Molecular dynamics simulations of sorption of organic compounds at the clay mineral/aqueous solution interface

The adsorption of trichloroethene, C₂HCl₃, on clay mineral surfaces in the presence of water has been modeled as an example describing a general program that uses molecular dynamics simulations to study the sorption of organic materials at the clay mineral/aqueous solution interface. Surfaces of the clay minerals kaolinite and pyrophyllite were hydrated at different water levels corresponding to partial and complete monolayers of water. In agreement with experimental trends, water was found to outcompete C₂HCl₃ for clay surface sites. The simulations suggest that at least three distinct mechanisms coexist for C₂HCl₃ on clay minerals in the environment. The most stable interaction of C₂HCl₃ with clay surfaces is by full molecular contact, coplanar with the basal surface. This kind of interaction is suppressed by increasing water loads. A second less stable and more reversible interaction involves adsorption through single-atom contact between one Cl atom and the surface. In a third mechanism, adsorbed C₂HCl₃ never contacts the clay directly but sorbs onto the first water layer. To test the efficacy of existing force field parameters of organic compounds in solid state simulations, molecular dynamics simulations of several representative organic crystals were also performed and compared with the experimental crystal structures. These investigations show that, in general, in condensed-phase studies, parameter evaluations are realistic only when thermal motion effects are included in the simulations. For chlorohydrocarbons in particular, further explorations are needed of atomic point charge assignments. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 144–153, 1998     

Adsorption of thymine and uracil on 1:1 clay mineral surfaces: comprehensive ab initio study on influence of sodium cation and water

This computational study performed using the density functional theory shows that hydrated and non-hydrated tetrahedral and octahedral kaolinite mineral surfaces in the presence of a cation adsorb the nucleic acid bases thymine and uracil well. Differences in the structure and chemistry of specific clay mineral surfaces led to a variety of DNA bases adsorption mechanisms. The energetically most predisposed positions for an adsorbate molecule on the mineral surface were revealed. The target molecule binding with the surface can be characterized as physisorption, which occurs mainly due to a cation-molecular oxygen interaction, with hydrogen bonds providing an additional stabilization. The adsorption strength is proportional to the number of intermolecular interactions formed between the target molecule and the surface. From the Atoms in Molecules analysis and comparison of binding energy values of studied systems it is concluded that the sorption activity of kaolinite minerals for thymine and uracil depends on various factors, among which are the structure and accessibility of the organic compounds. The adsorption is governed mostly by the surface type, its properties and presence of cation, which cause a selective binding of the nucleobase. Adsorbate stabilization on the mineral surface increases only slightly with explicit addition of water. Comparison of activity of different studied kaolinite mineral models reveals the following order for stabilization: octahedral-Na-water > octahedral-Na > tetrahedral-Na > tetrahedral-Na-water. Further investigation of the electrostatic potentials helps understanding of the adsorption process and confirmation of the active sites on the kaolinite mineral surfaces. Based on the conclusions that clay mineral affinity for DNA and RNA bases can vary due to different structural and chemical properties of the surface, a hypothesis on possible role of clays in the origin of life was made.     

Dual-scale modeling of benzene adsorption onto Ni(111) and Au(111) surfaces in explicit water.

We present a multiscale modeling approach for studying interactions of organic molecules with metal surfaces in explicit water. The approach is based on combining adsorption energies of isolated molecules on transition metal surfaces calculated by ab initio density functional methods and classical molecular dynamics simulations using atomistically detailed force fields. The interaction of benzene with Ni(111) and Au(111) surfaces was studied. It is shown that a strong affinity of water for the hydrophilic surfaces makes benzene adsorption on Au thermodynamically unfavorable, while on Ni there is no preference. The work presented here serves as a first step in modeling the interactions of larger organic molecules with metal surfaces.     

Molecular modeling of polymer-clay nanocomposite precursors: Lysine in montmorillonite interlayers

The layered structure of clays with interlayer cations leads to unique chemical and mechanical properties, which have been capitalized on in the field of polymer/layered silicate nanocomposites. Hydrophilic silica surfaces can become organophilic with the inclusion of alkylammonium cations, which improve the wetting characteristics of the polymer matrix. In fact, the molecular level interactions of amino acids, either natural or non-natural, with clay surfaces are at the heart of fields of study as diverse as nanocomposites fabrication, drug delivery, bio-remediation of soils and catalysis of biological polymers, to name a few. The ubiquity of these systems and the potential uses to which they could be put suggests the necessity of a deeper understanding of the interplay of bonds, conformations, and configurations between the molecules and the hosts. The interactions of the amino acid lysine with sodium montmorillonite were studied using theoretical molecular modeling methods. The interlayer spacing of montmorillonite was increased by incorporating water molecules and allowing the system to evolve with molecular mechanics. Care was taken to retain the sodium cations in the interlayer. The initial amino acid conformation was obtained surrounding the molecule with numerous discrete water molecules and minimizing the system at the semi empirical level. The optimized amino acid was then placed in the interlayer space in a series of initial positions. Molecular mechanics calculations were performed and the final positions were analyzed. The results tended to indicate the preponderance of configurations which included surface-sodium-amino acid complexes with a variety of spatial arrangements. These results were compared with molecular dynamics calculations of similar systems from the literature.     

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.     

Morphology and mechanical properties of surfactant aggregates at water-silica interfaces: molecular dynamics simulations

Dilute and concentrated surfactant systems at the solid-liquid interface are examined using classical molecular dynamics simulations. Particular emphasis is placed on understanding how surfactants aggregate and form the micellar structure, how micelles change shape at high concentrations in aqueous media and in the presence of hydrophilic surfaces, and at what force this micellar structure breaks apart during indentation of micelle-covered surfaces with a proximal probe microscope tip. The specific system of interest is C12TAB (n-dodecyltrimethylammonium bromide) surfactant in an aqueous medium that is modeled with empirical potentials. The simulations predict that the micelle structure in water is compact and either spherical or elliptical in shape. In the presence of a hydrophilic surface of silica, the structure evolves into a flat elliptical shape, in agreement with experimental findings. The simulated indentation of the micelle/silica system causes the micelle to break apart at an indentation force of about 1 nN and form a surfactant monolayer. The predicted force curve is in excellent agreement with experimental measurements.     

Non-bonded organo-mineral interactions and sorption of organic compounds on soil surfaces: a model approach

Molecular mechanics and molecular dynamics calculations have been performed on organo-mineral composites that model the sorption of high-molecular-weight humic polymers on mineral surfaces and the sorption of low-molecular-weight organic contaminants on both mineral and organic surfaces in soil. Muscovite mica was chosen as a mineral model; an oxidized topological lignin-carbohydrate complex was chosen as a humic model; benzene, sodium benzoate, atrazine, and DDT represent different classes of contaminants. Sorption energies were estimated based on molecular mechanics calculations. Flexible linear polymers undergo drastic conformational changes when approaching the mineral surface, to ensure a gain in the interaction energy that outweighs a loss in the conformational energy proper. Therefore, the gas-phase conformation composi tion of environmental organic polymers is not directly related to their spatial organization in soil composites. Molecular dynamics simulation suggests high stability of the organic polymer coatings of mineral surfaces in the environment. Low-molecular-weight organic molecules demonstrate much less affinity for the mineral surface, which implies unhindered exchanges between the surface and its near environment. Ionizable compounds, e.g. salts of organic acids, are different, because they can form strong associations with a mineral surface through cation bridges. Sorption energies are compound-specific and depend on the sorbate-sorbent orientation. The calculations suggest some preference for the edges of a model muscovite sheet in comparison with the basal oxygen surface as a sorption site. Coating of mineral surfaces with organic polymers does not hinder the sorption of organic molecules except in the special case of organic ions.     

AFM study of mineral wettability with reservoir oils

Wettability plays a key role in determining fluid distributions and consequently the multiphase flow and transport in petroleum reservoirs. Many crude oils have polar organic components that collect at oil-water interfaces and can adsorb onto the mineral surface if the brine film breaks, rendering the medium oil-wet or mixed-wet. Mica and silica surfaces have been aged with brine and crude oils to induce oil component adsorption. Bulk oil is eventually replaced by water in these experiments by washing with common solvents without ever drying the mineral surface. The organic deposit on the mineral surface is studied by atomic force microscopy in the tapping mode under water. Drying the surface during the removal of bulk oil induces artifacts; it is essential to keep the surface wet at all times before atomic force microscopy or contact angle measurement. As the mean thickness of the organic deposit increases, the oil-water contact angle increases. The organic deposits left behind after extraction of oil by common aromatic solvents used in core studies, such as toluene and decalin, are thinner than those left behind by non-aromatic solvents, such as cyclohexane. The force of adhesion with a probe sphere for minerals aged with just the asphaltene fraction is similar to that of the whole oil. The force of adhesion for the minerals aged with just the resin fraction is the highest of all SARA (saturates, aromatics, resins, and asphaltenes) fractions.     

Small molecule‐mediated control of hydroxyapatite growth: Free energy calculations benchmarked to density functional theory

The unique, plate‐like morphology of hydroxyapatite (HAP) nanocrystals in bone lends to the hierarchical structure and functions of bone. Proteins enriched in phosphoserine (Ser‐OPO₃) and glutamic acid (Glu) residues have been proposed to regulate crystal morphology; however, the atomic‐level mechanisms remain unclear. Previous molecular dynamics studies addressing biomineralization have used force fields with limited benchmarking, especially at the water/mineral interface, and often limited sampling for the binding free energy profile. Here, we use the umbrella sampling/weighted histogram analysis method to obtain the adsorption free energy of Ser‐OPO₃ and Glu on HAP (100) and (001) surfaces to understand organic‐mediated crystal growth. The calculated organic‐water–mineral interfacial energies are carefully benchmarked to density functional theory calculations, with explicit inclusion of solvating water molecules around the adsorbate plus the Poisson–Boltzmann continuum model for long‐range solvation effects. Both amino acids adsorb more strongly on the HAP (100) face than the (001) face. Growth rate along the [100] direction should then be slower than in the [001] direction, resulting in plate‐like crystal morphology with greater surface area for the (100) than the (001) face, consistent with bone HAP crystal morphology. Thus, even small molecules are capable of regulating bone crystal growth by preferential adsorption in specific directions. Furthermore, Ser‐OPO₃ is a more effective growth modifier by adsorbing more strongly than Glu on the (100) face, providing one possible explanation for the energetically expensive process of phosphorylation of some proteins involved in bone biomineralization. The current results have broader implications for designing routes for biomimetic crystal synthesis. © 2013 Wiley Periodicals, Inc.     

Molecular dynamics simulation study of water adsorption on hydroxylated graphite surfaces

In this paper, we present results from molecular dynamic simulations devoted to the characterization of the interaction between water molecules and hydroxylated graphite surfaces considered as models for surfaces of soot emitted by aircraft. The hydroxylated graphite surfaces are modeled by anchoring several OH groups on an infinite graphite plane. The molecular dynamics simulations are based on a classical potential issued from quantum chemical calculations. They are performed at three temperatures (100, 200, and 250 K) to provide a view of the structure and dynamics of water clusters on the model soot surface. These simulations show that the water-OH sites interaction is quite weak compared to the water-water interaction. This leads to the clustering of the water molecules above the surface, and the corresponding water aggregate can only be trapped by the OH sites when the temperature is sufficiently low, or when the density of OH sites is sufficiently high.     

Molecular dynamics simulations of peptide-surface interactions

Proteins, which are bioactive molecules, adsorb on implants placed in the body through complex and poorly understood mechanisms and directly influence biocompatibility. Molecular dynamics modeling using empirical force fields provides one of the most direct methods of theoretically analyzing the behavior of complex molecular systems and is well-suited for the simulation of protein adsorption behavior. To accurately simulate protein adsorption behavior, a force field must correctly represent the thermodynamic driving forces that govern peptide residue-surface interactions. However, since existing force fields were developed without specific consideration of protein-surface interactions, they may not accurately represent this type of molecular behavior. To address this concern, we developed a host-guest peptide adsorption model in the form of a G(4)-X-G(4) peptide (G is glycine, X is a variable residue) to enable determination of the contributions to adsorption free energy of different X residues when adsorbed to functionalized Au-alkanethiol self-assembled monolayers (SAMs). We have previously reported experimental results using surface plasmon resonance (SPR) spectroscopy to measure the free energy of peptide adsorption for this peptide model with X = G and K (lysine) on OH and COOH functionalized SAMs. The objectives of the present research were the development and assessment of methods to calculate adsorption free energy using molecular dynamics simulations with the GROMACS force field for these same peptide adsorption systems, with an oligoethylene oxide (OEG) functionalized SAM surface also being considered. By comparing simulation results to the experimental results, the accuracy of the selected force field to represent the behavior of these molecular systems can be evaluated. From our simulations, the G(4)-G-G(4) and G(4)-K-G(4) peptides showed minimal to no adsorption to the OH SAM surfaces and the G(4)-K-G(4) showed strong adsorption to the COOH SAM surface, which is in agreement with our SPR experiments. Contrary to our experimental results, however, the simulations predicted a relatively strong adsorption of G(4)-G-G(4) peptide to the COOH SAM surface. In addition, both peptides were unexpectedly predicted to adsorb to the OEG surface. These findings demonstrate the need for GROMACS force field parameters to be rebalanced for the simulation of peptide adsorption behavior on SAM surfaces. The developed methods provide a direct means of assessing, modifying, and validating force field performance for the simulation of peptide and protein adsorption to surfaces, without which little confidence can be placed in the simulation results that are generated with these types of systems.     

Investigation of ligand exchange reactions in aqueous uranyl carbonate complexes using computational approaches

Carbonate anion exchange reactions with water in the uranyl-carbonate and calcium-uranyl-carbonate aqueous systems have been investigated using computational methods. Classical molecular dynamics (MD) simulations with the umbrella sampling technique were employed to determine potentials of mean force for the exchange reactions of water and carbonate. The presence of calcium counter-ions is predicted to increase the stability of the uranyl-carbonate species in accordance with previous experimental observations. However, the free energy barrier to carbonate exchange with water is found to be comparable both in the presence and absence of calcium cations. Possible implications of these results for uranyl adsorption on mineral surfaces are discussed. Density functional theory (DFT) calculations were also used to confirm the trends observed in classical molecular dynamics simulations and to corroborate the validity of the potential parameters employed in the MD scheme.     

Adhesion of single polyelectrolyte molecules on silica, mica, and bitumen surfaces

In a recent study (Energy Fuels 2005, 19, 936), a partially hydrolyzed polyacrylamide (HPAM) was used as a process aid to recover bitumen from oil sand ores. It was found that HPAM addition at the bitumen extraction step not only improved bitumen recovery but also enhanced fine solids settling in the tailings stream. To understand the role of HPAM, single-molecule force spectroscopy was employed for the first time to measure the desorption/adhesion forces of single HPAM molecules on silica, mica, and bitumen surfaces using an atomic force microscope (AFM). Silicon wafers with an oxidized surface layer and newly cleaved mica were used, respectively, to represent sand grains and clays in oil sands. The force measurements were carried out in deionized water and in commercial plant process water under equilibrium conditions. The desorption/adhesion forces of HPAM obtained on mica, silica, and bitumen surfaces were approximately 200, 40, and 80 pN in deionized water and approximately 100, 50, and 40 pN in the plant process water, respectively. The measured adhesion forces together with the zeta potential values of these surfaces indicate that the polymer would preferentially adsorb onto clay surfaces rather than onto bitumen surfaces. It is the selective adsorption of HPAM that benefits both bitumen recovery and tailings settling when the polymer was added directly to the bitumen extraction process at an appropriate dosage.     

Interfacial water on hydrophobic surfaces recognized by ions and molecules

Recent spectrophotometric and molecular dynamics simulation studies have shown that the physicochemical properties and structures of water in the vicinity of hydrophobic surfaces differ from those of the bulk water. However, the interfacial water acting as a separation medium on hydrophobic surfaces has never been detected and quantified experimentally. In this study, we show that small inorganic ions and organic molecules differentiate the interfacial water formed on the surfaces of octadecyl-bonded (C(18)) silica particles from the bulk water and the chemical separation of these solutes in aqueous media with hydrophobic materials can be interpreted with a consistent mechanism, partition between the bulk water phase and the interfacial water formed on the hydrophobic surface. Thermal transition behaviour of the interfacial water incorporated in the nanopores of the C(18) silica materials and the solubility parameter of the water calculated from the distribution coefficients of organic compounds have indicated that the interfacial water may have a structure of disrupted hydrogen bonding. The thickness of the interfacial water or the limit of distance from the hydrophobic surface at which molecules and ions can sense the surface was estimated to be 1.25 ± 0.13 nm from the volume of the interfacial water obtained by a liquid chromatographic method and the surface area, suggesting that the hydrophobic effect may extend beyond the first solvation shell of water molecules directly surrounding the surfaces.     

Selective adsorption and chiral amplification of amino acids in vermiculite clay-implications for the origin of biochirality

Smectite clays are hydrated layer silicates that, like micas, occur naturally in abundance. Importantly, they have readily modifiable interlayer spaces that provide excellent sites for nanochemistry. Vermiculite is one such smectite clay and in the presence of small chain-length alkyl-NH(3)Cl ions forms sensitive, 1-D ordered model clay systems with expandable nano-pore inter-layer regions. These inter-layers readily adsorb organic molecules. n-Propyl NH(3)Cl vermiculite clay gels were used to determine the adsorption of alanine, lysine and histidine by chiral HPLC. The results show that during reaction with fresh vermiculite interlayers, significant chiral enrichment of either L- and D-enantiomers occurs depending on the amino acid. Chiral enrichment of the supernatant solutions is up to about 1% per pass. In contrast, addition to clay interlayers already reacted with amino acid solutions resulted in little or no change in D/L ratio during the time of the experiment. Adsorption of small amounts of amphiphilic organic molecules in clay inter-layers is known to produce Layer-by-Layer or Langmuir-Blodgett films. Moreover atomistic simulations show that self-organization of organic species in clay interlayers is important. These non-centrosymmetric, chirally active nanofilms may cause clays to act subsequently as chiral amplifiers, concentrating organic material from dilute solution and having different adsorption energetics for D- and L-enantiomers. The additional role of clays in RNA oligomerization already postulated by Ferris and others, together with the need for the organization of amphiphilic molecules and lipids noted by Szostak and others, suggests that such chiral separation by clays in lagoonal environments at normal biological temperatures might also have played a significant role in the origin of biochirality.     

Molecular dynamics simulations of the rehydration of folded and unfolded cytochrome C ions in the vapor phase.

Molecular dynamics (MD) simulations have been performed to study the rehydration of compact and unfolded cytochrome c ions in the vapor phase. Experimental studies have shown that the compact conformations adsorb many more water molecules than unfolded ones when exposed to water vapor. MD simulations performed with up to 150 water molecules reproduce the key experimental observations, including a partial refolding caused by hydration. According to the calculations it is more energetically favorable to hydrate the compact conformation in the initial stages of hydration, because it is easier for a water molecule to interact simultaneously with several polar groups (due to their proximity). The protonated side chains are not favored hydration sites in the simulations because they have "self-solvation" shells which must be disrupted for the water to penetrate. For both conformations, the adsorbed water molecules are mainly located in surface crevices.     

Assessing the accuracy of improved force‐matched water models derived from Ab initio molecular dynamics simulations

The accuracy of water models derived from ab initio molecular dynamics simulations by means on an improved force‐matching scheme is assessed for various thermodynamic, transport, and structural properties. It is found that although the resulting force‐matched water models are typically less accurate than fully empirical force fields in predicting thermodynamic properties, they are nevertheless much more accurate than generally appreciated in reproducing the structure of liquid water and in fact superseding most of the commonly used empirical water models. This development demonstrates the feasibility to routinely parametrize computationally efficient yet predictive potential energy functions based on accurate ab initio molecular dynamics simulations for a large variety of different systems. © 2016 Wiley Periodicals, Inc.     

Definition and computation of intermolecular contact in liquids using additively weighted Voronoi tessellation

We present a definition of intermolecular surface contact by applying weighted Voronoi tessellations to configurations of various organic liquids and water obtained from molecular dynamics simulations. This definition of surface contact is used to link the COSMO-RS model and molecular dynamics simulations. We demonstrate that additively weighted tessellation is the superior tessellation type to define intermolecular surface contact. Furthermore, we fit a set of weights for the elements C, H, O, N, F, and S for this tessellation type to obtain optimal agreement between the models. We use these radii to successfully predict contact statistics for compounds that were excluded from the fit and mixtures. The observed agreement between contact statistics from COSMO-RS and molecular dynamics simulations confirms the capability of the presented method to describe intermolecular contact. Furthermore, we observe that increasing polarity of the surfaces of the examined molecules leads to weaker agreement in the contact statistics. This is especially pronounced for pure water.     

Re-examining the properties of the aqueous vapor-liquid interface using dispersion corrected density functional theory

First-principles molecular dynamics simulations, in which the forces are computed from electronic structure calculations, have great potential to provide unique insight into structure, dynamics, electronic properties, and chemistry of interfacial systems that is not available from empirical force fields. The majority of current first-principles simulations are driven by forces derived from density functional theory with generalized gradient approximations to the exchange-correlation energy, which do not capture dispersion interactions. We have carried out first-principles molecular dynamics simulations of air-water interfaces employing a particular generalized gradient approximation to the exchange-correlation functional (BLYP), with and without empirical dispersion corrections. We assess the utility of the dispersion corrections by comparison of a variety of structural, dynamic, and thermodynamic properties of bulk and interfacial water with experimental data, as well as other first-principles and force field-based simulations.