Modelos contínuos do solvente: fundamentos

Continuum solvation models are nowadays widely used in the modeling of solvent effects and the range of applications goes from the calculation of partition coefficients to chemical reactions in solution. The present work presents a detailed explanation of the physical foundations of continuum models. We discuss the polarization of a dielectric and its representation through the volume and surface polarization charges. The Poisson equation for a dielectric was obtained and we have also derived and discuss the apparent surface charge method and its application for free energy of solvation calculations.

Exploración estocástica de las superficies de energía potencial de dímeros cis-trans y trans-trans del ácido fórmico

Potential energy surface (PES) of cis-trans and trans-trans formic acid dimers were sampled using a stochastic method, and the geometries, energies, and vibrational frequencies were computed at B3LYP/6-311++G(3df,2p) level of theory. The results show that molar free energy of dimerization deviated up to 108.4% when basis set superposition error (BSSE) and zero-point energy (ZPE) were not considered. For cis-trans dimers, C=O and O - H bond weakened, whereas C - O bonds strengthened due to dimerization. Also, trans-trans FA dimers did not show a trend regarding strengthening or weakening of the C=O, O - H and C - O bonds.

CÉLULAS SOLARES SENSIBILIZADAS POR CORANTES NATURAIS: UM EXPERIMENTO INTRODUTÓRIO SOBRE ENERGIA RENOVÁVEL PARA ALUNOS DE GRADUAÇÃO

An interesting practical experiment about the preparation of dye–sensitized solar cells (DSSC) using natural dyes were carried out by the undergraduate students in the chemistry course at UNICAMP . Natural dyes were extracted from blueberries (Vaccinium myrtillus L.), jabuticabas (Myrciaria cauliflora), raw and cooked beets (Beta vulgaris L.), and annattos (Bixa orellana L.), which were used to sensitize TiO2 films that composed the photoanode in the DSSC. A polymer electrolyte containing an iodide/triiodide redox couple was used in lieu of the use of liquid solutions to prevent any leakage in the devices. A maximum solar-to-electric energy conversion of 0.26 ± 0.02% was obtained for the solar cell prepared with annatto extracts. This experiment was an effective way to illustrate to the undergraduate students how to apply some of the chemical concepts that they learned during their chemistry course to produce electric energy from a clean and renewable energy source. Teachers could also exploit the basics of the electronic transitions in inorganic and organic compounds (e.g., metal-to-ligand charge transfer and ϖ-ϖ* transitions), thermodynamics (e.g., Gibbs free energy), acid–base reactions in the oxide solid surface and electrolyte, and band theory (i.e., the importance of the Fermi level energy).

Kinetic, thermodynamic properties, and optimization of barley hydration

The hydration kinetics of five barley cultivars was studied at six different temperatures ranging from 10 to 35 ºC for 32 hours applying the Peleg model. Response Surface was used to describe dynamic of the process and identify the hydration time for each cultivar. The activation energy (Ea), enthalpy (ΔH*), entropy (ΔS*), and Gibbs free energy (ΔG*) were estimated from the adjusted parameters and Arrhenius equation. Temperature had significant effect on the hydration of the five cultivars. At low temperatures, the stabilization time for hydration was faster. Peleg constants K1 and K2 decreased with increasing temperature. The cultivar BRS BRAU showed the lowest value of initial absorption rate (R0 = 0.149 kg.h-1) at 10 ºC, while the cultivar BRS BOREMA had the highest value of R0 (0.367 kg.h-1 at 35 ºC). The equilibrium moisture content (Me) increased with increasing temperature. The cultivars BRS CAUE and BRS BRAU showed the lowest values of Ea, ΔH*, ΔS* showed negative values, and ΔG* increased with increasing temperature, confirming the effect of temperature on hydration.

Um esquema geral para a discussão do movimento de materiais para as células vivas e tecidos

A generalized comprehensive scheme concerning the movement of materials into living cells and tissues is presented. It is designed for use by investigators and teachers who, is assumed, have a previous knowledge of the subject as well as familiarity with previously published literature on the subject. Footnotes to figure 2 X = a constituent component material, arising from extermal sources or through metabolism, capable of migration under favorable conditions. e, i, ec, ic, mc = subscripts indicating location. oC = oxidized cytoplasmic constituents specifically concerned in unidirectional (here invardly directed), diffetial translocation of a particular material X. rC = reduced cytoplasmic constituents specifically concerned. XF = specific free energy (2) of a constituent component in in external or internal phases or in cytoplasm. D = diffusion (4). EA = exchange adsorption (4). MA= metabolic accumulation (4), CI = differentially characteristic cytoplasmic interaction (4) between oC and X, determined by the genetic constitution of the biological species. ▬▬▬>= migration, where permeability to the material involved is relatively high; and ~~~~->, where relatively low. <▬▬▬>= chemical reactions. ▬▬▬>= energy changes of X; diffusion is characteristically with the direction in which the concentration or activity of the constituent decreases, exchange adsorption may be with or against the direction of concentration or activity decrease.

A nuclear ribosomal DNA pseudogene in triatomines opens a new research field of fundamental and applied implications in Chagas disease

A pseudogene, designated as "ps(5.8S+ITS-2)", paralogous to the 5.8S gene and internal transcribed spacer (ITS)-2 of the nuclear ribosomal DNA (rDNA), has been recently found in many triatomine species distributed throughout North America, Central America and northern South America. Among characteristics used as criteria for pseudogene verification, secondary structures and free energy are highlighted, showing a lower fit between minimum free energy, partition function and centroid structures, although in given cases the fit only appeared to be slightly lower. The unique characteristics of "ps(5.8S+ITS-2)" as a processed or retrotransposed pseudogenic unit of the ghost type are reviewed, with emphasis on its potential functionality compared to the functionality of genes and spacers of the normal rDNA operon. Besides the technical problem of the risk for erroneous sequence results, the usefulness of "ps(5.8S+ITS-2)" for specimen classification, phylogenetic analyses and systematic/taxonomic studies should be highlighted, based on consistence and retention index values, which in pseudogenic sequence trees were higher than in functional sequence trees. Additionally, intraindividual, interpopulational and interspecific differences in pseudogene amount and the fact that it is a pseudogene in the nuclear rDNA suggests a potential relationships with fitness, behaviour and adaptability of triatomine vectors and consequently its potential utility in Chagas disease epidemiology and control.

Computational drug design strategies applied to the modelling of human immunodeficiency virus-1 reverse transcriptase inhibitors

Reverse transcriptase (RT) is a multifunctional enzyme in the human immunodeficiency virus (HIV)-1 life cycle and represents a primary target for drug discovery efforts against HIV-1 infection. Two classes of RT inhibitors, the nucleoside RT inhibitors (NRTIs) and the nonnucleoside transcriptase inhibitors are prominently used in the highly active antiretroviral therapy in combination with other anti-HIV drugs. However, the rapid emergence of drug-resistant viral strains has limited the successful rate of the anti-HIV agents. Computational methods are a significant part of the drug design process and indispensable to study drug resistance. In this review, recent advances in computer-aided drug design for the rational design of new compounds against HIV-1 RT using methods such as molecular docking, molecular dynamics, free energy calculations, quantitative structure-activity relationships, pharmacophore modelling and absorption, distribution, metabolism, excretion and toxicity prediction are discussed. Successful applications of these methodologies are also highlighted.

Zinc adsorption in highly weathered soils

The objective of this work was to assess the effects of pH and ionic strength upon zinc adsorption, in three highly weathered variable charge soils. Adsorption isotherms were elaborated from batch adsorption experiments, with increasing Zn concentrations (0-80 mg L-1), and adsorption envelopes were constructed through soil samples reactions with 0.01, 0.1 and 1 mol L-1 Ca(NO3)2 solutions containing 5 mg L-1 of Zn, with an increasing pH value from 3 to 8. Driving force of reaction was quantified by Gibbs free energy and separation factor. Isotherms were C-, H- and L-type and experimental results were fitted to nonlinear Langmuir model. Maximum adsorption ranged from 59-810 mg kg-1, and Zn affinity was greater in subsoil (0.13-0.81 L kg-1) than in the topsoil samples (0.01-0.34 L kg-1). Zinc adsorption was favorable and spontaneous, and showed sharply increase (20-90%) in the 4-6 pH range. No effect of ionic strength was observed at pH values below 5, because specific adsorption mechanisms predominated in the 3-5 pH range. Above pH 5, and in subsoil samples, Zn was adsorbed by electrostatic mechanisms, since ionic strength effect was observed. Despite depth and ionic strength effects, Zn adsorption depends mainly on the pH.

Defeitos superficiais em 2H-WS2 observados por microscopia de tunelamento

Scanning tunnelling microscopy (STM) was used to characterise the basal surface of fresh cleaved crystals of 2H-WS2. Although no impurity or stacking faults could be detected by X-ray diffraction, STM images obtained with negative bias voltage showed two kinds of defects. These defects were attributed to an iodine derivative used as transport agent. In a flat surface free of defects, an image with atomic resolution was achieved with sulphur distances and angles as expected for hexagonal symmetry of 2H-WS2.

Termodinâmica estatística de líquidos com o método de Monte Carlo. I. Metodologia

Statistical mechanics Monte Carlo simulation is reviewed as a formalism to study thermodynamic properties of liquids. Considering the importance of free energy changes in chemical processes, the thermodynamic perturbation theory implemented in the Monte Carlo method is discussed. The representation of molecular interaction by the Lennard-Jones and Coulomb potential functions is also discussed. Charges derived from quantum molecular electrostatic potential are also discussed as an useful methodology to generate an adequate set of partial charges to be used in liquid simulation.

Termodinâmica estatística de líquidos com o método de Monte Carlo. II. O líquido clorofórmio

Thermodynamic properties and radial distribution functions for liquid chloroform were calculated using the Monte Carlo method implemented with Metropolis algorithm in the NpT ensemble at 298 K and 1 atm. A five site model was developed to represent the chloroform molecules. A force field composed by Lennard-Jones and Coulomb potential functions was used to calculate the intermolecular energy. The partial charges needed to represent the Coulombic interactions were obtained from quantum chemical ab initio calculations. The Lennard-Jones parameters were adjusted to reproduce experimental values for density and enthalpy of vaporization for pure liquid. All thermodynamic results are in excelent agreement with experimental data. The correlation functions calculated are in good accordance with theoretical results avaliable in the literature. The free energy for solvating one chloroform molecule into its own liquid at 298 K and 1 atm was computed as an additional test of the potential model. The result obtained compares well with the experimental value. The medium effects on cis/trans convertion of a hypotetical solute in water TIP4P and chloroform solvents were also accomplished. The results obtained from this investigation are in agreement with estimates of the continuous theory of solvation.

Estudo da geometria da uréia por métodos ab initio e simulação computacional de líquidos

A study was carried out on the urea geometries using ab initio calculation and Monte Carlo computational simulation of liquids. The ab initio calculated results showed that urea has a non-planar conformation in the gas phase in which the hydrogen atoms are out of the plane formed by the heavy atoms. Free energies associated to the rotation of the amino groups of urea in water were obtained using the Monte Carlo method in which the thermodynamic perturbation theory is implemented. The magnitude of the free energy obtained from this simulation did not permit us to conclude that urea is non-planar in water.

Review of the synthesis of layered double hydroxides: a thermodynamic approach

The synthesis of layered double hydroxides (LDHs) by hydrothermal-LDH reconstruction and coprecipitation methods is reviewed using a thermodynamic approach. A mixture model was used for the estimation of the thermodynamics of formation of LDHs. The synthesis and solubility of LDHs are discussed in terms of standard molar Gibbs free energy change of reaction. Data for numerous divalent and trivalent metals as well as for some monovalent and tetravalent metals that may be part of the LDH structure have been compiled. Good agreement is found between theoretical and experimental data. Diagrams and tables for the prediction of possible new LDH materials are provided.

Parâmetros termodinâmicos da reação de adsorção de boro em solos tropicais altamente intemperizados

The driving force of boron adsorption on some tropical soils was evaluated by means of thermodynamic parameters. The batch method was employed, and the reaction was monitored at different pH values. The Langmuir equation successfully fitted the experimental results and provided reasonable isotherm parameters. Boron adsorption increased as a function of the pH of the soil solution and the concentration of added boron. The reaction was favorable and proceeded spontaneously, being strongly exoergic, as indicated by a negative free energy (deltaG) and a separation factor (K R) < 1. The boron adsorption phenomenon and the soil-solution interface were thermodinamically described using a theoretical model.

Análise quiral por espectrometria de massas através da utilização do método cinético

Novel and quantitative mass spectrometry methods for rapid and accurate enantiomeric excess determination are presented. These methodologies use electrospray ionization (ESI) and mass spectrometry (MS) to detect and analyze, via collision-induced dissociation (CID), mass-selected transition metal complexes that promote enantio especific interactions. The data from CID are conveniently treated by the kinetic method, a sensitive linear free energy method of treating mass spectrometric results. Four different variations of this methodology are described: single ratio method (S R), quotient ratio method (Q R), fixed ligand method (S Rfixed), and quotient ratio method with fixed ligand (Q Rfixed). These individual methods are compared and their main features discussed in detail.