Manel Canales

Molecular dynamics simulation of liquid lithium

Liquid 7Li at 470 K is studied by molecular dynamics simulation. A recently proposed interionic effective potential with no adjustable parameters is assumed. Both structural and dynamical properties show very good agreement with the available experimental information.

Generalized Langevin dynamics simulations of NaCl electrolyte solutions

The stochastic simulation method called generalized Langevin dynamics has been employed in the study of NaCl aqueous solutions at several ionic concentrations. Only the ion pairs have been considered explicitly in the simulations. Every ion follows a generalized Langevin equation in which the total acceleration has a stochastic term, an integral time-dependent friction term, and a deterministic part that takes into account the interaction with the other ions in the system. Different solvent-averaged potentials and memory kernels have been tested in order to obtain a realistic behavior of the systems. The screening of electrostatic forces between ions has been analyzed too. The electric field around Na+ and Cl− ions has been calculated and the screening has been analyzed in terms of the structural features of the ionic surroundings.

Water absorbed by polyaniline emeraldine tends to organize, forming nanodrops

Interactions, in terms of both binding energies and microscopic organization, of water molecules absorbed by hydrophilic polyaniline emeraldine base have been investigated using quantum mechanical calculations, molecular dynamics simulation, FTIR spectroscopy, and (1)H NMR. From an enthalpic point of view, water molecules interact more favorably with imine nitrogen atoms than with amine ones, even though the latter are entropically favored with respect to the former because of their two binding sites. Quantum mechanical results show that interaction energies of water molecules reversibly absorbed but organized individually around a binding site range from 3.0 to 6.3 kcal/mol, which is in good agreement with activation energies of 3-5 kcal/mol previously determined by thermodynamic measurements. The irreversible absorption of water to produce C-OH groups in rings of diimine units has been examined considering a three steps process in which water molecules act as both acidic and nucleophilic reagent. Although calculations predict that the whole process is disfavored by 5-8 kcal/mol only, FTIR and (1)H NMR detected the existence of reversibly absorbed water but not of C-OH groups. Both the binding energies and the structural information provided by molecular dynamics simulations have been used to interpret the existence of two types of physisorbed water molecules: (i) those that interact individually with polymer chains and (ii) those immersed in nanodrops that are contained within the polymeric matrix. The binding energies calculated for these two types of water molecules are fully consistent with the thermodynamic activation energies previously reported.

A First Principle Analysis of the Structure of Oligoanilines Doped with Alkylsulfonic Acids

The interaction of polyaniline with alkylsulfonate dopants have been investigated at the atomic level using quantum mechanical methods. Calculations have been performed on complexes formed by dopant molecules with an alkyl group ranging from methyl to nonyl and model oligoanilines of different sizes. The stabilization provided by the formation of the alkylsulfonate...oligoaniline complexes (70-90 kcal/mol) is significantly higher than that found for conventional hydrogen bonds (5-12 kcal/mol) but lower than that obtained for methylsulfate...alkylammonium and methylsulfate...Na(+) systems (120-135 kcal/mol). On the other hand, the influence of size of the alkyl group contained in the dopant on the interaction is practically negligible, whereas, in opposition, the number of aniline units used to represent polyaniline significantly affects the energetics of the interaction. Specifically, the interaction energy of an alkyl-dopant molecule and an infinite polyaniline chain has been predicted to be around -65 kcal/mol. The overall results allow the conclusion that the interaction between alkylsulfonate dopants and polyaniline is a very local phenomenon.

On the mode-coupling theory for the velocity autocorrelation functions of simple liquids

The velocity autocorrelation functions and the corresponding memory functions for a set of liquid metals and Lennard-Jones fluids have been calculated using a mode-coupling theory. The data required for the theoretical calculations have been obtained from molecular dynamics simulations. The influence of both the short repulsive wall and the attractive well of the potential on the binary and mode-coupling terms of the memory function has been analysed. The mode-coupling theory has been tested by comparing the theoretical results with those directly obtained from computer simulations. The most marked discrepancies correspond to systems showing velocity autocorrelation functions with weak backscattering. In the case of the Lennard-Jones fluids, the binary term of the memory function is less well described using a gaussian function.

Polyaniline Emeraldine Salt in the Amorphous Solid State: Polaron versus Bipolaron

The polaronic and bipolaronic forms of polyaniline emeraldine salt (PAni-ES) in the amorphous solid state have been simulated using classical molecular dynamics (MD) and hybrid quantum mechanical/molecular mechanical-molecular dynamics (QM/MM-MD) approaches. It should be remarked that the electronic state of PAni-ES has been theoretically investigated in the gas phase, solution phase, and crystalline state, but this is the first study in the amorphous solid state, which is the most typical for this conducting polymer. MD simulations were carried out using force-field parametrizations explicitly developed for polaronic and bipolaronic models. QM/MM-MD calculations were performed using a quantum mechanical zone defined by four repeat units. In addition of the structural and electronic characteristics of the two forms of PAni-ES, MD and QM/MM-MD simulations indicate that the bipolaronic is the most stable state of amorphous PAni-ES. Complementary studies have been carried out using different experimental techniques. Although the morphology and topography of doped and undoped PAni are very similar, comparison of their UV-vis spectra supports the preference toward the bipolaronic form of PAni-ES.

Helical Dendronized Polymers with Chiral Second-Generation Dendrons: Atomistic View and Driving Forces for Structure Formation

The secondary structures of protected (neutral) and deprotected (charged) second generation dendronized polymethylmethacrylates carrying chiral 4-aminoproline-based dendrons were investigated using atomistic molecular dynamics simulations. Trajectories involving a total of approximately 280 ns on molecular systems containing up to 101,909 explicit particles allowed the correlation of the structural parameters, rigidity, and thermal stability with the microscopic interactions that govern these systems. In both the neutral and the charged systems a right-handed helix is found. This screw-sense is enforced by the packing of the dendrons and allows for a very similar arrangement of the polymethylmethacrylate backbones, independently of their tacticity. The properties of the secondary structures are mainly defined by the interdendron interactions, whereby the remarkable thermal stability and the rigid rod-like behavior found for the protected polymer is due to the interdendron network of hydrogen bonds. For the deprotected congener instead, where also a helical secondary structure is found, a specific arrangement of the dendritic side chains minimize the repulsive interactions between the positive charges of neighboring repeat units. In addition, the impact of the conformational changes produced when the protected system transforms into the deprotected one by the addition of acid has been evaluated.

Modeling of Amorphous Polyaniline Emeraldine Base

Amorphous polyaniline emeraldine base has been investigated using atomistic classical molecular dynamics simulations. Initially, different sets of force-field parameters, which differ in the atomic charges and/or the van der Waals parameters, were tested. The experimental density of polyaniline was satisfactorily reproduced using the following combination: (i) equilibrium bond lengths, equilibrium bond angles, and electrostatic charges derived from quantum mechanical calculations and (ii) van der Waals parameters extrapolated from GROMOS for all atoms with the exception of the CH pseudoparticles of the phenyl ring, which were taken from an anisotropic united atom potential. Next, this force field was used to investigate the structure of the polymer in the amorphous state, the trajectories performed for this purpose allowing accumulation of 750 ns. Analyses of the energies evidence that the interactions between one repeating unit containing an amine nitrogen atom and another unit with an imine nitrogen are favored with respect to those between two identical repeating units. This conclusion is also supported by quantum mechanical and quantum mechanical/molecular mechanics calculations. On the other hand, the partial radial distribution functions indicate that this material only exhibits short-range intramolecular correlation, which is in excellent agreement with experimental evidence.

On the analysis of conformational dynamics in polymers with several rotational isomers

The ability of different correlation functions to shed some light onto the conformational dynamics of an amorphous polymer has been analyzed. The study has been performed on a polyethylene model polymer, which has been simulated at decreasing temperatures towards its glass transition, via the molecular dynamics technique. Three rotational isomers are allowed by the considered torsional potential. The correlation times associated with the evaluated transition rates have shown to be Arrhenius in nature, with activation energies resulting basically from internal rotation barriers. Overall torsional autocorrelation functions have been calculated. We have observed that they are dominated by slow events. Alternatively, a set of torsional autocorrelation functions associated with every isomeric state has been evaluated. Stretched exponential fits lead to correlation times that display Vogel-Fulcher temperature dependence.

On the bond-angle distributions in liquids and liquid solutions

Abstract Bond-angle distributions are used for the study of local orientational order in liquid systems. Bond-angles between a central particle and particles in both the first and second coordination shells are considered. Molecular dynamics calculations are carried out for determining the bond-angle distributions in a Lennard Jones liquid. The resulting distributions are compared with those obtained from stochastic simulations of a subset of atoms (solute) of the same system (solution). Although the radial distribution functions from the two simulations are in agreement, the bond-angle distributions show noticeable difference. Computer simulation findings are compared with results obtained by using both the superposition and convolution approximations. The reliability of the generalized Langevin dynamics simulation method is discussed.