Monte Carlo Simulation Study of Adsorption Characteristics in Slit-Like Micropores Under Supercritical Conditions

Abstract

Adsorption characteristics of a solute diluted in supercritical fluids has been investigated by using the Monte Carlo simulation techniques. The Lennard-Jones potential function is used for describing interactions for a model system of CO₂ + benzene in slit-like micropores with infinite graphitic carbon walls. A modified μVT ensemble method with particle exchange proposed by Cracknell, Nicholson and Quirke (1993) is found to be much superior to the conventional μVT ensemble method especially for dense mixtures in a pore. Adsorption isotherms of CO₂ and benzene, in equilibrium with a dilute benzene mixture in CO₂ (mole fraction of benzene = 0.001), are computed by varying pressure, temperature, the benzene–surface interaction potential, and the slitwidth. Adsorption isotherm curve of CO₂ increases with an increase in pressure while that of benzene shows a maximum at a pressure far below the critical pressure of CO₂ and then it decreases with increasing pressure. The decrease in benzene adsorption with increasing pressure is attributable to both the enhanced solubility in supercritical CO₂ and the competitive adsorption of CO₂. The isotherm curves of each component at two temperatures, 313.2 K and 323.2 K, show to cross at a pressure near the critical pressure due to the “density effect” on the chemical potentials of a solute at supercritical fluid conditions. When the interaction between a solute and a surface increases, the adsorption isotherm increases. Narrowing the slitwidth results in the increase in the adsorption of solute since the external potential from two walls becomes deeper.     

Adsorption and structure of benzene confined in disordered porous carbons: effect of pore heterogeneity and surface chemistry

Molecular simulations are used to study the adsorption of benzene at 300?K in atomistic models of disordered nanoporous carbons. These models, named as CS400, CS1000 and CS1000a, differ in density and chemical compositions, and reproduce the morphological and topological features present in real nanoporous carbons. We found that the adsorption phenomena depend upon the local structure of nanoporous carbons. To understand the effect of surface chemistry on adsorption and structure of confined benzene, functional groups (–COOH and –C=O) were added to these models. The presence of functional groups led to the onset of adsorption process at a low pressure. The carboxyl groups (–COOH) have a greater impact on adsorption as compared to carbonyl (–C=O) groups. The CS1000a models have wide micropores and thus it exhibits a jump in adsorption isotherm. The jump shifts towards lower pressure on the addition of functional groups, with –COOH groups showing a larger shift. The presence of functional groups also increases the isosteric heat of adsorption, with –COOH groups showing higher values. The coulombic contribution to total fluid–wall interaction energy is higher for –COOH functional groups and decreases on increasing pressure. Benzene confined in CS1000a models exhibit a liquid-like structure.     

A Preliminary Study of the Surface Properties of Earthworms and Their Relations to Non-Stain Behaviour

The surface properties of earthworms were studied using nitrogen adsorption/desorption isotherm and dynamic contact angle measurement with the aim to understand their non-stain behaviour. The results obtained by applying dynamic contact angle technique using water, glycerol, cooking oil and dimethylsilicone show that the surface properties of earthworms are a function of time. The critical surface energy, calculated using advancing angle, is as low as 11 × 10~(-3) J·m~(-2). However this hydrophobic behaviour at the initial contact moment changes progressively into hydrophilic as time goes by. This behaviour together with the creeping movement of corrugated surface is believed to be responsible for the non-stain behaviour of earthworms. The nitrogen adsorption isotherm of dried skin of earthworms at 77.3 K exhibits more or less Type V isotherm with surface area of 13 m~2·g~(-1) calculated using the α_s plot. The Type V isotherm is the indication of weak interaction between nitrogen and the worm surface.     

New Insight on Biological Interaction Analysis: New Nanocrystalline Mixed Metal Oxide SPME Fiber for GC-FID Analysis of BTEX and Its Application in Human Hemoglobin-Benzene Interaction Studies

Nanocrystalline mixed metal oxides (MMO) of various metal cations were synthesized and were used for coating a piece of copper wire as a new high sensitive solid phase micro extraction (SPME) fiber in extraction and determination of BTEX compounds from the headspace of aqueous samples prior to GC-FID analysis. Under optimum extraction conditions, the proposed fiber exhibited low detection limits, and quantification limits, good reproducibility, simple and fast preparation method, high fiber capacity and high thermal and mechanical durability. These are some of the most important advantages of the new fiber. The proposed fiber was used for human hemoglobin upon interaction with benzene. Binding isotherm, Scatchard and Klotz logarithmic plots were constructed using HS-SPME-GC data, accurately. The obtained binding isotherm analyzed using Hill method. The Hill parameters have been obtained by calculating saturation parameter from the ratio of measured chromatographic peak areas in the presence and absence of hemoglobin. In this interaction, Hill coefficient and Hill constant determined as (n_H = 6.14 and log K_H = 6.47) respectively. These results reveal the cooperativity of hemoglobin upon interaction with benzene.     

Monitoring protein expression by proteomics: human plasma exposed to benzene

Low levels and long term exposure to benzene is associated with hematotoxicity including aplastic anemia, acute myelogenous leukemia, and lymphoma. Current biomonitoring methods such as urinary phenol, S-phenylmercapturic acid, and trans-trans muconic acid were found to be unreliable as analytical methods to detect benzene exposure. Therefore, to search for a specific protein for biomonitoring benzene exposure, we investigated plasma proteins from workers (n = 50) at a printing company who were exposed to benzene, by two-dimensional gel electrophoresis. The protein profiles are significantly different (p < 0.05) between benzene exposed and unexposed groups, as identified by matrix-assisted laser desorption ionization/time of flight mass spectrometry and confirmed by Western blot analyses. T cell receptor beta chain (TCR beta), FK506-binding protein, and matrix metalloproteinase-13 were expressed only in benzene exposed workers. In addition, interleukin-4 receptor alpha chain and T cell surface glycoprotein CD1b precursor were found to be up-regulated in the plasma of benzene exposed workers. When we treated Jurkat cells with benzene (10 microM-10 mM), TCR beta expression was increased in the membrane more than 6-9-fold compared to untreated cells. In addition, the amount of TCR beta released into the culture media, at benzene concentrations greater than 50 microM, increased up to 10 mM. Therefore, TCR beta levels in plasma could be used as a biomarker and a possible therapeutic target for benzene exposure.     

Partially induced transition from horizontal to vertical orientation of helical peptides at the air–water interface and the structure of their monolayers transferred on the solid substrates

To apply the Langmuir–Blodgett (LB) technique as a platform for investigating the fundamental properties of amphiphilic peptides (APs), we have investigated the structure of LB films using the APs. To vertically orient the helical APs like transmembrane proteins in the membrane, the primary structure of the APs was designed to have two domains: a hydrophilic domain (three amino acids) and a hydrophobic domain (ca. 20 amino acids). However, we are still far from having full control of their orientation. This study reports the contribution of the subphase temperature to the change in the orientation of helical APs. When the surface pressure–area isotherm of AP was observed at the subphase temperature at 41.5 °C, the isotherm exhibited a plateau, implying that a phase transition of the monolayer at the air–water interface occurred. Circular dichroism (CD) spectra of the monolayers transferred on the solid substrates revealed that the orientation of the helices changed at the pressure, where the plateau of the isotherm was observed. This change was not observed at 21.5 °C, i.e., the horizontal alignment of helixes was maintained. Atomic force microscopy (AFM) was used to systematically investigate the surface structure of the monolayers transferred at different surface pressures. A structural model of the monolayer that did not contradict with the results obtained by the three different techniques (the isotherm, CD spectroscopy, and AFM) was derived, and it was concluded that the horizontally oriented helices partially changed their orientation to vertical upon compression in the plateau region of the isotherm.     

The effects of structural parameters of zeolite on the adsorption of hydrogen: a molecular simulation study

The adsorption isotherm of hydrogen in zeolites FAU, LTA, KFI, RWY, RHO and TSC has been simulated employing grand canonical Monte Carlo procedure for a temperature range of 77 to 95 K and different pressures. The effects of structural composition, unit cell volume, framework density and specific surface area of zeolite on hydrogen adsorption in zeolites were investigated. The results clearly show that the adsorption of hydrogen in zeolites with the same silica density is a function of oxygen density at low pressures, and it is approximately the same at intermediate pressures. Nevertheless, at high pressures, the adsorption of hydrogen is a function of pore diameter for zeolites with same silica density. The effect of specific surface area on the adsorption isotherm of hydrogen on zeolites with approximately the same specific surface area is significant at low and high pressures. The results clearly indicate that the adsorption of hydrogen in RWY zeolite has maximum value at 77 K and at high pressures. The optimum condition of pressure for hydrogen adsorption isotherm in RWY zeolite is determined to be 600 bar. At a temperature of 77 K and a pressure of 600 bar, the adsorption of hydrogen in RWY zeolite is 6.93 wt %.     

A surface plasmon resonance immunosensor based on the streptavidin-biotin complex.

It is shown that a streptavidin monolayer immobilized onto an evaporated gold film with biotin forms the basis of a highly specific sensing element. As an example, we show that by immobilizing the biotinylated antibody sex hormone binding globulin (alpha-SHBG) to the bound streptavidin monolayer a specific sensor for the antigen SHBG is readily fabricated. The interaction between immobilized antibody and corresponding antigen is monitored by surface plasmon resonance spectroscopy and is shown to follow a classic Langmuir isotherm. Detection of SHBG at nanomolar concentrations is demonstrated.     

A method for probing the affinity of peptides for amphiphilic surfaces

We have developed a rapid method for probing the affinity of peptides toward an amphiphilic surface. Hydrophobic polystyrene-divinylbenzene beads of 5.7 +/- 1.5 micron diameter are coated with a monomolecular film of egg lecithin to achieve the equilibrium spreading density of the phospholipid, 6 X 10(-3) molecule/A2. The coated beads are ideally suited for assessing the affinity of peptides for phospholipid surfaces: Large quantities of lipid-coated beads of known surface area can be prepared easily and rapidly. Within the pH range 2.0 to 9.0, the adsorbed phospholipids are relatively resistant to hydrolysis and remain bound indefinitely. Following incubation with peptide ligands, beads can be separated from the reaction mixture by centrifugation. Peptides, such as melittin, which destroy or cause fusion of single bilayer phospholipid vesicles, cannot disrupt lecithin-coated beads in a comparable way, and do not displace lecithin from the surface of beads. After incubating these beads in solutions of peptides and proteins, we have determined the parameters for the binding of several ligands to the phospholipid surface. The binding of many amphiphilic peptides obeys a Langmuir adsorption isotherm, i.e., saturable reversible binding to independent and equivalent sites on the bead. That the binding is a true reversible equilibrium is shown by desorption of the ligand upon dilution. From the isotherm, the surface areas occupied by the ligand molecules were calculated, and were observed to be similar to those observed in monolayers at the air-water interface. In comparing the binding of amphiphilic peptides to that of completely hydrophilic peptides, we observed that only the former bind at levels measurable by our techniques. Thus, this method can serve as a rapid assay for detecting amphiphilicity in peptides of putative amphiphilic character.     

Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues

In CAPRI Rounds 1 and 2, we assumed that because there are many ionic charges that weaken electrostatic interaction forces in living cells, the hydrophobic interaction force might be important entropically. As a result of Rounds 1 and 2, the predictions for binding sites and geometric centers were acceptable, but those of the binding axes were poor, because only the largest benzene cluster was used for generating the initial docking structures. These were generated by fitting of benzene clusters formed on the surface of receptor and ligand. In CAPRI Rounds 3-5, the grid-scoring sum on the protein-protein interaction surface and the pairwise potential of the amino acid residues, which were indicated as coming easily into the protein-protein interaction regions, were used as the calculation methods, along with the smaller benzene clusters that participated in benzene cluster fitting. Good predicted models were obtained for Targets 11 and 12. When the modeled receptor proteins were superimposed on the experimental structures, the smallest ligand root-mean-square deviation (RMSD) values corresponding to the RMSD between the model and experimental structures were 6.2 A and 7.3 A, respectively.     

Adsorption of globular proteins on locally planar surfaces: models for the effect of excluded surface area and aggregation of adsorbed protein on adsorption equilibria.

Equilibrium statistical-thermodynamic models are presented for the surface adsorption of proteins modeled as regular convex hard particles. The adsorbed phase is treated as a two-dimensional fluid, and the chemical potential of adsorbed protein is obtained from scaled particle theory. Adsorption isotherms are calculated for nonassociating and self-associating adsorbing proteins. Area exclusion broadens adsorption isotherms relative to the Langmuir isotherm (negative cooperativity), whereas self-association steepens them (positive cooperativity). The calculated isotherm for adsorption of hard spheres using scaled particle theory for hard discs agrees well with that calculated from the hard disc virial expansion. As the cross section of the adsorbing protein in the plane of the surface becomes less discoidal, the apparent negative cooperativity manifested in the isotherm becomes more pronounced. The model is extended to the case of simultaneous adsorption of a tracer protein at low saturation and a competitor protein with a different size and/or shape at arbitrary fractional saturation. Area exclusion by competitor for tracer (and vice versa) is shown to substantially enhance the displacement of tracer by competitor and to qualitatively invalidate the standard interpretation of ligand competition experiments, according to which the fractional displacement of tracer by competitor is equal to the fractional saturation by competitor.     

The adsorption of phloretin to lipid monolayers and bilayers cannot be explained by langmuir adsorption isotherms alone.

Phloretin and its analogs adsorb to the surfaces of lipid monolayers and bilayers and decrease the dipole potential. This reduces the conductance for anions and increases that for cations on artificial and biological membranes. The relationship between the change in the dipole potential and the aqueous concentration of phloretin has been explained previously by a Langmuir adsorption isotherm and a weak and therefore negligible contribution of the dipole-dipole interactions in the lipid surface. We demonstrate here that the Langmuir adsorption isotherm alone is not able to properly describe the effects of dipole molecule binding to lipid surfaces--we found significant deviations between experimental data and the fit with the Langmuir adsorption isotherm. We present here an alternative theoretical treatment that takes into account the strong interaction between membrane (monolayer) dipole field and the dipole moment of the adsorbed molecule. This treatment provides a much better fit of the experimental results derived from the measurements of surface potentials of lipid monolayers in the presence of phloretin. Similarly, the theory provides a much better fit of the phloretin-induced changes in the dipole potential of lipid bilayers, as assessed by the transport kinetics of the lipophilic ion dipicrylamine.     

Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant

The atomic-level mechanisms that coordinate ligand release from protein pockets are only known for a handful of proteins. Here, we report results from accelerated molecular dynamics simulations for benzene dissociation from the buried cavity of the T4 lysozyme Leu99Ala mutant (L99A). In these simulations, benzene is released through a previously characterized, sparsely populated room-temperature excited state of the mutant, explaining the coincidence for experimentally measured benzene off rate and apo protein slow-timescale NMR relaxation rates between ground and excited states. The path observed for benzene egress is a multistep ligand migration from the buried cavity to ultimate release through an opening between the F/G-, H-, and I-helices and requires a number of cooperative multiresidue and secondary-structure rearrangements within the C-terminal domain of L99A. These rearrangements are identical to those observed along the ground state to excited state transitions characterized by molecular dynamic simulations run on the Anton supercomputer. Analyses of the molecular properties of the residues lining the egress path suggest that protein surface electrostatic potential may play a role in the release mechanism. Simulations of wild-type T4 lysozyme also reveal that benzene-egress-associated dynamics in the L99A mutant are potentially exaggerations of the substrate-processivity-related dynamics of the wild type.     

Tension at the Surface: Which Phase Is More Important,Liquid or Vapor?

Tension at the surface is a most fundamental physicochemical property of a liquid surface. The concept of surface tension has widespread implications in numerous natural, engineering and biomedical processes. Research to date has been largely focused on the liquid side; little attention has been paid to the vapor—the other side of the surface, despite over 100 years of study. However, the question remains as to whether the vapor plays any role, and to what extent it affects the surface tension of the liquid. Here we show a systematic study of the effect of vapor on the surface tension and in particular, a surprising observation that the vapor, not the liquid, plays a dominant role in determining the surface tension of a range of common volatile organic solutions. This is in stark contrast to results of common surfactants where the concentration in the liquid plays the major role. We further confirmed our results with a modified adsorption isotherm and molecular dynamics simulations, where highly structured, hydrogen bonded networks, and in particular a solute depletion layer just beneath the Gibbs dividing surface, were revealed.     

A comparative monomolecular film study of antibiotic A21978C homologues of various lipid chain length

A21978C is a calcium-dependent lipopeptide antibiotic whose biological properties are modulated by changes in its lipid chain length. This article reports on the monolayer characteristics of this cyclic lipopeptide and of LY146032 a semi synthetic homologue. The equilibrium spreading pressure pi e increases linearly with the ionic concentration of the subphase and is higher with divalent cations. The nature of the divalent cation plays a crucial role in the spreading as indicated by the variation in the molecular free energy delta Gs.delta Gs decreases in the order K+ greater than Mg2+ greater than Ca2+, which indicates privileged interactions with Ca2+. Also, the larger the lipid chain, the easier the spreading of antibiotic molecules. The compression isotherm curves are shown. The mean area of the uncompressed molecules is around 220-240 A 2 which is compatible with the size of the peptide cycle lying at the interface. The isotherm curves of the natural compounds show a transition region where the molecules are more compressible. At a given area/molecule, the surface pressures increase with the acyl chain length. When the molecules are spread on various salt solutions, the surface pressures increase in the order K+ less than Mg2+ less than Ca2+. The isotherm curves are not reversible upon a compression-expansion cycle and a wide amplitude hysteresis is observed. If a second compression is done, the curve shape is that of a liquid-expanded state and the transition region is no longer observed. This implies a conformational change of the molecules during the first compression process.     

Theoretical aspects of genomic variation screening using DNA microarrays

We present a theoretical model for typical microarray-based single nucleotide polymorphism (SNP) assay of small genomic DNA amount. We derived the adsorption isotherm expressing the on-array hybridization efficiency in terms of genomic target sequence and concentration, oligonucleotide probe sequence and surface density, hybridization buffer, and temperature. This isotherm correctly describes the surface probe density effects, the sensitivity peak, and the melting temperature depression, and is in accord with published experiments. We discuss optimization of parallel SNP genotyping. Our estimates show that SNP detection at a single temperature in aqueous hybridization buffer is restricted by DNA regions that differ by less than 20% in GC content. We predict that the variety of genotyped SNPs could be substantially extended using an assay design with high probe density and a large fraction of probes hybridized.     

Aliphatics vs. aromatics hydration thermodynamics

By comparing the hydration thermodynamics of benzene with that of a hypothetical aliphatic hydrocarbon having the same accessible surface area (ASA) of benzene, Makhatadze and Privalov concluded that the whole difference is due to the weak H-bonds that water forms with the aromatic ring. The formation of such H-bonds would be characterized by a negative Gibbs energy change, slightly increasing in magnitude with temperature, and a positive entropy change over a large temperature range. The latter thermodynamic feature is not physically reliable for the formation of H-bonds. In the present article, by using a statistical mechanical dissection scheme of hydration, a microscopic interpretation for the numbers obtained by Makhatadze and Privalov is proposed. The difference in hydration Gibbs energy should be attributed to the different strength of van der Waals interactions that benzene can do with water, owing to the larger polarizability of the aromatic ring with respect to an aliphatic hydrocarbon of equal size. In addition, the difference in hydration entropy should account for the different extent of H-bond reorganization upon the insertion of benzene and the corresponding aliphatic hydrocarbon in water.     

Phase transitions in 1,2- and 1,3-diacyl-sn-glycero-3-phosphocholine monolayers at the oil/water interface.

Moving the phosphatidylcholine group from the 3- to the 2-position in monolayers of distearoyl-sn-glycero-3-phosphocholine at the oil/water interface expands the surface pressure-area isotherm and markedly increases the surface pressure at which phase separation occurs with only a slight change in the monolayer surface density at the onset of the transition. This is interpreted in terms of a change in an ordering parameter in the solid-condensed state.     

Complexation of 1,2,4-benzenetriol with inorganic and ferritin-released iron in vitro.

The reactive metabolite(s) responsible for the expression of benzene toxicity is not clearly known despite extensive information on the metabolism and hematotoxicity of benzene. It is now widely believed that hematotoxicity of benzene is due to the concerted action of several metabolites which arise from multiple pathways of benzene. In our earlier study, we proposed iron polyphenol chelates as possible toxic metabolites of benzene due to their prooxidant activity. In continuation, we demonstrate the formation of an iron and 1,2,4-benzenetriol (BT) complex, when added together in an acetate buffer, 0.1 M, pH 5.6, by sephadex G-10 column chromatography. It was also observed that iron released from ferritin in the presence of BT formed a complex with BT.