Time-dependent density functional theory molecular dynamics simulation of doubly charged uracil in gas phase

We use time-dependent density functional theory and Born-Oppenheimer molecular dynamics methods to investigate the fragmentation of doubly ionized uracil in gas phase. Different initial electronic excited states of the dication are obtained by removing electrons from different inner-shell orbitals of the neutral species. We show that shape-equivalent orbitals lead to very different fragmentation patterns revealing the importance of the intramolecular chemical environment. The results are in good agreement with ionion coincidence measurements of uracil collision with 100 keV protons.     

Environmental effects on vibrational properties of carotenoids: experiments and calculations on peridinin

Carotenoids are employed in light-harvesting complexes of dinoflagellates with the two-fold aim to extend the spectral range of the antenna and to protect it from radiation damage. We have studied the effect of the environment on the vibrational properties of the carotenoid peridinin in different solvents by means of vibrational spectroscopies and QM/MM molecular dynamics simulations. Three prototypical solvents were considered: cyclohexane (an apolar/aprotic solvent), deuterated acetonitrile (a polar/aprotic solvent) and methanol (a polar/protic solvent). Thanks to effective normal mode analysis, we were able to assign the experimental Raman and IR bands and to clarify the effect of the solvent on band shifts. In the 1500-1650 cm(-1) region, seven vibrational modes of the polyene chain were identified and assigned to specific molecular vibrations. In the 1700-1800 cm(-1) region a strong progressive down-shift of the lactonic carbonyl frequency is observed passing from cyclohexane to methanol solutions. This has been rationalized here in terms of solvent polarity and solute-solvent hydrogen bond interactions. On the basis of our data we propose a classification of non-equivalent peridinins in the Peridinin-Chlorophyll-Proteins, light-harvesting complexes of dinoflagellates.     

Toward a DFT-based molecular dynamics description of Co(II) binding in sulfur-rich peptides

In this paper, we investigated the reliability of a Car-Parrinello molecular dynamics (CPMD) approach to characterize the binding of Co(II) metal cation to peptide molecules containing cysteine. To this end, we compared pseudo-potentials and DFT plane wave expansion, which are used as key ingredients in the CPMD method, with standard all-electron Gaussian basis set DFT calculations. The simulations presented here are the first attempts to characterize interactions and dynamics of Co(II) metal with the building blocks of phytochelatin peptide molecules. Benchmark calculations are performed on [Co(Cys-H)]+ and [Co(Glutathione-H)]+ complexes, since they are the main fragments of the Co(II)-Cys and Co(II)-glutathione systems found in gas phase electrospray ionisation mass spectrometry (ESI-MS) experiments done in our laboratory. We also present benchmark calculations on the [Co(H2O)6)]2+ cluster with direct comparisons to highly correlated ab initio calculations and experiments. In particular, we investigated the dissociation path of one water molecule from the first hydration shell of Co(II) with CPMD. Overall, our molecular dynamics simulations shed some light on the nature of the Co(II) interaction and reactivity in Co(II)-phytochelatin building block systems related to the biological and environmental activity of the metal, either in the gas or liquid phase.     

Proton transfers induced by lead(II) in a uracil nucleobase: a study based on quantum chemistry calculations

Within the context of metal biotoxicity, electrospray ionization mass spectrometry experiments (ESIMS) have recently been performed by us on the pyrimidine nucleobases (B) uracil and thymine complexed with lead(II) [Int. J. Mass. Spectrom. 2005, 243, 279]. Among the ions detected, [Pb(B)-H]+ complexes, where the base has been deprotonated, have been identified as producing intense signals. In the same study, quantum calculations based on density functional theory (DFT) have assessed the complexation sites and energies of [Pb(B)-H]+ ions. The present DFT investigations aim at giving an understanding on the energetics and mechanisms associated with uracil's loss of a proton. We specifically assess and quantify the role of lead binding in this process. For that purpose, intra- and intermolecular proton transfers have been considered. We have found that uracil (U) 1,3-tautomerization can be exergonic when uracil is complexed with Pb2+, in opposition to the situation without lead. The corresponding intramolecular processes were nonetheless found to occur at geological time scales. In contrast, the addition of a second body to [Pb(U)]2+ complexes, namely OH- or H2O (as found in the initial water droplet of ESIMS experiments), gives exergonic and fast uracil 1,3-proton transfers. Finally, we have shown that intermolecular proton transfers in uracil-H2O, uracil-OH-, or uracil-uracil complexes are able to explain the experimentally detected [Pb(U)-H]+ ions.     

Time‐Dependent Density Functional Theory Molecular Dynamics Simulations of Liquid Water Radiolysis

The early stages of the Coulomb explosion of a doubly ionized water molecule immersed in liquid water are investigated with time‐dependent density functional theory molecular dynamics (TD–DFT MD) simulations. Our aim is to verify that the double ionization of one target water molecule leads to the formation of atomic oxygen as a direct consequence of the Coulomb explosion of the molecule. To that end, we used TD–DFT MD simulations in which effective molecular orbitals are propagated in time. These molecular orbitals are constructed as a unitary transformation of maximally localized Wannier orbitals, and the ionization process was obtained by removing two electrons from the molecular orbitals with symmetry 1B₁, 3A₁, 1B₂ and 2A₁ in turn. We show that the doubly charged H₂O²⁺ molecule explodes into its three atomic fragments in less than 4 fs, which leads to the formation of one isolated oxygen atom whatever the ionized molecular orbital. This process is followed by the ultrafast transfer of an electron to the ionized molecule in the first femtosecond. A faster dissociation pattern can be observed when the electrons are removed from the molecular orbitals of the innermost shell. A Bader analysis of the charges carried by the molecules during the dissociation trajectories is also reported.     

Conservative methods for the Toda lattice equations

We are concerned with the numerical integration of the Todalattice equations by using different conservative methods. Numericalexperiments suggest that the global error for isospectral schemesdecreases exponentially with time but it is almost constantfor either symplectic or more general integrators. We providea theoretical explanation for these experimental findings.