Paola Cimino

Development and validation of the B3LYP/N07D computational model for structural parameter and magnetic tensors of large free radicals

Extensive calculations on a large set of free radicals containing atoms of the second and third row show that the B3LYP/N07D computational model provides remarkably accurate structural parameters and magnetic tensors at reasonable computational costs. The key of this success is the optimization of core-valence s functions for hyperfine coupling constants, while retaining (and even improving) the good performances of the parent 6-31+G(d,p) basis set for valence properties through reoptimization of polarization and diffuse p functions.

Validation of the B3LYP/N07D and PBE0/N07D Computational Models for the Calculation of Electronic g-Tensors

Calculations on a large set of free radicals containing atoms of the second and third row show that the computational model defined by the new N07D basis set and hybrid density functionals (B3LYP and PBE0) provides remarkably accurate g-tensor values at reasonable computational costs. Since in previous works it has been shown that the same computational model delivers reliable results also for structural parameters and hyperfine couplings, the route seems paved toward full a priori computation of EPR spectra of large free radicals both in vacuo and in condensed phases.

Extension of the AMBER force-field for the study of large nitroxides in condensed phases: an ab initio parameterization.

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.

Structural revision of halipeptins: synthesis of the thiazoline unit and isolation of halipeptin C

Abstract The structural revision of the anti-inflammatory marine metabolites halipeptin A ( 1 ) and B ( 2 ) along with the isolation of the new related product halipeptin C ( 3 ) are reported. In particular, the heterocyclic portion of the molecule, incorrectly assigned as an oxazetidine ring, has now been characterised as a thiazoline unit by comparison of the spectral data of the natural products ( 1–3 ) with an appropriate synthetic model ( 10 ). GIAO calculated 13C NMR chemical shifts for oxazetidine and thiazoline model compounds provide additional support to the revised structure.

An integrated computational protocol for the accurate prediction of EPR and PNMR parameters of aminoxyl radicals in solution.

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. Copyright

CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study

The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC calculations.

Double CH activation of ethane by metal-free SO2.+ radical cations

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.

Radiation-induced formation of DNA intrastrand crosslinks between thymine and adenine bases: a theoretical approach

The role of local geometric and stereo-electronic effects in tuning the radiation-induced formation of intrastrand crosslinks between adenine and thymine has been analyzed by a computational approach rooted in density functional theory. Our study points out that together with steric accessibility, stereo-electronic effects play a major role in determining the reaction mechanism and the observed predominance of the thymine-adenine lesion over the opposite sequence isomer.

Isolation and NMR characterization of rosacelose, a novel sulfated polysaccharide from the sponge Mixylla rosacea.

Rosacelose, a new anti-HIV polysaccharide composed of glucose and fucose sulfate, has been isolated from an aqueous extract of the marine sponge Mixylla rosacea. Extensive use of 1H and 13C multidimensional NMR spectroscopy, combined with chemical analysis were used to establish a linear polysaccharide structure composed mainly of 4,6-disulfated 3-O-glycosylated alpha-D-glucopyranosyl and 2,4-disulfated 3-O-glycosylated alpha-L-fucopyranosyl residues (in a 3:1 molar ratio).

Magnetic Interactions in Phenyl-Bridged Nitroxide Diradicals: Conformational Effects by Multireference and Broken Symmetry DFT Approaches

In the present paper we report the key results of a comprehensive computational study aimed at investigating the dependence of the singlet-triplet energy gap in phenyl-bridged bis-nitroxide diradicals, on the basis set and on soft structural parameters like torsion and pyramidalization. We have compared the BS-DFT technique with the post-Hartree-Fock DDCI2 multireference approach. With this latter method we have also studied the different role that sigma and pi core and virtual orbitals have in the resulting singlet-triplet energy gap.The results obtained represent one step forward in the definition of a protocol for an efficient and reliable computation of spin-spin coupling in diradical systems.