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     

The Mechanism of NO Bond Cleavage in Rhodium‐Catalyzed CH Bond Functionalization of Quinoline N‐oxides with Alkynes: A Computational Study

Metal‐catalyzed C?H activation not only offers important strategies to construct new bonds, it also allows the merge of important research areas. When quinoline N‐oxide is used as an arene source in C?H activation studies, the N?O bond can act as a directing group as well as an O‐atom donor. The newly reported density functional theory method, M11L, has been used to elucidate the mechanistic details of the coupling between quinoline N?O bond and alkynes, which results in C?H activation and O‐atom transfer. The computational results indicated that the most favorable pathway involves an electrophilic deprotonation, an insertion of an acetylene group into a Rh?C bond, a reductive elimination to form an oxazinoquinolinium‐coordinated Rh^I intermediate, an oxidative addition to break the N?O bond, and a protonation reaction to regenerate the active catalyst. The regioselectivity of the reaction has also been studied by using prop‐1‐yn‐1‐ylbenzene as a model unsymmetrical substrate. Theoretical calculations suggested that 1‐phenyl‐2‐quinolinylpropanone would be the major product because of better conjugation between the phenyl group and enolate moiety in the corresponding transition state of the regioselectivity‐determining step. These calculated data are consistent with the experimental observations.     

Reinvestigation into the ring‐opening process of monochloroethylene oxide by quantum chemical calculations

Density functional theory (DFT) computation with B3LYP/6‐31++G** has been performed for the ring‐opening process of monochloroethylene oxide. In this study, the energy changes of an isolated monochloroethylene oxide, an O‐protonated one and a Cl‐protonated one, were investigated with respect to the stretching of the C? O bond length. The increased energy in an O‐protonated system is fairly slow compared with that in a neutral system. In an O‐protonated system, rupturing of the C? O bond, in which the carbon atom in the bond binds to the chlorine atom, occurs more easily than another C? O bond rupture. This fact is in agreement with ideas accepted in organic chemistry. Intrinsic reaction coordinate (IRC) calculations were performed for the O‐protonated system, which gave the activation energy of the ring rupture as 3.89 kcal/mol. This also revealed that the production of an aldehyde occurred by a two‐step reaction, that is, the first ring‐opening process and following transfer of the chlorine atom. LMO wave functions were used to analyze the reaction mechanism. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

A comparative study of open‐close and related rotamers methods to evaluate the intramolecular hydrogen bond energies in 3‐imino‐propen‐1‐ol and its derivatives

MP2 study of O? H…N intramolecular hydrogen bond (IMHB) in 3‐imino‐propen‐1‐ol and its derivatives were performed and their IMHB energies were obtained using the related rotamers and open‐close methods. Also the topological properties of electron density distribution and charge transfer energy associated with IMHB were gained by quantum theory of atoms in molecules and natural bond orbital theory, respectively. The computational results reveal that the related rotamers method energies are well correlates with geometrical parameters, topological parameters at hydrogen bond and ring critical points, integrated properties, proton transfer barrier and charge transfer energy of O? H…N unit. Surprisingly, it was found that the open‐close hydrogen bond energies cannot represent good linear correlations with these parameters. Consequently, we extrapolate a number of equations that can be used in estimation of O? H…N IMHB energy in complex biological systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Quantum chemistry aspects of the solvent effects on the ene reaction of 1‐Phenyl‐1,3,4‐triazolin‐2,5‐dione and 2‐methyl‐2‐butene

A density functional theory study was used to investigate the quantum aspects of the solvent effects on the kinetic and mechanism of the ene reaction of 1‐phenyl‐1,3,4‐triazolin‐2,5‐dione and 2‐methyl‐2‐butene. Using the B3LYP/6–311++ G(d,p) level of the theory, reaction rates have been calculated in the various solvents and good agreement with the experimental data has been obtained. Natural bond orbital analysis has been applied to calculate the stabilization energy of N18? H19 bond during the reaction. Topological analysis of quantum theory of atom in molecule (QTAIM) studies for the electron charge density in the bond critical point (BCP) of N18? H19 bond of the transition states (TSs) in different solvents shows a linear correlation with the interaction energy. It is also seen form the QTAIM analysis that increase in the electron density in the BCP of N18? H19, raises the corresponding vibrational frequency. Average calculated ratio of 0.37 for kinetic energy density to local potential energy density at the BCPs as functions of N18? H19 bond length in different media confirmed covalent nature of this bond. Using the concepts of the global electrophilicity index, chemical hardness and electronic chemical potentials, some correlations with the rate constants and interaction energy have been established. Mechanism and kinetic studies on 1‐phenyl‐1,3,4‐triazolin‐2,5‐dione and 2‐methyl‐2‐butene ene reaction suggests that the reaction rate will boost with interaction energy enhancement. Interaction energy of the TS depends on the solvent nature and is directly related to electron density of the bonds involved in the reaction proceeding, global electrophilicity index and electronic chemical potential. However, the chemical hardness relationship is reversed. Finally, an interesting and direct correlation between the imaginary vibrational frequency of the N18? H19 critical bond and its electron density at the TS has been obtained. © 2014 Wiley Periodicals, Inc.     

Metal‐Free σ‐Bond Metathesis in 1,3,2‐Diazaphospholene‐Catalyzed Hydroboration of Carbonyl Compounds

The first metal‐free catalytic hydroboration of carbonyl derivatives has been developed in which a catalytic amount of 1,3,2‐diazaphospholene effectively promotes a hydroboration reaction of aliphatic and aromatic aldehydes and ketones. The reaction mechanism involves the cleavage of both the P? O bond of the alkoxyphosphine intermediate and the B? H bond of pinacolborane as well as the formation of P? H and B? O bonds. Thus, the reaction proceeds through a non‐metal σ‐bond metathesis. Kinetic and computational studies suggest that the σ‐bond metathesis occurred in a stepwise but nearly concerted manner.     

Comparative Analysis of Electron‐Density and Electron‐Localization Function for Dinuclear Manganese Complexes with Bridging Boron‐ and Carbon‐Centered Ligands

Bonding in borylene‐, carbene‐, and vinylidene‐bridged dinuclear manganese complexes [MnCp(CO)₂]₂X (X=B‐tBu, B=NMe₂, CH₂, C?CH₂) has been compared by analyses based on quantum theory of atoms in molecules (QTAIM), on the electron‐localization function (ELF), and by natural‐population analyses. All of the density functional theory based analyses agree on the absence of a significant direct Mn? Mn bond in these complexes and confirm a dominance of delocalized bonding via the bridging ligand. Interestingly, however, the topology of both charge density and ELF related to the Mn‐bridge‐Mn bonding depend qualitatively on the chosen density functional (except for the methylene‐bridged complex, which exhibits only one three‐center‐bonding attractor both in ??²ρ and in ELF). While gradient‐corrected functionals provide a picture with localized two‐center X? Mn bonding, increasing exact‐exchange admixture in hybrid functionals concentrates charge below the bridging atom and suggests a three‐center bonding situation. For example, the bridging boron ligands may be described either as substituted boranes (e.g., at BLYP or BP86 levels) or as true bridging borylenes (e.g., at BHLYP level). This dependence on the theoretical level appears to derive from a bifurcation between two different bonding situations and is discussed in terms of charge transfer between X and Mn, and in the context of self‐interaction errors exhibited by popular functionals.     

New insight into the electronic structure of iron(IV)‐oxo porphyrin compound I. A quantum chemical topological analysis

The electronic structure of iron‐oxo porphyrin π‐cation radical complex Por^·+Fe^IV?O (S? H) has been studied for doublet and quartet electronic states by means of two methods of the quantum chemical topology analysis: electron localization function (ELF) η(r) and electron density ρ(r). The formation of this complex leads to essential perturbation of the topological structure of the carbon–carbon bonds in porphyrin moiety. The double C?C bonds in the pyrrole anion subunits, represented by pair of bonding disynaptic basins V_i=1,2(C,C) in isolated porphyrin, are replaced by single attractor V(C,C)_i=1–20 after complexation with the Fe cation. The iron–nitrogen bonds are covalent dative bonds, N→Fe, described by the disynaptic bonding basins V(Fe,N)_i=1–4, where electron density is almost formed by the lone pairs of the N atoms. The nature of the iron–oxygen bond predicted by the ELF topological analysis, shows a main contribution of the electrostatic interaction, Fe^δ+···O^δ?, as long as no attractors between the C(Fe) and C(O) core basins were found, although there are common surfaces between the iron and oxygen basines and coupling between iron and oxygen lone pairs, that could be interpreted as a charge‐shift bond. The Fe? S bond, characterized by the disynaptic bonding basin V(Fe,S), is partially a dative bond with the lone pair donated from sulfur atom. The change of electronic state from the doublet (M = 2) to quartet (M = 4) leads to reorganization of spin polarization, which is observed only for the porphyrin skeleton (?0.43e to 0.50e) and S? H bond (?0.55e to 0.52e). © 2012 Wiley Periodicals, Inc.     

Substituent effect on structure,electron density,and intramolecular hydrogen bonding in nitroso‐oxime methane

Density functional calculations with Beck's three‐parameter hybrid method using the correlation functional of Lee, Yang, and Parr (B3LYP) were carried out for investigation of the intramolecular hydrogen bond strength in Nitroso‐oxime methane and its derivatives. Also, vibrational frequencies for them were calculated at the same level of theory. The π‐electron delocalization parameter (Q) and as a geometrical indicator of a local aromaticity, the geometry‐based harmonic oscillator measure of aromaticity index has been applied. Additionally, the linear correlation coefficients between substituent constants and selected parameters in R position have calculated. The obtained results show that the hydrogen bond strength is mainly governed by the resonance variations inside the chelate ring induced by the substituent groups. The topological properties of the electron density distributions for O? H ··· O intramolecular bridges have been analyzed in terms of the Bader theory of atoms in molecules (AIM). Correlations between the H‐bond strength and topological parameters have been also studied. The electron density (ρ) and Laplacian (?²ρ) properties, estimated by AIM calculations, show that O ··· H bond have low ρ and negative (?²ρ) values (consistent with covalent character of the HBs), whereas O? H bond have positive (?²ρ) Furthermore, the analysis of hydrogen bond in this molecule and its derivatives by quantum theory of natural bond orbital (NBO) methods fairly support the ab initio results. Natural population analysis data, the electron density, and Laplacian properties as well as υ(O? H) and γ(O? H) were further used for estimation of the hydrogen bonding interactions and the forces driving their formation. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Copper‐Catalyzed Domino Synthesis of 2‐Imino‐1H‐imidazol‐5(2H)‐ones and Quinoxalines Involving CC Bond Cleavage with a 1,3‐Dicarbonyl Unit as a Leaving Group

Although 2‐imino‐1H‐imidazol‐5(2H)‐ones have important biological activities in metabolism, their synthesis has rarely been investigated. Quinoxalines as “privileged scaffolds” in medicinal chemistry have been extensively investigated, but the development of novel and efficient synthetic methods remains very attractive. Herein, we have developed two copper‐catalyzed domino reactions for the synthesis of 2‐imino‐1H‐imidazol‐5(2H)‐ones and quinoxalines involving C?C bond‐cleavage with a 1,3‐dicarbonyl unit as a leaving group. The domino sequence for the synthesis of 2‐imino‐1H‐imidazol‐5(2H)‐ones includes aza‐Michael addition, intramolecular cyclization, C?C bond‐cleavage, 1,2‐rearrangement, and aerobic dehydrogenation reaction, whereas the domino sequence for the synthesis of quinoxalines includes aza‐Michael addition, intramolecular cyclization, elimination reaction, and C?C bond‐cleavage reaction. The two domino reactions have significant advantages including high efficiency, mild reaction conditions, and high tolerance of various functional groups.     

Chemoselectivity of the Reactions of Diazomethanes with 5‐Benzylidene‐3‐phenylrhodanine

The reactions of 5‐benzylidene‐3‐phenylrhodanine ( 2 ; rhodanine=2‐thioxo‐1,3‐thiazolidin‐4‐one) with diazomethane ( 7a ) and phenyldiazomethane ( 7b ) occurred chemoselectively at the exocyclic C?C bond to give the spirocyclopropane derivatives 9 and, in the case of 7a , also the C‐methylated products 8 (Scheme 1). In contrast, diphenyldiazomethane ( 7c ) reacted exclusively with the C?S group leading to the 2‐(diphenylmethylidene)‐1,3‐thiazolidine 11 via [2+3] cycloaddition and a ‘two‐fold extrusion reaction’. Treatment of 8 or 9b with an excess of 7a in refluxing CH₂Cl₂ and in THF at room temperature in the presence of [Rh₂(OAc)₄], respectively, led to the 1,3‐thiazolidine‐2,4‐diones 15 and 20 , respectively, i.e., the products of the hydrolysis of the intermediate thiocarbonyl ylide. On the other hand, the reactions with 7b and 7c in boiling toluene yielded the corresponding 2‐methylidene derivatives 16, 21a , and 21b . Finally, the reaction of 11 with 7a occurred exclusively at the electron‐poor C?C bond, which is conjugated with the C?O group. In addition to the spirocyclopropane 23 , the C‐methylated 22 was formed as a minor product. The structures of the products (Z)‐ 8, 9a, 9b, 11 , and 23 were established by X‐ray crystallography.     

Comprehensive Analysis of DNA Strand Breaks at the Guanosine Site Induced by Low‐Energy Electron Attachment

To elucidate the role of guanosine in DNA strand breaks caused by low‐energy electrons (LEEs), theoretical investigations of the LEE attachment‐induced C? O σ‐bonds and N‐glycosidic bond breaking of 2′‐deoxyguanosine‐3′,5′‐diphosphate (3′,5′‐dGMP) were performed using the B3LYP/DZP++ approach. The results reveal possible reaction pathways in the gas phase and in aqueous solutions. In the gas phase LEEs could attach to the phosphate group adjacent to the guanosine to form a radical anion. However, the small vertical detachment energy (VDE) of the radical anion of guanosine 3′,5′‐diphosphate in the gas phase excludes either C? O bond cleavage or N‐glycosidic bond breaking. In the presence of the polarizable surroundings, the solvent effects dramatically increase the electron affinities of the 3′,5′‐dGDP and the VDE of 3′,5′‐dGDP^?. Furthermore, the solvent–solute interactions greatly reduce the activation barriers of the C? O bond cleavage to 1.06–3.56 kcal mol^?1. These low‐energy barriers ensure that either C_5′? O_5′ or C_3′? O_3′ bond rupture takes place at the guanosine site in DNA single strands. On the other hand, the comparatively high energy barrier of the N‐glycosidic bond rupture implies that this reaction pathway is inferior to C? O bond cleavage. Qualitative agreement was found between the theoretical sequence of the bond breaking reaction pathways in the PCM model and the ratio for the corresponding bond breaks observed in the experiment of LEE‐induced damage in oligonucleotide tetramer CGTA. This concord suggests that the influence of the surroundings in the thin solid film on the LEE‐induced DNA damage resembles that of the solvent.     

A density functional theory study on the catalytic mechanism of hydroxycinnamoyl‐CoA hydratase‐lyase

Hydroxycinnamoyl‐CoA hydratase‐lyase (HCHL), a particular member of the crotonase superfamily, catalyzes the bioconversion of feruloyl‐CoA to the important flavor and fragrance compound vanillin. In this article, the catalytic mechanism of HCHL has been studied by using hybrid density functional theory method with simplified models. The calculated results reveal that the mechanism involves the hydration of the C?C double bond of feruloyl‐CoA and thence the cleavage of C? C single bond of β‐hydroxythioester. The hydration step is a typical concerted process, whereas C? C bond cleavage follows a concerted but asynchronous mechanism. The calculated energy barrier of hydration reaction is only slightly lower than that of cleavage process, implying both of two processes are rate limiting. By using three substrate analogs, the substrate specificity of HCHL was further examined. It is found that the p‐hydroxyl group of aromatic ring is necessary for the catalytic reaction. © 2013 Wiley Periodicals, Inc.     

Synthesis and Characterization of [XeOXe]2+ in the Adduct‐Cation Salt, [CH3CN‐ ‐ ‐XeOXe‐ ‐ ‐NCCH3][AsF6]2

Acetonitrile and [FXeOXe‐ ‐ ‐FXeF][AsF₆] react at ?60 °C in anhydrous HF (aHF) to form the CH₃CN adduct of the previously unknown [XeOXe]²⁺ cation. The low‐temperature X‐ray structure of [CH₃CN‐ ‐ ‐XeOXe‐ ‐ ‐NCCH₃][AsF₆]₂ exhibits a well‐isolated adduct‐cation that has among the shortest Xe?N distances obtained for an sp‐hybridized nitrogen base adducted to xenon. The Raman spectrum was fully assigned by comparison with the calculated vibrational frequencies and with the aid of ¹⁸O‐enrichment studies. Natural bond orbital (NBO), atoms in molecules (AIM), electron localization function (ELF), and molecular electrostatic potential surface (MEPS) analyses show that the Xe?O bonds are semi‐ionic whereas the Xe?N bonds may be described as strong electrostatic (σ‐hole) interactions.     

Blue‐shifted and red‐shifted hydrogen bonds: Theoretical study of the CH3CHO· · ·HNO complexes

The blue‐shifted and red‐shifted H‐bonds have been studied in complexes CH₃CHO…HNO. At the MP2/6‐31G(d), MP2/6‐31+G(d,p) MP2/6‐311++G(d,p), B3LYP/6‐31G(d), B3LYP/6‐31+G(d,p) and B3LYP/6‐311++G(d,p) levels, the geometric structures and vibrational frequencies of complexes CH₃CHO…HNO are calculated by both standard and CP‐corrected methods, respectively. Complex A exhibits simultaneously red‐shifted C? H…O and blue‐shifted N? H…O H‐bonds. Complex B possesses simultaneously two blue‐shifted H‐bonds: C? H…O and N? H…O. From NBO analysis, it becomes evident that the red‐shifted C? H…O H‐bond can be explained on the basis of the two opposite effects: hyperconjugation and rehybridization. The blue‐shifted C? H…O H‐bond is a result of conjunct C? H bond strengthening effects of the hyperconjugation and the rehybridization due to existence of the significant electron density redistribution effect. For the blue‐shifted N? H…O H‐bonds, the hyperconjugation is inhibited due to existence of the electron density redistribution effect. The large blue shift of the N? H stretching frequency is observed because the rehybridization dominates the hyperconjugation. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Theoretical investigations on the weak nonbonded CS···CH2 interactions: Chalcogen‐bonded complexes with singlet carbene as an electron donor

In this article, we explored the noncovalent bonding interactions between O?C?S, S?C?S, F₂C?S, Cl₂C?S, and singlet carbene. Six chalcogen‐bonded complexes were obtained. It is found that all the vibrational frequencies of C?S bond presented a red shift character. Interaction energy, topology property of the electron density and its Laplacian, and the donor–acceptor interaction have been investigated. All these results show that there exists a weak nonbonded interaction between the chalcogen bond donor and CH₂. An energy decomposition analysis was performed to disclose that the electrostatic interaction is the main stabilized factor in these nonbonded complexes. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Rhodium(III)‐Catalyzed CC and CO Coupling of Quinoline N‐Oxides with Alkynes: Combination of CH Activation with O‐Atom Transfer

[Cp*Rh^III]‐catalyzed C? H activation of arenes assisted by an oxidizing N? O or N? N directing group has allowed the construction of a number of hetercycles. In contrast, a polar N? O bond is well‐known to undergo O‐atom transfer (OAT) to alkynes. Despite the liability of N? O bonds in both C? H activation and OAT, these two important areas evolved separately. In this report, [Cp*Rh^III] catalysts integrate both areas in an efficient redox‐neutral coupling of quinoline N‐oxides with alkynes to afford α‐(8‐quinolyl)acetophenones. In this process the N? O bond acts as both a directing group for C? H activation and as an O‐atom donor.     

Blue‐shifted H‐bond in aromatic sulfines: An ab initio calculation

The intramolecular C? H···O?S H‐bond in the aromatic sulfines, HRC?S?O, was analyzed by NBO and QTAIM methods. The results of QTAIM analysis at the MP2/aug‐cc‐pVDZ level of theory show that the C? H···O?S H‐bond meets all the characteristics of an improper, blue shift hydrogen bond. NBO analysis at the MP2/6–31++G(d,p)//MP2/aug‐cc‐pVDZ level predicts a normal relationship between change of bond length and C? H rehybridization. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Copper‐Catalyzed Oxidative Reaction of β‐Keto Sulfones with Alcohols via C−S Bond Cleavage: Reaction Development and Mechanism Study

A Cu‐catalyzed cascade oxidative radical process of β‐keto sulfones with alcohols has been achieved by using oxygen as an oxidant. In this reaction, β‐keto sulfones were converted into sulfinate esters under the oxidative conditions via cleavage of C?S bond. Experimental and computational studies demonstrate that a new pathway is involved in this reaction, which proceeds through the formation of the key four‐coordinated Cu^II intermediate, O?O bond homolysis induced C?S bond cleavage and Cu‐catalyzed esterification to form the final products. This reaction provides a new strategy to sulfonate esters and enriches the research content of C?S bond cleavage and transformations.