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

Perfluorobicyclo[2.2.0]hex-1(4)-ene as unique partner for Diels–Alder reactions with benzene: a density functional theory study

The mechanism of the Diels–Alder reactions between perfluorobicyclo[2.2.0]hex-1(4)-ene (1a) and bicyclo[2.2.0]hex-1(4)-ene (1b) with benzene (2a) and naphthalene (2b) has been studied within the density functional theory at the MPWB1K/6-311G(d,p) level. The bonding pattern in these reactions is analyzed in the topology of the electron localization function within the bonding evolution theory perspective. The bonding electron density changes along the reaction paths reveal that the C–C bond formation takes place through a synchronous and non-concerted one-step mechanism and proceeds with a moderate activation energy. The reactivity order with 1a is 2a–2b. The reactions begin by the rupture of the double bond in the strained 1a-b molecules, and then two pseudoradical centers at the 1a-b fragments are created. Finally, at the same time, two new single bonds are formed in the cycloaddition products. The TSs proceed with high global electron density transfer providing a polar character at these reactions.

Unveiling the Unexpected Reactivity of Electrophilic Diazoalkanes in [3+2] Cycloaddition Reactions within Molecular Electron Density Theory

The [3+2] cycloaddition (32CA) reactions of strongly nucleophilic norbornadiene (NBD), with simplest diazoalkane (DAA) and three DAAs of increased electrophilicity, have been studied within the Molecular Electron Density Theory (MEDT) at the MPWB1K/6-311G (d,p) computational level. These pmr-type 32CA reactions follow an asynchronous one-step mechanism with activation enthalpies ranging from 17.7 to 27.9 kcal·mol−1 in acetonitrile. The high exergonic character of these reactions makes them irreversible. The presence of electron-withdrawing (EW) substituents in the DAA increases the activation enthalpies, in complete agreement with the experimental slowing-down of the reactions, but contrary to the Conceptual DFT prediction. Despite the nucleophilic and electrophilic character of the reagents, the global electron density transfer at the TSs indicates rather non-polar 32CA reactions. The present MEDT study establishes the depopulation of the N–N–C core in this series of DAAs with the increase of the EW character of the substituents present at the carbon center is responsible for the experimentally found deceleration.

A molecular electron density theory study for [3+2] cycloaddition reactions of N-benzylcyclohexylnitrone with methyl-3-butenoate

The [3+2] cycloaddition (32CA) reactions of N-benzylcyclohexylnitrone 1 with methyl-3-butenoate 2 have been studied within molecular electron density theory (MEDT) at the B3LYP/6-311++G(d,p) level of theory.

Deep eutectic solvent assisted synthesis of dihydropyrimidinones/thiones via Biginelli reaction: theoretical investigations on their electronic and global reactivity descriptors

DES 2 (ZrOCl2·8H2O-ethylene glycol at 1 : 2 ratio) was used as a catalyst for the synthesis of dihydropyrimidinones/thiones via a Biginelli reaction.

Exploring the antioxidant activity of thiaflavan compounds: a quantum chemical study

Conceptual DFT tools (HAT, SPLET, SET-PT, aromaticity index,…) have been used to explore the antioxidant activity of thiaflavan compounds, and predict which derivate should be the best one.

DFT Study on the Electronic Properties, Spectroscopic Profile, and Biological Activity of 2-Amino-5-trifluoromethyl-1,3,4-thiadiazole with Anticancer Properties

Extensive investigation on the molecular and electronic structure of 2-amino-5-trifluoromethyl-1,3,4-thiadiazole in the ground state and in the first excited state has been performed. The energy barrier corresponding to the conversion between imino and amino tautomers has been calculated, which indicates the existence of amino tautomer in solid state for the title compound. The FT-Raman and FT-IR spectra were recorded and compared with theoretical vibrational wavenumbers, and a good coherence has been observed. The MESP map, dipole moment, polarizability, and hyperpolarizability have been calculated to comprehend the properties of the title molecule. High polarizability value estimation of the title compound may enhance its bioactivity. Natural bonding orbital analysis has been done on monomer and dimer to investigate the charge delocalization and strength of hydrogen bonding, respectively. Strong hydrogen bonding interaction energies of 17.09/17.49 kcal mol^-1 have been calculated at the B3LYP/M06-2X functional. The UV-vis spectrum was recorded and related to the theoretical spectrum. The title compound was biologically examined for anticancer activity by studying the cytotoxic performance against two human cancer cell lines (A549 and HeLa) along with the molecular docking simulation. Both molecular docking and cytotoxic performance against cancer cell lines show positive outcomes, and the title compound appears to be a promising anticancer agent.

Participation of Phosphorylated Analogues of Nitroethene in Diels–Alder Reactions with Anthracene: A Molecular Electron Density Theory Study and Mechanistic Aspect

The structure and the contribution of the bis(2-chloroethyl) 2-nitro 1a and 2-bromo-2-nitroethenylphosphonates 1b with anthracene 2 in the Diels–Alder (DA) reactions have been studied within the Molecular Electron Density Theory (MEDT) at the B3LYP functional together with 6-31G(d), 6-31+G(d) and 6-31+G(d,p) basic sets. Analysis of the Conceptual Density Functional Theory (CDFT) reactivity indices indicates that 1a and 1b can be classified as a strong electrophile and marginal nucleophile, while 2 is classified as a strong electrophile and strong nucleophile. The studied DA reactions take place through a one-step mechanism. A Bonding Evolution Theory (BET) of the one path associated with the DA reaction of 1a with 2 indicates that it is associated with non-concerted two-stage one-step mechanism. BET analysis shows that the first C2-C3 single bond is formed in Phase VI, while the second C1-C6 single bond is formed in the Phase VIII. The formation of both single bonds occurs through the merging of two C2 and C3, C1 and C6 pseudoradical centers, respectively.

A DFT study of fulvic acid binding with bivalent metals: Cd, Cu, Mg, Ni, Pb, Zn

3,7,8-Trihydroxy-3-methyl-10-oxo-4,10-dihydro-1H,3H-pyrano [4,3-b]chromene-9-carboxylic acid is a structurally well-characterized fulvic acid (FA) capable to act as a polyfunctional bidentate ligand in the complexes with metal ions. Investigations of the formation mechanisms and structure of the above-mentioned FA complexes with bivalent metals [Cd(II), Cu(II), Mg(II), Ni(II), Pb(II) and Zn(II)] are presently an actual and trending topic in the modern chemistry of humic and fulvic acids. Furthermore, the importance of the theoretical DFT investigations of binding of metals with fulvic acids is stipulated by the lack of the relevant experimental structural data for such complexes. The quantum chemical calculations have shown that, of the four possible FA tautomers, the two FA forms are more stable. The wavefunction analysis and computed reactivity descriptors (electrostatic potential, Hirshfeld surface analysis, natural population analysis charges, and condensed Fukui indexes) give the insight on the properties and reactive ability of these two different forms of the FA. The computed thermochemical parameters of the ion-exchange reaction explain the metal binding affinity and selectivity of the FA forms.

A MEDT computational study of the mechanism, reactivity and selectivity of non-polar [3+2] cycloaddition between quinazoline-3-oxide and methyl 3-methoxyacrylate

The Molecular Electron Density Theory (MEDT) was used for the study of the mechanism and the selectivity of the [3+2] cycloaddition reaction between quinazoline-3-oxide and methyl 3-methoxyacrylate, using the B3LYP/6-31G(d,p) DFT method. In gas phase, this [3+2] cycloaddition reaction is characterized by a completely ortho regioselectivity and a moderate exo stereoselectivity. Dichloroethane solvent did not modify the selectivities obtained in gas phase but increase the activation energies and decrease the exothermic character. Analysis of thermodynamic characters indicates that by the inclusion of the experimental conditions, the reaction becomes endergonic and thereby under thermodynamic control favouring the formation of the most stable product as observed experimentally, explaining the exo stereoselectivity. The analysis of the global electron density transfer (GEDT) at the transition states and bond order (BO) show that this reaction takes place via a very slightly synchronous and non-polar one-step mechanism. Conceptual DFT reactivity indices analysis accounts for the electrophilic character of the reagents, explaining the high obtained free activation energies, while local Parr functions analysis allows us to explain the ortho regioselectivity observed experimentally. ELF topological analysis of the most favoured reactive pathways indicates that mechanism of this 32CA reaction is one stage, one step, synchronous and non-concerted. The stability of the favourable cycloadduct is attributed to the presence of different non-conventional hydrogen bonds interactions as indicated by NCI and QTAIM analyses. Graphical Abstract.

Understanding the Reactivity of Trimethylsilyldiazoalkanes Participating in [3+2] Cycloaddition Reactions towards Diethylfumarate with a Molecular Electron Density Theory Perspective

A Molecular Electron Density Theory (MEDT) study is presented here for [3+2] cycloaddition (32CA) reactions of three trimethylsilyldiazoalkanes with diethyl fumarate. The presence of silicon bonded to the carbon of these silyldiazoalkanes changes its structure and reactivity from a pseudomonoradical to that of a zwitterionic one. A one-step mechanism is predicted for these polar zw-type 32CA reactions with activation enthalpies in CCl4 between 8.0 and 19.7 kcal·mol−1 at the MPWB1K (PCM)/6-311G(d,p) level of theory. The negative reaction Gibbs energies between −3.1 and −13.2 kcal·mole−1 in CCl4 suggests exergonic character, making the reactions irreversible. Analysis of the sequential changes in the bonding pattern along the reaction paths characterizes these zw-type 32CA reactions. The increase in nucleophilic character of the trimethylsilyldiazoalkanes makes these 32CA reactions more polar. Consequently, the activation enthalpies are decreased and the TSs require less energy cost. Non-covalent interactions at the TSs account for the stereoselectivity found in these 32CA reactions involving the bulky trimethylsilyl group.

The effect of cation-π interactions on the stability and electronic properties of anticancer drug Altretamine: a theoretical study

The present work utilizes density functional theory (DFT) calculations to study the influence of cation-π interactions on the electronic properties of the complexes formed by Altretamine [2,4,6-tris(dimethylamino)-1,3,5-triazine], an anticancer drug, with mono- and divalent (Li⁺, Na⁺, K⁺, Be²⁺, Mg²⁺ and Ca²⁺) metal cations. The structures were optimized with the M06-2X method and the 6-311++G(d,p) basis set in the gas phase and in solution. The theory of `Atoms in Molecules' (AIM) was applied to study the nature of the interactions by calculating the electron density ρ(r) and its Laplacian at the bond critical points. The charge-transfer process during complexation was evaluated using natural bond orbital (NBO) analysis. The results of DFT calculations demonstrate that the strongest/weakest interactions belong to Be²⁺/K⁺ complexes. There are good correlations between the achieved densities and the amounts of charge transfer with the interaction energies. Finally, the stability and reactivity of the cation-π interactions can be determined by quantum chemical computation based on the molecular orbital (MO) theory.

Reactions of 3-aryl-1-(trifluoromethyl)prop-2-yn-1-iminium salts with 1,3-dienes and styrenes

3-Aryl-1-(trifluoromethyl)prop-2-yn-1-iminium triflate salts represent a novel, highly reactive class of acetylenic iminium salts. Herein we present several reactions which are based on the electron-poor acetylenic bond and on the high electrophilicity of the CF₃-substituted iminium group. These salts were found to be highly reactive dienophiles in Diels–Alder reactions with cyclopentadiene, 2,3-dimethylbutadiene and even anthracene. At higher temperature, the cycloadducts undergo an intramolecular S_E(Ar) reaction leading to condensed carbocycles incorporating a 1-(trifluoromethyl)-1-(dimethylamine)indene ring system. With styrenes and some substituted styrenes, cascade reactions take place, which likely include cyclobutene and several cationic intermediates and mainly yield 2-(1-phenylvinyl)indenes. In a similar reaction cascade, a fulvene derivative was obtained with 1,4-diphenylbutadiene as the substrate.

Unprecedented Regio- and Stereoselective Synthesis of Pyrene-Grafted Dispiro[indoline-3,2'-pyrrolidine-3',3″-indolines]: Expedient Experimental and Theoretical Insights into Polar [3 + 2] Cycloaddition

A series of dispiro[indoline-3,2'-pyrrolidine-3',3″-indolines] was synthesized via a multicomponent polar [3 + 2] cycloaddition (32CA) reaction of isatin derivatives, sarcosine and (E)-3-(2-oxo-2-(pyren-1-yl)ethylidene)indolin-2-one derivatives. The regio- and stereochemistries of the cycloadducts were established on the basis of one-dimensional (1D) (1H-, 13C-, 13C-CRAPT NMR) and two-dimensional (2D) homonuclear and heteronuclear correlation NMR spectrometry experiments (1H-1H gDQFCOSY, 13C-1H-HSQCAD, 13C-1H-HMBCAD, 1H-1H-ROESYAD). The molecular mechanism and regio- and stereoselectivities of the cycloaddition (CA) reaction have been investigated utilizing a density functional theory (DFT) method and were thoroughly explained based on the transition-state stabilities and global/local electrophilicity/nucleophilicity reactivity indices of the reactants.

Deciphering the Mechanism of Silver Catalysis of “Click” Chemistry in Water by Combining Experimental and MEDT Studies

A combined experimental study and molecular electron density theory (MEDT) analysis was carried out to investigate the click of 1,2,3-triazole derivatives by Ag(I)-catalyzed azide-alkyne cycloaddition (AgAAC) reaction as well as its corresponding mechanistic pathway. Such a synthetic protocol leads to the regioselective formation of 1,4-disubstituted-1,2,3-triazoles in the presence of AgCl as catalyst and water as reaction solvent at room temperature and pressure. The MEDT was performed by applying Density Functional Theory (DFT) calculations at both B3LYP/6-31G(d,p) (LANL2DZ for Ag) and ωB97XD/6-311G(d,p) (LANL2DZ for Ag) levels with a view to decipher the observed regioselectivity in AgAAC reactions, and so to set out the number of silver(I) species and their roles in the formation of 1,4-disubstituted-1,2,3-triazoles. The comparison of the values of the energy barriers for the mono- and dinuclear Ag(I)-acetylide in the AgAAC reaction paths shows that the calculated energy barriers of dinuclear processes are smaller than those of the mononuclear one. The type of intramolecular interactions in the investigated AgAAC click chemistry reaction accounts for the regioselective formation of the 1,4-regiosisomeric triazole isomer. The ionic character of the starting compounds, namely Ag-acetylide, is revealed for the first time. This finding rules out any type of covalent interaction, involving the silver(I) complexes, along the reaction pathway. Electron localization function (ELF) topological analysis of the electronic structure of the stationary points reaffirmed the zw-type (zwitterionic-type) mechanism of the AgAAC reactions.

In silico molecular investigations of pyridine N-Oxide compounds as potential inhibitors of SARS-CoV-2: 3D QSAR, molecular docking modeling, and ADMET screening

The new coronavirus SARS-CoV-2 virus is causing a severe pneumonia in human, provoking the serious outbreak epidemic CoV-2. Since its appearance in Wuhan, China on December 2019, CoV-2 becomes the biggest challenge the world is facing today, including the discovery of antiviral drug for SARS-CoV-2. In this study, the potential inhibitory of a class of human SARS inhibitors, namely pyridine N-oxide derivatives, against CoV-2 was addressed by quantitative structure-activity relationship 3 D-QSAR. The reliable CoMSIA developed model of 110 pyridine N-oxide based-antiviral compounds, showed Q²= 0.54 and rext2=0.71. The molecular surflex-docking was applied to identify the crystal structure of CoV-2 main protease 3CLpro (PDB: 6LU7) and two potentially and largely used antiviral molecules, namely chloroquine, hydroxychloroquine. The obtained free energy affinity and ADMET properties indicate that among the series of model antiviral compounds examined, the new antiviral compound A5 could be an excellent antiviral drug inhibitor against COVID-19. The inhibition activity of pyridine N-oxyde compounds against CoV-2 was compared with the activity of two common antiviral drug, namely chloroquine (CQ) and hydroxychloroquine (HCQ). DFT method was also used to define the sites of reactivity of pyridine N-oxyde derivatives as well as CQ and HCQ.Communicated by Ramaswamy H. Sarma.

Theoretical Characterization of Catalytically Active Species in Reductive Hydroxymethylation of Styrene with CO2 over a Bisphosphine-Ligated Copper Complex

In this work, a density functional theory (DFT) study was performed to identify the catalytically active species in the copper-catalyzed three-component reductive hydroxymethylation of styrene with CO₂ and hydrosilane. The calculations reveal that the dimeric copper(I) hydride species, formed in a mixture of the bisphosphine ligand, Cu(OAc)₂, and hydrosilane, probably acts as the catalyst precursor. In the beginning, this species is catalytically competent to trigger the hydrocupration of styrene, along with the formation of the dimeric copper(I) alkyl intermediate. Subsequently, CO₂ insertion into the dimeric copper(I) alkyl intermediate occurs, which is accompanied by the cleavage of the Cu-Cu bond and the generation of the monomeric copper(I) carboxylate intermediate. In the end, the sequential reduction of the monomeric copper(I) carboxylate intermediate with the hydrosilane produces the monomeric copper(I) hydride species as the actual catalyst and turns on the catalytic cycle. On the other hand, the monomeric copper(II) hydride species, yielded as the kinetic product in the initial reaction of the bisphosphine ligand, Cu(OAc)₂, and hydrosilane, is also reactive for the hydrocupration of styrene. However, the resulting monomeric copper(II) alkyl intermediate is found to be the catalyst resting state, because of the much higher energy barrier demanded for the subsequent nucleophilic attack toward CO₂. On the basis of the results of an activation-strain model (ASM) analysis and charge decomposition analysis (CDA), the low activity of the monomeric copper(II) alkyl intermediate can be ascribed to the more crowded environment around the central copper(II) ion and the weaker nucleophilicity of the alkyl moiety. Furthermore, all of the possible CuH species generated in the system are competent to promote the two-component hydrosilylation of CO₂ with hydrosilane, which is an inevitable side reaction along with the reductive hydroxymethylation of styrene with CO₂ and hydrosilane.

2-Aminobenzothiazole-Containing Copper(II) Complex as Catalyst in Click Chemistry: An Experimental and Theoretical Study

The reaction of copper(II) acetate with the 2-aminobenzothiazole (abt) heterocycle affords the new copper(II) complex of formula [Cu(abt)2(OOCCH3)2] (1) in a straightforward manner. Compound 1 served as a precatalyst for azide/alkyne cycloaddition reactions (CuAAC) in water, leading to 1,4-disubstituted-1,2,3-triazole derivatives in a regioselective manner and with excellent yields at room temperature. The main advantages of the coordination of such a heterocyclic ligand in 1 are its strong σ-donating ability (N-Cu), nontoxicity and biological properties. In addition, the click chemistry reaction conditions using 1 allow the formation of a great variety of 1,2,3-triazole-based heterocyclic compounds that make this protocol potentially relevant from biological and sustainable viewpoints. A molecular electron density theory (MEDT) study was performed by using density functional theory (DFT) calculations at the B3LYP/6-31G(d,p) (LANL2DZ for Cu) level to understand the observed regioselectivity in the CuAAC reaction. The intramolecular nature of this reaction accounts for the regioselective formation of the 1,4-regioisomeric triazole derivatives. The ionic nature of the starting copper-acetylide precludes any type of covalent interaction throughout the reaction, as supported by the electron localization function (ELF) topological analysis, reaffirming the zwitterionic-type (zw-type) mechanism of the copper(I)/aminobenzothiazole-catalysed azide-alkyne cycloaddition reactions.

Unravelling the regio- and stereoselective synthesis of bicyclic N,O-nucleoside analogues within the molecular electron density theory perspective

The [3 + 2] cycloaddition (32CA) reactions of 1-pyrroline-1-oxide with N-vinyl nucleobases leading to bicyclic N,O nucleoside analogues have been studied within the molecular electron density theory (MEDT) at the MPWB1K/6-311G(d,p) computational level. These non-polar zwitterionic type 32CA reactions take place through a one-step mechanism with minimal global electron density transfer (GEDT) at the TSs and the exo/ortho approach mode as the energetically favoured reaction path. The 32CA reactions of N-vinyl nucleobases with thymine and cytosine substituents respectively show the activation enthalpies of 15.2 and 12.5 kcal mol⁻¹ in toluene. The reactions are irreversible due to strong exothermic character of − 35.4–− 26.4 kcal mol⁻¹ in toluene. The bonding evolution theory (BET) study suggests that these 32CA reactions take place through the coupling of pseudoradical centres with earlier C–C bond formation and the formation of new C–C and C–O covalent bonds has not been started in the TSs. Non-covalent interactions (NCI) are predicted at the TSs from the visualization of NCI gradient isosurfaces.

Influence on the reactivity properties of the substitution by different halogens on the conjugated backbone of the 1,3,5-triaryl-2-pyrazoline skeleton in relation to the increasing alkyloxy chain length: a conceptual density functional theory study

A series of non-substituted 1,3,5-triaryl-2-pyrazolines and pyrazolines substituted with Fluoro (-F), Chloro (-Cl) and Bromo (-Br) groups at the 3-aryl position were studied. All calculations were done using the conceptual framework of density functional theory. The geometries and reactivity properties were analyzed according to an increase from one to twelve alkyl units in the 5-aryl of 2-pyrazoline ring. In order to be able to apply the particular methodology named KID procedure (for Koopmans in DFT), the KID descriptors were calculated and the results showed that the use of this approximation (Koopmans' theorem in DFT studies) is feasible. The results for the geometries determined that the increase of the chain with alkyl units does not affect the geometry of the systems. However, the solvation energy also calculated is affected by this increase in the allyl chain length. Due to this, as the chains increases, the solubility of the molecular systems diminishes. The chemical reactivity properties were determined by calculating the descriptors that arise from conceptual DFT and it could be demonstrated that they are not affected by the chain growth. Slight differences were found due to the different halogen substitutions. Finally, it could be observed that all the pyrazolines present an important electrophilic behavior. Graphical Abstract Properties changes in relation to the increasing alkyloxy chain length and halogens presence.

Unveiling the Lewis Acid Catalyzed Diels-Alder Reactions Through the Molecular Electron Density Theory

The effects of metal-based Lewis acid (LA) catalysts on the reaction rate and regioselectivity in polar Diels-Alder (P-DA) reactions has been analyzed within the molecular electron density theory (MEDT). A clear linear correlation between the reduction of the activation energies and the increase of the polar character of the reactions measured by analysis of the global electron density transfer at the corresponding transition state structures (TS) is found, a behavior easily predictable by analysis of the electrophilicity ω and nucleophilicity N indices of the reagents. The presence of a strong electron-releasing group in the diene changes the mechanism of these P-DA reactions from a two-stage one-step to a two-step one via formation of a zwitterionic intermediate. However, this change in the reaction mechanism does not have any chemical relevance. This MEDT study makes it possible to establish that the more favorable nucleophilic/electrophilic interactions taking place at the TSs of LA catalyzed P-DA reactions are responsible for the high acceleration and complete regioselectivity experimentally observed.

Theoretical analysis of the regio- and stereoselective synthesis of spiroisoxazolines

The [3+2] cycloaddition (32CA) reaction of benzonitrile oxide to α-methylene cyclopentanone and propionitrile oxide to γ-methyl-α-methylene-γ-butyrolactone, yielding regio- and stereochemically defined spiroisoxazolines, has been studied at the MPWB1K/6-311G(d,p) computational level. These processes proceed by a one-step mechanism through asynchronous transition states. Ortho regioselectivity and anti diastereofacial selectivity are predicted in complete agreement with the experimental outcomes.