Anomeric effect, hyperconjugation and electrostatics: lessons from complexity in a classic stereoelectronic phenomenon

Stereoselective Entry into α,α'-C-Oxepane Scaffolds through a Chalcogen Bonding Catalyzed Strain-Release C-Septanosylation Strategy

The utility of unconventional noncovalent interactions (NCIs) such as chalcogen bonding has lately emerged as a robust platform to access synthetically difficult glycosides stereoselectively. Herein, we disclose the versatility of a phosphonochalcogenide (PCH) catalyst to facilitate access into the challenging, but biologically interesting 7-membered ring α,α'-C-disubstituted oxepane core through an α-selective strain-release C-glycosylation. Methodically, this strategy represents a switch from more common but entropically less desired macrocyclizations to a thermodynamically favored ring-expansion approach. In light of the general lack of stereoselective methods to access C-septanosides, a remarkable palette of silyl-based nucleophiles can be reliably employed in our method. This include a broad variety of useful synthons, such as easily available silyl-allyl, silyl-enol ether, silyl-ketene acetal, vinylogous silyl-ketene acetal, silyl-alkyne and silylazide reagents. Mechanistic investigations suggest that a mechanistic shift towards an intramolecular aglycone transposition involving a pentacoordinate silicon intermediate is likely responsible in steering the stereoselectivity.

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 strategy for the controllable generation of organic superbases from benchtop-stable salts

Organic superbases are a distinct class of strong base that enable numerous modern reaction applications. Despite their great synthetic potential, widespread use and study of superbases are limited by their air sensitivity and difficult preparation. To address this, we report air-stable carboxylate salts of BTPP and P2-t-Bu phosphazene superbases that, when added to solution with an epoxide, spontaneously generate freebase. These systems function as effective precatalysts and stoichiometric prereagents for superbase-promoted addition, substitution and polymerization reactions. In addition to improving the synthesis, shelf stability, handling and recycling of phosphazenes, this approach enables precise regulation of the rate of base generation in situ. The activation strategy effectively mimics manual slow addition techniques, allowing for control over a reaction's rate or induction period and improvement of reactions that require strong base but are also sensitive to its presence, such as Pd-catalyzed coupling reactions.

A True Reverse Anomeric Effect Does Exist After All: A Hydrogen Bonding Stereocontrolling Effect in 2-Iminoaldoses

The reverse anomeric effect is usually associated with the equatorial preference of nitrogen substituents at the anomeric center. Once postulated as another anomeric effect with explanations ranging from electrostatic interactions to delocalization effects, it is now firmly considered to be essentially steric in nature. Through an extensive research on aryl imines from 2-amino-2-deoxyaldoses, spanning nearly two decades, we realized that such substances often show an anomalous anomeric behavior that cannot easily be rationalized on the basis of purely steric grounds. The apparent preference, or stabilization, of the β-anomer takes place to an extent that not only neutralizes but also overcomes the normal anomeric effect. Calculations indicate that there is no stereoelectronic effect opposing the anomeric effect, resulting from the repulsion between electron lone pairs on the imine nitrogen and the endocyclic oxygen. Such data and compelling structural evidence unravel why the exoanomeric effect is largely inhibited. We are now confident, as witnessed by 2-iminoaldoses, that elimination of the exo-anomeric effect in the α-anomer is due to the formation of an intramolecular hydrogen bond between the anomeric hydroxyl and the iminic nitrogen, thereby accounting for a true electronic effect. In addition, discrete solvation may help justify the observed preference for the β-anomer.

Hydroxyl Group as the 'Bridge' to Enhance the Single-Molecule Conductance by Hyperconjugation

For designing single-molecule devices that have both conjugation systems and structural flexibility, a hyperconjugated molecule with a σ-π bond interaction is considered an ideal candidate. In the investigation of conductance at the single-molecule level, since few hyperconjugation systems have been involved, the strategy of building hyperconjugation systems and the mechanism of electron transport within this system remain unexplored. Based on the skipped-conjugated structure, we present a rational approach to construct a hyperconjugation molecule using a hydroxyl group, which serves as a bridge to interact with the conjugated fragments. The measurement of single-molecule conductance reveals a two-fold conductance enhancement of the hyperconjugation system having the 'bridging' hydroxyl group compared to hydroxyl-free derivatives. Theoretical studies demonstrate that the hydroxyl group in the hyperconjugation system connects the LUMO of the two conjugated fragments and opens a through-space channel for electron transport to enhance the conductance.

Design, synthesis and application of a magnetic H-bond catalyst in the preparation of new nicotinonitriles via cooperative vinylogous anomeric-based oxidation

Herein, we designed and synthesized a new H-bond magnetic catalyst with 2-tosyl-N-(3-(triethoxysilyl)propyl)hydrazine-1-carboxamide as a sensitive H-bond donor/acceptor. We created an organic structure with a urea moiety on the magnetic nanoparticles, which can function as a hydrogen bond catalyst. Hydrogen bond catalysts serve as multi-donor/-acceptor sites. Additionally, we utilized magnetic nanoparticles in the production of the target catalyst, giving it the ability to be recycled and easily separated from the reaction medium with an external magnet. We evaluated the catalytic application of Fe3O4@SiO2@tosyl-carboxamide as a new magnetic H-bond catalyst in the synthesis of new nicotinonitrile compounds through a multicomponent reaction under solvent-free and green conditions with high yields (50-73%). We confirmed the structure of Fe3O4@SiO2@tosyl-carboxamide using various techniques. In addition, the structures of the desired nicotinonitriles were confirmed using melting point, 1H-NMR, 13C-NMR and HR-mass spectrometry analysis. The final step of the reaction mechanism was preceded via cooperative vinylogous anomeric-based oxidation (CVABO).

Systematic Study of Different Types of Interactions in α-, β- and γ-Cyclodextrin: Quantum Chemical Investigation

In this work, comprehensive ab initio quantum chemical calculations using the DFT level of theory were performed to characterize the stabilization interactions (H-bonding and hyperconjugation effects) of two stable symmetrical conformations of α-, β-, and γ-cyclodextrins (CDs). For this purpose, we analyzed the electron density using "Atom in molecules" (AIM), "Natural Bond Orbital" (NBO), and energy decomposition method (CECA) in 3D and in Hilbert space. We also calculated the H-bond lengths and OH vibrational frequencies. In every investigated CD, the quantum chemical descriptors characterizing the strength of the interactions between the H-bonds of the primary OH (or hydroxymethyl) and secondary OH groups are examined by comparing the same quantity calculated for ethylene glycol, α-d-glucose (α-d-Glcp) and a water cluster as reference systems. By using these external standards, we can characterize more quantitatively the properties of these bonds (e.g., strength). We have demonstrated that bond critical points (BCP) of intra-unit H-bonds are absent in cyclodextrins, similar to α-d-Glcp and ethylene glycol. In contrast, the CECA analysis showed the existence of an exchange (bond-like) interaction between the interacting O…H atoms. Consequently, the exchange interaction refers to a chemical bond, namely the H-bond between two atoms, unlike BCP, which is not suitable for its detection.

Interrupted Dance of Five Heteroatoms: Reinventing Ozonolysis to Make Geminal Alkoxyhydroperoxides from C═N Bonds

Four heteroatoms dance in the cascade of four pericyclic reactions initiated by ozonolysis of C═N bonds. Switching from imines to semicarbazones introduces the fifth heteroatom that slows this dance, delays reaching the thermodynamically favorable escape path, and allows efficient interception of carbonyl oxides (Criegee intermediates, CIs) by an external nucleophile. The new three-component reaction of alcohols, ozone, and oximes/semicarbazones greatly facilitates synthetic access to monoperoxyacetals (alkoxyhydroperoxides).

Conformational Analysis Explores the Role of Electrostatic Nonclassical CF···HC Hydrogen Bonding Interactions in Selectively Halogenated Cyclohexanes

The conformational equilibria of selectively halogenated cyclohexanes are explored both experimentally (VT-NMR) for 1,1,4,-trifluorocyclohexane 7 and by computational analysis (M06-2X/aug-cc-pVTZ level), with the latter approach extending to a wider range of more highly fluorinated cyclohexanes. Perhaps unexpectedly, 7ax is preferred over the 7eq conformation by ΔG = 1.06 kcal mol-1, contradicting the accepted norm for substituents on cyclohexanes. The axial preference is stronger again in 1,1,3,3,4,5,5,-heptafluorocyclohexane 9 (ΔG = 2.73 kcal mol-1) as the CF2 groups further polarize the isolated CH2 hydrogens. Theoretical decomposition of electrostatic and hyperconjugative effects by natural bond orbital analysis indicated that nonclassical hydrogen bonding (NCHB) between the C-4 fluorine and the diaxial hydrogens at C-2 and C-6 in cyclohexane 7 and 9 largely accounts for the observed bias. The study extended to changing fluorine (F) for chlorine (Cl) and bromine (Br) at the pseudoanomeric position in the cyclohexanes. Although these halogens do not become involved in NCHBs, they polarize the geminal -CHX- hydrogen at the pseudoanomeric position to a greater extent than fluorine, and consequent electrostatic interactions influence conformer stabilities.

Formaldehyde-Mediated Hydride Liberation of Alkylamines for Intermolecular Reactions in Hexafluoroisopropanol

The ability of alkylamines to spontaneously liberate hydride ions is typically restrained, except under specific intramolecular reaction settings. Herein, we demonstrate that this reactivity can be unlocked through simple treatment with formaldehyde in hexafluoroisopropanol (HFIP) solvent, thereby enabling various intermolecular hydride transfer reactions of alkylamines under mild conditions. Besides transformations of small molecules, these reactions enable unique late-stage modification of complex peptides. Mechanistic investigations uncover that the key to these intermolecular hydride transfer processes lies in the accommodating conformation of solvent-mediated macrocyclic transition states, where the aggregates of HFIP molecules act as dexterous proton shuttles. Importantly, negative hyperconjugation between the lone electron pair of nitrogen and the antibonding orbital of amine's α C-H bond plays a critical role in the C-H activation, promoting its hydride liberation.

Exploiting π and Chalcogen Interactions for the β-Selective Glycosylation of Indoles through Glycal Conformational Distortion

Harnessing unconventional noncovalent interactions (NCIs) is emerging as a formidable synthetic approach in difficult-to-access glycosidic chemical space. C-Glycosylation, in particular, has gained a flurry of recent attention. However, most reported methods are restricted to the relatively facile access to α-C-glycosides. Herein, we disclose a β-stereoselective glycosylation of indoles by employing a phosphonoselenide catalyst. The robustness of this protocol is exemplified by its amenability for reaction at both the indolyl C- and N- reactivity sites. In contrast to previous reports, in which the chalcogens were solely involved in Lewis acidic activation, our mechanistic investigation unraveled that the often neglected flanking aromatic substituents of phosphonoselenides can substantially contribute to catalysis by engaging in π-interactions. Computations and NMR spectroscopy indicated that the chalcogenic and aromatic components of the catalyst can be collectively exploited to foster conformational distortion of the glycal away from the usual half-chair to the boat conformation, which liberates the convex β-face for nucleophilic attack.

Exploring Ring Conformation in Uronate Monosaccharides: Insights from Ab Initio Calculations and Classical Molecular Dynamics Simulations

The study focuses on the conformational properties of biologically relevant monosaccharides belonging to the group of uronates: α-l-iduronate, O2-sulfated-α-l-iduronate, and O2-sulfated-α-l-guluronate, either unfunctionalized or O1-methylated. We applied the previously proposed two-step methodology, combining classical MD simulations and subsequent ab initio (QM) calculations, performed on a rationally subsampled set of molecular configurations. We found that, regardless of the number of molecular configurations considered, the level of theory, and the weighting scheme applied, none of the QM approaches is capable of predicting the correct conformational equilibrium of sulfated iduronates as long as the tight counterion binding is not considered. Multicenter, ring-shape-specific binding of either Na+ or Ca2+ ions drastically shifts the conformational equilibrium of the pyranose ring in sulfated iduronates toward 1C4 but does not significantly affect the conformation of non-sulfated compounds. A similar shift is observed upon the protonation of carboxyl groups in all iduronates. In addition, we report a set of average J-coupling constant values related to vicinal protons bound to the pyranose ring of iduronates and corresponding to each of the three main groups of ring conformers, i.e., 4C1, B/S (boat/skew boat), and 1C4. In combination with the conformational energies or with the experimental data, these values allowed the relative proportions of the ring conformers to be estimated and the Karplus-type equations linking the 3JHH-coupling constants to the torsion angles within the pyranose ring to be refined.

Synthetic Advantages of Defluorinative C-F Bond Functionalization

Much progress has been made in the development of methods to both create compounds that contain C-F bonds and to functionalize C-F bonds. As such, C-F bonds are becoming common and versatile synthetic functional handles. This review summarizes the advantages of defluorinative functionalization reactions for small molecule synthesis. The coverage is organized by the type of carbon framework the fluorine is attached to for mono- and polyfluorinated motifs. The main challenges, opportunities and advances of defluorinative functionalization are discussed for each class of organofluorine. Most of the text focuses on case studies that illustrate how defluorofunctionalization can improve routes to synthetic targets or how the properties of C-F bonds enable unique mechanisms and reactions. The broader goal is to showcase the opportunities for incorporating and exploiting C-F bonds in the design of synthetic routes, improvement of specific reactions and advent of new methods.

Advances in glycoside and oligosaccharide synthesis

The structural complexity of glycans poses a serious challenge in the chemical synthesis of glycosides, oligosaccharides and glycoconjugates. Glycan complexity, determined by composition, connectivity, and configuration far exceeds what nature achieves with nucleic acids and proteins. Consequently, glycoside synthesis ranks among the most complex tasks in organic synthesis, despite involving only a simple type of bond-forming reaction. Here, we introduce the fundamental principles of glycoside bond formation and summarize recent advances in glycoside bond formation and oligosaccharide synthesis.

Design of Cationic Lipids with Acetal Linkers: Conformational Preferences, Hydrolytic Stability, and High Drug-Loading Abilities

Lipids are key constituents of numerous biomedical drug delivery technologies. Here, we present the design, synthesis and biophysical characterizations of a library of cationic lipids containing an acetal residue in their linker region. These cationic acetal lipids (CALs) were conveniently prepared through a trans-acetalization protocol from commercially available precursors. NMR studies highlighted the conformational rigidity at the acetal residue and the high hydrolytic stability of these CALs. Fluorescence anisotropy studies revealed that the CAL with a pyridinium headgroup (CAL1) formed highly cohesive vesicular aggregates in water. These structural and self-assembly features of the CAL1 allowed up to 196 % w/w loading of curcumin (Cur) as a representative hydrophobic drug. A reconstitutable formulation of Cur was obtained as a result, which could deliver the drug inside mammalian cells with very high efficiency. The hemocompatibility and cytocompatibility of CAL1 was significantly enhanced by creating a coating of polydopamine (PDA) onto its vesicular assemblies to produce hybrid lipid-polymer nanocapsules. This work demonstrates rapid access to the useful synthetic lipid formulations with high potential in drug and gene delivery applications.

Electron-Poor Butenolides: The Missing Link between Acrylates and Maleic Anhydride in Radical Polymerization

Butenolides are a class of 5-membered lactones that hold great potential as bio-based monomers to replace oil-derived acrylates, of which they are cyclic analogues. Despite this structural resemblance, the reactivity of the unsaturated ester moiety of electron-poor butenolides leans toward that of maleic anhydride, another essential monomer that does not homopolymerize but copolymerizes in a highly alternating fashion with polarized electron-rich comonomers. By studying the reactivity of 5-methoxy and 5-acyloxy butenolides through a combination of kinetics and density functional theory (DFT) experiments, we explain why electron-poor butenolides constitute a missing link between acrylates and maleic anhydride in radical polymerization.

Stereoselective Synthesis of Z-Styryl Sulfides from Nucleophilic Addition of Arylacetylenes and Benzyl Thiols

The stereoselective synthesis of Z-anti-Markovnikov styryl sulfides via an anionic thiolate-alkyne addition reaction was achieved when the terminal alkynes and benzyl mercaptans were reacted using tBuOLi (0.5 equiv) in EtOH under ambient conditions. Exclusive stereoselectivity (ca. 100%) was achieved by stereoelectronic control via anti-periplanar and anti-Markovnikov addition of benzylthiolates to phenylacetylenes. Solvolysis of lithium thiolate ion pairs in ethanol significantly suppresses the competing formation of the E-isomer. A remarkable enhancement of the Z-selectivity under a longer reaction time was observed.

Synthesis of new hybrid pyridines catalyzed by Fe3O4@SiO2@urea-riched ligand/Ch-Cl

Herein, a new heterogeneous catalytic system through modification of urea functionalized magnetic nanoparticles with choline chloride [Fe₃O₄@SiO₂@urea-riched ligand/Ch-Cl] was designed and synthesized. Then, the synthesized Fe₃O₄@SiO₂@urea-riched ligand/Ch-Cl was characterized by using FT-IR spectroscopy, FESEM, TEM, EDS-Mapping, TGA/DTG and VSM techniques. After that, the catalytic usage of Fe₃O₄@SiO₂@urea-riched ligand/Ch-Cl was investigated for the synthesis of hybrid pyridines with sulfonate and/or indole moieties. Delightfully, the outcome was satisfactory and the applied strategy represents several advantages such as short reaction times, convenience of operation and relatively good yields of obtained products. Moreover, the catalytic behavior of several formal homogeneous DESs was investigated for the synthesis of target product. In addition, a cooperative vinylogous anomeric-based oxidation pathway was suggested as rational mechanism for the synthesis of new hybrid pyridines.

Application of Zr-MOFs based copper complex in synthesis of pyrazolo[3, 4-b]pyridine-5-carbonitriles via anomeric-based oxidation

In this research article, Zr-MOFs based copper complex as a novel heterogeneous and porous catalyst was designed and prepared. The structure of catalyst has verified by various techniques such as FT-IR, XRD, SEM, N₂ adsorption-desorption isotherms (BET), EDS, SEM-elemental mapping, TG and DTG analysis. UiO-66-NH₂/TCT/2-amino-Py@Cu(OAc)₂ was used as an efficient catalyst in the synthesis of pyrazolo[3,4-b]pyridine-5-carbonitrile derivatives. The aromatization of titled molecules is performed via a cooperative vinylogous anomeric-based oxidation both under air and inert atmospheres. The unique properties of the presented method are short reaction time, high yield, reusability of catalyst, synthesis of desired product under mild and green condition.

Application of Metal-Organic Frameworks with Sulfonic Acid Tags in the Synthesis of Pyrazolo[3,4-b]pyridines via a Cooperative Vinylogous Anomeric-Based Oxidation

Herein, we report the design and synthesis of Co-MOF-71/imidazole/SO₃H as a novel porous catalyst with sulfonic acid tags. The structure and morphology of the catalyst were investigated using various techniques such as Fourier transform-infrared spectroscopy (FT-IR), X-ray diffraction, scanning electron microscopy (SEM), SEM elemental mapping, energy-dispersive X-ray spectroscopy, Barret-Joyner-Halenda, and N₂ adsorption-desorption isotherms. Co-MOF-71/imidazole/SO₃H was studied in the preparation of novel pyrazolo[3,4-b]pyridines under mild and green conditions via a cooperative vinylogous anomeric-based oxidation. A wide range of mono and bis pyrazolo[3,4-b]pyridines were synthesized with good to excellent yields (65-82%). A hot filtration test for the heterogeneous nature of the catalyst indicated the high stability of the prepared catalyst. The recyclability of Co-MOF-71/imidazole/SO₃H is another advantage of the present methodology. The structures of the final products were confirmed using FT-IR, ¹H-NMR, and ¹³C-NMR spectroscopic techniques.

Application of Nanomagnetic Metal-Organic Frameworks in the Green Synthesis of Nicotinonitriles via Cooperative Vinylogous Anomeric-Based Oxidation

In the current study, we synthesized a new nanomagnetic metal-organic framework Fe₃O₄@MIL-53(Al)-N(CH₂PO₃)₂ and characterized it using various techniques. This nanomagnetic metal-organic framework was used for the synthesis of a wide range of nicotinonitrile derivatives as suitable drug candidates by a four-component reaction of 3-oxo-3-phenylpropanenitrile or 3-(4-chlorophenyl)-3-oxopropanenitrile, ammonium acetate (NH₄OAc), acetophenone derivatives, and various aldehydes including those bearing electron-donating, electron-withdrawing, and halogen groups, which afforded desired products (27 samples) via a cooperative vinylogous anomeric-based oxidation (CVABO) mechanism under solvent-free conditions in excellent yields (68-90%) and short reaction times (40-60 min). Increasing the surface-to-volume ratio, easy separation of the catalyst using an external magnet, and high chemical and temperature stability are the advantages of the described nanomagnetic metal-organic frameworks.

Conformational Distributions of Phenyl β-D-Glucopyranoside and Gastrodin in Solution by Vibrational Optical Activity and Theoretical Calculations

The conformational landscapes of two highly flexible monosaccharide derivatives, namely phenyl β-D-glucopyranoside (ph-β-glu) and 4-(hydroxymethyl)phenyl β-D-glucopyranoside, also commonly known as gastrodin, were explored using a combined experimental and theoretical approach. For the infrared, Raman, and the associated vibrational optical activity (VOA), i.e., vibrational circular dichroism and Raman optical activity, experiments of these two compounds in DMSO and in water were carried out. Extensive and systematic conformational searches were performed using a recently developed conformational searching tool called CREST (conformer-rotamer ensemble sampling tool) in the two solvents. Fourteen and twenty-four low-energy conformers were identified at the DFT level for ph-β-glu and gastrodin, respectively. The spectral simulations of individual conformers were done at the B3LYP-D3BJ/def2-TZVPD level with the polarizable continuum model of the solvents. The VOA spectral features exhibit much higher specificity to conformational differences than their parent infrared and Raman. The excellent agreements achieved between the experimental and simulated VOA spectra allow for the extraction of experimental conformational distributions of these two carbohydrates in solution directly. The experimental percentage abundances based on the hydroxymethyl (at the pyranose ring) conformations G+, G-, and T for ph-β-glu were obtained to be 15%, 75%, and 10% in DMSO and 53%, 40%, and 7% in water, respectively, in comparison to the previously reported gas phase values of 68%, 25%, and 7%, highlighting the important role of solvents in conformational preferences. The corresponding experimental distributions for gastrodin are 56%, 22%, and 22% in DMSO and 70%, 21%, and 9% in water.

Mechanistic Understanding and Reactivity Analyses for the Photochemistry of Disubstituted Tetrazoles

The photolysis of tetrazoles has undergone extensive research. However, there are still some problems to be solved in terms of mechanistic understanding and reactivity analyses, which leaves room for theoretical calculations. Herein, multiconfiguration perturbation theory at the CASPT2//CASSCF level was employed to account for electron correction effects involved in the photolysis of four disubstituted tetrazoles. Based on calculations of vertical excitation properties and evaluations of intersystem crossing (ISC) efficiencies in the Frank-Condon region, the combination of space and electronic effects is found in maximum-absorption excitation. Two types of ISC (¹ππ* → ³nπ*, ¹ππ* → ³ππ*) are determined in disubstituted tetrazoles, and the obtained rates follow the El-Sayed rule. Through mapping three representative types of minimum energy profiles for the photolysis of 1,5-, and 2,5-disubstituted tetrazoles, a conclusion can be drawn that the photolysis of tetrazoles exhibits reactivity characteristic of bond-breaking selectivity. Kinetic evaluations show that the photogeneration of singlet imidoylnitrene operates predominately over that in the triplet state, which can be confirmed by a double-well model in the triplet potential energy surface of 1,5-disubstituted tetrazole. Similar mechanistic explorations and reactivity analyses were also applied to the photolysis of 2,5-disubstituted tetrazole to unveil fragmentation patterns of nitrile imine generation. All computational efforts allow us to better understand the photoreactions of disubstituted tetrazoles and to provide useful strategies for regulating their unique reactivity.

Small Change, Big Impact: Reversal of Diastereoselection in Cuprate Conjugate Additions to α,β-Unsaturated Lactams and Identification of a Competing Mechanism

A seemingly minor change to a reactant is shown to cause a change in reaction mechanisms. Conjugate addition of organocopper reagents to bicyclic α,β-unsaturated lactams derived from pyroglutaminol is determined by the nature of the aminal group. Aminals derived from aldehydes give anti addition; those from ketones give syn addition. Divergence in diastereoselection occurs because the substrates react by different mechanisms, ultimately due to a small but significant difference in pyramidalization of the aminal nitrogen.

Quantum Mechanical-Cluster Approach to Solve the Bioisosteric Replacement Problem in Drug Design

Bioisosteres are molecules that differ in substituents but still have very similar shapes. Bioisosteric replacements are ubiquitous in modern drug design, where they are used to alter metabolism, change bioavailability, or modify activity of the lead compound. Prediction of relative affinities of bioisosteres with computational methods is a long-standing task; however, the very shape closeness makes bioisosteric substitutions almost intractable for computational methods, which use standard force fields. Here, we design a quantum mechanical (QM)-cluster approach based on the GFN2-xTB semi-empirical quantum-chemical method and apply it to a set of H → F bioisosteric replacements. The proposed methodology enables advanced prediction of biological activity change upon bioisosteric substitution of -H with -F, with the standard deviation of 0.60 kcal/mol, surpassing the ChemPLP scoring function (0.83 kcal/mol), and making QM-based ΔΔG estimation comparable to ∼0.42 kcal/mol standard deviation of in vitro experiment. The speed of the method and lack of tunable parameters makes it affordable in current drug research.

Bis(arylsulfonyl) Peroxide-Mediated Difunctionalization of Cyclic Enol Ethers

A bis(arylsulfonyl) peroxide-mediated 1,2-difunctionalization of cyclic enol ethers is reported. Bis(nosyl) peroxide selectively sulfonylates the 3-position of enol ethers, generating an oxocarbenium ion that is trapped by a carboxylic acid nucleophile at the 2-position. The reaction proceeds in a good yield and tolerates a variety of cyclic enol ethers, including glycals as well as various carboxylic acids, which act as the oxocarbeium ion trapping reagents.

Role and importance of solvents for the fractionation of lignocellulosic biomass

Lignocellulosic biomass is one of the most important renewable materials to replace carbon-based fossil resources. Solvent-based fractionation is a promising route for fractionation of biomass into its major components. Processing is governed by the employed solvent-systems properties. This review sheds light on the factors governing both dissolution and potential reactivities of the chemical structures present in lignocellulose, highlighting how proper understanding of the underlying mechanisms and interactions between solute and solvent help to choose proper systems for specific fractionation needs. Structural and chemical differences between the carbohydrate-based structural polymers and lignin require very different solvents capabilities in terms of causing and eventually stabilizing conformational changes and consequent activation of bonds to be cleaved by other active components in the. A consideration of potential depolymerization events during dissolution and energetic aspects of the dissolution process considering the contribution of polymer functionalities allow for a mapping of solvent suitability for biomass fractionation.

Contribution of Hyperconjugation and Inductive Effects to the Pseudo-anomeric Effect in 4-Substituted Methoxycyclohexanes

The importance of electrostatic nonconventional hydrogen bonds (NCHBs) to the pseudo-anomeric effect of 4-substituted methoxycyclohexanes is evaluated using theory [natural bond orbital (NBO)] to deconvolute electrostatic from other contributing effects. There is an interesting interplay between σ_CH → σ_CX^* hyperconjugation and the electropositive charge on 3,5-axial hydrogens (H_ax). In essence, better σ_CX^* (or π_CO^*) acceptors increase the charge on 3,5-CH_ax, which in turn strengthens C^δ+H_ax···^δ-OMe NCHB interactions.

Interheteromolecular Hyperconjugation Boosts (De)hydrogenation for Reversible H2 Storage

Interheteromolecular hyperconjugation is ubiquitous in organic systems, affecting bond length, dipole moments, conformations and so on, while its effect on (de)hydrogenation reactivity in a heterogeneous thermo-catalytic system has rarely been explored. Herein, the N-heterocycles containing a benzene ring and aliphatic chain [N-ethylcarbazole (NEC) and N-propylcarbazole (NPC)] were utilized to study the correlation between interheteromolecular hyperconjugation and catalytic (de)hydrogenation. Density functional theory calculations, variable-temperature ¹ H nuclear magnetic resonance spectroscopy, and catalytic experiments showed that the presented hyperconjugation between NEC and NPC weakened the electron cloud density of aromatic rings and thus facilitated the reactivity with hydrogen featuring unpaired electrons. Therefore, an extremely low temperature of 80 °C was enough for the hydrogenation. Moreover, this interheteromolecular hyperconjugation was general in other N-heterocycles (e. g., N-methyindole and NPC) and was also effective to (de)deuterate as revealed by isotope experiments. This work expands the application of interheteromolecular hyperconjugation to heterogeneous thermocatalysis for reversible H₂ storage.

A convenient catalytic method for preparation of new tetrahydropyrido[2,3-d]pyrimidines via a cooperative vinylogous anomeric based oxidation

In this study, a novel functionalized metal-organic frameworks MIL-125(Ti)-N(CH₂PO₃H₂)₂ was designed and synthesized via post-modification methodology. Then, MIL-125(Ti)-N(CH₂PO₃H₂)₂ as a mesoporous catalyst was applied for the synthesis of a wide range of novel tetrahydropyrido[2,3-d]pyrimidines as bioactive candidate compounds by one-pot condensation reaction of 3-(1-methyl-1H-pyrrol-2-yl)-3-oxopropanenitrile, 6-amino-1,3-dimethylpyrimidine-2,4(1H,3H)-dione and aromatic aldehydes at 100 °C under solvent-free condition. Interestingly, the preparation of tetrahydropyrido[2,3-d]pyrimidine was achieved via vinylogous anomeric based oxidation mechanism with a high yield and short reaction time.

Chemical Synthesis of the Nonreducing Hexasaccharide Fragment of Axinelloside A Based on a Stepwise Glycosylation Approach

An expedient synthesis of the nonreducing hexasaccharide fragment of axinelloside A has been completed via a linear stepwise glycosylation approach. Challenges involved in the synthesis include the highly stereoselective construction of five consecutive 1,2-cis-glycosidic linkages and the formation of a sterically crowded 2,3-disubstituted l-fucoside subunit. Protecting group-directing glycosylation strategies such as the remote participation effect of the benzoyl substituent and the stereocontrolling effect of the 4,6-O-benzylidene group were employed for the synthesis of the desired 1,2-cis-glycosidic linkages. Moreover, the 2,3-branched l-fucoside framework was established through a 3-O and then 2-O glycosylation sequence in which the 3-hydroxyl group of the core l-fucose unit was glycosylated first and then the 2-hydroxyl. The synthetic hexasaccharide is properly protected, so it can be employed as a precursor to synthesize its natural form.

Silicon-bridged (1→1)-disaccharides: an umpoled glycomimetic scaffold

Modification of the carbohydrate scaffold is an important theme in drug and vaccine discovery. Therefore, the preparation of novel types of glycomimetics is of interest in synthetic carbohydrate chemistry. In this manuscript, we present an early investigation of the synthesis, structure, and conformational behaviour of (1→1)-Si-disaccharides as a novel type of glycomimetics arising from the replacement of interglycosidic oxygen with a dimethyl-, methylpropyl-, or diisopropylsilyl linkage. We accomplished the preparation of this unusual group of umpoled compounds by the reaction of lithiated glycal or 2-oxyglycal units with dialkyldichlorosilanes. We demonstrated the good stability of the "Si-glycosidic" linkage under acidic conditions even at elevated temperatures. Next, we described the conformational landscape of these compounds by the combination of in silico modelling with spectroscopic and crystallographic methods. Finally, we explained the observed conformational flexibility of these compounds by the absence of gauche stabilizing effects that are typically at play in natural carbohydrates.

Diastereoselective Radical 1,4-Ester Migration: Radical Cyclizations of Acyclic Esters with SmI2

Reductive cyclizations of carbonyl compounds, mediated by samarium(II) diiodide (SmI₂, Kagan’s reagent), represent an invaluable platform to generate molecular complexity in a stereocontrolled manner. In addition to classical ketone and aldehyde substrates, recent advances in radical chemistry allow the cyclization of lactone and lactam-type substrates using SmI₂. In contrast, acyclic esters are considered to be unreactive to SmI₂ and their participation in reductive cyclizations is unprecedented. Here, we report a diastereoselective radical 1,4-ester migration process, mediated by SmI₂, that delivers stereodefined alkene hydrocarboxylation products via radical cyclization of acyclic ester groups in α-carbomethoxy δ-lactones. Isotopic labeling experiments and computational studies have been used to probe the mechanism of the migration. We propose that a switch in conformation redirects single electron transfer from SmI₂ to the acyclic ester group, rather than the “more reactive” lactone carbonyl. Our study paves the way for the use of elusive ketyl radicals, derived from acyclic esters, in SmI₂-mediated reductive cyclizations.

Structural, Electronic, Reactivity, and Conformational Features of 2,5,5-Trimethyl-1,3,2-diheterophosphinane-2-sulfide, and Its Derivatives: DFT, MEP, and NBO Calculations

In this study, we used density functional theory (DFT) and natural bond orbital (NBO) analysis to determine the structural, electronic, reactivity, and conformational features of 2,5,5-trimethyl-1,3,2-di-heteroatom (X) phosphinane-2-sulfide derivatives (X = O (compound 1), S (compound 2), and Se (compound 3)). We discovered that the features improve dramatically at 6-31G** and B3LYP/6-311+G** levels. The level of theory for the molecular structure was optimized first, followed by the frontier molecular orbital theory development to assess molecular stability and reactivity. Molecular orbital calculations, such as the HOMO–LUMO energy gap and the mapping of molecular electrostatic potential surfaces (MEP), were performed similarly to DFT calculations. In addition, the electrostatic potential of the molecule was used to map the electron density on a surface. In addition to revealing molecules’ size and shape distribution, this study also shows the sites on the surface where molecules are most chemically reactive.

Carboxylate as a Non-innocent L-Ligand: Computational and Experimental Search for Metal-Bound Carboxylate Radicals

We show that the carboxylate radical acts as an L-ligand with certain high-spin transition metal centers. Such coordination preserves the O-radical character needed for C-H activation via hydrogen atom transfer. Capture of the new C-radical by the metal and subsequent reductive elimination leads to formal C-H acyloxylation. Decarboxylation of the RCO₂ radical is minimized through hybridization effects introduced by spiro-cyclopropyl moiety.

Offsets between hyperconjugations, p→d donations and Pauli repulsions impact the bonding of E-O-E systems. Case study on elements of Group 14

The nature of the E-O chemical bond (E = C, Si, Ge, Sn) is investigated in a wide range of model derivatives, such as oxonium cations, hydrogenated/methylated/fluorinated/chlorinated ethers and acyclic oligomers incorporating the E-O-E moiety. By means of density functional theory (DFT) calculations and natural bond orbital (NBO) techniques, we propose a bonding mechanism that explains the structural contrast between the organic and the inorganic counterparts of all these derivatives: the interplay between stabilizing interactions like LP(O)→σ*(E-X) hyperconjugations and LP(O)→d(E) donations with LP(O)⋯σ(E-X) vicinal Pauli repulsions (X = H, C, O, F, Cl) dictates the equilibrium structures in terms of E-O-E angles and E-O bond lengths. In addition, the present work represents the first study of oxonium ions that describes the structural discrepancies among organic derivatives and their heavier analogues. Another novel outcome for ethers and oligomers is that the two non-equivalent lone pair electrons (LPs) at the oxygen atoms impact in different manners the geometries of such derivatives, i.e. the s/p LP is correlated with the bending behaviour of the E-O-E units, while the pure p LP mainly dictates the short E-O bond distances of inorganic derivatives. Lastly, we evaluate the impact of the number of electronegative substituents, e.g. F, Cl or OEH₃ groups, on the bond patterns developed for hydrogenated or methylated ethers.

Synthesis and application of novel urea-benzoic acid functionalized magnetic nanoparticles for the synthesis of 2,3-disubstituted thiazolidin-4-ones and hexahydroquinolines

In this work, we reported the synthesis and application of a new urea-benzoic acid containing ligand [(OEt)3Si(CH2)3-urea-benzoic acid] for the functionalization of silica coated magnetic nanoparticles. The resulting structure, namely Fe3O4@SiO2@(CH2)3-urea-benzoic acid, was characterized through different techniques including FT-IR, SEM, EDX-Mapping, VSM and TGA/DTG analysis. Then, Fe3O4@SiO2@(CH2)3-urea-benzoic acid was applied as a heterogeneous dual acidic and hydrogen bonding catalyst for the synthesis of 2,3-disubstituted thiazolidin-4-ones and hexahydroquinolines under mild and green reaction conditions. More importantly, all of the desired products were obtained with relatively good yields. Also, the catalyst was recovered and reused for four successive runs without significant reduction in yield of the model reaction.

Inverse α-Effect as the Ariadne's Thread on the Way to Tricyclic Aminoperoxides: Avoiding Thermodynamic Traps in the Labyrinth of Possibilities

Stable tricyclic aminoperoxides can be selectively assembled via a catalyst-free three-component condensation of β,δ'-triketones, H₂O₂, and an NH-group source such as aqueous ammonia or ammonium salts. This procedure is scalable and can produce gram quantities of tricyclic heterocycles, containing peroxide, nitrogen, and oxygen cycles in one molecule. Amazingly, such complex tricyclic molecules are selectively formed despite the multitude of alternative reaction routes, via equilibration of peroxide, hemiaminal, monoperoxyacetal, and peroxyhemiaminal functionalities! The reaction is initiated by the "stereoelectronic frustration" of H₂O₂ and combines elements of thermodynamic and kinetic control with a variety of mono-, bi-, and tricyclic structures evolving under the conditions of thermodynamic control until they reach a kinetic wall created by the inverse α-effect, that is, the stereoelectronic penalty for the formation of peroxycarbenium ions and related transition states. Under these conditions, the reaction stops before reaching the most thermodynamically stable products at a stage where three different heterocycles are assembled and fused at the acyclic precursor frame.

Remote Stereoelectronic Effects in Pyrrolidone- and Caprolactam-Substituted Phenols: Discrepancies in Antioxidant Properties Evaluated by Electrochemical Oxidation and H-Atom Transfer Reactivity

New antioxidants are commonly evaluated via two main approaches, i.e., the ability to donate an electron and the ability to intercept free radicals. We compared these approaches by evaluating the properties of 11 compounds containing both antioxidant moieties (mono- and polyphenols) and auxiliary pharmacophores (pyrrolidone and caprolactam). Several common antioxidants, such as butylated hydroxytoluene (BHT), 2,3,5-trimethylphenol (TMP), quercetin, and dihydroquercetin, were added for comparison. The antioxidant properties of these compounds were determined by their rates of reaction with 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical and their oxidation potentials from cyclic voltammetry. Although these methods test different chemical properties, their results correlate reasonably well. However, several exceptions exist where the two methods give opposite predictions! One of them is the different behavior of mono- and polyphenols: polyphenols can react with DPPH more than an order of magnitude faster than monophenols of a similar oxidation potential. The second exception stems from the size of a "bystander" lactam ring at the benzylic position. Although the phenols with a seven-membered lactam ring are harder to oxidize, the sterically nonhindered compounds react with DPPH about 2× faster than the analogous five-membered lactams. The limitations of computational methods, especially those based on a single parameter, are also evaluated and discussed.