Quantitative characterization of the global electrophilicity power of common diene/dienophile pairs in Diels–Alder reactions

Virtual Screening for Potential Phytobioactives as Therapeutic Leads to Inhibit NQO1 for Selective Anticancer Therapy

NAD(P)H:quinone acceptor oxidoreductase-1 (NQO1) is a ubiquitous flavin adenine dinucleotide-dependent flavoprotein that promotes obligatory two-electron reductions of quinones, quinonimines, nitroaromatics, and azo dyes. NQO1 is a multifunctional antioxidant enzyme whose expression and deletion are linked to reduced and increased oxidative stress susceptibilities. NQO1 acts as both a tumor suppressor and tumor promoter; thus, the inhibition of NQO1 results in less tumor burden. In addition, the high expression of NQO1 is associated with a shorter survival time of cancer patients. Inhibiting NQO1 also enables certain anticancer agents to evade the detoxification process. In this study, a series of phytobioactives were screened based on their chemical classes such as coumarins, flavonoids, and triterpenoids for their action on NQO1. The in silico evaluations were conducted using PyRx virtual screening tools, where the flavone compound, Orientin showed a better binding affinity score of -8.18 when compared with standard inhibitor Dicumarol with favorable ADME properties. An MD simulation study found that the Orientin binding to NQO1 away from the substrate-binding site induces a potential conformational change in the substrate-binding site, thereby inhibiting substrate accessibility towards the FAD-binding domain. Furthermore, with this computational approach we are offering a scope for validation of the new therapeutic components for their in vitro and in vivo efficacy against NQO1.

The Participation of 3,3,3-Trichloro-1-nitroprop-1-ene in the [3 + 2] Cycloaddition Reaction with Selected Nitrile N-Oxides in the Light of the Experimental and MEDT Quantum Chemical Study

The regioselective zw-type [3 + 2] cycloaddition (32CA) reactions of a series of aryl-substituted nitrile N-oxides (NOs) with trichloronitropropene (TNP) have been both experimentally and theoretically studied within the Molecular Electron Density Theory (MEDT). Zwitterionic NOs behave as moderate nucleophiles while TNP acts as a very strong electrophile in these polar 32CA reactions of forward electron density flux, which present moderate activation Gibbs free energies of 22.8-25.6 kcal·mol-1 and an exergonic character of 28.4 kcal·mol-1 that makes them irreversible and kinetically controlled. The most favorable reaction is that involving the most nucleophilic MeO-substituted NO. Despite Parr functions correctly predicting the experimental regioselectivity with the most favorable O-CCCl3 interaction, these reactions follow a two-stage one-step mechanism in which formation of the O-C(CCl3) bond takes place once the C-C(NO2) bond is already formed. The present MEDT concludes that the reactivity differences in the series of NOs come from their different nucleophilic activation and polar character of the reactions, rather than any mechanistic feature.

Synthesis, Computational Pharmacokinetics Report, Conceptual DFT-Based Calculations and Anti-Acetylcholinesterase Activity of Hydroxyapatite Nanoparticles Derived From Acorus Calamus Plant Extract

Over the years, Alzheimer's disease (AD) treatments have been a major focus, culminating in the identification of promising therapeutic targets. A herbal therapy approach has been required by the demand of AD stage-dependent optimal settings. Present study describes the evaluation of anti-acetylcholinesterase (AChE) activity of hydroxyapatite nanoparticles derived from an Acorus calamus rhizome extract (AC-HAp NPs). The structure and morphology of as-prepared (AC-HAp NPs) was confirmed using powder X-ray diffractometer (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM) and high-resolution transmission electron microscopy (HR-TEM). The crystalline nature of as-prepared AC-HAp NPs was evident from XRD pattern. The SEM analysis suggested the spherical nature of the synthesized material with an average diameter between 30 and 50 nm. Further, the TEM and HR-TEM images revealed the shape and size of as-prepared (AC-HAp NPs). The interplanar distance between two lattice fringes was found to be 0.342 nm, which further supported the crystalline nature of the material synthesized. The anti-acetylcholinesterase activity of AC-HAp NPs was greater as compared to that of pure HAp NPs. The mechanistic evaluation of such an activity carried out using in silico studies suggested that the anti-acetylcholinesterase activity of phytoconstituents derived from Acorus calamus rhizome extract was mediated by BNDF, APOE4, PKC-γ, BACE1 and γ-secretase proteins. The global and local descriptors, which are the underpinnings of Conceptual Density Functional Theory (CDFT), have been predicted through the MN12SX/Def2TZVP/H2O model chemistry to help in the comprehension of the chemical reactivity properties of the five ligands considered in this study. With the further objective of analyzing their bioactivity, the CDFT studies are complemented with the estimation of some useful computed pharmacokinetics indices, their predicted biological targets, and the ADMET parameters related to the bioavailability of the five ligands are also reported.

New α-Hydrazinophosphonic acid: Synthesis, characterization, DFT study and in silico prediction of its potential inhibition of SARS-CoV-2 main protease

A new α-Hydrazinophosphonic acid (HDZPA) has been synthesized and its molecular structure was determined using spectroscopic methods. The Density Functional Theory (DFT) at the B3LYP/6-31 G (d,p) level was utilized to determine the electronic properties, vibrational modes and active sites of the examined molecule. In this context, some quantum chemical parameters have been calculated in order to discuss the reactivity of the studied molecule. Also, the inhibition activity of the investigated α-Hydrazinophosphonic acid for SARS-CoV-2 main protease (Mpro) and RNA dependent RNA polymerase (RdRp) has been predicted using in silico docking.

In Silico Pharmacokinetics, ADMET Study and Conceptual DFT Analysis of Two Plant Cyclopeptides Isolated From Rosaceae as a Computational Peptidology Approach

This research presents the outcomes of a computational determination of the chemical reactivity and bioactivity properties of two plant cyclopeptides isolated from Rosaceae through the consideration of Computational Peptidology (CP), a protocol employed previously in the research of similar molecular systems. CP allows the prediction of the global and local descriptors that are the integral foundations of Conceptual Density Functional Theory (CDFT) and which could help in getting in the understanding of the chemical reactivity properties of the two plant cyclopeptides under study, hoping that they could be related to their bioactivity. The methodology based on the Koopmans in DFT (KID) approach and the MN12SX/Def2TZVP/H2O model chemistry has been successfully validated. Various Chemoinformatics tools have been used to improve the process of virtual screening, thus identifying some additional properties of these two plant cyclopeptides connected to their ability to behave as potentially useful drugs. With the further objective of analyzing their bioactivity, the CP protocol is complemented with the estimation of some useful parameters related to pharmacokinetics, their predicted biological targets, and the Absorption, Distribution, Metabolism, Excretion and Toxicity (ADMET) parameters related to the bioavailability of the two plant cyclopeptides under study are also reported.

Catalytic Asymmetric Aza-Diels-Alder Reaction of Ketimines and Unactivated Dienes

The enantioselective aza-Diels-Alder reaction is efficient for constructing chiral tetrahydropyridines, but the catalytic asymmetric aza-Diels-Alder reaction of ketimines with unactivated dienes is still a challenging topic. Herein, guided by computational screening, a highly enantioselective aza-Diels-Alder reaction of 2-aryl-3H-indol-3-ones with unactivated dienes was realized by using a B(C₆ F₅ )₃ /chiral phosphoric acid catalyst system under mild conditions. The reaction has a broad scope with respect to both aza-Diels-Alder reaction partners and hence offers rapid access to an array of tetrahydropyridine derivatives with pretty outcomes (up to 99 % yield, >20:1 dr and 98:2 er). The reaction is very efficient: lowering catalyst loadings for the model reaction to 0.1 mol %, enantioselectivity is still maintained. The synthetic utility was confirmed by transformations of the products. DFT calculations provide convincing evidence for the interpretation of stereoselection.

Understanding the reaction mechanism of the regioselective piperidinolysis of aryl 1-(2,4-dinitronaphthyl) ethers in DMSO: Kinetic and DFT studies

Reactions of aryl 1-(2,4-dinitronaphthyl) ethers with piperidine in dimethyl sulfoxide at 25oC resulted in substitution of the aryloxy group at the ipso carbon atom. The reaction was measured spectrophotochemically and the kinetic studies suggested that the titled reaction is accurately third order. The mechanism is began by fast nucleophilic attack of piperidine on C1 to form zwitterion intermediate (I) followed by deprotonation of zwitterion intermediate (I) to the Meisenheimer ion (II) in a slow step, that is, SB catalysis. The regular variation of activation parameters suggested that the reaction proceeded through a common mechanism. The Hammett equation using reaction constant σo values and Brønsted coefficient value showed that the reaction is poorly dependent on aryloxy substituent and the reaction was significantly associative and Meisenheimer intermediate-like. The mechanism of piperidinolysis has been theoretically investigated using density functional theory method using B3LYP/6-311G(d,p) computational level. The combination between experimental and computational studies predicts what mechanism is followed either through uncatalyzed or catalyzed reaction pathways, that is, SB and SB-GA. The global parameters of the reactants, the proposed activated complexes, and the local Fukui function analysis explained that C1 carbon atom is the most electrophilic center of ether. Also, kinetics and theoretical calculation of activation energies indicated that the mechanism of the piperidinolysis passed through a two-step mechanism and the proton transfer process was the rate determining step.

New insight into the mechanism of carbon dioxide activation on copper-based catalysts: A theoretical study

A combination of Artificial Bee Colony algorithm, eXtended Tight Binding and Density functional theory methods were performed to study the activation process of carbon dioxide (CO₂) over copper (Cu₄ cluster) based catalytic systems. The findings revealed that the activation of the C-O bond resulted from the electron transfer to σ*, π* - MO of CO₂. The more the electrons are transferred to CO₂, the more the C-O bond is activated and elongated. The suitability of several metal oxide supports (Fe₂O₃, Al₂O₃, MgO, ZnO) is estimated using calculated electronic parameters (global electrophilicity index, vertical ionization potential and vertical electron affinity). Aside from demonstrating the appropriateness of Al₂O₃ and ZnO, a thorough examination of MgO revealed that, due to the formation of stable carbonate products, this oxide is not really appropriate as a support for copper-based catalysts in CO₂ conversion. Our studies have also shown that the electron enrichment of copper atoms plays a key role in the activation of C-O bonds. Alkali metal doping (Li, K, Cs) significantly improves the catalytic efficiency of the Cu₄ cluster. Based on the results of electron transfer to the CO₂ molecule, the effect of doping alkali metal atoms may be organized in the following order: Cs > K > Li. A new core/shell catalytic system with potassium atoms in the core and copper atoms in the shell has been proposed and has proven to be a promising, efficient catalytic system in the CO₂ adsorption and activation.

Effect of the Nucleophile's Nature on Chloroacetanilide Herbicides Cleavage Reaction Mechanism. A DFT Study

In this study, the degradation mechanism of chloroacetanilide herbicides in the presence of four different nucleophiles, namely: Br^-, I^-, HS^-, and S₂O₃^-2, was theoretically evaluated using the dispersion-corrected hybrid functional wB97XD and the DGDZVP as a basis set. The comparison of computed activation energies with experimental data shows an excellent correlation (R² = 0.98 for alachlor and 0.97 for propachlor). The results suggest that the best nucleophiles are those where a sulfur atom performs the nucleophilic attack, whereas the other species are less reactive. Furthermore, it was observed that the different R groups of chloroacetanilide herbicides have a negligible effect on the activation energy of the process. Further insights into the mechanism show that geometrical changes and electronic rearrangements contribute 60% and 40% of the activation energy, respectively. A deeper analysis of the reaction coordinate was conducted, employing the evolution chemical potential, hardness, and electrophilicity index, as well as the electronic flux. The charge analysis shows that the electron density of chlorine increases as the nucleophilic attack occurs. Finally, NBO analysis indicates that the nucleophilic substitution in chloroacetanilides is an asynchronous process with a late transition state for all models except for the case of the iodide attack, which occurs through an early transition state in the reaction.

The use of minimal topological differences to inspire the design of novel tetrahydroisoquinoline analogues with antimalarial activity

A quantitative structure-activity relationship (QSAR) study was conducted using nineteen previously synthesized, and tested 1-aryl-6-hydroxy-1,2,3,4-tetrahydroisoquinolines with proven in vitro activities against Plasmodium falciparum. In order to computationally design and screen potent antimalarial agents, these compounds with known biological activity ranging from 0.697 to 35.978 μM were geometry optimized at the B3LYP/6-311 + G(d,p) level of theory, using the Gaussian 09W software. To calculate the topological differences, the series of the nineteen compounds was superimposed and a hypermolecule obtained with s¯ = 17 and 20 vertices. Other molecular descriptors were considered in order to build a highly predictive QSAR model. These include the minimal topological differences (MTD), LogP, two dimensional polarity surface area (TDPSA), dipole moment (μ), chemical hardness (η), electrophilicity (ω), potential energy (E_p), electrostatic energy (E_ele) and number of rotatable bonds (NRB). By using a training set composed of 15 randomly selected compounds from this series, several QSAR equations were derived. The QSAR equations obtained were then used to attempt to predict the IC₅₀ values of 4 remaining compounds in a test (or validation) set. Ten analogues were proposed by a fragment search of a fragment library containing the pharmacophore model of the active compounds contained in the training set. The most active proposed analogue showed a predicted activity within the lower micromolar range.

Optimization of Sibipiruna activated carbon preparation by simplex-centroid mixture design for simultaneous adsorption of rhodamine B and metformin

The present paper reports the application of augmented simplex-centroid mixture design to obtain a high BET surface area activated carbon using as reactants KOH, K₂CO₃ and K₂C₂O₄. The optimum mixture composition was 2.51 g of KOH, 0.49 g of K₂CO₃ and absence of K₂C₂O₄, generating an optimized AC (AC_op) with S_BET value equals to 1984 m² g^-1. The results herein obtained show that low amounts of K₂CO₃ can catalyze the pore development in the presence of KOH, increasing the surface area. Furthermore, the fractal dimensions of AC_op are greater than 2.72, indicating the material has a complex pore structure with irregularities self-similar upon variations of resolution, as seen by SEM images. The TPD curves showed that the AC_op has different oxygenated molecular fragments, which agrees with the pH_PZC value (5.05). The AC_op was applied in the adsorption of rhodamine B (RhB) and metformin (Met) in both binary and monocomponent systems. The simultaneous adsorption at 30 °C reveals that the adsorption capacity of RhB is 630.94 mg g^-1, while for Met the value is 103.83 mg g^-1.

Reactivity of 3-nitroindoles with electron-rich species

The indol(in)e building block is one of the "privileged-structures" for the pharmaceutical industry since this fragment plays a central role in drug discovery. While the electron-rich character of the indole motif has been investigated for decades, exploiting the electrophilic reactivity of 3-nitroindole derivatives has recently been put at the heart of a wide range of new, albeit challenging, chemical reactions. In particular, dearomatization processes have considerably enriched the scope of C2[double bond, length as m-dash]C3 functionalizations of these scaffolds. This feature article showcases this remarkable electrophilic reactivity of 3-nitroindoles with electron-rich species and highlights their value in generating diversely substituted indol(in)es. This compilation underlines how these heteroaromatic templates have gradually become model substrates for electron-poor aromatic compounds in dearomatization strategies.

Are There Only Fold Catastrophes in the Diels-Alder Reaction Between Ethylene and 1,3-Butadiene?

This work revisits the topological characterization of the Diels-Alder reaction between 1,3-butadiene and ethylene. In contrast to the currently accepted rationalization, we here provide strong evidence in support of a representation in terms of seven structural stability domains separated by a sequence of 10 elementary catastrophes, but all are only of the fold type (F and F^†), that is, C₄H₆ + C₂H₄:1-7-[FF]F[F^†F^†][F^†F^†][FF]F^†-0: C₆H₁₀. Such an unexpected finding provides fundamental new insights opening simplifying perspectives concerning the rationalization of the CC bond formation in pericyclic reactions in terms of the simplest Thom's elementary catastrophe, namely, the one-(state) variable, one-(control) parameter function.

Analysis of the possibility and molecular mechanism of carbon dioxide consumption in the Diels-Alder processes

The large and significant increase in carbon dioxide concentration in the Earth’s atmosphere is a serious problem for humanity. The amount of CO2 is increasing steadily which causes a harmful greenhouse effect that damages the Earth’s climate. Therefore, one of the current trends in modern chemistry and chemical technology are issues related to its utilization. This work includes the analysis of the possibility of chemical consumption of CO2 in Diels-Alder processes under non-catalytic and catalytic conditions after prior activation of the C=O bond. In addition to the obvious benefits associated with CO2 utilization, such processes open up the possibility of universal synthesis of a wide range of internal carboxylates. These studies have been performed in the framework of Molecular Electron Density Theory as a modern view of the chemical reactivity. It has been found, that explored DA reactions catalyzed by Lewis acids with the boron core, proceeds via unique stepwise mechanism with the zwitterionic intermediate. Bonding Evolution Theory (BET) analysis of the molecular mechanism associated with the DA reaction between cyclopentadiene and carbon dioxide indicates that it takes place thorough a two-stage one-step mechanism, which is initialized by formation of C–C single bond. In turn, the DA reaction between cyclopentadiene and carbon dioxide catalysed by BH3 extends in the environment of DCM, indicates that it takes place through a two-step mechanism. First path of catalysed DA reaction is characterized by 10 different phases, while the second by eight topologically different phases.

The Role of the Catalyst on the Reactivity and Mechanism in the Diels–Alder Cycloaddition Step of the Povarov Reaction for the Synthesis of a Biological Active Quinoline Derivative: Experimental and Theoretical Investigations

An experimental and theoretical study of the reactivity and mechanism of the non-catalyzed and catalyzed Povarov reaction for the preparation of a 4-ethoxy-2,3,4,4a-tetrahydro-2-phenylquinoline as a biological active quinoline derivative has been performed. The optimization of experimental conditions indicate that the use of a catalyst, namely Lewis acid with an electron-releasing group, creates the best experimental conditions for this kind of reaction. The chemical structure was characterized by the usual spectroscopic methods. The prepared quinoline derivative has been also tested in vitro for antibacterial activity, which displays moderate inhibitory activity against both Escherichia coli and Staphylococcus aureus. The antioxidant activity was investigated in vitro by evaluating their reaction with 1,1-diphenyl-2-picrylhydrazyl DPPH radical, which reveals high reactivity. The computational study was performed on the Diels–Alder step of the Povarov reaction using a B3LYP/6-31G(d,p) level of theory. The conceptual DFT reactivity indices explain well the reactivity and the meta regioselectivity experimentally observed. Both catalysts enhance the reactivity of the imine, favoring the formation of the meta regioisomers with a low activation energy, and they change the mechanism to highly synchronous for the Lewis acid and to stepwise for the Brønsted acid. The reaction of imine with allyl alcohol does not give any product, which requires high activation energy.

Theoretical Study of closo-Borate Anions [BnHn]2− (n = 5–12): Bonding, Atomic Charges, and Reactivity Analysis

This study has focused on the structure, bonding, and reactivity analysis of closo-borate anions [BnHn]2− (n = 5–12). Several descriptors of B–H interactions have been calculated. It has been found that the values of electron density and total energy at bond critical point are the most useful descriptors for investigation of B–H interactions. Using results from the descriptor analysis, one may conclude that orbital interactions in [BnHn]2− increase with increasing the boron cluster size. Several approaches to estimate atomic charges have been applied. Boron atoms in apical positions have more negative values of atomic charges as compared with atoms from equatorial positions. The mean values of boron and hydrogen atomic charges tend to be more positive with the increasing of boron cluster size. Global and local reactivity descriptors using conceptual density functional theory (DFT) theory have been calculated. Based on this theory, the closo-borate anions [BnHn]2− (n = 5–9) can be considered strong and moderate electrophiles, while the closo-borate anions [BnHn]2− (n = 10–12) can be considered marginal electrophiles. Fukui functions for electrophilic attack have been calculated. Fukui functions correlate well with atomic charges of the closo-borate anions. Boron atoms in apical positions have the most positive values of Fukui functions.

Flavonoid content of the Libyan Onosma Cyrenaicum: isolation, identification, electronic chemical reactivity, drug likeness, docking, and MD study

In this work, an attempt to identify the flavonoid content of the Libyan Onosma Cyrenaicum led to the isolation of three flavonoids 7,8-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one(GE-001), 5,7-dihydroxy-2-(3-hydroxy-4-methoxy phenyl)-4H-chromen-4-one (GE-002) and 5,7-dihydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one (GE-003), the isolated compounds were characterized using ¹H and ¹³C-NMR techniques. A further DFT study at ωB97-XD with 6-311++G** basis set in water was conducted to calculate the isolated compounds' global and local reactivity descriptors and Fukui indices along with their antioxidant activity. The drug-likeness and bioactivity properties of the isolated compounds were estimated and discussed. Finally, GE-001, GE-002, and GE-003 were docked into HCV NS5B polymerase active siteand this was followed by molecular dynamic simulation to certify the obtained docking result and to obtain the MM-GBSA free binding energyy of the isolated compounds. Communicated by Ramaswamy H. Sarma.

Unveiling the molecular mechanisms of the cycloaddition reactions of aryl hetaryl thioketones and C,N-disubstituted nitrilimines

Many synthetic routes to constructing biologically active heterocyclic compounds are made feasible through the (3 + 2) cycloaddition (32CA) reactions. Due to a large number of possible combinations of several heteroatoms from either the three-atom components (TACs) or the ethylene derivatives, the potential of the 32CA reactions in heterocyclic syntheses is versatile. Herein, the cycloaddition reaction of thiophene-2-carbothialdehyde derivatives and C,N-disubstituted nitrilimines have been studied through density functional theory (DFT) calculations at the B3LYP/6-311G(d,p) level of theory. In the present study, a one-step 32CA and two-step (4 + 3) cycloaddition (43CA) reaction mechanisms involved in TACs reactions and ethylene derivative have been investigated. In all reactions considered, the one-step 32CA cycloaddition is preferred over the two-step 43CA. The TAC chemoselectively adds across the thiocarbonyl group present in the ethylene derivative in a 32CA fashion to form the corresponding cycloadduct. Analysis of the electrophilic [Formula: see text] and nucleophilic [Formula: see text] Parr functions at the various reaction centers in the ethylene derivative show that the TAC adds across the atomic centers with the largest Parr functions, which is in total agreement with the experimental observation. The selectivities observed in the titled reactions are kinetically controlled.

The Cascade Reactions of Indigo with Propargyl Substrates for Heterocyclic and Photophysical Diversity

The synthesis of structurally diverse heterocycles for chemical space exploration was achieved via the cascade reactions of indigo with propargylic electrophiles. New pyrazinodiindolodione, naphthyridinedione, azepinodiindolone, oxazinoindolone and pyrrolodione products were prepared in one pot reactions by varying the leaving group (-Cl, -Br, -OMs, -OTs) or propargyl terminal functionality (-H, -Me, -Ph, -Ar). Mechanistic and density functional theory studies revealed that the unsaturated propargyl moiety can behave as an electrophile when aromatic terminal substitutions are made, and therefore competes with leaving group substitution for new outcomes. Selected products from the cascade reactions were investigated for their absorption and fluorescence properties, including transient absorption spectroscopy. This revealed polarity dependent excited state relaxation pathways, fluorescence, and triplet formation, thus highlighting these reactions as a means to access diverse functional materials rapidly.

The Azide-Allene Dipolar Cycloaddition: Is DFT Able to Predict Site- and Regio-Selectivity?

The site- and regio-selectivity of thermal, uncatalysed 1,3-dipolar cycloadditions between arylazides and mono- or tetra-substituted allenes with different electronic features have been investigated by both conceptual (reactivity indices) and computational (M08-HX, ωB97X-D, and B3LYP) DFT approaches. Both approaches show that these cycloadditions follow a nonpolar one-step mechanism. The experimental site- and regio-selectivity of arylazides towards methoxycarbonyl- and sulfonyl-allenes as well as tetramethyl- and tetrafluoro-allenes was calculated by DFT transition state calculations, achieving semiquantitative agreement to both previous and novel experimental findings. From the mechanistic standpoint, 1H-NMR evidence of a methylene-1,2,3-triazoline intermediate reinforces the reliability of the computational scheme.