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The formation and rearrangements of nitrile imines are of ongoing synthetic and theoretical interest. In this paper, we report a computational investigation at the M06/6-311 + G(d,p) level of the formation and rearrangement of propargylic N-phenyl-C-styrylnitrile imine 3 from 2-phenyl-5-styryltetrazole 1 by flash vacuum pyrolysis (FVP). Nitrile imine 3 cyclizes to 3aH-3-styrylindazole 4, which is also generated by H-shifts in the FVP of 3-styrylindazole 8. Tautomerization of 4 and N2-elimination afford cyclohexadienylidene 14, which by cyclization followed by H-shifts yields the primary pyrolysis product, 3-phenylindene 5. An alternate path via 7aH-3-styrylindazole, phenyl(styryl)diazomethane, and phenyl(styryl)carbene is potentially possible. The analogous pyrolysis of 2-phenyl-5-phenylethynyltetrazole 1' afforded cyclopenta[fg]fluorene and cyclopenta[def]phenanthrene via N-phenyl-C-phenylethynylnitrile imine 3' and 3aH-3-phenylethynylindazole 4'. In both cases, 3 and 3', rearrangement to diazocyclohexadienes and cyclohexadienylidenes (e.g., 14) is energetically preferred over alternate aryldiazomethane and arylcarbene intermediates.
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The unique potential of fullerene C60 for various biological applications has ignited significant interest. However, its inherent non-polarity poses a critical challenge for its effective integration within biological systems. This study delves into the intricate physicochemical characteristics of the innovative [C60 + NO] complex using density functional theory and time-dependent density functional theory. The computational analyses encompass molecular charge, surface electrostatic potential, and dipole moment evaluations. Impressively, the dipole moment of the [C60 + NO] complex significantly increases to 12.92 D. Meticulous surface analysis reveals a subtle interplay between molecular structures, indicating weak interactions. The analysis of the absorption spectrum unveils a noteworthy red-shift of 200 nm subsequent to complex formation. To elucidate the electron transfer mechanisms, we explore photo-induced electron transfer through CAM-B3LYP. This exploration elucidates intricate pathways governing electron transfer, with complementary insights gleaned from Marcus theory's outputs, especially the Gibbs free energy of electron transfer. Changes in the physicochemical properties of approaching C60 and NO molecules reveal interesting results compared to separate molecules. These findings resonate profoundly in the context of potential biological and pharmaceutical utilization. With implications for the biomedical area, the outcomes linked to the [C60 + NO] complex kindle optimism for pioneering biomedical applications.
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Fulerenos , Fulerenos/química , Óxido Nítrico , Modelos Moleculares , Transporte de Elétrons , Estrutura MolecularRESUMO
[This retracts the article DOI: 10.1039/C6RA12299J.].
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The mechanism(s) of thermal rearrangement of azulenes have been enigmatic for several decades. Herein, we have employed density functional theory (DFT) calculations at the M06-2X/6-311+G(d,p) level together with single-point calculations at the CCSD(T) level to assess possible mechanisms of the experimentally observed azulene and naphthalene automerizations. Of the two mechanisms proposed for naphthalene automerization, it is found that the benzofulvene (BF) route is favored over the naphthvalene mechanism by â¼6 kcal/mol and is energetically lower than the norcaradiene-vinylidene mechanism (NVM) for the azulene-naphthalene rearrangement (Ea â¼ 76.5 (74.6) kcal/mol). Moreover, contrary to older reports, we observe that a pathway involving indenylcarbene intermediates is a viable, alternate mechanism. Therefore, the naphthalene automerization is expected to take place during azulene pyrolysis, especially under conditions of low-pressure FVP, where it will be aided by chemical activation. Furthermore, thermal azulene-azulene isomerization is feasible through vinylidene-acetylene-vinylidene (VAV), dehydrotriquinacene (DTQ), and azulvalene (AV) pathways with activation energies lying below that required for the azulene-naphthalene conversion, i.e., the NVM. These results, together with the previously published NVM, provide reasonable explanations for most of the products of the thermal azulene-naphthalene rearrangement.
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The thermal rearrangement of azulene to naphthalene has been the subject of several experimental and computational studies. Here, we reexamine the proposed mechanisms at the DFT level. The use of different functionals showed that the HF-exchange contribution significantly affects reaction energies and barrier heights. Accordingly, all proposed pathways were investigated with the optimal method, M06-2X/6-311+G(d,p), which confirms the norcaradiene-vinylidene mechanism (A) as the dominant unimolecular route (Ea ≈ 76 kcal/mol) able to account for the major products of pyrolyses using 13C- or substituent-labeled azulenes. Moreover, a facile vinylidene-acetylene interconversion will scramble the terminal carbon atoms in the vinylidene. Several other potential intramolecular reaction mechanisms (B-E) are ruled out because of higher activation energies (>84 kcal/mol) and failure to reproduce the results obtained with substituted and 13C-labeled azulenes and benzazulenes. These experimental results also demonstrate that the proposed free radical or H atom-induced intermolecular methylene walk and spiran mechanisms cannot be major contributors, especially under flash vacuum pyrolysis conditions.
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In the Dimroth rearrangement of heterocycles, often pyrimidines, an exocyclic and a ring substituent are interchanged. However, the term Dimroth rearrangement is frequently used even when there is no knowledge of the reaction mechanism and alternatives are likely. Here, we have employed density functional theory (DFT) calculations at the M06-2X/6-311+G(d,p) level to determine the most plausible rearrangement pathways of 3-aminothiocarbonylquinazoline 5, tetrahydrofuranylpyrimidine 21, and 5-allyltriazocine 30. For the rearrangement of quinazoline 5 to 9, the [1,3]-sigmatropic shift of the thioamido group with an activation barrier of 26.7 kcal/mol is much preferred over the Dimroth rearrangement (â¼46 kcal/mol). An even lower barrier of 21.6 kcal/mol applies to a stepwise [1,3]-shift. The migration of the tetrahydrofuranyl unit in pyrimidines like 21 â 23 can take place by means of a [1,3]-sigmatropic shift with a low barrier (≤17.5 kcal/mol) rather than a Dimroth rearrangement under acidic conditions and most likely also under neutral conditions (â¼30 kcal/mol). In the rearrangement of 5-allyl-6-iminotriazocine 30 to 32, the [3,3]-sigmatropic shift (aza-Cope rearrangement) is preferred over the Dimroth mechanism under neutral conditions, but in the presence of acid, the azonia-Cope rearrangement of an allyl group and the true Dimroth rearrangement have comparable activation energies.
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Human Serum Albumin, a plasma protein existing in abundance, was selected as a template and reducing agent for the formation of CdNCs due to two factors: its stability and low cost. In the presence of human serum albumin (HSA), a selective and sensitive, low-cost, environmental friendly, and label-free off-on fluorescent sensor was synthesized and characterized for a bioaccumulating and toxic heavy metal, Hg2+ and biothiols. HSA - CdNCs can specifically recognize Hg2+ through aggregating NCs and causing fluorescence quenching. Subsequently, with increase in the concentration of biothiols, Hg2+ was eliminated from the surface of NC, while the fluorescence was restored. The calculated limits of detection (LOD) were 55â¯pM for Hg(II) and 14â¯nM for GSH, respectively. The assay was capable of detecting Hg2+ ions and GHS at different concentrations in the range of 0.008 to 8530â¯nM and 7.5-5157â¯nM, respectively. Furthermore, the appropriate molecular mechanics (MM) as well as quantum mechanical (QM) methods were performed to optimize and the theoretical investigation of the discussed HSA-profile structures and its interactions with the Cd-NCs (one atom of Cd), Hg2+ and glutathione (G).
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Cádmio , Mercúrio , Glutationa , Humanos , Limite de Detecção , Espectrometria de FluorescênciaRESUMO
Mechanism-based inactivation (MBI) refers to the metabolic bioactivation of a xenobiotic by cytochrome P450s to a highly reactive intermediate which subsequently binds to the enzyme and leads to the quasi-irreversible or irreversible inhibition. Xenobiotics, mainly drugs with specific functional units, are the major sources of MBI. Two possible consequences of MBI by medicinal compounds are drug-drug interaction and severe toxicity that are observed and highlighted by clinical experiments. Today almost all of these latent functional groups (e.g., thiophene, furan, alkylamines, etc.) are known, and their features and mechanisms of action, owing to the vast experimental and theoretical studies, are determined. In the past decade, molecular modeling techniques, mostly density functional theory, have revealed the most feasible mechanism that a drug undergoes by P450 enzymes to generate a highly reactive intermediate. In this review, we provide a comprehensive and detailed picture of computational advances toward the elucidation of the activation mechanisms of various known groups with MBI activity. To this aim, we briefly describe the computational concepts to carry out and analyze the mechanistic investigations, and then, we summarize the studies on compounds with known inhibition activity including thiophene, furan, alkylamines, terminal acetylene, etc. This study can be reference literature for both theoretical and experimental (bio)chemists in several different fields including rational drug design, the process of toxicity prevention, and the discovery of novel inhibitors and catalysts.
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Inibidores das Enzimas do Citocromo P-450/farmacologia , Sistema Enzimático do Citocromo P-450/metabolismo , Teoria da Densidade Funcional , Xenobióticos/farmacologia , Inibidores das Enzimas do Citocromo P-450/química , Humanos , Estrutura Molecular , Xenobióticos/químicaRESUMO
The diverse capabilities of self-propelled micro/nanomotors open up significant opportunities for various environmental and biomedical applications. Here, a synchronized two-lobed bubble exhaust drives micromotor comprising a metal (cobalt and gold) sandwiched polytryptophan body (Au/poly-Trp/Co) in a non-curved direction. The autonomous motion is achieved through the decomposition of chemical fuel to result in a kayak-like system. The ejected oxygen bubbles from the interfacial cobalt/polytryptophan layer, as well as the inert nature of the metal segments (Au-Co), were considered for some computational studies of the electronic properties of the composite and physical phenomena at the kayak/electrolyte interfaces, and confirmed the role of Co-Trp in the fuel decomposition. It is believed that the autonomous motion is the combined result of bubble recoil force, self-electrophoresis, and perturbation in the interfacial hydrogen-bond network of the poly-Trp body and water molecules. The velocity of the micromotor in the range 23±4 to 157±17â µm s-1 at different concentrations of H2 O2 from 1 % to 10 %. Depending on the method of fragmentation, it is possible to have both single and multiple motorized kayaks with lengths of 1.5 and 6â µm, respectively, that can be tailored for environmental applications.
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This study was focused on the geometries and properties of the structural isomers obtained from a random walk of methylpentynol-HN3 clusters. The theoretical aspects of hydrogen bonding effects on the discussed 1,3-dipolar cycloaddition (1,3-DC) reactions [between methylpentynol (a) as a dipolarophile and azide (b) as a 1,3-dipole] have shown regioselective output concepts. The dipolarophile methylpentynol (a) was applied for the treatment of insomnia. Both methylpentynol (a) and azide (b) can be H-bond acceptor and H-bond donor agents. Because of this trait of them, structures of H-bonding arrays (c-f) and methylpentynol-azide clusters (g-m) can be probable. In this work, regioselectivity of the 1,3-DC reaction [between methylpentynol (a) as a dipolarophile and azide (b) as a 1,3-dipole] was determined based on these structures (c-m) using density functional theory (DFT). The energy levels of the reactants (a and b) and the structures of H-bonding arrays (c-f), methylpentynol-azide clusters (g-m), transition states, and products (1 and 2) were studied, and also, the free energies of the reaction (Δr G and ΔG #, in kcal mol-1) and rate constants were determined using Eyring's equation (k). Structural data were calculated and obtained by the DFT/B3LYP method. Seven different basis sets have been used to obtain the most appropriate results from comparison of data.
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In this exploration, we reported the design and synthesis of a novel ionically tagged magnetic nanoparticles bearing urea linkers, namely, Fe3O4@SiO2@(CH2)3-urea-thiazole sulfonic acid chloride. The structure of the mentioned compound was fully characterized by using several techniques including Fourier transform infrared spectroscopy, energy-dispersive X-ray analysis, elemental mapping analysis, thermogravimetric analysis/differential thermal analysis, scanning electron microscopy, transmission electron microscopy, and vibrating sample magnetometer. In the presence of the novel reusable catalyst, applied starting materials including aryl aldehydes, pyruvic acid, and 1-naphthylamine condensed to afford the desired 2-aryl-quinoline-4-carboxylic acid derivatives via an anomeric-based oxidation pathway under solvent-free conditions.
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Protection techniques of functional groups within the structure of organic compounds are important synthetic methods against unwanted attacks from various reagents during synthetic sequences. Acetal and thioacetal groups are well known as protective functional groups in organic reactions. In this study, acetalization of carbonyl compounds with diols and dithiols and methoxymethylation of alcohols with formaldehyde dimethyl acetal (FDMA) have been carried out using sulfamic acid-functionalized magnetic Fe3O4 nanoparticles (SA-MNPs) as a heterogeneous solid acid catalyst. Products were characterized by FT-IR and NMR spectroscopies. The structural and electronic properties of some products were computed by quantum mechanical (QM) methods. Depending on the stereochemistry and electronic properties that were obtained by computational results, we have suggested that hyperconjugation plays a key role in the structural properties of 2-phenyl-1,3-dioxolane derivatives, and also the electron transfer between π-electrons of the aromatic ring with the 3d orbital of S-atoms influences the 2-phenyl-1,3-dithiane derivatives' structure.
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Electrochemical behavior and sensing of 2-methyl-4, 6-dinitrophenol as an herbicide has been investigated by cyclic voltammetry (CV) and square wave voltammetry (SWV). We have synthesized a cefazolin (CEF) immobilized nanomagnetic core-shell (Fe3O4@SiO2-(CH2)3-CEF) and attached it on the modified glassy carbon electrode (GCE/MWCNT) through electrostatic adsorption (GCE/MWCNT/CEF-SiO2@Fe3O4). 2-Methyl-4, 6-dinitrophenol has an oxidation peak that is related to the formation of nitrosamine from hydroxylamine species. This peak was applied for quantifying determination of 2-methyl-4, 6-dinitrophenol. The electrochemical oxidation involves two electron transfers accompanied by two protons. The electrochemical process was controlled by adsorption. The good agreement between the obtained computational studies and the experimental results has demonstrated that outer sphere electron transfer occurred on modified electrode. The new electrochemical sensor was applied to determination of 2-methyl-4, 6-dinitrophenol by SWV in the range of 1.0â¯×â¯10-10 to 1.5â¯×â¯10-7â¯M with a detection limit of 0.1â¯nM. The proposed sensor was applied for determination of 2-methyl-4, 6-dinitrophenol in water samples.
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Carbono/química , Dinitrofenóis/análise , Técnicas Eletroquímicas/métodos , Vidro/química , Nanopartículas de Magnetita/química , Nanotubos de Carbono/química , Cefazolina/química , Eletrodos , Concentração de Íons de Hidrogênio , Nanopartículas de Magnetita/ultraestrutura , Nanotubos de Carbono/ultraestrutura , Oxirredução , Propriedades de Superfície , Água/químicaRESUMO
This study introduces a signal amplification strategy rely on incorporating a specific polymer film between two typical nanostructured layers, aiming to improve the electrical properties of the platform to be able to transduce small binding event through sub-femtomolar detection of HIV-1 gene at the surface of the constructed biosensing device. The proposed composite was arrayed based on a conductive layer consist of p-aminobenzoic acid (PABA) sandwiched between the electrochemically reduced graphene oxide (ERGO) as the sub-layer, and the gold nanoparticles (AuNPs) as the interfacial layer. We computationally explored that how the use of such design enables the platform to transduce small changes in the interfacial properties of the biosensor, caused by low concentrations of HIV-1 gene, without needing any amplification strategy. Furthermore, it was found that the loin PABA conductive polymer sandwiched between two nanostructure layers play an artwork-ensemble role, which resulted in a good signal repeatability and stability during the relatively long successive incubation and detection procedures. The justification of using such an array of conductive layers was established on the attaining extra low-level of detection limit. The observed performance for probe-DNA immobilized on glassy carbon electrode (GC) modified with ERGO/PABA/AuNPs compared to the GC electrode modified with ERGO/AuNPs inspired us to perform computational calculations, a hybrid of ab-initio and semi-empirical quantum mechanics methods, to discover its probable molecular-scale reasons. A rapid single frequency impedance measurement (SFIM) was also employed to remarkably reduce the measurement time and diminish the probable nonspecific impedance changes. The proposed biosensor was used to evaluate the DNA target over an extremely wide concentration range from 0.1â¯fM to 10â¯nM, with a detection limit of 37 aM (S/Nâ¯=â¯3).
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Técnicas Biossensoriais/métodos , DNA/química , Condutividade Elétrica , Genes Virais , HIV-1/genética , Nanoestruturas/química , Polímeros/química , Sequência de Bases , DNA/genética , Ouro/química , Humanos , Limite de Detecção , Nanopartículas Metálicas/química , Fatores de TempoRESUMO
An innovative dual-emissive ratiometric nanohybrid probe comprised of red-emitting a (Ag/Au)@insulin nanoclusters (NCs) and blue-emitting carbon dots (CDs) was designed for sensitive and selective ratiometric determination of Hg2+ and Cu2+ ions.The fluorescence intensity of CDs (λex = 340 nm; λem = 420 nm) was unaffected in the presence of the metal ions tested, whereas the red emitting NCs (λex = 340 nm; λem = 640 nm) was strongly quenched by both Cu2+ and Hg2+ ions. Interestingly, the selectivity of the probe toward these two ions was simply switched by controlling the pH of probe solution without using any chelating agent. The probe selectively responded to Hg2+ ions at acidic condition (pH = 4.0), Cu2+ ions at basic condition (pH = 10.0), and Hg2+-Cu2+ mixtures at pHs within this range. The respective detection limitsfor determination of Cu2+ and Hg2+ ions at their specific pH conditions were estimated as 5 nM and 7 nM, over linear ranges of 20-600 nM and 20-2000 nM, respectively. The fabricated ratiometric probe also showed distinguished fluorescence color changes to visual detection of these ions. Finally, the probe was successfully applied to determination of Hg2+ and Cu2+ ions in tap and mineral water samples.
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It is known that tryptophan (Trp) tends to be electropolymerized over a potential window that is mostly applied for voltammetric determination of Trp. Furthermore, over the applied potential range, most of Trp-sensors suffer from some possible interferences. Knowing these challenges motivated us to establish a novel sensing device able to monitor Trp before approaching the mentioned potential range, decreasing memory-effects and some sources of non-linearity during electrochemical measurements. However, considering its molecular structure, it is unrealistic to expect tryptophan oxidation in negative potentials. This work reports the application of a surface-confined chromium-salen complex that delivered a redox couple attributed to Cr(II)/Cr(III) at a low positive potentials. The recorded cyclic voltammograms (CVs) clarified that Trp has a high inhibitory activity toward the chromium oxidation peak in the alkaline medium at a low potential of -0.18â¯V vs. Ag/AgCl. The positive shift of the anodic peak potential of redox reaction disclosed that Trp drastically influenced the capability of the interfacial charge transfer of the modified electrode, the features that was exploited in establishing a sensitive Trp detection method using electrochemical impedance spectroscopy. The proposed sensor was successfully employed to determine Trp over a concentration range of 4.0-60.0â¯nM with the calculated detection limit of 0.78â¯nM.
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Cromo/química , Técnicas Eletroquímicas , Etilenodiaminas/química , Triptofano/análise , Espectroscopia Dielétrica , Eletrodos , Etilenodiaminas/antagonistas & inibidores , Oxirredução , Propriedades de SuperfícieRESUMO
Despite many efforts focused on the emission origin of carbon dots (CDs), it is still a topic of debate. This is mainly due to the complex structure of these nanomaterials. Here, we developed an innovative method to evaluate the number and spectral characterizations of various emission centers in CDs. We monitored the photostability of a series of column-separated CDs under UV irradiation to obtain three-dimensional data sets and resolve them using multivariate decomposition methods. The obtained results clearly revealed the presence of three different types of emission centers in CDs, including molecular states, aromatic domain states, and carbon-core states so that their single or coexisting appearance was found to be deeply dependent on the reaction temperature. Furthermore, density functional theory and time-dependent density functional theory were used to investigate the electronic and optical properties of some different aza-polycyclic and corannulene molecules as possible polycyclic aromatic hydrocarbons responsible for the above-mentioned aromatic domain states.
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The C60 fullerene displays a considerable electronegativity. It has a unique photophysical and electrochemical behavior that can be used as a suitable drug carrier. In the present study, the interaction of C60 fullerene as an electron recipient with the Cefamandole antibiotic was investigated in both ground and excited states using DFT and TD-DFT methods. The study of the interaction of C60 and Cefamandole via electron localization function (ELF) and reduced density gradient (RDG) revealed that the complex formation is of van der Waals type. The data from natural bonding orbitals (NBO) analysis also confirmed the interaction type. The study of absorption and emission spectrum via CAM-B3LYP in the TD-SCF state showed that the emission peak of C60 fullerene in the 591.73nm after the complex formation results in the extinction of this emission spectrum due to charge transfer (CT) from chelator to fluorophore. The photoinduced electron transfer (PET) process was investigated using the electron hole theory.
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Cefamandol/química , Elétrons , Fulerenos/química , Luz , Modelos Moleculares , Nanopartículas/química , Teoria Quântica , Conformação MolecularRESUMO
Fluorescence spectroscopy, ultraviolet-visible absorption spectroscopy, circular dichroism spectroscopy, viscometry, cyclic voltammetry, and differential pulse voltammetry were applied to investigate the competitive interaction of DNA with the three new cycloalkyl α-aminobisphosphonates (D1-D3) and spectroscopic probe, neutral red dye, and Hoechst (HO), in a Tris-hydrogen chloride buffer (pH 7.4). The spectroscopic and voltammetric studies showed that the groove binding mode of interaction is predominant in the solution containing DNA and α-aminobisphosphonates. Furthermore, the results indicated that α-aminobisphosphonate with the lengthy N alkyl chains and larger heterocyclic ring size had a stronger interaction. The principal component analysis and theoretical quantum mechanical and molecular mechanics (QM-DFT B3LYP/6-31+G* and MM-SYBYL) methods were also applied to determine the number of chemical components presented in complexation equilibrium and identify the structure complexes of DNA with the three new cycloalkyl α-aminobisphosphonates (D1-D3), respectively.
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DNA/química , Difosfonatos/química , Animais , Sítios de Ligação , Ligação Competitiva , Bisbenzimidazol/química , Soluções Tampão , Bovinos , Técnicas Eletroquímicas , Corantes Fluorescentes/química , Cinética , Vermelho Neutro/química , Análise de Componente Principal , Teoria Quântica , Soluções , Espectrometria de Fluorescência , TermodinâmicaRESUMO
In this paper a novel electrochemical sensor based on nickel carbide (Ni3C) nanoparticles as a new modifier was constructed. Ni3C nanoparticle was synthesized and characterized by scanning electron microscopy, X-ray diffraction and first-principles study. Electrochemical impedance spectroscopy (EIS) and cyclic voltammetry (CV) studies confirmed the electrode modification. Afterwards, the new electrode for the first time was used for interaction study between vitamin K1 and warfarin as an anticoagulant drug by differential pulse voltammetry. The adduct formation between the drug and vitamin K1 was improved by decreasing in anodic peak current of warfarin in the presence of different amounts of vitamin K1. The binding constant between warfarin and vitamin K1 was obtained by voltammetric and UV-vis and fluorescence spectroscopic methods. The molecular modeling method was also performed to explore the structural features and binding mechanism of warfarin to vitamin K1. The different aspects of modeling of vitamin K1 and warfarin and their adduct structures confirmed the adduct formation by hydrogen bonding.