Biomedical subjects

Paul Fleurat-Lessard

Publications and source records attributed to Paul Fleurat-Lessard.

7 recordsLinked to original sources

PubMed2007

Assessment of the exchange-correlation functionals for the physical description of spin transition phenomena by density functional theory methods: all the same?

This study aims to assess present day density functionals in the description of spin crossover iron(II) complexes. Two recently synthesized spin crossover complexes were considered. Theoretical calculations were made using 53 of the most popular exchange-correlation density functionals with triple zeta plus polarization quality basis sets. The present work shows that even though different density functionals can lead to different energy gaps between spin states, most of them are very similar for these two compounds when a comparison between energy gaps is sought. The present work shows that even though different exchange correlations can lead to different energy gaps between spin states, the difference between these gaps calculated at different geometries and that calculated at a given reference geometry is surprisingly independent of the choice of functional. The reasons for the similarities and the differences among exchange and correlation functional combinations are discussed.

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PubMed2006

Simulating temperature programmed desorption of water on hydrated gamma-alumina from first-principles calculations.

The knowledge of the properties of gamma-alumina is of great importance in order to control its surface for numerous applications. We investigate the kinetic behavior of the hydrated alumina (110) surface toward water desorption: the minimum energy path is presented for successive desorption steps starting from the completely hydrated surface toward the dehydrated one. It appears that water desorption is a non activated process. A kinetic model is proposed based on an extension of the Eyring theory. This model is a useful tool to understand the evolution of water coverage during the pretreatment of alumina. It is then used to model temperature programmed desorption experiments for various heating rates. The shape of the desorption curve is qualitatively reproduced, and the differences between theory and experiments are discussed.

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PubMed2005

Tracing the minimum-energy path on the free-energy surface.

The free-energy profile of a reaction can be estimated in a molecular-dynamics approach by imposing a mechanical constraint along a reaction coordinate (RC). Many recent studies have shown that the temperature can greatly influence the path followed by the reactants. Here, we propose a practical way to construct the minimum-energy path directly on the free-energy surface at a given temperature. First, we follow the blue-moon ensemble method to derive the expression of the free-energy gradient for a given RC. These derivatives are then used to find the actual minimum-energy reaction path at finite temperature, in a way similar to the intrinsic reaction path of Fukui on the potential-energy surface. [K. Fukui, J. Phys. Chem. 74, 4161 (1970)]. Once the path is known, one can calculate the free-energy profile using thermodynamic integration. We also show that the mass-metric correction cancels for many types of constraints, making the procedure easy to use. Finally, the minimum-free-energy path at 300 K for the addition of CCl2 to ethylene is compared with a path based on a simple one-dimensional reaction coordinate. A comparison is also given with the reaction path at 0 K.

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PubMed2005

The effect of zero-point energy differences on the isotope dependence of the formation of ozone: a classical trajectory study.

The effect of zero-point energy differences (DeltaZPE) between the possible fragmentation channels of highly excited O(3) complexes on the isotope dependence of the formation of ozone is investigated by means of classical trajectory calculations and a strong-collision model. DeltaZPE is incorporated in the calculations in a phenomenological way by adjusting the potential energy surface in the product channels so that the correct exothermicities and endothermicities are matched. The model contains two parameters, the frequency of stabilizing collisions omega and an energy dependent parameter Delta(damp), which favors the lower energies in the Maxwell-Boltzmann distribution. The stabilization frequency is used to adjust the pressure dependence of the absolute formation rate while Delta(damp) is utilized to control its isotope dependence. The calculations for several isotope combinations of oxygen atoms show a clear dependence of relative formation rates on DeltaZPE. The results are similar to those of Gao and Marcus [J. Chem. Phys. 116, 137 (2002)] obtained within a statistical model. In particular, like in the statistical approach an ad hoc parameter eta approximately 1.14, which effectively reduces the formation rates of the symmetric ABA ozone molecules, has to be introduced in order to obtain good agreement with the measured relative rates of Janssen et al. [Phys. Chem. Chem. Phys. 3, 4718 (2001)]. The temperature dependence of the recombination rate is also addressed.

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PubMed2005

Optimizing the structures of minimum and transition state on the free energy surface.

Presented here is the application of a scheme for optimizing the structures of minima and transition states on the free energy surface (FES) for a path along a fixed reaction coordinate with the aid of ab initio molecular dynamics (AIMD) simulation. In the direction of the reaction coordinate, the values corresponding to the stationary points were optimized using the quasi-Newton method, in which the gradient of the free energy along the reaction coordinate was obtained by a constraint AIMD method, and the Bofill Hessian update scheme was used. The equilibrium values for the other directions were taken as the corresponding averages in the dynamic simulation. This scheme was applied to several elementary bimolecular addition reactions: (A) BH(3) + H(2)O --> H(2)O.BH(3); (B) BF(3) + NH(3) --> FB(3).NH(3); (C) SO(3) + NH(3) --> O(3)S.NH(3); (D) C(2)H(4) + CCl(2) --> H(4)C(2).CCl(2); (E) Ni(NH(2))(2) + PH(3) --> (NH(2))(2)Ni.PH(3); (F) W(CO)(5) + CO --> W(CO)(6). For reactions A, B, C, and F, no transition state (TS) exists on the potential energy surface (PES). However there is a TS on the FES. This stems from the curvature difference of the PES and -TDeltaS as a function of the reaction coordinate. For all reactions, it is found that the TS shifts toward the complexation product with increasing temperature because of the curvature increase of -TDeltaS. The equilibrium bond distances for the inactive coordinates perpendicular to the reaction coordinate always increase with temperature, which is due to the thermal excitation and anharmonicity of the PES.

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PubMed2004

The transition-state region of the O((3)P)+O(2)((3)Sigma(g) (-)) potential energy surface.

New electronic structure calculations for the transition-state region of the lowest ozone potential energy surface are reported. A two-dimensional potential energy surface in the asymptotic channel is calculated with the O(2) bond distance being fixed. The calculations are performed at the multireference average quadratic coupled cluster level of theory using full-valence complete active space self-consistent field wave functions and the augmented correlation consistent polarized V6Z atomic basis set. The general shape of the potential energy surface as predicted in earlier studies, that is, a narrow transition state below the O+O(2) asymptote, is confirmed by the present calculations. The transition state is 181 cm(-1) below the asymptote and 72 cm(-1) above the van der Waals-like minimum. The changes in the O+O(2)-->O(3) (*) capture cross section and rate constant when the new potential energy surface is employed are investigated by means of classical trajectory calculations.

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PubMed2002

Does back-bonding involve bonding orbitals in boryl complexes? A theoretical DFT study.

Theoretical calculations at the DFT (B3LYP) level have been undertaken on tris- and bis(boryl) complexes. Two model d(6) complexes [Rh(PH(3))(3)(BX(2))(3) and Rh(PH(3))(4)(BX(2))(2)(+), X = OH and H] have been studied. In the model tris(boryl) complex (X = OH) we find a fac structure as a minimum, in accordance with the experimental data. The mer geometries are found to be higher in energy. Analysis of the energetic ordering in mer isomers shows that back-bonding in these complexes involves a bonding Rh-B orbital (and not a d-block orbital as usual). This surprising behavior is rationalized through a qualitative MO analysis and quantitative NBO analysis. Results on the bis(boryl) complex confirm the preceding analysis. Full optimization of unsubstituted (X = H) complexes leads to structures in which the BH(2) moieties are coupled. In the optimal geometry of the bis(boryl) complex, the B(2)H(4) ligand resembles the transition state of the C(2v)-->D(2d) interconversion of the isolated B(2)H(4) species. In the tris(boryl) complex, we find a B(3)H(6) ligand in which the B(3) atoms define an isosceles triangle with one hydrogen bridging the shorter B-B bond.

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