INTERACTIONS: DESIGN, IMPLEMENTATION AND EVALUATION OF A COMPUTATIONAL TOOL FOR TEACHING INTERMOLECULAR FORCES IN HIGHER EDUCATION

Intermolecular forces are a useful concept that can explain the attraction between particulate matter as well as numerous phenomena in our lives such as viscosity, solubility, drug interactions, and dyeing of fibers. However, studies show that students have difficulty understanding this important concept, which has led us to develop a free educational software in English and Portuguese. The software can be used interactively by teachers and students, thus facilitating better understanding. Professors and students, both graduate and undergraduate, were questioned about the software quality and its intuitiveness of use, facility of navigation, and pedagogical application using a Likert scale. The results led to the conclusion that the developed computer application can be characterized as an auxiliary tool to assist teachers in their lectures and students in their learning process of intermolecular forces.

Binding of Dengue Virus Partitcles and Dengue Proteins onto Solid Surfaces

The interaction between dengue virus particles (DENV), sedimentation hemagglutinin particles (SHA), dengue virus envelope protein (Eprot), and solid surfaces was investigated by means of ellipsometry and atomic force microscopy (AFM). The surfaces chosen are bare Si/SiO(2) wafers and Si/SiO(2) wafers covered with concanavalin A (ConA), jacalin (Jac), polystyrene (PS), or poly(styrene sulfonate) (PSS) films. Adsorption experiments at pH 7.2 and pH 3 onto all surfaces revealed that (i) adsorption of DENV particles took place only onto ConA under pH 7.2, because of specific recognition between glycans on DENV surface and ConA binding site; (ii) DENV particles did not attach to any of the surfaces at pH 3, suggesting the presence of positive charges on DENV surface at this pH, which repel the positively charged lectin surfaces; (iii) SHA particles are positively charged at pH 7.2 and pH 3 because they adhered to negatively charged surfaces at pH 7.2 and repelled positively charged layers at pH 3; and (iv) SHA particles carry polar groups on the surface because they attached to silanol surfaces at pH 3 and avoided hydrophobic PS films at pH 3 and pH 7.2. The adsorption behavior of Eprot at pH 7.2 revealed affinity for ConA > Jac > PSS > PS approximate to bare Si/SiO(2) layers. These findings indicate that selectivity of the Eprot adsorption is higher when it is part of virus structure than when it is free in solution. The correlation between surface energy values determined by means of contact angle measurements and DENV, SHA, or Eprot adsorption behavior was used to understand the intermolecular forces at the interfaces. A direct correlation was not found because the contributions from surface energy were probably surpassed by specific contributions.

Synthesis of new peptide derivatives that self-assemble into nanostructured hydrogels for biomedical applications

Tese de Doutoramento em Ciências (área de especialização em Química)

Barrier for the reaction X20+ + X20+ -> X402+ in alkali-metal clusters related to electron density at the bond midpoint of the supermolecule (X20+)2

Using the extended Thomas-Fermi version of density-functional theory (DFT), calculations are presented for the barrier for the reaction Na20++Na20+¿Na402+. The deviation from the simple Coulomb barrier is shown to be proportional to the electron density at the bond midpoint of the supermolecule (Na20+)2. An extension of conventional quantum-chemical studies of homonuclear diatomic molecular ions is then effected to apply to the supermolecular ions of the alkali metals. This then allows the Na results to be utilized to make semiquantitative predictions of position and height of the maximum of the fusion barrier for other alkali clusters. These predictions are confirmed by means of similar DFT calculations for the K clusters.

Lipophilicity and its relationship with passive drug permeation.

In this review, we first summarize the structure and properties of biological membranes and the routes of passive drug transfer through physiological barriers. Lipophilicity is then introduced in terms of the intermolecular interactions it encodes. Finally, lipophilicity indices from isotropic solvent systems and from anisotropic membrane-like systems are discussed for their capacity to predict passive drug permeation across biological membranes such as the intestinal epithelium, the blood-brain barrier (BBB) or the skin. The broad evidence presented here shows that beyond the predictive power of lipophilicity parameters, the various intermolecular forces they encode allow a mechanistic interpretation of passive drug permeation.

A cartography of the Van der Waals territory

The distribution of distances from atoms of a particular element E to a probe atom X (oxygen in most cases), both bonded and intermolecular non-bonded contacts, has been analyzed. In general, the distribution is characterized by a maximum at short EX distances corresponding to chemical bonds, followed by a range of unpopulated distances the van der Waals gap and a second maximum at longer distances the van der Waals peak superimposed on a random distribution function that roughly follows a d3 dependence. The analysis of more than five million interatomic"non-bonded" distances has led to the proposal of a consistent set of van der Waals radii for most naturally occurring elements, and its applicability to other element pairs has been tested for a set of more than three million data, all of them compared to over one million bond distances.

Construção e avaliação de célula de fluxo para estudo da tensão interfacial dinâmica da interface fluxo líquido - sólido por despolarização da fluorescência

A simple low-cost flow cell was developed, built and optimized in order to observe dynamic interfacial tension of continuous flow systems. Distinct materials can be used in one of the cell walls in order to observe the intermolecular forces between the flowing liquid and the chemical constitution of the walls. The fluorescence depolarization was evaluated using Rhodamine B as fluorescent probe seeded in ethylene glycol. The effects of the positioning angles on the data acquired across the cell are reported. The reproducibility of the data was evaluated with a spectrometer assembled in-house and the relative standard deviation was below 3%.

A model for specific interactions of manganese-phthalocyanine in protic media

Extinction coefficients (e) changes of manganese phthalocyanine (Mn-Pc) were studied in different organic solvents and related to solvent polarity scales; (Kosower's values (Z), Dimroth's values (E T), donor numbers (DN) and linear solvation energy relationships (LSER) or linear free energy relationships (LFER));, theoretical molecular orbital calculations and ligand/solvent coordination processes in order to predict molecular interaction with the medium and identification of predominant intermolecular forces.

Studies on molecular structure and properties using microwave and infrared spectral data

The major objective of the thesis is essentially to evolve and apply certain computational procedures to evaluate the structure and properties of some simple polyatomic molecules making use of spectroscopic data available from the literature. It must be said that though there is dwindling interest in recent times in such analyses, there exists tremendous scope and utility for attempting such calculations as the precision and reliability of'experimental techniques in spectroscopy have increased vastly due to enormous sophistication of the instruments used for these measurements. In the present thesis an attempt is made to extract maximum amount of information regarding the geometrical structure and interatmic forces of simple molecules from the experimental data on microwave and infrared spectra of these molecules

O ensino por investigação abrindo espaços para a argumentação de alunos e professores do ensino médio

Pós-graduação em Educação para a Ciência - FC

Dinâmica não linear, caos, e controle na microscopia de força atômica

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Theoretical Models for Surface Forces and Adhesion and Their Measurement Using Atomic Force Microscopy

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Ability of the PM3 Quantum Mechanical Method to Model Intermolecular Hydrogen Bonding between Neutral Molecules

The PM3 semiempirical quantum-mechanical method was found to systematically describe intermolecular hydrogen bonding in small polar molecules. PM3 shows charge transfer from the donor to acceptor molecules on the order of 0.02-0.06 units of charge when strong hydrogen bonds are formed. The PM3 method is predictive; calculated hydrogen bond energies with an absolute magnitude greater than 2 kcal mol-' suggest that the global minimum is a hydrogen bonded complex; absolute energies less than 2 kcal mol-' imply that other van der Waals complexes are more stable. The geometries of the PM3 hydrogen bonded complexes agree with high-resolution spectroscopic observations, gas electron diffraction data, and high-level ab initio calculations. The main limitations in the PM3 method are the underestimation of hydrogen bond lengths by 0.1-0.2 for some systems and the underestimation of reliable experimental hydrogen bond energies by approximately 1-2 kcal mol-l. The PM3 method predicts that ammonia is a good hydrogen bond acceptor and a poor hydrogen donor when interacting with neutral molecules. Electronegativity differences between F, N, and 0 predict that donor strength follows the order F > 0 > N and acceptor strength follows the order N > 0 > F. In the calculations presented in this article, the PM3 method mirrors these electronegativity differences, predicting the F-H- - -N bond to be the strongest and the N-H- - -F bond the weakest. It appears that the PM3 Hamiltonian is able to model hydrogen bonding because of the reduction of two-center repulsive forces brought about by the parameterization of the Gaussian core-core interactions. The ability of the PM3 method to model intermolecular hydrogen bonding means reasonably accurate quantum-mechanical calculations can be applied to small biologic systems.

Raman spectral evidence for hydration forces between collagen triple helices

Hydration forces are thought to result from the energetic cost of water rearrangement near macromolecular surfaces. Raman spectra, collected on the same collagen samples on which these forces were measured, reveal a continuous change in water hydrogen-bonding structure as a function of separation between collagen triple helices. The varying spectral parameters track the force-distance curve. The energetic cost of water “restructuring,” estimated from the spectra, is consistent with the measured energy of intermolecular interaction. These correlations support the idea that the change in water structure underlies the exponentially varying forces seen in this system at least over the 13–18-Å range of interaxial separations.