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

A DFT Study on the Adsorption of Benzodiazepines to Clay Surfaces

Benzodiazepines (BDZ) belong to the group of psychiatric substances which act on the central nervous system, having anxiolytic, sedative and hypnotic effects and is one of the most prescribed groups of pharmaceuticals throughout the world. These compounds are not exclusively used for human therapeutics, their prescription is also common in veterinary treatments for anxiolytic and appetite stimulation effects. Nowadays, there are several benzodiazepines under international control for therapeutic use. The widespread use of these compounds doesn’t come without a cost and trace levels of it can now be found disseminated on the environment, what is a matter of ecological concern. In fact, over the last decade, there has been a significant number of studies reporting the occurrence of BDZ in environmental matrices, namely in wastewater treatment plants influents and effluents, surface waters and drinking waters . Some of the more frequently detected BDZ include alprazolam, diazepam, lorazepam and oxazepam . The main reason for the ubiquitous presence of BDZ in the environment is associated not only with the large use but also the generally low efficiency of conventional biological wastewater treatment to remove these pharmaceutical residues. It has been suggested that this inefficiency is due to the halogenated structure of these compounds that significantly reduces their susceptibility to biodegradation . Adsorption processes are the most promising and cheap alternative for removal of these kind of organic xenobiotic from wastewaters. In recent years, inexpensive widely available materials have been investigated for the selection of efficient adsorbents that can make adsorption processes an attractive solution at reasonable costs. Among some of the adsorbents studied, clay-based materials have received some attention due to their interesting properties such as the high cation exchange capacity, swelling properties and high specific surface areas. In particular for the treatment of wastewaters, these materials can overcome the limitations of biological processes, as used in conventional wastewater treatment. A better understanding of the interactions of these organic molecules with clay minerals may thus allow a more judicious selection of materials for water/wastewater treatment filters that present significant enhancements in the removal of BDZ. In this work, electronic structure calculations based on the density functional theory (DFT) are presented on the interaction of two BDZ molecules (diazepam and alprazolam) with a periodic model surface of the vermiculite mineral. Geometry changes of the molecules upon adsorption were compared and the interaction energies with the surfaces were determined for a few different molecular orientations in order to understand the way these molecules interact with the clay surface and the essential factor governing the adsorption processes

Identifying the Azobenzene/Aniline reaction intermediate on TiO2-(110) : a DFT Study

Density functional theory (DFT) calculations, both with and without dispersion corrections, have been performed to investigate the nature of the common surface reaction intermediate that has been shown to exist on TiO2(110) as a result of exposure to either azobenzene (C6H5N═NC6H5) or aniline (C6H5NH2). Our results confirm the results of a previous DFT study that dissociation of azobenzene into two adsorbed phenyl imide (C6H5N) fragments, as was originally proposed, is not energetically favorable. We also find that deprotonation of aniline to produce this surface species is even more strongly energetically disfavored. A range of alternative surface species has been considered, and while dissociation of azobenzene to form surface C6H4NH species is energetically favored, the same surface species cannot form from adsorbed aniline. On the contrary, adsorbed aniline is much the most stable surface species. Comparisons with experimental determinations of the local adsorption site, the Ti–N bond length, the molecular orientation, and the associated C 1s and N 1s photoelectron core level shifts are all consistent with the DFT results for adsorbed aniline and are inconsistent with other adsorbed species considered. Possible mechanisms for the hydrogenation of azobenzene required to produce this surface species are discussed

A DFT study on the adsorption of benzodiazepines to vermiculite surfaces

Widespread use of pharmaceuticals such as benzodiazepines has been resulting over the last decades in the dissemination of residues of these compounds in the environment, and such fact has been raising increasing concern. The generally low efficiencies of conventional wastewater treatment processes for the removal of this type of pollutants demands for the development of alternative or complementary water and wastewater treatment technologies, among which adsorption processes have been gaining popularity, provided that cheap efficient adsorbents are found. Clay materials have been one of the popular choices in this regard. In the present study, quantumchemical calculations have been performed by periodic DFT using the projector augmented-wave (PAW) method to characterize the interactions of two benzodiazepine molecules, alprazolam and diazepam, with a surface of clay mineral, vermiculite. It was observed that both molecules interact strongly with the vermiculite surface, both through a water-bridge binding and by cation-bridge provided by the exchangeable Mg2+ cations of the vermiculite surface. The results point to an interesting potential of vermiculite to be used efficiently as filter medium to remove these pollutants from water and wastewater

Removal of the Antibiotic Sulfamethoxazole by “Green” Clay Sorbents

Contamination of water resources with pharmaceuticals has been one of the top concerns of environmental sciences in the latest years [1, 2], the matter having received very significant media coverage recently [2, 3]. Antibiotics in particular have been gathering considerable attention and are amongst the most serious worries due to the development of antibiotic resistant bacteria as result of prolonged exposure [1, 2, 3]. In particular, antimicrobials and their metabolites are being detected in significant amounts in water supplies, and although no evidence exists that human health is affected by minute doses of antibiotics over long periods of time, changes have been observed in ecosystem functions [3,4]. In addition to antimicrobial resistance, other effects have been observed such as a delay in cell growth of bacteria, limited denitrification, and shifts in community composition [5]. Sulfamethoxazole (SMX), a broad-spectrum biostatic sulfanilamide, has become a point of interest because of its prevalence in contaminated wastewaters at concentrations correlated to bacterial resistance and genetic mutations in organisms [3,4,5]. Taking into account the widespread use of sulfonamides and their potential environmental effects, there is importance in developing new technologies for removing SMX and similar compounds from points of discharge. In fact, most wastewater treatment plants are inefficient for the removal of most micropollutants, especially hardly biodegradable organic xenobiotics which are present in wastewaters at low concentrations, as these conventional systems were only designed for removing bulk pollutants. Several advanced technologies have been evaluated as options to treat these contaminants, e.g. advanced oxidative processes or membrane filtration, but despite the sometimes high removal efficiencies attained, these technologies are too expensive to be considered as viable solutions on a large scale. Adsorption, alone or as part of a more complex water or wastewater treatment process, has been seen as playing a very important role in the removal of many organic xenobiotic pollutants [6, 7]. In this regard, the choice of adsorbent materials is crucial. However, pollutants removal efficiency is not the sole selection criterion, as the cost of the materials may provide or preclude economic viability of the water/wastewater treatment system. Therefore, the quest for efficient adsorbents that are widely available, and do not require expensive processing in order to be used (thereby allowing lower production costs) is a very important aspect of research aimed to manage this environmental problem. In this work we present the study of sorption properties of clay materials (LECA and vermiculite) for the removal of SMX from water. The dependence of removal efficiencies on the antibiotic initial concentrations, contact time with the adsorbents and other system/environment conditions was assessed. The two clay materials were compared in terms of their more balanced performance towards the removal of the pharmaceutical tested and the materials are suggested as a useful component of a water or wastewater treatment system designed for the removal of this contaminant (and others of similar type). Vermiculite was shown to be more efficient than LECA in the adsorption of the pharmaceutical and the one with faster kinetics. In other to gain a deeper insight into the characteristics that favor the removal of this compound by mineral surfaces, quantum chemical theoretical calculations were performed to illustrate the type of interactions that are responsible for the preferable adsorption of the compound to the vermiculite surface

T-20 and T-1249 HIV fusion inhibitors’ structure and conformational behavior in solution: a molecular dynamics study

Fusion of the HIV envelope with the target cell membrane is a critical step of HIV entry into the target cell. Several peptides based on the C-region of HIV gp41 have been used in clinical trials as possible HIV fusion inhibitors. Among these are T-1249 and T-20 (also known as enfurvitide; see fig. 1). Despite recent works, a detailed molecular picture of the inhibitory mechanism of these molecules is still lacking. These peptides are usually depicted as α-helices by analogy with the structure of the sequence of the gp41 protein with which they are homologous. However, structures like these would not explain the ability that the two fusion inhibitors have to both become solvated by water and interact effectively with cell membranes. This led us to study the structure and conformational behavior of all these peptides. To this effect, extensive molecular dynamics simulations (total time 400 ns) with explicit solvent (SPC water) were carried out to investigate the structure and conformational behavior of T-1249 and T-20, as well as shorter homologous peptides CTP and 3f5 (see fig. 1), which show no inhibitory action. The monitored parameters include mean square displacement relative to the initial conformation (α-helix structures in all cases), secondary structure, solvent accessible surface and radius of gyration. We found that the studied peptides have no stable structure in solution in the time scale studied. Additionally, the solvent accessible area varies significantly during the simulation. Our findings suggest that these peptides may assume not only one but several possible sets of structures in solution, some of which more adequate to interact with the solvent, whereas others might be better suited to interact with cell membranes

Influence of mordants in the colour of natural dyes: theoretical predictions and experimental results

Arraiolos tapestries are probably one of the richest artistic Portuguese expressions in terms of textile production and a cultural heritage that urges to preserve. The richness of colours displayed by some of the Arraiolos tapestries denotes the likely use of a wide variety of dyes. The different light-fastness of dyes combined with the use of different types of mordants can also explain the appearance of pale shades and fading in some tapestries due to different molecule interactions with the support fibres. The work we present is part of a major project (experimental and theoretical) that envisages the identification of the dyes and mordants used throughout the ages in the production of Arraiolos tapestries and the establishment of the major factors (like mordant, humidity and light) that are responsible for the colour and fading of the natural dyes as well as for the degradation of the fibres. It is well known that the colour of a dye depends on the type of mordant used, due to the formation of metal complexes that cause a change in the molecular orbitals energies and hence a shift in UV/Vis absorption bands. The electronic structure and transitions in the visible spectra of some dyes and mordants identified on Arraiolos rugs were predicted by the ZINDO-INDO/S semi-empirical molecular orbital method [1,2] in order to identify the origin of the colours and characterize the influence of metal coordination on colour modifications. The molecular geometry of each dye-mordant complex was optimized at DFT level using the Gaussian03 package [3] and a simulation of the UV/Vis absorption spectrum was calculated using ZINDO. Another important outcome of this study was the determination of the chromophore properties of fragment molecules produced by the dyes degradation processes that enabled the evaluation of the colour changes of the dyes and subsequent fading. Wool fibres were dyed with previously identified natural dyes and mordants and the colour parameters and the spectra were determined using a UV-Vis portable spectrometer. These parameters were compared with the results from the theoretical predictions

Excess Thermodynamics of Mixtures Involving Xenon and Light Linear Alkanes by Computer Simulation

Excess molar enthalpies and excess molar volumes as a function of composition for liquid mixtures of xenon + ethane (at 161.40 K), xenon + propane (at 161.40 K) and xenon + n-butane (at 182.34 K) have been obtained by Monte Carlo computer simulations and compared with available experimental data. Simulation conditions were chosen to closely match those of the corresponding experimental results. The TraPPE-UA force field was selected among other force fields to model all the alkanes studied, whereas the one-center Lennard−Jones potential from Bohn et al. was used for xenon. The calculated and for all systems are negative, increasing in magnitude as the alkane chain length increases. The results for these systems were compared with experimental data and with other theoretical calculations using the SAFT approach. An excellent agreement between simulation and experimental results was found for xenon + ethane system, whereas for the remaining two systems, some deviations that become progressively more significant as the alkane chain length increases were observed

Influence of the sterol aliphatic side chain on membrane properties: a molecular dynamics study

Following a recent experimental investigation of the effect of the length of the alkyl side chain in a series of cholesterol analogues (Angew. Chem., Int. Ed., 2013, 52, 12848–12851), we report here an atomistic molecular dynamics characterization of the behaviour of methyl-branched side chain sterols (iso series) in POPC bilayers. The studied sterols included androstenol (i-C0-sterol) and cholesterol (i-C8-sterol), as well as four other derivatives (i-C5, i-C10, i-C12 and i-C14-sterol). For each sterol, both subtle local effects and more substantial differential alterations of membrane properties along the iso series were investigated. The location and orientation of the tetracyclic ring system is almost identical in all compounds. Among all the studied sterols, cholesterol is the sterol that presents the best matching with the hydrophobic length of POPC acyl chains, whereas longer-chained sterols interdigitate into the opposing membrane leaflet. In accordance with the experimental observations, a maximal ordering effect is observed for intermediate sterol chain length (i-C5, cholesterol, i-C10). Only for these sterols a preferential interaction with the saturated sn-1 chain of POPC (compared to the unsaturated sn-2 chain) was observed, but not for either shorter or longer-chained derivatives. This work highlights the importance of the sterol alkyl chain in the modulation of membrane properties and lateral organization in biological membranes

Estimation of Hyperpolarizabilities of Organometallic Complexes by DFT

The research of nonlinear optical (NLO) materials has grown in the past decades due to the potential application in optical device technology, like data storage, communication and bio-sensing. For obtaining large molecular second-order nonlinear optical (SONLO) responses, i.e. large hyperpolarizabilities (β), molecules have to possess typical “push-pull” asymmetric structures. η5- Monocyclopentadienylruthenium(II) and iron(II) complexes presenting heterocyclic organic chromophores have proven to be promising systems in this field. Also the presence of a transition metal suggests that it is possible to switch the SONLO response of the material by changing its oxidation state, by electrochemical means for example. In this case, two distinct forms would be expected: the “switched on” form, with high β value; and the “switched-off” form, with negligible or substantially lower β. Herein, we show the application of Density Functional Theory (DFT) to the studies of SONLO properties of several organometallic complexes bearing thiophene based organic ligands as active NLO chromophores