Modeling sorption of soil organic matter on mineral surfaces: wood-derived polymers on mica

Molecular mechanics and molecular dynamics calculations were carried out on model organo–mineral composites typical of both paper products and soil. Sorption energy of neutral model linear chains of lignin, carbohydrate, and humic substances on muscovite mica depends on the mutual orientation of organic and mineral components, spatial organization and functionality of the organic chain, and the presence of metal cations. Carbohydrates are characterized by their higher affinity towards the mineral surface than the more flexible helical aromatic polymers. In the model calculations, sorption energies are twice as high. Oxidation of lignin into respective humic acids does not lead to better sorption. Unlike metal cations, water molecules interlacing between organic and mineral surfaces do not act as bridges and sharply decrease sorption energy. Flexible linear polymers may undergo drastic conformational changes when approaching the mineral surface, to ensure a gain in the interaction energy that more than compensates a loss in the conformational energy proper.     

The conformational dynamics of humic polyanions in model organic and organo-mineral aggregates

Molecular mechanics calculations and simulated annealing were applied to model humic polyanions originating from lignin. The dynamic behavior of such oxidized lignins in model soil organic complexes, such as an oxidized lignin-carbohydrate complex (LCC) and humic (oxidized LCC)-clay aggregates, was analyzed. Neither ionization nor hydrogen bonding bring significant changes in the conformational properties of oxidized lignin and LCC. Oxidized lignin and LCC oligomers (humic substances in soil) bind to the mineral surfaces, a process that was exemplified in computational experiments on complexes with muscovite. Upon ionization, a lignin-derived oligomer develops strong attractive organo-mineral interactions through cation bridges. Without metal cations, electrostatic repulsion between negatively charged anions and the oxygen-mineral surface prevails, and the two parts of the organo-mineral complex drift apart. This tendency is typical of an oxidized lignin oligomer but not of a topological oxidized LCC.     

Retention of Metamitron by Model and Natural Particulate Matter

Abstract

Adsorption isotherms of metamitron on model soil colloidal components: kaolinite, illite, montmorillonite, iron oxide and humic acid, and their binary associations were obtained using a batch equilibration procedure. Sorption parameters, K_f and n_f, were calculated by fitting the sorption data to the Freundlich equation and results obtained for binary associations were compared with those obtained for the individual model components. The sorption efficiency of the humic acids and their binary associations was measured as Koc. The adsorption behaviour of the < 2 μm fraction of two soils from Southern Spain was also studied as natural particulate matter. Montmorillonite and humic acids were found to be the most important components responsible for metamitron retention by the model adsorbents studied. On the contrary, metamitron showed little interaction with kaolinite, illite or iron oxide. These individual adsorption behaviours were reproduced in the montmorillonite-iron oxide-humic acid binary systems, but with differences suggesting changes on the surface properties upon association. Differences in Koc values of isolated humic acids and their associations indicate that the interaction transforms the humic acid surfaces and suggest different types of bonding between colloids and metamitron. The results obtained with model adsorbents and their associations were in agreement with the highest adsorption of metamitron found for the natural clay fraction of two soils which displayed the largest adsorption in that with the highest content in montmorillonite and organic carbon. The importance of organic matter and montmorillonite in metamitron adsorption by colloidal components was also shown by the decrease in K_f and the increase in Koc observed after removal of organic matter from the soil clay fraction with the highest organic carbon content.     

Conformational sensitivity of polyether macrocycles to electrostatic potential: Partial atomic charges,molecular mechanics,and conformational prediction

Molecular recognition (whether by enzymes, the immune system, or chelating ligands) depends critically on molecular conformation. Molecular mechanics predicts energetically favorable molecular conformations by locating low energy conformations using an empirical fit of molecular potential energy as a function of internal coordinates. Molecular mechanics analysis of 18-crown-6 demonstrates that the nonbonded term (primarily the electrostatic part) is the largest contributor to the conformational energy. Nevertheless, common methods of treating the electrostatic interaction for 18-crown-6 yield inconsistent values for conformational energies partly because partial charges assigned to each atom can change with conformation due to through-space inductive effects which are not considered in most molecular mechanics programs. Similar findings from several other groups are reviewed to support our conclusions. We argue for care and caution in predicting conformational preferences of molecules with two or more highly polar atoms. We also discuss the desirability of using an empirical method of partial charge determination such as the charge equilibration algorithm of Rappé and Goddard (or a suitable generalization which includes polarization) as a method of including these effects in molecular mechanics and molecular dynamics calculations.     

Sorption of two aromatic acids onto iron oxides: experimental study and modeling

The transport of aromatic carboxylate compounds in the environment can be strongly influenced by adsorption onto certain minerals, such as iron oxides and hydroxides, found in ground water and soils. Batch experiments with five iron oxides were conducted to quantify the contributions to adsorption from different iron mineral surfaces and compare adsorption characteristics of selected organic acids (gentisic acid (GA) and 1-hydroxy-2-naphthoic acid (HNA)). Because of their widespread abundance in soils and sediments, goethite, lepidocrocite, ferrihydrite, hematite, and magnetite were investigated. Sorption of two organic acids onto iron oxides was examined over a wide range of conditions (pH, ionic strength, and sorbate concentration). Specific surface area and mineral surface charge proved be important for the adsorption of these compounds. The sorption isotherm was described well by the Tempkin equation for both organic acids, with the adsorption constant higher for HNA than GA. For modeling the sorption edges of ferrihydrite and hematite, surface reactions involving the formation of mononuclear (1:1) surface species were proposed. These results indicate that the generalized two-layer model, with the assumption of homogeneous surface sites, could predict sorption on iron oxides over a range of pH conditions. The results of this study suggest that the mineralogy of the iron oxides and the pH value should be considered when predicting sorption of aromatic acids onto iron oxides and their fate in the soil and the environment.     

Probing the conformational space available to inhibitors in the thermolysin active site using Monte Carlo/energy minimization techniques

The conformational space available to four inhibitors of the bacterial enzyme thermolysin has been searched in the enzyme binding site using a method that combines Monte Carlo type techniques with energy minimization for exploration of the conformational potential energy hypersurface. Molecular mechanics methodology using the AMBER force field was employed for computation of the molecular energetics. Solvation energies were also included in the calculations by employing a technique that estimates hydration energies based on the exposed solvent accessible surface area for each atom of the inhibitor and active site. It was found that in each case, the crystallographically observed conformation was among the low energy conformers discovered. In fact, in three of the calculations it was the lowest energy conformation. The methodology described in this article is expected to be quite useful for studies involving computer aided design and evaluation of enzyme inhibitors.     

Force field development for poly(dimethylsilylenemethylene) with the aid of ab initio calculations

The molecular geometries, conformational energies, and zero-point energies of di(trimethylsilylene)methylene have been determined from high-level quantum chemistry calculations. The results are further used in the parametrization of a classical potential energy function suitable for performing simulations of the corresponding polymer, namely, poly(dimethylsilylenemethylene). Di(trimethylsilylene)methylene geometrical parameter optimizations for a proper location of the global minimum and other local minima, constrained at certain dihedral and bond angles, were performed at both the B3LYP/6-311G and MP2(full)/6-311G levels of theory. The global minimum configuration is slightly displaced from a perfectly staggered geometry, approximately by 16.0 degrees, at both levels of theory. Molecular mechanics and Monte Carlo calculations for isolated polymer chains together with molecular dynamics runs for the modeled dimer provide very good results in terms of conformational and thermodynamic properties.     

Simultaneous removal of uranium and humic acid by cyclodextrin modified graphene oxide nanosheets

Cyclodextrin-modified graphene oxide nanosheets (denoted as CD/GO) were synthesized by an in-situ polymerization method and characterized by as well as Fourier transform-infrared spectroscopy, X-ray photoelectron spectroscopy, Raman spectroscopy and potentiometric acid-base titration. The characterization results indicated that CD was successfully grafted onto GO surfaces by forming a chemical bond. Mutual effects on the simultaneous removal of hexavalent uranium and humic acid by CD/GO from aqueous solution were investigated. The results indicated that U(VI) and humic acid (HA) sorption on CD/GO were greatly affected by pH and ionic strength. The presence of HA enhanced U(VI) sorption at low pH and reduced U(VI) sorption at high pH, whereas the presence of U(VI) enhanced HA sorption. The surface adsorbed HA acted as a “bridge” between U(VI) and CD/GO, and formed strong inner-sphere surface complexes with U(VI). Sorption isotherms of U(VI) or HA on CD/GO could be well fitted by the Langmuir model. This work highlights that CD/GO can be used as a promising material in the enrichment of U(VI) and HA from wastewater in U(VI) and humic substances obtained by environmental pollution cleanup.     

The Structure of Cellulose by Conformational Analysis. Part 5. The Cellulose Ii Water Sorption IsothermXS

Exact values of the sorption energies of single molecules of water on all available sorption sites of crystalline cellulose II have been obtained by conformational analysis. The sorption energies are equated to the total energy (E_tot ) of interaction between the water molecule and all the suitable atomic groups of the cellulose. E_tot is composed of van der Waals, H-bond, and electrostatic energies. The interferences of water molecules on vicinal sorption sites were obtained. Sites in which such interference can occur were identified for crystalline cellulose II. Sorption energy in crystalline cellulose II appears to depend only on the interaction of water with surface sorption sites of the crystal. There appears to be favorable sorption on 1) sites exerting high attractive forces, and 2) sites which are exposed and protrude from the crystal surface. Sites recessed from the crystal surface are generally repulsive due to strong interactions with neighboring groups. All the sorption energies of the “monolayer” were calculated. Very strong sorption sites cannot always form a second layer because of strong steric hindrance from vicinal groups. Sorption capacities of crystalline cellulose II were calculated, and the isotherm of the schematic five chain crystallite used was constructed by theoretical means. The results obtained were briefly compared with those for cellulose I crystallites and amorphous cellulose. The inflection points of the isotherm and the variability of Dent's k ₁ constant for the water monolayer with relative humidity for the cellulose I and II isotherms were also calculated by theoretical means.     

Entrapment of Humic Acid in a Sol-Gel Matrix—A New Tool for Sorption Studies

Humic substances are natural complexed mixtures of organic compounds originated from the decomposition of plant and animal residues. These compounds are ubiquitous in soils, sediments, surface waters and groundwaters. They contain both hydrophobic and hydrophilic moieties, able to interact with hydrophobic organic contaminants and with heavy metals. These sorption interactions play a crucial role in contaminants fate and transport and their understanding and quantification are essential for modeling and predictions. However, sorption analyses frequently suffer from experimental problems. A novel idea presented in this study is to use sol-gel as an inert matrix to immobilize (entrap) specific, well defined, humic molecules which then be used in sorption studies. We developed a successful procedure for the immobilization of humic acid (HA) in a sol-gel matrix. After gelation and drying, the doped gel was crushed and washed several times, yielding a very stable product. It was then used in a series of batch experiments, studying the sorption of several polycyclic aromatic hydrocarbons (PAHs) with Aldrich HA. The sorption coefficients (K _oc) obtained with the immobilized HA were highly correlated with the values expected based on the hydrophobicity of the contaminants. We concluded that the entrapped HA retained its original properties and that it was accessible to the external contaminants through the pore network.     

Micropollutant sorption to membrane polymers: a review of mechanisms for estrogens

Organic micropollutants such as estrogens occur in water in increasing quantities from predominantly anthropogenic sources. In water such micropollutants partition not only to surfaces such as membrane polymers but also to any other natural or treatment related surfaces. Such interactions are often observed as sorption in treatment processes and this phenomenon is exploited in activated carbon filtration, for example. Sorption is important for polymeric materials and this is used for the concentration of such micropollutants for analytical purposes in solid phase extraction. In membrane filtration the mechanism of micropollutant sorption is a relatively new discovery that was facilitated through new analytical techniques. This sorption plays an important role in micropollutant retention by membranes although mechanisms of interaction are to date not understood. This review is focused on sorption of estrogens on polymeric surfaces, specifically membrane polymers. Such sorption has been observed to a large extent with values of up to 1.2 ng/cm(2) measured. Sorption is dependent on the type of polymer, micropollutant characteristics, solution chemistry, membrane operating conditions as well as membrane morphology. Likely contributors to sorption are the surface roughness as well as the microporosity of such polymers. While retention-and/or reflection coefficient as well as solute to effective pore size ratio-controls the access of such micropollutants to the inner surface, pore size, porosity and thickness as well as morphology or shape of inner voids determines the available area for sorption. The interaction mechanisms are governed, most likely, by hydrophobic as well as solvation effects and interplay of molecular and supramolecular interactions such as hydrogen bonding, π-cation/anion interactions, π-π stacking, ion-dipole and dipole-dipole interactions, the extent of which is naturally dependent on micropollutant and polymer characteristics. Systematic investigations are required to identify and quantify both relative contributions and strength of such interactions and develop suitable surface characterisation tools. This is a difficult endeavour given the complexity of systems, the possibility of several interactions taking place simultaneously and the generally weaker forces involved.     

Kinetic study on the sorption of dissolved natural organic matter onto different aquifer materials: the effects of hydrophobicity and functional groups

The subsurface sorption of Suwannee River fulvic acid (SRFA) and humic acid (SRHA) onto a synthetic aquifer material (iron-oxide-coated quartz) and two natural aquifer materials (Ringold sediment and Bemidji soils) was studied in both batch and column experiments. The hypothesis that hydrophobic effects followed by ligand exchange are the dominant mechanism contributing to the chemical sorption happening between dissolved natural organic matter (NOM) and the mineral surfaces is supported by observations of several phenomena: nonlinear isotherms, faster sorption rates versus slower desorption rates, phosphate competition, a solution pH increase during NOM sorption, and functional groups and aromaticity-related sorption. In addition, high-pressure size exclusion chromatography (HPSEC) and carboxylic acidity showed that lower molecular weight NOM components of SRHA are preferentially sorbed to iron oxide, a result in contrast to that for SRFA. Phosphate increased the desorption of sorbed NOM as well as soil organic matter. All of these trends support ligand exchange as the dominant reaction between NOM and the iron oxide surfaces; however, if the soil surface has been occupied by soil organic matter, then the sorption of NOM is more due to hydrophobic effect.     

AFM study on the adsorption and aggregation behavior of dissolved humic substances on mica

Humic substances (HS) are a category of naturally occurring, biogenic, heterogeneous organic materials found in or extracted from soils, sediments, and natu- ral waters that can generally be characterized as being yellow-to-black in color, of highly variable relative molecular masses, and refractory[1,2]. Derived from a variety of organic precursors (plant biopolymers such as lignin etc.), plant residues and animal debris via both transformation and synthesis processes[3] under the profound ge…     

Interfacial energy exchange and reaction dynamics in collisions of gases on model organic surfaces

Molecular beam scattering experiments and molecular dynamics simulations have been combined to develop an atomic-level understanding of energy transfer, accommodation, and reactions during collisions between gases and model organic surfaces. The work highlighted in this progress report has been motivated by the scientific importance of understanding fundamental interfacial chemical reactions and the relevance of reactions on organic surfaces to many areas of environmental chemistry. The experimental investigations have been accomplished by molecular beam scattering from ω-functionalized self-assembled monolayers (SAMs) on gold. Molecular beams provide a source of reactant molecules with precisely characterized collision energy and flux; SAMs afford control over the order, structure, and chemical nature of the surface. The details of molecular motion that affect energy exchange and scattering have been elucidated through classical-trajectory simulations of the experimental data using potential energy surfaces derived from ab initio calculations. Our investigations began by employing rare-gas scattering to explore how alkanethiol chain length and packing density, terminal group relative mass, orientation, and chemical functionality influence energy transfer and accommodation at organic surfaces. Subsequent studies of small molecule scattering dynamics provided insight into the influence of internal energy, molecular orientation, and gas–surface attractive forces in interfacial energy exchange. Building on the understanding of scattering dynamics in non-reactive systems, our work has recently explored the reaction probabilities and mechanisms for O₃ and atomic fluorine in collisions with a variety of functionalized SAM surfaces. Together, this body of work has helped construct a more comprehensive understanding of reaction dynamics at organic surfaces.     

Modeling adsorption of the uranyl dication on the hydroxylated alpha-Al2O3(0001) surface in an aqueous medium. Density functional study

As a first step toward modeling the interaction of dissolved actinide contaminants with mineral surfaces, we studied low-coverage adsorption of aqueous uranyl, UO2(2+), on the hydroxylated alpha-Al2O3(0001) surface. We carried out density functional periodic slab model calculations and modeled solvation effects by explicit aqua ligands. We explored the formation of both inner- and outer-sphere complexes and estimated the corresponding adsorption energies. Effects of solvation were accounted for by explicit consideration of the first hydration shell of uranyl and by means of a posteriori corrections for long-range solvent effect. With energetics described at the GGA-PW91 level and under the assumption of a fully protonated ideal surface, we predict a weakly bound outer-sphere adsorption complex.     

Effect of humic acid, pH and ionic strength on the sorption of Eu(III) on red earth and its solid component

Sorption and desorption of radioeuropium on red earth and its solid components to remove organic matter was studied at pH 5.3±0.1 and 4.5±0.1, and in 0.01M and 0.001M NaClO₄ solutions, respectively. Eu(III) sorption showed strong pH and humic acid concentration dependency, and NaClO₄ concentration independency. The sorption increased with increasing pH and amount of HA adsorbed on red earth. The sorption of Eu(III) on red earth was mainly dominated by surface complexation. Humic acid and high pH had a great tendency to immobilize the movement of Eu(III) in red earth. Sorption-desorption hysteresis of Eu(III) on red earth indicated that the sorption was irreversible.     

A computer modeling study of the competitive adsorption of water and organic surfactants at surfaces of the mineral scheelite

Atomistic computer simulation techniques were employed to investigate the interaction of a selection of organic surfactant molecules with a range of scheelite surfaces. The adsorbates coordinate mainly to the surfaces through interaction between their oxygen (or nitrogen) atoms to surface calcium ions, followed by hydrogen-bonded interactions to surface oxygen ions. Bridging between two surface calcium ions is the preferred mode of adsorption, but a bidentate interaction by two adsorbate oxygen ions to the same surface calcium ion is also a stable configuration and multiple interactions between surfaces and adsorbate molecules lead to the largest adsorption energies. All adsorbates containing carbonyl and hydroxy groups interact strongly with the surfaces, releasing energies between approximately 80 and 170 kJ mol(-1), but methylamine containing only the -NH2 functional group adsorbs to the surfaces to a much lesser extent (55-86 kJ mol(-1)). Both hydroxymethanamide and hydroxyethanal adsorb to some surfaces in an eclipsed conformation, which is a requisite for these functional groups. Sorption of the organic material by replacement of preadsorbed water at different surface features is calculated to be mainly exothermic for methanoic acid, but less so for the hydroxymethanamide and hydroxyethanal molecules, whereas methylamine would not replace preadsorbed water at the scheelite surfaces. The efficacy of the surfactant molecules is hence calculated to be carboxylic acids > alkyl hydroxamates > hydroxyaldehydes > alkylamines. The results from this study suggest that computer simulations may provide a route to the identification or even design of particular organic surfactants for use in mineral separation processes.     

Analysis of transport behavior in polymer powders

Vapor sorption studies on powder samples of glassy polymers have provided data which supplement results obtained on conventional film specimens and aid in the elucidation of glassy-state transport mechanisms. For uniform spherical particles of sub-micron size, sorption kinetics at very low activities of organic vapors follow a simple Fickian diffusion model. The short diffusion path in such samples allows determination of the very low diffusivities characteristic of the glassy state in experiments of conveniently short duration. Deviations from the Fickian, uniform-sphere model are observed in several circumstances: Particle size non-uniformity retards the approach to diffusion equilibrium. Sorption data at substantial vapor activities show an apparently similar slow approach to equilibrium which can be related to the contribution of a relaxation-controlled mode of sorption. The effects of particle non-uniformity and of relaxation processes can be distinguished by appropriate experimental design, and models for both have been developed. Sorption rate data obtained under Fickian diffusion conditions can be used to characterize particle size distribution. Sorption kinetics on uniform-sphere powders, conversely, can be analyzed through a diffusion-plus-relaxation model to distinguish and quantify the roles of the two transport modes more clearly than is possible with polymer film specimens. Polymer powder vapor solubility isotherms show significant variations with sample history which can be interpreted in terms of free volume changes and glassy state relaxations. This discussion, based on a study of vapor sorption by poly(vinyl chloride) samples, indicates that powder sorption measurements are also likely to be of general value in the study of other glassy polymers.     

Adsorption of dicarboxylic acids by clay minerals as examined by in situ ATR-FTIR and ex situ DRIFT

The adsorption of dicarboxylic acids by kaolinite and montmorillonite at different pH conditions was investigated using in situ attenuated total reflectance Fourier transform infrared (ATR-FTIR) and ex situ diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy. The sorption capacity of montmorillonite was greater than that of kaolinite. Adsorption of dicarboxylic acids (succinic acid, glutaric acid, adipic acid, and azelaic acid) was the highest at pH 4 as compared with those at pH 7 and 9. These results indicate that sorption is highly pH-dependent and related to the surface characteristics of minerals. The aliphatic chain length of the dicarboxylic acids highly influenced the sorption amount at acidic pH, regardless of the clay mineral species: succinic acid [HOOC(CH2)2COOH] < glutaric acid [HOOC(CH2)3COOH] < adipic acid [HOOC(CH2)4COOH] < azelaic acid [HOOC(CH2)7COOH]. With in situ ATR-FTIR analysis, most samples tend to have outer-sphere adsorption with the mineral surfaces at all tested pHs. However, inner-sphere coordination between the carboxyl groups and mineral surfaces at pH 4 was dominant from DRIFT analysis with freeze-dried complex samples. The complexation types, inner- or outer-sphere, depended on dicarboxylic acid species, pH, mineral surfaces, and solvent conditions. From the experimental data, we suggest that organic acids in an aqueous environment prefer to adsorb onto the test minerals by outer-sphere complexation, but inner-sphere complexation is favored under dry conditions. Thus, organic acid binding onto clay minerals under dry conditions is stronger than that under wet conditions, and we expect different conformations and aggregations of sorbed organic acids as influenced by complexation types. In the environment, natural organic material (NOM) may adsorb predominantly on positively charged mineral surfaces at the aqueous interface, which can convert into inner-sphere coordination during dehydration. The stable NOM/mineral complexes formed by frequent wetting-drying cycles in nature may resist chemical/microbial degradation of the NOM, which will affect carbon storage in the environment and influence the sorption of organic contaminants.