Search Results (43)

The rapid advancement of 3D packaging technology has emerged as a key solution to overcome the scaling-down limitation of advanced memory and logic devices. Redistribution layer (RDL) fabrication, a critical process in 3D packaging, requires the use of polyimide (PI) films with thicknesses in the micrometer range. However, these polyimide films present surface topography variations in the range of hundreds of nanometers, necessitating chemical–mechanical planarization (CMP) to achieve nanometer-level surface flatness. Polyimide films, composed of copolymers of pyromellitimide and diphenyl ether, possess strong covalent bonds such as C–C, C–O, C=O, and C–N, leading to inherently low polishing rates during CMP. To address this challenge, the introduction of Fe(NO₃)₃ into CMP slurries has been proposed as a polishing rate accelerator. During CMP, this Fe(NO₃)₃ deformed the surface of a polyimide film into strongly positively charged 1,2,4,5-benzenetetracarbonyliron and weakly negatively charged 4,4′-oxydianiline (ODA). The chemically dominant polishing rate enhanced with the concentration of the Fe(NO₃)₃ due to accelerated surface interactions. However, higher Fe(NO₃)₃ concentrations reduce the attractive electrostatic force between the positively charged wet ceria abrasives and the negatively charged deformed surface of the polyimide film, thereby decreasing the mechanically dominant polishing rate. A comprehensive investigation of the chemical and mechanical polishing rate dynamics revealed that the optimal Fe(NO₃)₃ concentration to achieve the maximum polyimide film removal rate was 0.05 wt%. Full article

Studies have shown that the incorporation of fluorine into materials can improve their properties, but C–F bonds are not readily formed in nature. Although some researchers have studied the reaction of fluorinating alkenes catalyzed by hypervalent iodine, far too little attention has been paid to its reaction mechanism. This study aimed to explore the mechanism of the hypervalent iodine-catalyzed 1,4-difluorination of dienes. We found that the catalyst is favorable for the activation of C1=C2 double bonds through halogen bonds, and then two HFs interact with one F atom in the catalyst via hydrogen bonds, resulting in the cleavage of I–F bonds and the formation of [F–H∙∙∙F]⁻. Subsequently, the catalyst interacts with C1, and the roaming [F–H···F]⁻ attacks C4 from the opposite side of the catalyst. After the fluorination step is completed, the nucleophile F⁻ substitutes the catalyst via the S_N2 mechanism. Our calculations demonstrated that the interaction between HF and F⁻ is favorable for the stabilization of the transition state within the fluorination process for which the presence of two HFs in the reaction is the best. We also observed that [F–H∙∙∙F]⁻ attacking C4 from the opposite side of the catalyst is more advantageous than attacking from the same side. This study therefore offers a novel perspective on the mechanism of the hypervalent iodine-catalyzed fluoridation of dienes. Full article

Tuberculosis (TB) continues to be a major global health challenge and a leading cause of death from infectious diseases. Inspired by the results from a previous work by our group on antimycobacterial N-alkylnitrobenzamides, which are structurally related to the nitrobenzamide family of decaprenylphosphoryl-β-d-ribose oxidase (DprE1) inhibitors, the present study explored a broad array of substituted benzamides. We particularly focused on previously unexplored 3,5-dinitrobenzamide derivatives. Starting with 3,5-dinitrobenzoic acid, we synthesized a diverse library of amides, incorporating both linear and cyclic amine moieties and also assessed the impact of terminal aromatic groups connected through ether, ester, or amide bonds on the bioactivity of the compounds. The synthesis primarily utilized nucleophilic addition/elimination, S_N2, and Mitsunobu reactions. The activity was impacted mainly by two structural features, the addition of an aromatic moiety as a terminal group and the type of linker. The most interesting compounds (c2, d1, and d2, MIC = 0.031 μg/mL) exhibited activities against Mycobacterium Tuberculosis (Mtb) H37Rv comparable to isoniazid. Complementary computational studies helped elucidate potential interactions with DprE1, enhancing our understanding of the molecular basis of their action. Our findings suggest that the most active compounds provide a promising foundation for the continued development of new antimycobacterial agents. Full article

Thiols can react with readily available organic substrates under benign conditions, making them suitable for use in chemical, biological, physical, and materials and engineering research areas. In particular, the highly efficient thiol-based click reaction includes the reaction of radicals with electron-rich enes, Michael addition with electron-poor enes, carbonyl addition with isocyanate S_N2 ring opening with epoxies, and S_N2 nucleophilic substitution with halogens. This mini review provides insights into emerging venues for their industrial applications, especially for the applications of thiol-ene, thiol–isocyanate, and thiol–epoxy reactions, highlighting a brief chemistry of thiols as well as various approaches to polythiol synthesis. Full article

Fusion is a key event for enveloped viruses, through which viral and cell membranes come into close contact. This event is mediated by viral fusion proteins, which are divided into three structural and functional classes. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein belongs to class I fusion proteins, characterized by a trimer of helical hairpins and an internal fusion peptide (FP), which is exposed once fusion occurs. Many efforts have been directed at finding antivirals capable of interfering with the fusion mechanism, mainly by designing peptides on the two heptad-repeat regions present in class I viral fusion proteins. Here, we aimed to evaluate the anti-SARS-CoV-2 activity of the FP sequence conjugated to a tetravalent dendrimer through a classical organic nucleophilic substitution reaction (S_N2) using a synthetic bromoacetylated peptide mimicking the FP and a branched scaffold of poly-L-Lysine functionalized with cysteine residues. We found that the FP peptide conjugated to the dendrimer, unlike the monomeric FP sequence, has virucidal activity by impairing the attachment of SARS-CoV-2 to cells. Furthermore, we found that the peptide dendrimer does not have the same effects on other coronaviruses, demonstrating that it is selective against SARS-CoV-2. Full article

The competition between base-induced elimination (E2) and bimolecular nucleophilic substitution (S_N2) is of significant importance in organic chemistry and is influenced by many factors. The electronic structure calculations for the gas-phase reactions of F⁻ + RY (R = CH₃, C₂H₅, ⁱC₃H₇, ^tC₄H₉, and Y = Cl, I) are executed at the MP2 level with aug-cc-pVDZ or ECP/d basis set to investigate the α-methyl substitution effect. The variation in barrier height, reaction enthalpy, and competition of S_N2/E2 as a function of methyl-substitution and leaving group ability has been emphasized. And the nature of these rules has been explored. As the degree of methyl substitution on α-carbon increases, the E2 channel becomes more competitive and dominant with R varying from C₂H₅, ⁱC₃H₇, to ^tC₄H₉. Energy decomposition analysis offers new insights into the competition between E2 and S_N2 processes, which suggests that the drop in interaction energy with an increasing degree of substitution cannot compensate for the rapid growth of preparation energy, leading to a rapid increase in the S_N2 energy barrier. By altering the leaving group from Cl to I, the barriers of both S_N2 and E2 monotonically decrease, and, with the increased number of substituents, they reduce more dramatically, which is attributed to the looser transition state structures with the stronger leaving group ability. Interestingly, ∆E₀^‡ exhibits a positive linear correlation with reaction enthalpy (∆H) and halogen electronegativity. With the added number of substituents, the differences in ∆E₀^‡ and ∆H between Y = Cl and I likewise exhibit good linearity. Full article

Mechanisms are part of the high school curriculum in many countries. Although research shows that university students struggle with mechanistic reasoning, very little is known about learning mechanisms in high school. Understanding the cognitive resources that high school students intuitively activate is critical to fostering meaningful learning. A readily available tool for modeling dynamic processes are stop-motion animations (SMAs). In this study, 55 high school students were asked to create SMAs of their intuitive ideas of nucleophilic substitution reactions. In a second step, the students evaluated two pre-made SMAs modeling the textbook-based stepwise (S_N1) and concerted (S_N2) mechanisms. Within the student-generated SMAs, S_N1- and S_N2-like mechanisms were equally distributed; after viewing the textbook-style animations, most students rated an S_N2 mechanism as more likely. However, no group modeled both types of mechanisms or reasoned that both mechanisms were possible. Students used diverse chemical concepts as well as plausibility in their reasoning. However, simultaneous movement of atoms, conformational changes, and the idea of competing and boundary mechanisms do not seem intuitive. In conclusion, SMAs were found to be an appropriate tool for activating, analyzing, and discussing students’ resources “on the fly”, and these ideas can serve as a starting point for promoting productive mechanistic reasoning. Full article

Organic chemical reactions have been used to functionalize preformed conducting polymers (CPs). The extensive work performed on polyaniline (PANI), polypyrrole (PPy), and polythiophene (PT) is described together with the more limited work on other CPs. Two approaches have been taken for the functionalization: (i) direct reactions on the CP chains and (ii) reaction with substituted CPs bearing reactive groups (e.g., ester). Electrophilic aromatic substitution, S_EAr, is directly made on the non-conductive (reduced form) of the CPs. In PANI and PPy, the N-H can be electrophilically substituted. The nitrogen nucleophile could produce nucleophilic substitutions (SN) on alkyl or acyl groups. Another direct reaction is the nucleophilic conjugate addition on the oxidized form of the polymer (PANI, PPy or PT). In the case of PT, the main functionalization method was indirect, and the linking of functional groups via attachment to reactive groups was already present in the monomer. The same is the case for most other conducting polymers, such as poly(fluorene). The target properties which are improved by the functionalization of the different polymers is also discussed. Full article

Nanoscale control of chemical reactivity, manipulation of reaction pathways, and ultimately driving the outcome of chemical reactions are quickly becoming reality. A variety of tools are concurring to establish such capability. The confinement of guest molecules inside nanoreactors, such as the hollow nanostructures of carbon nanotubes (CNTs), is a straightforward and highly fascinating approach. It mechanically hinders some molecular movements but also decreases the free energy of translation of the system with respect to that of a macroscopic solution. Here, we examined, at the quantum mechanics/molecular mechanics (QM/MM) level, the effect of confinement inside CNTs on nucleophilic substitution (S_N2) and elimination (syn-E2 and anti-E2) using as a model system the reaction between ethyl chloride and chloride. Our results show that the three reaction mechanisms are kinetically and thermodynamically affected by the CNT host. The size of the nanoreactor, i.e., the CNT diameter, represents the key factor to control the energy profiles of the reactions. A careful analysis of the interactions between the CNTs and the reactive system allowed us to identify the driving force of the catalytic process. The electrostatic term controls the reaction kinetics in the S_N2 and syn/anti-E2 reactions. The van der Waals interactions play an important role in the stabilization of the product of the elimination process. Full article

A straightforward method for the synthesis of 5-substituted tetrazolo[1,5-a]pyrido[2,3-e]pyrimidines from 2,4-diazidopyrido[3,2-d]pyrimidine in SnAr reactions with N-, O-, and S- nucleophiles has been developed. The various N- and S-substituted products were obtained with yields from 47% to 98%, but the substitution with O-nucleophiles gave lower yields (20–32%). Furthermore, the fused tetrazolo[1,5-a]pyrimidine derivatives can be regarded as 2-azidopyrimidines and functionalized in copper(I)-catalyzed azide-alkyne dipolar cycloaddition (CuAAC) and Staudinger reactions due to the presence of a sufficient concentration of the reactive azide tautomer in solution. In total, seven products were fully characterized by their single crystal X-ray studies, while five of them were representatives of the tetrazolo[1,5-a]pyrido[2,3-e]pyrimidine heterocyclic system. Equilibrium constants and thermodynamic values were determined using variable temperature ¹H NMR and are in agreement of favoring the tetrazole tautomeric form (ΔG₂₉₈ = −3.33 to −7.52 (kJ/mol), ΔH = −19.92 to −48.02 (kJ/mol) and ΔS = −43.74 to −143.27 (J/mol·K)). The key starting material 2,4-diazidopyrido[3,2-d]pyrimidine presents a high degree of tautomerization in different solvents. Full article

Many viruses from the realm Riboviria infecting eukaryotic hosts encode protein domains with sequence similarity to S-adenosylmethionine-dependent methyltransferases. These protein domains are thought to be involved in methylation of the 5′-terminal cap structures in virus mRNAs. Some methyltransferase-like domains of Riboviria are homologous to the widespread cellular FtsJ/RrmJ-like methyltransferases involved in modification of cellular RNAs; other methyltransferases, found in a subset of positive-strand RNA viruses, have been assigned to a separate “Sindbis-like” family; and coronavirus-specific Nsp13/14-like methyltransferases appeared to be different from both those classes. The representative structures of proteins from all three groups belong to a specific variety of the Rossmann fold with a seven-stranded β-sheet, but it was unclear whether this structural similarity extends to the level of conserved sequence signatures. Here I survey methyltransferases in Riboviria and derive a joint sequence alignment model that covers all groups of virus methyltransferases and subsumes the previously defined conserved sequence motifs. Analysis of the spatial structures indicates that two highly conserved residues, a lysine and an aspartate, frequently contact a water molecule, which is located in the enzyme active center next to the methyl group of S-adenosylmethionine cofactor and could play a key role in the catalytic mechanism of the enzyme. Phylogenetic evidence indicates a likely origin of all methyltransferases of Riboviria from cellular RrmJ-like enzymes and their rapid divergence with infrequent horizontal transfer between distantly related viruses. Full article

Commercialization of anion exchange membrane fuel cells (AEMFCs) has been limited due to the chemical degradation of various quaternary ammonium (QA) head groups, which affects the transportation of hydroxide (${\mathrm{OH}}^{-}$) ions in AEMs. Understanding how various QA head groups bind and interact with hydroxide ions at the molecular level is of fundamental importance to developing high-performance AEMs. In this work, the binding and degradation reaction of hydroxide ions with several QA head groups—(a) pyridinium, (b) 1,4-diazabicyclo [2.2.2] octane (DABCO), (c) benzyltrimethylammonium (BTMA), (d) n-methyl piperidinium, (e) guanidium, and (f) trimethylhexylammonium (TMHA)—are investigated using the density functional theory (DFT) method. Results of binding energies (“∆” EBinding) show the following order of the binding strength of hydroxide ions with the six QA head groups: (a) > (c) > (f) > (d) > (e) > (b), suggesting that the group (b) has a high transportation rate of hydroxide ions via QA head groups of the AEM. This trend is in good agreement with the trend of ion exchange capacity from experimental data. Further analysis of the absolute values of the LUMO energies for the six QA head groups suggests the following order for chemical stability: (a) < (b)~(c) < (d) < (e) < (f). Considering the comprehensive studies of the nucleophilic substitution (S_N2) degradation reactions for QA head groups (c) and (f), the chemical stability of QA (f) is found to be higher than that of QA (c), because the activation energy (“∆” EA) of QA (c) is lower than that of QA (f), while the reaction energies (“∆” ER) for QA (c) and QA (f) are similar at the different hydration levels (HLs). These results are also in line with the trends of LUMO energies and available chemical stability data found through experiments. Full article

Nitrobenzenesulfochlorination of β-aminopropioamidoximes leads to a set of products depending on the structure of the initial interacting substances and reaction conditions. Amidoximes, functionalized at the terminal C atom with six-membered N-heterocycles (piperidine, morpholine, thiomorpholine and phenylpiperazine), as a result of the spontaneous intramolecular heterocyclization of the intermediate reaction product of an S_N2 substitution of a hydrogen atom in the oxime group of the amidoxime fragment by a nitrobenzenesulfonyl group, produce spiropyrazolinium ortho- or para-nitrobenzenesulfonates. An exception is ortho-nitrobenzenesulfochlorination of β-(thiomorpholin-1-yl)propioamidoxime, which is regioselective at room temperature, producing two spiropyrazolinium salts (ortho-nitrobezenesulfonate and chloride), and regiospecific at the boiling point of the solvent, when only chloride is formed. The para-Nitrobezenesulfochlorination of β-(benzimidazol-1-yl)propioamidoxime, due to the reduced nucleophilicity of the aromatic β-amine nitrogen atom, is regiospecific at both temperatures, and produces the O-para-nitrobenzenesulfochlorination product. The antidiabetic screening of the new nitrobezenesulfochlorination amidoximes found promising samples with in vitro α-glucosidase activity higher than the reference drug acarbose. ¹H-NMR spectroscopy and X-ray analysis revealed the slow inversion of six-membered heterocycles, and experimentally confirmed the presence of an unfavorable stereoisomer with an axial N–N bond in the pyrazolinium heterocycle. Full article

LTA₄H is a bifunctional zinc metalloenzyme that converts leukotriene A₄ (LTA₄) into leukotriene B₄ (LTB₄), one of the most potent chemotactic agents involved in acute and chronic inflammatory diseases. In this reaction, LTA₄H acts as an epoxide hydrolase with a unique and fascinating mechanism, which includes the stereoselective attachment of one water molecule to the carbon backbone of LTA₄ several methylene units away from the epoxide moiety. By combining Molecular Dynamics simulations and Quantum Mechanics/Molecular Mechanics calculations, we obtained a very detailed molecular picture of the different consecutive steps of that mechanism. By means of a rather unusual 1,7-nucleophilic substitution through a clear S_N1 mechanism, the epoxide opens and the triene moiety of the substrate twists in such a way that the bond C₆-C₇ adopts its cis (Z) configuration, thus exposing the R face of C₁₂ to the addition of a water molecule hydrogen-bonded to ASP375. Thus, the two stereochemical features that are required for the bioactivity of LTB₄ appear to be closely related. The noncovalent π-π stacking interactions between the triene moiety and two tyrosines (TYR267 and, especially, TYR378) that wrap the triene system along the whole reaction explain the preference for the cis configuration inside LTA₄H. Full article