Topological Analysis Of Electron Localization Function Research Articles

Understanding the mechanism and regio- and stereo selectivity of [3 + 2] cycloaddition reactions between substituted azomethine ylide and 3,3,3-trifluoro-1-nitroprop-1-ene, within the molecular electron density theory.

The selectivity and the nature of the molecular mechanism of the [3 + 2] cycloaddition (32CA) reaction between 2-(dimethylamino)-1H-indene-1,3(2H)-dione (AY11) and trans(E)-3,3,3-trifluoro-1-nitroprop-1-ene(FNP10) has been studied, in which the molecular electron density theory using density functional theory methods at the MPWB1K/6-31G(d) computational level was used. Analysis of the global reactivity indices permits us to characterize FNP10 as a strong electrophile and AY11 as a strong nucleophile. Four reactive pathways associated with the ortho/meta regioselective channels and endo/exo stereoselective approaches modes have been explored and characterized in the gas phase and in the benzene solvent. The analysis of the relative energies associated with the different reaction pathways indicates that the 32CA reactions of the azomethine ylide (AY) with the nitroalkene (FNP) is meta regioselective with high endo stereoselectivity. This result is in good agreement with the experimental observations. electron localization function topological analysis of the most favored reactive pathways allows for characterizing the mechanism of this 32CA reactions as a non-concerted two-stage one-step mechanism. Finally, non-covalent interactions and quantum theory of atoms in molecule analyses at the meta/endo transition state structure indicate that the presence of different several weak interactions, namely, CF and NH contributed in favoring the formation of a meta-endo cycloadduct.

Probing the Structure-Property Relationships of Na+···Cl-@C50N5H5 under the External Electric Field.

Endohedral open-cage fullerenes are one of the attractive types of fullerenes due to their interesting electronic properties which make it potentially promising for applications in molecular electronics. In this paper, a novel structure of Na+···Cl-@C50N5H5 with Na+ inside the cavity and Cl- at the opening of the open-cage fullerene is designed to explore the chemical bonding and interaction between the open-cage fullerene system C50N5H5 and NaCl salt. Further, the directional migration of Na+ was achieved by applying an external electric field (EEF) along the X-axis. Notably, when the EEF ranges from -85 to -86 × 10-4 au, Na+ sharply approaches Cl- to regain its ionic bonding character. In addition, the Wiberg bond index, electron localization function topological analysis, and interaction energy (Eint) of the structure under the effect of the EEF also experienced a series of interesting changes. We hope that this work will provide a new strategy for the design of innovative materials for molecular electronics.

Understanding the Participation of Fluorinated Azomethine Ylides in Carbenoid-Type [3 + 2] Cycloaddition Reactions with Ynal Systems: A Molecular Electron Density Theory Study.

The carbenoid-type (cb-type) 32CA reaction of 1,1-difluoroated azomethine ylide (DFAY) with phenylpropynal has been studied using the molecular electron density theory (MEDT). Electron localization function (ELF) characterizes DFAY as a carbenoid species participating in cb-type 32CA reactions. The supernucleophilic character of DFAY and the strong electrophilic character of the ynal cause this polar 32CA reaction to have an unappreciable barrier; the reaction, which is highly exothermic, presents total chemo- and regioselectivity. ELF topological analysis of the bonding changes along the reaction establishes its non-concerted two-stage one-step mechanism, in which the nucleophilic attack of the carbenoid carbon of DFAY on the electrophilic carbonyl carbon of the ynal characterizes the cb-type reactivity of this three-atom component (TAC). The presence of two fluorines at DFAY modifies the pseudodiradical structure and reactivity of the simplest azomethine ylide to that of a carbenoid TAC participating in cb-type 32CA reactions toward electrophilic ethylenes.

Unveiling the Intramolecular Ionic Diels–Alder Reactions within Molecular Electron Density Theory

The intramolecular ionic Diels–Alder (IIDA) reactions of two dieniminiums were studied within the Molecular Electron Density Theory (MEDT) at the ωB97XD/6-311G(d,p) computational level. Topological analysis of the electron localization function (ELF) of dieniminiums showed that their electronic structures can been seen as the sum of those of butadiene and ethaniminium. The superelectrophilic character of dieniminiums accounts for the high intramolecular global electron density transfer taking place from the diene framework to the iminium one at the transition state structures (TSs) of these IIDA reactions, which are classified as the forward electro density flux. The activation enthalpy associated with the IIDA reaction of the experimental dieniminium, 8.7 kcal·mol−1, was closer to that of the ionic Diels–Alder (I-DA) reaction between butadiene and ethaniminium, 9.3 kcal·mol−1. However, the activation Gibbs free energy of the IIDA reaction was 12.7 kcal·mol−1 lower than that of the intermolecular I-DA reaction. The strong exergonic character of the IIDA reaction, higher than 20.5 kcal·mol−1, makes the reaction irreversible. These IIDA reactions present a total re/exo and si/endo diastereoselectivity, which is controlled by the most favorable chair conformation of the tetramethylene chain. ELF topological analysis of the single bond formation indicated that these IIDA reactions take place through a non-concerted two-stage one-step mechanism. Finally, ELF and atoms-in-molecules (AIM) topological analyses of the TS associated with the inter and intramolecular processes showed the great similarity between them.

QTAIM and ELF topological analyses of zinc-amido complexes

The structures of three dinuclear zinc-amido complexes, involved in the very first step of the preparation of zinc oxide nanoparticles via an organometallic route, have been investigated by density functional theory computational studies. The various zinc–nitrogen and zinc–cyclohexyl bonds are finely characterized using quantum theory of atoms in molecules and electron localization function (ELF) topological analyses. The results are compared to the topological analyses of parent zinc-amido or zinc-alkyl complexes, for which an experimental structure has been already reported. The original two-component dative zinc-amido bond is unravelled by ELF topological analysis. Fukui indices condensed on the ELF basins allow for the comparison of the chemical reactivity of the three dinuclear zinc-amido complexes. The larger sensitivity to electrophilic attack of the terminal zinc-amido bonds with respect to the bridging intracyclic zinc-amido bonds or with respect to the terminal zinc–cyclohexyl bonds is evidenced.

Understanding the Influence of the Trifluoromethyl Group on the Selectivities of the [3+2] Cycloadditions of Thiocarbonyl S‐methanides with α,β‐Unsaturated Ketones. A MEDT study

AbstractExperimentally (G. Mlostoń et al., J. Fluor. Chem. 2016, 190, 56–60), it has been found that the type of the obtained cycloadduct of the [3+2] cycloaddition (32CA) reaction of thiocarbonyl S‐methanides with α,β‐unsaturated ketones depends strongly on the location of the trifluoromethyl group. In the case of enones containing the CF3CH=CH moiety, the 32CA reaction occurs chemo‐ and regioselectively onto the C=C double bond giving trifluoromethylated tetrahydrothiophene derivatives. On the other hand, enones containing the CF3−C=O fragment react as carbonyl heteroethylenes leading to trifluoromethylated 1,3‐oxathiolanes also in a chemo‐ and regioselective manner. Our aim in the present work is to perform a theoretical study of the all chemo‐, regio‐, and stereo‐isomeric reaction paths of these 32CA reactions within the Molecular Electron Density Theory. Activation Gibbs free energies, calculated at the B3LYP/6‐311G(d,p) level in tetrahydrofurane at −40 °C, show that the ortho/endo reaction path giving the trifluoromethylated tetrahydrothiophene is more favoured, while the meta/endo reaction path leading to trifluoromethylated 1,3‐oxathiolanes is more preferred in total agreement with experimental findings. The low activation barriers in combination of the Electron Localization Function topological analysis of the most relevant points along the Intrinsic Reaction Coordinate reveals the pseudomonoradical character of the studied 32CA reactions.

Insights into the mechanism and regiochemistry of the 1,3-dipolar cycloaddition reaction between benzaldehyde and diazomethane

The 1,3-dipolar cycloaddition reaction of benzaldehyde with diazomethane is investigated, in gas phase and in diverse polar solvents, using the molecular electron density theory through density functional theory calculations at the B3LYP(+D3)/6-31G(d) level. Analysis of the reaction pathway reveals that this reaction takes place along a concerted but asynchronous mechanism. Computations show that the acetophenone product is kinetically and thermodynamically more favored than 2-phenylacetaldehyde product in agreement with experimental outcomes. The favored cyclization mode and the observed regioselectivity of this cycloaddition are rationalized by both activation energy calculations, frontier molecular orbital analysis and reactivity indices. Also, polar solvents effect favors the reaction. Furthermore, we performed electron localization function (ELF) topological analysis. The ELF topological analysis of diazomethane indicates that this reactant presents an allenic pseudoradical electronic structure.

The nature of the triple B[tbnd]B, double, B[dbnd]B, single, B–B, and one-electron, B.B boron-boron bonds from the topological analysis of electron localisation function (ELF) perspective

Local nature of the boron-boron (BB) bond has been investigated in 23 molecules using the topological analysis of Electron Localisation Function (ELF) and the electron density (AIM) frameworks. The wave function has been approximated using the CCSD//CCSD(T), CASSCF and DFT(M062x) methods and triple-zeta basis sets. The calculations yielded a formally triple bond, BB, with population of 5.87–4.67e, a double bond BB with population of 4.39–3.58e, a single bond, B–B with population of 2.49–2.04e and one electron bond, B.B with 0.38e. Topological analysis of ρ(r) field has shown the non-nuclear attractor, NNA, for the BB bond in ten molecules (CCSD, DFT) with ropt(B,B) smaller than 1.6 Å. Population of the pseudo-atom basin ranges from 0.28e to 1.42e (CCSD) and from 0.32e to 1.27e (DFT). An overview of the results from topological analysis of ELF together with a detailed discussion of electronic structure for 14 small molecules has been presented.

A molecular electron density theory study of the [3 + 2] cycloaddition reaction of 1,4-diphosphorinium-3-olates with methyl acrylate and methyl methacrylate

The [3 + 2] cycloaddition (32CA) reactions between the unsubstituted, P1 and C-methyl substituted 1,4-diphosphorinium-3-olates (DPOs) with methyl acrylate (MA) and methyl methacrylate (MMA) were studied within the molecular electron density theory using the B3LYP/6-31G(d) method in the gas phase, THF and MeCN. An analysis of the kinetic and thermodynamic parameters associated to these 32CA reactions indicates that the formation of the 6-exo cycloadducts (CAs) is preferred. The theoretical findings of the 32CA reactions of DPOs with MA and MMA were compared with those of phosphorinium-3-olate and the nitrogen analogs. These zw-type 32CA reactions have very low polar character as a consequence of the low electrophilic character of MA and MMA. The electron localization function topological analysis of the bonding changes along the most favorable reaction path associated with the unsubstituted and highly substituted 32CA reactions indicates that these reactions take place through a non-concerted two-stage one-step mechanism. These reactions may be used to examine 32CA reactions involving complex phosphorus moieties. The major outcome of these investigations is promising for the study of phosphorus containing heterocycles due to their rising applications and limited research.

A Study of the Effects of the Lewis Acid Catalysts on Oxa‐Diels‐Alder Reactions through Molecular Electron Density Theory

AbstractThe effects of the Lewis acid (LA) AlCl3 catalyst on the oxa‐Diels‐Alder (ODA) reaction of 2‐aryl‐butadiene 1 toward benzaldehyde 2 have been studied within the molecular electron density theory at the M06‐2X/6‐311G(d,p) computational level. Coordination of the LA AlCl3 to the carbonyl oxygen of benzaldehyde 2 not only considerably accelerates the reaction, but also facilitates the ODA reaction along a high polar two‐step mechanism. The complete regioselectivity and endo‐stereoselectivity experimentally observed are explained through Parr functions, respectively, non‐covalent interactions analyses. Electron localization function topological analysis along the most favorable meta/endo reaction path permits characterizing the C‐C and C‐O single bond formation along this two‐step mechanism.

Understanding the origin of the enantioselectivity and the mechanism of the asymmetric reduction of ketimine generated from acetophenone with oxazaborolidine catalyst

The enantioselectivity of the oxazaborolidine-catalysed asymmetric reduction reaction of ketimine generated from acetophenone has been investigated by transition state theory at the hydride transfer step using DFT methods at the B3LYP/6-31G(d,p) level of theory. The obtained results indicate that the hydride attack at the Si face is more favourable than the Re one. Analyses of non-covalent interactions and molecular electrostatic potential indicate that the several favourable interactions at the Si hydrogen transfer mode are the origin of the enantioselectivity observed experimentally. Electron Localisation Function topological analysis indicates that the studied hydride transfer step takes place via a non-concerted three-stage mechanism.

Participation of furoxancarbonitrile oxide in [3+2] cycloaddition reaction toward C–N triple bond: a Molecular Electron Density Theory study of regioselectivity and mechanistic aspect

The [3+2] cycloaddition (32CA) reaction between furoxancarbonitrile oxide (FNO 2) and electron-deficient 2,2,2-trichloroacetonitrile (TCAN 3) in the presence of chloroform was studied within the Molecular Electron Density Theory (MEDT), at the DFT-B3LYP/6-311G(d,p) computational level. This zwitterionic-type (zw-type) 32CA reaction takes place in a highly chemo- and regioselective manner, yielding oxadiazole 4 as the sole product of the reaction, in excellent agreement with the experimental findings. The very low polar character of this zw-type 32CA reaction accounts for the high activation barrier found for this 32CA reaction. A topological analysis of the electron localization function (ELF) over some relevant points of the reaction path permits establishing that this zw-type 32CA reaction takes place along a non-concerted two-stage one-step molecular mechanism. The ELF topological analysis evidences that formation of the C1–N8 and O3–C7 single bonds take place through the sharing of the part of the electron density of the N8 nitrogen and that of the O3 lone pairs toward, respectively, the C1 and C7 pseudoradical centers created along the reaction path.

A Molecular Electron Density Theory Study of the Role of the Copper Metalation of Azomethine Ylides in [3 + 2] Cycloaddition Reactions

The copper metalation of azomethine ylides (AYs) in [3 + 2] cycloaddition (32CA) reactions with electron-deficient ethylenes has been studied within the Molecular Electron Density Theory (MEDT) at the MPWB1K/6-311G(d,p) level, in order to shed light on the electronic effect of the metalation in the course of the reaction. Analysis of the Conceptual Density Functional Theory reactivity indices indicates that the metalation of AYs markedly enhances the nucleophilicity of these species given the anionic character of the AY framework. These 32CA reactions take place through stepwise mechanisms characterized by the formation of a molecular complex. Both nonmetalated and metalated 32CA reactions present similar activation energies. While metalated 32CA reactions are completely regioselective, their stereoselectivity depends on the bulk of the ligand as well as the nature of the ethylene derivative. The metalation of the AY slightly increases the asynchronicity of the C-C single bond formation. Electron Localization Function topological analysis of the C-C bond formation processes makes it possible to characterize the mechanism of these 32CA reactions as a two-stage one-step mechanism. The present MEDT study rules out any catalytic role of the Cu(I) cation in the kinetics of the 32CA reactions of metalated AYs.

An investigation of molecular mechanism and the role of Te-bridged-atom in the formation of polysubstituted pyridines via Hetero-Diels–Alder reaction of isotellurazole with acetylenic dienophile: a molecular electron density study

An electron localization function (ELF) analysis and a detailed computational study of the hetero-Diels-Alder (HDA) reaction between isotellurazole and acetylenic dienophile have been performed. Then, B3LYP/Lanl2dz + 6-31+g(d) basis set level has been used to characterize the molecular mechanism and reactivity. The conceptual and computational DFT show that the most favorable regioisomeric product is the ortho/endo adduct, for which the energetic cost is 39.4 kcal/mol. Furthermore, ELF topological analysis envisages that the electron density of the pseudo-radical centers of the most electrophilic and nucleophilic atoms of the molecules come mainly from the charge transfer which takes place along the reaction pathway. The high asynchronicity of the bond formation means that two-stage one-step is the most appropriate mechanism for this reaction. However, the weak electronic contribution of the heavy chalcogen-bridged Tellurium atom in the C1-Te-N2 sequence has increased the activation barrier of the reaction. Otherwise, it has assisted the easy removal of the atom in the intermediary cycloadduct in the end of the reaction leading to the polysubstituted pyridine. So, despite the fact that Te atom is electronically rich, it plays a marginal role for improving reactivity of this [4+2] cycloaddition process. Synopsis. The mechanism of the Hetero-Diels-Alder (HDA) reaction of isotellurazole with acetylenic dienophile has been studied carefully. The quantum chemical calculations and an electron localization function analysis show that the weak electronic contribution of the heavy chalcogen-bridged Tellurium atom in the C1-Te-N2 sequence has decreased the activation barrier of the reaction. Besides, it has assisted the easy removal of this atom in the intermediary cycloadduct at the end of the reaction to make possible the synthesis of pyridine ring system (high polarized bonds). Equally, the electronic density analysis of several formed radicals permits us to conclude that two-stage one-step is the mechanism of the HDA reaction

A molecular electron density theory study of the [3 + 2] cycloaddition reaction between an azomethine imine and electron deficient ethylenes

AbstractThe selectivity and the nature of the molecular mechanism of the [3 + 2] cycloaddition (32CA) reaction of an azomethine imine (AI 12) with p‐nitrobenzylidenemalononitrile (NBMN, 13) have been theoretically studied within the Molecular Electron Density Theory using DFT methods at the MPWB1K/6‐31G(d) computational level. Analysis of the Conceptual DFT reactivity indices indicates that the strong nucleophilic character of AI 12 together with the high electrophilic character of NBMN 13 accounts for the strong polar character of this 32CA reaction, which demands very low activation energy. Analysis of the energy profiles indicates that this polar zw‐type 32CA reaction proceeds completely with a meta/exo selective pathway, in great agreement with the experimental data. Analyses of both molecular electrostatic potential and the non‐covalent interactions at the meta regioisomeric TSs allow explaining the observed exo stereoselectivity. Electron Localisation Function topological analysis indicates that the studied 32CA reaction takes place via a non‐concerted two‐stage one‐step mechanism as a [2n + 2τ] process.

DFT exploration of [3 + 2] cycloaddition reaction of 1H-phosphorinium-3-olate and 1-methylphosphorinium-3-olate with methyl methacrylate.

A Molecular Electron Density Theory (MEDT) study of the regio- and stereoselectivity of the [3 + 2] cycloaddition (32CA) reaction of 1H-phosphorinium-3-olate and 1-methylphosphorinium-3-olate with methyl methacrylate was carried out using the B3LYP/6-31G(d) method. In order to test the method dependence for the most favorable reaction path leading to the 1H-substituted 6-exo cycloadduct (CA) various functionals using higher basis sets were taken into consideration in the gas phase. An analysis of the energetic parameters indicates that the reaction path leading to 6-exo CA are kinetically as well as thermodynamically favored in the gas phase, THF and ethanol. The calculated energetic parameters of the 32CA reaction of these phosphorus derivatives were compared with those of methyl acrylate and their nitrogen analogues. Investigation of the global electron density transfer at the TSs indicates that these 32CA reactions have non-polar character, while electron localisation function topological analysis of the C–C bond formation along the most favorable reaction path indicates that these 32CA reactions take place through a non-concerted two-stage one-step mechanism, via highly asynchronous TSs.

Understanding the Intramolecular Diels‐Alder Reactions of N‐Substituted N‐Allyl‐Furfurylamines: An MEDT Study

AbstractThe intramolecular Diels‐Alder (IMDA) reactions of N‐allyl‐furfurylamine (1a) and N‐trityl‐allyl‐furfurylamine (1b), were studied within the molecular electron density theory (MEDT) using density functional theory method [B3LYP/6‐31G(d)]. In spite of the high activation enthalpies, the low unfavourable activation entropies associated to these intramolecular processes permit these IMDA reactions to take place. The IMDA reaction of 1a is thermodynamically unfavourable. The presence of the bulky −CPh3 group in the amine nitrogen atom that destabilises the extended conformation of 1b turns the process into an exergonic one. This behaviour does not only affect the thermochemistry of the reaction, but also the kinetic parameters, thus accelerating the reaction. Electron localisation function topological analysis of the C−C single bond formation along the IMDA reaction of 1a shows a bonding pattern similar to non‐polar intermolecular Diels‐Alder reactions. The present MEDT study explains the experimental results; although the steric buttress is able to change the direction of these reversible IMDA reactions, this change is only possible due to the aromatic nature of the furanyl diene system.

Aromaticity in Pericyclic Transition State Structures? A Critical Rationalisation Based on the Topological Analysis of Electron Density

AbstractThe nature of the electron delocalisation pattern within a cyclic structure, i. e. the aromatic character, is examined for six‐membered pseudocyclic transition state structures (TSs) involved in five representative examples of so‐called pericyclic reactions. Results of the electron localisation function (ELF) and the quantum theory of atoms in molecules (QTAIM) analyses of the electron density evidence that in four of the cases, at least one pair of atoms are not bound at the TS configuration, thus precluding a possible cyclic conjugation. These findings make it possible to rule out the aromatic character of these TSs. High values of the synchronicity Sy index at the TSs contrast with the bonding changes evidenced by ELF topological analysis. The magnitude of the nucleus independent chemical shift (NICS) computed for the five TSs becomes much more negative than that of the reference system, benzene, with no obvious relation to the strong evidence of the pattern of delocalisation revealed by the topological analysis of ELF and QTAIM for each TS. The topology of the anisotropy of current induced density (ACID) at each TS reveals the actual existence of strong non‐symmetrical patterns of electron delocalisation of the five TSs.

A density functional theory study on the reaction mechanism of hydrazones with α-oxo-ketenes: Comparison between stepwise 1,3-dipolar cycloaddition and Diels–Alder pathways

Density functional theory calculations have been performed at the B3LYP/6-311+G(d,p) and M06-2X/6-31G(d,p) levels to obtain an insight into the nature of the stepwise cycloaddition reactions of hydrazones with α-oxo-ketenes. Three reaction pathways are possible, two Diels–Alder reactions and a 1,3-dipolar cycloaddition (1,3-DC) reaction. Despite the high energy required for 1,2-hydrogen shift in hydrazone to form an azomethine imine, 1,3-DC reaction among the possible pathways is the most favorable. The mechanism has been explained on the basis of transition state stabilities, global and local reactivity indices of the reactants, intrinsic reaction coordinate calculation, and the electron localization function topological analysis of the bonding changes along the 1,3-DC reaction. The computed free energies and enthalpies agree with the experimental outcome.

Understanding the kinetics and mechanism of thermal cheletropic elimination of N2 from (2,5-dihydro-1H-pyrrol-1-ium-1-ylidene) amide using RRKM and ELF theories

The cheletropic elimination process of N2 from (2,5-dihydro-1H-pyrrol-1-ium-1-ylidene) amide (C4H6N2) has been studied computationally using density functional theory, along with the M06-2X/aug-cc-pVTZ level of theory. The calculated energy profile has been supplemented with calculations of kinetic rate constants using transition state theory (TST) and statistical Rice–Ramsperger–Kassel–Marcus (RRKM) theory. This elimination process takes place spontaneously with an activation energy around 33 kJ/mol. Pressure dependence of the rate constants revealed that the TST approximation breaks down and fall-off expression is necessary for the kinetic modeling. At temperatures ranging from 240 to 360 K and atmospheric pressure, the unimolecular rate constant is evaluated from RRKM theory as $$k_{{(240 - 360\,{\text{K}})}}^{{1.0{\text{atm}}}} = 1.0249 \times 10^{12} \times {\text{e}}^{{ - \frac{{33.11\;{\text{kJ}}/{\text{mol}}}}{RT}}} \,{\text{s}}^{ - 1}$$ . Bonding changes along the reaction coordinate have been studied using bonding evolution theory. Electron localization function topological analysis reveals that the cheletropic elimination is characterized topologically by four successive structural stability domains (SSDs). Breaking of C–N bonds (Rx = 0.1992 amu1/2 Bohr) and the other selected points separating the SSDs along the reaction coordinate occur in the vicinity of the transition state.