Search

General acid catalysis is a powerful and widely used strategy in enzymatic nucleophilic displacement reactions. For example, hydrolysis/phosphorolysis of the N-glycosidic bond in nucleosides and nucleotides commonly involves the protonation of the leaving nucleobase concomitant with nucleophilic attack. However, in the nucleoside hydrolase of the parasite Trypanosoma vivax, crystallographic and mutagenesis studies failed to identify a general acid. This enzyme binds the purine base of the substrate between the aromatic side-chains of Trp83 and Trp260. Here, we show via quantum chemical calculations that face-to-face stacking can raise the pKa of a heterocyclic aromatic compound by several units. Site-directed mutagenesis combined with substrate engineering demonstrates that Trp260 catalyzes the cleavage of the glycosidic bond by promoting the protonation of the purine base at N-7, hence functioning as an alternative to general acid catalysis.

International audience; The adsorption behavior of the butene isomers on NaY zeolite is studied experimentally and compared with quantum chemical predictions. The adsorption experiments were carried out with the pulse chromatographic method, the calculations were performed both on the HF as on the DFT-B3LYP level in combination with the 6-31G* and the 6-311+G** basis set. The results of the calculations are in line with the experimental ones for the cation-butene isomer interaction in the gas phase; the same adsorption trend in the zeolite cluster, however, could not be recovered. The calculated interaction energies for a Na+ zeolite cluster are close to the experimental ones with a magnitude of deviation of only 2 kcal/mol, showing the reliability of the model chosen. The trends obtained are discussed in the framework of the HSAB principle and purely electrostatic and inductive interactions.

International audience; The vibrational properties of p-chloro-, p-methoxy- and p-nitrobenzohydroxamic acids (BHA) and of the unsubstituted BHA were investigated and the spectra were assigned. The assignment was made on the basis of the experimental information available about the Raman peaks of mono- and disubstituted benzenes and the procedure was greatly facilitated by the data obtained from high-level DFT quantum-chemical calculations. In order to support an intended assignment of the SER spectra of BHA on copper, the molecular electrostatic maps and Fukui functions were derived. from ab initio calculations. Both quantum-chemical descriptors were shown to provide similar information about the possible BHA molecule-copper surface interaction sites. Copyright (C) 2003 John Wiley Sons, Ltd.

We present a DFT study on the reactivity of an alkoxide and a thiolate towards the neutral and all ionic forms of arsenate and phosphate. The isolated neutral, mono-, di- and trianionic arsenate/phosphate (electrophiles) and thiolate/methanolate (nucleophiles) species are used as model systems of reacting partners in the enzymatic reactions catalyzed by arsenate reductase and phosphatase. The onset of the displacement reaction at the electrophilic center by the attacking nucleophile is described by the DFT descriptor local softness, applied in a HSAB context. The instability of multiply charged anions in gas phase necessitates the use of a solvent model with an appropriate dielectric constant mimicking the enzymatic environment. Gas phase and solvent reactivity studies of isolated compounds indicate that the nucleophilic attack of a thiolate during the first catalysis step of ArsC and LMWPTPase preferably occurs via the dianionic arsenate and phosphate. This computational approach confirms and supplements earlier experimental data.

It is an understatement that Density Functional theory (DFT) played an important role in the development of quantum chemistry in the past decade : it would be more correct to state that DFT revolutionarized quantum chemistry, offering a computational technique partly including electron correlation at a much better quality/cost ratio than the conventional post Hartree Fock (Moller Plesset, CI, Coupled Cluster …) wave function methods [1][2].

In the analysis of molecular similarity and chirality of enantiomers performed in this paper, we introduce a new local similarity index based on the Hirshfeld partitioning. In the framework of conceptual density functional theory and considering the enantiomers of the halomethane CHFClBr and of the amino acids alanine and leucine, this index is used to investigate the dissimilarity of chiral molecules. Furthermore, we illustrate Mezey's holographic electron density theorem.

Atomic dipole moments, derived within the Hirshfeld partitioning of the molecular electron density, have been studied for compounds of the type H-X and Cl-X, for a series of functional groups X frequently encountered in organic molecules. In the case of the H-X compounds, the component of the atomic dipole moment on H along the axis connecting H with the central atom in X is found to be linearly correlated with the electronegativity of X, the hardness of X playing no significant role. In the case of the Cl-X compounds, the situation is less clear. However, evidence seems to point to the conclusion that for these compounds, also the group hardness plays an important role.

International audience; A perturbational approach is used to study the adsorption behavior of small molecules in faujasite type zeolites. From the evaluated interaction energies. iso-interaction energy plots for N-2, O-2, CO2 and C2H4 in LSX faujasite exchanged with Na+ are calculated. From these plots the preferential adsorption sites in the zeolite cavity were located. The interaction energies on the preferential sites were found to predict rough trends for the separation behavior of the considered zeolites. A study of the different cation sites. based on an ab initio calculation of the atomic charges at the HF/3-21G level showed a good agreement with existing experimental results and previous theoretical calculations. (C) 2002 Elsevier Science B.V. All rights reserved.

International audience; Experimental results for the adsorption frequencies of SCN- on a silver electrode obtained with the surface-enhanced Raman spectrometry (SERS) method are presented and discussed. These results were confronted with a quantum chemical DFT-based study. Different clusters were used from the simple monoatomic case to a much more realistic representation of the silver electrode by means of a Ag-23 cluster simulating the (100) surface. The calculations were performed at the B3PW91/LanL2DZ and the BP86/TZP level. The interaction energies indicate the importance of the cluster size and calculation level. The cluster size was increased until the results were converged. Calculated vibrational frequencies for the different possible adsorption geometries on a (100) surface are compared with experiment. Together with the interaction energy results, they indicate that the preferred interaction via the sulfur atom on a hollow site of the silver electrode is in agreement with the hard and soft acids and bases principle.

We present the results of a theoretical investigation focusing on the solvent structure surrounding the -1, 0 and +1 charged species of F, Cl, Br and I halogen atoms and F2, Cl2, Br2 and I2 di-halogen molecules in a methanol solvent and its influence on the electronic structure of the solute molecules. Our results show a large stabilizing effect arising from the solute-solvent interactions. Well-formed first solvation shells are observed for all species, the structure of which is strongly influenced by the charge of the solute species. Detailed analysis reveals that coordination number, CN, solvent orientation, θ, and solute-solvent distance, d, are important structural characteristics which are coupled to changes in the electronic structure of the solute. We propose that the fundamental chemistry of any solute species is generally regulated by these solvent degrees of freedom.

Within the context of reactivity descriptors known in conceptual DFT, the linear response function (χ(r,r')) remained nearly unexploited. Although well known, in its time dependent form, in the solid state physics and time-dependent DFT communities the study of the "chemistry" present in the kernel was, until recently, relatively unexplored. The evaluation of the linear response function as such and its study in the time independent form are highlighted in the present review. On the fundamental side, the focus is on the approaches of increasing complexity to compute and represent χ(r,r'), its visualisation going from plots of the unintegrated χ(r,r') to an atom condensed matrix. The study on atoms reveals its physical significance, retrieving atomic shell structure, while the results on molecules illustrate that a variety of chemical concepts are retrieved: inductive and mesomeric effects, electron delocalisation, aromaticity and anti-aromaticity, σ and π aromaticity,…. The applications show that the chemistry of aliphatic (saturated and unsaturated) chains, saturated and aromatic/anti-aromatic rings, organic, inorganic or metallic in nature, can be retrieved via the linear response function, including the variation of the electronic structure of the reagents along a reaction path. The connection of the linear response function with the concept of nearsightedness and the alchemical derivatives is also highlighted.

The [2 + 1] cycloadditions of carbon monoxide and carbon monothioxide CX (X = O, S) to acetylenes (R1C triple bond CR2 with R1 = H, OH and R2 = CH3, OH, NH2, C6H5) have been studied at the B3LYP/6-311G(d,p) level. It has been shown that the reaction proceeds in two steps forming first an intermediate having the properties of both a carbene and a zwitterion followed by a ring closure leading to cyclopropenones or cyclopropenethiones. The solvent effect does not play an important role in the course of the cycloaddition. The estimation of the first vertical excitation energies by CIS and TD-B3LYP methods shows that the reactions likely take place in the ground state rather than in an excited state. All the studied cyclopropenones and cyclopropenethiones are aromatic as shown by their NICS values and confirmed by calculated and experimental NMR chemical shifts. Different reactivity criteria including HOMO coefficient, local softness, hardness, polarizability, and NICS are used to predict the site selectivity in all studied cases, and the NICS criterion seems to yield the best results among them.

The electron paramagnetic resonance (EPR) spectra of irradiated mono and oligosaccharides are very complex because of their multicomponent character. A multivariate statistical method called MLCFA (maximum likelihood common factor analysis) predicts at least four components contributing to the total EPR spectrum of irradiated D-fructose powder at room temperature. To elucidate the nature of the induced paramagnetic defects, we have applied magnetic resonance techniques to irradiated D-fructose single crystals. After X-irradiation the single crystals have been investigated with electron nuclear double resonance (ENDOR) and ENDOR induced EPR (EI-EPR) at 60 K. Two dominant EPR components could be isolated and interpreted in terms of three non-equivalent proton splittings. By comparing the experimental proton hyperfine tensors with the corresponding quantities calculated using density functional theory, a plausible structure for the two detected radicals will be presented.

International audience; Six different exchange-correlation functionals were assessed in a quantum chemical study of the geometry and energetics of silanol, its conjugated base and both conformers of disiloxane, using Dunning's augmented correlation consistent basis set. It was found that the B3LYP and the B3PW91 hybrid functionals perform the best, their performance was comparable with MP2/VQZ calculations. A deprotonation energy of -365.4 kcal/mol for silanol was obtained at the B3PWB1/AVQZ level. For disiloxane, a very small difference between both disiloxane conformers, 0.037 kcal/mol (extra stabilization for the doubly staggered conformation) and 149.3 degrees for the very sensible Si-O-Si angle was found, or 154.7 degrees temperature corrected (300 K). degrees 2001 Elsevier Science B.V. All rights reserved.

Symposium on Material Simulation for the 21st Century, CATHOLIC UNIV, ARENBERG CASTLE, LEUVEN, BELGIUM, AUG 03, 1999; International audience; A perturbational approach (M-method) for the calculation of the interaction energies of N(2), O(2), Ar and CO in zeolite cavities is presented. The calculation method is compared with the `molecule in point charge environment' calculation and a full ab initio calculation tested along an axis connecting the center of the cavity with a site II cation. The Henry constants, heats of adsorption and separation constants for N(2), O(2) and Ar in a NaY zeolite are obtained using the `molecule in point charge environment' method and the present approximation. Different grid sizes were considered depending on the distance between adsorbing system and cation. A promising result, in particular for the separation constants. was found using the Van der Waals and ionic radii for the grid delimitation and the M-method calculated on the B3LYP/6-31G* level. CO was added as a final test system with lower symmetry. (C) 2001 Elsevier Science B.V. All rights reserved.

5th World Congress of Theoretically Oriented Chemists (WATOC), IMPERIAL COLL, LONDON, ENGLAND, AUG 01-06, 1999; International audience; A study is presented concerning the performance and basis set dependence of density functional methods in the calculation of dipole and quadrupole moments. A set of some small molecules was thereby used, together with seven commonly used exchange correlation functionals and Dunnings correlation consistent aug-cc-pVDZ, aug-cc-pVTZ, aug-cc-pVQZ and aug-cc-pV5Z basis sets. The results were compared with experiment and previously published values obtained with traditional ab initio molecular orbital methods. The best performance in the calculation of dipole and quadrupole moments is due to the hybrid functionals B3LYP and B3PW91. Moreover, the results seem to be essentially converged at the aug-cc-pVTZ level. Comparison of the LDA/aug-cc-pV5Z results with the numerical LDA results of Dickson and Becke, reveals that both sets of values are identical for most cases. (C) 2000 Elsevier Science B.V. All rights reserved.

The first all-electron ab initio study of Young's modulus and Poisson ratio for a number of closed single-walled nanotubes is presented. At the Hartree–Fock 6-31G ∗ level, the results obtained compare well with experimental as well as previous theoretical studies, predicting a Young's modulus higher than 1 TPa. The calculated Young's modulus for a graphene layer is found to be smaller than for its (5,5)-nanotube counterpart.

International audience; The influence of Al/Si substitutions on the stability and acidic characteristics of a zeolite system is investigated. The 12-membered ring present in a number of zeolites was chosen as a realistic model system for this purpose. The stability of this system upon different double Al/Si substitutions was investigated in order to find evidence for both Lowenstein's and Dempsey's rules. It was found that both rules hold for the chosen model system. The acidity of the bridging hydroxyls was studied using the calculated deprotonation energy and the Mulliken and ChelpG electronic populations on the H-atom and on the O atom in the conjugated base. (C) 2000 Elsevier Science B.V. All rights reserved.