Biomedical subjects

Laurent Joubert

Publications and source records attributed to Laurent Joubert.

5 recordsLinked to original sources

PubMed2006

A combined experimental and theoretical study on the conformational behavior of a calix[6]arene.

An experimental and theoretical study on the conformational behavior of the 1,3,5-OMe-2,4,6-OCH(2)CONHOH-p-tert-butylcalix[6]arene has been carried out. In particular, semiempirical (AM1) and density functional theory (DFT) calculations have been performed in order to identify the possible conformers. The obtained results show that the cone structure is the most stable conformer at any level of theory, even if significant differences have been obtained for the other species. The inclusion of solvent effect, through a continuum model, also points out the relevant role played by the solvent in the stabilization of the cone structure in solution. These latter results have been confirmed by NMR experiments, which clearly show the presence of only the cone conformer in a polar solvent, such as DMSO. Finally, (1)H and (13)C NMR spectra on model systems, i.e., two successive phenol rings (Ar(1)-CH(2)-Ar(2)), have been computed at the DFT level and compared with the experimental spectra of the complete molecule. The results show an overall good agreement with the experimental data, thus leading to an unambiguous assignment of the experimental spectra.

Calixarenes↗

PubMed2006

Bridging the gap between the topological and orbital description of hydrogen bonding: the case of the formic acid dimer and its sulfur derivatives.

Several molecular descriptors, based on topological approaches as well as on a more traditional orbital-based decomposition, have been used to asses relations with hydrogen bond strengths in a series of formic acid dimers and its sulfur derivatives. Particular attention has been devoted to the analysis of the core-valence bifurcation topological index and to the bond order index. Their values are seen to be linearly related to bond energies estimated through a bond-energy-bond-order relationship; also, the mean value of the topological index appears to be related to the complexation energy computed by methods based on density functional theory. The dependence of the index upon the donor-acceptor couple in relation to its applicability is discussed.

Computer Simulation↗

PubMed2006

A comprehensive theoretical view of the bonding in actinide molecular complexes.

While usual atomic population methods give a consistent view of trivalent lanthanide or a uranium-ligand bond, the description of the bonding of americium(III), which is a key element for nuclear fuel processes, is a challenge. Neither experimental data nor theoretical calculations have been able so far to evidence covalency effects in the americium-ligand bond. We show herein that the use of more sophisticated methods based on a topological approach (AIM and ELF) gives a consistent view of such an interaction for the first time, showing a weak covalent back-bonding interaction with the CO ligand.

Journal Article↗

PubMed2005

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.

Journal Article↗

PubMed2002

The elusive atomic rationale for DNA base pair stability.

A systematic analysis of the electrostatic interaction between 27 natural DNA base pairs was carried out, based on ab initio correlated wave functions and the topology of the electron density. Using high rank multipole moments we show that the atomic partitioning of the interaction energy contains many substantial contributions between distant atoms. Profiles of cumulative energy versus internuclear distance show large fluctuations and provide an electrostatic fingerprint of the partitioning of interaction energy in a complex. A quantified comparison between each pair of energy profiles, one for each base pair, makes clear that there is no correlation between the total base pair interaction energy and the shape of the profile. In other words, base pairs with similar interaction energy are not stable for the same reasons in terms of atomic partitioning. In summary, simple rules to rationalize the pattern of energetic stability of naturally occurring base pairs in terms of subsets of atoms are elusive. Our work cautions against inappropriate use of Jorgensen's secondary interaction hypothesis.

Base Pairing↗