The Franck-Condon factors for vibronic transitions from the ground states of the HF and DF molecu... more The Franck-Condon factors for vibronic transitions from the ground states of the HF and DF molecules to the X 2Πand A 2Σ + states of the corresponding parent ions are computed in the Born-Oppenheimer approximation. The distribution of these Franck-Condon factors between bound and unbound vibrational A 2Σ + states are employed to predict the percentage of A 2Σ + ions leading to molecular fragmentation. The results are compared with the available experimental data.
The potential energy curves of the X 2Πand A 2Σ + electronic states of the HF + molecular ion ar... more The potential energy curves of the X 2Πand A 2Σ + electronic states of the HF + molecular ion are determined by CI expansions employing several one-particle Gaussian basis sets. The radiative lifetimes of the vibrational Born—Oppenheimer levels of the A state are then evaluated in both the length and velocity forms of the transition operator. With respect to improvements of the wavefunctions, the transition moments and lifetimes are found to be much more stable in the length gauge than in the velocity gauge. Thus the observed gauge disagreement of the computed observables is mainly ascribable to the inaccuracy of the velocity gauge transition moments and therefore the more commonly employed length gauge seems to be the preferred one in the present computational context.
... Volume 1 58, number 3,4 CHEMICAL PHYSICS LETTERS 9 June 1989 AR INITIO CALCULATION OF THE FRA... more ... Volume 1 58, number 3,4 CHEMICAL PHYSICS LETTERS 9 June 1989 AR INITIO CALCULATION OF THE FRANCK-CONDON FACTORS FOR IONIZATION OF HF AND DF TO X ~fl AND A 2L4 STATES Ivo CACELLI Scuo!a Norma/c Superiore, Piazza dci Cavalieri, 56100 Fist ...
This paper concern the theoretical study of the dissociation dynamics of the HF + and DF + molecu... more This paper concern the theoretical study of the dissociation dynamics of the HF + and DF + molecular ions in the B 2Σ + state. The adiabatic curves of the lowest twelve electronic states belonging to the 2Σ + symmetry are computed by a limited CI calculation. The nuclear motion is treated by a classical trajectory approach in which the initial conditions are selected according to the Wigner distribution function. The decay pattern shows complex non-adiabatic interactions involving simultaneous coupling among several adiabatic states. The results are discussed in the light of the available experimental data.
The dissociative pathway of the HF+ molecular ion, initially in its B 2Σ+ electronic state, is st... more The dissociative pathway of the HF+ molecular ion, initially in its B 2Σ+ electronic state, is studied by a full quantum-mechanical technique. The vibronic time-dependent wave function is expanded on the twelve lowest 2Σ+ electronic states computed by a limited configuration-interaction calculation. The nuclear functions are projected on a monodimensional grid and the time-evolution operator is represented by its (1,1) Padè approximant. The calculations are performed both in the adiabatic and in a semidiabatic representation of the electronic states. The decay pattern shows strong vibronic interactions often involving several states at a time. The results are compared with those obtained in a previous calculation, where the nuclear motion was treated by a classical trajectories approach.
Journal of Chemical Information and Modeling, 2005
A new methodology for the theoretical evaluation of the hydrogen bond acidity ΣR 2 H and basicity... more A new methodology for the theoretical evaluation of the hydrogen bond acidity ΣR 2 H and basicity Σ 2 H Abraham descriptors is presented. The first step is a quantum mechanical calculation at the Hartree-Fock level using a moderate basis set, including the solute-solvent interaction through a Reaction Field method, namely the Polarizable Continuum Model (PCM). The density charge on the surface of the cavity surrounding the solute, which contains the signature of the specificity of the molecule, is then translated into effective atomic charges through a suitable algorithm. These atomic charges can be related to the acidity and basicity properties of the molecule by a proper parametrization of empirical atomic factors, which account for the specific H-bonding capabilities of the individual atoms and group of atoms. The Abraham descriptors can be then evaluated with a high degree of accuracy for a large number of classes of molecules. Calculations performed for a set of 55 compounds give a standard deviation of 0.029 and 0.044 for ΣR 2 H and Σ 2 H , respectively. The correlation coefficients are 0.994 and 0.974.
Reductive elimination of methane from methyl hydride half-sandwich phosphane complexes of the Gro... more Reductive elimination of methane from methyl hydride half-sandwich phosphane complexes of the Group 9 metals has been investigated by DFT calculations on the model system [CpM(PH(3))(CH(3))(H)] (M = Co, Rh, Ir). For each metal, the unsaturated product has a triplet ground state; thus, spin crossover occurs during the reaction. All relevant stationary points on the two potential energy surfaces (PES) and the minimum energy crossing point (MECP) were optimized. Spin crossover occurs very near the sigma-CH(4) complex local minimum for the Co system, whereas the heavier Rh and Ir systems remain in the singlet state until the CH(4) molecule is almost completely expelled from the metal coordination sphere. No local sigma-CH(4) minimum was found for the Ir system. The energetic profiles agree with the nonexistence of the Co(III) methyl hydride complex and with the greater thermal stability of the Ir complex relative to the Rh complex. Reductive elimination of methane from the related oxidized complexes [CpM(PH(3))(CH(3))(H)](+) (M = Rh, Ir) proceeds entirely on the spin doublet PES, because the 15-electron [CpM(PH(3))](+) products have a doublet ground state. This process is thermodynamically favored by about 25 kcal mol(-1) relative to the corresponding neutral system. It is essentially barrierless for the Rh system and has a relatively small barrier (ca. 7.5 kcal mol(-1)) for the Ir system. In both cases, the reaction involves a sigma-CH(4) intermediate. Reductive elimination of ethane from [CpM(PH(3))(CH(3))(2)](+) (M = Rh, Ir) shows a similar thermodynamic profile, but is kinetically quite different from methane elimination from [CpM(PH(3))(CH(3))(H)](+): the reductive elimination barrier is much greater and does not involve a sigma-complex intermediate. The large difference in the calculated activation barriers (ca. 12.0 and ca. 30.5 kcal mol(-1) for the Rh and Ir systems, respectively) agrees with the experimental observation, for related systems, of oxidatively induced ethane elimination when M = Rh, whereas the related Ir systems prefer to decompose by alternative pathways.
The reasons why colchicine undergoes photochemical cyclization to give lumicolchicine, whereas th... more The reasons why colchicine undergoes photochemical cyclization to give lumicolchicine, whereas thiocolchicine does not, are investigated by theoretical methods. The relative stability of the reagent and of the products is computed at DFT level of theory and indicates that such a photochemical reaction is energetically possible. The photochemical reaction path of thiocolchicine is studied within the relaxed energy scan, at MC-SCF level of theory. The results are again rather similar to those of colchicine. Finally, the spin-orbit coupling between S 1 and T 1 has been computed and are two order of magnitude greater than those of colchicine, that makes plausible that spin-orbit is the main reason of the observed reaction quenching.
... Volume 1 58, number 3,4 CHEMICAL PHYSICS LETTERS 9 June 1989 AR INITIO CALCULATION OF THE FRA... more ... Volume 1 58, number 3,4 CHEMICAL PHYSICS LETTERS 9 June 1989 AR INITIO CALCULATION OF THE FRANCK-CONDON FACTORS FOR IONIZATION OF HF AND DF TO X ~fl AND A 2L4 STATES Ivo CACELLI Scuo!a Norma/c Superiore, Piazza dci Cavalieri, 56100 Fist ...
Pccp Physical Chemistry Chemical Physics, Jun 9, 2011
Molecular dynamics simulations (90 ns) of different DNA complexes attached to a functionalized su... more Molecular dynamics simulations (90 ns) of different DNA complexes attached to a functionalized substrate in solution were performed in order to clarify the behavior of mismatched DNA sequences captured by a tethered DNA probe (biochip). Examination of the trajectories revealed that the substrate influence and a series of cooperative events, including recognition, reorientation and reorganization of the bases, could induce the formation of stable duplexes having non-canonical arrangements. Major adjustment of the structures was observed when the mutated base was located in the end region of the chain close to the surface.
The photoionization cross sections and asymmetry parameters of the four main valence ionization p... more The photoionization cross sections and asymmetry parameters of the four main valence ionization processes in H 2S, corresponding to the formation of respectively 2b 1, 5a 1, 2b 2 and 4a 1 holes, have been calculated in the random phase approximation (RPA). By resorting to a recently proposed computational procedure, based on the K-matrix technique, the RPA equations for the four coupled ionization channels have been projected on a basis set of L 2 functions and solved, at any excitation energy above the ionization threshold, in a way that allows to recover the electronic continuum degeneracy.
The title compound has been first synthesized and fully characterized as both tetraphenylborate a... more The title compound has been first synthesized and fully characterized as both tetraphenylborate and perchlorate salt. Its 300-900 nm absorption spectrum, recorded in nitromethane, water, and dimethyl sulfoxide, reveals the peculiar existence of two distinct bands whose intensities depend on the solvent donor number. This feature can be attributed to two separate metal-to-ligand charge-transfer transitions, in agreement with the theoretical predictions obtained by extensive configuration interaction calculations, which take into account the solvent effects. The calculation of the potential energy curves of the ground and excited states along the Ru-tetrazine coordinate allows the interpretation of the relative intensities of the observed bands, as well as the interpretation of their line-shape profiles.
The absorption spectrum of [(NH3) 5Ru-(4, 4'-bipyridine)] 2+ in the visible has been stu... more The absorption spectrum of [(NH3) 5Ru-(4, 4'-bipyridine)] 2+ in the visible has been studied by ab initio methods, taking into account solvent effects by means of the polarizable continuum model and performing extensive CI calculations. The dependence of the ...
Pccp Physical Chemistry Chemical Physics, Apr 1, 2010
The stretching, bending, and torsional force-field parameters for modelling Si (111) surfaces fun... more The stretching, bending, and torsional force-field parameters for modelling Si (111) surfaces functionalized with alkylamines have been derived from energies, optimized geometries and harmonic frequencies obtained by accurate quantum mechanical calculations. Addition of inter-chain non-bonded parameters from a literature force field leads to computed energies in good agreement with their quantum mechanical counterparts for a large set of geometrical arrangements. The overall force-field was tested through molecular dynamics simulations performed on several models of Si functionalized surfaces, with different coverage percentages. Preliminary results indicate that the presence of a polar terminal amine group yields a surface coating of around 50%.
The Franck-Condon factors for vibronic transitions from the ground states of the HF and DF molecu... more The Franck-Condon factors for vibronic transitions from the ground states of the HF and DF molecules to the X 2Πand A 2Σ + states of the corresponding parent ions are computed in the Born-Oppenheimer approximation. The distribution of these Franck-Condon factors between bound and unbound vibrational A 2Σ + states are employed to predict the percentage of A 2Σ + ions leading to molecular fragmentation. The results are compared with the available experimental data.
The potential energy curves of the X 2Πand A 2Σ + electronic states of the HF + molecular ion ar... more The potential energy curves of the X 2Πand A 2Σ + electronic states of the HF + molecular ion are determined by CI expansions employing several one-particle Gaussian basis sets. The radiative lifetimes of the vibrational Born—Oppenheimer levels of the A state are then evaluated in both the length and velocity forms of the transition operator. With respect to improvements of the wavefunctions, the transition moments and lifetimes are found to be much more stable in the length gauge than in the velocity gauge. Thus the observed gauge disagreement of the computed observables is mainly ascribable to the inaccuracy of the velocity gauge transition moments and therefore the more commonly employed length gauge seems to be the preferred one in the present computational context.
... Volume 1 58, number 3,4 CHEMICAL PHYSICS LETTERS 9 June 1989 AR INITIO CALCULATION OF THE FRA... more ... Volume 1 58, number 3,4 CHEMICAL PHYSICS LETTERS 9 June 1989 AR INITIO CALCULATION OF THE FRANCK-CONDON FACTORS FOR IONIZATION OF HF AND DF TO X ~fl AND A 2L4 STATES Ivo CACELLI Scuo!a Norma/c Superiore, Piazza dci Cavalieri, 56100 Fist ...
This paper concern the theoretical study of the dissociation dynamics of the HF + and DF + molecu... more This paper concern the theoretical study of the dissociation dynamics of the HF + and DF + molecular ions in the B 2Σ + state. The adiabatic curves of the lowest twelve electronic states belonging to the 2Σ + symmetry are computed by a limited CI calculation. The nuclear motion is treated by a classical trajectory approach in which the initial conditions are selected according to the Wigner distribution function. The decay pattern shows complex non-adiabatic interactions involving simultaneous coupling among several adiabatic states. The results are discussed in the light of the available experimental data.
The dissociative pathway of the HF+ molecular ion, initially in its B 2Σ+ electronic state, is st... more The dissociative pathway of the HF+ molecular ion, initially in its B 2Σ+ electronic state, is studied by a full quantum-mechanical technique. The vibronic time-dependent wave function is expanded on the twelve lowest 2Σ+ electronic states computed by a limited configuration-interaction calculation. The nuclear functions are projected on a monodimensional grid and the time-evolution operator is represented by its (1,1) Padè approximant. The calculations are performed both in the adiabatic and in a semidiabatic representation of the electronic states. The decay pattern shows strong vibronic interactions often involving several states at a time. The results are compared with those obtained in a previous calculation, where the nuclear motion was treated by a classical trajectories approach.
Journal of Chemical Information and Modeling, 2005
A new methodology for the theoretical evaluation of the hydrogen bond acidity ΣR 2 H and basicity... more A new methodology for the theoretical evaluation of the hydrogen bond acidity ΣR 2 H and basicity Σ 2 H Abraham descriptors is presented. The first step is a quantum mechanical calculation at the Hartree-Fock level using a moderate basis set, including the solute-solvent interaction through a Reaction Field method, namely the Polarizable Continuum Model (PCM). The density charge on the surface of the cavity surrounding the solute, which contains the signature of the specificity of the molecule, is then translated into effective atomic charges through a suitable algorithm. These atomic charges can be related to the acidity and basicity properties of the molecule by a proper parametrization of empirical atomic factors, which account for the specific H-bonding capabilities of the individual atoms and group of atoms. The Abraham descriptors can be then evaluated with a high degree of accuracy for a large number of classes of molecules. Calculations performed for a set of 55 compounds give a standard deviation of 0.029 and 0.044 for ΣR 2 H and Σ 2 H , respectively. The correlation coefficients are 0.994 and 0.974.
Reductive elimination of methane from methyl hydride half-sandwich phosphane complexes of the Gro... more Reductive elimination of methane from methyl hydride half-sandwich phosphane complexes of the Group 9 metals has been investigated by DFT calculations on the model system [CpM(PH(3))(CH(3))(H)] (M = Co, Rh, Ir). For each metal, the unsaturated product has a triplet ground state; thus, spin crossover occurs during the reaction. All relevant stationary points on the two potential energy surfaces (PES) and the minimum energy crossing point (MECP) were optimized. Spin crossover occurs very near the sigma-CH(4) complex local minimum for the Co system, whereas the heavier Rh and Ir systems remain in the singlet state until the CH(4) molecule is almost completely expelled from the metal coordination sphere. No local sigma-CH(4) minimum was found for the Ir system. The energetic profiles agree with the nonexistence of the Co(III) methyl hydride complex and with the greater thermal stability of the Ir complex relative to the Rh complex. Reductive elimination of methane from the related oxidized complexes [CpM(PH(3))(CH(3))(H)](+) (M = Rh, Ir) proceeds entirely on the spin doublet PES, because the 15-electron [CpM(PH(3))](+) products have a doublet ground state. This process is thermodynamically favored by about 25 kcal mol(-1) relative to the corresponding neutral system. It is essentially barrierless for the Rh system and has a relatively small barrier (ca. 7.5 kcal mol(-1)) for the Ir system. In both cases, the reaction involves a sigma-CH(4) intermediate. Reductive elimination of ethane from [CpM(PH(3))(CH(3))(2)](+) (M = Rh, Ir) shows a similar thermodynamic profile, but is kinetically quite different from methane elimination from [CpM(PH(3))(CH(3))(H)](+): the reductive elimination barrier is much greater and does not involve a sigma-complex intermediate. The large difference in the calculated activation barriers (ca. 12.0 and ca. 30.5 kcal mol(-1) for the Rh and Ir systems, respectively) agrees with the experimental observation, for related systems, of oxidatively induced ethane elimination when M = Rh, whereas the related Ir systems prefer to decompose by alternative pathways.
The reasons why colchicine undergoes photochemical cyclization to give lumicolchicine, whereas th... more The reasons why colchicine undergoes photochemical cyclization to give lumicolchicine, whereas thiocolchicine does not, are investigated by theoretical methods. The relative stability of the reagent and of the products is computed at DFT level of theory and indicates that such a photochemical reaction is energetically possible. The photochemical reaction path of thiocolchicine is studied within the relaxed energy scan, at MC-SCF level of theory. The results are again rather similar to those of colchicine. Finally, the spin-orbit coupling between S 1 and T 1 has been computed and are two order of magnitude greater than those of colchicine, that makes plausible that spin-orbit is the main reason of the observed reaction quenching.
... Volume 1 58, number 3,4 CHEMICAL PHYSICS LETTERS 9 June 1989 AR INITIO CALCULATION OF THE FRA... more ... Volume 1 58, number 3,4 CHEMICAL PHYSICS LETTERS 9 June 1989 AR INITIO CALCULATION OF THE FRANCK-CONDON FACTORS FOR IONIZATION OF HF AND DF TO X ~fl AND A 2L4 STATES Ivo CACELLI Scuo!a Norma/c Superiore, Piazza dci Cavalieri, 56100 Fist ...
Pccp Physical Chemistry Chemical Physics, Jun 9, 2011
Molecular dynamics simulations (90 ns) of different DNA complexes attached to a functionalized su... more Molecular dynamics simulations (90 ns) of different DNA complexes attached to a functionalized substrate in solution were performed in order to clarify the behavior of mismatched DNA sequences captured by a tethered DNA probe (biochip). Examination of the trajectories revealed that the substrate influence and a series of cooperative events, including recognition, reorientation and reorganization of the bases, could induce the formation of stable duplexes having non-canonical arrangements. Major adjustment of the structures was observed when the mutated base was located in the end region of the chain close to the surface.
The photoionization cross sections and asymmetry parameters of the four main valence ionization p... more The photoionization cross sections and asymmetry parameters of the four main valence ionization processes in H 2S, corresponding to the formation of respectively 2b 1, 5a 1, 2b 2 and 4a 1 holes, have been calculated in the random phase approximation (RPA). By resorting to a recently proposed computational procedure, based on the K-matrix technique, the RPA equations for the four coupled ionization channels have been projected on a basis set of L 2 functions and solved, at any excitation energy above the ionization threshold, in a way that allows to recover the electronic continuum degeneracy.
The title compound has been first synthesized and fully characterized as both tetraphenylborate a... more The title compound has been first synthesized and fully characterized as both tetraphenylborate and perchlorate salt. Its 300-900 nm absorption spectrum, recorded in nitromethane, water, and dimethyl sulfoxide, reveals the peculiar existence of two distinct bands whose intensities depend on the solvent donor number. This feature can be attributed to two separate metal-to-ligand charge-transfer transitions, in agreement with the theoretical predictions obtained by extensive configuration interaction calculations, which take into account the solvent effects. The calculation of the potential energy curves of the ground and excited states along the Ru-tetrazine coordinate allows the interpretation of the relative intensities of the observed bands, as well as the interpretation of their line-shape profiles.
The absorption spectrum of [(NH3) 5Ru-(4, 4'-bipyridine)] 2+ in the visible has been stu... more The absorption spectrum of [(NH3) 5Ru-(4, 4'-bipyridine)] 2+ in the visible has been studied by ab initio methods, taking into account solvent effects by means of the polarizable continuum model and performing extensive CI calculations. The dependence of the ...
Pccp Physical Chemistry Chemical Physics, Apr 1, 2010
The stretching, bending, and torsional force-field parameters for modelling Si (111) surfaces fun... more The stretching, bending, and torsional force-field parameters for modelling Si (111) surfaces functionalized with alkylamines have been derived from energies, optimized geometries and harmonic frequencies obtained by accurate quantum mechanical calculations. Addition of inter-chain non-bonded parameters from a literature force field leads to computed energies in good agreement with their quantum mechanical counterparts for a large set of geometrical arrangements. The overall force-field was tested through molecular dynamics simulations performed on several models of Si functionalized surfaces, with different coverage percentages. Preliminary results indicate that the presence of a polar terminal amine group yields a surface coating of around 50%.
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