Can one predict changes from S(N)1 to S(N)2 mechanisms?

Cyano-Hydrol green derivatives: Expanding the 9-cyanopyronin-based resonance Raman vibrational palette

9-cyanopyronin is a promising scaffold that exploits resonance Raman enhancement to enable sensitive, highly multiplexed biological imaging. Here, we developed cyano-Hydrol Green (CN-HG) derivatives as resonance Raman scaffolds to expand the color palette of 9-cyanopyronins. CN-HG derivatives exhibit sufficiently long wavelength absorption to produce strong resonance Raman enhancement for near-infrared (NIR) excitation, and their nitrile peaks are shifted to a lower frequency than those of 9-cyanopyronins. The fluorescence of CN-HG derivatives is strongly quenched due to the lack of the 10th atom, unlike pyronin derivatives, and this enabled us to detect spontaneous Raman spectra with high signal-to-noise ratios. CN-HG derivatives are powerful candidates for high performance vibrational imaging.

Regioselective Fluorohydrin Synthesis from Allylsilanes and Evidence for a Silicon-Fluorine Gauche Effect

Allylsilanes can be regioselectively transformed into the corresponding 3-silylfluorohydrin in good yield using a sequence of epoxidation followed by treatment with HF·Et3N with or without isolation of the intermediate epoxide. Various silicon-substitutions are tolerated, resulting in a range of 2-fluoro-3-silylpropan-1-ol products from this method. Whereas other fluorohydrin syntheses by epoxide opening using HF·Et3N generally require more forcing conditions (e.g., higher reaction temperature), opening of allylsilane-derived epoxides with this reagent occurs at room temperature. We attribute this rate acceleration along with the observed regioselectivity to a β-silyl effect that stabilizes a proposed cationic intermediate. The use of enantioenriched epoxides indicates that both SN1- and SN2-type mechanisms may be operable depending on substitution at silicon. Conformational analysis by NMR and theory along with a crystal structure obtained by X-ray diffraction points to a preference for silicon and fluorine to be proximal to one another in the products, perhaps favored due to electrostatic interactions.

Exploring borderline SN1-SN2 mechanisms: the role of explicit solvation protocols in the DFT investigation of isopropyl chloride

Nucleophilic substitution at saturated carbon is a crucial class of organic reactions, playing a pivotal role in various chemical transformations that yield valuable compounds for society. Despite the well-established SN1 and SN2 mechanisms, secondary substrates, particularly in solvolysis reactions, often exhibit a borderline pathway. A molecular-level understanding of these processes is fundamental for developing more efficient chemical transformations. Typically, quantum-chemical simulations of the solvent medium combine explicit and implicit solvation methods. The configuration of explicit molecules can be defined through top-down approaches, such as Monte Carlo (MC) calculations for generating initial configurations, and bottom-up methods that involve user-dependent protocols to add solvent molecules around the substrate. Herein, we investigated the borderline mechanism of the hydrolysis of a secondary substrate, isopropyl chloride (iPrCl), at DFT-M06-2X/aug-cc-pVDZ level, employing explicit and explicit + implicit protocols. Top-down and bottom-up approaches were employed to generate substrate-solvent complexes of varying number (n = 1, 3, 5, 7, 9, and 12) and configurations of H2O molecules. Our findings consistently reveal that regardless of the solvation approach, the hydrolysis of iPrCl follows a loose-SN2-like mechanism with nucleophilic solvent assistance. Increasing the water cluster around the substrate in most cases led to reaction barriers of ΔH‡ ≈ 21 kcal mol-1, with nine water molecules from MC configurations sufficient to describe the reaction. The More O'Ferrall-Jencks plot demonstrates an SN1-like character for all transition state structures, showing a clear merged profile. The fragmentation activation strain analyses indicate that energy barriers are predominantly controlled by solvent-substrate interactions, supported by the leaving group stabilization assessed through CHELPG atomic charges.

Unraveling the promoter effect and the roles of counterion exchange in glycosylation reaction

The stereoselectivity of glycosidic bond formation continues to pose a noteworthy hurdle in synthesizing carbohydrates, primarily due to the simultaneous occurrence of SN1 and SN2 processes during the glycosylation reaction. Here, we applied an in-depth analysis of the glycosylation mechanism by using low-temperature nuclear magnetic resonance and statistical approaches. A pathway driven by counterion exchanges and reaction byproducts was first discovered to outline the stereocontributions of intermediates. Moreover, the relative reactivity values, acceptor nucleophilic constants, and Hammett substituent constants (σ values) provided a general index to indicate the mechanistic pathways. These results could allow building block tailoring and reaction condition optimization in carbohydrate synthesis to be greatly facilitated and simplified.

Guidelines for O-Glycoside Formation from First Principles

With a view to reducing the notorious complexity and irreproducibility of glycosylation reactions, 12 guidelines for the choice of concentration, temperature, and counterions are adumbrated.

Nucleophilicity Prediction via Multivariate Linear Regression Analysis

The concept of nucleophilicity is at the basis of most transformations in chemistry. Understanding and predicting the relative reactivity of different nucleophiles is therefore of paramount importance. Mayr’s nucleophilicity scale likely represents the most complete collection of reactivity data, which currently includes over 1200 nucleophiles. Several attempts have been made to theoretically predict Mayr’s nucleophilicity parameters N based on calculation of molecular properties, but a general model accounting for different classes of nucleophiles could not be obtained so far. We herein show that multivariate linear regression analysis is a suitable tool for obtaining a simple model predicting N for virtually any class of nucleophiles in different solvents for a set of 341 data points. The key descriptors of the model were found to account for the proton affinity, solvation energies, and sterics.

Flow synthesis kinetics for lomustine, an anti-cancer active pharmaceutical ingredient

An original reaction mechanism and kinetic parameter estimation has been achieved for lomustine, an anti-cancer active pharmaceutical ingredient (API).

Predicting glycosylation stereoselectivity using machine learning

Predicting the stereochemical outcome of chemical reactions is challenging in mechanistically ambiguous transformations. The stereoselectivity of glycosylation reactions is influenced by at least eleven factors across four chemical participants and temperature. A random forest algorithm was trained using a highly reproducible, concise dataset to accurately predict the stereoselective outcome of glycosylations. The steric and electronic contributions of all chemical reagents and solvents were quantified by quantum mechanical calculations. The trained model accurately predicts stereoselectivities for unseen nucleophiles, electrophiles, acid catalyst, and solvents across a wide temperature range (overall root mean square error 6.8%). All predictions were validated experimentally on a standardized microreactor platform. The model helped to identify novel ways to control glycosylation stereoselectivity and accurately predicts previously unknown means of stereocontrol. By quantifying the degree of influence of each variable, we begin to gain a better general understanding of the transformation, for example that environmental factors influence the stereoselectivity of glycosylations more than the coupling partners in this area of chemical space.

Catalytic Room-Temperature C-N Coupling of Amides and Isocyanates by Using Mechanochemistry

A mechanochemical route is developed for room-temperature and solvent-free derivatization of different types of amides into carbamoyl isatins (up to 96 % conversion or yield), benzamides (up to 81 % yield), and imides (up to 92 % yield). In solution, this copper-catalyzed coupling either does not take place or requires high temperatures at which it may also be competing with alternative thermal reactivity, highlighting the beneficial role of mechanochemistry for this reaction. Such behavior resembles the previously investigated coupling with sulfonamide substrates, suggesting that this type of C-N coupling is an example of a mechanochemically favored reaction, for which mechanochemistry appears to be a favored environment over solution.

Transacylation in Ferrocenoyl-Purines. NMR and Computational Study of the Isomerization Mechanism

In the reaction of purines with ferrocenoyl chloride in dimethylformamide (DMF), a regioselective acylation occurred. The two products have been isolated and, according to detailed NMR analysis, identified as N7- and N9-ferrocenoylated isomers. In a more polar solvent, for example, in dimethylsulfoxide (DMSO), the two isomers interconvert to each other. The N7/N9 isomerization was followed by ¹H NMR spectroscopy, until dynamic equilibrium was reached. Both kinetics and thermodynamics of the transacylation process are governed by a C6-substituent on the purine ring (R = NH₂, Me, NHBz, OBz). The observed rate constant for the N7/N9-isomerization in the adenine system (R = NH₂) is k_obs = 0.3668 h^-1, whereas the corresponding process in the C6-benzyloxypurine is 56 times slower. By use of density functional theory calculations and molecular dynamics simulations, several reaction pathways were considered and explored. Only the reaction mechanism involving DMSO as a nucleophilic reactant is in harmony with the experimental kinetic data. The calculated barrier (ΔG^⧧ = 107.9 kJ/mol; at the M06L/6-311+G(d,p)/SDD level of theory) for this S_N2-like reaction in the adenine system agrees well with the experimental value of 102.7 kJ/mol. No isomerization was detected in other organic solvents, for example, acetonitrile, N,N-dimethylformamide, or acetone, which indicated the exceptional nucleophilicity of DMSO. Our results raise a warning when treating or dissolving acylated purines in DMSO as they are prone to isomerization. We observed that the N7/N9-group transfer was specific not only for the organometallic moiety only, but for other acyl groups in purines as well. The relevance of this isomerization may be expected for a series of nucleobases and heterocyclic systems in general.

Intramolecular substitutions of secondary and tertiary alcohols with chirality transfer by an iron(III) catalyst

Optically pure alcohols are abundant in nature and attractive as feedstock for organic synthesis but challenging for further transformation using atom efficient and sustainable methodologies, particularly when there is a desire to conserve the chirality. Usually, substitution of the OH group of stereogenic alcohols with conservation of chirality requires derivatization as part of a complex, stoichiometric procedure. We herein demonstrate that a simple, inexpensive, and environmentally benign iron(III) catalyst promotes the direct intramolecular substitution of enantiomerically enriched secondary and tertiary alcohols with O-, N-, and S-centered nucleophiles to generate valuable 5-membered, 6-membered and aryl-fused 6-membered heterocyclic compounds with chirality transfer and water as the only byproduct. The power of the methodology is demonstrated in the total synthesis of (+)-lentiginosine from D-glucose where iron-catalysis is used in a key step. Adoption of this methodology will contribute towards the transition to sustainable and bio-based processes in the pharmaceutical and agrochemical industries.

The direct substitution of the OH group of stereogenic alcohols are reported rarely in literature. Here, the authors demonstrate direct substitution of both secondary and tertiary alcohols with chirality transfer leading to enantioenriched 5-membered, 6-membered and aryl-fused 6-membered heterocyclic compounds.

Stable Benzylic (1-Ethynylcyclohexanyl)carbonates Protect Hydroxyl Moieties by the Synergistic Action of [Au]/[Ag] Catalytic System

Chemical syntheses of oligosaccharides and glycosides call utilization of many protecting groups that can be installed or deprotected without affecting other functional groups present. Benzyl ethers are routinely used in the synthesis of glycans as they can be subjected to hydrogenolysis under neutral conditions. However, installation of benzyl ethers is often carried out under strong basic conditions using benzyl halides. Many a times, strongly basic conditions will be detrimental for some of the other sensitive functionalities (e.g., esters). Later introduced reagents such as benzyl trichloroacetimidate and BnOTf are not shelf-stable, and hence, a new method is highly desirable. Taking a cue from the [Au]/[Ag]-catalyzed glycosidations, we have identified a method that enables protection of hydroxyl groups as benzyl, p-methoxybenzyl, or naphthylenemethyl ethers using easily accessible and stable carbonate reagent. A number of saccharide-derived alcohols were subjected to the benzylation successfully using a catalytic amount of gold phosphite and silver triflate. Furthermore, the protocol is suitable for even protecting menthol, cholesterol, serine, disaccharide OH, and furanosyl-derived alcohol easily. The often-utilized olefins and benzoates, as well as benzylidene-, silyl-, Troc-, and Fmoc-protecting groups do not get affected during the newly identified protocol. Regioselective protection and one-pot installation of benzyl and p-methoxybenzyl ethers are demonstrated.

Nonclassical Mechanism in the Cyclodehydration of Diols Catalyzed by a Bifunctional Iridium Complex

1,4- and 1,5-diols undergo cyclodehydration upon treatment with cationic N-heterocyclic carbene (NHC)-IrIII complexes to give tetrahydrofurans and tetrahydropyrans, respectively. The mechanism was investigated, and a metal-hydride-driven pathway was proposed for all substrates, except for very electron-rich ones. This contrasts with the well-established classical pathways that involve nucleophilic substitution.

The Experimental Evidence in Support of Glycosylation Mechanisms at the SN1-SN2 Interface

A critical review of the state-of-the-art evidence in support of the mechanisms of glycosylation reactions is provided. Factors affecting the stability of putative oxocarbenium ions as intermediates at the SN1 end of the mechanistic continuum are first surveyed before the evidence, spectroscopic and indirect, for the existence of such species on the time scale of glycosylation reactions is presented. Current models for diastereoselectivity in nucleophilic attack on oxocarbenium ions are then described. Evidence in support of the intermediacy of activated covalent glycosyl donors is reviewed, before the influences of the structure of the nucleophile, of the solvent, of temperature, and of donor-acceptor hydrogen bonding on the mechanism of glycosylation reactions are surveyed. Studies on the kinetics of glycosylation reactions and the use of kinetic isotope effects for the determination of transition-state structure are presented, before computational models are finally surveyed. The review concludes with a critical appraisal of the state of the art.

Nucleophilic Substitution (SN 2): Dependence on Nucleophile, Leaving Group, Central Atom, Substituents, and Solvent

The reaction potential energy surface (PES), and thus the mechanism of bimolecular nucleophilic substitution (SN 2), depends profoundly on the nature of the nucleophile and leaving group, but also on the central, electrophilic atom, its substituents, as well as on the medium in which the reaction takes place. Here, we provide an overview of recent studies and demonstrate how changes in any one of the aforementioned factors affect the SN 2 mechanism. One of the most striking effects is the transition from a double-well to a single-well PES when the central atom is changed from a second-period (e. g. carbon) to a higher-period element (e.g, silicon, germanium). Variations in nucleophilicity, leaving group ability, and bulky substituents around a second-row element central atom can then be exploited to change the single-well PES back into a double-well. Reversely, these variations can also be used to produce a single-well PES for second-period elements, for example, a stable pentavalent carbon species.

Electrogenerated Cationic Reactive Intermediates: The Pool Method and Further Advances

Electrochemistry serves as a powerful method for generating reactive intermediates, such as organic cations. In general, there are two ways to use reactive intermediates for chemical reactions: (1) generation in the presence of a reaction partner and (2) generation in the absence of a reaction partner with accumulation in solution as a "pool" followed by reaction with a subsequently added reaction partner. The former approach is more popular because reactive intermediates are usually short-lived transient species, but the latter method is more flexible and versatile. This review focuses on the latter approach and provides a concise overview of the current methods for the generation and accumulation of cationic reactive intermediates as a pool using modern techniques of electrochemistry and their reactions with subsequently added nucleophilic reaction partners.

Discovery, Optimization, and Characterization of Novel Chlorcyclizine Derivatives for the Treatment of Hepatitis C Virus Infection

Recently, we reported that chlorcyclizine (CCZ, Rac-2), an over-the-counter antihistamine piperazine drug, possesses in vitro and in vivo activity against hepatitis C virus. Here, we describe structure-activity relationship (SAR) efforts that resulted in the optimization of novel chlorcyclizine derivatives as anti-HCV agents. Several compounds exhibited EC50 values below 10 nM against HCV infection, cytotoxicity selectivity indices above 2000, and showed improved in vivo pharmacokinetic properties. The optimized molecules can serve as lead preclinical candidates for the treatment of hepatitis C virus infection and as probes to study hepatitis C virus pathogenesis and host-virus interaction.

Spiropyran as a reusable chemosensor for selective colorimetric detection of aromatic thiols

Design of optical molecular probes for selective detection of aromatic thiols has attracted much attention. Although several types of probes have been proposed, all of them exhibit colorimetric or fluorometric response via irreversible reaction with aromatic thiols and cannot be reused. Here we report that a spiropyran dye is the first example of a reusable chemosensor for aromatic thiols. A colorless spiropyran dye () dissolved in aqueous media containing aromatic thiols is selectively isomerized to the colored merocyanine form in the dark. In contrast, visible light irradiation of the merocyanine form promotes successful reversion to the colorless spirocyclic form. Kinetic absorption analysis and ab initio calculations of the transition states revealed that this colorimetric response in the dark is ascribed to the decrease in activation energy for isomerization via the nucleophilic interaction between the aromatic thiol and the olefinic carbon of the dye.

Switching the reaction pathways of electrochemically generated β-haloalkoxysulfonium ions - synthesis of halohydrins and epoxides

β-Haloalkoxysulfonium ions generated by the reaction of electrogenerated Br(+) and I(+) ions stabilized by dimethyl sulfoxide (DMSO) reacted with sodium hydroxide and sodium methoxide to give the corresponding halohydrins and epoxides, respectively, whereas the treatment with triethylamine gave α-halocarbonyl compounds.

Investigation of diastereoselective acyclic α-alkoxydithioacetal substitutions involving thiacarbenium intermediates

Reported herein is an experimental and theoretical study that elucidates why silylated nucleobase additions to acyclic α-alkoxythiacarbenium intermediates proceed with high 1,2-syn stereocontrol (anti-Felkin-Anh), which is opposite to what would be expected with corresponding activated aldehydes. The acyclic thioaminals formed undergo intramolecular cyclizations to provide nucleoside analogues with anticancer and antiviral properties. The factors influencing the selectivity of the substitution reaction have been examined thoroughly. Halothioether species initially form, ionize in the presence (low dielectric media) or absence (higher dielectric media) of the nucleophile, and react through SN2-like transition structures (TS A and D), where the α-alkoxy group is gauche to the thioether moiety. An important, and perhaps counterintuitive, observation in this work was that calculations done in the gas phase or low dielectric media (toluene) are essential to locate the product- and rate-determining transition structures (C-N bond formation) that allow the most reasonable prediction of selectivity and isotope effects for more polar solvents (THF, MeCN). The ΔΔG(⧧) (G(TSA-TSD)) obtained in silico are consistent with the preferential formation of 1,2-syn product and with the trends of stereocontrol displayed by 2,3-anti and 2,3-syn α,β-bis-alkoxydithioacetals.

A computational study of acid catalyzed aerosol reactions of atmospherically relevant epoxides

Epoxides are important intermediates of atmospheric isoprene oxidation. Their subsequent reactions in the particle phase lead to the production of organic compounds detected in ambient aerosols. We apply density functional theory to determine the important kinetic factors that drive epoxide reactions in the particle phase. Specifically, the importance of acid catalysis and solvent polarity are investigated using a variety of epoxides and nucleophiles. The condensed phase is modeled using molecular clusters immersed in a dielectric continuum and a majority of the calculations are performed with the M062x density functional and the 6-311++G** basis set. Calculations of acid catalyzed epoxide hydrolysis transition states for simple primary, secondary and tertiary epoxides are consistent with an A-2 mechanism where the nucleophile (water) interacts with an epoxide carbon in the transition state. By applying transition state theory to this mechanism, the overall rate constants of epoxide reactions such as hydrolysis, organosulfate formation, organonitrate formation and oligomerization are determined. The calculations indicate that the acid catalyzed hydrolysis rate constant of 2-methyl-2,3-epoxybutane-1,4-diol (β-IEPOX--an isoprene epoxide produced under low NOx conditions) is approximately 30 times greater than 2-methyl-2,3-epoxypropanoic acid (MAE--methacrylic acid epoxide derived from isoprene and produced at high NOx concentrations). Furthermore, acid catalyzed organosulfate formation and epoxide oligomerization reactions are competitive and appear to be kinetically favorable over the hydrolysis of IEPOX.

Halogen and chalcogen cation pools stabilized by DMSO. Versatile reagents for alkene difunctionalization

Halogen and chalcogen cations (X(+) = Br(+), I(+), ArS(+), and ArSe(+)) were generated by low-temperature electrochemical oxidation in the presence of dimethyl sulfoxide (DMSO) and were accumulated in the solution. DFT calculations indicated that DMSO stabilizes these cations by coordination. The complexes of I(+) with one and two DMSO molecules were observed by cold-spray-ionization MS analyses. The stability of the resulting cation pools of X(+) increased in the order of Br(+) < I(+) < ArS(+) < ArSe(+), which could be explained in terms of the electronegativity of X. The cation pools served as versatile reagents for organic synthesis; the reactions with alkenes gave β-X-substituted alkoxysulfonium ions, which were converted to the corresponding carbonyl compounds by the treatment with triethylamine, whereas the treatment with methanol gave the corresponding alcohols. The reactions with aminoalkenes and 1,6-dienes gave the cyclized products.

Cation clock permits distinction between the mechanisms of α- and β-O- and β-C-glycosylation in the mannopyranose series: evidence for the existence of a mannopyranosyl oxocarbenium ion

The use of a cationic cyclization reaction as a probe of the glycosylation mechanism has been developed and applied to the 4,6-O-benzylidene-protected mannopyranoside system. Cyclization results in the formation of both cis- and trans-fused tricyclic systems, invoking an intermediate glycosyl oxocarbenium ion reacting through a boat conformation. Competition reactions with isopropanol and trimethyl(methallyl)silane are interpreted as indicating that β-O-mannosylation proceeds via an associative S(N)2-like mechanism, whereas α-O-mannosylation and β-C-mannosylation are dissociative and S(N)1-like. Relative rate constants for reactions going via a common intermediate can be estimated.