J. P. Prates Ramalho

INFLUENCE OF SURFACE IONIZATION ON THE ADSORPTION OF AQUEOUS ZINC SPECIES BY ACTIVATED CARBONS

A surface ionization and adsorption model is used to simulate the adsorption of zinc species from aqueous solutions of varying pH on a number of different activated carbons and the results compared with experimental data. In all cases good agreement is obtained between theory and experiment. It is shown that for most of the carbons the uptake of zinc is due to adsorption of Zn2+ ions on ionized acid sites, the calculated equilibrium constants being of the order of 106–107. On the other hand, one of the carbons used (NORIT AZO) contains virtually no acid sites, but a high concentration of strong basic sites, and the uptake of zinc in this case appears to be due to adsorption of a negatively charged hydroxy complex on protonated basic sites, the estimated equilibrium constant being 108.

Structure and Phase Transformations of DPPC Lipid Bilayers in the Presence of Nanoparticles: Insights from Coarse-Grained Molecular Dynamics Simulations

In this article, we investigate fluid-gel transformations of a DPPC lipid bilayer in the presence of nanoparticles, using coarse-grained molecular dynamics. Two types of nanoparticles are considered, specifically a 3 nm hydrophobic nanoparticle located in the core of the bilayer and a 6 nm charged nanoparticle located at the interface between the bilayer and water phase. Both negatively and positively charged nanoparticles at the bilayer interface are investigated. We demonstrate that the presence of all types of nanoparticles induces disorder effects in the structure of the lipid bilayer. These effects are characterized using computer visualization of the gel phase in the presence of nanoparticles, radial distribution functions, and order parameters. The 3 nm hydrophobic nanoparticle immersed in the bilayer core and the positively charged nanoparticle at the bilayer surface have no effect on the temperature of the fluid-gel transformation, compared to the bulk case. Interestingly, a negatively charged hydrophobic nanoparticle located at the surface of the bilayer causes slight shift of the fluid-gel transformation to a lower temperature, compared to the bulk bilayer case.

Recent developments in molecular dynamics simulations of fluorescent membrane probes.

Due to their sensitivity and versatility, the use of fluorescence techniques in membrane biophysics is widespread. Because membrane lipids are non-fluorescent, extrinsic membrane probes are widely used. However, the behaviour of these probes when inserted in the bilayer is often poorly understood, and it can be hard to distinguish between legitimate membrane properties and perturbation resulting from probe incorporation. Atomistic molecular dynamics simulations present a convenient way to address these issues and have been increasingly used in recent years in this context. This article reviews the application of molecular dynamics to the study of fluorescent membrane probes, focusing on recent work with complex design fluorophores and ordered bilayer systems.

NBD-Labeled Cholesterol Analogues in Phospholipid Bilayers: Insights from Molecular Dynamics

Nitrobenzoxadiazole (NBD)-labeled sterols are commonly used as fluorescent cholesterol analogues in membrane biophysics. However, some experimental reports have questioned their ability to emulate the behavior of cholesterol in phospholipid bilayers. For the purpose of a detailed clarification of this matter, atomistic molecular dynamics simulations of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers, containing either cholesterol or one of two fluorescent cholesterol analogues, 22-NBD-cholesterol or 25-NBD-cholesterol, were carried out. It is found that these sterol probes tend to adopt conformations in which their tail-labeled fluorophore is oriented toward the lipid/water interface, with a location similar to that observed in molecular dynamics simulations of other NBD probes. This implies that in these molecules the long sterol axis is no longer aligned with the membrane normal, and preferentially adopts orientations approximately parallel to the bilayer plane. In turn, these stretched conformations, together with NBD-POPC atomic interactions, lead to slowed-down lateral diffusion of both fluorescent sterols, compared to cholesterol. From computation of the deuterium order parameter and acyl chain tilts of POPC chains for varying POPC-sterol distance, it is observed that the local ordering effect of sterol is altered in both fluorescent derivatives. In agreement with reported experimental data, both fluorescent sterols are able to increase the order of POPC at 20 mol % concentration (as some molecules adopt an upright conformation, possibly related to formation of transbilayer aggregates), albeit to a smaller extent to that of cholesterol. Altogether, this study indicates that both 22- and 25-NBD-cholesterol are unable to mimic the most important features of cholesterols behavior in lipid bilayers.

Behavior of Fluorescent Cholesterol Analogues Dehydroergosterol and Cholestatrienol in Lipid Bilayers: A Molecular Dynamics Study

Molecular dynamics simulations of bilayer systems consisting of varying proportions of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), cholesterol (Chol), and intrinsically fluorescent Chol analogues dehydroergosterol (DHE) or cholestatrienol (CTL) were carried out to study in detail the extent to which these fluorescent probes mimic Chols behavior (location, orientation, dynamics) in membranes as well as their effect on host bilayer structure and dynamics (namely their ability to induce membrane ordering in comparison with Chol). Control properties of POPC and POPC/Chol bilayers agree well with published experimental and simulation work. Both probes and Chol share similar structural and dynamical properties within the bilayers. Additionally, the fluorescent sterols induce membrane ordering to a similar (slightly lower) extent to that of Chol. These findings combined demonstrate that the two studied fluorescent sterols are adequate analogues of Chol, and may be used with advantage over side-chain labeled sterols. The small structural differences between the three studied sterols are responsible for the slight variations in the calculated properties, with CTL presenting a more similar behavior to Chol (correlating with its larger structural similarity to Chol) compared to DHE.

Fluorescent membrane probes’ behavior in lipid bilayers: insights from molecular dynamics simulations

Fluorescence spectroscopy and microscopy have been used as tools to study membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Two major points of concern arise regarding this matter, namely the incomplete understanding of the probe behavior inside the bilayer and the perturbation of the latter resulting from probe incorporation. To this effect, molecular dynamics (MD) simulations, by providing detailed atomic-scale information, represent a valuable way to characterize the location and dynamics of bilayer-inserted membrane probes, as well as the magnitude of perturbation they induce on the host lipid structure, and several important classes of reporter molecules have been studied in recent years. This article reviews the state of the art of MD simulations of bilayer-inserted fluorescent probes, focusing on the information that has been obtained from previous studies and hinting at future perspectives in this rapidly emerging field.

Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

Fluorescence spectroscopy and microscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in these membranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3-4Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using them as membrane reporters.

Numerical simulation of surface ionisation and specific adsorption on a two-site model of a carbon surface

A two-site (one acidic, one basic) model of the ionisation of a carbon-type surface, in the presence or absence of specifically adsorbing ions, is analysed. The effect of various parameters, such as site concentration and strength, ion-adsorption equilibrium constants and solution composition, are considered and it is shown how these parameters influence the extent of surface ionisation and adsorption, as well as the surface charge. Special consideration is given to the point of zero charge (pzc) and the factors which determine its value. Of particular note is the finding that when specific adsorption occurs the value of the pzc depends not only on the strength of the adsorption itself, but also on the concentration and ionisation constant of the acidic site (for cation adsorption) or basic site (for anion adsorption). One of the consequences of this dependence is that, although cation adsorption tends to decrease the pzc and anion adsorption tends to increase it, equal adsorptions will not necessarily cancel out the opposing changes. Furthermore, under appropriate circumstances the pzc can decrease even though the anion is adsorbed more strongly and vice versa. A graphical proof that the mass-titration method for the determination of the pzc is valid, even when specific adsorption of ions occurs, is also presented.

Mechanisms of removal of three widespread pharmaceuticals by two clay materials

Pharmaceutical residues presence in the environment is among nowadays top emergent environmental issues. For removal of such pollutants, adsorption is a generally efficient process that can be complementary to conventional treatment. Research of cheap, widely available adsorbents may make this process economically attractive. The aim of the present work was to evaluate the capacity of two clay materials (exfoliated vermiculite, LECA) to adsorb gemfibrozil, mefenamic acid and naproxen in lab-scale batch assays. Results show that both adsorbents are able to remove the pharmaceuticals from aqueous medium. Although vermiculite exhibited higher adsorption capacities per unit mass of adsorbent, LECA yielded higher absolute removals of the pharmaceuticals due to the larger mass of adsorbent. Quantum chemistry calculations predicted that the forms of binding of the three molecules to the vermiculite surface are essentially identical, but the adsorption isotherm of naproxen differs substantially from the other twos. The linear forms of the latter impose limits at lower concentrations to the removal efficiencies of these pharmaceuticals by vermiculite, thereby electing LECA as more efficient. Notwithstanding, vermiculites high specific adsorption capacity and also its much faster adsorption kinetics suggest that there may be some benefits in combining both materials as a composite adsorbent solution.

Switchable Nonlinear Optical Properties of η5-Monocyclopentadienylmetal Complexes: A DFT Approach

Density functional theory (DFT) calculations have been carried out to investigate the switching of the second-order nonlinear optical (NLO) properties of η(5)-monocyclopentadienyliron(II) and ruthenium(II) model complexes presenting 5-(3-(thiophen-2-yl)benzo[c]thiophen-1-yl)thiophene-2-carbonitrile as a ligand. The switching properties were induced by redox means. Both oxidation and reduction stimulus have been considered, and calculations have been performed both for the complexes and for the free benzo[c]thiophene derivative ligand in order to elucidate the role played by the organometallic fragment on the second-order NLO properties of these complexes. B3LYP, CAM-B3LYP, and M06 functionals were used for our calculations. The results show some important structural changes upon oxidation/reduction that are accompanied by significant differences on the corresponding second-order NLO properties. TD-DFT calculations show that these differences on the second-order NLO response upon oxidation/reduction are due to a change in the charge transfer pattern, in which the organometallic iron and ruthenium moieties play an important role. The calculated static hyperpolarizabilities were found to be strongly functional dependent. CAM-B3LYP, however, seems to predict more reliable structural and optical data as well as hyperpolarizabilities when compared to experimental data. The use of this functional predicts that the studied complexes can be viewed as acting as redox second-order NLO switches, in particular using oxidation stimulus. The β(tot) value of one-electron oxidized species is at least ~8.3 times (for Ru complex) and ~5.5 times (for Fe complex) as large as that of its nonoxidized counterparts.