The structure of cis-5-hydroperoxy-6-hydroxy-5,6-dihydrothymine was obtained using X-ray crystallography [space group P21n (Z = 4) with a = 11.428(2) Å, b = 6.284(1) Å, c = 11.882(2) Å and β = 110.56(3) °]. Electronic properties of the thymine hydroxyhydroperoxide were determined, both in the solid state form and in the free molecule form, using LSD-DFT theory calculations. Only slight differences between the crystal structure and the optimized geometry are observed. On the other hand, the two structures exhibit significant differences in their electronic properties. In particular, the dipole moment of the crystal structure is larger than that of the theoretical geometry. This is probably due to the occurrence of hydrogen bonds in the crystal. A large hydrogen bond network, as well as unusual coulombic interactions between the different molecules in the crystal, are responsible for the molecular packing. These observations lead to a better understanding of the structural changes that occur during the hydroxyl radical-mediated decomposition of thymine.

A recently developed quantum mechanical approach devoted to the study of unstable species in solution was applied to isomeric radicals resulting from the addition of hydrogen atoms to thymine. The computational protocol includes either post-Hartree-Fock or density functional electronic computations, together with simulation of the solvent by a polarizable continuum, and averaging of spectroscopic properties over thr most important vibrational motions. Concerning electronic computations, hybrid Hartree-Fock/density functional models (here B3LYP) provide reliable results both for structural and spectroscopic parameters. In contrast. pure Hartree-Fock or low-order perturbative many-body approaches (here MP2) stand against considerable difficulties in the treatment of open-shell systems. Starting from B3LYP computations, vibrational averaging by the out of plane motions and, to a lower extent, consideration of solvent effects lend to remarkable agreement between the computed hyperfine coupling constants and experimental data.

Extensive post-Hartree–Fock calculations are reported for the geometrical structures and hyperfine parameters of cyclopropyl and bicyclobutyl radicals. Computations for the parent molecules, whose structures are experimentally well characterized, show that reliable geometrical parameters are obtained, especially for bicyclobutane, only when using sufficiently flexible basis sets including f functions on carbon. Isotropic hyperfine splittings obtained by purposely tailored basis sets, proper treatment of correlation, and inclusion of vibrational averaging effects are in remarkable agreement with experiment. Our results suggest a revision of the accepted assignment for bicyclobtyl radical and suggest that long-range couplings are not governed by the well-known W rule but rather by a syn rule.

A comparative post-Hartree–Fock study has been performed on cyclopropyl and oxiranyl radicals in order to ascertain the role of the oxygen atom in modifying the hyperfine structure and height of the barrier governing inversion at the radical center. The structural parameters and harmonic force fields obtained for the parent molecules using second-order many-body perturbation theory with a large basis set are in good agreement with experiment. The same approach points out significant distortions upon breaking of a CH bond and a larger pyramidality for the radical center in oxiranyl with respect to cyclopropyl. Also inversion barriers of both radicals are in remarkable agreement with experimental estimates. Isotropic hyperfine parameters in good agreement with those obtained from electron spin resonance spectra can be computed only when using purposely tailored basis sets in the framework of a coupled cluster approach and taking into account vibrational averaging effects induced by the inversion motion. Interpretation of the results in terms of direct and spin polarization effects points out a number of general trends for germinal and vicinal atoms. Furthermore, it is well evidenced that replacement of a methylenic group by an oxygen atom modifies the hyperfine parameters through geometric rather than direct electronic effects.

Hyperfine coupling constants provide a direct experimental measure of the distribution of unpaired spin density in paramagnetic molecules and can serve as a critical benchmark for electronic wave functions [1,2]. Conversely, given an accurate theoretical model, one can obtain considerable information on the equilibrium structure of a free radical from the computed hyperfine coupling constants and from their dependence on temperature. In this scenario, proper account of vibrational modulation effects is not less important than the use of a high quality electronic wave function.

The exchange coupling of Ullman's nitroxide biradicals, bis[2,2'-(1-oxy-3-oxido-4,4,5,5-tetramethyldihydro-1H-imidazolyl)] (1) and bis[2,2'-(1-oxy-4,4,5,5-tetramethyldihydro-1H-imidazolyl)] (2), has been determined by performing ab initio calculations followed by a specific configuration interaction on model compounds where the methyl groups have been substituted by hydrogen atoms, C1 and C2, respectively. The analysis of the dependence of the coupling on the conformation angle between each nitroxide moiety shows that even in the perpendicular structure the singlet state is found below the triplet. The calculated singlet-triplet gaps for the experimental value of the twist angle, -364 cm(-1) for C1 and -175 cm(-1) for C2, are in very good agreement with recent experimental results for 1 and 2.

A general quantum mechanical protocol for the study of flexible open-shell systems has been applied to a simple model of the glycine radical engaged in peptide chains. The conformational freedom of the resulting dipeptide; analogue is severely restricted with respect to that of standard amino acid residues. Only planar or quasi-planar conformations are energetically accessible due to pi-electron delocalization on the whole compound. As a consequence, the structural parameters and the vibrational frequencies involving the C-alpha atom are typical of ethylenic systems. The hyperfine coupling constants of the (CH)-H-alpha moiety remain, however, similar to those of the prototype methyl radical and show the same strong dependence on out-of-plane deformations. The hyperfine coupling constants of the NH moiety are, instead, only dependent on the backbone conformation. Vibrationally averaged hyperfine coupling constants both of (CH)-H-alpha and NH moieties are in fair agreement with experimental values of glycine radicals produced in some proteins.

Extensive post Hartree-Fock calculations are reported for the geometrical structure and hyperfine parameters of the carbon-centered glycine radical in its zwitterionic form. Vibrational averaging effects connected to inversion at the radical center are significant for Cα and Hα atoms. The good agreement between computed and experimental hyperfine splittings confirms the nature of one of the radicals obtained from irradiation of glycine crystals. On the other hand, the ESR spectrum obtained in aqueous solution cannot be due to the zwitterionic form.

The structure, conformational behavior, and ESR features of the glycine radical have been investigated by an established quantum-mechanical protocol with the aim of better elucidating the role of intrinsic and environmental effects in determining the physicochemical properties of amino acid radicals involved in biological systems. From a structural point of view, extraction of a hydrogen atom from glycine modifies only the local environment of the C(alpha)atom. The conformational freedom of the radical is, however, severely restricted with respect to its closed-shell parent. In particular, only planar or nearly planar structures are energetically accessible. These are characterized by very similar hyperfine splittings, which ate in agreement with experiment for C-alpha and N, but are significantly too large for H-alpha. Although the average value of H(N) splittings is not far from the experimental value, the two protons are strongly not equivalent. The computed torsional barrier around the N-C-alpha bond is too high to allow an effective rotational averaging and also inversion of the NH2 moiety, which is governed by a low-energy barrier (approximate to 3 kJ/mol), cannot restore agreement with experiment. Inclusion of solvent-induced structural modifications significantly improves matters for H-alpha, whereas the equivalence of H(N) atoms in acidic solution can be explained in terms of a mixture between the neutral species and a nonclassical cationic form.

A quantum mechanical protocol for the study of flexible open-shell systems has been applied in a reinvestigation of the isotropic hyperfine coupling constants of the bicyclobutyl radical. Our computations indicate that the most stable structure of the radical corresponds to the exo-form and is characterized by a strongly pyramidal radical center. The hyperfine coupling constants computed for this form are in good agreement with experiment, but indicate that the accepted assignment of H α and H γ endo protons should be reversed. The energy difference between the exo and endo form is sufficiently large to avoid thermal averaging of observables at reasonable temperatures. Vibrational averaging effects in the potential well corresponding to the exo minimum are significant for the C α atom, but do not alter results for H atoms. A striking outcome of this study is the demonstration that stereo-electronic can lead to the counterintuitive results that long range couplings are larger than α ones.

Ab initio calculations at various levels of theory (HF/6-31G*//6-31G* up to MP4SDTQ/6-31G*//MP2(full)/6-31G*) were used to compute the total energies of alpha- and beta-propyl radicals and their parent molecules. Isodesmic/homodesmic reactions have been studied for the purpose of obtaining theoretical enthalpies of formation of these compounds. Tle choice of the theoretical model as well as the choice of the isodesmic reaction has been discussed. These data were used to calculate the thermodynamic stabilization energies of these species according to Leroys definition, in order to examine the influence of alpha and beta substitution on their stability. Homolytic bond dissociation energies (BDEs) were also deduced; it appears that the BDE cannot be used to analyse the substituent effects on the stability of substituted propyl radicals.

The structure and EPR parameters of dihydronitrosyl radical H2NO have been investigated by highly correlated ab-initio methods. The relative stabilities of planar and pyramidal structures have been analyzed in detail, taking also into account the effect of small-amplitude vibrations perpendicular to the inversion motion. Vibrational averaging of hyperfine coupling constants has been computed by a quantum-mechanical treatment based on the vibrational adiabatic zero curvature approximation. The general picture emerging from this study, substantiated by several checks, consists in a quasi-planar molecule with a nearly free inversion motion for out-of-plane angles as large as 30-degrees. Due to compensation of different terms, vibrational averaging gives results very close to those obtained from a static treatment at an out-of-plane angle of about 20-degrees. An equally important outcome of this work is the introduction of a general and reliable ab-initio strategy for the study of magnetic properties in nonrigid radicals.

Ab initio calculations at various levels of theory (HF/6-31G∗//6-31G∗ up to MP4SDTQ/6-31G∗//MP2(full)/6-31G∗) were used to compute the total energies of α- and β-propyl radicals and their parent molecules. Isodesmic/ homodesmic reactions have been studied for the purpose of obtaining theoretical enthalpies of formation of these compounds. The choice of the theoretical model as well as the choice of the isodesmic reaction has been discussed. These data were used to calculate the thennodynamic stabilization energies of these species according to Leroys definition, in order to examine the influence of α and β substitution on their stability. Homolytic bond dissociation energies (BDEs) were also deduced; it appears that the BDE cannot be used to analyse the substituent effects on the stability of substituted propyl radicals.

A complete ab initio optimization of the unsubstituted nitronyl and iminonitroxides was performed at the UHF-SCF level, using a 6-311G** basis set, followed by a gradient optimization of the NO bond at the MP2 level. Experimental structural and spectroscopic findings are well reproduced by the calculations. A precise attribution of the couplings of the two inequivalent nitrogens in the iminonitroxide has been achieved, underlining the need for highly correlated wave functions in order to obtain accurate results.

A general quantum-mechanical protocol recently introduced for the theoretical study of non-rigid radicals has been used in the investigation of the structure, inversion rate, and EPR spectrum of the cyclopropyl radical. The results are in close agreement with experiment and can be interpreted in terms of the interplay between the variation of the potential energy and the different properties along the inversion coordinate.

A general quantum-mechanical protocol for the study of nonrigid free radicals has been applied to the series CH3, CH2F, CHF2, and CF3. Electronic structures have been computed by highly correlated ab initio methods and vibrational modulation effects have been studied by a nonrigid invertor Hamiltonian. The effect of small amplitude vibrations perpendicular to the inversion motion has been taken into account by an adiabatic model. The results are in close agreement with experiment, and can be interpreted quite straightforwardly in terms of the interplay between the potential energy and the property hypersurfaces. This allows a more dynamically based analysis of hyperfine coupling constants extensible to large, nonrigid radicals.

A complete ab initio optimization of the simplest nitronyl and imino nitroxides was performed at the UHF-SCF level, using a 3-21G basis set. The molecular electrostatic potential maps were drawn and correctly predict the coordinating ability of oxygen and nitrogen in both radicals. The largest fraction of the unpaired electron is always found on the oxygens, but the imino nitrogen bears a noticeable part of the spin population in agreement with experimental findings. All the trends of experimental EPR spectra are well reproduced by the calculated spin-projected densities at nuclei, the imino nitrogen being found to have the largest coupling constant at the SCF level.

EHT calculations on nickel(111) and nickel aluminium two-layer clusters show that an electron transfer takes place from Al to Ni 3d orbitals. Interaction of Ni11-xAlx and Ni10-xAlx with ethylene and formaldehyde, respectively, has been analyzed in terms of fragments, showing that both Π and Π* orbitals of ethylene interact with the cluster d band, while only the Π* orbital of H2CO significantly interacts with the cluster. Residual aluminium in the nickel catalyst destabilizes the four-electron interaction between solid and ethylene, so the chemisorption step becomes less favourable.

AbstractThe adducts (I)‐(IV) of rhodium trifluoroacetate dimer with nitroxyl free radicals are prepared (yields 87, 69, 47, 58%) and their structural and magnetic properties studied.