Publications (32) View all
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Article: Effects of molecular dynamics and solvation on the electronic structure of molecular probes
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ABSTRACT: Most spectroscopic parameters are influenced by nuclear dynamics and by the chemical environment. However, proper inclusion of these effects still represents a challenge in computational spectroscopy studies. In many cases, a route coupling satisfactory accuracy with reason- able computational costs consists in the integration of DFT-based methods to compute spectroscopic parameters, with ab initio molecular dynamics simulations to sample from the classical phase space of the system. Here, we discuss the application of this approach in two case studies of remarkable practical interest, namely the simulation of the absorption spectrum of 9-methyladenine, an adenine nucleoside model; and the prediction of electron spin res- onance parameters for nitroxyl radicals, the prototypical spin probes. In both cases, the accuracy of the results increases significantly when the subtle interplay of intra- molecular dynamics and solvent effects is introduced.Theoretical Chemistry Accounts 04/2012; 131:1211. · 2.16 Impact Factor -
Article: An integrated computational protocol for the accurate prediction of EPR and PNMR parameters of aminoxyl radicals in solution.
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ABSTRACT: Magnetic spectroscopic techniques such as electron paramagnetic resonance (EPR) and paramagnetic NMR (PNMR) are valuable tools for understanding the structure and dynamics of complex systems such as, for example, biomolecules or nanomaterials labeled with suitable free radicals. Unfortunately, such spectra do not give direct access to the radical structure because of the subtle interplay between several different effects not easily separable and evaluable by experimentalists alone. In this respect, computational spectroscopy is becoming an essential and versatile tool for the assignment and interpretation of experimental spectra. In this article, the new integrated computational approaches developed in the recent years in our research group are reviewed. Such approaches have been applied to two widely used spin probes showing that proper account of stereo-electronic, environmental and dynamical effects leads to magnetic properties in remarkable agreement with experimental results.Magnetic Resonance in Chemistry 12/2010; 48 Suppl 1:S11-22. · 1.44 Impact Factor -
Article: Extension of the AMBER force-field for the study of large nitroxides in condensed phases: an ab initio parameterization.
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ABSTRACT: The popular AMBER force-field has been extended to provide an accurate description of large and flexible nitroxide free-radicals in condensed phases. New atom types have been included, and relevant parameters have been fitted based on geometries, vibrational frequencies and potential energy surfaces computed at the DFT level for several different classes of nitroxides, both in vacuo and in different solvents. The resulting computational tool is capable of providing reliable structures, vibrational frequencies, relative energies and spectroscopic observables for large and flexible nitroxide systems, including those typically used as spin labels. The modified force field has been employed in the context of an integrated approach, based on classical molecular dynamics and discrete-continuum solvent models, for the investigation of environmental and short-time dynamic effects on the hyperfine and gyromagnetic tensors of PROXYL, TEMPO and INDCO spin probes. The computed magnetic parameters are in very good agreement with the available experimental values, and the procedure allows for an unbiased evaluation of the role of different effects in tuning the overall EPR observables.Physical Chemistry Chemical Physics 10/2010; 12(37):11697-709. · 3.57 Impact Factor -
Article: Double C-H activation of ethane by metal-free SO2*+ radical cations.
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ABSTRACT: The room-temperature C-H activation of ethane by metal-free SO(2)(*+) radical cations has been investigated under different pressure regimes by mass spectrometric techniques. The major reaction channel is the conversion of ethane to ethylene accompanied by the formation of H(2)SO(2)(*+), the radical cation of sulfoxylic acid. The mechanism of the double C-H activation, in the absence of the single activation product HSO(2)(+), is elucidated by kinetic studies and quantum chemical calculations. Under near single-collision conditions the reaction occurs with rate constant k=1.0 x 10(-9) (+/-30%) cm(3) s(-1) molecule(-1), efficiency=90%, kinetic isotope effect k(H)/k(D)=1.1, and partial H/D scrambling. The theoretical analysis shows that the interaction of SO(2)(*+) with ethane through an oxygen atom directly leads to the C-H activation intermediate. The interaction through sulfur leads to an encounter complex that rapidly converts to the same intermediate. The double C-H activation occurs by a reaction path that lies below the reactants and involves intermediates separated by very low energy barriers, which include a complex of the ethyl cation suitable to undergo H/D scrambling. Key issues in the observed reactivity are electron-transfer processes, in which a crucial role is played by geometrical constraints. The work shows how mechanistic details disclosed by the reactions of metal-free electrophiles may contribute to the current understanding of the C-H activation of ethane.Chemistry 06/2010; 16(21):6234-42. · 5.93 Impact Factor -
Article: Interplay of stereo-electronic, environmental, and dynamical effects in determining the EPR parameters of aromatic spin-probes: INDCO as a test case.
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ABSTRACT: An integrated computational strategy for the evaluation of reliable structures and magnetic properties of spin probes and spin labels has been extended to aromatic species. From an electronic point of view, delocalization of the unpaired electron density over aromatic moieties reduces significantly the computed nitrogen isotropic hyperfine coupling constant (A(N)) with respect to values characteristic of aliphatic nitroxides. Solvent effects in not too high polarity media are quite small, but not negligible. At this stage computed A(N) are lower than their experimental counterparts by more than 1 G. Inclusion of vibrational averaging effects by molecular dynamics simulations with a new reliable force field restores full agreement with experiment pointing out the limits of static approaches irrespective of the sophistication of the electronic quantum mechanical method. The generality and computational effectiveness of the proposed integrated approach paves the route toward a reliable analysis of the interplay of stereo-electronic, environmental, and dynamical effects in tuning the properties of large flexible magnetic systems of biological and technological interest.Physical Chemistry Chemical Physics 04/2010; 12(15):3741-6. · 3.57 Impact Factor
