Molecular dynamics simulation study of probe diffusion in liquid n-alkanes

We performed molecular dynamics simulations for the probe diffusion and friction dynamics of Lennard-Jones (LJ) particles modelled for methyl yellow (MY) in liquid n-alkanes of C₁₂–C₂₀₀ at temperatures of 318, 418, 518 and 618 K. Two LJ particles are chosen: MY1 with a mass of 114 g/mol, LJ parameters of σ = 4.0 Å and ? = 0.4 kJ/mol, and MY2 with a mass of 225 g/mol, σ = 6.0 Å and ? = 0.6 kJ/mol. We observed a clear transition in the power law dependence of MY2 diffusion on the molecular weight of n-alkanes at lower temperatures of 318 and 418 K. The sharp transitions occur near n-dotriacontane (C₃₂). However, no such transition is found for MY1 at all the temperatures and for MY2 at higher temperatures of 518 and 618 K. We also calculated the friction constants of both MY probe molecules in liquid n-alkanes. For the larger probe molecule (MY2), at lower temperatures, a large deviation of slope from the linear dependence of the friction of MY2 on the chain length of n-alkane is observed, which indicates a large reduction of friction in longer chains when compared with the shorter chains, enhancing the diffusion of the probe molecules (MY2).     

Phytoremediation of petroleum hydrocarbons by using a freshwater fern species Azolla filiculoides Lam

In this study, the phytoremediation capacity of Azolla filiculoides Lam. for the water resources contaminated with petroleum hydrocarbons was investigated. The plants were grown in nitrogen-free Hoagland nutrient solution containing 0.005%, 0.01%, 0.05%, 0.1%, 0.2%, 0.3%, 0.4%, and 0.5% crude oil under greenhouse conditions for 15 days. Although the growth rate of the plants were not negatively influenced by the presence of crude oil in the media for the concentration of 0.005% and 0.01% v/v, a gradual impeding effect of crude oil in the growth media has been observed at concentrations 0.05–0.1%. More than 0.1% crude oil in the growth medium ostensibly retarded the growth. For example, 0.2% oil in the media reduced growth approximately 50% relative to the control, and the presence of crude oil at concentrations 0.3% or more were lethal. The data about the percentage of plant growth, fresh weight increase and root growth clearly indicated that the tolerance level of A. filiculoides plants to crude oil ranges between 0.1% and 0.2%. In comparison to control samples, the biodegradation rate of total aliphatic and aromatic (phenathrene) hydrocarbons at 0.05–0.2% oil concentrations, was 94–73% and 81–77%, respectively. On the other hand, in case of further increases in oil concentration in media, i.e.; 0.3–0.5%, the biodegradation rate was still higher in the experimental samples, respectively 71–63% and 75–71%. The high biodegradation rates of petroleum hydrocarbons in the experimental samples suggested that A. filiculoides plants could be a promising candidate to be used for the phytoremediation of low crude oil contaminated precious freshwater resources.     

Chemotaxonomic Differentiation of Pinus Species Based on n-Alkane and Long-Chain Alcohol Profiles of Needle Cuticular Waxes

n-Alkane and long-chain alcohol (LCOH) profiles of needle cuticular waxes of nine provenances of three Pinus species (P. taeda. P. pinaster and P. pinea) were determined and their chemotaxonomic importance was studied. n-Alkanes concentrations were very low in all Pinus spp. A lack of ability of these compounds to differentiate Pinus spp. and their provenances was observed. LCOH concentrations were much higher, being nonacosan-10-ol (10-C₂₉-OH) the most abundant one in all Pinus spp. Total LCOH concentrations varied (P<0.001) between Pinus spp. with P. taeda presenting the highest (P<0.05) value and P. pinea the lowest one. Differences in LCOH profiles were large (P<0.001) and allowed separation of Pinus spp. in the Principal Component Analysis (PCA). Although a noticeable separation of individuals was not observed. cluster analysis on LCOH concentrations allowed a clear distinction between species, indicating their potential to be used as chemotaxonomic markers to differentiate provenances of different Pinus spp.     

Molecular-Dynamics Simulation of the Surface Diffusion of n-Alkanes on Pt(111)

Abstract

In the present study, the equilibrium adsorption and the dynamics of surface diffusion in a model of ethane and n-butane on a Pt(111) surface were simulated with molecular dynamics. At low temperatures, we found that both admolecules adsorb in a specific binding site. Through analysis of the trajectories, several features of the dynamics were resolved. At low temperature, we observed that diffusion occurs through a nearest-neighbor hopping mechanism involving both lateral rotation and axial translation. At high temperatures, the admolecule makes multiple-site hops and nonlocalized long flights. The temperature dependence of the diffusion coefficients was analyzed and was found to exhibit good Arrhenius behavior. The apparent diffusion coefficients follow trends seen in related experimental studies. In the case of ethane, a comparison between the diffusion barrier measured in the molecular-dynamics simulations and the theoretical barrier predicted by transition-state theory indicates that the simulated barrier is larger than the theoretical value. This finding is consistent with conclusions in recent studies of metal-atom diffusion on metal surfaces, where it was found that systems with low corrugation exhibit a non-unique relationship between the dynamical diffusion barrier and the potential-energy-surface topology.     

Methanogenic Microbial Community Composition of Oily Sludge and Its Enrichment Amended with Alkanes Incubated for Over 500 Days

Methanogenic microbial community is responsive to the availability of hydrocarbons and such information is critical for the assessment of hydrocarbon degradation in remediation and also in biologically enhanced recovery of energy from non-producing oil reserves. In this study, methanogenic enrichment cultures from oily sludge amended with n-alkanes (C₁₅-C₂₀) showed a development of active methanogenic alkanes-degrading consortium for over a total of 1000 days of incubation at 37°C. Total genomic DNAs were extracted from three types of samples, the original oily sludge (OS), the sludge after incubation for 500 days under methanogenic condition without any external carbon addition (EC), and the enrichment culture from the EC amended with n-alkanes (ET) incubated for another 500 days. The phylogenetic diversities of microbial communities of the three samples were analyzed by PCR amplification of partial 16S rRNA genes. The catabolic genes encoding benzylsuccinate synthase (bssA) and alkylsuccinate synthase (assA) were also examined by PCR amplification. These results provide important evidence in that microbial populations in an oily sludge shifted from methanogenic aromatic compounds degrading communities to potential methanogenic alkane-degrading communities when the enrichment was supplemented with n-alkanes and incubated under anaerobic conditions.     

Evaluation of n-alkanes and their carbon isotope enrichments (δ(13)C) as diet composition markers

Plant cuticular n-alkanes have been successfully used as markers to estimate diet composition and intake of grazing herbivores. However, additional markers may be required under grazing conditions in botanically diverse vegetation. This study was conducted to describe the n-alkane profiles and the carbon isotope enrichment of n-alkanes of common plant species from the Mid Rift Valley rangelands of Ethiopia, and evaluate their potential use as nutritional markers. A total of 23 plant species were collected and analysed for long-chain n-alkanes ranging from heptacosane to hexatriacontane (C(27) to C(36)), as well as their carbon isotopic ratio ((13)C/(12)C). The analysis was conducted by gas chromatography/combustion isotope ratio mass spectrometry following saponification, extraction and purification. The isotopic composition of the n-alkanes is reported in the delta notation (δ(13)C) relative to the Vienna Pee Dee Belemnite standard. The dominant n-alkanes in the species were C(31) (mean ± s.d., 283 ± 246 mg/kg dry matter) and C(33) (149 ± 98 mg/kg dry matter). The carbon isotopic enrichment of the n-alkanes ranged from -19.37‰ to -37.40‰. Principal component analysis was used to examine interspecies differences based on n-alkane profiles and the carbon isotopic enrichments of individual n-alkanes. Large variability among the pasture species was observed. The first three principal components explained most of the interspecies variances. Comparison of the principal component scores using orthogonal procrustes rotation indicated that about 0.84 of the interspecies variances explained by the two types of data sets were independent of each other, suggesting that the use of a combination of the two markers can improve diet composition estimations. It was concluded that, while the n-alkane profile of the pasture species remains a useful marker for use in the study region, the δ(13)C values of n-alkanes can provide additional information in discriminating diet components of grazing animals.     

leaf cuticular alkanes of cultivated Polyscias

Leaf cuticular alkane analysis of 34 cultivars of Polyscias generally supported morphological classifications of this genus, but variability within groups such as P. crispatum suggested that alkane data by itself is insufficient for classification of the various cultivars into species. Alkanes with 27–33 carbon atoms were present in most species, with C₃₁ predominating.     

Biostimulation-based bioremediation of diesel fuel: field demonstration

Ex-situ bioremediation of leached cynamonic forest soilat initial diesel oil contamination of 6000 mg kg^-1, 4000 mg kg^-1 and 2000 mg kg^-1 was investigated afterbiostimulation with inorganic fertilizers. It was foundthat the added nutrients had no effect on the decontamination of polluted soils. A precise and reliable approach for evaluation of the biodegradation process is proposed. It comprisesapplication of sensitive and easily accessible diagnostic parameters and relations, calculated on the basis of n-alkanes andisoprenoids – pristane (2.6.10.14-tetramethylpentadecane,i-C₁₉H₄₀) andphytane (2.6.10.14-tetramethylhexadecane,i-C₂₀H₄₂) distribution.     

Abundance of Macroalgal Organic Matter in Biofilms: Evidence from n-Alkane Biomarkers

Biofilm development on titanium panels immersed in the surface waters of Dona Paula Bay was investigated using molecular biomarkers such as n-alkanes and other chemical and biological parameters. Biofilm biomass measured as organic carbon (OC), organic nitrogen (ON), chlorophyll a, diatoms and bacterial numbers on the titanium panels generally increased over the period of immersion. Total lipids and n-alkane concentration also showed similar trends. n-alkanes from C₁₂ to C₃₀ were detected in the biofilm samples, which showed a bimodal distribution. The first mode consisted of n-alkanes > C₂₃ with a strong even over odd predominance. In the second mode, the n-alkanes < C₂₃ were more abundant with odd carbon number maxima at C₁₅, C₁₇ and C₁₉ and a strong odd over even carbon number predominance (Carbon Preference Index > 2). The predominance of these odd-chain n-alkanes strongly indicates that the organic matter derived from macroalgal sources was the major contributor to the biofilm organic matter developed on the titanium panels over the 15 d period of study. The data suggest that molecular characterization is a useful tool in understanding the sources of biofilm organic matter. The observed abundance of macroalgal organic matter during the 15 d period of biofilm development may play an important role in subsequent fouling by micro- and macrofouling organisms.