In this paper, a new dual descriptor for nucleophilicity and electrophilicity is introduced. The new index is defined in terms of the variation of hardness with respect to the external potential, and it is written as the difference between nucleophilic and electrophilic Fukui functions, thus being able to characterize both reactive behaviors. It is shown that the new descriptor correctly predicts the site reactivity induced by different donor and acceptor groups in substituted phenyl molecules. Also, the Dunitz-Burgi attack on ketones and aldehydes has been revisited to illustrate the stereoselective capability of this new index. Finally, its predictive ability has been tested successfully on different series of conjugated and nonconjugated carbonyl compounds.

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The Woodward-Hoffmann rules for pericyclic reactions are explained entirely in terms of directly observable physical properties of molecules (specifically changes in electron density) without any recourse to model-dependent concepts, such as orbitals and aromaticity. This results in a fundamental explanation of how the physics of molecular interactions gives rise to the chemistry of pericyclic reactions. This construction removes one of the key outstanding problems in the qualitative density-functional theory of chemical reactivity (the so-called conceptual DFT). One innovation in this paper is that the link between molecular-orbital theory and conceptual DFT is treated very explicitly, revealing how molecular-orbital theory can be used to provide "back-of-the-envelope" approximations to the reactivity indicators of conceptual DFT.

The second-order response of the electron density with respect to changes in electron number, known as the dual descriptor, has been established as a key reactivity indicator for reactions like pericyclic reactions, where reagents accept and donate electrons concurrently. Here we establish that the dual descriptor is also the key reactivity indicator for ambiphilic reagents: reagents that can act either as electrophiles or as nucleophiles, depending on the reaction partner. Specifically, we study dual atoms (which are proposed to act, simultaneously, as an electron acceptor and an electron donor), dual molecules (which react with both electrophiles and nucleophiles, generally at different sites), and dual ion-molecule complexes (which react with both cations and anions). On the basis of our analysis, the dual atom (an Al(I) that has been purported to be dual in the literature) is actually pseudodual in the sense that it does not truly accept electrons from a nucleophiles; rather, it serves as a conduit through which an electrophile can donate electrons to the attached aromatic ring. For understanding dual ion-molecule complexes, it helps to understand that the dual descriptor makes a key contribution to the long-range portion of the quadratic hyperpolarization. In all cases, a complete description of the reactivity of the ambiphilic reagent requires considering both an orbital-based descriptor of electron transfer (the dual descriptor or the local hypersoftness) and the electrostatic potential. The local hypersoftness strongly resembles the dual descriptor.

The reaction of singlet molecular oxygen with purine DNA bases is investigated by computational means. We support the formation of a transient endoperoxide for guanine and by classical molecular dynamics simulations we demonstrate that the formation of this adduct does not affect the B-helicity. We thus identify the guanine endoperoxide as a key intermediate, confirming a low-temperature nuclear magnetic resonance proof of its existence, and we delineate its degradation pathway, tracing back the preferential formation of 8-oxoguanine versus spiro-derivates in B-DNA. Finally, the latter oxidized 8-oxodGuo product exhibits an almost barrierless reaction profile, and hence is found, coherently with experience, to be much more reactive than guanine itself. On the contrary, in agreement with experimental observations, singlet-oxygen reactivity onto adenine is kinetically blocked by a higher energy transition state.

Clustered apurinic/apyrimidinic (AP; abasic) DNA lesions produced by ionizing radiation are by far more cytotoxic than isolated AP lesion entities. The structure and dynamics of a series of seven 23-bp oligonucleotides featuring simple bistranded clustered damage sites, comprising of two AP sites, zero, one, three or five bases 3′ or 5′ apart from each other, were investigated through 400 ns explicit solvent molecular dynamics simulations. They provide representative structures of synthetically engineered multiply damage sites-containing oligonucleotides whose repair was investigated experimentally (Nucl. Acids Res. 2004, 32:5609-5620; Nucl. Acids Res. 2002, 30: 2800–2808). The inspection of extrahelical positioning of the AP sites, bulge and non Watson–Crick hydrogen bonding corroborates the experimental measurements of repair efficiencies by bacterial or human AP endonucleases Nfo and APE1, respectively. This study provides unprecedented knowledge into the structure and dynamics of clustered abasic DNA lesions, notably rationalizing the non-symmetry with respect to 3′ to 5′ position. In addition, it provides strong mechanistic insights and basis for future studies on the effects of clustered DNA damage on the recognition and processing of these lesions by bacterial or human DNA repair enzymes specialized in the processing of such lesions.

In this paper, we introduce new local descriptors in the framework of Conceptual Density Functional Theory. They can be considered as an extension of the dual descriptor [Morell et al., J. Phys. Chem. A, 2005, 109, 205]. These indices are particularly suited for the discrimination between electrophilic and nucleophilic sites inside a molecule. They are computed using the densities of the electronic excited states, giving a picture of the polarization of the electron density induced by the approach of a reactant. Links with the linear-response function are discussed, and the first examples of applications are given, highlighting how these new descriptors can be used in practice for reactivity studies. It has been found that this extension of the dual descriptor can handle tricky cases, such as nitrobenzene or isoquinoline, for which Frontier Molecular Orbital Theory fails.