Biomedical subjects

Francesco Tarantelli

Publications and source records attributed to Francesco Tarantelli.

9 recordsLinked to original sources

PubMed2006

Site-selected Auger electron spectroscopy of N2O.

The N 1s Auger spectra for the two nonequivalent N atoms in N2O have been measured via Auger electron-photoelectron coincidence spectroscopy. The site-selected Auger spectra are compared with the normal Auger spectrum and with accurate theoretical calculations accounting for the effects of the dynamics of the nuclei on the energy and linewidth of the Auger bands. Such effects are found to be crucial factors in determining the different band shapes in the site-selected spectra.

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PubMed2006

Ab initio molecular dynamics simulations of elimination reactions in water solution: exploring the borderline region between the E1cb and E2 reaction mechanisms.

We report a theoretical study, based on ab initio molecular dynamics simulations in water solution, of the mechanism of base-induced beta-elimination reactions in systems activated by the pyridyl ring, with halogen leaving groups. The systems investigated represent borderline cases, where it is uncertain whether the reaction proceeds via a carbanion intermediate (E1cb, A(xh)D(H) + D(N)) or via the concerted loss of a proton and the halide (E2, A(N)D(E)D(N)) upon base attack. Recent theoretical and experimental evidence points toward the lack of a net distinction between the E1cb and E2 reaction paths, which seem to merge smoothly into each other in these borderline cases (Alunni, S.; De Angelis, F.; Ottavi, L.; Papavasileiou, M.; Tarantelli, F. J. Am.Chem. Soc. 2005, 127, 15151-15160). In this study, we explore the dynamics on the potential energy surface for the reaction of 2-(2-fluoroethyl)-1-methyl pyridinium with OH- by means of Car-Parrinello simulations in water solution. Our results indicate that the reaction mechanism effectively evolves through the potential energy region of the carbanion: the carbon-fluoride bond breaks only after the carbon-hydrogen bond, confirming the conclusions of a recently reported study of the potential energy surface for this system.

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PubMed2006

The electronic structure of alkali aurides. A four-component Dirac-Kohn-Sham study.

Spectroscopic constants, including dissociation energies, harmonic and anharmonic vibrational frequencies, and dipole moments, are calculated for the complete alkali auride series (LiAu, NaAu, KAu, RbAu, CsAu). The four-component formulation of relativistic density functional theory has been employed in this study, using the G-spinor basis sets implemented recently in the program BERTHA. The performance of four standard nonrelativistic density functionals employed is investigated by comparing the results with the best available theoretical and experimental data. The present work provides the first theoretical predictions on the molecular properties of RbAu. The intermetallic bond that occurs in the alkali auride series is highly polar and is characterized by a large charge transfer from the alkali metals to gold. The extent of this electron transfer has been investigated using several different charge analysis methods, enabling us to reach some general conclusions on their relative performance. We further report a detailed analysis of the topological properties of relativistic electron density in the bonding region, discussing the features of this approach which characterize the nature of the chemical bond. We have also computed the fully relativistic density for the alkali halides MBr and MI (M = Li, Na, K, Rb, and Cs). The comparative study shows that, on the basis of several topological properties and the variation in bond lengths, the gold atom behaves similarly to a halogen intermediate between Br and I.

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PubMed2006

Electron density fitting for the Coulomb problem in relativistic density-functional theory.

A density fitting approach for the Coulomb matrix representation within the four-component formulation of relativistic density-functional theory is presented. Our implementation, which uses G-spinor basis sets, shares all the advantages of those found in nonrelativistic quantum chemistry. We show that very accurate Coulomb energies may be obtained using a modest number of scalar auxiliary basis functions for molecules containing heavy atoms. The efficiency of this new implementation is demonstrated in a detailed study of the spectroscopic properties of the gold dimer, and its scaling behavior has been tested by calculations of some closed-shell gold clusters (Au2, Au3+, Au4, Au5+). The algorithm is found to scale as O(N3), just as it does in the nonrelativistic case, and represents a dramatic improvement in efficiency over the conventional approach in the calculation of the Coulomb matrix, with computation times that are reduced to less than 3% for Au2 and up to 1% in the case of Au5+.

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PubMed2005

Evidence of a borderline region between E1cb and E2 elimination reaction mechanisms: a combined experimental and theoretical study of systems activated by the pyridine ring.

We report a combined experimental and theoretical study to characterize the mechanism of base-induced beta-elimination reactions in systems activated by the pyridyl ring, with halogen leaving groups. The systems investigated represent borderline cases, where it is uncertain whether the reaction proceeds via a carbanion intermediate (E1cb, A(xh)D(H) + D(N)) or via the concerted loss of a proton and the halide (E2, A(N)D(E)D(N)) upon base attack. Experimentally, the Taft correlation for H/D exchange, in OD(-)/D(2)O with noneliminating substrates (1-methyl-2-(2-Xethyl)pyridinium iodide), is used to predict the expected values of the rate constants for the elimination reactions with N-methylated substrates and F, Cl, Br as the leaving group. The comparison indicates an E1cb irreversible mechanism with F, but the deviation observed with Cl and Br does not allow a conclusive assignment. The theoretical calculations show that for the N-methylated substrate with a fluoride leaving group the elimination proceeds via formation of a moderately stable carbanion. No stable anionic intermediate is instead found when the leaving group is Cl or Br, as well as for any of the nonmethylated species, indicating a concerted elimination. The methylated substrate with Cl shows however only a moderate increase in reactivity compared to the fluorinated substrate, despite the change in mechanism. Very interestingly, our analysis of the computed two-dimensional potential energy surface for the reaction with a F leaving group indeed evidences the lack of a net distinction between the E1cb and E2 reaction paths, which appear to merge smoothly into each other in these borderline cases.

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PubMed2005

Computational strategies for a four-component Dirac-Kohn-Sham program: implementation and first applications.

An implementation of the generalized gradient approximation within the four-component formulation of relativistic density-functional theory using G-spinor basis sets is presented. This approach is based on the direct evaluation of the relativistic density and its gradient from the G-spinor amplitudes and gradients without explicit reference to the total density matrix. This proves to be a particularly efficient scheme, with an intrinsic computational cost that scales linearly with the number of G-spinor basis functions. In order to validate this new implementation, incorporated in the parallel version of the program BERTHA, a detailed study of the diatomic system CsAu is also reported. The spectroscopic constants D(e),r(e),omega(e), and x(e)omega(e) and the dipole moment mu have been calculated and compared with the best available theoretical and experimental data. The sensitivity of our results to the details of the numerical schemes used to evaluate the matrix elements is analyzed in detail. Also presented is a comparative study of molecular properties in the alkali auride series which have been obtained using several standard non-relativistic density functionals.

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PubMed2005

Penning ionization of N2O molecules by He(2(3,1)S) and Ne(3P2,0) metastable atoms: a crossed beam study.

The energetics of [Rg... N2O]* autoionizing collision complexes (where Rg=He or Ne) and their dynamical evolution have been studied in a crossed beam apparatus, respectively, by Penning ionization electron spectroscopy (PIES) and by mass spectrometry (MS) techniques in the thermal energy range. The PIES spectra, detected by an electron energy analyzer, were recorded for both complexes at four different collision energies. Such spectra allowed the determination of the energy shifts for Penning electron energy distributions, and the branching ratios for the population of different electronic states and for the vibrational population in the molecular nascent ions. For the [Ne...N2O]* collision complex it was found, by MS, that the autoionization leads to the formation of N2O+, NO+, O+, and NeN2O+ product ions whose total and partial cross sections were measured in the collision energy range between 0.03 and 0.2 eV. The results are analyzed exploiting current models for the Penning ionization process: the observed collision energy dependence in the PIES spectra as well as in the cross sections are correlated with the nature of the N2O molecule orbitals involved in the ionization and are discussed in term of the Rg-N2O interaction potentials, which are estimated by using a semiempirical method developed in our laboratory.

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PubMed2005

Penning ionization of N2O molecules by He(2(3,1)S) and Ne(3P2,0) metastable atoms: theoretical considerations about the intermolecular interactions.

A theoretical investigation of the intermolecular interaction, operative in collision complexes of He*(2 3S1), He*(2 1S0), and Ne*(3P2,0) with N2O, is carried out to explain the main results of the experimental study reported in the preceding paper. The analysis is carried out by means of a semiempirical method based on the identification, modeling, and combination of the leading interaction components, including the effect of the selective polarization of the more external electronic cloud of the metastable atom in the intermolecular electric field. These and other crucial aspects of our approach have been quantitatively verified by ab initio calculations. The proposed method permits to evaluate the interaction at any configuration of the complexes and provides a useful and inexpensive representation of the intermolecular potential energy for dynamics studies. The main experimental findings can be rationalized taking into account the critical balancing between molecular orientation effects in the intermolecular interaction field and the ionization probability. These orientation effects tend to become less pronounced with increasing collision energy.

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PubMed2004

Double ionization of fluorinated benzenes: hole localization and delocalization effects.

The dense double ionization spectra of all the twelve fluoro-substituted benzene molecules are investigated in great detail by Green's function ADC2 calculations and a two-hole density mapping. Double ionization is shown to provide an extremely sensitive tool of electronic structure analysis. The calculations evidence and measure quantitatively how the charge distribution is dictated by the complex interplay between the resilience of the aromatic ring electronic structure and the disruptive effect of the electronegative halogen substituents. Successive substitutions are found not to have any synergic effect, but affect the spectra in very identifiable ways. The Auger spectra of the fluorobenzenes are interpreted in the light of the charge distribution results, using the foreign-imaging model. The double charge transfer spectra are also analyzed and discussed.

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