A molecular modeling analysis of polycyclic aromatic hydrocarbon biodegradation by naphthalene dioxygenase

Removing polycyclic aromatic hydrocarbons from water using granular activated carbon: kinetic and equilibrium adsorption studies

Polycyclic aromatic hydrocarbons (PAHs) constitute a group of highly persistent, toxic and widespread environmental micropollutants that are increasingly found in water. A study was conducted in removing five PAHs, specifically naphthalene, acenaphthylene, acenaphthene, fluorene and phenanthrene, from water by adsorption onto granular activated carbon (GAC). The pseudo-first-order (PFO) model satisfactorily described the kinetics of adsorption of the PAHs. The Weber and Morris diffusion model's fit to the data showed that there were faster and slower rates of intra-particle diffusion probably into the mesopores and micropores of the GAC, respectively. These rates were negatively related to the molar volumes of the PAHs. Batch equilibrium adsorption data fitted well to the Langmuir, Freundlich and Dubinin-Radushkevich models, of which the Freundlich model exhibited the best fit. The adsorption affinities were related to the hydrophobicity of the PAHs as determined by the log K_ow values. Free energies of adsorption calculated from the Dubinin-Radushkevich model and the satisfactory kinetic data fitting to the PFO model suggested physical adsorption of the PAHs. Adsorption of naphthalene, acenaphthylene and acenaphthene in fixed-bed columns containing a mixture of GAC (0.5 g) + sand (24.5 g) was satisfactorily simulated by the Thomas model.

Static and dynamic electronic (hyper)polarizabilities of dimethylnaphthalene isomers: characterization of spatial contributions by density analysis

Static and frequency-dependent electronic (hyper)polarizabilities of the dimethylnaphthalene (DMN) isomers were computed in vacuum using the Coulomb-attenuating Density Functional Theory method. The nonlinear optical Second Harmonic Generation (SHG) and Electro-Optical Pockels Effect (EOPE) were investigated at the characteristic Nd:YAG laser wavelength of 1064 nm. The response electric properties especially the longitudinal polarizability, polarizability anisotropy, and first-order hyperpolarizability are significantly affected by the position of the methyl groups. The SHG and EOPE techniques can be potentially useful to discriminate the α,α-DMN isomers (2,6-DMN < 2,7-DMN < 2,3-DMN) as well as the β,β-DMN isomers (1,5-DMN < 1,4-DMN < 1,8-DMN). The (hyper)polarizability differences among the investigated DMNs were elucidated through density analysis calculations. The predicted polarizabilities exhibit good linear relationships with the experimental first-order biomass-normalized rate coefficient, a physicochemical property connected to the rates of biodegradation processes of polycyclic aromatic hydrocarbons.

Substrate specificity and structural characteristics of the novel Rieske nonheme iron aromatic ring-hydroxylating oxygenases NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1

The Rieske nonheme iron aromatic ring-hydroxylating oxygenases (RHOs) NidAB and NidA3B3 from Mycobacterium vanbaalenii PYR-1 have been implicated in the initial oxidation of high-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs), forming cis-dihydrodiols. To clarify how these two RHOs are functionally different with respect to the degradation of HMW PAHs, we investigated their substrate specificities to 13 representative aromatic substrates (toluene, m-xylene, phthalate, biphenyl, naphthalene, phenanthrene, anthracene, fluoranthene, pyrene, benz[a]anthracene, benzo[a]pyrene, carbazole, and dibenzothiophene) by enzyme reconstitution studies of Escherichia coli. Both Nid systems were identified to be compatible with type V electron transport chain (ETC) components, consisting of a [3Fe-4S]-type ferredoxin and a glutathione reductase (GR)-type reductase. Metabolite profiles indicated that the Nid systems oxidize a wide range of aromatic hydrocarbon compounds, producing various isomeric dihydrodiol and phenolic compounds. NidAB and NidA3B3 showed the highest conversion rates for pyrene and fluoranthene, respectively, with high product regiospecificity, whereas other aromatic substrates were converted at relatively low regiospecificity. Structural characteristics of the active sites of the Nid systems were investigated and compared to those of other RHOs. The NidAB and NidA3B3 systems showed the largest substrate-binding pockets in the active sites, which satisfies spatial requirements for accepting HMW PAHs. Spatially conserved aromatic amino acids, Phe-Phe-Phe, in the substrate-binding pockets of the Nid systems appeared to play an important role in keeping aromatic substrates within the reactive distance from the iron atom, which allows each oxygen to attack the neighboring carbons.