Deciphering the influence of PdII and PdIV oxidation states on non-standard chemical bonds within bis(jN-heterocyclic carbene) complexes: insights from DFT.

Bis-N-heterocyclic carbene ligands (bis(NHC)) have introduced a new approach to designing homogeneous and heterogeneous catalysts, demonstrating the versatility of ligand concepts in catalysis. This study presents a computational analysis of palladium (+ii and +iv) complexes containing either a normally (bis(nNHC)) or an abnormally (bis(aNHC)) bound CH2-bridged bis-N-heterocyclic carbene ligand; in addition, ancillary ligands are permuted from chlorides (X = Cl) to bromides (X = Br). Density functional theory at the B3PW91/6-31G(d)/Lanl2DZ level in the gas phase was used to investigate the electronic structure and bonding properties of bis(NHC)PdIIX2 and bis(NHC)PdIVX4 for bis(NHC) palladium(ii) dihalide and palladium(iv) tetrachloride complexes, respectively. Results indicate that all of the palladium complex structures prefer a flexible boat-type conformation with an average C 2v symmetry, according to bond property (Ccarbene-Pd and Pd-Cl[Br]) analysis. The strength of these bonds depends on coordinating halide ions (Cl- and Br-), the type of ligand (bis(nNHC) and bis(aNHC)), and the palladium oxidation state (+ii and +iv). Analysis of thermodynamic parameters (ΔH 0, ΔG 0, and ΔE bind) shows an increase in values from an abnormal to normal chelating mode in tetrahalides, whereas the opposite is observed for dihalide complexes. The lower π-backbonding ability of the metal, which is influenced by the quantity and size of halide ions involved, could be one possible explanation for this deficiency.

Exploring the Mechanism of the Intramolecular Diels-Alder Reaction of (2E,4Z,6Z)-2(allyloxy)cycloocta-2,4,6-trien-1-one Using Bonding Evolution Theory.

In the present work, the bond breaking/forming events along the intramolecular Diels-Alder (IMDA) reaction of (2E,4Z,6Z)-2(allyloxy)cycloocta-2,4,6-trien-1-one have been revealed within bonding evolution theory (BET) at the density functional theory level, using the M05-2X functional with the cc-pVTZ basis set. Prior to achieving this task, the energy profiles and stationary points at the potential energy surface (PES) have been characterized. The analysis of the results finds that this rearrangement can proceed along three alternative reaction pathways (a-c). Paths a and b involve two steps, while path c is a one-step process. The first step in path b is kinetically favored, and leads to the formation of an intermediate step, Int-b. Further evolution from Int-b leads mainly to 3-b1. However, 2 is the thermodynamically preferred product and is obtained at high temperatures, in agreement with the experimental observations. Regarding the BET analysis along path b, the breaking/forming process is described by four structural stability domains (SSDs) during the first step, which can be summarized as follows: (1) the breaking of the C-O bond with the transfer of its population to the lone pair (V(O)), (2) the reorganization of the electron density with the creation of two V(C) basins, and (3) the formation of a new C-C single bond via the merger of the two previous V(C) basins. Finally, the conversion of Int-b (via TS2-b1) occurs via the reorganization of the electron density during the first stage (the creation of different pseudoradical centers on the carbon atoms as a result of the depopulation of the C-C double bond involved in the formation of new single bonds), while the last stage corresponds to the non-concerted formation of the two new C-C bonds via the disappearance of the population of the four pseudoradical centers formed in the previous stage. On the other hand, along path a, the first step displays three SSDs, associated with the depopulation of the V(C2,C3) and V(C6,C7) basins, the appearance of the new monosynaptic basins V(C2) and V(C7), and finally the merging of these new monosynaptic basins through the creation of the C2-C7 single bond. The second step is described by a series of five SSDs, that account for the reorganization of the electron density within Int-a via the creation of four pseudoradical centers on the C12, C13, C3 and C6 carbon atoms. The last two SSDs deal with the formation of two C-C bonds via the merging of the monosynaptic basins formed in the previous domains.

Unraveling the sequence of electron flow along the cyclocondensation reaction between ciprofloxacin and thiosemicarbazide through the bonding evolution theory.

We have theoretically conducted a comprehensive investigation on the cyclocondensation reaction between ciprofloxacin and thiosemicarbazide at the MN15/6-311++G(d,p) level of approximation. In order to revisit and understand the sequence of electronic flow rearrangement, as described in terms of electron pair distribution, within the framework of Bonding Evolution Theory (BET) approach as provided by the application of Thom's elementary Catastrophe Theory (CT) to the changes, along the intrinsic reaction coordinate, of the gradient vector field of the electron localization function (ELF). This reaction has two channels (a and b) and each one takes place via three steps. The CDFT results show that ciprofloxacin and thiosemicarbazide have an electrophilic and nucleophilic characters respectively and therefore allowing this reaction to have a polar character. All the transition state (TS) of all reaction steps have been localized and characterized. In addition, the analysis of activation energy predicts the formation of ciprofloxacin thiosemicarbazone 3a (channels a) as a main product in good agreement with experimental outcomes. The BET analysis results along channel a reveal that the mechanism for each reaction step is divided into four structural stability domains. During the first step, a new N2-C2 bond occurs at the SSD-II, followed by a rupture of the H1-N2 single bond (SSD-III) illustrating the restoration of lone pairs of the N2 nitrogen atom, and finally, the formation of a new H1-O1 single bond. For the second step, the process involves the breaking of O1-C2 and N2-H3 bonds at the SSD-II and SSD-III, respectively, followed by the formation of O1-H3 bond at the SSD-IV. For the last step, it is noted the formation of C4-N8 bond at the SSD-II, followed by the breaking of N8-H9 and C4-O6 bonds simultaneously at the SSD-III with water elimination at the last domain (SSD-IV).

Exploring The Sequence of Electron Density Along The Chemical Reactions Between Carbonyl Oxides And Ammonia/Water Using Bond Evolution Theory.

The molecular mechanism of the reactions between four carbonyl oxides and ammonia/water are investigated using the M06-2X functional together with 6-311++G(d,p) basis set. The analysis of activation and reaction enthalpy shows that the exothermicity of each process increased with the substitution of electron donating substituents (methyl and ethenyl). Along each reaction pathway, two new chemical bonds C-N/C-O and O-H are expected to form. A detailed analysis of the flow of the electron density during their formation have been characterized from the perspective of bonding evolution theory (BET). For all reaction pathways, BET revealed that the process of C-N and O-H bond formation takes place within four structural stability domains (SSD), which can be summarized as follows: the depopulation of V(N) basin with the formation of first C-N bond (appearance of V(C,N) basin), cleavage of N-H bond with the creation of V(N) and V(H) monosynaptic basin, and finally the V(H,O) disynaptic basin related to O-H bond. On the other hand, in the case of water, the cleavage of O-H bond with the formation of V(O) and V(H) basins is the first stage, followed by the formation of the O-H bond as a second stage, and finally the creation of C-O bond.

Topological investigation of the reaction mechanism of glycerol carbonate decomposition by bond evolution theory.

The reaction mechanisms of the decomposition of glycerol carbonate have been investigated at the density functional theory level within the bond evolution theory. The four reaction pathways yield to 3-hydroxypropanal (TS1), glycidol (TS2a and TS2b), and 4-methylene-1,3-dioxolan-2-one (TS3). The study reveals non-concerted processes with the same number (four) of structural stability domains for each reaction pathway. For the two decarboxylation mechanisms, the two first steps are similar. They correspond to the cleavage of two single CO bonds to the detriment of the increased population of the lone pairs of two O atoms. These are followed, along TS1, by the transformation of a CO single bond into a double bond together with a proton transfer to create a CH bond. For TS2a and TS2b, the last step is a cyclization by CO bond formation. For the TS3 pathway, the first stage consists in the cleavage of a CH bond and the transfer of its electron population to both a proton and a C atom, the second step corresponds to the formation of an OH bond, and the last one describes the formation of a CC double bond. Moreover, the analysis of the energies, enthalpies, and free enthalpies of reaction and of activation leads to the conclusion that 3-hydroxypropanal is both the thermodynamic and kinetic product, independent of the method of calculation.

Deciphering the Curly Arrow Representation and Electron Flow for the 1,3-Dipolar Rearrangement between Acetonitrile Oxide and (1S,2R,4S)-2-Cyano-7-oxabicyclo[2.2.1]hept-5-en-2-yl Acetate Derivatives.

This study is focused on describing the molecular mechanism beyond the molecular picture provided by the evolution of molecular orbitals, valence bond structures along the reaction progress, or conceptual density functional theory. Using bonding evolution theory (BET) analysis, we have deciphered the mechanism of the 1,3-dipolar rearrangement between acetonitrile oxide and (1S,2R,4S)-2-cyano-7-oxabicyclo[2.2.1]hept-5-en-2-yl acetate derivatives. The BET study revealed that the formation of the C-C bond takes place via a usual sharing model before the O-C one that is also formed in the halogenated species through a not very usual sharing model. The mechanism includes depopulation of the electron density at the N-C triple bond and creation of the V(N) and V(C) monosynaptic basins, depopulation of the former C-C double bond with the creation of V(C,C) basins, and final formation of the V(O,C) basin associated with the O-C bond. The topological changes along the reaction pathway take place in a highly synchronous way. BET provides a convenient quantitative method for deriving curly arrows and electron flow representation to unravel molecular mechanisms.

Density Functional Theory Investigation of the Binding of ThioTEPA to Purine Bases: Thermodynamics and Bond Evolution Theory Analysis.

Density functional theory with the ωB97X-D exchange-correlation functional together with implicit as well as explicit solvation is used to describe the reactions of the adenine and guanine purine bases on N,N',N″-triethylenethiophosphoramide (thioTEPA), an alkylating agent used as an anticancer drug. This reaction is decomposed into (i) a nucleophilic addition and (ii) a proton "migration" that is mediated by the solvent molecules. The calculations reveal that the first step is rate determining and that the presence of an explicit water molecule to mediate the proton migration has a negligible role on the kinetics of the first step, so that the focus is set on the first step of the reaction. ωB97X-D calculations highlight (i) the activation energy (Gibbs free enthalpy) is smaller for imine nitrogens than amine nitrogens, (ii) for the imine functions, the activation energy is slightly smaller for adenine than for guanine together with a larger exergonicity for the alkylation by adenine, and (iii) among the amine nitrogens, the presence of stabilizing H-bonds in the case of exocyclic amines leads to smaller activation energy than for the endocyclic ones. The reaction mechanisms are unraveled by employing the bond evolution theory, combining the use of electronic localization functions, and their evolution along the intrinsic reaction coordinate, with Thom's catastrophe theory. These analyses, suitable for highlighting the populations of the major monosynaptic and disynaptic basins, show (i) the reaction with imine nitrogens begins by the cleavage of the C-N aziridine bond and is followed by the simultaneous formation of the new C-N bond and the disappearance of the nitrogen lone pair, (ii) the reaction with the nitrogen atom of an endocyclic or exocyclic amine proceeds first by the formation of the cross-linking C-N bond and then by the cleavage of the C-N aziridine bond and the disappearance of the nitrogen lone pair, and (iii) in case ii, this bond breaking and forming occur before the transition state, which has been correlated to the increased Gibbs enthalpy of activation with respect to the reaction with the nitrogen atom of imine functions.

Intramolecular [3 + 2] Cycloaddition Reactions of Unsaturated Nitrile Oxides. A Study from the Perspective of Bond Evolution Theory (BET).

The reaction mechanism of the [3 + 2] intramolecular cycloaddition of 3,3-dimethyl-2-(prop-2-en-1-yloxy) and (prop-2-en-1-ylsulfanyl) nitrile oxides is analyzed using different DFT functionals with the 6-311++G(d,p) basis set. The activation and the reaction energies for the cis and trans pathways are evaluated at the DFT, MP2, and CCSD(T) levels of theory as well as their Gibbs free energy counterparts. It is shown that the trans regioisomers are both thermodynamic and kinetic compounds, in agreement with experimental outcomes. For a deeper understanding of the reaction mechanism, a BET analysis along the reaction channel ( trans and cis) has been carried out. This analysis reveals that the lone pair on the nitrogen atom is formed first, then the C-C bond, and finally the O-C one. The global mechanism is similar for the two compounds and for the two pathways even if some small differences are observed, for instance, in the values of the reaction coordinates of appeareance of the different basins.