A theoretical study on the reaction mechanism for the bergman cyclization from the perspective of the electron localization function and catastrophe theory

The reaction mechanism associated with the Bergman cyclization of the (Z)-hexa-1,5-diyne-3-ene to render p-benzyne has been analyzed by means of a combined use of the electron localization function (ELF) and the catastrophe theory on the basis of density functional theory (DFT) calculations (B3LYP/6-31G(d)). The complex electronic rearrangements of this reaction can be highlighted using this novel quantum mechanical perspective. Five domains of structural stability of the ELF occurring along the intrinsic reaction path as well as four catastrophes (fold-cusp-fold-cusp) responsible for the changes in the topology of the system have been identified. The multiple factors that occur along the intrinsic reaction coordinate path are presented and discussed in a consistent way. The topological analysis of ELF and catastrophe theory reveals that mechanical deformation of the C1-C2-C3 unit and closed-shell repulsion between terminal acetylene groups lead to an early formation of diradicaloid character at C2 and C5 atoms. Immediately after the transition structure (TS) is reached, the open-shell-singlet biradical becomes stable. Meanwhile, C1 and C6 atoms are preparing to be covalently bonded; that will finally occur at a distance of 1.791 A. In addition, a separation of the ELF into in-plane (sigma) and out-of-plane (pi) contributions allows us to discuss the aromaticity profiles; sigma-aromaticity appears in the vicinities of the TS, while pi-aromaticity takes place in the final stage of the reaction path, once the ring has been formed.     

Electronic fluxes during diels‐alder reactions involving 1,2‐benzoquinones: mechanistic insights from the analysis of electron localization function and catastrophe theory

By means of the joint use of electron localization function (ELF) and Thom's catastrophe theory, a theoretical analysis of the energy profile for the hetero‐Diels‐Alder reaction of 4‐methoxy‐1,2‐benzoquinone 1 and methoxyethylene 2 has been carried out. The 12 different structural stability domains obtained by the bonding evolution theory have been identified as well as the bifurcation catastrophes (fold and cusp) responsible for the changes in the topology of the system. This analysis permits finding a relationship between the ELF topology and the evolution of the bond breaking/forming processes and electron pair rearrangements through the reaction progress in terms of the different ways of pairing up the electrons. The reaction mechanism corresponds to an asynchronous electronic flux; first, the O1? C5 bond is formed by the nucleophilic attack of the C5 carbon of the electron rich ethylene 2 on the most electrophilically activated carbonyl O1 oxygen of 1 , and once the σ bond has been completed, the formation process of the second O4? C6 bond takes place. In addition, the values of the local electrophilicity and local nucleophilcity indices in the framework of conceptual density functional theory accounts for the asychronicity of the process as well as for the observed regioselectivity. © 2012 Wiley Periodicals, Inc.     

Nature of the ring-closure process along the rearrangement of octa-1,3,5,7-tetraene to cycloocta-1,3,5-triene from the perspective of the electron localization function and catastrophe theory

We analyze the behavior of the energy profile of the ring‐closure process for the transformation of (3Z,5Z)‐octa‐1,3,5,7‐tetraene 5 to (1Z,3Z,5Z)‐cycloocta‐1,3,5‐triene 6 through a combination of electron localization function (ELF) and catastrophe theory (CT). From this analysis, concepts such as bond breaking/forming processes, formation/annihilation of lone pairs, and other electron pair rearrangements arise naturally through the reaction progress simply in terms of the different ways of pairing up the electrons. A relationship between the topology and the nature of the bond breaking/forming processes along this rearrangement is reported. The different domains of structural stability of the ELF occurring along the intrinsic reaction path have been identified. The reaction mechanism consists of six steps separated by fold and cusp catastrophes. The transition structure is observed in the third step, d(C1? C8) = 2.342 Å, where all bonds have topological signature of single bonds (C? C). The “new” C1? C8 single bond is not formed in transition state and respective catastrophe of the ELF field (cusp) is localized in the last step, d(C1? C8) ≈ 1.97 Å, where the two monosynaptic nonbonding basins V(C1) and V(C8) are joined into single disynaptic bonding basin V(C1,C8). The V(C1,C8) basin corresponds to classical picture of the C1? C8 bond in the Lewis formula. In cycloocta‐1,3,5‐triene 6 the single C1? C8 bond is characterized by relatively small basin population 1.72e, which is much smaller than other single bonds with 2.03 and 2.26e. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

DFT study of the active intermediate in the Fenton reaction

Density functional theory has been used to investigate the nature of the oxidizing agent in the Fenton reaction. Starting from the primary intermediate [FeII(H2O)5H2O2]2+, we show that the oxygen-oxygen bond breaking mechanism has a small activation energy and could therefore demonstrate the catalytic effect of the metal complex. The O-O bond cleavage of the coordinated H2O2, however, does not lead to a free hydroxyl radical. Instead, the leaving hydroxyl radical abstracts a hydrogen from an adjacent coordinated water leading to the formation of a second Fe-OH bond and of a water molecule. Along this reaction path the primary intermediate transforms into the [FeIV(H2O)4(OH)2]2+ complex and in a second step into a more stable high valent ferryl-oxo complex [FeIV(H2O)5O]2+. We show that the energy profile along the reaction path is strongly affected by the presence of an extra water molecule located near the iron complex. The alternative intermediate [FeII(H2O)4(OOH-)(H3O+)]2+ suggested in the literature has been also investigated, but it is found to be unstable against the primary intermediate. Our results support a picture in which an FeIV-oxo complex is the most likely candidate as the active intermediate in the Fenton reaction, as indeed first proposed by Bray and Gorin already in 1932.     

New findings on the Diels-Alder reactions. An analysis based on the bonding evolution theory

Two Diels-Alder type reactions, i.e., normal electron demand (NED) between 1,3-butadiene (BD) and acrolein (Acr) and inverse electron demand (IED) between 2,4-pentadienal (PDA) and methyl vinyl ether (MVE), have been investigated using the bonding evolution theory (BET). BET combines topological analysis of the electron localization function (ELF) and catastrophe theory. Catalyst effect has been incorporated through Lewis acid BH3. The B3LYP hybrid HF/DFT method along with 6-31G(d), 6-311++G(d,p) basis sets have been used. All reactions yield two-stage mechanism and there is no topological evidence that they might be concerted with two bonds partially formed during transition structure. A formation of six-membered ring requires 10 (or 11) steps separated by two types of catastrophes: fold and cusp. The first "intermolecular" bond (C1-C6) is formed at 1.93, 1.92 A (NED) and 1.92, 1.97 A (IED). The six-membered ring is "closed" at 2.11, 2.13 A (NED) and 2.5, 2.6 A (IED) via formation of the second bond C4-C5. All reactions begin with "reduction" of C=C bonds to single C-C (cusp catastrophes). Subsequently, the nonbonding electron density is concentrated (fold catastrophes) on terminal C atoms. Finally the new bonds, C1-C6 and C4-C5, are established (cusp catastrophes). Both magnitude and regularity of the electron redistribution, happening during reactions enable us to distinguish two effects: (1) the "ring effect", where a large amount of electron density is regularly transferred from double C=C bonds to intermolecular regions and single C-C bonds, (2) the "side chain effect"--usually weaker and irregular--involving substituents' bonds. In the transition structure, well formed bonding basin V(C1,C6), is observed only for the PDA...BH3/MVE reaction. For other reactions only the nonbonding basins: V(C1) and V(C6), are found in the interaction region C1...C6.     

Static and dynamic descriptions of bond breaking/formation: a complementary view?

Ab initio molecular-dynamic simulations using density-functional theory and the recent atom-centered density-matrix propagation (ADMP) method were used to study the bond breaking and formation for a case-study substitution nucleophilic bimolecular reaction, namely, the Walden inversion. Using the atoms-in-molecule approach, we have performed a detailed analysis to investigate intra- and intermolecular charge transfer along the ADMP trajectory. These results were compared to those obtained considering a static approach, such as the intrinsic reaction path. In particular, the topological properties computed along the dynamic trajectory well evidence a stronger electron exchange tending to spontaneously maximize the rising covalent interaction. Furthermore, their analysis suggests that the bond formation mechanism involves a reactive intermediate with a bonding interaction stronger than in the final product.     

Reactivity of Pt- and Pd-bound nitriles towards nitrile oxides and nitrones: substitution vs. cycloaddition

Reactions of the nitrone CH3CH=N(CH3)O and the nitrile oxide CH3C[triple bond]NO with the nitrile complexes trans-[MCl2(N[triple bond]CCH3)2] (M = Pt, 1; Pd, 2) were investigated by theoretical methods at B3LYP and, for some processes, CCSD(T) levels of theory. The mechanisms of substitutions and cycloadditions were studied in detail. The former occur via a concerted asynchronous mechanism of dissociative type. The calculations of the metal-ligand bond energies in the starting complexes and substitution products and the analysis of structural features of the transition states indicate that the M-N bond dissociation (rather than M-O bond formation) is the step, which controls the reactivity of and in substitutions. The different chemical behaviours of the Pt and Pd complexes towards the 1,3-dipoles were investigated. The exclusive isolation of cycloaddition rather than substitution products in any solvents in the case of is both kinetically and thermodynamically controlled.The switch of the reaction mode from cycloaddition to substitution for 2 in CH2Cl2 solution is caused by the significantly lower Pd-N bond energy in comparison with the Pt-N bond energy, consistent with the higher lability of the Pd complexes. The different chemical behaviour of 2 in CH3CN and CH2Cl2 solvents is accounted for by the great excess of acetonitrile in the CH3CN solution rather than a different solvation character. The relative variation of Wiberg bond indices along the reaction path is proposed as a quantitative criterion for the classification of the reaction mechanism.     

Theoretical study on the reactions of Zr<Superscript>+</Superscript> and Zr with CO<Subscript>2</Subscript> in gas phase

Density functional theory (DFT) calculations have been performed to explore the potential energy surfaces of C-O bond activation in CO₂ molecule by gas-phase Zr⁺ cation and Zr atom, for better understanding the mechanism of second-row transition metal reacting with CO₂. The minimum energy reaction path is found to involve the spin inversion in the different reaction steps. This potential energy curvecrossing dramatically affects reaction energetics. The present results show that the reaction mechanism is insertion-elimination mechanism along the C-O bond activation. All theoretical results not only support the existing conclusions inferred from early experiment, but also complement the pathway and mechanism for this reaction.     

Mechanism of TBD-catalyzed hydrolysis of acetonitrile

1,5,7-Triazabicyclo[4.4.0]dec-5-ene (TBD) has recently been shown to be an effective organocatalyst for the hydrolysis reaction of acetonitrile. This reaction involves the acetamide-forming reaction of acetonitrile hydrolysis and the further hydrolysis of acetamide to form acetic acid and NH₃. Density functional theory (DFT) and Hartree–Fock (HF) methods were employed to comprehensively investigate these two hydrolysis steps to elucidate the TBD-catalyzation mechanism. Structures and energies of the reactants, intermediates, transition states and products along the reaction path were presented. Charge population and bond orders were given by natural bond orbital (NBO) analysis to clarify the computed atomic and molecular behaviors. The results showed that compared with the noncatalyzed reaction, the TBD-catalyzed process had significantly lower energy barriers in both the hydration steps and the isomerization steps. As a result, the whole reaction process could be accelerated and the TBD-catalyzation mechanism was clarified.     

A spin-coupled study of the Claisen rearrangement of allyl vinyl ether

The spin-coupled (SC) form of modern valence bond (VB) theory is utilised to examine the electronic structure of the transition state (TS) and the electronic reaction mechanism of the Claisen rearrangement of allyl vinyl ether. The differences between the spin-coupling patterns and orbital overlap integrals at the optimised TS geometries obtained using B3LYP/6-31G^*, MP2/6-31G^* and MP4(SDQ)/6-31G^* wavefunctions are minimal, and the SC picture suggests that the TS is non-aromatic. SC calculations along the intrinsic reaction coordinates computed at these three levels of theory also produce near identical results. The SC wavefunctions at different stages of the reaction provide easily interpretable orbital diagrams which, in combination with the changes in the orbital overlap integrals, indicate an electronic reaction mechanism involving concerted, though not entirely synchronous, bond breaking and bond formation processes. The evolution of the active space spin-coupling pattern, which is closely related to the classical VB concept of resonance, combined with the changes in the orbital overlap integrals, show that the reaction path involves a region in which the electronic structure of the reacting system becomes similar to that of benzene. This suggests that during the Claisen rearrangement the reacting system can attain moderately aromatic character but that this does not necessarily happen at the TS. The results of the SC analysis indicate that the most appropriate schematic representation of the Claisen rearrangement is furnished by a homolytic mechanism in which six harpoons describe the changes in the bonding pattern from reactant to product     

Thermal dissociation of 1,2-dioxethane. II. Quantum topology of the charge distributions

The topological properties of the charge distribution of 1,2-dioxethane along the dissociation path (to formaldehyde products) and in different Hartree–Fock solutions are presented. At the equilibrium geometry of 1,2-dioxethane, all bond paths do not coincide with the corresponding internuclear axes. The outward curvature of the O? O bond path elaborates upon the concept of strain in the dioxethane ring. This weak binding of the ring is further confirmed by the considerably low ρ(r) value at the ring (3, +1) saddle point. An extension of the theory to the dynamic case has been discussed in terms of the topological changes in ρ(r) along the reaction path. The catastrophe of the chemical change, i.e., rupture of the dioxethane ring, takes the form of gradual merging and annhilation of the O? O (3, ?1) and the ring (3, +1) critical points. The values of ρ(r) at the positions of the critical points along the reaction path provide a topological characterization and definition of “partial valence.” The difference between the topological behavior of ρ(r), as obtained by different HF solutions, along the reaction path is analyzed and discussed.     

Origin of the synchronicity in bond formation in polar Diels-Alder reactions: an ELF analysis of the reaction between cyclopentadiene and tetracyanoethylene

The origin of the synchronicity in C-C bond formation in polar Diels-Alder (P-DA) reactions involving symmetrically substituted electrophilic ethylenes has been studied by an ELF analysis of the electron reorganization along the P-DA reaction of cyclopentadiene (Cp) with tetracyanoethylene (TCE) at the B3LYP/6-31G* level. The present study makes it possible to establish that the synchronicity in C-C bond formation in P-DA reactions is controlled by the symmetric distribution of the electron-density excess reached in the electrophile through the charge transfer process, which can be anticipated by an analysis of the spin electron-density at the corresponding radical anion. The ELF comparative analysis of bonding along the DA reactions of Cp with ethylene and with TCE asserts that these DA reactions, which have a symmetric electron reorganization, do not have a cyclic electron reorganization as the pericyclic mechanism states. Due to the very limited number of cases of symmetrically substituted ethylenes, we can conclude that the synchronous mechanism is an exception of DA reactions.     

H原子和(CH3)2SiH2抽提反应的理论研究

采用UMP2/6-31G(d)理论水平优化了H原子和(CH3)2SiH2抽提反应势能面上的所有驻点,并在此水平基础上进行了内禀反应坐标(IRC)的计算,得到该反应的反应途径(MEP)。应用变分过渡态理论及最小能量途径半经典绝热基态隧道效应校正(MEPSAG)、小曲率半经典绝热基态隧道效应校正(SCSAG)等方法对上述反应进行了动力学研究,期望从理论上提供一套温度范围较宽、精度较高的动力学数据,为阐明反应机理和解释实验结果提供理论依据。     

Theoretical analysis on the hydrogen bonding and reactivity that associated with the proton transfer reaction of carboxylic acid dimers and their monosulfur derivatives

Carboxylic acid dimers and their monosulfur derivatives are investigated by density functional theory calculations. Basis set superposition error (BSSE) counterpoise correction is included to compare the influence of BSSE on the interaction energies as well as on the geometries. The nature of hydrogen bond is determined on the basis of atoms in molecules (AIM) and natural bond orbital (NBO) analyses. Good correlations have been established between H‐bond length versus AIM topological parameter, orbital interaction, and barrier height for proton transfer. The reactivity behavior along the reaction path of the double proton transfer reaction has also been studied. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Theoretical study of the reaction of Sc with SCO in gas phase

In order to elucidate the mechanism of reaction M⁺ + SCO, both triplet and singlet potential energy surfaces (PESs) for the reaction of Sc⁺ + SCO have been theoretically investigated using the DFT (B3LYP/6-311+G*) level of theory. The geometries for reactants, intermediates, transition states and products were completely optimized. All the transition states were verified by the vibrational analysis and the intrinsic reaction coordinate calculations. The involving potential energy curve-crossing dramatically affects reaction mechanism, reaction rate has been discussed, and the crossing points (CPs) have been localized by the approach suggested by Yoshizawa et al. The present results show that the reaction mechanism are insertion–elimination mechanism both along the C–S and C–O bond activation branches, but the C–S bond activation is much more favorable in energy than the C–O bond activation. All theoretical results not only support the existing conclusions inferred from early experiment, but also complement the pathway and mechanism for this reaction.     

Theoretical study on the reactions of Nb and Nb+ with CO2 in gas phase

Density functional theory calculations have been performed to explore the potential energy surfaces of C? O bond activation in CO₂ molecule by gas‐phase Nb atom and Nb⁺ cation for better understanding the reaction mechanism of second‐row metal with CO₂. The minimum‐energy reaction path is found to involve the spin inversion in the different reaction steps. This potential energy curve‐crossing dramatically affects the reaction energetic. The present results show that the mechanism is insertion‐elimination mechanism along the C? O bond activation reaction. All theoretical results not only support the existing conclusions inferred from early experiment but also complement the pathway and mechanism for this reaction. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

A theoretical study of the reaction between cyclopentadiene and protonated imine derivatives: a shift from a concerted to a stepwise molecular mechanism

The reaction between cyclopentadiene and protonated pyridine-2-carboxaldehyde imine derivatives has been studied by using Hartree-Fock (HF) and B3LYP methods together with the 6-31G basis set. The molecular mechanism is stepwise along an inverted energy profile. This results from the protonation on both nitrogen atoms of the imine group and the pyridine framework. The first step corresponds to the nucleophilic attack of cyclopentadiene on the electron-poor carbon atom of the iminium cation group to give an acyclic cation intermediate, and the second step is associated with the ring closure of this intermediate via the formation of a C-N single bond yielding the final cycloadduct. Two reactive channels have been characterized corresponding to the endo and exo approach modes of the cyclopentadiene to the iminium cation. The role of the pyridium cation substituent and the nitrogen position (ortho, meta, and para) along the reaction pathway has been also considered. Solvent effects (dichloromethane) by means of a continuum model have been taken into account to model the experimental environment.     

Effect of a complex formation on the calculated low-pressure rate constant of a bimolecular gas-phase reaction governed by tunneling

Many important bimolecular hydrogen-transfer processes that take place in the atmosphere proceed via a potential energy minimum (hydrogen-bonded complex) that precedes along the minimum energy path the unique saddle point of the reaction, the one corresponding to the hydrogen transfer. It is clear that the one-step low-pressure rate constant of such a reaction does not depend on the existence of any complex along the minimum energy path below the reactant if the reaction takes place by thermal activation over a transition state that lies quite above the reactants (for instance 10 kcal/mol). However, we have quantitatively shown in this article that the scenario notoriously changes if the reaction involves significant tunneling. In this work, we have theoretically calculated the rate constants and their temperature dependence for the reaction HO+HOH→HOH+OH by means of a canonical variational transition state theory and a canonical unified statistical theory (when necessary). Multidimensional tunneling effects have been included with a semiclassical transmission coefficient. Two kinds of modified potential energy surfaces (PESs), obtained from an original ab initio potential energy surface, previously calculated by us, have been used. The Eckart-modified PESs serve to model the hydrogen-abstraction profiles with no complexes along the path, while the Gaussian-modified PESs model the energy profiles with two complexes along the path symmetrically distributed at each side of the abstraction saddle point. Our results show that the existence of those complexes reduces the thickness of the classically forbidden region for energies below the adiabatic barrier, and then tunneling is promoted and the reaction is accelerated. The effect of the complex formation in several kinetic magnitudes, as the Arrhenius parameters and the kinetic isotope effect has also been analyzed. © 1999 John Wiley & Sons, Inc. J Comput Chem 20: 1685–1692, 1999     

Energetic and topological analyses of the oxidation reaction between Mo(n) (n = 1, 2) and N2O

The interaction between molybdenum, atom, and dimer, with nitrous oxide has been investigated using density functional theory. The analysis of the potential energy surfaces for both reactions has revealed that a single molybdenum atom can activate the N--O bond of N2O requiring a small activation energy. However, the presence of several intersystem crossings between three different spin states, namely, septet, quintet and triplet states, seems to be the major constraint to the Mo + N2O reaction. Contrarily, the low-lying excited states (triplet and quintet) do not participate in the reaction between the molybdenum dimer and N2O. The latter reaction fully evolves on the singlet spin surface. Three different regions have been distinguished along the pathway: formation of an adduct complex, formation of an inserted compound, and the N2 detachment. The connection between the two first regions has been characterized by the formation of a special complex in which the N--O bond is so weakened that it could be considered as a first step in the insertion process. It has been shown that the topological changes along the pathways provide a clear explanation for the geometrical changes that occur along the reaction pathway. In summary, the detachment of the N2 molecule is found to be kinetically an effective process for both reactions, owing to the high exothermicity and consequently to the high internal energy of the insertion intermediates. However, in the case of Mo atom, the reaction should be a slow process due to the presence of spin-forbidden transitions. These results fully agree with previous experimental works.