RESUMO

The zwitterions resulting from the covalent attachment of 3- or 4-hydroxy benzene to the 1,3-dimethylimidazolium cation represent basic compounds (pKa of 8.68 and 8.99 in aqueous solutions, respectively) that chemisorb in aqueous solutions 0.58 mol/mol of carbon dioxide at 1.3 bar (absolute) and 40 °C. Equimolar amounts of chemisorbed CO2 in these solutions are obtained at 10 bar and 40 °C. Chemisorption takes place through the formation of bicarbonate in the aqueous solution using imidazolium-containing phenolate. CO2 is liberated by simple pressure relief and heating, regenerating the base. The enthalpy of absorption was estimated to be -38 kJ/mol, which is about 30 % lower than the enthalpy of industrially employed aqueous solutions of MDEA (estimated at -53 kJ/mol using the same experimental apparatus). The physisorption of CO2 becomes relevant at higher pressures (>10 bar) in these aqueous solutions. Combined physio- and chemisorption of up to 1.3 mol/mol at 40 bar and 40 °C can be attained with these aqueous zwitterionic solutions that are thermally stable and can be recycled at least 20 times.

RESUMO

Plant RNases T2 are involved in several physiological and developmental processes, including inorganic phosphate starvation, senescence, wounding, defense against pathogens, and the self-incompatibility system. Solanaceae RNases form three main clades, one composed exclusively of S-RNases and two that include S-like RNases. We identified several positively selected amino acids located in highly flexible regions of these molecules, mainly close to the B1 and B2 substrate-binding sites in S-like RNases and the hypervariable regions of S-RNases. These differences between S- and S-like RNases in the flexibility of amino acids in substrate-binding regions are essential to understand the RNA-binding process. For example, in the S-like RNase NT, two positively selected amino acid residues (Tyr156 and Asn134) are located at the most flexible sites on the molecular surface. RNase NT is induced in response to tobacco mosaic virus infection; these sites may thus be regions of interaction with pathogen proteins or viral RNA. Differential selective pressures acting on plant ribonucleases have increased amino acid variability and, consequently, structural differences within and among S-like RNases and S-RNases that seem to be essential for these proteins play different functions.

RESUMO

We performed classical Molecular Dynamics computer simulations to analyze solutions of the gases CO2, N2, and CH4 in four 1-n-butyl-3-methylimidazolium-based ionic liquids (1-n-butyl-3-methylimidazolium acetate, 1-n-butyl-3-methylimidazolium prolinate, 1-n-butyl-3-methylimidazolium bromide, and 1-n-butyl-3-methylimidazolium tetrafluoroborate). Typical experimental conditions (10 bar gas pressure and room temperature) have been chosen to study mixtures of the ionic liquids with the gases at a single gas molar fraction of 0.25. Structural aspects are discussed to judge the absorption capacities of the ionic liquids. We observed that CO2 coordinates preferentially within the polar domain of the ionic liquids with the bromide and tetrafluoroborate anions presenting the best performances. The other gases, N2 and CH4, remain in the less polar domains of the ionic liquids. Cluster size analysis indicates phase separation for these two gases. Considering both, the absorption tendency and gas separation capacity of the ionic liquids, the anion is desired to be small and possessing multiple coordination sites. In this aspect, the tetrafluoroborate anion accomplished the best results.

Assuntos

Gases/química , Imidazóis/química , Líquidos Iônicos/química , Simulação de Dinâmica Molecular , Absorção Fisico-Química , Conformação Molecular , Pressão , Temperatura

RESUMO

The simple photolysis of CO2 in aqueous solutions to generate CO and/or hydrocarbons and derivatives in the presence of a catalyst is considered to be a clean and efficient approach for utilizing CO2 as a C1 building block. Despite the huge efforts dedicated to this transformation using either semiconductors or homogeneous catalysts, only small improvements of the catalytic activity have been achieved so far. This article reports that simple aqueous solutions of organic salts-denominated as ionic liquids-can efficiently photo-reduce CO2 to CO without using photosensitizers or sacrificial agents. The system relies on the formation of the [CO2 ].- intermediate through homolytic C-C bond cleavage in a cation-CO2 adduct of imidazolium-based ionic liquids (ILs). The system continuously produced CO up to 2.88 mmol g-1 of IL after 40 h of irradiation by using an aqueous solution of 1-n-butyl-3-methylimidazolium-2-carboxylate (BMIm.CO2 ) IL, representing an apparent quantum yield of 3.9 %. The organophotocatalytic principles of our system may help to develop more simple and efficient organic materials for the production of solar fuels from CO2 under mild conditions, which represents a real alternative to those based on semiconductors and homogeneous metal-based catalysts.

RESUMO

Prions are proteins that cause a group of invariably fatal neurodegenerative diseases, one of the most known being bovine spongiform encephalopathy. The three-dimensional structure of PrPSc , the altered isoform of the prion protein, has not been fully elucidated yet, and studies on prion conversion mechanisms must rely on hypothetical ß-rich structures. Experimental and computational studies indicate that the use of low pH is capable to produce a gain of ß-structure content in the otherwise unstructured N-terminal region. These in silico studies have used different PrP fragments from distinct organisms, and with different lengths and simulation protocols, making it difficult to identify the influence of the force fields on the formation of such structures. Here, we performed a systematic study of the influence of six well-established force fields (GROMOS96 53a6, GROMOS96 43a1, AMBER99SB, AMBER99SB-ILDN, CHARMM27, and OPLS-AA/L) on the process of structural conversion of the Syrian hamster cellular prion protein simulated at acidic and neutral pH. From our analysis, we observe a strong dependence of the results with the different force fields employed. Additionally, only GROMOS96 53A6 and AMBER99SB force fields are capable to capture a high ß-sheet formation at acidic pH and adequately reproduce the neutral pH. In both cases, the ß-sheet elongation seems to be guided by the movement of the N-terminal tail toward the N-terminal of α-helix HB under acidic condition. These results comprise the most wide-ranging study to date correlating force fields to structural changes in the cellular prion protein. © 2018 Wiley Periodicals, Inc.

Assuntos

Simulação de Dinâmica Molecular , Proteínas Priônicas/química , Animais , Bovinos , Concentração de Íons de Hidrogênio , Estrutura Secundária de Proteína

RESUMO

A series of functionalized N-alkylimidazolium based ionic liquids (ImILs) were designed, through anion (carboxylates and halogenated) and cation (N-alkyl side chains) structural modifications, and studied as potential sorbents for CO2 . The sorption capacities of as prepared bare ImILs could be enhanced from 0.20 to 0.60 molar fraction by variation of cation-anion-CO2 and IL-CO2 -water interaction. By combining NMR spectroscopy with molecular dynamics simulations, a good description of interactions between ImIL and CO2 can be obtained. Three types of CO2 sorption modes have been evidenced depending on the structure of the ImIL ion pair: Physisorption, formation of bicarbonate, and covalent interaction through the nucleophilic addition of CO2 to the cation or anion. The highest CO2 sorption capacity was observed with the ImIL containing the 1-n-butyl-3-methylimidazolium cation associated with the carboxylate anions (succinate and malonate). This study provides helpful clues for better understanding the structure-activity relationship of this class of materials and the ion pair influence on CO2 capture.

RESUMO

Emodin is one of the most abundant anthraquinone derivatives found in nature. It is the active principle of some traditional herbal medicines with known biological activities. In this work, we combined experimental and theoretical studies to reveal information about location, orientation, interaction and perturbing effects of Emodin on lipid bilayers, where we have taken into account the neutral form of the Emodin (EMH) and its anionic/deprotonated form (EM-). Using both UV/Visible spectrophotometric techniques and molecular dynamics (MD) simulations, we showed that both EMH and EM- are located in a lipid membrane. Additionally, using MD simulations, we revealed that both forms of Emodin are very close to glycerol groups of the lipid molecules, with the EMH inserted more deeply into the bilayer and more disoriented relative to the normal of the membrane when compared with the EM-, which is more exposed to interfacial water. Analysis of several structural properties of acyl chains of the lipids in a hydrated pure DMPC bilayer and in the presence of Emodin revealed that both EMH and EM- affect the lipid bilayer, resulting in a remarkable disorder of the bilayer in the vicinity of the Emodin. However, the disorder caused by EMH is weaker than that caused by EM-. Our results suggest that these disorders caused by Emodin might lead to distinct effects on lipid bilayers including its disruption which are reported in the literature.

RESUMO

The rational synthesis of alternative materials is highly demanding due to the outbreak of infectious diseases and resistance to antibiotics. Herein, we report a tailored nanoantibiotic synthesis protocol where the antibiotic binding was optimized on the silver-silica core-shell nanoparticles surface to maximize biological responses. The obtained silver nanoparticles coated with mesoporous silica functionalized with ampicillin presented remarkable antimicrobial effects against susceptible and antibiotic-resistant Escherichia coli. In addition, these structures were not cell-death inducers and different steps of the mitotic cell cycle (prophase, anaphase and metaphase) were clearly identified. The superior biological results were attributed to a proper and tailored synthesis strategy.

Assuntos

Ampicilina/farmacologia , Antibacterianos/farmacologia , Escherichia coli/efeitos dos fármacos , Nanopartículas Metálicas/química , Ampicilina/química , Antibacterianos/química , Sobrevivência Celular/efeitos dos fármacos , Sistemas de Liberação de Medicamentos/instrumentação , Sistemas de Liberação de Medicamentos/métodos , Células HEK293 , Humanos , Dióxido de Silício/química , Prata/química

RESUMO

It is well known that the macroscopic physico-chemical properties of ionic liquids (ILs) are influenced by the presence of water that strongly interferes with the supramolecular organization of these fluids. However, little is known about the function of water traces within this confined space and restricted ionic environments, i.e. between cations and anions. Using specially designed ILs namely 1,2,3-trimethyl-1H-imidazol-3-ium imidazol-1-ide (MMMI·Im) and 3-n-butyl-1,2-dimethyl-1H-imidazol-3-ium imidazol-1-ide (BMMI·Im), the structure and function of water have been determined in condensed, solution and gas phases by X-ray diffraction studies, NMR, molecular dynamics simulations (MDS) and DFT calculations. In the solid state the water molecule is trapped inside the ionic network (constituted of contact ion pairs formed by π(+)-π(-) interaction) through strong H-bonds involving the water hydrogens and the nitrogens of two imidazolate anions forming a guest@host supramolecular structure. A similar structural arrangement was corroborated by DFT calculations and MDS. The presence of a guest@host species (H2O@ILpair) is maintained to a great extent even in solution as detected by (1)H-(1)H NOESY-experiments of the ILs dissolved in solvents with low and high dielectric constants. This confined water catalyses the H/D exchange with other substrates containing acidic-H such as chloroform.

RESUMO

Molecular dynamics computer simulations have been performed to identify preferred positions of the fluorescent probe PRODAN in a fully hydrated DLPC bilayer in the fluid phase. In addition to the intramolecular charge-transfer first vertical excited state, we considered different charge distributions for the electronic ground state of the PRODAN molecule by distinct atomic charge models corresponding to the probe molecule in vacuum as well as polarized in a weak and a strong dielectric solvent (cyclohexane and water). Independent on the charge distribution model of PRODAN, we observed a preferential orientation of this molecule in the bilayer with the dimethylamino group pointing toward the membrane's center and the carbonyl oxygen toward the membrane's interface. However, changing the charge distribution model of PRODAN, independent of its initial position in the equilibrated DLPC membrane, we observed different preferential positions. For the ground state representation without polarization and the in-cyclohexane polarization, the probe maintains its position close to the membrane's center. Considering the in-water polarization model, the probe approaches more of the polar headgroup region of the bilayer, with a strong structural correlation with the choline group, exposing its oxygen atom to water molecules. PRODAN's representation of the first vertical excited state with the in-water polarization also approaches the polar region of the membrane with the oxygen atom exposed to the bilayer's hydration shell. However, this model presents a stronger structural correlation with the phosphate groups than the ground state. Therefore, we conclude that the orientation of the PRODAN molecule inside the DLPC membrane is well-defined, but its position is very sensitive to the effect of the medium polarization included here by different models for the atomic charge distribution of the probe.

Assuntos

Bicamadas Lipídicas , Simulação de Dinâmica Molecular , Fosfatidilcolinas/química

RESUMO

Jaburetox-2Ec, a recombinant peptide derived from an urease isoform (JBURE-II), displays high insecticidal activity against important pests such as Spodoptera frugiperda and Dysdercus peruvianus. Although the molecular mechanism of action of ureases-derived peptides remains unclear, previous ab initio data suggest the presence of structural motifs in Jaburetox-2Ec with characteristics similar to those found in a class of pore-forming peptides. Here, we investigated the molecular aspects of the interaction between Jaburetox-2Ec and large unilamellar vesicles. Jaburetox-2Ec displays membrane-disruptive ability on acidic lipid bilayers and this effect is greatly influenced by peptide aggregation. Corroborating with this finding, molecular modeling studies revealed that Jaburetox-2Ec might adopt a well-defined beta-hairpin conformation similar to those found in antimicrobial peptides with membrane disruption properties. In addition, molecular dynamics simulations suggest that the protein is able to anchor at a polar/non-polar interface. In the light of these findings, for the first time it was possible to point out some evidence that the peptide Jaburetox-2Ec interacting with lipid vesicles promotes membrane permeabilization.

Assuntos

Inseticidas/química , Inseticidas/farmacologia , Urease/química , Urease/farmacologia , Sequência de Aminoácidos , Animais , Canavalia/enzimologia , Canavalia/genética , Heterópteros , Bicamadas Lipídicas , Modelos Moleculares , Dados de Sequência Molecular , Proteínas de Plantas/química , Proteínas de Plantas/genética , Proteínas de Plantas/farmacologia , Estrutura Terciária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/farmacologia , Homologia de Sequência de Aminoácidos , Spodoptera , Lipossomas Unilamelares , Urease/genética

RESUMO

Microscopic insights for effects of the alkyl chain length on macroscopic physical properties of 1-alkyl-3-methylimidazolium ionic liquids are provided from molecular dynamics computer simulation and quantum mechanical calculations. In particular, the liquid densities, internal energies, and hydrogen bonding behavior of the ions were studied. The effect of the alkyl chain size on the hydrogen bonding behavior of these liquids, in terms of both radial distribution functions and pair energetics, is demonstrated. Finally, studies of the ion pair stabilization were performed at the quantum mechanical level by means of the Kitaura-Morokuma energy partition. The fitting of atomic charges to the ion pairs has been performed to illustrate the charge transfer effect between cation and anion.

RESUMO

We present a detailed computational study of the structure of ionic liquids based on the imidazolium cation. Both imidazolium-ring stacking and hydrogen bonding behavior are investigated from radial and spatial orientational distribution functions, as well as orientational correlation functions. The alkyl chain size and anion effect on the liquid structure are provided and discussed. Our results support models for liquid organization comparable to those formulated on the basis of experimental observations.

RESUMO

Echinococcus granulosus antigen B is an oligomeric protein of 120-160 kDa composed by 8-kDa (AgB8) subunits. Here, we demonstrated that the AgB8 recombinant subunits AgB8/1, AgB8/2 and AgB8/3 are able to self-associate into high order homo-oligomers, showing similar properties to that of parasite-produced AgB, making them valuable tools to study AgB structure. Dynamic light scattering, size exclusion chromatography and cross-linking assays revealed approximately 120- to 160-kDa recombinant oligomers, with a tendency to form populations with different aggregation states. Recombinant oligomers showed helical circular dichroism spectra and thermostability similar to those of purified AgB. Cross-linking and limited proteolysis experiments indicated different degrees of stability and compactness between the recombinant oligomers, with the AgB8/3 one showing a more stable and compact structure. We have also built AgB8 subunit structural models in order to predict the surfaces possibly involved in electrostatic and hydrophobic interactions during oligomerization.

Assuntos

Antígenos de Helmintos/química , Echinococcus granulosus/imunologia , Sequência de Aminoácidos , Animais , Antígenos de Helmintos/imunologia , Biopolímeros , Cromatografia em Gel , Dicroísmo Circular , Modelos Moleculares , Dados de Sequência Molecular , Conformação Proteica , Estrutura Secundária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/imunologia , Homologia de Sequência de Aminoácidos , Espectrometria de Fluorescência , Eletricidade Estática

RESUMO

The free energy of solvation for a large number of representative solutes in various solvents has been calculated from the polarizable continuum model coupled to molecular dynamics computer simulation. A new algorithm based on the Voronoi-Delaunay triangulation of atom-atom contact points between the solute and the solvent molecules is presented for the estimation of the solvent-accessible surface surrounding the solute. The volume of the inscribed cavity is used to rescale the cavitational contribution to the solvation free energy for each atom of the solute atom within scaled particle theory. The computation of the electrostatic free energy of solvation is performed using the Voronoi-Delaunay surface around the solute as the boundary for the polarizable continuum model. Additional short-range contributions to the solvation free energy are included directly from the solute-solvent force field for the van der Waals-type interactions. Calculated solvation free energies for neutral molecules dissolved in benzene, water, CCl4, and octanol are compared with experimental data. We found an excellent correlation between the experimental and computed free energies of solvation for all the solvents. In addition, the employed algorithm for the cavity creation by Voronoi-Delaunay triangulation is compared with the GEPOL algorithm and is shown to predict more accurate free energies of solvation, especially in solvents composed by molecules with nonspherical molecular shapes.

RESUMO

Binary liquid mixtures of dimethyl sulfoxide and acetonitrile at the three molar fractions 0.25, 0.50, and 0.75 have been investigated by molecular dynamics computer simulations. Thermodynamic states corresponding to liquid-vapor coexistence at a temperature of 298 K were considered. Intermolecular interactions were described by potential models of the site-site (12-6) Lennard-Jones plus Coulomb type that have been developed for the description of the pure liquids. Dimethyl sulfoxide has been represented by four interactions sites and acetonitrile by a three- as well as a six-site potential model. We have calculated thermodynamic properties and the intermolecular pair distribution functions. Intermolecular interaction energies indicate deviations from the behavior of ideal mixtures. The local mole fraction analysis demonstrates that dimethyl sulfoxide is preferentially solvated by acetonitrile and that the first solvation shell surrounding acetonitrile molecules is significantly enriched by dimethyl sulfoxide. The nonideal behavior in the mixtures is not affected by the choice of the three- or the six-site potential model for acetonitrile. Orientational correlations of dipole vectors within the first solvation shells indicate that the relative molecular orientations found in pure acetonitrile and dimethyl sulfoxide are maintained in the mixtures. Parallel and antiparallel dipole-dipole configurations determine first shell acetonitrile-dimethyl sulfoxide configurations. Dynamical features of the mixtures are discussed in terms of diffusion constants and orientational correlation times as obtained from the time correlation functions for linear velocities and molecular dipole moments, respectively. Computed relaxation times indicate faster reorientational motion for dimethyl sulfoxide if acetonitrile is added. In contrast, the orientational dynamics of acetonitrile becomes stronger correlated upon dilution with dimethyl sulfoxide. The diffusion coefficients for both compounds follow this tendency.

RESUMO

Using molecular dynamics simulation, we present new results for the free energy of solvation for solvents with low dielectric constants (CCl(4), CHCl(3), benzene). The solvation free energy is computed as the sum of three contributions originated at the cavitation of the solute by the solvent, the solute-solvent repulsion and dispersion interactions, and the electrostatic solvation of the solute. The cavitational contribution has been obtained from the Claverie-Pierotti model applied to excluded volumes obtained from distances for nearest neighbor configurations between the solute's atoms and a spherical solvent description. An electrostatic continuum model has been adapted for the computation of the electrostatic free energy of solvation, whereas the van der Waals contribution has been calculated directly from the intermolecular interactions defined by the force fields applied to the simulations. For each solvent, a large set of solute molecules containing most of the chemically interesting functionalities has been treated. The simulated solvation free energies are in very good agreement with experimental data, although a small systematical overestimation of the free energy of solvation indicates a failure of the spherical approach to the solvent molecules in the case of benzene.

RESUMO

A new approach to the calculation of the free energy of solvation from trajectories obtained by molecular dynamics simulation is presented. The free energy of solvation is computed as the sum of three contributions originated at the cavitation of the solute by the solvent, the solute-solvent nonpolar (repulsion and dispersion) interactions, and the electrostatic solvation of the solute. The electrostatic term is calculated based on ideas developed for the broadly used continuum models, the cavitational contribution from the excluded volume by the Claverie-Pierotti model, and the Van der Waals term directly from the molecular dynamics simulation. The proposed model is tested for diluted aqueous solutions of simple molecules containing a variety of chemically important functions: methanol, methylamine, water, methanethiol, and dichloromethane. These solutions were treated by molecular dynamics simulations using SPC/E water and the OPLS force field for the organic molecules. Obtained free energies of solvation are in very good agreement with experimental data.