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Odorant receptors (ORs) are the largest subfamily within class A G protein-coupled receptors (GPCRs). No experimental structural data of any OR is available to date and atomic-level insights are likely to be obtained by means of molecular modeling. In this article, we critically align sequences of ORs with those GPCRs for which a structure is available. Here, an alignment consistent with available site-directed mutagenesis data on various ORs is proposed. Using this alignment, the choice of the template is deemed rather minor for identifying residues that constitute the wall of the binding cavity or those involved in G protein recognition.

Oxygen transfer reactions mediated by transition metals, such as olefin epoxidation [1] and dihydroxylation, [2] are currently attracting much interest from both experimentalists and theoreticians. Many investigations, several of them of computational thrust, have unraveled details of olefin dihydroxylation as catalyzed by oxo complexes of the type MO 4

Quercetin, one of the most representative flavonoid compounds, is involved in antiradical, antioxidant, and prooxidant biological processes. Despite a constant increase of knowledge on both positive and negative activities of quercetin, it is unclear which activated form (quinone, semiquinone, or deprotonated) actually plays a role in each of these processes. Structural, electronic, and energetic characteristics of quercetin, as well as the influence of a copper ion on all of these parameters, are studied by means of quantum chemical electronic structure calculations. Introduction of thermodynamic cycles together with the role of coreactive compounds, such as reactive oxygen species, gives a glimpse of the most probable reaction schemes. Such a theoretical approach provides another hint to clarify which reaction is likely to occur within the broad range of quercetin biological activities.

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The hydrolysis by thermolysin of formamide, considered as a model of a peptide bond, has been studied with semiempirical and mixed QM/MM methods. The study has been carried out for two catalystsa molecular complex of a Zn2+ ion with two imidazole molecules and a formate ion, modeling the active site of the enzyme, and the whole enzymeand for two mechanisms involving one and two water molecules. In every case, the first step of the reaction is a nucleophilic attack of the carbon atom by the oxygen of a water molecule or a water dimer. The mechanism involving an ancillary water molecule (water-assisted process) is always favored compared to the process in which a single water molecule reacts. The fact is explained by a better nucleophilicity of the oxygen atom in the water dimer and a less constrained transition state. The zinc atom of the catalytic center acts as a Lewis acid and the ligands as an electron reservoir. The slight differences between the reactions catalyzed by the model complex and by the whole enzyme are explained on the basis of small geometry distortions induced by the amino acids residues surrounding the active center.

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