Molecular Dynamics Simulation of Basal Spacing, Energetics, and Structure Evolution of a Kaolinite–Formamide Intercalation Complex and Their Interfacial Interaction

Molecular dynamics simulations were performed on kaolinite–formamide complex models with various numbers of formamide molecules loaded in the kaolinite interlayer to explore the basal spacing, energetics, and structure evolution of the kaolinite–formamide complex during the intercalation process. Additionally, the interfacial interactions of formamide with kaolinite interlayer surfaces were calculated. The calculation revealed that the basal spacing of kaolinite was enlarged to 9.6 Å at the beginning of intercalation. Formamide was arranged as a monolayer structure in the kaolinite interlayer with the molecular plane oriented at small angles with respect to the interlayer surface. With continuous intercalation, the basal spacing readily reached a stable stage at 10.6 Å, where formamide rearranged its structure by rotating the molecule plane along the C–N bond that was parallel to the interlayer surface, which resulted in the molecular plane orienting at higher angles with respect to the interlayer surface. During this process, the CO groups oriented toward the hydroxyl groups on the interlayer octahedral surface, and one of N–H bonds progressively pointed toward the basal oxygens on the opposing interlayer tetrahedral surface. Continuous intercalation can enlarge the basal spacing to more than 14 Å with the prerequisite of overcoming the energy barrier, and then formamide evolved to a disordered bilayer structure in the kaolinite interlayer. The affinity of kaolinite interlayer surfaces for formamide motivated the intercalation process. The octahedral surface displayed a relatively larger affinity toward formamide compared to the tetrahedral surface partially due to the presence of hydroxyl groups that are more active in the intermolecular interactions with formamide

Reduction of Carbadox Mediated by Reaction of Mn(III) with Oxalic Acid

Manganese­(III) geocomponents are commonly found in the soil environment, yet their roles in many biogeochemical processes remain unknown. In this study, we demonstrated that Mn^III generated from the reaction of MnO₂ and oxalic acid caused rapid and extensive decompositions of a quinoxaline-di-<i>N</i>-oxide antibiotics, viz carbadox. The reaction occurred primarily at the quinoxaline-di-<i>N</i>-oxide moiety resulting in the removal of one O from N1-oxide and formation of desoxycarbadox. The reaction rate was accelerated by increasing amounts of Mn^III, carbadox and oxalate. The critical step in the overall reaction was the formation of a quinoxaline-di-<i>N</i>-oxide/Mn^III/oxalate ternary complex in which Mn^III functioned as the central complexing cation and electron conduit in which the arrangement of ligands facilitated electron transfer from oxalate to carbadox. In the complex, the CC bond in oxalate was cleaved to create CO₂^–• radicals, followed by electron transfer to carbadox through the Mn^III center. This proposed reaction mechanism is supported by the reaction products formed, reaction kinetics, and quantum mechanical calculations. The results obtained from this study suggest that naturally occurring Mn^III–oxalic acid complexes could reductively decompose certain organic compounds in the environment such as the antibiotic quinoxaline-di-<i>N</i>-oxide

Role of Tetracycline Speciation in the Bioavailability to <i>Escherichia coli</i> for Uptake and Expression of Antibiotic Resistance

Tetracycline contains ionizable functional groups that manifest several species with charges at different locales and differing net charge; the fractional distribution of each species depends on pH-p<i>K</i>_a relationship in the aqueous phase. In nature, these species interact with naturally abundant cations (e.g., Ca²⁺ and Mg²⁺) to form metal-tetracycline complexes in water. In this study, we used <i>Escherichia coli</i> MC4100/pTGM whole-cell bioreporter to investigate tetracycline uptake from solution under varying conditions of pH, salt composition and concentration by quantifying the corresponding expression of antibiotic resistance gene. The expression of antibiotic resistance gene in the <i>E. coli</i> bioreporter responded linearly to intracellular tetracycline concentration. Less tetracycline entered <i>E. coli</i> cells at solution pH of 8.0 than at pH 6.0 or 7.0 indicating reduced bioavailability of the antibiotic at higher pH. Both Mg²⁺ and Ca²⁺ in solution formed metal-tetracycline complexes which reduced uptake of tetracycline by <i>E. coli</i> hence diminishing the bioresponse. Among the various tetracycline species present in solution, including both metal-complexed and free (noncomplexed) species, zwitterionic tetracycline was identified as the predominant species that most readily passed through the cell membrane eliciting activation of the antibiotic resistance gene in <i>E. coli</i>. The results indicate that the same total concentration of tetracycline in ambient solution can evoke very different expression of antibiotic resistance gene in the exposed bacteria due to differential antibiotic uptake. Accordingly, geochemical factors such as pH and metal cations can modulate the selective pressure exerted by tetracycline for development and enrichment of antibiotic resistant bacteria. We suggest that tetracycline speciation analysis should be incorporated into the risk assessment framework for evaluating environmental exposure and the corresponding development of antibiotic resistance

Thermodynamic Mechanism and Interfacial Structure of Kaolinite Intercalation and Surface Modification by Alkane Surfactants with Neutral and Ionic Head Groups

Intercalation and surface modification of clays with surfactants are the essential process to tailor the clays’ surface chemistry for their extended applications. A full understanding of the interaction mechanism of surfactants with clay surfaces is crucial to engineer clay surfaces for meeting a particular requirement of industrial applications. In this study, the thermodynamic mechanism involved in the intercalation and surface modification of methanol preintercalated kaolinite by three representative alkane surfactants with different head groups, dodecylamine, cetyl­trimethyl­ammonium chloride (CTAC), and sodium stearate, were investigated using the adaptive biasing force accelerated molecular dynamics simulations. In addition, the interaction energies of surfactants with an interlayer environment (alumina surface, siloxane surface, and interlayer methanol) of methanol preintercalated kaolinite were also calculated. It was found that the intercalation free energy of CTAC with a cationic head group was relatively larger than that of stearate with an anionic head group and dodecylamine with a neutral head group. The attractive electrostatic and van der Waals interactions of surfactants with an interlayer environment contributed to the intercalation and surface modification process with the electrostatic force playing the significant role. This study revealed the underlying mechanism involved in the intercalation and surface modification process of methanol preintercalated kaolinite by surfactants, which can help in further design of kaolinite-based organic clays with desired properties for specific applications

Integrating Structural and Thermodynamic Mechanisms for Sorption of PCBs by Montmorillonite

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 (<i>K</i>_w) was observed for coplanar 3,3′,5-trichlorobiphenyl (PCB 36); log<i> K</i>_w 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 (<i>d</i>-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 <i>d</i>-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 <i>K</i>_w, manifesting enhanced sorption of coplanar PCBs was attributed to shape selectivity and hydrophobic interactions

Bioavailability of Soil-Sorbed Tetracycline to <i>Escherichia coli</i> under Unsaturated Conditions

Increasing concentrations of anthropogenic antibiotics in soils are partly responsible for the proliferation of bacterial antibiotic resistance. However, little is known about how soil-sorbed antibiotics exert selective pressure on bacteria in unsaturated soils. This study investigated the bioavailability of tetracycline sorbed on three soils (Webster clay loam, Capac sandy clay loam, and Oshtemo loamy sand) to a fluorescent <i>Escherichia coli</i> bioreporter under unsaturated conditions using agar diffusion assay, microscopic visualization, and model simulation. Tetracycline sorbed on the soils could be desorbed and become bioavailable to the <i>E. coli</i> cells at matric water potentials of −2.95 to −13.75 kPa. Bright fluorescent rings were formed around the tetracycline-loaded soils on the unsaturated agar surfaces, likely due to radial diffusion of tetracycline desorbed from the soils, tetracycline uptake by the <i>E. coli</i> cells, and its inhibition on <i>E. coli</i> growth, which was supported by the model simulation. The bioavailability of soil-sorbed tetracycline was much higher for the Oshtemo soil, probably due to faster diffusion of tetracycline in coarse-textured soils. Decreased bioavailability of soil-sorbed tetracycline at lower soil water potential likely resulted from reduced tetracycline diffusion in soil pore water at smaller matric potential and/or suppressed tetracycline uptake by <i>E. coli</i> at lower osmotic potential. Therefore, soil-sorbed tetracycline could still exert selective pressure on the exposed bacteria, which was influenced by soil physical processes controlled by soil texture and soil water potential

Mechanism Associated with Kaolinite Intercalation with Urea: Combination of Infrared Spectroscopy and Molecular Dynamics Simulation Studies

Intercalation of urea in kaolinite was investigated using infrared spectroscopy and molecular dynamics simulation. Infrared spectroscopic results indicated the formation of hydrogen bonds between urea and siloxane/alumina surfaces of kaolinite. The carbonyl group (−CO) of urea acted as H-acceptors for the hydroxyl groups on alumina surfaces. The amine group (−NH₂) of urea functioned as H-donors interacting with basal oxygens on siloxane surfaces and/or the oxygens of hydroxyl groups on alumina surfaces. The H-bonds of urea formed with kaolinite surfaces calculated directly from molecular dynamics simulation was consistent with the infrared spectroscopic results. Additionally, MD simulations further provided insight into the interaction energies of urea with the kaolinite interlayer environment. The calculated interaction energies of urea molecules with kaolinite alumina and siloxane surfaces suggest that the intercalation of urea within kaolinite interlayers is energetically favorable. The interaction energy of urea with alumina surfaces was greater than that with siloxane surfaces, indicating that the alumina surface plays a primary role in the intercalation of kaolinite by urea. The siloxane surfaces function as H-acceptors to facilitate the intercalation of urea. The present study offers a direct view of the specific driving force involved in urea intercalation in kaolinite. The results obtained can help develop appropriate protocol to intercalate and delaminate clay layers for clay-based applications and products

Bioavailability of Soil-Sorbed Tetracycline to <i>Escherichia coli</i> under Unsaturated Conditions

Increasing concentrations of anthropogenic antibiotics in soils are partly responsible for the proliferation of bacterial antibiotic resistance. However, little is known about how soil-sorbed antibiotics exert selective pressure on bacteria in unsaturated soils. This study investigated the bioavailability of tetracycline sorbed on three soils (Webster clay loam, Capac sandy clay loam, and Oshtemo loamy sand) to a fluorescent <i>Escherichia coli</i> bioreporter under unsaturated conditions using agar diffusion assay, microscopic visualization, and model simulation. Tetracycline sorbed on the soils could be desorbed and become bioavailable to the <i>E. coli</i> cells at matric water potentials of −2.95 to −13.75 kPa. Bright fluorescent rings were formed around the tetracycline-loaded soils on the unsaturated agar surfaces, likely due to radial diffusion of tetracycline desorbed from the soils, tetracycline uptake by the <i>E. coli</i> cells, and its inhibition on <i>E. coli</i> growth, which was supported by the model simulation. The bioavailability of soil-sorbed tetracycline was much higher for the Oshtemo soil, probably due to faster diffusion of tetracycline in coarse-textured soils. Decreased bioavailability of soil-sorbed tetracycline at lower soil water potential likely resulted from reduced tetracycline diffusion in soil pore water at smaller matric potential and/or suppressed tetracycline uptake by <i>E. coli</i> at lower osmotic potential. Therefore, soil-sorbed tetracycline could still exert selective pressure on the exposed bacteria, which was influenced by soil physical processes controlled by soil texture and soil water potential

Numbers of up- and down-regulated genes, relative to SUC, in DD and DF grown cells, and relative to DF, in DD grown cells, by COG category.

<p>The numbers in red are total genes in each COG. Some genes are assigned to multiple COG categories and counted in each.</p

Lower pathways of dibenzo-<i>p</i>-dioxin and dibenzofuran degradation.

<p>Up-regulated genes are indicated in bold and * with DF and † with DD.</p