Resumo em Inglês:

We present a review on the intermolecular dynamics of liquid aqueous systems focusing mainly on Molecular Dynamics simulation work that has been carried out at the State University of Campinas in recent years. Emphasis is given on simulation results that are more directly related to modern experimental spectroscopic measurements.

Resumo em Inglês:

In the first part of this paper I review the understanding of anomalous properties of water in terms of particles interacting by core-softened potentials. I discuss the origin of the bulk anomalies in terms of the two different configurations of neighbor particles: low energy-high volume and high energy-low volume. In the second part I study some anomalies of water under strong spatial confinement, namely when it lubricates a contact between two solid surfaces. Solvation and friction forces are studied as a function of lubricant thickness. Whereas for hard core particles maxima in the solvation force are correlated with maxima in the friction force, for soft core particles and appropriately chosen parameters the opposite is true. This leads to a reduction of the friction coefficient of about one order of magnitude in the second case. I argue that materials that expand when freeze may be modeled in terms of soft core particles, and that these materials are naturally good boundary lubricants.

Resumo em Inglês:

In this work, we describe how the anomalous diffusivity is related to the structural anomalies. For this purpose, we study how the thermodynamics and the dynamics of low-temperature water are affected by the decrease of the density.

Resumo em Inglês:

Hydrogen bonded liquids like water present a rich thermodynamic behaviour due to the strength and directionality of the bonds. In a recent paper a geometric model based on Bernal's model for liquids was proposed to study the effects of the hydrogen bonds on the phase transitions of water, under pressure and temperature variations. Water molecules were assumed to stay at the vertices of coordination r (r = 4; 5; 6) of perfectly tiled polygons, and to have four links which allow up to four hydrogen bonds per particle. Mean field calculations yielded a phase diagram with three phases of different densities and a critical point at the end of the coexistence line between the high and low density phases. The three phases were considered to be liquids of different densities. In the present work we have shown that applying some geometric constraints to particle arrangements (thus correcting the system entropy, which was overestimated in the previous work), and allowing a variable number of links per molecule, leads to substantial alteration of the phase diagram. Three phases of different densities are still present, but no critical point appears. Two of the phases are solid, and one phase is amorphous.

Resumo em Inglês:

In order to simulate the effects of hydrostatic pressure on protein folding/unfolding it is necessary to accurately describe the behavior of the dielectric constant and the density of the solvent (water), in the range of pressures (between 0.1 MPa and 2.0 GPa) and temperatures (below 75 ° C) required for pressure-induced unfolding. A simple equation of the form X = X (T, Pi) + a0 ln (a i+ P)/(a i + Pi) [were X is the property, Pi (in MPa) is the reference pressure and a i are coefficients adjusted to fit experimental values] is proposed to describe both properties as function of pressure, at constant temperatures. The equation reproduces available data for dielectric constant and density of water to an accuracy of 0.1%. Because of its simplicity and accuracy, the proposed equation is useful for simulation studies and for any other problem where the knowledge of those properties as a function of pressure is needed.

Resumo em Inglês:

Electronic properties of liquid water were investigated by sequential Monte Carlo/Quantum mechanics calculations. The density of states (DOS) and HOMO-LUMO gap (E G) of liquid water have been determined by Hartree-Fock and Density Functional Theory (DFT) calculations. The quantum mechanical calculations were carried out over uncorrelated supermolecular structures generated by the Monte Carlo simulations. The DFT calculations were performed with a modified B3LYP exchange-correlation functional proposed by Abu-Awwad and Politzer which was parametrized to reproduce valence orbital energies in agreement with experimental ionization potentials of the water molecule. We have analyzed the dependence of the DOS and HOMO-LUMO gap on the number of water molecules and on surface effects. Our prediction for E G is 6:5 ± 0:5 eV in good agreement with a recent experimental prediction of 6.9 eV.

Resumo em Inglês:

Group contributions to the free energy of solvation in water and octanol as well as to the octanol/water partition coefficient have been determined from Miertus-Scrocco-Tomasi continuum calculations. Particular attention is paid to the influence exerted by the procedure used to carry out the charge normalization in the MST model, as well as to the formalism of the partitioning scheme. A good agreement is found between the group contributions calculated by using different charge normalization and partitioning schemes in a series of structurally related drug-like molecule. Finally, the transferability of the group contributions determined for common chemical fragments along the series of molecules is discussed.

Resumo em Inglês:

The influence that urea has on the conformation of water-soluble globular protein, bovine serum albumin (BSA), exposed directly to the aqueous solution as compared to the condition where the macromolecule is confined in the Aerosol-OT (AOT - sodium bis-2-ethylhexyl sulfosuccinate)/n-hexane/water reverse micelle (RM) is addressed. Small angle X-ray scattering (SAXS), tryptophan (Trp) fluorescence emission and circular dichroism (CD) spectra of aqueous BSA solution in the absence and in the presence of urea (3M and 5M) confirm the known denaturating effect of urea in proteins. The loss of the globular native structure is observed by the increase in the protein maximum dimension and gyration radius, through the Trp emission increase and maximum red-shift as well as the decrease in alpha-helix content. In RMs, the Trp fluorescence and CD spectra show that BSA is mainly located in its interfacial region independently of the micellar size. Addition of urea in this BSA/RM system also causes changes in the Trp fluorescence (emission decrease and maximum red-shift) and in the BSA CD spectra (decrease in alpha-helix content), which are compatible with the denaturation of the protein and Trp exposition to a more apolar environment in the RM. The fact that urea causes changes in the protein structure when it is located in the interfacial region (evidenced by CD) is interpreted as an indication that the direct interaction of urea with the protein is the major factor to explain its denaturating effect.

Resumo em Inglês:

We have performed a series of 10 ns Molecular Dynamics simulations of the sodium octanoate micelle in aqueous solution in the constant NpT ensemble, at p = 1 bar and T = 300 K. Two molecular topologies were studied, one with all internal degrees of freedom and the other constraining bond stretching and angle bending degrees of freedom. Two Lennard-Jones parameters for sodium ions, namely the OPLS and ° Aqvist parameters, were used. The results show an artificial enhancement of stable sodium bridges between octanoate anions when the OPLS parameters for sodium are used. The ° Aqvist parameters give a micellar structure in good agreement with experimental and thermodynamical evidences. It is also observed that the aggregation of monomers is strongly dependent on the molecular topology. When the ° Aqvist parameters were employed, the model system without constraining geometry had one dissociated monomer after 10 ns, while the model system with bond length and bond angle constraining had five dissociated monomers after a 10 ns trajectory.

Resumo em Inglês:

This paper discusses water at interfaces with emphasis on the electrical properties of adsorbed films. Two issues are addressed, namely adsorption of organic molecules at the air/water interface in Langmuir monolayers and the influence of adsorbed water on the electrical properties of nanostructured organic films deposited onto solid substrates. In Langmuir monolayers the focus will be on the interaction of the adsorbed molecules with the underlying water, particularly with regard to the surface potential and lateral conductance of the monolayers. It will be shown that these electrical measurements are extremely sensitive to small changes in the subphase, including trace amounts of impurities. Phase transitions due to structuring of the monolayer will be discussed at the light of theoretical models that deal with proton transfer along the monolayers. Attempts will be made to connect the interpretation at the molecular level with experimental findings from techniques such as Brewster angle microscopy and fluorescence microscopy, which provide information at the mesoscopic or microscopic scale. The gradient of the dielectric constant for water at the monolayer interface is inferred from modeling the monolayer surface potential in terms of the dipole moments of the molecules. For deposited films, the discussion will be centered on the electrical properties of nanostructured films produced with either the Langmuir-Blodgett (LB) or the layer-by-layer (LBL) methods. The strong effects from adsorbed water will be presented, with mention to sensor applications where the extreme sensitivity of the electrical properties to water is exploited and to doping of a conducting polymer induced by X-ray irradiation.

Resumo em Inglês:

The importance of hydration on the equilibrium involving internal rotation around carbon-carbon single bond is investigated for the furfural molecule dissolved in water. To analyze the solvent effects in stabilizing any preferred conformation of furfural, we perform Monte Carlo (MC) NPT simulations corresponding to different rotation angles of the carbonyl group. The hydrogen bonds formed between solute and solvent are also analyzed along the conformational equilibrium. They are found to be equivalent, both in number and in binding energy, for all rotation angles. These results give a strong evidence that the conformational stability and the rotation barrier of the furfural molecule in water relate to the bulk properties rater than solute-solvent hydrogen bonds.

Resumo em Inglês:

Globular proteins are produced as a linear chain of aminoacids in water solution in the cell and, in the same aqueous environment, fold into their respective unique and functional native structures. In spite of this, many theoretical studies have tried to explain the folding process in vacuum, but in this paper we adopt an alternative point of view: the folding problem of heteropolymers is analyzed from the solvent perspective. The thermodynamics of the folding process is discussed for a non homogeneous system composed by the chain and solvent together; hydrophobic effects, modulated by the polar/nonpolar attributes of the residue sequence and by its corresponding steric specificities, are proposed as basic ingredients for the mechanisms of the folding process. These ideas are incorporated in both lattice and off-lattice models and treated by Monte Carlo simulations. Configurational and thermodynamical results are compared with properties of real proteins. The results suggest that the folding problem of small globular protein can be considered as a process in which the mechanism to reach the native structure and the requirements for the globule stability are uncoupled.

Resumo em Inglês:

The role of the supporting medium of water molecules in some protein activities is examined under different aspects as in the cases of a monomeric peptide, the basic fibroblast growth factor, of a dimeric peptide, the human neutrophil peptide 3, of a peptide that acts in non-aqueous environment, the gramicidin A dimer, of a water molecule present in the binding of a co-factor in a phospholipase peptide, and under the general point of view of the hydrophilic/hydrophobic properties described by a hydropathy scale. These examples illustrate the importance of water in the hydrogen bond formation that is, of main importance in keeping the peptide structures that cannot be defined without the water contributions. The conclusions confirm that living systems are like they are because water is an outstanding and abundant molecule present everywhere in living matter.

Resumo em Inglês:

We investigated the performance of the recently developed SPC/L model for liquid water, as a pure liquid, in binary mixtures with DMSO, and as a solvent model in a peptide folding simulation. Additionally, in order to test the compatibility with the GROMOS biomolecular force field, free energies of hydration of a set of representative compounds were computed. The results are compared to those for the well established SPC water model, which is generally used as a solvent model in conjunction with the GROMOS force field already for more than two decades. It turns out that as a pure liquid and in binary mixtures with DMSO the SPC/L model outperforms SPC, whereas as solvent in combination with the GROMOS force field both models perform equally well.

Resumo em Inglês:

Computer simulations of biomolecular systems have achieved a significant importance in science as they provide information regarding structure, dynamics, and energetics of biomolecules that are inaccessible to experimental measuring techniques. In this work, some important aspects of the simulation of biomolecular systems are described. An overview of the most popular protein force fields, simple explicit water models for the simulation of liquid water, and different approaches to treat the boundaries of the system is presented. Also, studies conducted in our group illustrating successful simulations of three biomolecules (thrombin, L-type calcium channel and human Cytomegalovirus protease) through the application of simple explicit water models combined with protein force fields are discussed.

Resumo em Inglês:

A method to obtain the components of the broad Raman band assigned to the OH stretching vibrations of liquid water was developed, by considering the subtraction of spectra at several temperatures. From these subtractions a set of six components, that we denominate "basis", was determined corresponding to several water structures. This procedure fixes the number of components in the fitting as well as the values of the frequencies, generating a set of six gaussian bands from which the water spectrum can be calculated at any temperature. With such bands the spectrum of lithium perchlorate was calculated at several concentrations and temperatures. It was verified that the spectrum so obtained was identical to that of pure water at a higher temperature. The presence of an isosbestic point is a proof of the existence of equilibrium between the several structures. The enthalpy and entropy values were determined for the isosbestic point and for pairs of structures corresponding to the gaussian bands.

Resumo em Inglês:

Deep Inelastic Neutron Scattering (Neutron Compton Scattering), is used to measure the momentum distribution of the protons in water from temperatures slightly below freezing to the supercritical phase. The momentum distribution is determined almost entirely by quantum localization effects, and hence is a sensitive probe of the local environment of the proton. The distribution shows dramatic changes as the hydrogen bond network becomes more disordered. Within a single particle interpretation, the proton moves from an essentially harmonic well in ice to a slightly anharmonic well in room temperature water, to a deeply anharmonic potential in the supercritical phase that is best described by a double well potential with a separation of the wells along the bond axis of about 0.3 Angstrom. Confining the supercritical water in the interstices of a C60 powder enhances this anharmonicity and enhances the localization of the protons. The changes in the distribution are consistent with gas phase formation at the hydrophobic boundaries and inconsistent with the formation of ice there.