Fig 4 - uploaded by Mya A. Norman
Content may be subject to copyright.
In the presence of several layers of water, an organic molecule can adsorb at a mineral surface via a single group, while the bulk of its structure is immersed in the aqueous phase, as shown here for DNOC on montmorillonite (snapshot after 250 ps of MD simulations). For graphic clarity, water molecules are rendered in the line-drawing mode, while the ball and stick mode was chosen for DNOC and the mineral lattice.
Source publication
Computational studies of the sorption of organic compounds at clay mineral surfaces are described. Molecular dynamics simulations were performed with a recently developed empirical force field for dioctahedral clays. The studies allow the identification of three general mechanisms of adsorption. In the absence of water, organic compounds adsorb to...
Context in source publication
Context 1
... [3] for the 1:1 clay mineral kaolinite can be used to construct a surface for simulations by fusing several unit cells together to form a supercell. A supercell with com- position Al 32 Si 32 O 80 (OH) 64 , for example, offers a nearly rectangular repeat unit base of 20.61 by 17.88 A ̊ in the crystallographic ab -plane [57]. Unlike smectites, kaolinite does not typically swell along the c -axis upon hydration. The layers can never- theless be separated in the simulations, increasing the c axis from 7.4 A, ̊ the crystal spacing [3], to some 20.0 A ̊ or larger, in order to create an interlayer space of de- sired dimension, where the behavior of water and adsorbed molecules can be modeled. Kaolinite is an interesting model mineral, since it presents two very different types of surfaces to aqueous solutions. The artificial expansion of the interlayer space creates a pore, which provides both types of basal external surface found on a kaolinite mineral grain. Slit pores of this type are found in kaolinite books [61] and perhaps at interfaces between silicate grains and aluminum oxide coatings. Systems with an artificially expanded interlayer space are modeled under NVT (constant mass, volume and temperature) conditions, if the intention is to keep the d (001) spacing constant. In order to equilibrate an expanded system, simulations are subjected to NPT (constant mass, pressure, and temperature) conditions. During that process, the separated layers spontaneously anneal, restoring the equilibrium interlayer spacing characteristic of a given system. In other MD simulations [59], we have used the crystallographic structure [4] of pyrophyllite, an uncharged, 2:1, dioctahedral phyllosilicate, to construct a model system for studying adsorption. For example, fusing six unit cells of pyrophyllite will yield an Al 24 Si 48 O 120 (OH) 24 supercell of a neutral, idealized 2:1 clay. Pyrophyllite is well suited for study because it has the same structure as the smectites, but it is a neutral clay and the interlayer space is thus devoid of any hydrated counter ions. When Si ions in the tetrahedral sheet of a pyrophyllite supercell are iso- morphically substituted with Al, an idealized beidellite system results with a cation-exchange capacity dependent on the chosen extent of substitution. Alternatively, model montmorillonite systems can be constructed by isomor- phic substitutions of Al in the octahedral sheet by Mg. The mineral surfaces constructed in this way are usu- ally hydrated at various levels, producing various layers of water, as needed. Subsequently, the adsorbates to be studied are added to the interlayer space or pore surface and subjected to MD simulations for time periods of, typically, several hundred picoseconds, using a time step of 0.5 fs. The structures of two pesticides, 2-chloro-4- ethylamino-6-isopropylamino- S -triazine, commonly called atrazine (ATZ), and of 2-methyl-4,6-dinitro phenol, commonly called DNOC, are shown in Fig. 1. We are currently studying the adsorption of both systems on a model montmorillonite with a cation-exchange capacity of 105 meq/100 g, using K + as counter ions. Other counter ions are also considered because they affect the transport properties of pesticides on soils [62]. The behavior of DNOC and ATZ on clays follows trends generally found for the sorption of organic compounds [57–60]. When organic compounds like ATZ and DNOC are placed with random orientations in the clay interlayer space, as shown for DNOC in Fig. 2, they will move spontaneously during MD simulations to the mineral surface and adsorb coplanar with the mineral basal plane (Fig. 2). During this process, the counter ions will perform a simi- lar movement, sometimes forming ion bridges, as seen for DNOC in Fig. 2. Interestingly, no ion bridging was found for ATZ. The tendency to maximize contact area is a general characteristic for organic compounds on dry mineral surfaces, when no water is present. In the case of peptides and proteins [60] it is the cause of significant denaturing, i.e., large changes in φ , ψ -torsional angles [60]. Details of how adsorbed species in this state interact with siloxane surfaces are shown in Fig. 3. In a characteristic way, adsorbing species tend to point a functional group to the inside of a hexagonal siloxane cavity, but not to the ex- act center. Off-center adsorption is particularly clear for single ions (Fig. 3). In the presence of water, the adsorption mechanism can change significantly because water can displace organic compounds from surface sites, and because polar compounds show an affinity of their own for aqueous solutions. Basically, two different processes are possible in the presence of water. When the amount of water in the interlayer space is sufficiently high for forming several water layers (see below), organic compounds can attach to a mineral surface via a single functional group, while its bulk is immersed in the aqueous phase. Such a case is shown in Fig. 4, in which DNOC is seen to sorb via one of its NO 2 groups, while the main part of its body remains immersed in the aqueous phase. Similarly, ATZ was found to interact with a mineral surface by penetrating a water layer with its C-Cl bond. The same mechanism was previously obtained for trichloroethene [57]. In the single-group adsorption mode, the adsorbates are typically mobile and able to diffuse significantly, jumping from one surface site to another. In contrast, coplanar adsorbates are effectively immobilized. The ability of pesticides to form complexes with counter ions is an important factor in their transport properties in soils [62]. To investigate whether such complexes are being formed to a statistically significant extent between DNOC and K + , the histogram of Fig. 5 was gen- erated, involving distances between DNOC–oxygen and K + on montmorillonite. From that analysis (Fig. 5), short- range interactions between DNOC–NO 2 and K + appear as relatively infrequent. Further analyses with different ions, such as Ca 2 + , are currently under investigation. When the interlayer space is soaked with a large amount of water, DNOC and ATZ show a tendency to remain completely in the aqueous phase without mak- ing contact with the mineral surface. We have obtained the same result before for TCE [57] and methylene blue [59]. For proteins in proximity to mineral surfaces, large amounts of water allow for retaining the globular structure, which dry surfaces destroy. Figure 6 shows the protein, rubredoxin, in the presence of DNOC and some 2000 water molecules on pyrophyllite. It is seen that, after 150 ps of dynamics, the essential globular structure has been pre- served. In a system of this kind, a given pesticide can interact with both the surfaces of the mineral and of the protein. In our studies of hydrated clay surfaces, we noticed that dynamics relaxation will lead in a short time from per- fectly disordered starting configurations to highly structured arrangements of water. The phenomenon is illus- trated in Fig. 7, where three distinct water layers are seen in a typical snapshot of hydrated DNOC on montmorillonite. When the loading is very high, as in the system shown in Fig. 8, narrow water layers will form adjacent to a surface and are visibly separated from the bulk phase in the interior of the interlayer space. To study the dependence of water structures on state variables, a model beidellite system, with a 4 × 2 × 1 supercell, 178 water molecules, and six charges compen- sated by Ca 2 + , was subjected to MD equilibrations at a pressure of 1 atm and temperatures of 300, 350, 400, 450, and 500 K; and at a temperature of 300 K and external pressures of 1, 2, 3, 5, and 10 atm. In the first series, d (001) spacings were found at 20.46, 20.66, 20.89, 21.20, and 21.75 A, ̊ respectively (averages of batch averages of 50 steps taken during the last 5 ps of 30 ps runs). As the temperature increased, the layer structure was destroyed by the high kinetic energy. In contrast, in the second series (80 ps runs), changes in pressure had no effect on the water layers, and also the d (001) spacing was practically unaffected (at 20.46, 20.40, 20.47, 20.45, and 20.40 A, ̊ respectively). The ordering of water in interlayer spaces is an interesting phenomenon [27–29]. Plots of the distances between water oxygen atoms and mineral surfaces (Fig. 9) show that the water arranges not only in layers along the c -axis, but also along the other axes. These trends are apparent in single snapshots of equilibrated systems, as well as in ensemble averages (Figs. 10 and 11). We think that the extent of the ordering is perhaps exaggerated by the calculations. Some ordering of the kind revealed by Figs. 9–11 must be expected, [27–29], but the absence of polarization functions in the current empirical force fields may very well lead to a higher order than is realistic. Molecules are more strongly adsorbed on dry surfaces than on hydrated ones. The siloxane cavity of clay minerals plays a major role in neutral molecule adsorption as it does in the adsorption of ions. Ions as well as polar functional groups (NO 2 in DNOC and C Cl in ATZ) position themselves in a characteristically off- center arrangement relative to the hexagonal siloxane cavity. In the presence of water, the organic compounds can make contact with clay surfaces by single functional groups and can then be expected to move rapidly through soils. When adsorbed by full molecular contact, coplanar with the basal surface, the adsorbates are essentially immobilized. From that position desorption by water can occur, with different rates, depending on surface type and type of compound adsorbed. The current work was based entirely on empirical computational techniques. In the future, quantum molecular dynamics simulations, using techniques such as those implemented by program CASTEP [63] can be expected to be of increasing importance. The authors gratefully ...
Citations
... -17 of 28 that organic inhibitors typically have long-chain structures containing multiple binding sites, it could be difficult for them to reach equilibrium on the calcite surface within the limited simulation time. Besides, Yu et al. [264] discovered that organic molecules often bind the mineral surfaces with a single functional group in aqueous solutions with the rest being immersed in the water. Therefore, investigating the adsorption properties of key functional groups seems to be a more practical approach. ...
Calcium carbonate (CaCO3) is a crucial mineral with great scientific relevance in biomineralization and geoscience. However, excessive precipitation of CaCO3 is posing a threat to industrial production and the aquatic environment. The utilization of chemical inhibitors is typically considered an economical and successful route for addressing the scaling issues, while the underlying mechanism is still debated and needs to be further investigated. In this context, a deep understanding of the crystallization process of CaCO3 and how the inhibitors interact with CaCO3 nuclei and crystals are of great significance in evaluating the performance of scale inhibitors. In recent years, with the rapid development of computing facilities, computer simulations have provided an atomic‐level perspective on the kinetics and thermodynamics of possible association events in CaCO3 solutions as well as the predictions of nucleation pathway and growth mechanism of CaCO3 crystals as a complement to experiment. This review surveys several computational methods and their achievements in this field with a focus on analyzing the functional mechanisms of different types of inhibitors. A general discussion of the current challenges and future directions in applying atomistic simulations to the discovery, design, and development of more effective water‐scale inhibitors is also discussed.
... The number of load step in each calculated run is 6:0 × 10 6 , in which the balance step number is 3:0 × 10 6 and the process step number is 3:0 × 10 6 . This GCMC method was successfully used to calculate the absorption of CO 2 in magnesite in our previous works [35], and its validity also was proved by different works [31,[36][37][38][39][40]. ...
CO2 transports in the Earth’s interior play a crucial role in understanding the deep carbon cycle and the global climate changes. Currently, CO2 transports inside of the Earth under extreme condition of pressure and temperature have not been understood well. In this study, the molecular dynamics (MD) calculations were performed to study CO2 transports under different CO2 pressures in slit-like magnesite pores with different pore sizes at 350~2500 K and 3~50 GPa are presented. Diffusion of CO2 in magnesite was improved as the temperature increases but showed the different features as a function of pressure. The diffusion coefficients of CO2 in magnesite were found in the range of 9×10−12 m2 s−1~28000×10−12 m2 s−1. Magnesite with the pore size of 20~25 Å corresponds to the highest transports. Anisotropic diffusion of CO2 in magnesite may help to understand the inhomogeneous distribution of carbon in the upper mantle. The time of CO2 diffusion from the mantle to Earth surface was estimated to be around several tens of Ma and has an important effect on deep carbon cycle. The simulation of CO2 transports based on the Earth condition provides new insights to revealing the deep carbon cycle in the Earth’s interiors.
... With the current high-performance computational resources, molecular simulations have become powerful tools for understanding the molecular-scale structural 18,19 , thermodynamic 20 , mechanical 21 and dynamic [22][23][24][25] properties of clay. Grand-canonical Monte Carlo (GCMC) method was used to examine the adsorption of CO 2 with H 2 O 23 , CH 4 26-28 and organic molecules 25,29 in clay. Yang et al. used molecular dynamics (MD) to study the structure and self-diffusion coefficient (SDC) of CO 2 in uncharged clay-like slit pores 24 . ...
Storing CO2 in underground saline aquifers is an important way to reduce CO2 emission in atmosphere, where gas/fluid diffusion in clay plays a key role in CO2 leakage and migration. Various diffusivities, self-diffusivity, Maxwell–Stefan (M–S) diffusivity and Fick diffusivity, in clay interlayer are investigated by molecular dynamics (MD). Self-diffusivity varies with CO2 concentration, and reaches the maximum value at 2 molecules/unit-cell. High fluid concentration leads to clay swelling, thereby increasing self-diffusivity. However, the fractional free volume of clay explains the trend of CO2 self-diffusivity, which does not decrease with CO2 concentration monotonously but reaches the maximum when CO2 concentration reaches 2. Displacement distribution of CO2 molecules is analysed to explore the microscopic diffusion mechanism, which is characterised by logarithmic normal distribution. The mean value of such distribution further explains the self-diffusivity dependence on CO2 concentration. M–S and Fick diffusivities of CO2 are calculated by MD for the first time, both of which increase with increasing CO2 and H2O concentration and temperature. Based on self-diffusivity and M–S diffusivity, a quantity representing the coupling strength between CO2 molecules is presented; it increases firstly with CO2 concentration but begins to decrease when CO2 concentration is beyond 2.
... Several studies, summarized by Kalbitz [21], have shown that after heavy rainfall events and during snowmelt in the early stages, preferential flow through macropores in structure soils can affect DOC output by reducing contact time between the solid and solution phase. According to the laboratory experiments of Yu et al. [38], in the absence of water, organic compounds adsorb on the mineral surfaces in such a way that contact area is maximized. ...
This study demonstrates the potential of the electrochemical methods for the characterization of dissolved organic matter (DOM) in the drainage water of hydroameliorated agricultural areas. A study of drainage water could lead to a better understanding of the distribution and fate of terrestrial DOM in the freshwater systems. We have applied the voltammetric techniques which were developed by our group for the characterization of organic matter in the natural waters in general. Studied samples were collected in the experimental amelioration fields in the Sava river valley (45° 33′ 52″ N/16° 31′ 33″ E, 100 m above sea level), in the hydroameliorated agricultural areas in Croatia. The rough characterization of the type, nature and reactivity of DOM was done through the study of surface activity (SA) of dissolved organic carbon (DOC), copper complexing capacity (CuCC) and apperent stability constants, and measurements of organic and inorganic reduced sulfur species (RSS) fractions. The results confirm that the electrochemical approach gives a valuable and comprehensive insight into physicochemical characteristics of DOM in the drainage water and could be successfully applied to temporal studies in different terrestrial ecosystem.
... No attempt has been made to quantify the effect of methylgroup orientation because these rearrangements in general have a minor role in adsorption structure or energetics. At higher concentrations, aggregates of adsorbed MB + consist mainly of MB + oriented perpendicular to the surface ( Figure 4b), in agreement with MD simulations of MB + trimers and pentamers adsorbed on a dry mica surface ( Yu et al., 2003). Details of this surface structure will be explored in more detail below. ...
Organic dyes such as methylene blue (MB) are often used in the characterization of clays and related minerals, but details of the adsorption mechanisms of such dyes are only partially understood from spectroscopic data, which indicate the presence of monomers, dimers, and higher aggregates for varying mineral surfaces. A combination of quantum (density functional theory) and classical molecular simulation methods was used to provide molecular detail of such adsorption processes, specifically the adsorption of MB onto kaolinite basal surfaces. Slab models with vacuum-terminated surfaces were used to obtain detailed structural properties and binding energies at both levels of theory, while classical molecular dynamics simulations of aqueous pores were used to characterize MB adsorption at infinite dilution and at higher concentration in which MB dimers and one-dimensional chains formed. Results for the neutral MB molecules are compared with those for the corresponding cation. Simulations of the aqueous pore indicate preferred adsorption on the hydrophobic siloxane surface, while charge-balancing chloride ions adsorb at the aluminol surface. At infinite dilution and in the gas-phase models, MB adsorbs with its primary molecular plane parallel to the siloxane surface to enhance hydrophobic interactions. Sandwiched dimers and chains are oriented perpendicular to the surface to facilitate the strong hydrophobic intermolecular interactions. Compared with quantum results, the hybrid force field predicts a weaker MB adsorption energy but a stronger dimerization energy. The structure and energetics of adsorbed MB at infinite dilution are consistent with the gas-phase binding results, which indicate that monomer adsorption is driven by strong interfacial forces rather than by the hydration properties of the dye. These results inform spectroscopic studies of MB adsorption on mineral surfaces while also revealing critical areas for development of improved hybrid force fields.
... Perhaps only calculations on the basis of molecular dynamics in 3D simulations of fully hydrated clay environments can supply the desired predictive power if these models are sufficiently optimized to deliver quantitative output on sorption energies in fully hydrated clay systems. 45,46 Until then, the VxNAi model in combination with continuously updated empirical corrective increments can be used for chemicals that fall inside the chemical applicability domain. For chemicals that are clearly outside the chemical domain, sorption isotherms should be measured experimentally on a single relevant phyllosilicate clay mineral at least. ...
Sorption to the phyllosilicate clay minerals illite, kaolinite, and bentonite, has been studied for a wide variety of organic cations, using a flow-through method with fully aqueous medium as eluent. Linear isotherms were observed at concentrations below 10% of the cation exchange capacity (CEC) for illite and kaolinite, and below 1 mmol/kg (<1% CEC) for bentonite. Sorption to clays was strongly influenced by electrolyte composition of the eluent, but with a consistent trend for a diverse set of compounds on all clays, thus allowing for empirical correction factors. When sorption affinities for a given compound to a given clay are normalized to the CEC of the clay, the differences in sorption affinities between clays are reduced to less than 0.5 log units for most compounds. While CEC-normalized sorption of quaternary ammonium compounds to clay was up to 10-fold higher than CEC-normalized sorption to soil organic matter, CEC-normalized sorption for most compounds was comparable between clays and soil organic matter. The clay fraction is thus a potentially relevant sorption phase for organic cations in many soils. The sorption data for organic cations to clay showed several regular trends with molecular structure, but also showed quite a few systematic effects that we cannot explain yet. A model based on molecular size and charge density at the ionized nitrogen is used here as tool to obtain benchmark values that elucidate the effect of specific polar moieties on the sorption affinity.
... Schulten and Schnitzer, 1997;Shevchenko and Bailey, 1998) or (ii) by submersing the model in a defined water box containing several hundreds of water molecules (condensed phase; e.g. Sutton et al., 2005;Yu et al., 2003). ...
... Schulten and Schnitzer, 1997;Shevchenko and Bailey, 1998) or (ii) by submersing the model in a defined water box containing several hundreds of water molecules (condensed phase; e.g. Sutton et al., 2005;Yu et al., 2003). ...
The structure of soil organic matter (SOM) and humic substances (HS) has been discussed from different viewpoints including molecular conformation, molecular aggregation, macromolecularity, supramolecular characteristics, domain mobility, and many others. Until now, the individual models appear partly contradictory, although each viewpoint provides important information on the structural and functional properties of SOM. This is most probably due to the huge heterogeneity of SOM. Therefore, the question: “How can molecular modeling help to further understand structure and functioning of soil organic matter?” needs to be addressed with care. This contribution reviews and discusses the potential of important molecular modeling approaches currently applied in soil organic matter science.
... Thus, the most stable distribution with no Mg– Mg pairs in the octahedral sheet was used in our calculations. In the study of Yu et al. [6], it was shown that the influence of water could not be neglected in the interlayer of MMT– organic compounds systems. In the presence of sufficient amount of water molecules in the interlayer, the bulk of organic molecules (2-methyl-4,6-dinitro phenol and antrazine ) is immersed in aqua phase while molecule's functional groups are connected to the silicate layer. ...
... The optimal configurations of four and eight phenols arranged into the pyramid and layer of irregularly tilted molecules, respectively, are shown in Figures 3 and 4. In addition, the thin water layer was favourably formed above MMT and tended to push phenols away as demonstrated in the first two rows ofTable 4. It is not surprising because non-ionised phenol has low polarity as demonstrated by its K OW (see above). The tendency of the water layer formed on the surfaces of clay minerals to exclude organic adsorbates backward to the aqueous phase has also been demonstrated by molecular dynamics simulations [6]. Phenol solvated by water molecules in the MMT interlayer space was recognised by the Monte Carlo and molecular dynamics computer simulations [4]. ...
Natural and intercalated Wyoming montmorillonite (MMT) with the tetramethylammonium (TMA) cations were used for the adsorption of phenol and aniline. Laboratory experiments characterised by adsorption isotherms were compared with the results of molecular modelling simulations. Aniline adsorbed itself strongly on MMT; while using the TMA intercalates (TMA-MMT), its adsorption decreased. On the contrary, the adsorption of phenol on TMA-MMT was moderately higher than on the MMT surface. The MMT surface models were described by empirical force-field used in molecular mechanics and dynamics. The Burchart–Universal force-field was used in the Cerius2 modelling environment. The modelling results revealed the important role of water forming a moderately concentrated layer on the pure MMT surface. Water molecules enable the adsorption of aniline on MMT and, on the contrary, repeal phenol molecules from MMT. In the case of TMA-MMT, lower amount of water near a silicate layer caused decrease of the aniline adsorption and, on the contrary, increase of the phenol adsorption.
... Yu et al. 178 point out the differences between excluding and including water in their simulations of organic molecules on mineral surfaces. The range of behaviors they observe has been seen by several other studies since. ...
Simulation methods applied to the challenges of biomineralization has steadily advanced in recent times. Improvements on these methods are presented focusing on coarse-grained model that can be calibrated or validated against molecular dynamics simulations. Another approach is to concentrate on the use of a coarse-grained model to model the long time scale evolution of a system, as well as to create models that are explicitly based on rules. This last strategy will work by showing the types of behavior that are possible and how these behaviors depend on the rules that are chosen. Such new models and simulation are needed since biomineralization still presents a challenge to present theories of nucleation and growth.
