Molecular Electron Density Theory Study Research Articles

Utilizing MEDT analysis of [3 + 2] cycloaddition reaction: x-ray crystallography of spirooxindole linked with thiophene/furan heterocycles and triazole framework.

Hybridization of spirooxindole with different pharmacophores such as triazole and heterocycle such as thiophene and furan moiety was achieved by the [3 + 2] cycloaddition (32CA) reaction approach. Structural investigations of the compounds 4a and 4b were performed using X-ray single crystal structure determinations and Hirshfeld analysis. Both compounds crystallized in monoclinic crystal system. The space group is P21/c for 4a and P21/n for 4b. The crystal parameters are a = 10.2619(3) Å, b = 13.6776(3) Å, c = 10.9318(3), β = 116.640(4)° for the former while a = 13.0012(1) Å, b = 14.9692(1) Å, c = 14.1178(1) Å, β = 97.101(1)° for the latter. In both compounds, the aryl group and the triazole moieties are twisted from one another. The twist angle is 84.75˚for 4a while 86.64˚ for 4b. Based on Hirshfeld calculations, the Cl…H, O…H, N…H and C…H non-covalent interactions in 4a while the O…H interactions in 4b are the most important. The molecular mechanism of the key 32CA reaction between the in situ generated azomethine ylides and the corresponding chalcones has been studied within the Molecular Electron Density Theory (MEDT). The MEDT study reveals that the low activation energies and high experimental selectivity are the result of the supernucleophilic character of the ylides and the strong electrophilicity of the chalcones, which favour the process through a high polar character. This high polar character accounts for the total endo selectivity experimentally found.

An MEDT Study of the Reaction Mechanism and Selectivity of the Hetero-Diels-Alder Reaction Between 3-Methylene-2,4-Chromandione and Methyl Vinyl Ether.

The hetero-Diels-Alder (HDA) reaction between the ambident heterodiene 3-methylene-2,4-chromandione (MCDO) and non-symmetric methyl vinyl ether (MVE) is investigated using the molecular electron density theory (MEDT) at the B3LYP/6-311G(d,p) computational level. The aim of this study is to gain insight into its molecular mechanism and to elucidate the factors that control the selectivity found experimentally. DFT-based reactivity indices reveal that MCDO exhibits strong electrophilic characteristics, while MVE displays a strong nucleophilic character. Meanwhile, the Parr function explains the ortho regioselectivity of this HDA reaction. The highly polar nature of this HDA reaction, supported by the high global electron density transfer (GEDT) taking place at the transition state structures (TSs), accounts for the very low activation energy associated with the most favorable TS-4on. The ambident nature of MCDO allows for the formation of two constitutional isomeric cycloadducts. In the case of MVE, pseudocyclic selectivity is attained using a thermodynamic control. This polar HDA reaction displays an endo stereoselectivity and a complete ortho regioselectivity. A comparative relative interacting atomic energy (RIAE) analysis of the two diastereomeric structures TS-4on and TS-6on indicates a high degree of likeness, which explains the low pseudocyclic selectivity under kinetic control.

Synthesis, Molecular Electron Density Theory Study, Molecular Docking, and Pharmacological Evaluation of New Coumarin-Sulfonamide-Nitroindazolyl-Triazole Hybrids as Monoamine Oxidase Inhibitors.

Inhibitors of monoamine oxidases (MAOs) are of interest for the treatment of neurodegenerative disorders and other human pathologies. In this frame, the present work describes different synthetic strategies to obtain MAO inhibitors via the coupling of the aminocoumarin core with arylsulfonyl chlorides followed by copper azide-alkyne cycloaddition, leading to coumarin-sulfonamide-nitroindazolyl-triazole hybrids. The nitration position on the coumarin moiety was confirmed through nuclear magnetic resonance spectroscopy and molecular electron density theory in order to elucidate the molecular mechanism and selectivity of the electrophilic aromatic substitution reaction. The coumarin derivatives were evaluated for their inhibitory potency against monoamine oxidases and cholinesterases. Molecular docking calculations provided a rational binding mode of the best compounds in the series with MAO A and B. The work identified hybrids 14a-c as novel MAO inhibitors, with a selective action against isoform B, of potential interest to combat neurological diseases.

A molecular electron density theory study on the [3 + 2] cycloaddition reaction of a 2,4-dienone and a nitrone: regioselectivity, diastereoselectivity, energetic aspects, and molecular mechanism

A molecular electron density theory study on the [3 + 2] cycloaddition reaction of a 2,4-dienone and a nitrone: regioselectivity, diastereoselectivity, energetic aspects, and molecular mechanism

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.

A molecular electron density theory study of hydrogen bond catalysed polar Diels–Alder reactions of α,β-unsaturated carbonyl compounds

The hydrogen bond (HB) catalysed Diels-Alder (DA) reactions of acrolein with cyclopentadiene have been investigated within the Molecular Electron Density Theory (MEDT) at the ωB97X-D/6-311G(d,p) computational level. The formation of HBs increases the electrophilicity of these species, suggesting an acceleration of these polar Diels-Alder (P-DA) reactions with forward electron density flux. Formation of one or two HBs with acrolein decreases the activation energies of the HB-catalysed P-DA reactions by 1.7 (methanol) and 4.0 (squaramide) kcal·mol−1, with the corresponding DA reactions exhibiting low endo stereoselectivity. These HB-catalysed DA reactions proceed through non-concerted one-step mechanisms via asynchronous transition state structures (TSs). An Interacting Quantum Atoms (IQA) energy partitioning analysis of the TSs indicates that the intra-atomic stabilization of the acrolein framework, coupled with the increase of the global electron density transfer, plays a crucial role in reducing the activation energies of these HB-catalysed DA reactions.

A molecular electron density theory study to understand intramolecular [3 + 2] cycloaddition reactions of azides and diazoalkanes

A molecular electron density theory study to understand intramolecular [3 + 2] cycloaddition reactions of azides and diazoalkanes

A molecular electron density theory study of the bimolecular nucleophilic substitution reactions on monosubstituted methyl compounds.

The nucleophilic substitution reactions involving methyl monosubstituted compounds have been studied within the Molecular Electron Density Theory (MEDT) at the ωB97X-D/6-311+G(d,p) computational level in DMSO. This study aims to characterize the electronic nature of the transition state structures (TSs) involved in the so-called SN2 and SNi reactions. Both electron localization function and atom-in-molecules topological analyses indicate that the TSs involved in these nucleophilic substitutions can be described as a central methyl CH3+ carbocation, which is strongly stabilized by the presence of two neighbouring nucleophilic species through electron density transfer. This MEDT study establishes a significant electronic similarity between the so-called SN1 and SN2 reactions. Due to the weak electrophilic character of the methyl tetrahedral carbons, the departure of the leaving group should be expected with the approach of the nucleophile. However, while along the SN1 reactions, the strong stabilization of the tertiary carbocation does not demand the participation of the nucleophile, along the SN2 and SNi reactions involving primary tetrahedral carbons, the nucleophiles should participate in the reaction to stabilize the unstable methyl carbocation.

MEDT Study, hemisynthesis via regioselective ring opening of α-Himachalene-Epoxides, ADME survey and docking studies designed to target coronavirus and HIV-1

The ring-opening reaction of the two diepoxides, α-himachalenes 6 and 7, with aluminum lithium hydride (LiAlH4) in ether produced the title compounds C15H24O2 sesquiterpene alcohol. Both experimentally and conceptually, the regio- and stereospecificity of this ring opening reaction were investigated using the Molecular Electron Density Theory (MEDT). The Parr functions and the energy study correctly predicted the best interaction to be between the C13 carbon and the hydride, as evidenced by the attained regio- and stereo-specificity revealed through the experimental research. Moreover, the alcohol 8 is obtained from a kinetic and thermodynamic control while the alcohol 9 is obtained only by a kinetic control, in the maximum conformity with the findings of the experiments. In addition, the performed docking calculations to examine the coronavirus and HIV-1 activities of the products 1–9 revealed that alcohol 9 has a higher affinity against coronavirus while β-himachalene 1 against the HIV-1.

A molecular electron density theory study of asymmetric Diels-Alder [4 + 2] reaction's mechanism of furan with three substituted alkynes (5-R substituted-3-(3-(phenylsulfonyl)-propioloyl)-oxazolidin-2-one).

The [4 +2 ] cycloaddition reactions between furan and three substituted alkynes (5-R-substituted-3-(3-(phenylsulfonyl)-propioloyl)-oxazolidin-2-one) have been investigated using the MEDT approach. Reactivity indices, reaction pathways, and activation energies are calculated. In an investigation of conceptual DFT indices, furan acts as a nucleophile, while the three substituted alkynes (5-R-substituted-3-(3-(phenylsulfonyl)-propioloyl)-oxazolidin-2-one) function as electrophiles in this reaction. The cycloaddition is regioiselective, as demonstrated by the activation and reaction energies, in clear agreement with the experiment's results. Hetero Diels-Alder [4 + 2] cycloadditions occur following a non-concerted two stages one-step molecular mechanism. For the purpose of this study, all calculations were performed using the Gaussian 09 software. Optimization was achieved through Berny's computational gradient optimization method, employing the B3LYP functional and the 6-31G(d) basis set. Analysis of both local and global reactivity indices provided insights into the reactivity tendencies of the reactants, distinguishing between electrophilic and nucleophilic characteristics via Parr functions. Frequency calculations were employed to identify and characterize stationary points, with transition states indicated by a single imaginary frequency and positive values of all frequencies for reactants and product. The electron localization function (ELF) was investigated using the Multiwfn software within the context of topological analyses.

A Molecular Electron Density Theory Study of the Domino Reaction of N-Phenyl Iminoboranes with Benzaldehyde Yielding Fused Bicyclic Compounds.

The reaction of N-phenyl iminoborane with benzaldehyde yielding a fused aromatic compound, recently reported by Liu et al., has been studied within the Molecular Electron Density Theory (MEDT). Formation of the fused aromatic compound is a domino process that comprises three consecutive reactions: (i) formation of a weak molecular complex between the reagents; (ii) an intramolecular electrophilic attack of the activated carbonyl carbon of benzaldehyde on the ortho position of the N-phenyl substituent of iminoborane; and (iii) a formal 1,3-hydrogen shift yielding the final fused aromatic compound. The two last steps correspond to a Friedel-Crafts acylation reaction, the product of the second reaction being the tetrahedral intermediate of an electrophilic aromatic substitution reaction. However, the presence of the imino group adjacent to the aromatic ring strongly stabilizes the corresponding intermediate, being the reaction product when the ortho positions are occupied by t-butyl substituents. This domino reaction shows a great similitude with the Brønsted acid catalyzed Povarov reaction. Although N-phenyl iminoborane can experience a formal [2+2] cycloaddition reaction with benzaldehyde, its higher activation Gibbs free energy compared to the intramolecular electrophilic attack of the activated carbonyl carbon of benzaldehyde on the ortho position of the N-phenyl substituent, 6.6 kcal·mol-1, prevents the formation of the formal [2+2] cycloadduct. The present MEDT study provides a different vision of the molecular mechanism of these reactions based on the electron density.

Investigation of the molecular mechanism and diastereoselectivity in the [3 + 2] cycloaddition reaction between acetonitrile oxide and Cis-3,4-Dichlorocyclobutene: Insights from MEDT and docking study

[3 + 2] cycloaddition (32CA) reactions involving acetonitrile oxide 1 and cis-3,4-dichlorocyclobutene 2 has been investigated via Molecular Electron Density Theory (MEDT) at B3LYP and M06-2X associated with the basis 6–311++G(d,p). The calculated energy profile demonstrates clearly that this reaction is considerably high diastereoselectivity, which is perfectly in accordance with the results of the experiments. The cycloaddition reaction's molecular mechanism has been examined in bonding evolution theory (BET) terms that displays several changes in electron densities along the reaction pathway and demonstrates a one-step process with highly asynchronous transition states. The acetonitrile oxide under study was classified as zwitter-ionic species from the topological analysis of the electron localization function (ELF). In addition, the optimum solvent for performing this cycloaddition is cyclohexane, which is followed by ether and then chloroform. In a further step, a docking survey was carried out for cycloadducts 3, 3-F, 4 and 4-F docked to the main protease of SARS-CoV2 (6LU7) in comparison with ribavirin, revealing that these cycloadducts have lower binding energies than ribavirin.

Synthesis of tetrazoles through a domino reaction: A molecular electron density theory study of energetics, selectivities, and molecular mechanistic aspects

This study corresponds to a molecular electron density theory (MEDT) investigation to shed light on the energetics, selectivities, and molecular mechanistic aspects of an experimental domino reaction. Theoretical evidences at the M06–2X/6-31G(d) level indicates that this domino reaction includes three different successive steps and is initialized by a stepwise HCl elimination from precursor chlorohydrazone NPCH to yield nitrile imine NI-2. A subsequent stepwise and highly regioselective [3 + 2] cycloaddition (32CA) reaction of NI-2 toward tetramethylguanidine TMG-3 affords corresponding formal [3 + 2] cycloadduct CA-1 as the sole product. Finally, a stepwise HNMe2 elimination experienced by CA-1 leads to amino triazole ATA as an aromatic five-membered target product. Computed rate constants reveal that the HCl elimination step should be considered as the bottleneck of this domino reaction. However, a topological analysis of electron localization function (ELF) of NI-2 demonstrates a zwitterionic type (zw-type) 32 C A reaction is expected between NI-2 and TMG-3. This 32CA reaction also displays an almost noticeable polar character arising from moderate electrophilicity and strong nucleophilicity of NI-2 and TMG-3, respectively. The regioselectivity of 32CA reaction can be explained via analysis of Parr functions values calculated at the reactive sites of reagents. The molecular mechanism of the 32CA reaction was explored through portraying bond forming/breaking patterns involved in this polar, stepwise, and zw-type reaction by means of the ELF analysis. Indeed, formation of both C–N single bonds along the first and second steps takes place through coupling of the corresponding pseudoradical centers.

Unveiling substituent effects in [3+2] cycloaddition reactions of benzonitrile N-oxide and benzylideneanilines from the molecular electron density theory perspective

The zw- type [3+2] cycloaddition (32CA) reactions of benzonitrile N-oxide with a series of substituted benzylideneanilines have been studied within the Molecular Electron Density Theory (MEDT) at the B3LYP/6-31G(d) computational level. The presence of dimethylamino and methoxy substituents in the aromatic rings of benzylideneaniline makes the reaction more facile relative to the unsubstituted one, while the electron withdrawing nitro substituents relatively induce minimal changes in the energy profile complying with the experimentally observed reaction rates. The presence of non-bonding electron density at the nitrogen atom and the formation of pseudoradical centre at the carbon atom of benzonitrile N-oxide characterise the difference in electronic structure of the TSs relative to the reagents, while the topological analysis of the electron localization function (ELF) and the atoms-in-molecules (AIM) reveal no covalent bond formation at the early TSs. The present MEDT study analyses the experimentally observed substituent effects and complete regioselectivity in the studied 32CA reactions.

Exploring the factors controlling the mechanism and the high stereoselectivity of the polar [3+2] cycloaddition reaction of the N,N'-cyclic azomethine imine with 3-nitro-2-phenyl-2H-chromene. A molecular electron density theory study

Exploring the factors controlling the mechanism and the high stereoselectivity of the polar [3+2] cycloaddition reaction of the N,N'-cyclic azomethine imine with 3-nitro-2-phenyl-2H-chromene. A molecular electron density theory study

A molecular electron density theory study of mechanism and selectivity of the intramolecular [3+2] cycloaddition reaction of a nitrone–vinylphosphonate adduct

A molecular electron density theory study of mechanism and selectivity of the intramolecular [3+2] cycloaddition reaction of a nitrone–vinylphosphonate adduct

A Molecular Electron Density Theory Study of the Polar Diels-Alder Reaction of Naphtoquinone:Cr(CO)3 Complex with Cyclic Dienes

The role of the Cr(CO)3 coordination to the aromatic ring of naphtoquinone (NQ) in the polar Diels-Alder (P-DA) reactions with cyclic dienes, cyclopentadiene (Cp), cyclohexadiene (Ch), and 1-methoxy-cyclohexadiene (ChOMe), has been studied within Molecular Electron Density Theory (MEDT). Electron Localization Function (ELF) of the NQ:Cr(CO)3 complex indicates that Cr(CO)3 does not cause any remarkable change in the electronic structure of NQ. While the NQ:Cr(CO)3 complex is categorized as a strong electrophile, the cyclic dienes are categorized as strong nucleophiles, suggesting P-DA reactions. Formation of the NQ:Cr(CO)3 complex reduces the activation energy by only 0.7 kcal·mol−1. While Ch shows a lower reactivity than Cp, ChOMe presents the highest reactivity of this series of cyclic dienes. Analysis of the activation Gibbs free energies of the P-DA reaction with Cp indicates that the reaction is completely endo and anti stereoselective. The present MEDT study shows that the Cr(CO)3 complex has no effective catalytic activity in the P-DA reactions of NQ with cyclic dienes, but only permits the reaction to take place experimentally with a total endo and anti facial stereoselectivity, yielding a single cycloadduct.

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 Diels-Alder reaction between (E)-N-benzylidene-2,2-difluoro-1-phenylethenamine and 2-vinyl pyridine: A molecular electron density theory study

A MEDT study is carried out on dehydrofluorination of benzyltrifluoromethylketimine (BFK) to (E)-N-benzylidene-2,2-difluoro-1-phenylethenamine (BFPA), and the Diels-Alder (DA) reaction of BFPA with 2-vinylpyridine (2VP), which has been performed experimentally by Fu and co-workers. PES analysis indicated that in the dehydrofluorination reaction, the deprotonation of BFK is the RDS in the presence of 2,2,6,6-tetramethylpiperidine (TMP), and the presence of 2,2,6,6-tetramethylpiperidinium ion generated in the deprotonation step, is essential for defluorination. In consistent with the experimental work, it was found that the formation of cis ortho disubstituted cycloadduct from the DA reaction is more favorable kinetically. The high activation barriers rationalize the performing of reactions in harsh conditions. The ELF analysis suggested that the DA reaction takes place through a two-stage one-step mechanism via the coupling of pseudoradical centers. IGM analysis confirmed the endo stereoselectivity predominance of the reaction. Finally, it was found that the BF3 Lewis acid makes the reaction unfavorable.

Unveiling thecb‐typeIntramolecular [3+2] Cycloaddition Reactions of Fluorinated Azomethine Ylides to Ester Carbonyls with a Molecular Electron Density Theory Perspective

AbstractThe carbenoid‐type (cb‐type) intramolecular [3+2] cycloaddition (IM32CA) reactions of four fluorinated azomethine ylides (AYs) bearing an ester carbonyl substituent have been studied from the molecular electron density theory (MEDT) perspective. The presence of two fluorine atoms in these species changes thepseudodiradicalstructure of the simplest AY to that of a carbenoid one, according to thecb‐typemolecular reactivity of these IM32CA reactions. These IM32CA reactions present low activation energies, lesser than 3.0 kcal ⋅ mol−1, and a strongly exothermic character, more than −34.0 kcal ⋅ mol−1, showing a complete chemo‐ and regioselectivity. The presence of the electron‐withdrawing −CN group at the aryl ester framework increases the global electron density transfer (GEDT) at the transition state structure (TS), which fluxes from the nucleophilic AY moiety to the electrophilic carbonyl ester, diminishing the activation energy by 2 kcal ⋅ mol−1relative to that of the phenyl substituent. Electron Localization Function and Atom‐in‐Molecules topological analyses of the most favorable TSs show the early character of thesecb‐typeIM32CA reactions. The present MEDT study makes it possible to establish that the carbenoid structure of these fluorinated AYs together with their supernucleophilic character are responsible for the high reactivity and selectivities shown by these three‐atom‐components participating incb‐type32CA reactions towards carbonyl compounds.