Revealing the Critical Role of Global Electron Density Transfer in the Reaction Rate of Polar Organic Reactions within Molecular Electron Density Theory.

The critical role of global electron density transfer (GEDT) in increasing the reaction rate of polar organic reactions has been studied within the framework of Molecular Electron Density Theory (MEDT). To this end, the series of the polar Diels-Alder (P-DA) reactions of cyclopentadiene with cyanoethylene derivatives, for which experimental kinetic data are available, have been chosen. A complete linear correlation between the computed activation Gibbs free energies and the GEDT taking place at the polar transition state structures (TSs) is found; the higher the GEDT at the TS, the lower the activation Gibbs free energy. An interacting quantum atoms energy partitioning analysis allows for establishing a complete linear correlation between the electronic stabilization of the electrophilic ethylene frameworks and the GEDT taking place at the polar TSs. This finding supports Parr's proposal for the definition of the electrophilicity ω index. The present MEDT study establishes the critical role of the GEDT in the acceleration of polar reactions, since the electronic stabilization of the electrophilic framework with the electron density gain is greater than the destabilization of the nucleophilic one, making a net favorable electronic contribution to the decrease in the activation energy.

Understanding of the stability of acyclic nitronic acids in the light of molecular electron density theory.

In the present work, the electronic structure and stability of acyclic nitronic acids were studied. Depending on the different substituents, the analyzed compounds can be classified as pseudo(mono)radical or zwitterionic nitronic acids. ELF topological analysis of the electron density of nitronic acids containing in their structure EWG substituent (-NO2 (1); -COOCH3 (2); -NO2, -CH3 (5); -COOCH3, -OCH3 (6); -NO2, -H (7); -COOH3, -H (8)) permits establishing a pseudo(mono)radical electronic structure with a pseudoradical centers at the C1 carbon atom. In turn, ELF analysis of the compounds 3, 4, 9 and 10 containing substituent belonging to the EGD group (-CH3 (3); -OCH3 (4); -CH3, -H (9); -COH3, -H (10)) and based on the presence of C1-N2 double bond and absence of pseudoradical centre allows for the classification of these compounds as a zwitterionic nitronic acids. Nitronic acids containing EDG substituents in their structure are the most stable among the analyzed nitronic acids. In turn, nitronic acids containing EWG groups are characterized by higher reactivity in chemical reactions compared to other analyzed nitronic acids.

On the Question of Zwitterionic Intermediates in the [3+2] Cycloaddition Reactions between Aryl Azides and Ethyl Propiolate.

The molecular mechanism of the [3+2] cycloaddition reactions between aryl azides and ethyl propiolate was evaluated in the framework of the Molecular Electron Density Theory. It was found that independently of the nature of the substituent within the azide molecule, the cycloaddition process is realized via a polar but single-step mechanism. All attempts of localization as postulated earlier by Abu-Orabi and coworkers' zwitterionic intermediates were not successful. At the same time, the formation of zwitterions with an "extended" conformation is possible on parallel reaction paths. The ELF analysis shows that the studied cycloaddition reaction leading to the 1,4-triazole proceeds by a two-stage one-step mechanism. It also revealed that both zwitterions are created by the donation of the nitrogen atom's nonbonding electron densities to carbon atoms of ethyl propiolate.

New spiro-indeno[1,2-b]quinoxalines clubbed with benzimidazole scaffold as CDK2 inhibitors for halting non-small cell lung cancer; stereoselective synthesis, molecular dynamics and structural insights.

Despite the crucial role of CDK2 in tumorigenesis, few inhibitors reached clinical trials for managing lung cancer, the leading cause of cancer death. Herein, we report combinatorial stereoselective synthesis of rationally designed spiroindeno[1,2-b]quinoxaline-based CDK2 inhibitors for NSCLC therapy. The design relied on merging pharmacophoric motifs and biomimetic scaffold hopping into this privileged skeleton via cost-effective one-pot multicomponent [3 + 2] cycloaddition reaction. Absolute configuration was assigned by single crystal x-ray diffraction analysis and reaction mechanism was studied by Molecular Electron Density Theory. Initial MTT screening of the series against A549 cells and normal lung fibroblasts Wi-38 elected 6b as the study hit regarding potency (IC50 = 54 nM) and safety (SI = 6.64). In vitro CDK2 inhibition assay revealed that 6b (IC50 = 177 nM) was comparable to roscovitine (IC50 = 141 nM). Docking and molecular dynamic simulations suggested that 6b was stabilised into CDK2 cavity by hydrophobic interactions with key aminoacids.

Synthesis and Characterization of New Spirooxindoles Including Triazole and Benzimidazole Pharmacophores via [3+2] Cycloaddition Reaction: An MEDT Study of the Mechanism and Selectivity.

A new series of spirooxindoles based on benzimidazole, triazole, and isatin moieties were synthesized via a [3+2] cycloaddition reaction protocol in one step. The single X-ray crystal structure of the intermediate triazole-benzimidazole 4 was solved. The new chemical structures of these spirooxindole molecules have been achieved for the first time. The final synthesized chemical architecture has differently characterized electronic effects. An MEDT study of the key 32CA reaction between in situ generated azomethine ylide (AY) and chalcones explained the low reaction rates and the total selectivities observed. The supernucleophilic character of AY and the strong electrophilicity of chalcones favor these reactions through a highly polar two-stage one-step mechanism in which bond formation at the ß-conjugated carbon of the chalcones is more advanced. The present combined experimental and theoretical study reports the synthesis of new spirooxindoles with potential biological activities and fully characterizes the molecular mechanisms for their formation through the key 32CA reaction step.

A novel alpha-amylase inhibitor-based spirooxindole-pyrrolidine-clubbed thiochromene-pyrzaole pharmacophores: Unveiling the [3+2] cycloaddition reaction by molecular electron density theory.

A novel spirooxindole-pyrrolidine clubbed thiochromene and pyrazole motifs were synthesized by [3+2] cycloaddition (32CA) reactions in one step process starting from the ethylene-based thiochromene and pyrazole scaffolds with the secondary amino-acids and substituted isatins in high yield. The 32CA reaction of AY 10 with ethylene derivative 6 has also been studied with Molecular Electron Density Theory. The high nucleophilic character of AY 10, N = 4.39 eV, allows explaining that the most favorable TS-on is 13.9 kcal mol-1 below the separated reagent. This 32CA, which takes place through a non-concerted one-step mechanism, presents a total ortho regio- and endo stereoselectivity, which is controlled by the formation of two intramolecular H… O hydrogen bonds. The design of spirooxindole-pyrrolidines engrafted thiochromene and pyrazole was tested for alpha-amylase inhibition and show a high efficacy in nanoscale range of reactivity. The key interaction between the most active hybrids and the receptor was studied by molecular docking. The physiochemical properties of the designed spirooxindole-pyrrolidines were carried out by in silico ADMET prediction. The newly synthesized most potent hybrid could be considered as a lead compound for drug discovery development for type 2 diabetes mellitus (T2DM).

Understanding the Molecular Mechanism of Thermal and LA-Catalysed Diels-Alder Reactions between Cyclopentadiene and Isopropyl 3-Nitroprop-2-Enate.

The molecular mechanism of the Diels-Alder reaction with the participation of cyclopentadiene and isopropyl 3-nitroprop-2-enate was examined based on wb97xd/6-311+G(d) (PCM) quantum chemical calculations. It was found that the type of mechanism for the conversion of addends depends significantly on the reaction conditions. In less-polar environments, a one-step polar mechanism is realised. In more polar solvents, the formation of "extended"-type zwitterionic intermediates is possible. In contrast, in the presence of an LA-type catalyst, the one-step mechanisms are replaced by respective stepwise mechanisms with zwitterionic or heterocyclic intermediates.

Fully Selective Synthesis of Spirocyclic-1,2-oxazine N-Oxides via Non-Catalysed Hetero Diels-Alder Reactions with the Participation of Cyanofunctionalysed Conjugated Nitroalkenes.

Hetero Diels-Alder (HDA) reactions with the participation of E-2-aryl-1-cyano-1-nitroethenes and methylenecyclopentane were evaluated on the basis of experimental as well as quantumchemical data. It was found that contrary to most known HDA reactions, title processes are realised under non-catalytic conditions and with full regiocontrol. The DFT study shows, without any doubt, the polar but single-step reaction mechanism. Deeper exploration using Bonding Evolution Theory (BET) techniques gives a clear image of the sequences of electron density reorganisation along the reaction coordinate. The first C4-C5 bond is created in phase VII by merging two monosynaptic basins, while the second O1-C6 bond is created in the last phase by a donation of the nonbonding electron density of O1 to C6. Based on the research, we can conclude that the analysed reaction proceeds according to a two-stage one-step mechanism.

Unveiling the Stereoselectivity and Regioselectivity of the [3+2] Cycloaddition Reaction between N-methyl-C-4-methylphenyl-nitrone and 2-Propynamide from a MEDT Perspective.

[3+2] cycloaddition reactions play a crucial role in synthesizing complex organic molecules and have significant applications in drug discovery and materials science. In this study, the [3+2] cycloaddition (32CA) reactions of N-methyl-C-4-methyl phenyl-nitrone 1 and 2-propynamide 2, which have not been extensively studied before, were investigated using molecular electron density theory (MEDT) at the B3LYP/6-311++G(d,p) level of theory. According to an electron localization function (ELF) study, N-methyl-C-4-methyl phenyl-nitrone 1 is a zwitterionic species with no pseudoradical or carbenoid centers. Conceptual density functional theory (CDFT) indices were used to predict the global electronic flux from the strong nucleophilic N-methyl-C-4-methyl phenylnitrone 1 to the electrophilic 2-propynamide 2 functions. The 32CA reactions proceeded through two pairs of stereo- and regioisomeric reaction pathways to generate four different products: 3, 4, 5, and 6. The reaction pathways were irreversible owing to their exothermic characters: -136.48, -130.08, -130.99, and -140.81 kJ mol-1, respectively. The enthalpy of the 32CA reaction leading to the formation of cycloadduct 6 was lower compared with the other path owing to a slight increase in its polar character, observed through the global electron density transfer (GEDT) during the transition states and along the reaction path. A bonding evolution theory (BET) analysis showed that these 32CA reactions proceed through the coupling of pseudoradical centers, and the formation of new C-C and C-O covalent bonds did not begin in the transition states.

Full Regio- and Stereoselective Protocol for the Synthesis of New Nicotinoids via Cycloaddition Processes with the Participation of Trans-Substituted Nitroethenes: Comprehensive Experimental and MEDT Study.

[3 + 2] Cycloaddition reactions with the participation of Z-C-(3-pyridyl)-N-methylnitrone and series of E-2-R-nitroethenes were both experimentally and theoretically explored in the framework of Molecular Electron Density Theory. It was found that all considered processes are realized under mild conditions and in full regio- and stereocontrol. The ELF analysis additionally showed that the studied reaction proceeds by a two-stage, one-step mechanism.

On the Question of the Formation of Nitro-Functionalized 2,4-Pyrazole Analogs on the Basis of Nitrylimine Molecular Systems and 3,3,3-Trichloro-1-Nitroprop-1-Ene.

Experimental and theoretical studies on the reaction between (E)-3,3,3-trichloro-1-nitroprop-1-ene and N-(4-bromophenyl)-C-arylnitrylimine were performed. It was found that the title process unexpectedly led to 1-(4-bromophenyl)-3-phenyl-5-nitropyrazole instead of the expected Δ2-pyrazoline molecular system. This was the result of a unique CHCl3 elimination process. The observed mechanism of transformation was explained in the framework of the molecular electron density theory (MEDT). The theoretical results showed that both of the possible channels of [3 + 2] cycloaddition were favorable from a kinetic point of view, due to which the creation of 1-(4-bromophenyl)-3-aryl-4-tricholomethyl-5-nitro-Δ2-pyrazoline was more probable. On the other hand, according to the experimental data, the presented reactions occurred with full regioselectivity.

Understanding the Regioselectivity and the Molecular Mechanism of [3 + 2] Cycloaddition Reactions between Nitrous Oxide and Conjugated Nitroalkenes: A DFT Computational Study.

Regiochemical aspects and the molecular mechanism of the [3 + 2] cycloaddition between nitrous oxide and conjugated nitroalkenes were evaluated on the basis of the wb97xd/6-311 + G(d) (PCM) computational study. It was found that, independently of the nature of the nitroalkene, all considered processes are realized via polar, single-step mechanisms. All attempts at the localization of hypothetical zwitterionic intermediates were unsuccessful. Additionally, the DFT computational study suggested that, in the course of the reaction, the formation of respective Δ2-4-nitro-4-R1-5-R2-1-oxa-2,3-diazolines was preferred from the kinetic point of view.

The First Examples of [3+2] Cycloadditions with the Participation of (E)-3,3,3-Tribromo-1-Nitroprop-1-Ene.

The first examples of [3+2] cycloaddition reactions between 3,3,3-tribromo-1-nitroprop-1-ene (TBMN) were explored on the basis of experimental and theoretical approaches. It was found that reactions involving TBMN and diarylnitrones realized with full regio- and stereoselectivity lead to respective 3,4-cis-4,5-trans-4-nitroisoxazolidines. The regioselecticity and the molecular mechanism of title processes was analyzed on the basis of the advanced DFT computational study.

A Molecular Electron Density Theory Study of the [3+2] Cycloaddition Reaction of an Azomethine Ylide with an Electrophilic Ethylene Linked to Triazole and Ferrocene Units.

The [3+2] cycloaddition (32CA) reaction of an azomethine ylide (AY) with an electrophilic ethylene linked to triazole and ferrocene units has been studied within the Molecular Electron Density Theory (MEDT) at the ωB97X-D/6-311G(d,p) level. The topology of the electron localization function (ELF) of this AY allows classifying it as a pseudo(mono)radical species characterized by the presence of two monosynaptic basins, integrating a total of 0.76 e, at the C1 carbon. While the ferrocene ethylene has a strong electrophilic character, the AY is a supernucleophile, suggesting that the corresponding 32CA reaction has a high polar character and a low activation energy. The most favorable ortho/endo reaction path presents an activation enthalpy of 8.7 kcal·mol-1, with the 32CA reaction being exergonic by -42.1 kcal·mol-1. This reaction presents a total endo stereoselectivity and a total ortho regioselectivity. Analysis of the global electron density transfer (GEDT) at the most favorable TS-on (0.23 e) accounts for the high polar character of this 32CA reaction, classified as forward electron density flux (FEDF). The formation of two intermolecular hydrogen bonds between the two interacting frameworks at the most favorable TS-on accounts for the unexpected ortho regioselectivity experimentally observed.

Mechanistic aspects of the synthesis of seven-membered internal nitronates via stepwise [4 + 3] cycloaddition involving conjugated nitroalkenes: Molecular Electron Density Theory computational study.

The density functional theory computational study indicates the possibility of the synthesis of seven-membered internal nitronates via cycloaddition reactions involving Z-C-aryl-N-methylnitrones and E-2-aryl-1-cyano-1-nitroethenes. The detailed exploration of the reaction paths indicates a polar, stepwise reaction mechanism through the zwitterionic intermediate. Using bonding evolution theory (BET), we have deciphered the molecular mechanism of the [4 + 3] cycloaddition reaction between E-2-phenyl-1-cyano-1-nitroethene and Z-C-phenyl-N-methylnitrone. The BET study has revealed that the formation of two CO single bonds takes place in the same way, through the depopulation of NC and CC bonding regions and monosynaptic basins, respectively. The first O1C7 single bond was formed in the sixth phase, while the second C3O4 bond was formed in the last ninth phase.

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.

A DFT Study on the Molecular Mechanism of Additions of Electrophilic and Nucleophilic Carbenes to Non-Enolizable Cycloaliphatic Thioketones.

The molecular mechanisms of addition of dihalocarbenes and dimethoxycarbene to thioketones derived from 2,2,4,4-tetrmethylcyclobutane-1,3-dione were examined on the basis of the DFT wb97xd/6-311g(d,p)(PCM) calculations. Obtained results demonstrated that the examined processes exhibit polar nature and in the case of electrophilic dichloro-, and dibromocarbenes are initiated by the attack of carbene species onto the sulfur atom of the C=S group. Remarkably, reactions involving more electrophilic carbenes (dichloro-, and dibromocarbene) proceeds via stepwise mechanism involving thiocarbonyl ylide as a transient intermediate. In contrast, analogous reactions with nucleophilic dimethoxycarbene occur via a single step reaction, which can be considered as the [2 + 1] cycloaddition reaction initiated by the attack onto the C=S bond. A computational study showed that difluorocarbene tends to react as a nucleophilic species and resembles rather dimethoxycarbene and not typical dihalocarbene species. Significantly higher reactivity of the thioketone unit in comparison to the ketone group, both present in 3-thioxo-2,2,4,4-tetramthylcyclobutanone molecule, was rationalized in the light of DFT computational study.

The Molecular Mechanism of the Formation of Four-Membered Cyclic Nitronates and Their Retro (3 + 2) Cycloaddition: A DFT Mechanistic Study.

In the present work, the formation of the four-membered cyclic nitronates and the retro (3 + 2) cycloaddition (retro-32CA) reaction of the 4H-[1,2]oxazete 2-oxide were studied using the density functional theory method at the MPWB1K/6-311G(d,p) theoretical level. The electronic structure of 3-tert-butyl-4,4-dimethyl-1,2-dinitro-pent-2-ene was known through electron localization function analysis, natural population analysis, and molecular electrostatic potential analysis. The formation of 4,4-di-tert-butyl-3-nitromethyl-4H-[1,2]oxazete 2-oxide proceeds through a one-step mechanism. The mechanism of the retro-32CA leading to di-tert-butyl ketone and nitrile oxide derivative should be described as an asynchronous two-stage one-step process. The bonding evolution theory study was carried out to clarify the mechanisms of the formation of 4H-[1,2]oxazete 2-oxide and their retro-32CA.

Unveiling the Ionic Diels-Alder Reactions within the Molecular Electron Density Theory.

The ionic Diels-Alder (I-DA) reactions of a series of six iminium cations with cyclopentadiene have been studied within the Molecular Electron Density Theory (MEDT). The superelectrophilic character of iminium cations, ω > 8.20 eV, accounts for the high reactivity of these species participating in I-DA reactions. The activation energies are found to be between 13 and 20 kcal·mol-1 lower in energy than those associated with the corresponding Diels-Alder (DA) reactions of neutral imines. These reactions are low endo selective as a consequence of the cationic character of the TSs, but highly regioselective. Solvents have poor effects on the relative energies, and an unappreciable effect on the geometries. In acetonitrile, the activation energies increase slightly as a consequence of the better solvation of the iminium cations than the cationic TSs. Electron localization function (ELF) topological analysis of the bonding changes along the I-DA reactions shows that they are very similar to those in polar DA reactions. The present MEDT study establishes that the global electron density transfer (GEDT) taking place at the TSs of I-DA reactions, and not steric (Pauli) repulsions such as have been recently proposed, are responsible for the features of these types of DA reactions.

Experimental and Theoretical Mechanistic Study on the Thermal Decomposition of 3,3-diphenyl-4-(trichloromethyl)-5-nitropyrazoline.

The present paper is a continuation of comprehensive study regarding to synthesis and properties of pyrazoles and their derivatives. In its framework an experimental and theoretical studies of thermal decomposition of the 3,3-diphenyl-4-(trichloromethyl)-5-nitropyrazoline were performed. It was found, that the decompositions of the mentioned pyrazoline system in the solution and at the melted state proceed via completely different molecular mechanisms. These mechanisms have been explained in the framework of the Molecular Electron Density Theory (MEDT) with the computational level of B3LYP/6-31G(d). A Bonding Evolution Theory (BET) examination of dehydrochlorination of the 3,3-diphenyl-4-(trichloromethyl)-5-nitropyrazoline permits elucidation of the molecular mechanism. It was found, that on the contrary for most known HCl extrusion processes in solution, this reaction is realised via single-step mechanism.