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Integrating structural and thermodynamic mechanisms for sorption of PCBs by montmorillonite.

ABSTRACT: Strong sorption of planar nonionic organic chemicals by clay minerals has been observed for important classes of organic contaminants including polyaromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and dioxins, and such affinity was hypothesized to relate to the interlayer hydrophobicity of smectite clays. In batch sorption experiments of two trichlorobiphenyls on homoionic Na-, K-, Cs-montmorillonites, considerably greater sorption coefficient (Kw) was observed for coplanar 3,3',5-trichlorobiphenyl (PCB 36); log Kw for Na-, K-, and Cs-montmorillonite were 3.69, 3.72, and 4.53 for coplanar PCB 36 vs 1.21, 1.46, and 0.87 for the nonplanar 2,2',6-trichlorobiphenyl (PCB 19). MD simulations were conducted utilizing X-ray diffraction determined clay interlayer distances (d-spacing). The trajectory, density distribution, and radial distribution function of interlayer cation, water, and PCBs collectively indicated that the hydrophobic nature of the interlayer regions was determined by the hydration status of exchangeable cations and the associated d-spacing. The sorption free energies calculated for both coplanar and nonplanar PCB molecules by adaptive biasing force (ABF) method with an extended interlayer-micropore two-phase model consisting of cleaved clay hydrates and "bulk water" are consistent with the Gibbs free energies derived from the measured log Kw, manifesting enhanced sorption of coplanar PCBs was attributed to shape selectivity and hydrophobic interactions.

SUBMITTER: Liu C

PROVIDER: S-EPMC5896315 | biostudies-literature | 2015 Mar

REPOSITORIES: biostudies-literature

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Integrating structural and thermodynamic mechanisms for sorption of PCBs by montmorillonite.

Liu Cun C Gu Cheng C Yu Kai K Li Hui H Teppen Brian J BJ Johnston Cliff T CT Boyd Stephen A SA Zhou Dongmei D

Environmental science & technology 20150217 5

Strong sorption of planar nonionic organic chemicals by clay minerals has been observed for important classes of organic contaminants including polyaromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and dioxins, and such affinity was hypothesized to relate to the interlayer hydrophobicity of smectite clays. In batch sorption experiments of two trichlorobiphenyls on homoionic Na-, K-, Cs-montmorillonites, considerably greater sorption coefficient (Kw) was observed for coplanar 3,3',5 ...[more]

PMID: 25629399

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Project description:Conformational entropy for atomic-level, three dimensional biomolecules is known experimentally to play an important role in protein-ligand discrimination, yet reliable computation of entropy remains a difficult problem. Here we describe the first two accurate and efficient algorithms to compute the conformational entropy for RNA secondary structures, with respect to the Turner energy model, where free energy parameters are determined from UV absorption experiments. An algorithm to compute the derivational entropy for RNA secondary structures had previously been introduced, using stochastic context free grammars (SCFGs). However, the numerical value of derivational entropy depends heavily on the chosen context free grammar and on the training set used to estimate rule probabilities. Using data from the Rfam database, we determine that both of our thermodynamic methods, which agree in numerical value, are substantially faster than the SCFG method. Thermodynamic structural entropy is much smaller than derivational entropy, and the correlation between length-normalized thermodynamic entropy and derivational entropy is moderately weak to poor. In applications, we plot the structural entropy as a function of temperature for known thermoswitches, such as the repression of heat shock gene expression (ROSE) element, we determine that the correlation between hammerhead ribozyme cleavage activity and total free energy is improved by including an additional free energy term arising from conformational entropy, and we plot the structural entropy of windows of the HIV-1 genome. Our software RNAentropy can compute structural entropy for any user-specified temperature, and supports both the Turner'99 and Turner'04 energy parameters. It follows that RNAentropy is state-of-the-art software to compute RNA secondary structure conformational entropy. Source code is available at https://github.com/clotelab/RNAentropy/; a full web server is available at http://bioinformatics.bc.edu/clotelab/RNAentropy, including source code and ancillary programs.

Dataset Information

Integrating structural and thermodynamic mechanisms for sorption of PCBs by montmorillonite.

Publications

Integrating structural and thermodynamic mechanisms for sorption of PCBs by montmorillonite.

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