• Bulletin of the Korean Chemical Society
• /
• v.29 no.8
• /
• pp.1554-1560
• /
• 2008

The probe diffusion and friction constants of methyl yellow (MY) in liquid n-alkanes of increasing chain length were calculated by equilibrium molecular dynamics (MD) simulations at temperatures of 318, 418, 518 and 618 K. Lennard-Jones particles with masses of 225 and 114 g/mol are modeled for MY. We observed that the diffusion constant of the probe molecule follows a power law dependence on the molecular weight of nalkanes, DMY${\sim}M^{-\gamma}$ well. As the molecular weight of n-alkanes increases, the exponent $\gamma$ shows sharp transitions near n-dotriacontane ($C_{32}$) for the large probe molecule (MY2) at low temperatures of 318 and 418 K. For the small probe molecule (MY1) $D_{MY1}$ in $C_{12}$ to C80 at all the temperatures are always larger than Dself of n-alkanes and longer chain n-alkanes offer a reduced friction relative to the shorter chain n-alkanes, but this reduction in the microscopic friction for MY1 is not large enough to cause a transition in the power law exponent in the log-log plot of DMY1 vs M of n-alkane. For the large probe molecule (MY2) at high temperatures, the situation is very similar to that for MY1. At low temperatures and at low molecular weights of n-alkanes, $D_{MY2}$ are smaller than $D_{self}$ of n-alkanes due to the relatively large molecular size of MY2, and MY2 experiences the full shear viscosity of the medium. As the molecular weight of n-alkane increases, $D_{self}$ of n-alkanes decreases much faster than $D_{MY2}$ and at the higher molecular weights of n-alkane, MY2 diffuses faster than the solvent fluctuations. Therefore there is a large reduction of friction in longer chains compared to the shorter chains, which enhances the diffusion of MY2. The calculated friction constants of MY1 and MY2 in liquid n-alkanes supported these observations. We deem that this is the origin of the so-called“solventoligomer”transition.

• Bulletin of the Korean Chemical Society
• /
• v.23 no.3
• /
• pp.459-468
• /
• 2002

Literature data measured by the author have been processed to report on the effect of solute structure on gas liquid partition coefficients of eleven normal, branched and cyclic alkanes ranging in carbon number from five to nine in sixty nine low molecular weight liquids. The alkane solutes are n-pentane(p), n-hexane(hx), n-heptane(hp), n-octane(o), n-nonane(n), 2-methylpentane(mp), 2,5-dimethylpentane(dp), 2,5-dimethylhexane(dh), 2,3,4-trimethylpentane(tp), cyclohexane(ch), and ethylcyclohexane(ec). The solvent set encompasses most of those studied by Rohrschneider as well as three homologous series of solvents (n-alkanes, 1-alcohols and 1-nitriles) and several perfluorinated alkanes and highly fluorinated alcohols. An excellent linear relationship was observed between lnK and the carbon number of n-alkanes. The effective carbon numbers of branched and cyclic alkanes were determined in a similar fashion to the method of Kovats index. We found that the logarithm of solute vapor pressure multiplied by solute molar volume was a perfect descriptor for the linear relationship with the median effective carbon number.

• Bulletin of the Korean Chemical Society
• /
• v.18 no.5
• /
• pp.478-484
• /
• 1997

In a recent paper[Bull. Kor. Chem. Soc. 17, 735 (1996)] we reported results of molecular dynamic (MD) simulations for the thermodynamic and structural properties of liquid n-alkanes, from n-butane to n-heptadecane, using three different models. Two of the three classes of models are collapsed atomic models while the third class is an atomistically detailed model. In the present paper we present results of MD simulations for the dynamic properties of liquid n-alkanes using the same models. The agreement of two self-diffusion coefficients of liquid n-alkanes calculated from the mean square displacements (MSD) via the Einstein equation and the velocity auto-correlation (VAC) functions via the Green-Kubo relation is excellent. The viscosities of n-butane to n-nonane calculated from the stress auto-correlation (SAC) functions and the thermal conductivities of n-pentane to n-decane calculated from the heat-flux auto-correlation (HFAC) functions via the Green-Kubo relations are smaller than the experimental values by approximately a factor of 2 and 4, respectively.

• Bulletin of the Korean Chemical Society
• /
• v.24 no.11
• /
• pp.1590-1598
• /
• 2003

In this paper we have presented the results for viscosity and self-diffusion constants of model systems for four liquid n-alkanes ($C_{12}, C_{20}, C_{32}, and C_{44}$) in a canonical ensemble at several temperatures using molecular dynamics (MD) simulations. The small chains of these n-alkanes are clearly $<{R_{ee}}^2>/6<{R_g}^2>>1$, which leads to the conclusion that the liquid n-alkanes over the whole temperatures considered are far away from the Rouse regime. Calculated viscosity ${\eta}$ and self-diffusion constants D are comparable with experimental results and the temperature dependence of both ${\eta}$ and D is suitably described by the Arrhenius plot. The behavior of both activation energies, $E_{\eta}$ and $E_D$, with increasing chain length indicates that the activation energies approach asymptotic values as n increases to the higher value, which is experimentally observed. Two calculated monomeric friction constants ${\zeta}$ and ${\zeta}_D$ give a correct qualitative trend: decrease with increasing temperature and increase with increasing chain length n. Comparison of the time auto-correlation functions of the end-to-end vector calculated from the Rouse model for n-dodecane ($C_{12}$) at 273 K and for n-tetratetracontane ($C_{44}$) at 473 K with those extracted directly from our MD simulations confirms that the short chain n-alkanes considered in this study are far away from the Rouse regime.

• Bulletin of the Korean Chemical Society
• /
• v.17 no.8
• /
• pp.735-744
• /
• 1996

We present results of molecular dynamic (MD) simulations for the thermodynamic and structural properties of liquid n-alkanes, from n-butane to n-heptadecane, using three different models Ⅰ-Ⅲ. Two of the three classes of models are collapsed atomic models while the third class is an atomistically detailed model. Model Ⅰ is the original Ryckaert and Bellemans' collapsed atomic model [Discuss. Faraday Soc. 1978, 66, 95] and model Ⅱ is the expanded collapsed model which includes C-C bond stretching and C-C-C bond angle bending potentials in addition to Lennard-Jones and torsional potentials of model Ⅰ. In model Ⅲ all the carbon and hydrogen atoms in the monomeric units are represented explicitly for the alkane molecules. Excellent agreement of the results of our MD simulations of model Ⅰ for n-butane with those of Edberg et al.[J. Chem. Phys. 1986, 84, 6933], who used a different algorithm confirms the validity of our algorithms for MD simulations of model Ⅱ for 14 liquid n-alkanes and of models Ⅰ and Ⅲ for liquid n-butane, n-decane, and n-heptadecane. The thermodynamic and structural properties of models Ⅰ and Ⅱ are very similar to each other and the thermodynamic properties of model Ⅲ for the three n-alkanes are not much different from those of models Ⅰ and Ⅱ. However, the structural properties of model Ⅲ are very different from those of models Ⅰ and Ⅱ as observed by comparing the radial distribution functions, the average end-to-end distances and the root-mean-squared radii of gyrations.

• Bulletin of the Korean Chemical Society
• /
• v.23 no.11
• /
• pp.1595-1603
• /
• 2002

In this paper we have presented the results of diffusion behavior of model systems for eight liquid n-alkanes ($C_{12}$-$C_{44}$) in a canonical (NVT) ensemble at several temperatures using molecular dynamics simulations. For these n-alkanes of small chain length n, the chains are clearly <$R_{ee}^2$>/6<$R_g^2$>>1 and non-Gaussian. This result implies that the liquid n-alkanes over the whole temperatures considered are far away from the Rouse regime, though the ratio becomes close to the unity as n increases. Calculated self-diffusion constants $D_{self}$ are comparable with experimental results and the Arrhenius plot of self-diffusion constants versus inverse temperature shows a different temperature dependence of diffusion on the chain length. The global rotational motion of n-alkanes is examined by characterizing the orientation relaxation of the end-to-end vector and it is found that the ratio ${\tau}1/{\tau}2$ is less than 3, the value expected for a isotropically diffusive rotational process. The friction constants ${\xi}$of the whole molecules of n-alkanes are calculated directly from the force auto-correlation (FAC) functions and compared with the monomeric friction constants ${\xi}_D$ extracted from $D_{self}$. Both the friction constants give a correct qualitative trends: decrease with increasing temperature and increase with increasing chain length. The friction constant calculated from the FAC's decreases very slowly with increasing temperature, while the monomeric friction constant varies rapidly with temperature. By considering the orientation relaxation of local vectors and diffusion of each site, it is found that rotational and translational diffusions of the ends are faster than those of the center.

• Journal of Korean Society for Atmospheric Environment
• /
• v.34 no.1
• /
• pp.166-176
• /
• 2018

The n-alkanes which are stable compounds in the atmosphere are emitted by anthropogenic sources and biological sources. The goal of this study is to understand characteristics of n-alkane distributions in $PM_{2.5}$ of the Anmyeon Island which is one of background site in Korea. The concentration of n-alkanes in $PM_{2.5}$ was measured at Anmyeon Island for one year from June 2015 to May 2016. The average concentration of total n-alkanes (${\sum}$ n-alkanes) from C20 to C34 was $14.02{\pm}10.26ng\;m^{-3}$ and ranged from 1.77 to $47.65ng\;m^{-3}$. Various diagnostic parameters were used to identify the source. As a result, it is considered that Anmyeon Island had a large influence of biological sources during non-heating period, while the influence of anthropogenic emission during the heating period was significant. Principle Component Analysis (PCA) was performed and yielded three components that accounted for 93.6% of the total variance in n-alkanes. Factor 1, which accounted for 42.3% of the total variance, indicated anthropogenic source including fossil fuel and biomass combustion, while, Factor 3 was interpreted as the biological sources such as plant wax.

• Ocean and Polar Research
• /
• v.41 no.2
• /
• pp.89-97
• /
• 2019

Long chain plant waxes (n-alkanes, n-alkanoic acids, and n-alcohols) and their carbon isotopic compositions (${\delta}^{13}C$) in geologic archives are valuable tools for paleovegetation reconstruction. However, the sensitivity of different plant wax constituents to vegetation shift is not well understood. This study explores controls on the variation in ${\delta}^{13}C$ values of long-chain n-alkanes ($C_{27}$ to $C_{33}$) and n-alkanoic acids ($C_{26}-C_{30}$) in the Gulf of Mexico core sediments (ODP 625B) near the Mississippi River delta. n-Alkanoic acids' ${\delta}^{13}C$ values were higher than those of n-alkanes by 1-2‰ on average and such a pattern is the opposite from their isotope fractionation observed in living plants: 1-2‰ smaller in n-alkanes than n-alkanoic acids. We attribute this offset to contributions from aquatic plants or microbes that produce high concentrations of $^{13}C-enriched$ long-chain n-alkanoic acids. The sensitivity of n-alkanes and n-alkanoic acids to vegetation and climate varied among chain lengths. The $n-C_{33}$ alkanes were most sensitive to $C_4$ grassland expansion among n-alkane homologues, while no specific trend was observed in n-alkanoic acids. This is due to the similarity in n-alkanoic acid concentrations between $C_3$ and $C_4$ plants by homologues and low terrestrial plant-derived n-alkanoic acid contributions to the sediments. The results of this study suggest that long chain n-alkanoic acids' ${\delta}^{13}C$ values in sediments may be influenced by contributions from different sources such as aquatic plants or microbial inputs and therefore interpretations regarding this matter should be cautiously formulated. We suggest that there is a need for further studies on characterizing long-chain n-alkanoic acids ($C_{26}-C_{34}$) in aquatic plants and microbes from various climates and environments in order to investigate their production and integration into sedimentary archives.

• Journal of Microbiology and Biotechnology
• /
• v.11 no.1
• /
• pp.56-60
• /
• 2001

A kerosene fungus of Cladosporium resinae NK-1 was examined for its ability to degrade individual n-alkanes and aromatic hydrocarbons by gas chromatography-mass spectrometry, and its organic solvent-tolerance was investigated by making use of the water-organic solvent suspension culture method. It grew on a wide range of solvents of varying hydrophobicities and it was found to have tolerance to various kinds of toxic organic solvents (10%, v/v) such as n-alkanes, cyclohexane, xylene, styrene, and toluene. A hydrocarbon degradation experiment indicated that NK-1 had a greater n-alkane degrading ability compared to that of the other selected strains. C. resinae NK-1, which could utilize 8-16 carbon chain-length n-alkanes of medium chain-length as a carbon source, could not assimilate the shorter chain-length n-alkanes and aromatic hydrocarbons tested so far. The n-alkane degrading enzyme activity was found in the mycelial extract of the organism.

• Bulletin of the Korean Chemical Society
• /
• v.18 no.5
• /
• pp.501-509
• /
• 1997

In recent papers[Bull. Kor. Chem. Soc. 1996, 17, 735; ibid 1997, 18, 478] we reported results of molecular dynamics (MD) simulations for the thermodynamic, structural, and dynamic properties of liquid normal alkanes, from n-butane to n-heptadecane, using three different models. Two of the three classes of models are collapsed atomic models while the third class is an atomistically detailed model. In the present paper we present results of MD simulations for the corresponding properties of liquid branched-chain alkanes using the same models. The thermodynamic property reflects that the intermolecular interactions become weaker as the shape of the molecule tends to approach that of a sphere and the surface area decreases with branching. Not like observed in the straight-chain alkanes, the structural properties of model Ⅲ from the site-site radial distribution function, the distribution functions of the average end-to-end distance and the root-mean-squared radii of gyration are not much different from those of models Ⅰ and Ⅱ. The branching effect on the self diffusion of liquid alkanes is well predicted from our MD simulation results but not on the viscosity and thermal conductivity.