Molecular dynamics simulation of free and forced BSA adsorption on a hydrophobic graphite surface

The adsorption of bovine serum albumin (BSA) onto a hydrophobic graphite surface is studied using molecular-dynamics simulation. In addition to the free, that is, unsteered, adsorption, we also investigate forced adsorption, in which the action of an AFM tip pushing the protein with constant force to the surface is modeled. Using an implicit inviscid water model, the adsorption dynamics and energetics are monitored for two different initial protein orientations toward the surface. In all cases, we find that the protein partially unfolds and spreads on the surface. The spreading is in agreement with the well-known high biocompatibility of graphite-based implants. The denaturation is, however, greatly enhanced in the case of forced adsorption. We follow the position of the so-called lipid-binding pocket found in subdomain IIIA (Sudlow site II) during adsorption and find that it is tilted and moved toward the graphite surface in all cases, in agreement with its hydrophobic character. The relevance of our findings for the common measurement procedure of studying protein adhesion using AFM experiments is discussed.     

Molecular dynamics simulation of aqueous NaF and NaI solutions near a hydrophobic surface

We present results from molecular dynamics simulation of aqueous solutions of alkali halide salts (NaI and NaF) at the interface with hydrophobic objects. The primary objective of this study is to investigate the structural properties of the salt solutions at the hydrophobic surface. An alkane crystal has been taken as the parent model for a hydrophobic surface. A hexagonal hole was created on it, which was half a nm deep and 2.5 nm wide. The density distributions of different species (water, anions, and cations) are studied as a function of distance from the surface. While iodide prefers the interface, the fluoride ions stay inside the bulk water region. The higher concentration of iodide ions at the interface drags sodium counterions to the interface. It also decreases the water density at the interface because of steric effects of the iodide ions. The number of contacts between the surface carbons and water decreases in the case of NaI solutions but is unchanged for NaF solutions. The orientation of the water-ion and the water-water hydrogen bond vector orientations near the interface is discussed in detail.     

Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface

We report atomistic simulations of the adsorption of a fibronectin type I module on a hydrophobic graphite surface. This module comprises only beta-sheets, unlike the albumin fragments previously investigated by us which contained only alpha-helices (Raffaini, G.; Ganazzoli, F. Langmuir 2003, 19, 3403-3412). As done in the latter case, most simulations are carried out in an effective dielectric medium by energy minimizations and molecular dynamics (MD). Further optimizations and MD runs in the explicit presence of water are also performed to assess the stability of the geometries found and to describe the solvation of the adsorbed fibronectin module. The initial adsorption is accompanied by local rearrangements of the strands in contact with the surface, but the overall molecular structure is largely preserved. Much larger rearrangements take place at longer times as found through the MD runs, with the molecule spreading as much as possible so as to maximize the surface coverage, hence the interaction energy, despite a significant strain energy. Energetic aspects of adsorption together with the concomitant size change are discussed in comparison with our previous results for two albumin fragments.     

Protein adsorption on the hydrophilic surface of a glassy polymer: a computer simulation study

Using atomistic computer simulations, we study the adsorption of different globular protein fragments with different secondary structures on the surface of a hydrophilic glassy polymer, poly(vinyl alcohol), or PVA, and compare the results with our earlier calculations on hydrophobic graphite. The simulations were mainly carried out with implicit solvent in an effective dielectric medium by energy minimizations and molecular dynamics at room temperature. We find that on the hydrophilic PVA surface the fragments basically retain their globular shape with an incomplete denaturation, at variance with our earlier results for the same fragments on graphite. Correspondingly, the interaction energy between the fragments and the surface is significantly smaller than on graphite, both because less residues are in contact with the surface, and because they interact more weakly. Moreover, very few hydrogen bonds are formed between the adsorbate and the PVA surface, since both the protein fragments and the polymer chains separately optimize these interactions. Additional molecular dynamics simulations in explicit solvent were also performed to study the hydration of the adsorbed fragments and to estimate the possible solvation effects.     

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 simulation study of interaction between model rough hydrophobic surfaces

We study some aspects of hydrophobic interaction between molecular rough and flexible model surfaces. The model we use in this work is based on a model we used previously (Eun, C.; Berkowitz, M. L. J. Phys. Chem. B 2009, 113, 13222-13228), when we studied the interaction between model patches of lipid membranes. Our original model consisted of two graphene plates with attached polar headgroups; the plates were immersed in a water bath. The interaction between such plates can be considered as an example of a hydrophilic interaction. In the present work, we modify our previous model by removing the charge from the zwitterionic headgroups. As a result of this procedure, the plate character changes: it becomes hydrophobic. By separating the total interaction (or potential of mean force, PMF) between plates into the direct and the water-mediated interactions, we observe that the latter changes from repulsive to attractive, clearly emphasizing the important role of water as a medium. We also investigate the effect of roughness and flexibility of the headgroups on the interaction between plates and observe that roughness enhances the character of the hydrophobic interaction. The presence of a dewetting transition in a confined space between charge-removed plates confirms that the interaction between plates is strongly hydrophobic. In addition, we notice that there is a shallow local minimum in the PMF in the case of the charge-removed plates. We find that this minimum is associated with the configurational changes that flexible headgroups undergo as the two plates are brought together.     

Molecular dynamics simulation study of xyloglucan adsorption on cellulose surfaces: effects of surface hydrophobicity and side-chain variation

The effect of surface hydrophobicity and side-chain variation on xyloglucan adsorption onto cellulose microfibrils (CMF) is investigated via molecular dynamics simulations. A molecular model of CMF with (100), (010), (1–10), (110) and (200) crystal faces was built. We considered xylogluco-oligosaccharides (XGO) with three repeating units, namely (XXXG)_3, (XXLG)₃, and (XXFG)₃ (where each (1,4)-β-d-glucosyl residue in the backbone is given a one-letter code according to its substituents: G = β-d-Glc; X = α-d-Xyl-(1,6)-β-d-Glc; L = β-d-Gal-(1,2)-α-d-Xyl-(1,6)-β-d-Glc; F = α-l-Fuc-(1,2)-β-d-Gal-(1,2)-α-d-Xyl-(1,6)-β-d-Glc). Our work shows that (XXXG)₃ binds more favorably to the CMF (100) and (200) hydrophobic surfaces than to the (110), (010) and (1–10) hydrophilic surfaces. The origin of this behavior is attributed to the topography of hydrophobic CMF surface, which stabilizes (XXXG)₃ in flat conformation. In contrast, on the rough hydrophilic CMF surface (XXXG)₃ adopts a less favorable random-coil conformation to facilitate more hydrogen bonds with the surface. Extending the xyloglucan side chains from (XXXG)₃ to (XXLG)₃ hinders their stacking on the CMF hydrophobic surface. For (XXFG)₃, the interaction with the hydrophobic surface is as strong as (XXXG)₃. All three XGOs have similar binding to the hydrophilic surface. Steered molecular dynamics simulation was performed on an adhesive model where (XXXG)₃ was sandwiched between two CMF hydrophobic surfaces. Our analysis suggests that this sandwich structure might help provide mechanical strength for plant cell walls. Our study relates to a recently revised model of primary cell walls in which extensibility is largely determined by xyloglucan located in limited regions of tight contact between CMFs.     

Molecular dynamics simulation study of drugs adsorption in UiO-66

Metal-organic frameworks (MOFs) are novel porous materials that have been extensively used in sensors, catalysis, gas storage and separation, and drug deliver owing to their adjustable pore size, large surface area and high porosity. Among diverse MOFs, UiO-66 can be a promising carrier for drug delivery due to high porosity and chemical stability. However, the adsorption mechanism of drugs in UiO-66 has not been identified and need a further investigation. Hence, we utilized molecular dynamic (MD) simulation to investigate the adsorption mechanism of UiO-66 as drug carriers. The MD simulation of UiO-66 exhibits the busulfan loading of 80 %, ibuprofen of 20 % and 5-fluorouracil of 30 %, respectively. We also demonstrated that the host-guest interaction between UiO-66 and drugs is dominated by the Van der Waals force. UiO-66 shows the highest affinity for busulfan compared with ibuprofen and 5-fluorouracil. In addition, it is certified the linear relation between the adsorption atoms and the interaction energy, which could help us to predict the interaction energy between drugs and UiO-66 by the contact atoms.     

Molecular dynamics simulation of TCDD adsorption on organo-montmorillonite

In this work, molecular dynamics simulation was applied to investigate the adsorption of Tetrachlorodibenzo-p-Dioxin (TCDD) on tetramethylammonium (TMA) and tetrapropylammonium (TPA) modified montmorillonite, with the aim of providing novel information for understanding the adsorptive characteristics of organo-montmorillonite toward organic contaminants. The simulation results showed that on both outer surface and interlayer space of TPA modified montmorillonite (TPA-mont), TCDD was adsorbed between the TPA cations with the molecular edge facing siloxane surface. Similar result was observed for the adsorption on the outer surface of TMA modified montmorillonite (TMA-mont). These results indicated that TCDD had stronger interaction with organic cation than with siloxane surface. While in the interlayer space of TMA-mont, TCDD showed a coplanar orientation with the siloxane surfaces, which could be ascribed to the limited gallery height within TMA-mont interlayer. Comparing with TMA-mont, TPA-mont had larger adsorption energy toward TCDD but smaller interlayer space to accommodate TCDD. Our results indicated that molecular dynamics simulation can be a powerful tool in characterizing the adsorptive characteristics of organoclays and provided additional proof that for the organo-montmorillonite synthesized with small organic cations, the available interlayer space rather than the attractive force plays the dominant role for their adsorption capacity toward HOCs.     

Molecular simulation study of adsorption and diffusion on silicalite for a benzene/CO2 mixture

The adsorption and diffusion of a binary mixture of supercritical CO2 and benzene on silicalite (MFI-type) have been studied through the grand canonical Monte Carlo and molecular dynamics (MD) simulations. The adsorption behavior of pure CO2 on silicalite was discussed in detail from the adsorption isotherms, adsorption sites, interaction energies, and isosteric heats of adsorption. For the mixture, the influences of temperature, pressure and composition on the adsorption isotherms have been examined. The adsorption site behavior of the mixture has been analyzed, and benzene molecules get adsorbed preferentially in the more spacious channel intersection positions. These simulation results suggest that SC-CO2 fluid can be used as an efficient desorbent of larger aromatics in the zeolite material. The diffusion characteristic for the benzene/CO2 mixture was studied on the basis of MD simulation. It was found that the large coadsorbed benzene molecule has a pronounced effect on the CO2 diffusion in the mixture, while the mobility of benzene molecules is very small due to geometrical restrictions.     

Cationic electrolyte adsorption layers on hydrophilic and hydrophobic surfaces

The capillary electrokinetics method (measurements of streaming potential and current in original and hydrophobized fused quartz capillaries with radii of 5–7 μm) is employed to study the formation of adsorption layers upon contact with solutions containing a cationic polyelectrolyte, poly(diallyldimethylammonium chloride). It is shown that polyelectrolyte adsorption causes the charge reversal of both hydrophilic and hydrophobic surfaces, with a smaller amount of the substance being adsorbed on the hydrophobic than on the hydrophilic surface. The adsorption on both surfaces increases with the polymer solution concentration. The cationic polyelectrolyte adsorption on the pure quartz surface occurs mainly due to the electrostatic attraction, while, in the case of the hydrophobic surface, the contribution of hydrophobic interactions increases. The study of the layer deformability shows that, on the hydrophilic surfaces, the layer ages and its structure depends on the polymer solution concentration. On the modified surface, the deformation of even freshly formed layers is slight, which suggests that a denser layer is formed on the hydrophobic surface. In contrast to the hydrophilic surface, the polyelectrolyte is partly desorbed from the hydrophobic surface.     

Monte Carlo simulation of water adsorption in hydrophobic MFI zeolites with hydrophilic sites

The effect of strong and weak hydrophilic sites, Al atoms with associated extraframework Na cations and silanol nests, respectively, in high-silica MFI zeolites on water adsorption was investigated using Monte Carlo simulations. For this purpose, a new empirical model to represent potential energy interactions between water molecules and the MFI framework was developed, which reproduced the hydrophobic characteristics of a siliceous MFI-type zeolite, silicalite-1, with both the vapor-phase adsorption isotherm and heats of adsorption at 298 K being in good agreement with experimental data. The proposed model is also compatible with previous hydrocarbon potential models and can be used in the adsorption simulations of VOC-water mixtures. Adsorption simulations revealed that strongly hydrophilic Al sites in Na-ZSM-5 zeolites coordinate two water molecules per site at low coverage, which promotes water clustering in the vicinity of these sites. However, weakly hydrophilic silanol nests in silicalite-1 are in coordination with a single water molecule per site, which does not affect the adsorption capacity significantly as expected. However, even in the presence of 0.125 silanol nest per unit cell, the increase in the heat of adsorption at low coverage is drastic.     

Adsorption of a single polymer chain on a surface: A molecular dynamics simulation study

We performed simulations of the physical adsorption of a single globular chain on a surface of hemispherical shape by means of molecular dynamics simulations. For the chain, we took advantage of a united atom model. Interactions within the chain were limited to stretching, bending, and torsional as well as nonbonded interactions between the nonadjacent atoms. The interaction between each chain element and the surface formation are reigned by a Lennard–Jones potential. In this article, we focused on differences in the behavior of the adsorbed globule to the free unadsorbed one particularly in two different zones of the immediate vicinity of the surface. There were strong indications for a localized acceleration of the dynamics as compared with the bulk that appears in an increase of trans–gauche switches. For explanation we came up with an adsorption scenario. Special attention was given to the shift of the percentage of trans and gauche conformations within the globule in dependence on the strength of the adsorption potential that might be related to crystallization or glass transition. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 2333–2339, 2001     

Polypeptide friction and adhesion on hydrophobic and hydrophilic surfaces: a molecular dynamics case study

Using all-atomistic MD simulations including explicit water, the mobility and adhesion of a mildly hydrophobic single polypeptide chain adsorbed on hydrophobic and hydrophilic diamond surfaces is investigated by application of lateral and vertical pulling forces. Forced motion on the hydrophilic surface exhibits stick-slip due to breaking and reformation of hydrogen bonds; in contrast, on the hydrophobic surface, the motion is smooth. By carefully tuning the driving force magnitude, the linear-response regime is reached on a hydrophobic surface and equilibrium values for mobility and adhesive strength are obtained. On the hydrophilic surface, on the other hand, slow hydrogen-bond kinetics prevents equilibration and only upper bounds for adhesion force and mobility can be estimated. Whereas the desorption force is rather comparable on the two surfaces and differs at most by a factor of 2, the mobility on the hydrophilic surface is at least 30-fold reduced compared to the hydrophobic one. A simple model based on a single particle diffusing in a corrugated potential landscape suggests that cooperativity is rather limited and that the small mobility on a hydrophilic surface can be rationalized in terms of incoherently moving monomers. The experimentally well-known peptide mobility in bulk water is quantitatively reproduced in our simulations, which serves as a sensitive test on our methodology employed.     

Molecular dynamics simulation of the crystal nucleation behavior of a single chain touching a substrate surface

Molecular dynamics simulation has been used in exploring the crystal nucleation behaviour of a single chain touching a substrate surface. It shows that a polyethylene chain (980 CH₂) changed its overall shape from an isotropic coil to an oriented one in the case of touching a substrate surface of amorphous carbons at 300 K. Most repeats of the chain were aligned and ordered in a zigzag package. Surprisingly, the direction of the package is not parallel to the plane of the substrate, but almost perpendicular to it. This is in accordance with experimental observations.     

Molecular dynamics simulation study on controlling the adsorption behavior of polyethylene by fine tuning the surface nanodecoration of graphite

Molecular dynamics simulations are applied to study the adsorption of polyethylene with different chain lengths on patterned graphite surfaces that contain nanoscale protrusions. The influence of the nanostructure on the strong attractive interaction inherently in the hydrophobic polyethylene and hydrophobic graphite system is investigated by modifying the top surface area and the height and the shape of the protrusions. The results are analyzed in terms of the chain configuration, the adsorption energy, the global orientational order parameter, and the normalized surface-chain contacting pair number in the first adsorption layer. When the size of the protrusion increases, the adsorption energy, the order parameter, and the normalized surface-chain contacting pair number decrease at a fixed chain length. When the size of the protrusion is fixed, the average adsorption energy per monomer and the order parameter decrease with increasing chain length because of the stronger intramolecular interactions between the monomers. Changing the protrusion shape in a suitable way will effectively reduce the strong surface-chain interaction.     

Nascent crystallization of a growing chain on a catalyst surface: a nonequilibrium molecular dynamics simulation study

The growing chain molecular dynamics (GCMD) simulation method, a new nonequilibrium molecular dynamics code, is proposed to simulate the polymer chain aggregation behavior during polymerization on a catalyst surface. We found that the growing chain crystallizes on the surface in two stages: the nucleation stage and the crystal growth stage. In the first part of the nucleation period, the short polymerizing chain first absorbs on the surface and can be in either an ordered or disordered structure. Still in the nucleation period, when the chain reaches a degree of polymerization, about 100 bonds, the chain folds into a stable nucleus on the substrate with 3-5 stems. In the crystal growth stage where the polymerization also proceeds, we observed a stem elongation process in combination with a chain folding process. In the stem elongation step, the number of stems in the nucleus remains constant, and all the stems expand together to a length of ca. 5-25 ns. In the subsequent chain folding step, the stem length decreases about 20 bonds within a period of ca. 0.1-0.5 ns. During chain growth, the elongation process and the folding process occur in an alternating and repeated fashion. The crystallization mechanism of the polymerizing chain was discussed.     

Molecular dynamics simulation on crystalline nucleation behaviour of a single chain touching a substrate surface II. Temperature dependence

Molecular dynamics simulation has been used in exploring the crystalline nucleation behaviour of a single chain touching a substrate surface at different temperatures. It shows that a polyethylene chain (980 CH₂) changed its overall shape from an isotropic coil to an oriented one nearly normal to the substrate surface of amorphous carbons at 200, 300, 400 and 500 K. Most repeats of the chain were getting ordered in a zigzag package for the first three temperatures, but not for the one at 500 K. It was found that the ordering rate was bothered by the substrate surface. The rate of forming the ordered package at 300 K is larger than that at 200 K and at 400 K, indicating the whole process simulated is nucleation dependent in nature.