Molecular dynamics study of the active site of methylamine dehydrogenase

We have obtained AMBER94 force-field parameters for the TTQ cofactor of the enzyme methylamine dehydrogenase (MADH). This enzyme catalyzes the oxidation of methylamine to produce formaldehyde and ammonia. In the rate-determining step of the catalyzed reaction, a proton is transferred from the methyl group of the substrate to residue Asp76. We used the new parameters to perform molecular dynamics simulations of MADH in order to characterize the dynamics of the active site prior to the proton-transfer step. We found that only one of the oxygen atoms of Asp76 can act as an acceptor of the proton. The other oxygen interacts with Thr122 via a strong hydrogen bond. In contrast, because of the rotation the methyl group of the substrate, the three methyl hydrogen atoms are alternately in position to be transferred. The distance that the proton has to travel presents a broad distribution with a peak between 1.0 and 1.1 A and reaches values as short as 0.8 A. The fluctuation of the distance between the donor and the acceptor has the largest frequency component at 50 cm(-1), but the spectrum presents a rich structure between 10 and 400 cm(-1). The more important peaks appear below 250 cm(-1).     

Electroanalytical determination of eugenol in clove oil by voltammetry of immobilized microdroplets

Journal of Solid State Electrochemistry - The determination of eugenol employing voltammetry of immobilized microdroplets (VIM) is reported in this work. The construction of the electrode was based...     

An efficient methodology to study cyclodextrin clusters: application to α-CD hydrated monomer, dimer, trimer and tetramer

The hydrated α-cyclodextrin (α-CD) clusters resulting from the following process: nα-CD + n(H₂O)₆ → α-CD_n · 6nH₂O, with n = 1, 2, 3, 4, have been investigated using semiempirical (PM3), ab initio Hartree-Fock and Density Functional Theory (BLYP functional) levels of theory. The largest structure containing 576 atoms and 5,760 contracted basis functions (6-31G(d,p) basis set) poses as a considerable hard task for quantum chemical calculations. As the number of basis function increases rapidly with the cluster size, an alternative procedure to make the calculations feasible is certainly welcome, in order to perform BLYP calculations with an adequate basis set. Through the aid of a computer program that we developed, it became of practical use the selection of atom by atom basis sets, using the common chemical sense, enabling quantum mechanical calculations to be performed for very large molecular interacting systems (inclusion complexes), at an affordable computational cost. In this article we show how an appropriate selection of basis functions, leaving the CH_n groups with a minimal basis set and the oxygen atoms (and OH groups) with a better quality basis set, lower considerably the computational cost with no significant loss in the calculated interaction energies. A regular pattern is observed for α-CD hydrated monomer, dimer, trimer and tetramer, therefore adding support to the use of this procedure when studying larger hydrogen bonded clusters where electron correlation effects are important. We show that the procedure reported here enables DFT calculations for hydrated cyclodextrin using basis set up to the 6-311++G(3df,3pd) triple zeta quality .     

Photoredox Properties of Iron(III) Fluoro Complexes Containing Tetradentate Open-Chain N2O2Ligands

Tetradentate open-chain Schiff base N₂O₂-ligands of acacen, benacen or salen type and fluoride anions F^? coordinate to the iron(III) central atom in methanol forming the complexes [Fe(N₂O₂)(CH₃OH)F]. The complexes do not undergo spontaneous redox changes when kept in the dark. Their irradiation into intraligand or ligand-to-metal charge transfer bands causes the photoreduction of Fe(III) to Fe(II) associated with oxidation of metanol to its radical CH₂OH. The final products of the primary photoredox and secondary dark redox processes, Fe(II) and CH₂O, are formed in a 2:1 molar ratio. The efficiency of the axial methanol ligand photooxidation is strongly wavelength dependent and influenced by the peripheral groups R of the tetradentate ligands     

High purity anatase TiO(2) nanocrystals: near room-temperature synthesis, grain growth kinetics, and surface hydration chemistry

High purity, spherical anatase nanocrystals were prepared by a modified sol-gel method. Mixing of anhydrous TiCl(4) with ethanol at about 0 degrees C yielded a yellowish sol that was transformed into phase-pure anatase of 7.7 nm in size after baking at 87 degrees C for 3 days. This synthesis route eliminates the presence of fine seeds of the nanoscale brookite phase that frequently occurs in low-temperature formation reactions and also significantly retards the phase transformation to rutile at high temperatures. Heating the as-is 7.7 nm anatase for 2 h at temperatures up to 600 degrees C leads to an increase in grain size of the anatase nanoparticles to 32 nm. By varying the calcination time from 2 to 48 h at 300 degrees C, the particle size could be controlled between 12 and 15.3 nm. The grain growth kinetics of anatase nanoparticles was found to follow the equation, D(2) - D(0)(2) = k(0)t(m)e((-)(E)(a)/(RT)) with a time exponent m = 0.286(+/-9) and an activation energy of E(a) = 32 +/- 2 kJ x mol(-)(1). Thermogravimetric analysis in combination with infrared and X-ray photoemission spectroscopies has shown the anatase nanocrystals at different sizes to be composed of an interior anatase lattice with surfaces that are hydrogen-bonded to a wide set of energetically nonequivalent groups. With a decrease in particle size, the anatase lattice volume contracts, while the surface hydration increases. The removal of the surface hydration layers causes coarsening of the nanoparticles.     

Responsive hydrogels from the intramolecular folding and self-assembly of a designed peptide

A general peptide design is presented that links the pH-dependent intramolecular folding of beta-hairpin peptides to their propensity to self-assemble, affording hydrogels rich in beta-sheet. Chemical responsiveness has been specifically engineered into the material by linking intramolecular folding to changes in solution pH, and mechanical responsiveness, by linking hydrogelation to self-assembly. Circular dichroic and infrared spectroscopies show that at low pH individual peptides are unstructured, affording a low-viscosity aqueous solution. Under basic conditions, intramolecular folding takes place, affording amphiphilic beta-hairpins that intermolecularly self-assemble. Rheology shows that the resulting hydrogel is rigid but is shear-thinning. However, quick mechanical strength recovery after cessation of shear is observed due to the inherent self-assembled nature of the scaffold. Characterization of the gelation process, from the molecular level up through the macroscopic properties of the material, suggests that by linking the intramolecular folding of small designed peptides to their ability to self-assemble, responsive materials can be prepared. Cryo-transmission electron and laser scanning confocal microscopies reveal a water-filled porous scaffold on both the nano- and microscale. The environmental responsiveness, morphology, and peptidic nature make this hydrogel a possible material candidate for biomedical and engineering technology.     

Spectral Properties of Interval Exchange Maps

 In [7], Nogueira and Rudolph proved that for irreducible permutations not of rotation class almost every (a.e.) interval exchange transformation (i.e.t.) is topological weak mixing. It is conjectured that the claim holds if topological weak mixing is replaced by weak mixing. Here we study the behaviour of eigenfunctions of i.e.t. Our analysis gives alternative proofs of results due to Katok and Stepin [4] and Veech [10]: for certain permutations a.e. i.e.t. is weak mixing and for irreducible permutations a.e. i.e.t. is totally ergodic. (Received 1 February 2001)     

Characterizing gonality for two-component stable curves

Geometriae Dedicata - It is a well-known result that a stable curve of compact type over $${\mathbb {C}}$$ having two components is hyperelliptic if and only if both components are hyperelliptic...     

6-Hydroxyhexyl 4-(E)-4-alkoxy/halostyryl)benzoates: synthesis,characterisation and study of mesomorphic and fluorescent properties

Hydroxyhexyl esters of alkoxy and halostilbene carboxylic acids were prepared and studied for thermal, liquid crystalline and fluorescent properties. The decomposition temperatures were determined thermogravimetrically and the compounds were found stable at least up to 200°C. Differential scanning calorimetry (DSC) indicated two mesophases in alkoxystilbene caboxylates. The smectic nature of the liquid crystal (LC) compounds was identified from the optical textures and confirmed through X-ray diffraction (XRD) measurements, where SmA, SmB and CrE mesophases were observed. The compounds 3a-g and 3h-k show single absorption maxima in UV-visible spectra at around 338 and 322 nm, respectively. All the alkoxy compounds emit blue light in solution and in solid state in the wavelength range of 422–425 nm.