Stéphane Humbel

On the link atom distance in the ONIOM scheme. An harmonic approximation analysis

Abstract The link atom distance of the ONIOM scheme is studied and analyzed with a harmonic approximation. It is shown that, when an appropriate low level is used, the ONIOM absolute energy does not depend on the choice of this distance, except for clearly ‘unreasonable’ distances. A strategy to analyze the low level is proposed on the basis of this harmonic approximation. Geometry optimizations are found even less sensitive to the choice of this link atom distance.

Modelling the two-dimensional polymerization of 1,4-benzene diboronic acid on a Ag surface

Modelling of the two-dimensional polymerization of 1,4-benzene diboronic acid molecules on the Ag(111) surface, which leads to the formation of a covalent organic framework, is reported. An estimation of free enthalpy is given that takes into account the constraints induced by the molecular adsorption on the surface. The various thermodynamic functions, enthalpies, entropies, and free enthalpies, are obtained from DFT calculations. The entropic effect of the surface plays an important role in the polymerization free energy. A germination threshold is obtained.

Specific solvent effect on R2ZrCl2 (R=butyl, ethyl) reactivity, a density functional study

The reactivity of ZrCl2Bu2 is modeled for the formation of ZrCl2(butene). Two pathways are computed: the β- and the γ-Hydrogen migration. It is found that the β-H pathway is favored by about 13 kcal mol−1. The specific effect of dimethyl ether as a model of the THF solvent is analyzed and found to greatly facilitate the reaction. Solvent or ligand complexation on the zirconium is found more important in product ZrCl2(butene) than in the reagent ZrCl2Bu2. These results are commented in regard to the experimental evidences of reactivity differences depending on the solvent used.

Theoretical description of [2+2] photocycloadditions: enone and ethylene as a model of the reactivity of cycloenones

Abstract The photoinitiated [2+2] cycloaddition of acrolein plus ethylene, as a model of cyclobutanes formation, has been studied using semi-empirical, ab initio and DFT methods. Singlet and triplet potential energy surfaces and their relative position were investigated. The intersystem crossing (spin–orbit coupling) and retrocleavage processes are also reported. The values obtained by usual methods (AM1, HF, MP2, B3LYP) are compared to the Coupled Cluster results. It is shown that the different parts of the reaction pathways have to be described by different levels of approximation. On the triplet surface, we found a severe spin contamination of the UHF wavefunction, which precludes further use of perturbative methods (MP2). In the intersystem crossing, we show how the physically wrong RHF wavefunction (singlet) leads to erroneous results which are not corrected, even using the CCSD(T) level of theory. In the ultimate part of the reaction profile (singlet surface), we report the overestimation by the UHF method of the energies of the transition states, especially for the one leading to the cycloadducts, and the poor quality of the B3LYP potential energy surface.

Localized Structures at the Hückel Level, a Hückel-Derived Valence Bond Method

A simple Huckel Hamiltonian is used and modified to describe localized states, where the electron pairs are confined to bonds between two atoms, or to lone pairs. The electronic delocalization can be considered either as a mixture of these localized states, or through a standard Huckel calculation. The two Huckel-Lewis methods described here attempt to find the coefficients of the mixture, based on energy or overlap consistence with the standard Huckel results. After the description of the two methods, test examples are used to show advantages and drawbacks of the different approaches. In any case, the results are compared to the NBO-NRT approach which is used on the electronic density obtained from standard DFT hybrids calculations such as B3LYP/6-31+G(d). This chapter ends with an introduction to the HuLiS program in which the two methods are implemented.

Differentiation of heterocyclic regioisomers: a combined tandem mass spectrometry and computational study of N-acridin-4-ylbenzylamide and N-acridin-2-yl-benzylamide.

Electrospray ionization (ESI) tandem mass spectrometry (MS/MS) has been used to differentiate two positional isomers of acridine derivatives, N-acridin-4-ylbenzylamide and N-acridin-2-ylbenzylamide. The study revealed that the isomeric ion structures produced by these heterocycles could be distinguished upon collision-induced dissociations (CID). In particular, the loss of a water molecule was shown to be a regiospecific reaction of the protonated N-acridin-4-ylbenzylamide, in which the location of the benzylamide substituent with respect to the acridinic nitrogen greatly assists proton migration by allowing the creation of intramolecular hydrogen bonds. To a lesser extent, the two isomers could also be distinguished by the difference in the abundance of the benzoyl cation in the MS/MS spectra of the [M+H]+ ions, as this ion is produced with a much higher rate from N-acridin-4-ylbenzylamide. Calculations based on quantum-mechanical models have been performed to evaluate the stability of the ion structures and to support mechanisms proposed for these two dissociation reactions.

Palladium-catalysed oxidation of alcohols to carbonyl compounds with 1,2-dichloroethane as the primary oxidant: a theoretical study

Homogeneous palladium chloride catalyses the oxidation of alcohols to aldehydes or ketones in 1,2-dichloroethane (DCE). The active catalytic species is regenerated by the dechlorination of DCE to ethylene. This catalytic cycle is studied here using non-local density functional theory. The insertions of “naked” Pd, of HPdCl, and of PdCl2 into the C–Cl bond of DCE are examined in detail, and it is shown that the most likely inserting species is Pd, then HPdCl and PdCl2. Two distinct reaction pathways are proposed and investigated, namely insertion of HPdCl into the C–Cl bond, followed by HCl abstraction, and abstraction of HCl from HPdCl, followed by oxidative insertion of a “naked” Pd atom into the C–Cl bond. Both paths converge on the same species but the former is found to involve lower energies. Entropy effects, ligand effects and possible mechanisms for the formation of ethylene in this system are discussed. Based on these results, the complete oxidation cycle from methanol to formaldehyde is calculated as a model reaction for the dehydrogenation of alcohols in this system. It is shown that the original catalytic species does not necessarily need to be regenerated to complete a the catalytic cycle. Ligand effects and entropy effects are considered. The choice of methanol as a model of alcohol is discussed.