Oscar Bertran

Poly(2-thiophen-3-yl-malonic acid), a polythiophene with two carboxylic acids per repeating unit.

A new substituted polythiophene derivative bearing malonic acid, poly(2-thiophen-3-yl-malonic acid), has been prepared and characterized using a strategy that combines both experimental and theoretical methodologies. The chemical structure of this material has been investigated using FTIR and (1)H NMR, and its molecular conformation has been determined using quantum mechanical calculations. Interestingly, the arrangement of the inter-ring dihedral angles was found to depend on the ionization degree of the material, that is, on the pH, which has been found completely soluble in aqueous base solution. Thus, the preferred anti-gauche conformation changes to syn-gauche when the negatively charged carboxylate groups transforms into neutral carboxylic acid. UV-vis experiments and quantum mechanical calculations on model systems with a head-to-tail regiochemistry showed that the lowest pi-pi* transition energy is 2.25 and 2.39 eV for the negatively charged and the neutral polymer, respectively. These values are slightly larger than those previously reported for other polythiophenes with bulky polar side groups. The polymer presents a good thermal stability with a decomposition temperature above 215 degrees C and an electrical conductivity of 10(-5) S/cm, which is characteristic of semiconductor materials. Scanning electron microscopy micrographs showed that, after doping, the surface of this material displays regular distribution pores with irregular sizes. This surface suggests that poly(2-thiophen-3-yl-malonic acid) is a candidate for potential applications such as selective membranes for electrodialysis, wastewater treatment, or ion-selective membranes for biomedical uses.

Computer simulation of dendronized polymers : organization and characterization at the atomistic level

Atomistic molecular dynamics simulations in chloroform and solvent-free environments are used to build and study a homologous series of neutral dendronized linear polymers (DPs), whose repeat units are regularly branched dendrons of generations g = 1–7, excluding g = 5. We find that a DP with g ≤ 4 displays an elongated conformation, while a DP with g = 6 exhibits a helical backbone. The conformations essentially differ in their alternating (elongated) or regular (helical) twist with respect to the macromolecular axis, at similar average distance between repeat units (2.1–2.3 A). With increasing g the dendrons tend to induce an increasing strain, stiffness and overall cylindrical shape onto the DP; the existence of DPs with g ≥ 7 is excluded. The fractal dimensionality of the backbone appears similar for DPs with g ≤ 4, while a discontinuous fractal behavior found for g = 6 is consistent with its helical backbone. Profiles describing the variation of the density as a function of the distance to the molecular backbone are extracted to analyze conformational effects of both backbone and sidegroups. For the solvent-free case the average density grows from 0.97 to 1.11 g cm−3 upon increasing g, while the radial density profile is basically constant at 1.1–1.2 g cm−3 and insensitive to g at intermediate distances, where dendrons are able to interpenetrate. The variation of obtained DP thicknesses is successfully compared with experimental estimates deduced from transmission electron microscopy measurements of polymers deposited onto attractive mica surfaces. Finally, we examine and discuss the distribution of solvent molecules inside elongated structures.

Modeling biominerals formed by apatites and DNA

Different aspects of biominerals formed by apatite and DNA have been investigated using computer modeling tools. Firstly, the structure and stability of biominerals in which DNA molecules are embedded into hydroxyapatite and fluoroapatite nanopores have been examined by combining different molecular mechanics methods. After this, the early processes in the nucleation of hydroxyapatite at a DNA template have been investigated using molecular dynamics simulations. Results indicate that duplexes of DNA adopting a B double helix can be encapsulated inside nanopores of hydroxyapatite without undergoing significant distortions in the inter-strand hydrogen bonds and the intra-strand stacking. This ability of hydroxyapatite is practically independent of the DNA sequence, which has been attributed to the stabilizing role of the interactions between the calcium atoms of the mineral and the phosphate groups of the biomolecule. In contrast, the fluorine atoms of fluoroapatite induce pronounced structural distortions in the double helix when embedded in a pore of the same dimensions, resulting in the loss of its most relevant characteristics. On the other hand, molecular dynamics simulations have allowed us to observe the formation of calcium phosphate clusters at the surface of the B-DNA template. Electrostatic interactions between the phosphate groups of DNA and Ca2+ have been found to essential for the formation of stable ion complexes, which were the starting point of calcium phosphate clusters by incorporating from the solution.

DNA adsorbed on hydroxyapatite surfaces

Hydroxyapatite (HAp) particles with very different surface charges and compositions (i.e. different Ca/P and CO3 2-/PO4 3- ratios) have been obtained by varying the experimental conditions used during the chemical precipitation process. The DNA adsorption capacity and protection imparted against the attack of nucleases of HAp particles have been proved to depend on the surface charge while the buffering capacity is affected by the chemical composition. On the basis of both the surface charge and the crystallinity, the predominant planes at the surfaces of HAp particles have been identified. Atomistic molecular dynamics simulations of surfaces constructed with these planes (i.e. (001) and the two terminations of (010)) with the adsorbed B-DNA double helix have been performed to get microscopic understanding of the influence of the mineral in the biomolecule structure and the interaction energies. The results indicate that the DNA secondary structure is perfectly preserved on the (001) surface, this stability being accompanied by an attractive binding energy. In contrast, the (010) surface with PO4 3-, OH- and Ca2+ ions in the termination induces significant local and global deformations in the double helix, repulsive OH-(HAp)PO4 3- (DNA) interactions provoking the desorption of the biomolecule. Finally, although the termination of the (010) surface with PO4 3- and Ca2+ ions also deforms the double helix, it forms very strong attractive interactions with the biomolecule. These binding characteristics are in excellent agreement with the DNA adsorption and protection abilities experimentally determined for the HAp samples. Finally, the surface charge has been found less decisive than the chemical composition in the efficacy of the transfection process.

Synergistic Approach to Elucidate the Incorporation of Magnesium Ions into Hydroxyapatite

Although the content of Mg(2+) in hard tissues is very low (typically ≤1.5 wt %), its incorporation into synthetic hydroxyapatite (HAp) particles and its role in the minerals properties are still subject of intensive debate. A combined experimental-computational approach is used to answer many of the open questions. Mg(2+) -enriched HAp particles are prepared using different synthetic approaches and considering different concentrations of Mg(2+) in the reaction medium. The composition, morphology and structure of the resulting particles are investigated using X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy, scanning and transmission electron microscopies, FTIR, and wide-angle X-ray diffraction. After this scrutiny, the role of the Mg(2+) in the first nucleation stages, before HAp formation, is investigated using atomistic molecular dynamics simulations. Saturated solutions are simulated with and without the presence of DNA, which has been recently used as a soft template in the biomineralization process. This synergistic investigation provides a complete picture of how Mg(2+) ions affect the mineralization from the first stages onwards.

Interactions in dendronized polymers: intramolecular dominates intermolecular

In an attempt to relate atomistic information to the rheological response of a large dendritic object, interand intramolecular hydrogen bonds and p,p-interactions have been characterized in a dendronized polymer (DP) that consists of a polymethylmethacrylate backbone with tree-like branches of generation four (PG4) and contains both amide and aromatic groups. Extensive atomistic molecular dynamics simulations have been carried out on (i) an isolated PG4 chain and (ii) ten dimers formed by two PG4 chains associated with different degrees of interpenetration. Results indicate that the amount of nitrogen atoms involved in hydrogen bonding is ~11% while ~15% of aromatic groups participate in p,pinteractions. Furthermore, in both cases intramolecular interactions clearly dominate over intermolecular ones, while exhibiting markedly different behaviors. Specifically, the amount of intramolecular hydrogen bonds increases when the interpenetration of the two chains decreases, whereas intramolecular p,pinteractions remain practically insensitive to the amount of interpenetration. In contrast, the strength of the corresponding two types of intermolecular interactions decreases with interpenetration. Although the influence of complexation on the density and cross-sectional radius is relatively small, interpenetration affects significantly the molecular length of the DP. These results support the idea of treating DPs as long colloidal molecules.

Structural and electronic properties of poly(thiaheterohelicene)s

Quantum chemical methods have been applied on model oligomers of poly(thiaheterohelicene)s to investigate the structural and electronic properties of these systems. Specifically, the properties of the helical structures found for poly(heterohelicene) and poly(methyl-sulfonium), which were calculated using density functional theory calculations, are in good agreement with available experimental data. The geometrical parameters obtained for poly(methyl-sulfonium) reflect the enlargement of the inner carbon-carbon bond lengths at the thiophene rings, which are those closer to the helical screw axes, and lead to reduce their aromaticity of such heterocycles. On this basis, a relationship between the aromaticity and the lowest pi-pi* transition energy has been established. Finally, the lowest pi-pi* transitions have been extrapolated for infinite polymer chains of poly(heterohelicene) and poly(methyl-sulfonium) using different theoretical approaches.

Dissolving Hydroxyolite: A DNA Molecule into Its Hydroxyapatite Mold

In spite of the clinical importance of hydroxyapatite (HAp), the mechanism that controls its dissolution in acidic environments remains unclear. Knowledge of such a process is highly desirable to provide better understanding of different pathologies, as for example osteoporosis, and of the HAp potential as vehicle for gene delivery to replace damaged DNA. In this work, the mechanism of dissolution in acid conditions of HAp nanoparticles encapsulating double-stranded DNA has been investigated at the atomistic level using computer simulations. For this purpose, four consecutive (multi-step) molecular dynamics simulations, involving different temperatures and proton transfer processes, have been carried out. Results are consistent with a polynuclear decalcification mechanism in which proton transfer processes, from the surface to the internal regions of the particle, play a crucial role. In addition, the DNA remains protected by the mineral mold and transferred proton from both temperature and chemicals. These results, which indicate that biomineralization imparts very effective protection to DNA, also have important implications in other biomedical fields, as for example in the design of artificial bones or in the fight against osteoporosis by promoting the fixation of Ca(2+) ions.

On the modeling of aggregates of an optically active regioregular polythiophene

The conformational properties of the optically active regioregular poly[(R)-3-(4-(4-ethyl-2-oxazolin-2-yl) phenyl) thiophene] (PEOPT) were explored by molecular dynamics on a single chain using several solvents of increasing polarity. Furthermore, their aggregate formation was studied over a wide range of temperatures using a replica exchange molecular dynamics simulation providing simulation data representative of the equilibrium behaviour of their aggregates. Results show a clear tendency of PEOPT to keep a syn–gauche conformation between continuous backbone thiophene rings favouring a bent chain structure in solvent. After studying their aggregation behaviour in acetonitrile, a strong tendency to pack stabilizing structures that reinforce the chirality of the polymer, in concordance with experimental data, was found. Two different aggregated structures were observed depending on oligomer length, a self-assembled helical aggregate based on stacked octamers and a bent double helix aggregate in large oligomers.

Atomistic organization and characterization of tube-like assemblies comprising peptide-polymer conjugates: computer simulation studies.

The structure and stability of the nanotube obtained by assembling peptide-polymer conjugates consisting of two poly(n-butyl acrylate) blocks coupled to the cyclic (D-alt-L)-octapeptide cyc[(L-Gln-D-Ala-L-Lys-D-Ala)2], have been investigated at the molecular level using atomistic molecular dynamics simulations. The effect of the wrapping polymer shells in the tube-like core, which consists of stacked beta-sheet cyclopeptides, has been examined by simulating assemblies of both unsubstituted cyclopeptides, and conjugates in chloroform and N,N-dimethylformamide solutions. Furthermore, the influence of the environment has been investigated by comparing conjugate assemblies in solution with those deposited on mica. In addition, nanotubes stabilized by beta-sheet-like hydrogen bonds between both parallel and antiparallel oriented cyclopeptides have been considered in all cases. The results, which have been analysed in terms of energy contributions, partial radial distribution functions, inter-subunit distances, shape of the cyclopeptide ring, internal van der Waals diameters, and both height and width of the nanostructures deposited on mica, have provided important microscopic insights. For example, analysis of both the energy terms and the structural dynamics obtained for the different assemblies indicate that the mica surface interacts more favourably with the parallel assembly than with the antiparallel ones, whereas the only configuration that is structurally stable in solution is the latter. Furthermore, adsorption onto the solid substrate produces a small deformation of the cylindrical molecular system.