A quantum-mechanical study of the reaction mechanism of sulfite oxidase.

The oxidation of sulfite to sulfate by two different models of the active site of sulfite oxidase has been studied. Both protonated and deprotonated substrates were tested. Geometries were optimized with density functional theory (TPSS/def2-SV(P)) and energies were calculated either with hybrid functionals and large basis sets (B3LYP/def2-TZVPD) including corrections for dispersion, solvation, and entropy, or with coupled-cluster theory (LCCSD(T0)) extrapolated toward a complete basis set. Three suggested reaction mechanisms have been compared and the results show that the lowest barriers are obtained for a mechanism where the substrate attacks a Mo-bound oxo ligand, directly forming a Mo-bound sulfate complex, which then dissociates into the products. Such a mechanism is more favorable than mechanisms involving a Mo-sulfite complex with the substrate coordinating either by the S or O atom. The activation energy is dominated by the Coulomb repulsion between the Mo complex and the substrate, which both have a negative charge of -1 or -2.

Application of the topological analysis of the electronic localization function to archetypical [Pb(II)Ln]p complexes: the bonding of Pb2+ revisited.

The coordination of neutral ligands (L = OC, HCN, NH3, PH3, SH2, HNCO and H2O) to Pb2+ is investigated and analyzed by means of the topological analysis of the Electronic Localization Function (ELF). It is shown that the mean charge density of the V(Pb) basin ((V(Pb))) can reach a ligand-independent limiting value from n = 6, a coordination number from which the [PbL(n)]2+ complexes adopt holodirected structures. The investigations performed on anionic series (L = HS-, OH-, CN-, F-, Cl-, and Br-) lead to optimized stable structures in which the coordination number does not exceed n = 4, even in the presence of a model aqueous solvent. This different behavior with respect to the neutral ligand series is interpreted by means of natural populations and electrostatic repulsions. The main result of this contribution is that stable Pb(II) complexes could be those exhibiting reasonable values of (V(Pb)), namely those not exceeding the saturation plateau evidenced in the present piece of work.

QM/MM study of the reaction mechanism of sulfite oxidase.

Sulfite oxidase is a mononuclear molybdenum enzyme that oxidises sulfite to sulfate in many organisms, including man. Three different reaction mechanisms have been suggested, based on experimental and computational studies. Here, we study all three with combined quantum mechanical (QM) and molecular mechanical (QM/MM) methods, including calculations with large basis sets, very large QM regions (803 atoms) and QM/MM free-energy perturbations. Our results show that the enzyme is set up to follow a mechanism in which the sulfur atom of the sulfite substrate reacts directly with the equatorial oxo ligand of the Mo ion, forming a Mo-bound sulfate product, which dissociates in the second step. The first step is rate limiting, with a barrier of 39-49 kJ/mol. The low barrier is obtained by an intricate hydrogen-bond network around the substrate, which is preserved during the reaction. This network favours the deprotonated substrate and disfavours the other two reaction mechanisms. We have studied the reaction with both an oxidised and a reduced form of the molybdopterin ligand and quantum-refinement calculations indicate that it is in the normal reduced tetrahydro form in this protein.

Straightforward synthesis of (S)- and (R)-alpha-trifluoromethyl proline from chiral oxazolidines derived from ethyl trifluoropyruvate.

[Structure: see text] A concise synthesis of both enantiomers of alpha-Tfm-proline and (S)-alpha-Tfm-prolinol from ethyl trifluoropyruvate is reported. The key step is a diastereoselective allylation reaction of ethyl trifluoropyruvate and (R)-phenylglycinol-based oxazolidines or imine. The lactone obtained by cyclization of the resulting hydroxy ester proved to be a valuable intermediate for the synthesis of (S)-alpha-Tfm-allylglycine and (S)-alpha-Tfm-norvaline in enantiopure form.

Understanding the Chemistry of Lead at a Molecular Level: The Pb(II) 6s6p Lone Pair Can Be Bisdirected in Proteins.

Pb(2+) complexes can attain several different topologies, depending of the shape of the Pb 6s6p lone pair. In this paper, we study structures with a bisdirected Pb lone pair with quantum mechanics (DFT) and QM/MM calculations. We study small symmetric Pb(2+) models to see what factors are needed to get a bisdirected lone pair. Two important mechanisms have been found: First, the repulsion of the lone pair of Pb(2+) with other lone pairs in the equatorial plane leads to a bisdirected structure. Second, a bisdirected lone pair can also arise due to interactions with double bonds, lone pairs, or hydrogen atoms. Moreover, we have analyzed Pb(2+) sites in proteins and to see if a bisdirected lone pair can exist in an asymmetrical environment. Several instances of bisdirected lone pairs were discovered.

Role of Cation Polarization in holo- and hemi-Directed [Pb(H2O)n](2+) Complexes and Development of a Pb(2+) Polarizable Force Field.

Reduced Variational Space (RVS) calculations are reported that afford insight into the energetic origins of the hemi- and holo-directing behavior of [Pb(H2O)n](2+) complexes. It is shown that the distribution of ligands around the Pb(2+) center arises from a delicate balance between the first-order Coulomb plus exchange-repulsion energy that favors holo-directionality, and the second-order charge transfer plus polarization term that favors hemi-directionality. It is additionally demonstrated that the pseudopotential/basis set combination used to study such complexes should be carefully selected, as artifacts can arise when using large-core pseudopotentials. Finally, based on these findings, we introduce a new SIBFA force field parametrization for Pb(2+). Results yield close agreement with ab initio complexation energies in a series of [Pb(H2O)n](2+) complexes and successfully encapsulate the hemi- and holo-directing properties. SIBFA thus appears to be the first classical force field to be able to model the holo-/hemi-directed transition within Pb complexes, avoiding the need for explicit wave function treatment and consequently providing the opportunity to deal with large leaded systems of biological interest.