Molecular Dynamics Simulations Of Adsorption Research Articles

A LA-BTC MOF as a sensor element of an electronic nose for selective adsorption of biomarkers of diseases: Molecular dynamics simulations of adsorption

The advanced non-invasive diagnostic method is an analysis of exhaled volatile organic compounds (VOCs), which are regarded as biomarkers of various diseases. A gravimetric-type electronic nose (e-nose) has shown great promise in exhaled VOC-pattern identification, and its efficiency is determined by the adsorption capacity of the sensing materials towards a specific VOC. The present study employed molecular dynamics (MD) calculations with the OPLS all-atom force field to investigate the adsorption of an isolated molecule of volatile fatty acids, acetone, ethanol, methanol, acetic aldehyde, neopentane, and ethane in a unit cell of the lanthanum-based metal-organic framework (La-BTC MOF), which was proposed as a potential sensing material for the gravimetric-type e-nose. The adsorption potential determined as a change in the potential energy, ΔEp, of the total simulation system upon the penetration of a single molecule into a unit pore of La-BTC MOF was calculated for all the targeted VOCs and water to be 1.56–10.78 kJ·mol−1, following the order: ethane < neopentane < acetic aldehyde < ethanol < methanol < water < acetone < butanoic acid < caproic acid. Therefore, the biomarkers with ΔEp > ΔEp(water) ∼ 7.3 kJ/mol can be captured from the exhaled breath. According to the MD calculations, an oxygen-containing biomarker molecule in the adsorbed state was oriented by its oxygen atom towards the La3+ cation, so that the O---La3+ distance of 0.28–0.32 nm was the shortest among those for other constituent atoms. Thus, the strong electrostatic interactions between the oxygen atoms of the adsorbate molecules and the La3+ cation of the adsorbent were most responsible for the capture of the oxygen-containing biomarkers by the La-BTC MOF. The competing adsorption effect between water and oxygen-containing biomarker molecules was examined in dependence on the water content and the way the water molecules were introduced into the simulation system.

Different anionic MIL structure optimization and molecular dynamics simulation of adsorption on coal surface

Surfactants can regulate the surface wettability of low-rank coal (LRC), resulting in highly efficient coal usage. Magnetic ionic liquids (MILs), a novel form of surfactants, provide environmental protection, excellent designability, and recyclability. In this study, quantum chemical simulations were performed to optimize the structures of [C12mim]FeCl4, [C12mim]2CoCl4, and [C12mim]2NiCl4 and the structural parameters were verified. The effect of MILs on the surface wettability of LRC was investigated by measuring the critical micelle concentration (CMC) using a conductivity technique and computing the adhesion work; thus, the micro-control mechanism of wettability was clarified. The wettability investigation revealed that the three different types of MILs had higher critical micelle concentrations as the temperature increased. Molecular dynamics modeling was utilized to calculate the adsorption process simultaneously, and the results demonstrated that the three different MILs may spontaneously complete adsorption on the surface of the LRC. Thermogravimetric and X-ray photoelectron spectroscopy analyses demonstrated that after the addition of the three different types of MILs, the oxygen-containing functional groups in the LRC were covered, the LRC surface became more hydrophobic, the water content of the LRC decreased, and the wettability of the LRC was effectively controlled.

Molecular Dynamics Simulation of Adsorption and Absorption Behavior of Shale Oil in Realistic Kerogen Slits

Exploring the occurrence of shale oil is of guiding significance to the exploration and recovery of shale oil. However, most studies focus on adsorption and neglect absorption or study it independently, which weakens the understanding of the coupling relationship between adsorption and absorption and the occurrence mechanism of shale oil in kerogen and its associated pores. Based on molecular dynamics (MD) simulation, the kerogen matrix with a smooth surface is constructed, and the general amber force field is adopted to calculate the adsorption and absorption of shale oil in a type II kerogen slit, and the influences of temperature, pressure, and pore diameter on the occurrence of shale oil are also discussed. Molecules absorbed in the kerogen matrix are mainly retained in the free space formed by the accumulation of aliphatic carbon. The effects of temperature on the distribution of shale oil in adsorption and absorption are opposite. High temperature improves the desorption of molecules from the adsorption sites and causes a lower adsorption and greater absorption. In contrast, pressure and pore diameter only slightly influence the distribution of shale oil. Unexpectedly, the result under aqueous conditions shows that the shale oil was absorbed quickly before the formation of water clusters. Once the water clusters are formed due to the strong hydrogen bonding and adsorbed near the N-, S-, and O-containing groups on the kerogen surface, the matrix gaps are blocked due to the size exclusion, and the absorption is suppressed. Additionally, we established the evolution of the ratio of free-adsorbed–absorbed oil at different temperatures and pressures, which provides a new idea and a new method for detecting the occurrence and mobility evaluation of shale oil under reservoir conditions.

Molecular dynamics simulation of adsorption and diffusion of partially hydrolyzed polyacrylamide on kaolinite surface

In tertiary oil recovery in oilfields, polymer solutions (partially hydrolyzed polyacrylamide) are often used for enhancing oil recovery. In view of the limitations of the current indoor flooding experiments, such as the limited scope of application and many assumptions, it is difficult to deeply reveal the mechanism of polymer flooding. In this paper, the molecular dynamics simulation method (MD) is used to establish an interaction model based on the construction of rock model, polymer molecular model and polymer solution system model to simulate the transport of polymers in nanopores from the microscopic level, and to study molecular. The interaction between them is described, and their diffusion and adsorption behaviors and viscoelastic properties are described, which provides a theoretical basis for the optimization of oil-displacing agents and the characterization of macro-rheological properties and flow parameters.

Molecular Dynamics Simulations of Adsorption of SARS-CoV-2 Spike Protein on Polystyrene Surface.

A prominent feature of coronaviruses is the presence of a large glycoprotein spike (S) protruding from the viral particle. The specific interactions of a material with S determine key aspects such as its possible role for indirect transmission or its suitability as a virucidal material. Here, we consider all-atom molecular dynamics simulations of the interaction between a polymer surface (polystyrene) and S in its up and down conformations. Polystyrene is a commonly used plastic found in electronics, toys, and many other common objects. Also, previous atomic force microscopy (AFM) experiments showed substantial adhesion of S over polystyrene, stronger than in other common materials. Our results show that the main driving forces for the adsorption of the S protein over polystyrene were hydrophobic and π–π interactions with S amino acids and glycans. The interaction was stronger for the case of S in the up conformation, which exposes one highly flexible receptor binding domain (RBD) that adjusts its conformation to interact with the polymer surface. In this case, the interaction has similar contributions from the RBD and glycans. In the case of S in the down conformation, the interaction with the polystyrene surface was weaker and it was dominated by glycans located near the RBD. We do not find significant structural changes in the conformation of S, a result which is in deep contrast to our previous results with another hydrophobic surface (graphite). Our results suggest that SARS-CoV-2 virions may adsorb strongly over plastic surfaces without significantly affecting their infectivity.

Molecular Dynamics Simulation of Adsorption in Two–dimensional Interlayer of Layered Clay Minerals

Molecular Dynamics Simulation of Adsorption in Two–dimensional Interlayer of Layered Clay Minerals

Molecular dynamics simulation of adsorption and separation of xylene isomers by Cu-HKUST-1.

Metal-organic frameworks (MOFs) are widely used in the adsorption separation of various gases. A fundamental understanding of the effective separation of xylene isomers helps improve aromatic products' separation efficiency and reduce industrial separation costs. Grand Canonical Monte Carlo (GCMC) simulations combined with Molecular Science is widely used to predict gas adsorption and diffusion in single crystals with metal-organic frameworks. We performed a GCMC + MD combined approach to study xylene isomers' adsorption and separation in Cu-HKUST-1 to predict the permeability and selectivity of the ternary gas mixture in the MOF with the adsorption and diffusion usage data. Most current studies take into account the computational cost and difficulty. Most recent research models are limited to the adsorption of a single or specific molecule, such as hydrogen, methane, carbon dioxide, etc. For this reason, we report an attempt to study the adsorption separation of aromatic gases (p-xylene/o-xylene/m-xylene) based on Cu-HKUST-1 single-crystal materials based on some previous research methods with an appropriate increase in computational cost. To predict the adsorption selectivity and permeability of the ternary mixture of xylene isomers on the MOF surface, the model simulation calculates key parameters of gas adsorption, including gas adsorption volume (N), the heat of adsorption (Q st), Henry coefficient (K), and diffusion coefficient (D).

Study of adsorption interactions between nitrous oxide and Zeolitic Imidazolate framework-8 (ZIF-8) by molecular modeling

Nitrous oxide (N2O) is a greenhouse gas (GHG) mainly issued from agriculture and waste management activities. Since N2O has a global warming potential 298 times higher than CO2 and an annual emission equivalent to 5.1 % v/v of total GHG emissions, the control of its emissions becomes essential. One of the main challenges to control N2O emissions is to capture them under the main sources’ conditions, i.e. atmospheric pressure and ambient temperature. The available technologies to control N2O emissions operate presently at medium/high pressure, being high energy consuming.The development of new and specific adsorbents for capturing N2O is important. Molecular modeling is a helpful tool to develop engineered adsorbents, generating virtual molecular interactions as a prior adsorbate-adsorbent system before experimental studies. Zeolitic Imidazolate Framework-8 (ZIF-8) has been selected in this study as an adsorbent because of its easy and reproducible synthesis, thermal stability, flexible structure, hydrophobicity and high adsorption capacity of gases, including GHGs.In the present study, the interactions between N2O and ZIF-8 were studied by molecular modeling methods, PM6 and DFT. Optimized geometries of N2O and ZIF-8, adsorption energy and ligand point length parameters were analyzed as part of a physical adsorption process. Three adsorption sites were identified on the four-membered and six-membered windows of ZIF-8. The two possible N2O interaction configurations (–ONN and –NNO) were simulated and compared in order to determine the most probable behavior of N2O. The study showed that the –ONN configuration produces more stable interactions with ZIF-8 than –NNO configuration. The six-membered window of ZIF-8 seems to be the pore where the most stable interactions occur based on the adsorption energy and the approach distance. The present study was concentrated on the interactions of one N2O molecule and a fragment of the ZIF-8, and it will be the basis for molecular dynamics simulations of adsorption with a control volume, containing several N2O molecules and a representative surface of ZIF-8 under different pressures and temperatures.

Quantum chemical and molecular dynamics modeling of interaction of isomolecular dipeptides of α-l-alanyl-α-l-alanine and β-alanyl-β-alanine with sodium dodecyl sulfate micelles

Quantum chemical investigation of α-l-alanyl-α-l-alanine and β-alanyl-β-alanine complexes with SDS dimer as an anion micelle fragment in polarizable continuum has been carried out by using of DFT method with B97-D/6-311++G(3d,3p) level. The variation of peptide structure and the difference in energies of free peptides, SDS dimer and their complexes have been analyzed. Optimized configurations of complexes are stabilized by hydrogen bonds of (H2)NH…O(S) type. The localization of α-l-alanyl-α-l-alanine among the charged groups of SDS dimer is more preferable. The localization of β-alanyl-β-alanine among the charged groups or in the dimer hydrophpbic canal results in close values of the complex formation energy. More favorite change of energy and shorter length of hydrogen bond of (H2)NH…O(S) type have been revealed for complex formation between SDS dimer and β-alanyl-β-alanine as opposed to α-l-alanyl-α-l-alanine. Molecular dynamics simulation of adsorption of the peptides on SDS micelle has been performed in NPT ensemble at 0.1 MPa and 298 K. The cell under study contained 14,678 water molecules, one peptide zwitter-ion, and the micelle including 64 SDS monomers. Most probable localization of peptide atoms relative the micelle has been analyzed. The peptide – SDS micelle interaction is accompanied by diminish of average number of peptide – water H-bonds and the formation of at the mean two H-bonds with SDS. Some peculiarities of adsorption of the isomolecular peptides on SDS micelle are appeared in different values of H-bond lifetimes, different probability of formation of H-bond of NH3+…−O3SO or NH3+…O(SO3−) types, and localization of peptide zwitter-ions outside or within double electrical layer of the micelle.

Polarizable force field for molecular dynamics simulations of silver nanoparticles

Contact of silver metal surfaces with water, ions and organic ligands experiences induced charges, leading to attractive polarization. These forces play an important role at inorganic/organic interfaces and complement other non-bonded surface interactions. Despite the importance of these interactions, it, however, remains difficult to implement polarization effects to classical molecular dynamics (MD) simulations. In this contribution, we first present an overview of two popular polarizable models, such as Drude oscillator and the rigid rod model, which are utilized to mimic the polarizability of bulk metals. Second, we implemented the rigid rod model to the polarizable force field (FF) for a silver atom, which was further adapted for atomistic MD simulations of silver nanoparticles (AgNPs) composed of 1397 atoms. In our model, induced charge polarization is represented by the displacement of a charge-carrying virtual site attached rigidly to an original Ag atom. To explore the role of polarization, we compared the performance of the classical nonpolarizable FF and the new polarizable model in the MD simulations of adsorption of water and ions onto quasi-spherical AgNP and the flat crystalline silver surface. The analysis of the radial distribution function of Ag-Ag atoms demonstrated that the introduction of the polarization effect had minor effects on face-centered cubic (fcc) packing of silver atoms of bare and water-solvated AgNPs. We found that the polarizable FF causes some increase in attractive interactions between the silver surface and water molecules and Na+ ions. As a crucial test of the developed polarizable model, the structure of adsorbed interfacial water molecules was analyzed. Our data suggest that the environment-induced polarization of the silver surface contributes significantly to the structure of adsorbed interfacial water layers and it also plays an important role in the adsorption of positive ions. However, it was also found out that the polarization effect has a rather short-range effect, so that a minor contribution of silver polarization was seen for adsorption of water molecules and ions from distant solvation shells.

Molecular dynamics simulations of adsorption and desorption of bone morphogenetic protein-2 on textured hydroxyapatite surfaces

Interactions between bone morphogenetic protein-2 (BMP-2) and biomaterial surfaces are of great significance in the fields of regenerative medicine and bone tissue engineering. In this work, the adsorption and desorption behaviors of BMP-2 on a series of nano-textured hydroxyapatite (HAP) surfaces were systematically investigated by combined molecular dynamic (MD) simulations and steered molecular dynamic (SMD) simulations. The textured HAP surfaces exhibited nanostructured topographies and played a critical role in the mediation of dynamic behaviors of BMP-2. Compared to the HAP-flat model, the HAP-1:1 group (means ridge vs groove = 1:1) showed the excellent ability to capture BMP-2, less conformation change of BMP-2 molecule, and high cysteine-knot stability during the adsorption and desorption processes. These findings suggest that nano-textured HAP surfaces are more capable of loading BMP-2 molecules, and most importantly, they can help maintain a higher biological activity of BMP-2 cargos. In the present study, for the first time, we have deeply clarified the adsorption and desorption dynamics of BMP-2 on various nano-textured HAP surfaces at the atomic level, which can provide significant guidelines for the future design of BMP-2-based tissue engineering implants/scaffolds. Statement of SignificanceBy using combined molecular dynamic (MD) simulations and steered molecular dynamic (SMD) simulations, the adsorption and desorption dynamics of bone morphogenetic protein-2 (BMP-2) dimer on a series of nano-textured hydroxyapatite (HAP) surfaces at the atomic level were presented in details for the first time. We have proved that the HAP-1:1 model (means ridge vs groove = 1:1) possessed excellent ability to capture BMP-2, less conformation change, and high cysteine-knot stability. As a result, the nano-textured topography of HAP-1:1 could maintain a relatively high biological activity of BMP-2 cargos. This work could provide theoretical guidelines for the design of BMP-2-based implants/scaffolds for bone tissue engineering.

Molecular Dynamics Simulations of Adsorption of CH4 in Nanocone

Adsorption is an important issue in the estimation of natural gas reserves. In this paper, the sorption behavior and configurations of methane (CH4) along the axial and radial direction of the nanocone are investigated based on molecular simulation. The simulation results show that the equilibrium distance between centroid of CH4 and nanocone tip is 2.25 nm. The corresponding adsorption energy of CH4 is -17.38635 kcal/mol and the smallest radius of the nanocone that CH4 can enter is 0.380 nm. The equilibrium distance between CH4 and nanocone wall is 0.30 nm. The corresponding adsorption varied along nanocone wall. Our findings and related analyses may help reveal the underlying mechanisms behind the adsorption phenomena, provide new idea in shale gas exploitation technology.

Correcting for solvent replacement effects in quartz crystal microbalance measurements

The quartz crystal microbalance (QCM) is frequently used to measure the adsorption of molecules from a liquid bulk phase onto surfaces. However, determining the true mass adsorbed onto the surface from the raw frequency shift values often involves various correction factors. In this paper, we highlight yet another correction factor that arises from correcting for the bulk, Kanazawa–Gordon-like solvent contribution to the total frequency shift. This correction factor depends on the cross-sectional size of the solute and solvent molecules on the surface, and shows that the apparent mass adsorbed reported by the QCM can significantly differ from the true mass. By performing molecular dynamics simulations of adsorption from a liquid phase, we are able to accurately estimate the molecular sizes of the solvent and solute. Using stearic acid in heptane solutions, and iron oxide surfaces, we quantify the magnitude of the correction factor by comparing the uncorrected and corrected QCM data. This paper emphasizes the importance of accounting for deviations from widely used models in analyzing measured frequency shifts in QCM experiments, to accurately obtain the true adsorbed mass.

Molecular Dynamics Simulation of Adsorption and Replacement of Methane in Kerogen Micropores

Characteristics of CH4 adsorption and CH4 replacement with CO2 in kerogen micropores were investigated by molecular dynamics (MD) simulations to obtain accurate estimates of CH4 volume and reduction of environmental load by applying multi-stage CO2 fracking for shale gas development. Firstly, CH4 density in the kerogen micropores was found to be about 1.8 times higher than in the mesopores outside the kerogen, indicating that an adsorption model accounting for the micropore filling is essential to correctly evaluate the volume of CH4 adsorption. Secondly, CO2 molecules with linear shape easily passed through the throat of the kerogen micropore, whereas CH4 molecules with regular tetrahedron shape did not. Thirdly, CH4 was easily replaced by CO2 in the kerogen micropores due to the higher affinity for CO2 than CH4 of oxygen atoms, which are much more common than other heteroatoms in the kerogen molecule. Finally, H2O molecules in the kerogen micropores and mesopores were aggregated by hydrogen bonding around the heteroatoms and prevented the replacement of CH4 by blocking the pathways.

Molecular Dynamics Simulations of Adsorption of Polymer Chains on the Surface of BmNn Graphyne-Like Monolayers

Molecular dynamics simulations are used here to study the interactions between BmNn graphyne-like monolayers and four different polymer chains. BN, B1N9, and B2N8 graphyne-like monolayers are selected from the family of BmNn graphyne-like monolayers. It is observed that increasing the number of B atoms in the structure of BmNn graphyne-like monolayers results in larger interaction energies of nanosheet/polymer systems. It is also shown that the polymer chains with the linear adsorbed configurations on the nanosheets have larger interaction energies with the nanosheets. Investigating the effect of number of polymer repeat units on the polymer/nanosheet interaction energy, it is observed that increasing the number of repeat units of polymers leads to enhancing the polymer/nanosheet interaction energy.

Molecular Dynamics Simulations of Adsorption of Poly(acrylic acid) and Poly(methacrylic acid) on Dodecyltrimethylammonium Chloride Micelle in Water: Effect of Charge Density.

We have investigated the interaction of dodecyltrimethylammonium chloride (DoTA) micelle with weak polyelectrolytes, poly(acrylic acid) and poly(methacrylic acid). Anionic as well as un-ionized forms of the polyelectrolytes were studied. Polyelectrolyte-surfactant complexes were formed within 5-11 ns of the simulation time and were found to be stable. Association is driven purely by electrostatic interactions for anionic chains whereas dispersion interactions also play a dominant role in the case of un-ionized chains. Surfactant headgroup nitrogen atoms are in close contact with the carboxylic oxygens of the polyelectrolyte chain at a distance of 0.35 nm. In the complexes, the polyelectrolyte chains are adsorbed on to the hydrophilic micellar surface and do not penetrate into the hydrophobic core of the micelle. Polyacrylate chain shows higher affinity for complex formation with DoTA as compared to polymethacrylate chain. Anionic polyelectrolyte chains show higher interaction strength as compared to corresponding un-ionized chains. Anionic chains act as polymeric counterion in the complexes, resulting in the displacement of counterions (Na(+) and Cl(-)) into the bulk solution. Anionic chains show distinct shrinkage upon adsorption onto the micelle. Detailed information about the microscopic structure and binding characteristics of these complexes is in agreement with available experimental literature.

Molecular Dynamics Simulations of Adsorption of Catechol and Related Phenolic Compounds to Alumina Surfaces

We performed atomistically detailed molecular dynamics simulations to study adsorption behaviors of catechol, which is a key functional group in marine bioadhesives, to two different alumina surfaces in both anhydrous and aqueous conditions. In anhydrous conditions, without competing interactions from water molecules, catechol adsorbed to both hydroxylated and nonhydroxylated alumina surfaces. In aqueous conditions, catechol and several analogous phenolic compounds displaced water molecules and were strongly attracted to the nonhydroxylated alumina surface, which is more hydrophobic. When comparing the phenolic moieties near the hydroxylated alumina surface in aqueous conditions, the catechol molecules displayed the strongest adsorptions mainly through cooperative hydrogen bonding interactions of two neighboring hydroxyl groups with the surface hydroxyl groups of alumina as evidenced by the longer hydrogen bonding lifetimes and the larger number of adsorbed molecules near the surface. Insights gained from...

Molecular-level understanding of the adsorption mechanism of a graphite-binding peptide at the water/graphite interface.

The association of proteins and peptides with inorganic material has vast technological potential. An understanding of the adsorption of peptides at liquid/solid interfaces on a molecular-level is fundamental to fully realising this potential. Combining our prior work along with the statistical analysis of 100+ molecular dynamics simulations of adsorption of an experimentally identified graphite binding peptide, GrBP5, at the water/graphite interface has been used here to propose a model for the adsorption of a peptide at a liquid/solid interface. This bottom-up model splits the adsorption process into three reversible phases: biased diffusion, anchoring and lockdown. Statistical analysis highlighted the distinct roles played by regions of the peptide studied here throughout the adsorption process: the hydrophobic domain plays a significant role in the biased diffusion and anchoring phases suggesting that the initial impetus for association between the peptide and the interface may be hydrophobic in origin; aromatic residues dominate the interaction between the peptide and the surface in the adsorbed state and the polar region in the middle of the peptide affords a high conformational flexibility allowing strongly interacting residues to maximise favourable interactions with the surface. Reversible adsorption was observed here, unlike in our prior work focused on a more strongly interacting surface. However, this reversibility is unlikely to be seen once the peptide-surface interaction exceeds 10 kcal mol(-1).

Molecular dynamics simulation of adsorption of pyrene–polyethylene glycol onto graphene

The nonvalent interaction between amphiphilic polymers and graphenes is important to provide the surface functionalization of graphene. Herein, molecular dynamics simulations were carried out to investigate the interaction of pyrene–polyethylene glycol (Py–PEG) with graphene. The dynamic adsorption process and self-assembly morphology of Py–PEG onto nanoscale graphene surface have been demonstrated. The effects of the graphene size and the length of polymer chain were explored. It was shown that Py–PEG could spontaneously adsorb onto graphene surface. The Py–PEG polymer generally exhibits a coil structure with the hydrophobic pyrene surrounded by the PEG chain. However, once the Py–PEG molecule approaches the graphene surface, the PEG chain can unfold its structure on the graphene surface and the pyrene group can display a flat binding mode with the surface. Comparatively, the water solvent has an obvious impeding effect on the surface adsorption due to the hydrogen bonding interaction between PEG chain and water molecules. The thermodynamic free energy shows that the interaction between pyrene and carbon surface provides the main interaction contribution to the adsorption performance.

Molecular dynamics simulation of adsorption of ozone and nitrate ions by water clusters

Coadsorption of ozone molecules and nitrate ions by water clusters was studied by the molecular dynamics technique. The maximum value of an average O-H…O bond length in a water carcass is realized at the minimum specific number of such bonds when the ratio of adsorbed ozone molecules to nitrate ions captured by a cluster is two. IR absorption and reflection spectra were reshaped significantly, and new peaks appeared at Raman spectra due to the addition of ozone and nitrate ions to the disperse water system. After ozone and nitrate ions were captured, the average (in frequency) IR reflection coefficient of the water disperse system increased drastically and the absorption coefficient fell.