Biomedical subjects

Gilles H Peslherbe

Publications and source records attributed to Gilles H Peslherbe.

10 recordsLinked to original sources

PubMed2006

Nonadiabatic ladder climbing during molecular collisions.

Combining classical molecular dynamics simulations with high level, multiconfigurational ab initio calculations, we demonstrate that even relatively mild collisions between ground state oxygen molecules can readily lead to the formation of highly reactive singlet oxygen molecules via a novel "ladder climbing" mechanism. We employ our findings to shed some light on two recent experiments that have remained poorly understood until now. The first one concerns the highly efficient cluster-catalyzed etching of silicon surfaces, whereas the second one involves a yet to be explained "dark channel" observed for the ozone photolysis in the stratosphere.

Journal Article↗

PubMed2006

Toward a reversible isolation of a C20 fullerene inside a tetraureacalix[4]arene dimer. A theoretical study.

The potential stabilization of normally unstable C20, the smallest fullerene, via its encapsulation inside a tetraureacalix[4]arene dimer has been analyzed using molecular mechanics calculations with different force fields, the self-consistent-charge density-functional tight-binding with dispersion correction (SCC-DFTB-D) model, and standard density-functional-theory (DFT) calculations. The interaction energies obtained for the C20 complex have been compared with analogous values calculated for numerous complexes of the tetraureacalix[4]arene dimer with other guests. Results of the calculations with all force fields and SCC-DFTB-D predict that the binding of C20 occurs with the highest selectivity. On the other hand, standard DFT calculations fail to correctly describe the stabilization of the complexes under study as standard DFT generally does not treat dispersion interactions properly. Predicted relative stabilities of the complexes are discussed in conjunction with available experimental data. Molecular dynamics simulations reveal the instability of the guest-free capsular dimer, which decomposes on a 1-ns time scale, while dimeric complexes with guests remained intact during the 5-ns simulation time, indicating the guest-driven formation of the molecular capsule.

Journal Article↗

PubMed2006

On the statistical nature of collision and surface-induced dissociation: a theoretical investigation of aluminum clusters.

The unimolecular dissociation dynamics of aluminum clusters following collision with either a rare gas atom or a surface is investigated by classical trajectory simulations with model potentials. Two conformers of Al(6) with very distinct shapes, i.e., the spherical O(h) and planar C(2)(h) clusters, are considered in this work. The initial vibrational energy and angular momentum distributions resulting from collision, as well as the energy and angular momentum resolved lifetime distributions, of excited clusters were determined for both collision-induced dissociation (CID) and surface-induced dissociation (SID) processes. The partitioning of excitation energy acquired upon collision was found to depend on the excitation mechanism (CID or SID), as well as on the cluster molecular shape, especially in the case of CID. For both types of processes, the energy and angular momentum resolved excited cluster lifetime distributions were found to decay exponentially, in agreement with statistical theories of chemical reactions, suggesting intrinsic Rice-Ramsperger-Kassel-Marcus (RRKM) behavior. Moreover, the simulated microcanonical rate constants determined from the cluster lifetime distributions are in good agreement with the predictions of the orbiting transition state model of phase space theory (OTS/PST), which further supports the statistical character of cluster CID and SID. Thus, in the CID and SID of highly fluxional systems such as aluminum clusters, the rate of intramolecular vibrational energy redistribution (IVR) is much faster than the dissociation rate, which validates one of the key assumptions, i.e., post-collision statistical behavior, underlying the models that are routinely used to determine cluster binding energies from experimental CID/SID cross sections.

Journal Article↗

PubMed2006

Nonadiabatic trajectory studies of NaI(H2O)n photodissociation dynamics.

We have investigated the photodissociation dynamics of NaI(H(2)O)(n) [n = 1-4] clusters using the molecular dynamics with quantum transitions method and a quantum mechanics/molecular mechanics description of NaI(H(2)O)(n), which involves a semiempirical valence-bond approach to describe the NaI electronic structure and classical solvent-solvent and solute-solvent interaction potentials. Our simulation results show that the NaI(H(2)O)(n) excited-state population decay upon reaching the NaI curve-crossing region increases with cluster size due to the stabilization of the ionic branch of the NaI excited state by the surrounding water molecules, and the resulting increase in nonadiabatic transition probability. After reaching the curve-crossing region for the first time, however, the excited-state population decay resembles that of bare NaI because of rapid evaporation of 99% and 95% of the water molecules for NaI(H(2)O) and NaI(H(2)O)(n) [n = 2-4], respectively. This extensive evaporation is due to the reversed NaI polarity in the Franck-Condon region of the NaI first excited state, which causes strong repulsive NaI-H(2)O forces and induces rapid nonstatistical water evaporation, where product water molecules are formed more rotationally than translationally hot. A few water molecules (5% or less) remain transiently or permanently bound to NaI, forming long-lived clusters, when NaI remains predominantly ionic, i.e., remains in the excited state, after reaching the curve-crossing region. To connect simulation results with experiment, we have simulated femtosecond probe signals resulting from two-photon and one-photon excitation to the X and I NaI(+) probe states. In agreement with experimental findings, the probe signals resulting from the two-photon probe scheme, where excitation occurs from the covalent branch of the excited state, decay exponentially over the NaI first excited-state vibrational period, with very little evidence of long-time dynamics. The one-photon probe scheme (not used for experimental cluster studies) is shown to be less sensitive to solvation, in that excitation energies will remain similar over a range of cluster sizes, as the ionic branch of the excited state and the NaI(+) probe states are stabilized to the same extent by the presence of water molecules. The resulting probe signals are also more revealing of the NaI(H(2)O)(n) photodissociation dynamics than the two-photon probe signals, as they may allow monitoring of solvation effects on the NaI nonadiabatic dynamics and of successive evaporation of water molecules. Time-resolved photoelectron spectra provide limited additional information regarding the NaI(H(2)O)(n) photodissociation dynamics. A key consequence of the rapid water evaporation demonstrated here is that experimentally observed signals may arise from the photodissociation of much larger NaI(H(2)O)(n) parent clusters.

Computer Simulation↗

PubMed2006

Accurate ab initio potential for the Na+...I* complex.

High-level ab initio calculations employing the multireference configuration interaction and coupled clusters methods with a correlation-consistent sequence of basis sets have been used to obtain accurate potential energy curves for the complex of the sodium cation with the iodine atom. Potential curves for the first two electronic Lambda-S states have very different characters: the potential for the 2pi state has a well depth of approximately 10 kcal/mol, while the 2sigma state is essentially unbound. This difference is rationalized in terms of the anisotropic interaction of the quadrupole moment of the iodine atom with the sodium cation, which is stabilizing in the case of the 2pi state and destabilizing in the case of the 2sigma state. The effects of spin-orbit coupling have been accounted for with both ab initio and semiempirical approaches, which have been found to give practically the same results. Inclusion of spin-orbit interactions does not affect the X(omega = 32) ground state, which retains its 2pi character, but it results in two omega = 12 spin-orbit states, with mixed 2sigma and 2pi characters and binding energies roughly half of that of the ground spin-orbit state. Complete basis set (CBS) extrapolations of potential curves, binding energies, and equilibrium geometries were also performed, and used to calculate a number of rovibronic parameters for the Na+...I* complex and to parameterize model potentials. The final CBS-extrapolated and zero-point vibrational energy-corrected binding energy is 10.2 kcal/mol. Applications of the present results for simulations of NaI photodissociation femtosecond spectroscopy are discussed.

Journal Article↗

PubMed2005

Substituent effects and the role of negative hyperconjugation in siloxycarbene rearrangements.

Substituent effects and the role of negative hyperconjugation in 1,2-silyl migration and decarbonylation of methoxy(substituted-siloxy)carbenes have been investigated using quantum chemical calculations and natural bond orbital analysis. It has been found that sigma-electron-withdrawing substituents generally lower the barriers for 1,2-silyl migration and decarbonylation, consistent with symmetry-forbidden concerted rearrangements involving intramolecular front-side nucleophilic attack by the carbene lone pair at silicon and by the methoxy oxygen at silicon, respectively. However, while good linear Hammett correlations are obtained for 1,2-silyl migration, those obtained for decarbonylation are poor. In addition, there appears to be a relationship between the extent of pertinent hyperconjugative interactions in the siloxycarbene conformers and the ease of intramolecular reactivity. As a matter of fact, the finding that 1,2-silyl migration is more favorable than decarbonylation seems to be primarily related to stronger negative hyperconjugation between the carbene lone pair and the O-Si antibonding orbital, compared to that between the methoxy oxygen n(sigma) lone pair and the O-Si antibonding orbital. Moreover, the activation enthalpies for 1,2-silyl migration decrease linearly with stronger negative hyperconjugation, although no such correlation could be established for decarbonylation.

Journal Article↗

PubMed2004

The electronic structure of nitrilimines revisited.

A combination of density-functional theory and natural resonance theory has been used to show that a complete description of the electronic structure of nitrilimines, R(1)CNNR(2), requires four resonance structures (propargylic, allenic, 1,3-dipolar and carbenic); appropriate substituents were shown to enhance the carbene character of nitrilimines to the point where they may be considered stable carbenes.

Journal Article↗

PubMed2003

Further insight into the relaxation dynamics of photoexcited I-(H2O)n clusters.

First-principles molecular dynamics simulations of the excited-state dynamics of I-(H2O)3 have been performed to gain some insight into the general features of the relaxation process of photoexcited I-(H2O)n clusters. The relaxation of excited I-(H2O)3 is characterized by rapid motion of water molecules and slow recoil motion of the iodine atom. Both solvent reorganization and iodine atom motion appear to be important for interpreting the existing femtosecond photoelectron spectroscopy experimental results.

Journal Article↗

PubMed2002

Theoretical evidence that Cu(I) complexation promotes degradation of S-nitrosothiols.

The degradation of S-nitrosothiols (RSNOs) to release NO is believed to be catalyzed by CuI ions, but the mechanism remains unclear. Kinetic experiments have shown that decomposition rates vary significantly with the chemical nature of the RSNO considered. On the basis of first-principles calculations, the catalytic role of CuI ion is investigated for the decomposition of S-nitrosocysteine and its N-acetylated and ethyl ester derivatives, and for S-nitrosohomocysteine. This preliminary study focuses on the CuI-RSNO intermediates involved in the decomposition pathway. The model chemistry has been validated by comparing calculated CuI-ligand binding energies and S-N bond homolysis energies with available experimental data. Calculations show that the formation of CuI-RSNO intermediates results in weakening of the S-N bond and strengthening of the N-O bond, which would promote S-N bond breaking and NO release from S-nitrosothiols.

Copper↗

PubMedDate not supplied

Ultraviolet absorption spectra of substituted phenols: a computational study.

Vertical excitation energies for electronic transitions from the ground state to the first two excited states of phenol, mono- and disubstituted methoxyphenols and methyl-substituted phenols have been characterized with the Time-Dependent Density Functional Theory (TD-DFT), the Complete Active Space Self-Consistent Field method (CASSCF) and the Coupled Cluster with Single and Double Excitations Equation-of-Motion approach (CCSD-EOM) to simulate and interpret experimental ultraviolet absorption spectra. While CASSCF excitation energies for the first two transitions either are grossly overestimated or exhibit a weak correlation with experimental data, both TD-DFT and CCSD-EOM perform very well, reproducing the spectral shifts of both the primary band and secondary band observed upon substitution. The conformational dependence of the calculated excitation energies is generally smaller than the shifts caused by substitution.

Computer Simulation↗