Adsorptive behavior of multi-walled carbon nanotubes immobilized magnetic nanoparticles for removing selected pesticides from aqueous matrices.

The present work synthesized two new materials of functionalized multi-walled carbon nanotubes (MWCNT-OH and MWCNT-COOH) impregnated with magnetite (Fe3O4) using solution precipitation methodology. The resulting MWCNT-OH-Mag and MWCNT-COOH-Mag materials were characterized by scanning electron microscopy coupled with energy dispersion X-ray spectroscopy, Fourier transform infrared, X-ray diffraction, atomic force microscopy, and electrical force microscopy. The characterization results indicate that the -OH functional groups in the MWCNT interact effectively with magnetite iron favoring impregnation and indicating the regular distribution of nanoparticles on the surface of the synthesized materials. The adsorption efficiency of the MWCNT-OH-Mag and MWCNT-COOH-Mag materials was tested using the pollutants 2,4-D and Atrazine. Over batch studies carried out under different pH ranges, it was found that the optimal condition for 2,4-D adsorption was at pH 2, while for Atrazine, it was found at pH 6. The rapid adsorption kinetics of 2,4-D and Atrazine reaches equilibrium within 30 min. The pseudo-first-order model described 2,4-D adsorption well. The General-order model described better atrazine adsorption. The magnetically doped adsorbent functionalized with -OH surface groups (MWCNT-OH-Mag) demonstrated superior adsorption performance and increased Fe-doped sites. The Sips model described the adsorption isotherms accurately. MWCNT-OH-Mag presented the greatest adsorption capacity at 51.4 and 47.7 mg g-1 for 2,4-D and Atrazine, respectively. Besides, electrostatic forces and complexation rule the molecular interactions between metals and pesticides. The leaching and regeneration tests of the synthesized materials indicate high stability in an aqueous solution. Furthermore, experiments with wastewater samples contaminated with the model pollutants indicate that the novel adsorbents are highly promising for enhancing water purification by adsorptive separation.

Pollution caused by nanoplastics: adverse effects and mechanisms of interaction via molecular simulation.

The continuous increase in the production of synthetic plastics for decades and the inadequate disposal of plastic waste have resulted in a considerable increase of these materials in aquatic environments, which has developed into a major environmental concern. In addition to conventional parameters, the relevance of the environmental monitoring of microplastics (MPs) and nanoplastics (NPs) has been highlighted by the scientific community due to the potential adverse effects these materials pose to the ecosystem as well as to human health. The literature has registered an increasing interest in understanding the mechanisms, at the molecular level, of the interaction between NPs and other compounds using molecular simulation techniques. The present review aims to: (i) summarize the force fields conventionally used to describe NPs by molecular simulations; (ii) discuss the effects of NPs in the structural and dynamical properties of biological membranes; (iii) evaluate how NPs affect the folding of proteins; (iv) discuss the mechanisms by which NPs adsorb contaminants from the environment. NPs can affect the secondary structure of proteins and change the lateral organization and diffusion of lipid membranes. As a result, they may alter the lipid digestion in the gastrointestinal system representing a risk to the assimilation of the nutrients by humans. The adsorption of contaminants on MPs and NPs can potentiate their harmful effects on human health, due to a possible synergism. Therefore, understanding the mechanisms involved in these interactions is crucial to predict dangerous combinations and outline action strategies that reduce negative impacts on ecosystems and human health. Depending on the chemical properties of contaminants and NPs, electrostatic and/or van der Waals interactions can be more relevant in explaining the adsorption process. Finally, we conclude by highlighting gaps in the literature and the critical aspects for future investigations.

Determination of liquid-vapor equilibrium and critical properties of fatty acids for biodiesel production through molecular dynamics.

In recent years, biodiesel production has emerged as an option for renewable and green fuel generation due to the constant reduction of fossil fuel reservoirs. Biofuels as biodiesel also show valuable attributes, environmentally speaking, due to their low environmental impact, contributing to the achievement of sustainability. However, costs are not allowable for large-scale production. Thereby, several novel processes have been proposed (e.g., reactive distillation) to solve this issue. An inconvenience for the development of these processes is the little information in the literature about the critical properties of fatty acids, which are precursors of biodiesel. Determination of critical properties for fatty acids through experimentation is difficult. The reason is that fatty acids tend to self-associate (to dimerize) due to carboxylic groups presence through hydrogen bonds, and consequently, have higher boiling points than other compounds of similar molecular mass (e.g., hydrocarbons, esters). Therefore, alternative methods for this determination are required. One choice is the group-contribution method, which is based on the structure of the molecule; however, results can significantly vary among different group-contribution approaches. Another alternative (and the focus of this research) for the determination of these properties is molecular simulation techniques. In this work, the liquid-vapor equilibrium as a function of temperature and the surface tension of three pure fatty acids of long chain (linoleic, oleic, and palmitic acid) have been calculated. Simulations have been performed by molecular dynamics using the method of direct determination of phase coexistence with the software GROMACS; in which the transferable potentials for phase equilibria united atom forcefield (TraPPE-UA) have been implemented for these specific molecules. Orthobaric densities and surface tension values have been reported at temperatures near the critical point (from 650 K to 800 K). Critical properties (temperature, pressure, density) have been extrapolated from trajectories obtained in these simulations using scaling law relations. Critical properties for these compounds are not available experimentally, therefore, group contribution calculations from the literature were used as a reference. In this comparison, the palmitic acid properties calculated in this work, show the best agreement among the three substances investigated.

Prediction of chlorophenols adsorption on activated carbons by representative pores method.

The specification of a particular activated carbon adsorbents for removal of phenol and related derivatives, from dilute aqueous solutions, is still based on lengthy trial and error experimental tests. A predictive model of adsorption of these compounds would considerably reduce the carbon selection time and could also bring new information to support more efficient carbon synthesis. The use of molecular simulation and the methodology of representative pores proved to be adequate for quantitative prediction of phenol adsorption. Here the methodology is being extended to chlorophenols, an important class of phenol-derived pollutants. A set of ortho- and para-chlorophenol isotherms were simulated for different representative pores in order to predict carbon adsorption and determine the most significative pore size. At low concentrations (1 × 10-4 mol/L), the pores of 8.9 and 18.5 Å are the most effective. For concentrations above 3 × 10-4 mol/L, pores in the range of 27.9 Å must be present in the activated carbon. The simulation predicts a step for the 27.9 Å pore that can be correlated with experimental steps in literature. Finally, the adsorption isotherms of chlorophenols for other activated carbons were predicted with the help of the model.

Insights into ß-amyloid transition prevention by cucurbit[7]uril from molecular modeling.

In this study, comparable molecular dynamic (MD) simulations of 1.2 microseconds were performed to clarify the prevention of the ß-amyloid peptide (Aß1-42) aggregation by cucurbit[7]uril (CB[7]). The accumulation of this peptide in the brain is one of the most harmful in Alzheimer's disease. The inhibition mechanism of Aß1-42 aggregation by different molecules is attributed to preventing of Aß1-42 conformational transition from α-helix to the ß-sheet structure. However, our structural analysis shows that the pure water and aqueous solution of the CB[7] denature the native Aß1-42 α-helix structure forming different compactness and unfolded conformations, not in ß-sheet form. On the other hand, in the three CB[7]@Aß1-42 complexes, it was observed the encapsulation of N-terminal (Asp1), Lys16, and Val36 by CB[7] along the MD trajectory, and not with aromatic residues as suggested by the literature. Only in one CB[7]@Aß1-42 complex was observed stable Asp23-Lys28 salt bridge with an average distance of 0.36 nm. All CB[7]@Aß1-42 complexes are very stable with binding free energy lowest than ∼-50 kcal/mol between the CB[7] and Aß1-42 monomer from MM/PBSA calculation. Therefore, herein we show that the mechanism of the prevention of elongation protofibril by CB[7] is due to the disruption of the Asp23-Lys28 salt bridge and steric effects of CB[7]@Aß1-42 complex with the fibril lattice, and not due to the transition from α-helix to ß-sheet following the dock-lock mechanism.Communicated by Ramaswamy H. Sarma.

Representative Pores: An Efficient Method to Characterize Activated Carbons.

We propose a pore size analysis methodology for carbonaceous materials that reduces complexity while maintaining the significant elements of the structure-property relationship. This method chooses a limited number of representative pores, which will constitute a simplified kernel to describe the pore size distribution (PSD) of an activated carbon. In this study we use the representative pore sizes of 7.0, 8.9, 18.5, and 27.9 Å and N2 isotherms at 77.4 K to determine the PSD which is later applied to predict the adsorption equilibrium of other gases. In this study we demonstrate the ability to predict adsorption of different gas molecules on activated carbon from the PSD generated with representative pores (PSDrep). The methodology allows quick solutions for large-scale calculations for carbonaceous materials screening, in addition to make accessible an easily understood and prompt evaluation of the structure-property relationship of activated carbons. In addition to the details of the methodology already tested in different fields of application of carbonaceous materials, we present a new application related to the removal of organic contaminants in dilute aqueous solutions.

A thermo-responsive adsorbent-heater-thermometer nanomaterial for controlled drug release: (ZIF-8,EuxTby)@AuNP core-shell.

An adsorbent-heater-thermometer nanomaterial, (ZIF-8,EuxTby)@AuNP, based on ZIF-8 (adsorbent), containing Eu3+ and/or Tb3+ ions (thermometer) and gold nanoparticles (AuNPs, heater) was designed, synthetized, characterized, and applied to controlled drug release. These composite materials were characterized as core-shell nanocrystals with the AuNPs being the core, around which the crystalline ZIF-8 has grown (shell) and onto which the lanthanide ions have been incorporated or chemosorbed. This shell of ZIF-8 acts as adsorbent of the drugs, the AuNPs act as heaters, while the luminescence intensities of the ligand and the lanthanide ions are used for temperature monitoring. This thermo-responsive material can be activated by visible irradiation to release small molecules in a controlled manner as established for the model pharmaceutical compounds 5-fluorouracil and caffeine. Computer simulations and transition state theory calculations shown that the diffusion of small molecules between neighboring pores in ZIF-8 is severely restricted and involves high-energy barriers. These findings imply that these molecules are uploaded onto and released from the ZIF-8 surface instead of being inside the cavities. This is the first report of ZIF-8 nanocrystals (adsorbents) containing simultaneously lanthanide ions as sensitive nanothermometers and AuNPs as heaters for controlled drug release in a physiological temperature range. These results provide a proof-of-concept that can be applied to other classes of materials, and offer a novel perspective on the design of self-assembly multifunctional thermo-responsive adsorbing materials that are easily prepared and promptly controllable.

Rotavirus VP6 protein as a bio-electrochemical scaffold: Molecular dynamics and experimental electrochemistry.

This paper reports a theoretical and experimental investigation on the recombinant protein rotavirus VP6 as a bioelectrochemical interface. Our motivation arises from the highly active zones of VP6 which can interact with biological structures and metals, as well as its useful features such as self-assembly, polymorphism, and active surface charge. A molecular simulation study was performed to analyze the charge transfer properties of theVP6 trimer under an applied electric field. The electrostatic properties were evaluated via the nonlinear second-order Poisson-Boltzmann equation, using finite element methods based on parameter discretization and calculation of solute/solvent interaction forces, which account for mean-field screening effects. The electrochemical study validated the theoretical predictions for VP6 in their different assemblies (trimers and nanotubes) when they are used as electrodes in 10 mM K3[Fe(CN)6], 1 M KCl. Applying a potential sweep promotes charge transfer, facilitates redox activity of the ferricyanide ion. Furthermore, protein assemblies decreased electrode electrical resistance and enabled gold particle electrodeposition on the protein VP6. These results suggest that VP6 is a promising conductive biomaterial that promotes charge transfer of redox probes and could be used as a new scaffold to create bio-electrochemical interfaces.

New red-shifted fluorescent biosensor for monitoring intracellular redox changes.

Maintenance of intracellular redox homeostasis is critical for cell survival, proliferation, differentiation, and signaling. In this regard, major changes in the intracellular redox milieu may lead to cell death whereas subtle increases in the level of certain oxidizing species may act as signals that regulate a plethora of cellular processes. Redox-sensitive variants of green fluorescent proteins (roGFP2 and rxYFP) were developed and proved useful to monitor intracellular redox changes in a non-invasive and online manner. With the aim to extend the spectral range of the fluorescent redox biosensors, we here describe the generation, biochemical characterization and biological validation of a new redox reporter based on the red-shifted mRuby2 protein (rxmRuby2). Spectrofluorimetric analysis performed with the recombinant biosensor shows a reversible redox response produced by two redox-active cysteine residues predicted by molecular modeling. rxmRuby2 is highly selective for the couple glutathione/glutathione disulfide in the presence of the oxidoreductase glutaredoxin. The estimated redox potential of rxmRuby2 (E° -265 ±â€¯22 mV) makes it suitable for its use in reducing subcellular compartments. Titration assays demonstrated the capacity of rxmRuby2 to monitor redox changes within a physiological pH range. rxmRuby2 responded sensitively and reversibly to different redox stimuli applied to HeLa and HEK293 cells expressing transiently and/or stable the biosensor. Fusing rxmRuby2 to the Clover fluorescent protein allowed normalization of the redox signal to the expression level of the reporter protein and/or to other factors that may affect fluorescence. The new red-shifted redox biosensor show promises for deep-tissue and in vivo imaging applications.

Penetration of antimicrobial peptides in a lung surfactant model.

Molecular dynamics simulations were successfully performed to understand the absorption mechanism of antimicrobial peptides LL-37, CATH-2, and SMAP-29 in a lung surfactant model. The antimicrobial peptides quickly penetrate in the lung surfactant model in dozens or hundreds nanoseconds, but they electrostatically interact with the lipid polar heads during the simulation time of 2 µs. This electrostatic interaction should be the explanation for the inactivation of the antimicrobial peptides when co-administrated with lung surfactant. As they strongly interact with the lipid polar heads of the lung surfactant, there is no positive charge available on the antimicrobial peptide to attack the negatively charged bacteria membrane. In order to avoid the interaction of peptides with the lipid polar heads, sodium cholate was used to form nanoparticles which act as an absorption enhancer of all antimicrobial peptides used in this investigation. The nanoparticles of 150 molecules of sodium cholate with one peptide were inserted on the top of the lung surfactant model. The nanoparticles penetrated into the lung surfactant model, spreading the sodium cholate molecules around the lipid polar heads. The sodium cholate molecules seem to protect the peptides from the interaction with the lipid polar heads, leaving them free to be delivered to the water phase. The penetration of peptides alone or even the peptide nanoparticles with sodium cholate do not collapse the lung surfactant model, indicating to be a promisor drug delivery system to the lung. The implications of this finding are that antimicrobial peptides may only be co-administered with an absorption enhancer such as sodium cholate into lung surfactant in order to avoid inactivation of their antimicrobial activity.

Rational Development of a Novel Hydrogel as a pH-Sensitive Controlled Release System for Nifedipine.

This work depicts the rational development (in-silico design, synthesis, characterization and in-vitro evaluation) of polyvinyl alcohol hydrogels (PVAH) cross-linked with maleic acid (MA) and linked to γ-cyclodextrin molecules (γ-CDPVAHMA) as systems for the controlled and sustained release of nifedipine (NFD). Through computational studies, the structural blocks (PVA chain + dicarboxylic acid + γ-CD) of 20 different hydrogels were evaluated to test their interaction energies (ΔE) with NFD. According to the ΔE obtained, the hydrogel cross-linked with maleic acid was selected. To characterize the intermolecular interactions between NFD and γ-CDPVAHMA, molecular dynamics simulation studies were carried out. Experimentally, three hydrogel formulations with different proportions of γ-CD (2.43%, 3.61% and 4.76%) were synthesized and characterized. Both loading and release of NFD from the hydrogels were evaluated at acid and basic pH. The computational and experimental results show that γ-CDs linked to the hydrogels were able to form 1:1 inclusion complexes with NFD molecules. Finally, γ-CDPVAHMA-3 demonstrated to be the best pH-sensitive release platform for nifedipine. Its effectiveness could significantly reduce the adverse effects caused by the anticipated release of NFD in the stomach of patients.

Design, synthesis and biological evaluation of 1,3-dihydroxyxanthone derivatives: Effective agents against acetylcholinesterase.

The present work concerns the rational design and development of new inhibitors of acetylcholinesterase (AChE) based on the privileged xanthone scaffold. In order to understand and rationalize the mode of action of these target structures a theoretical study was initially conducted. From the results of rational design, a new variety of amphiphilic xanthone derivatives were synthesized, structurally characterized and evaluated as potential anti-Alzheimer agents. The results showed that most of the synthesized compounds exhibited high AChE inhibitory activity at the micromolar range (IC50, 0.46-12.09µM). The synthetic xanthone 11 showed the best inhibitory effect on AChE and a molecular modeling study revealed that 11 targeted both the catalytic active site (CAS) and the peripheral anionic site (PAS) of AChE. Therefore, this compound could be considered asa potential lead compound towards new drugs for the treatment of Alzheimer's disease.

Viscosity of heptane-toluene mixtures. Comparison of molecular dynamics and group contribution methods.

Three methods of molecular dynamics simulation [Green-Kubo (G-K), non-equilibrium molecular dynamics (NEMD) and reversed non-equilibrium molecular dynamics (RNEMD)], and two group contribution methods [UNIFAC-VISCO and Grunberg-Nissan (G-N)] were used to calculate the viscosity of mixtures of n-heptane and toluene (known as heptol). The results obtained for the viscosity and density of heptol were compared with reported experimental data, and the advantages and disadvantages of each method are discussed. Overall, the five methods showed good agreement between calculated and experimental viscosities. In all cases, the deviation was lower than 9%. It was found that, as the concentration of toluene increases, the deviation of the density of the mixture (as calculated with molecular dynamics methods) also increases, which directly affects the viscosity result obtained. Among the molecular simulation techniques evaluated here, G-K produced the best results, and represents the optimal balance between quality of result and time required for simulation. The NEMD method produced acceptable results for the viscosity of the system but required more simulation time as well as the determination of an appropriate shear rate. The RNEMD method was fast and eliminated the need to determine a set of values for shear rate, but introduced large fluctuations in measurements of shear rate and viscosity. The two group contribution methods were accurate and fast when used to calculate viscosity, but require knowledge of the viscosity of the pure compounds, which is a serious limitation for applications in complex multicomponent systems.

Accessing gap-junction channel structure-function relationships through molecular modeling and simulations.

BACKGROUND: Gap junction channels (GJCs) are massive protein channels connecting the cytoplasm of adjacent cells. These channels allow intercellular transfer of molecules up to ~1 kDa, including water, ions and other metabolites. Unveiling structure-function relationships coded into the molecular architecture of these channels is necessary to gain insight on their vast biological function including electrical synapse, inflammation, development and tissular homeostasis. From early works, computational methods have been critical to analyze and interpret experimental observations. Upon the availability of crystallographic structures, molecular modeling and simulations have become a valuable tool to assess structure-function relationships in GJCs. Modeling different connexin isoforms, simulating the transport process, and exploring molecular variants, have provided new hypotheses and out-of-the-box approaches to the study of these important channels. METHODS: Here, we review foundational structural studies and recent developments on GJCs using molecular modeling and simulation techniques, highlighting the methods and the cross-talk with experimental evidence. RESULTS AND DISCUSSION: By comparing results obtained by molecular modeling and simulations techniques with structural and functional information obtained from both recent literature and structural databases, we provide a critical assesment of structure-function relationships that can be obtained from the junction between theoretical and experimental evidence.

MDWiZ: a platform for the automated translation of molecular dynamics simulations.

A variety of popular molecular dynamics (MD) simulation packages were independently developed in the last decades to reach diverse scientific goals. However, such non-coordinated development of software, force fields, and analysis tools for molecular simulations gave rise to an array of software formats and arbitrary conventions for routine preparation and analysis of simulation input and output data. Different formats and/or parameter definitions are used at each stage of the modeling process despite largely contain redundant information between alternative software tools. Such Babel of languages that cannot be easily and univocally translated one into another poses one of the major technical obstacles to the preparation, translation, and comparison of molecular simulation data that users face on a daily basis. Here, we present the MDWiZ platform, a freely accessed online portal designed to aid the fast and reliable preparation and conversion of file formats that allows researchers to reproduce or generate data from MD simulations using different setups, including force fields and models with different underlying potential forms. The general structure of MDWiZ is presented, the features of version 1.0 are detailed, and an extensive validation based on GROMACS to LAMMPS conversion is presented. We believe that MDWiZ will be largely useful to the molecular dynamics community. Such fast format and force field exchange for a given system allows tailoring the chosen system to a given computer platform and/or taking advantage of a specific capabilities offered by different software engines.

Nanoinformatics: an emerging area of information technology at the intersection of bioinformatics, computational chemistry and nanobiotechnology

After the progress made during the genomics era, bioinformatics was tasked with supporting the flow of information generated by nanobiotechnology efforts. This challenge requires adapting classical bioinformatic and computational chemistry tools to store, standardize, analyze, and visualize nanobiotechnological information. Thus, old and new bioinformatic and computational chemistry tools have been merged into a new sub-discipline: nanoinformatics. This review takes a second look at the development of this new and exciting area as seen from the perspective of the evolution of nanobiotechnology applied to the life sciences. The knowledge obtained at the nano-scale level implies answers to new questions and the development of new concepts in different fields. The rapid convergence of technologies around nanobiotechnologies has spun off collaborative networks and web platforms created for sharing and discussing the knowledge generated in nanobiotechnology. The implementation of new database schemes suitable for storage, processing and integrating physical, chemical, and biological properties of nanoparticles will be a key element in achieving the promises in this convergent field. In this work, we will review some applications of nanobiotechnology to life sciences in generating new requirements for diverse scientific fields, such as bioinformatics and computational chemistry.