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Vincenzo Barone

Publications and source records attributed to Vincenzo Barone.

At least 55 records · Page 3Linked to original sources
PubMed2005

A combined theoretical and experimental approach to determining order parameters of solutes in liquid crystals from 13C NMR data.

The ordering properties of an anisotropic liquid crystal can be studied by recording 13C NMR spectra at different temperatures for a number of rigid solutes. The traditional difficulty in analyzing 13C data comes from the scarcity of experimental information about the carbon shielding tensors and from their limited transferability among different solutes. We show that these obstacles can be overcome by computing high-level ab initio shielding tensors, also including the solvent effects by the polarizable continuum model. The reliability of this combined approach is carefully verified, and the order parameters of several solutes are obtained by reanalyzing previously published spectra. The quality of the results is shown to be comparable to deuterium NMR without the need of isotopic substitution.

Journal Article↗
PubMed2005

Understanding electron transfer across negatively-charged Aib oligopeptides.

The physicochemical effects modulating the conformational behavior and the rate of intramolecular dissociative electron transfer in phthalimide-Aibn-peroxide peptides (n = 0-3) have been studied by an integrated density functional/continuum solvent model. We found that three different orientations of the phthalimide ring are possible, labeled Phihel, PhiC7, and PhipII. In the condensed phase, they are very close in energy when the system is neutral and short. When the peptide chain length increases and the system is negatively charged, Phihel becomes instead the most stable conformer. Our calculations confirm that the 3(10)-helix is the most stable secondary structure for the peptide bridge. However, upon charge injection in the phthalimide end of the phthalimide-Aib3-peroxide, the peptide bridge can adopt an alpha-helix conformation as well. The study of the dependence of the frontier orbitals on the length and on the conformation of the peptide bridge (in agreement with experimental indications) suggests that for n = 3 the process could be influenced by a 3(10) --> alpha-helix conformational transition of the peptide chain.

Computer Simulation↗
PubMed2005

Solvent effects on the UV (n --> pi*) and NMR (13C and 17O) spectra of acetone in aqueous solution. An integrated car-parrinello and DFT/PCM approach.

The accurate reproduction of ultraviolet and nuclear magnetic resonance spectra of acetone in aqueous solution is used as a test of an integrated computational tool rooted in the density functional theory, the polarizable continuum model, and the Car-Parrinello dynamics. The analysis and solution of several conceptual and practical issues results in a robust and effective approach, which also can be used by nonspecialists and provides a general and powerful complement to experimental techniques.

Journal Article↗
PubMed2005

Vibrational computations beyond the harmonic approximation: performances of the B3LYP density functional for semirigid molecules.

The performances of the B3LYP density functional in the computation of harmonic and anharmonic frequencies were tested using 14 standard basis sets of double and triple zeta quality for a set of semirigid molecules containing from 4 to 12 atoms. The quality of the results is assessed by comparison with the most reliable computations available in the literature. The study reveals that the relatively cheap 6-31+G(d,p) basis set performs a very good job for harmonic frequency calculations and that B3LYP anharmonicities are in close agreement with the reference values irrespective of the basis set used. On these grounds "hybrid force fields" are proposed to achieve the best compromise between computer time and quality of the results.

Journal Article↗
PubMed2005

Building cavities in a fluid of spherical or rod-like particles: a contribution to the solvation free energy in isotropic and anisotropic polarizable continuum model.

A general formalism for the calculation of cavitation energies in the framework of the scaled particle theory has been implemented in the Polarizable Continuum Model (PCM), contributing to the nonelectrostatic part of the molecular free energy in solution. The solute cavity and the solvent molecules are described as hard spherocylinders, whose radius and length are related to the actual molecular shape, while the solvent density is estimated from experimental data, or from the solvent molecular volume, suitably scaled. The present model can describe isotropic solutions of spherical and rod-like molecules in spherical or rod-like solvents, and also anisotropic solutions in which the solvent molecules are oriented in space: in this case, the cavitation energy also depends on the relative orientation of solute and solvent molecules. Test calculations have been performed on simple systems to evaluate the accuracy of the present approach, in comparison with other methods and with the available experimental estimates of the cavitation energy, giving encouraging results.

Journal Article↗
PubMed2004

Absorption and fluorescence spectra of uracil in the gas phase and in aqueous solution: a TD-DFT quantum mechanical study.

Here we present the first computations of fluorescence spectra in aqueous solution at an accurate quantum mechanical level. From a methodological point of view, our study shows that by only taking into account both bulk effects and explicit solvent molecules it is possible to reproduce solvent effects on the energy and the intensities of the electronic spectra, especially for what concerns pi/pi* transition. The computed absorption and fluorescence spectra are in a good agreement with the available experimental results. The energy ordering between the lowest energy n-pi* and the pi/pi* transitions in uracil strongly depends on the nature of the embedding medium. The geometry of the first solvation shell is remarkably sensitive to the specific electronic state, suggesting that solvent degrees of freedom can act as S1/S2 coupling modes.

Gases↗
PubMed2004

Regioselectivity and nucleophilic control in the cyclopropane ring opening of duocarmycin SA derivatives under neutral and acid conditions: a quantum mechanical study in the gas phase and in solution.

We present a quantum mechanical investigation of the nucleophilic addition to the cyclopropane ring of a representative member of antitumor antibiotics related to CC-1065. We have analyzed, in particular, the regioselectivity of the reaction and its tuning by the nature of the etheroatom (O or N) in the nucleophile under both neutral and acidic conditions. Our results are in agreement with the experimental trends and suggest that, contrary to methanol, N-bases can be effective also under neutral conditions, irrespective of the additional steric constraints experienced in the biologically active substrate (DNA). The reliability of the computational protocol, rooted in the density functional theory coupled to a refined continuum solvent model, allows us to put forward reliable structure/reactivity relationships and to interpret the results in terms of reactivity indexes (hardness, electrophilic character).

Cyclopropanes↗
PubMed2004

Complete structural and magnetic characterization of biological radicals in solution by an integrated quantum mechanical approach: glycyl radical as a case study.

An integrated quantum mechanical approach for the structural and magnetic characterization of flexible free radicals in solution has been applied to a model of the glycyl radical engaged in peptidic chains. The hyperfine couplings computed using hybrid density functionals and purposely tailored basis sets are in good agreement with experiment when vibrational averaging effects from low frequency motions and solvent effects (both direct H bonding and bulk) are taken into the proper account. The g tensor shows a smaller dependence on the specific form of the density functional, the extension of the basis set over a standard double-zeta+polarization level, vibrational averaging, and bulk solvent effects. However, hydrogen bridges with solvent molecules belonging to the first solvation shell play a significant role. Together with their intrinsic interest, our results show that a comprehensive and reliable computational approach is becoming available for the complete characterization of open-shell systems of biological interest in their natural environment.

Dipeptides↗
PubMed2004

Checking the pH-induced conformational transition of prion protein by molecular dynamics simulations: effect of protonation of histidine residues.

The role of acidic pH in the conversion of human prion protein to the pathogenic isoform is investigated by means of molecular dynamics simulations, focusing the attention on the effect of protonation of histidine residues on the conformational behavior of human PrPC globular domain. Our simulations reveal a significant loss of alpha-helix content under mildly acidic conditions, due to destructuration of the C-terminal part of HB (thus suggesting a possible involvement of HB into the conformational transition leading to the pathogenic isoform) and a transient lengthening of the native beta-sheet. Protonation of His-187 and His-155 seems to be crucial for the onset of the conformational rearrangement. This finding can be related to the existence of a pathogenic mutation, H187R, which is associated with GSS syndrome. Finally, the relevance of our results for the location of a Cu2+-binding pocket in the C-terminal part of the prion is discussed.

Computer Simulation↗
PubMed2004

Thiazolidin-4-one formation. Mechanistic and synthetic aspects of the reaction of imines and mercaptoacetic acid under microwave and conventional heating.

Microwave irradiation of a mixture of benzylidene-anilines and mercaptoacetic acid in benzene gives 1,3-thiazolidin-4-ones in very high yield (65-90%), whereas the same reaction performed through using the conventional method, at reflux temperature, requires a much longer time and gives a much lower yield (25-69%). This difference seems to be due to some intermediates and by-products formed during the conventional reaction. On the basis of 1H NMR studies, two different mechanisms, acting in benzene and in DMF, respectively, have been hypothesized for the thiazolidin-4-one system formation.

Hot Temperature↗
PubMed2004

First-principle molecular dynamics of the Berry pseudorotation: insights on 19F NMR in SF4.

First-principles [density-functional theory (DFT)] molecular-dynamic simulations of the Berry pseudorotation mechanism in SF4 were performed using the atom-centered density-matrix propagation method. The reaction was monitored by following the chemical shieldings of the fluorine atoms, computed on snapshots along the trajectories. In particular we compared the results obtained using a standard functional based on the generalized gradient approximation with those issuing from its hybrid Hartree-Fock-DFT counterpart using a number of basis sets. Our results show that both the basis set and the functional choice rule the quality of the molecular properties monitored as well as the trajectory over the potential-energy surface.

Journal Article↗
PubMed2004

Observed and calculated 1H- and 13C-NMR chemical shifts of substituted 5H-pyrido[3,2-a]- and 5H-pyrido[2,3-a]phenoxazin-5-ones and of some 3H-phenoxazin-3-one derivatives.

Carbon and proton NMR spectra of several substituted 5H-pyrido[3,2-a]-, 5H-pyrido[2,3-a]phenoxazin-5-ones and 3H-phenoxazin-3-one derivatives have been assigned, and the experimental chemical shifts have been compared with the results of density functional calculations employing large basis sets. Solvent effects were explored by means of the polarizable continuum method (PCM), while the (limited) side-chain flexibility of the compounds has been addressed by Boltzmann averaging of the computed spectral parameters over different conformational minima. Overall, the calculated shifts reproduce well the experiment results; thus, the computational procedure represents a feasible and useful complement to multidimensional NMR experiments in the assignment process.

Journal Article↗
PubMed2004

Vibrational zero-point energies and thermodynamic functions beyond the harmonic approximation.

This paper compares harmonic and anharmonic zero-point energies and thermodynamic functions for a number of molecules of small and medium size. Anharmonic corrections cannot be neglected for quantitative studies, but can be obtained quite effectively by a perturbative treatment including cubic force constants to the second order and semidiagonal quartic constants to the first order. Simple finite difference equations provide all the necessary terms by at most 6N-11 Hessian evaluations, where N is the number of atoms in the system. Accurate values are obtained by this method using the Becke three parameter Lee-Yang-Parr functional, medium size basis sets, and, when needed, proper treatment of internal rotations. The whole model has been completely automated in the Gaussian package.

Journal Article↗
PubMed2004

Assessing the reliability of density functional methods in the conformational study of polypeptides: the treatment of intraresidue nonbonding interactions.

The role of intraresidue interactions in determining the conformational behavior of polypeptides is analyzed by means of density functional and post-Hartree-Fock computations on the alanine dipeptide analog and other model compounds. Our computations show that the accuracy of current density functionals is sufficient for H-bond, electrostatic, inductive, and short-range repulsive interactions, whereas medium-range attractions between electron-rich atoms and/or bonds are underestimated. This leads, in turn, to an underestimation of the stability of helical structures w.r.t. extended or folded conformers involving H-bonds. Those results could pave the route for devising local ad hoc corrections able to significantly improve structural and dynamic predictions for polypeptides issuing from DFT computations.

Alanine↗
PubMed2004

Reliable NMR chemical shifts for molecules in solution by methods rooted in density functional theory.

The conceptual and numerical problems involved in the computation of reliable NMR chemical shifts for molecules in condensed phases are analyzed with reference to a number of case studies ranging from aromatic compounds in low-polarity solvents to carbonyl and amidic models in aqueous solution and to large polypeptides. The results show that an integrated tool including the most recent density functionals, mixed discrete-continuum solvent models, hybrid QM/MM approaches and, when needed, averaging from molecular dynamics simulations are becoming an invaluable complement to experimental results.

Journal Article↗
PubMed2003

Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model.

The conductor-like solvation model, as developed in the framework of the polarizable continuum model (PCM), has been reformulated and newly implemented in order to compute energies, geometric structures, harmonic frequencies, and electronic properties in solution for any chemical system that can be studied in vacuo. Particular attention is devoted to large systems requiring suitable iterative algorithms to compute the solvation charges: the fast multipole method (FMM) has been extensively used to ensure a linear scaling of the computational times with the size of the solute. A number of test applications are presented to evaluate the performances of the method.

Journal Article↗