Estudos computacionais de esfingomielinases D: docking, dinâmica molecular e métodos híbridos QM/MM

Pós-graduação em Biofísica Molecular - IBILCE

Influence of Particle Size, Applied Compression, and Substratum Material on Particle-Surface Adhesion Force Using the Centrifuge Technique

The centrifuge technique was used to investigate the influence of particle size, applied compression, and substrate material (stainless steel, glass, Teflon, and poly(vinyl chloride)) on particle-surface adhesion force. For this purpose, phosphatic rock (rho(p) = 3090 kg/m(3)) and manioc starch particles (rho(p) = 1480 kg/m(3)) were used as test particles. A microcentrifuge that reached a maximum rotation speed of 14 000 rpm and which contained specially designed centrifuge tubes was used in the adhesion force measurements. The curves showed that the adhesion force profile followed a normal log distribution. The adhesion force increased linearly with particle size and with the increase of each increment of compression force. The manioc starch particles presented greater adhesion forces than the phosphatic rock particles for all particle sizes studied. The glass substrate showed a higher adherence than the other materials, probably due to its smoother topographic surface roughness in relation to the other substrata.

Comparison of predicted and experimental DSC curves for vegetable oils

We compare experimental and predicted differential scanning calorimetry (DSC) curves for palm oil (PO), peanut oil (PeO) and grapeseed oil (GO). The predicted curves are computed from the solid-liquid equilibrium modelling and direct minimization of the Gibbs free energy. For PO, the lower the scan rate, the better the agreement. The temperature transitions of PeO and GO were predicted with an average deviation of -0.72 degrees C and -1.29 degrees C respectively, in relation to experimental data from literature. However, the predicted curves showed other peaks not reported experimentally, as computed DSC curves correspond to equilibrium hypothesis which is reached experimentally for an infinitely small scan rate. The results revealed that predicted transitions temperatures using equilibrium hypotheses can be useful in pre-experimental evaluation of vegetable oils formulations seeking for desired melting profiles. (C) 2012 Elsevier B.V. All rights reserved.

Enhancement of Nematic Order and Global Phase Diagram of a Lattice Model for Coupled Nematic Systems

We use an infinite-range Maier-Saupe model, with two sets of local quadrupolar variables and restricted orientations, to investigate the global phase diagram of a coupled system of two nematic subsystems. The free energy and the equations of state are exactly calculated by standard techniques of statistical mechanics. The nematic-isotropic transition temperature of system A increases with both the interaction energy among mesogens of system B, and the two-subsystem coupling J. This enhancement of the nematic phase is manifested in a global phase diagram in terms of the interaction parameters and the temperature T. We make some comments on the connections of these results with experimental findings for a system of diluted ferroelectric nanoparticles embedded in a nematic liquid-crystalline environment.

Automatic design of decision-tree induction algorithms tailored to flexible-receptor docking data

Background: This paper addresses the prediction of the free energy of binding of a drug candidate with enzyme InhA associated with Mycobacterium tuberculosis. This problem is found within rational drug design, where interactions between drug candidates and target proteins are verified through molecular docking simulations. In this application, it is important not only to correctly predict the free energy of binding, but also to provide a comprehensible model that could be validated by a domain specialist. Decision-tree induction algorithms have been successfully used in drug-design related applications, specially considering that decision trees are simple to understand, interpret, and validate. There are several decision-tree induction algorithms available for general-use, but each one has a bias that makes it more suitable for a particular data distribution. In this article, we propose and investigate the automatic design of decision-tree induction algorithms tailored to particular drug-enzyme binding data sets. We investigate the performance of our new method for evaluating binding conformations of different drug candidates to InhA, and we analyze our findings with respect to decision tree accuracy, comprehensibility, and biological relevance. Results: The empirical analysis indicates that our method is capable of automatically generating decision-tree induction algorithms that significantly outperform the traditional C4.5 algorithm with respect to both accuracy and comprehensibility. In addition, we provide the biological interpretation of the rules generated by our approach, reinforcing the importance of comprehensible predictive models in this particular bioinformatics application. Conclusions: We conclude that automatically designing a decision-tree algorithm tailored to molecular docking data is a promising alternative for the prediction of the free energy from the binding of a drug candidate with a flexible-receptor.

New insights on reaction pathway selectivity promoted by crown ether phase-transfer catalysis: Model ab initio calculations of nucleophilic fluorination

Crown ethers have the ability of solubilizing inorganic salts in apolar solvents and to promote chemical reactions by phase-transfer catalysis. However, details on how crown ethers catalyze ionic S(N)2 reactions and control selectivity are not well understood. In this work, we have used high level theoretical calculations to shed light on the details of phase-transfer catalysis mechanism of KF reaction with alkyl halides promoted by 18-crown-6. A complete analysis of the of the model reaction between KF(18-crown-6) and ethyl bromide reveals that the calculations can accurately predict the product ratio and the overall kinetics. Our results point out the importance of the K* ion and of the crown ether ring in determining product selectivity. While the K* ion favors the S(N)2 over the E2 anti pathway, the crown ether ring favors the S(N)2 over E2 syn route. The combination effects lead to a predicted 94% for the S(N)2 pathway in excellent agreement with the experimental value of 92%. A detailed analysis of the overall mechanism of the reaction under phase-transfer conditions also reveals that the KBr product generated in the nucleophilic fluorination acts as an inhibitor of the 18-crown-6 catalyst and it is responsible for the observed slow reaction rate. (C) 2012 Elsevier B.V. All rights reserved.

On the Reaction of Lupulones, Hops beta-Acids, with 1-Hydroxyethyl Radical

Lupulones, hops beta-acids, are one of the main constituents of the hops resin and have an important contribution to the overall bacteriostatic activity of hops during beer brewing. The use of lupulones as natural alternatives to antibiotics is increasing in the food industry and also in bioethanol production. However, lupulones are easy oxidizable and have been shown to be very reactive toward 1-hydroxyethyl radical with apparent bimolecular rate constants close to diffusion control k = 2.9 x 10(8) and 2.6 x 10(8) L mol(-1) s(-1) at 25.0 +/- 0.2 degrees C in ethanol water solution (10% of ethanol (v/v)) as probed by EPR and ESI-IT-MS/MS spin-trapping competitive kinetics, respectively. The free energy change for an electron-transfer mechanism is Delta G degrees = 106 kJ/mol as calculated from the oxidation peak potential experimentally determined for lupulones (1.1 V vs NHE) by cyclic voltammetry and the reported reduction potential for 1-hydroxyethyl radical. The major reaction products identified by LC-ESI-IT-MS/MS and ultrahigh-resolution accurate mass spectrometry (orbitrap FT-MS) are hydroxylated lupulone derivatives and 1-hydroxyethyl radical adducts. The lack of pH dependence for the reaction rate constant, the calculated free energy change for electron transfer, and the main reaction products strongly suggest the prenyl side chains at the hops beta-acids as the reaction centers rather than the beta,beta'-triketone moiety.

Effect of amino-terminated substrates onto surface properties of cellulose esters and their interaction with lectins

Films of cellulose acetate butyrate (CAB) and carboxymethylcellulose acetate butyrate (CMCAB) were deposited from ethyl acetate solutions onto bare silicon wafers (Si/SiO2) or amino-terminated surfaces (APS) by means of equilibrium adsorption. All surfaces were characterized by means of ellipsometry, atomic force microscopy (AFM) and contact angle measurements. The presence of amino groups on the support surface favored the adsorption of CAB and CMCAB, inducing the orientation almost polar groups to the surface and the exposition of alkyl group to the air. Such molecular orientation caused increase of the dispersive component of surface energy (gamma(d)(s)) and decrease of the polar component of surface energy (gamma(p)(s)) of cellulose esters in comparison to those values determined for films deposited onto bare Si/SiO2 wafers. Adsorption behavior of jacalin or concanavalin A onto CAB and CMCAB films was also investigated. The adsorbed amounts of lectins were more pronounced on cellulose esters with high (gamma(p)(s)) and total surface energy (gamma(t)(s)) values. (C) 2011 Elsevier B.V. All rights reserved.

Biaxial nematic phase in the Maier-Saupe model for a mixture of discs and cylinders

We analyze the global phase diagram of a Maier-Saupe lattice model with the inclusion of shape-disordered degrees of freedom to mimic a mixture of oblate and prolate molecules (discs and cylinders). In the neighborhood of a Landau multicritical point, solutions of the statistical problem can be written as a Landau-de Gennes expansion for the free energy. If the shape-disordered degrees of freedom are quenched, we confirm the existence of a biaxial nematic structure. If orientational and disorder degrees of freedom are allowed to thermalize, this biaxial solution becomes thermodynamically unstable. Also, we use a two-temperature formalism to mimic the presence of two distinct relaxation times, and show that a slight departure from complete thermalization is enough to stabilize a biaxial nematic phase.

Structure and electronic properties of hydrated mesityl oxide: a sequential quantum mechanics/molecular mechanics approach

The hydration of mesityl oxide (MOx) was investigated through a sequential quantum mechanics/molecular mechanics approach. Emphasis was placed on the analysis of the role played by water in the MOx syn-anti equilibrium and the electronic absorption spectrum. Results for the structure of the MOx-water solution, free energy of solvation and polarization effects are also reported. Our main conclusion was that in gas-phase and in low-polarity solvents, the MOx exists dominantly in syn-form and in aqueous solution in anti-form. This conclusion was supported by Gibbs free energy calculations in gas phase and in-water by quantum mechanical calculations with polarizable continuum model and thermodynamic perturbation theory in Monte Carlo simulations using a polarized MOx model. The consideration of the in-water polarization of the MOx is very important to correctly describe the solute-solvent electrostatic interaction. Our best estimate for the shift of the pi-pi* transition energy of MOx, when it changes from gas-phase to water solvent, shows a red-shift of -2,520 +/- 90 cm(-1), which is only 110 cm(-1) (0.014 eV) below the experimental extrapolation of -2,410 +/- 90 cm(-1). This red-shift of around -2,500 cm(-1) can be divided in two distinct and opposite contributions. One contribution is related to the syn -> anti conformational change leading to a blue-shift of similar to 1,700 cm(-1). Other contribution is the solvent effect on the electronic structure of the MOx leading to a red-shift of around -4,200 cm(-1). Additionally, this red-shift caused by the solvent effect on the electronic structure can by composed by approximately 60 % due to the electrostatic bulk effect, 10 % due to the explicit inclusion of the hydrogen-bonded water molecules and 30 % due to the explicit inclusion of the nearest water molecules.

Hybrid Scaffolds Built From PET and Collagen as a Model For Vascular Graft Architecture

A hybrid material with excellent mechanical and biological properties is produced by electrospinning a co-solution of PET and collagen. The fibers are mapped using SEM, confocal Raman microscopy and collagenase digestion assays. Fibers of different compositions and morphologies are intermingled within the same membrane, resulting in a heterogeneous scaffold. The collagen distribution and exposure are found to depend on the PET/collagen ratio. The materials are chemically and mechanically characterized and biologically tested with fibroblasts (3T3-L1) and a HUVEC culture in vitro. All of the hybrid scaffolds show better cell attachment and proliferation than PET. These materials are potential candidates to be used as vascular grafts.

X-ray diffraction and theoretical investigation of the Gedunin crystal structure

The Gedunin compound (C28H34O6) is a natural product extracted from Trichilia pallida that has shown a wide activity. The crystallographic structure shows two conformers in the asymmetric unit, which differ in a rotation of the furan group. To understand this molecular arrangement, the density functional calculations. Molecular Electrostatic Potential (MEP) and thermodynamic function calculation have been performed at the B3LYP/6-311++g(d,p) level. Both conformers were optimized and the agreement with the experimental structure was very good, making possible further theoretical analysis of the structure. The inter-conversion between two conformers depends on the energy barrier. This process is studied in the vacuum and shows two transition states with a low energetic barrier for a potential energy curve scanning rigid around furan group: 4.37 kcal/mol and 16.52 kcal/mol. As the first transition state has a notably lower energetic barrier, the preferred inter-conversion pathway between the conformers involves the first rather than the second transition state. Understanding this transition state in detail led us to perform its optimization, showing an energetic barrier around 3.66 kcal/mol. The negative free energy and low enthalpy confirm that the process is spontaneous and exothermic. The results show that this requirement makes the existence of the two conformers in the asymmetric unit possible. The structure of molecules in the asymmetric unit is better understood when the MEP is used on the interaction between molecules. For Gedunin, both molecules have shown MEP with well-defined regions, and this behavior contributes to the observed link between molecules and for the negative regions complementing positive regions of another molecule. (C) 2011 Elsevier B.V. All rights reserved.

Triboelectricity: Macroscopic Charge Patterns Formed by Self-Arraying Ions on Polymer Surfaces

Tribocharged polymers display macroscopically patterned positive and negative domains, verifying the fractal geometry of electrostatic mosaics previously detected by electric probe microscopy. Excess charge on contacting polyethylene (PE) and polytetrafluoroethylene (PTFE) follows the triboelectric series but with one caveat: net charge is the arithmetic sum of patterned positive and negative charges, as opposed to the usual assumption of uniform but opposite signal charging on each surface. Extraction with n-hexane preferentially removes positive charges from PTFE, while 1,1-difluoroethane and ethanol largely remove both positive and negative charges. Using suitable analytical techniques (electron energy-loss spectral imaging, infrared microspectrophotometry and carbonization/colorimetry) and theoretical calculations, the positive species were identified as hydrocarbocations and the negative species were identified as fluorocarbanions. A comprehensive model is presented for PTFE tribocharging with PE: mechanochemical chain homolytic rupture is followed by electron transfer from hydrocarbon free radicals to the more electronegative fluorocarbon radicals. Polymer ions self-assemble according to Flory-Huggins theory, thus forming the experimentally observed macroscopic patterns. These results show that tribocharging can only be understood by considering the complex chemical events triggered by mechanical action, coupled to well-established physicochemical concepts. Patterned polymers can be cut and mounted to make macroscopic electrets and multipoles.

Variance Reduction in Analytical Chemistry : New Numerical Methods in Chemometrics and Molecular Simulation

This thesis is based on five papers addressing variance reduction in different ways. The papers have in common that they all present new numerical methods. Paper I investigates quantitative structure-retention relationships from an image processing perspective, using an artificial neural network to preprocess three-dimensional structural descriptions of the studied steroid molecules. Paper II presents a new method for computing free energies. Free energy is the quantity that determines chemical equilibria and partition coefficients. The proposed method may be used for estimating, e.g., chromatographic retention without performing experiments. Two papers (III and IV) deal with correcting deviations from bilinearity by so-called peak alignment. Bilinearity is a theoretical assumption about the distribution of instrumental data that is often violated by measured data. Deviations from bilinearity lead to increased variance, both in the data and in inferences from the data, unless invariance to the deviations is built into the model, e.g., by the use of the method proposed in paper III and extended in paper IV. Paper V addresses a generic problem in classification; namely, how to measure the goodness of different data representations, so that the best classifier may be constructed. Variance reduction is one of the pillars on which analytical chemistry rests. This thesis considers two aspects on variance reduction: before and after experiments are performed. Before experimenting, theoretical predictions of experimental outcomes may be used to direct which experiments to perform, and how to perform them (papers I and II). After experiments are performed, the variance of inferences from the measured data are affected by the method of data analysis (papers III-V).

Neue Methoden zur Computersimulation von Polymersystemen auf verschiedenen Längenskalen und ihre Anwendungen

In dieser Dissertation stellen wir einen neuen Ansatz zurModellierungvon Polymersystemen vor. Es werden (von methodischer Seiteher) zweiautomatisierte Iterationschemata dazu eingeführt,Kraftfeldparametermesoskopischer Polymersysteme systematisch zu optimieren:DasSimplex-Verfahren und das Struktur-Differenzen-Verfahren. Sowerdendiejenigen Freiheitsgrade aus Polymersystemen eliminiert,die einehohe Auflösung erfordern, was die Modellierung größerersystemeermöglicht. Nach Tests an einfachen Flüssigkeiten werdenvergröberteModelle von drei prototypischen Polymeren (Polyacrylsäure,Polyvinylalkohol und Polyisopren) in unterschiedlichenUmgebungen(gutes Lösungsmittel und Schmelze) entwickelt und ihrVerhalten aufder Mesoskala ausgiebig geprüft. Die zugehörige Abbildung(vonphysikalischer Seite her) so zu gestalten, daß sie dieunverwechselbaren Charakteristiken jedes systems auf diemesoskopischeLängenskala überträgt, stellt eine entscheidende Anforderungan dieautomatisierten Verfahren dar. Unsere Studien belegen, daß mesoskopische Kraftfeldertemperatur- unddichtespezifisch sind und daher bei geändernden Bedingungennachoptimiert werden müssen. Gleichzeitig läßt sichabschätzen, beiwelchen Umgebungsbedingungen dies noch nicht notwendig wird.In allenFällen reichen effektive Paarpotentiale aus, einrealistischesmesoskopisches Modell zu konstruieren. VergröberteSimulationenwerden im Falle der Polyacrylsäure erfolgreich gegenexperimentelleLichtstreudaten getestet. Wir erzielen für Molmassen bis zu300000g/mol eine hervorragende Übereinstimmung für denhydrodynamischenRadius. Unsere Ergebnisse erklären auch Korrekturen zudessenVerhalten als Funktion der Kettenlänge ('Skalenverhalten'). Im Fallevon Polyisopren untersuchen wir sowohl statische als auchdynamischeGrößen und stellen klare Unterschiede unserer Ergebnisse zudeneneines einfachen semi-flexiblen Mesoskalenmodells fest. InderProteinforschung werden aus Datenbanken gewonnene effektivePaarwechselwirkungen dazu verwendet, die freie Energie einesneuensystems vorherzusagen. Wir belegen in einem Exkurs mittelsGittersimulationen, daß es selbst in einfachsten Fällennicht gelingt,dies auch nur qualitativ korrekt zu bewerkstelligen.