (2) featuring a double nucleophilic substitution and Shi epoxidation as key steps. One of the applications of its benzyl ether derivative to asymmetric sulfur ylide-mediated epoxidation with up to 92% ee (14 examples) was also demonstrated herein.

Relative Stabilities of Transition States Determine Diastereocontrol in Sulfur Ylide Additions onto Chiral N-Sulfinyl Imines

Additions of methylphenylsulfonium methylide onto chiral non-racemic N-sulfinyl imines (R'-SO-N=CH-R, R'=t-butyl, R=protected diol), followed by ring closure, yield terminal aziridines with high diastereoselectivity. Control reactions have established that both N- and C- iminyl substituents impact product preference, and when properly matched, one addition product is selected almost exclusively. Using solution-phase density functional computational methods, minima and transition state searches have been performed to reveal the structural origins of the diastereoselectivity. Our computational findings indicate that ring closure is fast and irreversible, and consequently, the relative energies of the transition states for the competing Re/Si addition steps determine the product diastereomeric ratios. Analysis of addition transition state structures reveals the causes of selectivity as arising from the N- and C- iminyl substituents, and we identify the S (R) configuration of the N-sulfinyl sulfur atom as the dominant director of Si (Re) addition. The control attributed to the sulfur configuration is tied to an important favorable internal interaction between the sulfinyl oxygen and the iminyl hydrogen. The protected diol acts as a secondary director, owing to steric/electrostatic interactions with the approaching ylide.

Structural and conformational analysis of 1-oxaspiro[2.5]octane and 1-oxa-2-azaspiro[2.5]octane derivatives by (1) H, (13) C, and (15) N NMR

A structural and conformational analysis of 1-oxaspiro[2.5]octane and 1-oxa-2-azaspiro[2.5]octane derivatives was performed using (1) H, (13)  C, and (15)  N NMR spectroscopy. The relative configuration and preferred conformations were determined by analyzing the homonuclear coupling constants and chemical shifts of the protons and carbon atoms in the aliphatic rings. These parameters directly reflected the steric and electronic effects of the substituent bonded to the aliphatic six-membered ring or to C3 or N2. The parameters also were sensitive to the anisotropic positions of these atoms in the three-atom ring. The preferred orientation of the exocyclic substituents directed the oxidative attack.

Chemo-, regio-, and diastereoselectivity preferences in the reaction of a sulfur ylide with a dienal and an enone

Mechanistic insights into an interesting class of reaction between sulfur ylides with (i) a dienal, and (ii) an enone, obtained by using density functional theory, is reported. The kinetic and thermodynamic factors responsible for chemo-, regio-, and diastereoselectivities are established by identifying all key transition states and intermediates along the reaction pathway for 1,2-, 1,4-, and 1,6- modes of attack of dimethylsulfonium benzylide to 5-phenylpenta-2,4-dienal. The reaction profiles for 1,2- and 1,4- modes of addition are also evaluated for the reaction between dimethylsulfonium benzylide and pent-3-en-2-one. Our results show that the final outcome of the reaction with both these substrates would be decided by the interplay between kinetic and thermodynamic factors. It is found that the addition of a semi-stabilized ylide to conjugated carbonyl compounds prefers to proceed through a 1,4- (conjugate) pathway under thermodynamic conditions, which is in accordance with the available experimental reports. However, the formation of epoxides via a 1,2- (direct) addition pathway is computed to be equally competitive, which could be the favored pathway under kinetic conditions. Even though the lower barrier for the initial addition step is kinetically advantageous for the direct (or 1,2-) addition pathway, the higher energy of the betaine intermediates--as well as the reversibility of the accompanying elementary step--may disfavor product formation in this route. Thus, high diastereoselectivity in favor of 2,3-trans cyclopropanecarbaldehyde is predicted in the case of the dienal, using the most favored conjugate addition (1,4-addition) pathway. Along similar lines, ylide addition to the enone is identified to exhibit a preference toward conjugate addition over direct (1,2-) addition. The importance of transition state analysis in delineating the controlling factors towards product distribution and diastereoselectivity is established.

Origins of selectivity in Brønsted acid-promoted diazoalkane-azomethine reactions (the aza-Darzens aziridine synthesis)

The mechanism of the Brønsted acid-catalyzed aza-Darzens reaction is explored by charting the stereochemical outcome of the triflic acid-promoted conversion of trans-triazolines to cis-aziridines. These experiments are consistent with the intermediacy of an α-diazonium-β-amino ester intermediate.