Biomedical subjects

Vincenzo Barone

Publications and source records attributed to Vincenzo Barone.

At least 37 records · Page 2Linked to original sources

PubMed2006

Interplay of stereoelectronic and enviromental effects in tuning the structural and magnetic properties of a prototypical spin probe: further insights from a first principle dynamical approach.

The nitrogen isotropic hyperfine coupling constant (hcc) and the g tensor of a prototypical spin probe (di-tert-butyl nitroxide, DTBN) in aqueous solution have been investigated by means of an integrated computational approach including Car-Parrinello molecular dynamics and quantum mechanical calculations involving a discrete-continuum embedding. The quantitative agreement between computed and experimental parameters fully validates our integrated approach. Decoupling of the structural, dynamical, and environmental contributions acting onto the spectral observables allows an unbiased judgment of the role played by different effects in determining the overall experimental observables and highlights the importance of finite-temperature vibrational averaging. Together with their intrinsic interest, our results pave the route toward more reliable interpretations of EPR parameters of complex systems of biological and technological relevance.

Journal Article↗

PubMed2006

Geometries and properties of excited states in the gas phase and in solution: theory and application of a time-dependent density functional theory polarizable continuum model.

In this paper we present the theory and implementation of analytic derivatives of time-dependent density functional theory (TDDFT) excited states energies, both in vacuo and including solvent effects by means of the polarizable continuum model. The method is applied to two case studies: p-nitroaniline and 4-(dimethyl)aminobenzonitrile. For both molecules PCM-TDDFT is shown to be successful in supporting the analysis of experimental data with useful insights for a better understanding of photophysical and photochemical pathways in solution.

Journal Article↗

PubMed2006

On the role of stereo-electronic effects in tuning the selectivity and rate of DNA alkylation by duocarmycins.

The role of local geometric and stereo-electronic effects in tuning the alkylation of DNA by duocarmycins has been analyzed by an integrated computational tool rooted in the density functional theory and the polarizable continuum model. Our study points out that together with steric accessibility, different electronic delocalisations also contribute to determine the higher reactivity of adenine with respect to guanine. Also the effect of the methyl ester group on the alkylating agent has an electronic origin. Furthermore, deviations from the planarity in the drug structure (conformational catalysis) could be less important than currently accepted since, according to our computations, compounds with strongly different reactivity have nearly constant and very similar out of plane distortions before and after the reaction. Model computations suggest, instead, that specific non covalent interactions could discriminate between different drugs selectively reducing some activation energies with respect to the corresponding processes in solution.

Adenine↗

PubMed2006

The catecholic antioxidant piceatannol is an effective nitrosation inhibitor via an unusual double bond nitration.

Piceatannol (1) was found to be more effective than caffeic acid, an established antinitrosating agent, in inhibiting N-nitrosation of 2,3-diaminonaphthalene. Product analysis of the reaction mixture of 1 (20 microM) with nitrite ions (80 microM) at pH 3.0 and at 37 degrees C showed conversion to a single major nitration product, (E)-3,3',4,5'-tetrahydroxy-beta-nitrostilbene (2) (68% yield). This would result from an unexpected nitration at the double bond sector via the 4-phenoxyl radical, which was analyzed at the unrestricted DFT level.

Antioxidants↗

PubMed2006

Periodic and high-temperature disordered conformations of polytetrafluoroethylene chains: an ab initio modeling.

We report here the main results of a successful attempt to predict some macroscopic properties of representative polymers of technological relevance both in regular and disordered forms by using first principle quantum mechanical approaches at microscopic level. Until now, the prediction of the structural and thermal properties of those polymers has been mostly a domain of molecular mechanics methods. To overcome the limits of those classical computational tools whenever physical properties are significantly influenced by stereoelectronic effects (e.g., electron rich substituents), we employed methods rooted in the Density Functional Theory (DFT). A general computational strategy including the proper choice of periodic boundary conditions (PBC), functional, basis set, and model system size, has been tested and validated for saturated polymers such as polyethylene and isotactic/syndiotactic polypropylenes. On the basis of these results, a comprehensive study of poly(tetrafluoroethylene) (PTFE) chains in both regular periodic and disordered conformations has been performed. A statistical approach has been next applied to obtain the thermal concentration of defects and to reproduce the thermal behavior of the investigated polymer. At the end, a very good agreement with experimental X-ray diffraction and IR results has been achieved, definitely reaching a good understanding of the widely studied disorder phenomenon determining the main technological properties of poly(tetrafluoroethylene) (the trade Teflon) and, at the same time, identifying the proper computational tools to investigate perfluoro-compounds and other complex polymeric systems.

Journal Article↗

PubMed2006

Singlet excited-state behavior of uracil and thymine in aqueous solution: a combined experimental and computational study of 11 uracil derivatives.

The excited-state properties of uracil, thymine, and nine other derivatives of uracil have been studied by steady-state and time-resolved spectroscopy. The excited-state lifetimes were measured using femtosecond fluorescence upconversion in the UV. The absorption and emission spectra of five representative compounds have been computed at the TD-DFT level, using the PBE0 exchange-correlation functional for ground- and excited-state geometry optimization and the Polarizable Continuum Model (PCM) to simulate the aqueous solution. The calculated spectra are in good agreement with the experimental ones. Experiments show that the excited-state lifetimes of all the compounds examined are dominated by an ultrafast (<100 fs) component. Only 5-substituted compounds show more complex behavior than uracil, exhibiting longer excited-state lifetimes and biexponential fluorescence decays. The S(0)/S(1) conical intersection, located at CASSCF (8/8) level, is indeed characterized by pyramidalization and out of plane motion of the substituents on the C5 atom. A thorough analysis of the excited-state Potential Energy Surfaces, performed at the PCM/TD-DFT(PBE0) level in aqueous solution, shows that the energy barrier separating the local S(1) minimum from the conical intersection increases going from uracil through thymine to 5-fluorouracil, in agreement with the ordering of the experimental excited-state lifetime.

Models, Molecular↗

PubMed2006

Spectroscopic properties in the liquid phase: combining high-level ab initio calculations and classical molecular dynamics.

We present an integrated computational tool, rooted in density functional theory, the polarizable continuum model, and classical molecular dynamics employing spherical boundary conditions, to study the spectroscopic observables of molecules in solution. As a test case, a modified OPLS-AA force field has been developed and used to compute the UV and NMR spectra of acetone in aqueous solution. The results show that provided the classical force fields are carefully reparameterized and validated, the proposed approach is robust and effective, and can also be used by nonspecialists to provide a general and powerful complement to experimental techniques.

Journal Article↗

PubMed2006

A computational protocol to probe the role of solvation effects on the reduction potential of azurin mutants.

Semiquantitative relationships between thermodynamic parameters of Cu2+ reduction experimentally measured for a series of azurin mutants and the solvation free energy of the oxidized state of the proteins were derived. Solvation free energy calculations were carried out within an ONIOM/PCM scheme specifically adapted to this protein series. The method proved to be able to capture the main determinants of the measured reduction parameters, providing satisfactory predictions of the E degrees '.

Algorithms↗

PubMed2005

Harmonic and anharmonic contributions to parity-violating vibrational frequency difference between enantiomers of chiral molecules.

A general perturbative procedure for the computation of harmonic and anharmonic contributions to parity-violating vibrational shifts is introduced and applied to PHBrF and AsHBrF. The results point out the importance of both diagonal and off-diagonal anharmonic contributions and indicate that some parity-violating shift of AsHBrF approaches the resolution forecasted for next generation experiments. The proposed approach is sufficiently general and computationally effective to allow studies of similar and larger molecular systems.

Journal Article↗

PubMed2005

MD simulation of the Na+-phenylalanine complex in water: competition between cation-pi interaction and aqueous solvation.

The competition between cation-pi interaction and aqueous solvation for the Na+ ion has been investigated by molecular dynamics simulations, using the phenylalanine amino acid as the test pi system. Starting from one of the best standard force fields, we have developed new parameters that significantly improve the agreement with experimental and high quality quantum mechanical results for the complexes of Na+ with phenylalanine, benzene, and water. The modified force field performs very well in forecasting energy and geometry of cation coordination for the complexes. Next, analysis of MD trajectories and steered MD simulations indicate that the Na+-phenylalanine complex survives for a significant time in aqueous solution and that the free energy barrier opposing dissociation of the complex is sizable. Finally, we analyze the role of different intermolecular interactions in determining the preference for cation-pi bonding with respect to aqueous solvation. We thus confirm that the Na+-phenylalanine stabilization energy may overcome the interactions with water.

Journal Article↗

PubMed2005

Accurate prediction of electron-paramagnetic-resonance tensors for spin probes dissolved in liquid crystals.

High-level ab initio g and A tensor components have been calculated for PD-tempone and tempo-palmitate (TP) radical spin probes dissolved in n-pentyl and n-hexyl cyanobiphenyl liquid crystals. Solvent effects have been included in the proposed approach by means of the polarizable continuum model, allowing for solvent anisotropy. An in-depth analysis of the electronic structure of probes was performed to choose a suitable model for TP and make the calculations more accessible. Computed magnetic tensor components have been compared with corresponding values measured in the rigid limit. The quality of the results suggests the use of quantum-mechanical data to determine the order parameter of the nematic from experimental electron-spin resonance measurements.

Anisotropy↗

PubMed2005

New hints on the Ph-driven tautomeric equilibria of the topotecan anticancer drug in aqueous solutions from an integrated spectroscopic and quantum-mechanical approach.

The equilibria between the different forms of the topotecan anticancer drug have been studied at moderately acidic and physiological pH by an integrated computational tool rooted in the density functional theory and its time-dependent extension together with the polarizable continuum model. The results allow an unbiased selection between the different possible tautomeric forms and provide invaluable complements to experimental data. The ultraviolet-visible topotecan spectrum, recorded at moderately acidic pH, is accurately reproduced only by TD-DFT computations including solvent effects. Comparison of the experimental and calculated bands of the UV-vis spectrum at physiological pH indicates the presence of an equilibrium among different forms that is tuned by the microenvironment embedding the drug. The quantitative agreement between TD-DFT/PCM computations and experiments allows the identification of unequivocal spectroscopic signatures for different forms of topotecan.

Antineoplastic Agents↗

PubMed2005

Accurate vibrational spectra and magnetic properties of organic free radicals: the case of H2CN.

We present the structural, magnetic, and vibrational properties of H2CN computed using a second-order perturbative approach in which equilibrium values and harmonic frequencies evaluated at the coupled-cluster level are combined with anharmonic and vibrational averaging contributions obtained by hybrid Hartree-Fock/Kohn-Sham methods. Our computations lead to remarkably accurate results and suggest some revision of the experimental vibrational assignments.

Journal Article↗

PubMed2005

Experimental evidence for a variable first coordination shell of the cadmium(II) ion in aqueous, dimethyl sulfoxide, and N,N'-dimethylpropyleneurea solution.

A combined extended X-ray absorption fine structure (EXAFS) and large angle X-ray scattering (LAXS) investigation has been performed to evaluate the coordination structure of the cadmium(II) ion in aqueous, dimethyl sulfoxide, and N,N'-dimethylpropyleneurea (dmpu) solutions. This approach has singled out the existence of a flexible coordination shell around the cadmium(II) ion in aqueous and dimethyl sulfoxide solutions, whereas a regular octahedral complex is detected in dmpu. The EXAFS and LAXS techniques provide different values of the Cd-O first shell distance (2.27(1) A and 2.302(5) A, respectively) for the hydrated and dimethyl sulfoxide solvated complexes, and this discrepancy is originated by the simultaneous presence of hexa- and heptacoordinated complexes in solution, giving rise to a broad distribution of distances around the ion. These findings demonstrate that, in solution, the cadmium(II) ion forms quite flexible hydration and dimethyl sulfoxide solvate complexes undergoing a solvent exchange with unusually stable seven-coordinated intermediate complexes, and therefore the mean ion-solvent distance is longer in solution than in the solid state. In the dmpu solution, due to the bulkiness of the solvent molecules, the octahedral cadmium(II) solvate is extremely crowded and it is not possible for a seventh ligand to enter the inner-coordination shell. This investigation shows that the combined analysis of the EXAFS and LAXS data allows a reliable determination of the structural properties of electrolyte solutions, also in the presence of flexible coordination shell with a variable number of coordinating molecules.

Cadmium↗

PubMed2005

Computational evidence for a variable first shell coordination of the cadmium(II) ion in aqueous solution.

In this paper, we present a state-of-the-art 100 ns molecular dynamics simulation of a cadmium(II) aqueous solution that highlights a very flexible ion first coordination shell which transits between hexa- and heptahydrated complexes. From this investigation, a dynamical picture of the water exchange process emerges that takes place through an associative mechanism for the solvent substitution reaction. Our procedure starts from the generation of an effective two-body potential from quantum mechanical ab initio calculations in which the many-body ion-water terms are accounted for by the polarizable continuum method (PCM). This approach is computationally very efficient and has allowed us to carry out extremely long molecular dynamics simulations, indispensable to reproduce the dynamic properties of the cadmium(II) aqueous solution. Quantum mechanical ab initio calculations of the hexa- and heptahydrated complexes extracted from MD configurations have revealed stable minima for both clusters with the water molecules arranged in T(h)() and C(2) symmetries in the hexa- and heptahydrated complexes, respectively, with a slight energetic preference for the heptahydrated one. Finally, a comparison of the calculated hexa- and heptahydrated cluster IR and Raman spectra with the experimental data in the literature, has demonstrated that the IR spectroscopy is not able to distinguish between the two species, whereas the Raman spectrum of the Cd(2+)-(H(2)O)(7) cluster provides a better agreement with the experimental data.

Journal Article↗

PubMed2005

A first-principle study of the adsorption of 1-amino-3-cyclopentene on the (100) silicon surface.

The adsorption of 1-amino-3-cyclopentene on the (100) silicon surface has been studied by methods rooted in the density-functional theory using both delocalized (plane waves, PWs) and localized (Gaussian-type orbitals, GTOs) basis functions. The results obtained by modeling the surface by silicon clusters of different sizes are quite similar, thus confirming that the reaction is quite localized. Furthermore, PW and GTO computations give comparable results, provided that the same density functional and carefully chosen computational parameters (contraction of GTO, pseudopotentials, etc.) are used. Slab computations performed in the PW framework show that the cluster results are retrieved when low-coverage adsorption on the surface is considered. On these grounds, we are quite confident that reaction parameters obtained by the more reliable hybrid density functional (PBE0) are essentially converged, our best estimates of reaction and activation free energies are thus -40 and 6 kcal/mol, respectively.

Journal Article↗

PubMed2005

A mean field approach for molecular simulations of fluid systems.

In this paper we introduce a mean field method for simulating complex molecular systems like liquids and solutions. Using well-established theoretical principles and models, we obtained a relatively simple approach which seems to provide a reliable description of the bulk molecular behavior of liquid water. Moreover, we have applied this approach to study simple solutes in solution, like sodium and chloride ions and acetone. Comparison with standard simulations, performed with periodic boundary conditions, shows that such a mean field method can reproduce the same structural and thermodynamical properties at low computational costs and represents a valid alternative for simulating solute-solvent systems, like solutions of large biomolecules.

Journal Article↗

PubMed2005

Oxidative chemistry of 2-nitro and 4-nitroestradiol: Dichotomous behavior of radical intermediates and novel potential routes for oxyfunctionalization and B-ring fission of steroidal scaffolds.

Oxidation of 4-nitro-17beta-estradiol (1) with the peroxidase/H(2)O(2) system gave the symmetric C(2)-linked dimer (3) through phenoxy radical coupling. Similar oxidation of 2-nitro-17beta-estradiol (2), in which the nitro group is coplanar with the aromatic ring, yielded 9alpha- and 9beta-hydroxy-2-nitro-17beta-estradiol (4a,b), (17beta)-2-nitroestra-1(10),2,4,9(11)-tetraene-3,17-diol (5), and (12alpha,17beta)-2-nitroestra-1(10),2,4,9(11)-tetraene-3,12,17-triol (6). With higher concentrations of H(2)O(2), the novel secoestra-1(10),2,4-trien-9-one derivative 7 was obtained from 2. Theoretical calculations suggested that the peculiar behavior of 2 may be due to the generation of a relatively stable radical intermediate at C(9), which would then be converted to the reactive quinone methide 8. The chemistry described in this paper appears to be an intriguing example of control of the site of substitution over evolution of phenoxy radicals, and opens new vistas toward selective oxyfunctionalization of the estrane skeleton.

Estradiol↗