Quantum mechanical models of the resting state of the vanadium-dependent haloperoxidase

Density functional theory has been used to investigate structural and electronic properties of complexes related to the resting form of the active site of vanadium haloperoxidase as a function of environment and protonation state. Results obtained by studying models of varying size and complexity highlight the influence of environment and protonation state on the structure and stability of the metal cofactor. The study shows that, in the trigonal bipyramidal active site, where one axial position is occupied by a key histidine, the trans position cannot contain a terminal oxo group. Further, a highly negatively charged vanadate unit is not stable. Protonation of at least one equatorial oxo ligand appears necessary to stabilize the metal cofactor. The study also indicates that, while at rest within the protein, the vanadate unit is most likely an anion with an axial hydroxide and an equatorial plane containing two oxos and a hydroxide. For the neutral, protonated state of the vanadate unit, there were two minima found. The first structure is characterized by an axial water with two oxo and one hydroxo group in the equatorial plane. The second structure contains an axial hydroxo group and an equatorial plane composed of one oxo and two hydroxo oxygen atoms. These two species are not significantly different in energy, indicating that either form may be important during the catalytic cycle. These data support the initial crystallographic assignment of an axially bound hydroxide, but an axial water is also a possibility. This study also shows that the protonation state of the vanadate ion is most likely greater than previously proposed.     

Direct minimization of the energy functional in the LCAO-MO density matrix formalism

A previously proposed method of energy minimization is developed for MC SCF wavefunctions formed by all-pair excitations for a closed-shell system. The orbital coefficients are optimized by a gradient approach using a suitable orthogonal transformation of the atomic basis, while optimum CI coefficients are determined solving the usual secular problem for the lowest eigenvalue, after each optimization of the orbitals. Applications to LiH and NH₃ molecules show that the method is numerically well stable, and is capable of accounting for a large part of the correlation energy giving results which compare well with those of the conventional CI method.     

Thermoanalytical and spectroscopic characterization ofβ-cyclodextrin/ketoprofen inclusion complexes

A method to determine the composition and hydration state of the complexes formed in aqueous solution by cyclodextrins (CD) is presented and applied to the -CD/ketoprofen system; it is based on a combination of spectroscopic, calorimetric, and thermogravimetric analyses. The complexes have, on average and per -CD mole, more than eleven water molecules, which are present in completely different bound states.     

Synthesis of magnetic gradients for NMR tomography

A numerical method is applied to calculate an optimal distribution of currents in air which generate the magnetic field gradients required to spatially encode the radiofrequency signal in a NMR tomographic experiment. We compare the performances of the gradient circuits for the whole body air-core electromagnet described by Bangert and Mansfield (J. Phys. E 15; 1982) with the results of our optimization.     

Probing the effects of one-electron reduction and protonation on the electronic properties of the Fe-S clusters in the active-ready form of [FeFe]-hydrogenases. A QM/MM investigation

A QM/MM investigation of the active-ready (H(ox)) form of [FeFe]-hydrogenase from D. desulfuricans, in which the electronic properties of all Fe-S clusters (H, F and F') have been simultaneously described using DFT, was carried out with the aim of disclosing a possible interplay between the H-cluster and the accessory iron-sulfur clusters in the initial steps of the catalytic process leading to H(2) formation. It turned out that one-electron addition to the active-ready form leads to reduction of the F'-cluster and not of the H-cluster. Protonation of the H-cluster in H(ox) is unlikely, and in any case it would not trigger electron transfer from the accessory Fe(4)S(4) clusters to the active site. Instead, one-electron reduction and protonation of the active-ready form trigger electron transfer within the protein, a key event in the catalytic cycle. In particular, protonation of the H-cluster after one-electron reduction of the enzyme lowers the energy of the lowest unoccupied molecular orbitals localized on the H-cluster to such an extent that a long-range electron transfer from the F'-cluster towards the H-cluster itself is allowed.     

A DFT study of EPR parameters in Cu(II) complexes of the octarepeat region of the prion protein

The present paper shows how theoretically determined electron paramagnetic resonance (EPR) parameters can help in assigning the most favorable structure of Cu(ii) complexes in octarepeat (OR) regions (PHGGGWGQ) of the prion protein (PrP). This could contribute to a better understanding of the molecular structure of the Cu(OR) complexes, as some features of such species in solution are still unclear. The present theoretical investigation on [Cu(ii)(HGGG)] and [Cu(ii)(HGGGW)] complexes was carried out to confirm the stability of relevant isomers, and in particular, to evaluate the hyperfine coupling constants (hcc) with (63)Cu, (14)N and (17)O nuclei, as well as the g values. The hcc (and to a lesser extent the g components) are useful probes for checking whether the computed EPR parameters for specific isomers fit the experimental data, thus permitting the association of the observed spectra with a specific complex structure. The results obtained suggest that the Cu(ii) ion in the [Cu(HGGG)] isomers prefers a square pyramidal coordination with three nitrogen atoms of the peptide and one carbonyl oxygen atom in the basal plane. Also the Cu(ii) ion in the [Cu(HGGGW)] complex is penta-coordinated. The penta-coordination does not actually involve the tryptophan residue but an additional water molecule, forced to occupy the axial coordination position by a rather extended hydrogen-bond network, promoted by the tryptophan residue.The comparison between the calculated and experimental values of EPR parameters allows one to suggest the assignment of the coordination mode of the Cu(ii) ion in the considered peptide ligands. The computed values of the g components seem to be little affected by a particular coordination mode. In particular, the g( parallel) component is always underestimated by about 0.1 with respect to the experiment. The calculated values of the hcc, in contrast, are in acceptable agreement with the experimental values, in spite of the fact that the large size of the species under consideration forced us to accept a certain level of approximation in the computational procedure. Nevertheless, the present study must be considered as one of the first examples of truly ab initio calculations of EPR parameters for systems as large as the Cu(OR)-type complexes.     

Cation distribution in LiMgVO4 and LiZnVO4: structural and spectroscopic study

The room temperature cation occupancy in LiMgVO(4) and LiZnVO(4) crystallographic sites is obtained by means of the combined use of X-ray powder diffraction (XRPD), (7)Li and (51)V magic angle spinning nuclear magnetic resonance (MAS NMR), and micro-Raman measurements. In the LiMgVO(4) Cmcm orthorhombic structure, the 4c (C(2)(v) symmetry) tetrahedral vanadium site is fully ordered; on the contrary, the Li 4c tetrahedral site and the 4b (C(2)(h) symmetry) Mg octahedral site display about 22% of reciprocal cationic exchange. Higher cationic disorder is observed in LiZnVO(4): the three cations can distribute on the three tetrahedral and distinct sites of the R-3 structure. XRPD and MAS NMR analysis results highly agree for what concerns vanadium ion distribution on the three cationic sites (about 25, 26, and 47%). From the full profile fitting of XRPD patterns with the Rietveld method, it is also obtained that Li(+) displays a slightly preferred occupation of the T1 position (approximately 55%) and Zn(2+) of the T2 position (approximately 46%). The vibrational spectra of the two compounds are characterized by different peak positions and broadening of the Raman modes, reflecting the cation distribution and the local vibrational unit distortion. A comparison is also made with recent Raman results on Li(3)VO(4). High temperature XRPD measurements rule out possible structural transitions up to 673 K for both compounds.     

Insight into the catalytic mechanism of vanadium haloperoxidases. DFT investigation of vanadium cofactor reactivity

Density functional theory (DFT) has been used to investigate the catalytic properties of the isolated vanadium cofactor found in vanadium haloperoxidases, with a particular emphasis on the steps going from the resting form of the cofactor to the peroxo complex. Computation of transition states, intermediate species, and UV-vis spectra, as well as comparison of reaction energies, demonstrated the important role of protonation in cofactor activation. This illustrates that the resting form of the vanadium cofactor reacts with hydrogen peroxide according to a mechanism that implies formation of an aqua complex, release of the apical water molecule according to a dissociative pathway, and binding of hydrogen peroxide to vanadium. This process leads to a side-on peroxo species corresponding to the peroxo form observed in the enzyme. In addition, it appears that an acid-base catalysts strongly accelerates the conversion to the side-on peroxo form. The comparison of computed and experimental UV-vis spectra corroborated the proposed reaction pathway and allowed us to explain the effects of the vanadium ligands on the electronic properties of the cofactor.