Self-assembly pathways in a triphenylalanine peptide capped with aromatic groups.

Peptide derivatives and, most specifically, their self-assembled supramolecular structures are being considered in the design of novel biofunctional materials. Although the self-assembly of triphenylalanine homopeptides has been found to be more versatile than that of homopeptides containing an even number of residues (i.e. diphenylalanine and tetraphenylalanine), only uncapped triphenylalanine (FFF) and a highly aromatic analog blocked at both the N- and C-termini with fluorenyl-containing groups (Fmoc-FFF-OFm), have been deeply studied before. In this work, we have examined the self-assembly of a triphenylalanine derivative bearing 9-fluorenylmethyloxycarbonyl and benzyl ester end-capping groups at the N- and C-termini, respectively (Fmoc-FFF-OBzl). The antiparallel arrangement clearly dominates in ß-sheets formed by Fmoc-FFF-OBzl, whereas the parallel and antiparallel dispositions are almost isoenergetic in Fmoc-FFF-OFm ß-sheets and the parallel one is slightly favored for FFF. The effects of both the peptide concentration and the medium on the self-assembly process have been examined considering Fmoc-FFF-OBzl solutions in a wide variety of solvent:co-solvent mixtures. In addition, Fmoc-FFF-OBzl supramolecular structures have been compared to those obtained for FFF and Fmoc-FFF-OFm under identical experimental conditions. The strength of π-π stacking interactions involving the end-capping groups plays a crucial role in the nucleation and growth of supramolecular structures, which determines the resulting morphology. Finally, the influence of a non-invasive external stimulus, ultrasounds, on the nucleation and growth of supramolecular structures has been examined. Overall, FFF-based peptides provide a wide range of supramolecular structures that can be of interest in the biotechnological field.

Plasma-Functionalized Isotactic Polypropylene Assembled with Conducting Polymers for Bacterial Quantification by NADH Sensing.

Rapid detection of bacterial presence on implantable medical devices is essential to prevent biofilm formation, which consists of densely packed bacteria colonies able to withstand antibiotic-mediated killing. In this work, a smart approach is presented to integrate electrochemical sensors for detecting bacterial infections in biomedical implants made of isotactic polypropylene (i-PP) using chemical assembly. The electrochemical detection is based on the capacity of conducting polymers (CPs) to detect extracellular nicotinamide adenine dinucleotide (NADH) released from cellular respiration of bacteria, which allows distinguishing prokaryotic from eukaryotic cells. Oxygen plasma-functionalized free-standing i-PP, coated with a layer (≈1.1 µm in thickness) of CP nanoparticles obtained by oxidative polymerization, is used as working electrode for the anodic polymerization of a second CP layer (≈8.2 µm in thickness), which provides very high electrochemical activity and stability. The resulting layered material, i-PPf /CP2 , detects the electro-oxidation of NADH in physiological media with a sensitivity 417 µA cm-2 and a detection limit up to 0.14 × 10-3 m, which is below the concentration of extracellular NADH found for bacterial cultures of biofilm-positive and biofilm-negative strains.

Heterochirality Restricts the Self-Assembly of Phenylalanine Dipeptides Capped with Highly Aromatic Groups.

The influence of stereochemistry on the self-assembly of phenylalanine (Phe) dipeptides bearing aromatic fluorenyl groups at both the N- and C-termini (Fmoc, OFm) has been investigated. For this purpose, Fmoc-d-Phe-l-Phe-OFm and Fmoc-l-Phe-l-Phe-OFm have been examined considering a wide variety of solvents, which differ in dielectric constant and volatility. Results reveal that replacement of l-Phe by d-Phe has a major impact on the self-assembly propensities, restricting drastically the structural diversity and polymorphism shown by the homochiral dipeptide. Thus, the analogous heterochiral dipeptide shows a great propensity to form micro/nanofibers, independently of the environmental conditions. Theoretical calculations revealed that the stability of antiparallel disposition is much higher (a factor of ca. 15) for Fmoc-d-Phe-l-Phe-OFm than that for Fmoc-l-Phe-l-Phe-OFm, which has been attributed to the hydrophobic core formed in the former. Overall, results suggest that control of the backbone chirality is a potent and versatile strategy to drive and finely tune the self-assembly propensities of highly aromatic peptides.

Amyloid fibrils from organic solutions of an amphiphilic dipeptide.

Non-hydrated organic solutions of a diphenylalanine amphiphile blocked at the C-terminus with a fluorenylmethyl ester and stabilized at the N-terminus with a trifluoroacetate have been used to prepare amyloid fibrils. The solvent used to prepare the stock solution together with the co-solvent added enables regulation of the characteristics of the fibrils, which is important for their use in technological applications.

Paradigm Shift for Preparing Versatile M2+-Free Gels from Unmodified Sodium Alginate.

This manuscript describes a new route to prepare rapidly Ca2+-free hydrogels from unmodified sodium alginate by simply mixing with small organic molecules such as poly(carboxylic acid) compounds as cross-linker agents instead of classical divalent metal salts such as CaCl2. Dimethyl sulfoxide (DMSO) was also found to induce the rapid gelation of aqueous alginate solutions. The gelation process takes place at room temperature, and depending on the composition, gels with good thermal (90-100 °C) and mechanical properties compared to classical metal-containing analogs are obtained. DMSO-based gels showed remarkable self-supporting and thixotropic properties, which can be tuned by the biopolymer concentration. Furthermore, oxalic acid-based gels show superior elasticity than HCl, CaCl2 and DMSO-based gels. The possibility to prepare monoliths, beads, and films of these gels provide them with significant versatility. In particular, films made of alginate and oxalic acid show good potential as synergistic anticancer drug delivery carrier. Computational studies using both quantum mechanical and classical force-field methodologies reveal that hydrogen bonding networks between water and DMSO molecules located close to the alginate chains are responsible for the stability of DMSO-based gels. In contrast, the cohesion of oxalic acid-based gels is a consequence of the coexistence of multiple ionic associations involving oxalate, alginate, and Na+ counterions, which stabilize the system and keep all the interacting species grouped.

Measurement of Vibrations in Two Tower-Typed Assistant Personal Robot Implementations with and without a Passive Suspension System.

This paper presents the vibration pattern measurement of two tower-typed holonomic mobile robot prototypes: one based on a rigid mechanical structure, and the other including a passive suspension system. Specific to the tower-typed mobile robots is that the vibrations that originate in the lower part of the structure are transmitted and amplified to the higher areas of the tower, causing an unpleasant visual effect and mechanical stress. This paper assesses the use of a suspension system aimed at minimizing the generation and propagation of vibrations in the upper part of the tower-typed holonomic robots. The two robots analyzed were equipped with onboard accelerometers to register the acceleration over the X, Y, and Z axes in different locations and at different velocities. In all the experiments, the amplitude of the vibrations showed a typical Gaussian pattern which has been modeled with the value of the standard deviation. The results have shown that the measured vibrations in the head of the mobile robots, including a passive suspension system, were reduced by a factor of 16.

Diversity and Hierarchy in Supramolecular Assemblies of Triphenylalanine: From Laminated Helical Ribbons to Toroids.

Microstructures from small phenylalanine-based peptides have attracted great attention lately because these compounds are considered to be a new class of tunable materials. In spite of the extensive studies on uncapped diphenylalanine and tetraphenylalanine peptides, studies on the self-assembly of uncapped triphenylananine (FFF) are very scarce and nonsystematic. In this work, we demonstrate that FFF assemblies can organize in a wide number of well-defined supramolecular structures, which include laminated helical-ribbons, leaflike dendrimers, doughnut-, needle-, and flower-shapes. These organizations are produced by the attractive or repulsive interactions between already formed assemblies and therefore can be controlled through the choice of solvents used as the incubation medium. Thus, the formation of the desired supramolecular structures is regulated through the protonation/deprotonation of the terminal groups, the polarity of the incubation medium, which affects both peptide···solvent interactions and the cavity solvation energy (i.e., solvent···solvent interactions), and the steric interactions between own assemblies that act as building blocks. Finally, the ß-sheet disposition in the latter structural motifs has been examined using both theoretical calculations and Fourier transform infrared spectroscopy. Results indicate that FFF molecules can adopt both parallel and antiparallel ß-sheets. However, the former one is the most energetically favored because of the formation of π-π stacking interactions between the aromatic rings of hydrogen-bonded strands.

Distribution of dopant ions around poly(3,4-ethylenedioxythiophene) chains: a theoretical study.

The effect of counterions and multiple polymer chains on the properties and structure of poly(3,4-ethylenedioxythiophene) (PEDOT) doped with ClO4- has been examined using density functional theory (DFT) calculations with periodic boundary conditions (PBCs). Calculations on a one-dimensional periodic model with four explicit polymer repeat units and two ClO4- molecules indicate that the latter are separated as much as possible, with the salt structure and band gap obtained from such ClO4- distribution being in excellent agreement with those determined experimentally. On the other hand, DFT calculations on periodic models that include two chains indicate that neighboring PEDOT chains are shifted along the molecular axis by a half of the repeat unit length, with dopant ions intercalated between the polymer molecules acting as cement. In order to support these structural features, classical molecular dynamics (MD) simulations have been performed on a multiphasic system consisting of 69 explicit PEDOT chains anchored onto a steel surface, explicit ClO4- anions embedded in the polymer matrix, and an acetonitrile phase layer onto the polymer matrix. Analyses of the radial distribution functions indicate that the all-anti conformation, the relative disposition of adjacent PEDOT chains and the distribution of ClO4- dopant ions are fully consistent with periodic DFT predictions. The agreement between two such different methodologies allows reinforcing the microscopic understanding of the PEDOT film structure.

Design, Implementation and Validation of the Three-Wheel Holonomic Motion System of the Assistant Personal Robot (APR).

This paper presents the design, implementation and validation of the three-wheel holonomic motion system of a mobile robot designed to operate in homes. The holonomic motion system is described in terms of mechanical design and electronic control. The paper analyzes the kinematics of the motion system and validates the estimation of the trajectory comparing the displacement estimated with the internal odometry of the motors and the displacement estimated with a SLAM procedure based on LIDAR information. Results obtained in different experiments have shown a difference on less than 30 mm between the position estimated with the SLAM and odometry, and a difference in the angular orientation of the mobile robot lower than 5° in absolute displacements up to 1000 mm.

Hierarchical self-assembly of di-, tri- and tetraphenylalanine peptides capped with two fluorenyl functionalities: from polymorphs to dendrites.

Homopeptides with 2, 3 and 4 phenylalanine (Phe) residues and capped with fluorenylmethoxycarbonyl and fluorenylmethyl esters at the N-terminus and C-terminus, respectively, have been synthesized to examine their self-assembly capabilities. Depending on the conditions, the di- and triphenylalanine derivatives self-organize into a wide variety of stable polymorphic structures, which have been characterized: stacked braids, doughnut-like shapes, bundled arrays of nanotubes, corkscrew-like shapes and spherulitic microstructures. These highly aromatic Phe-based peptides also form incipient branched dendritic microstructures, even though they are highly unstable, making their manipulation very difficult. Conversely, the tetraphenylalanine derivative spontaneously self-assembles into stable dendritic microarchitectures made of branches growing from nucleated primary frameworks. The fractal dimension of these microstructures is ∼1.70, which provides evidence for self-similarity and two-dimensional diffusion controlled growth. DFT calculations at the M06L/6-31G(d) level have been carried out on model ß-sheets since this is the most elementary building block of Phe-based peptide polymorphs. The results indicate that the antiparallel ß-sheet is more stable than the parallel one, with the difference between them growing with the number of Phe residues. Thus, the cooperative effects associated with the antiparallel disposition become more favorable when the number of Phe residues increases from 2 to 4, while those of the parallel disposition remained practically constant.

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.

Self-assembled fibrillar networks of a multifaceted chiral squaramide: supramolecular multistimuli-responsive alcogels.

Chiral N,N'-disubstituted squaramide has been found to undergo self-assembly in a variety of alcoholic solvents at low concentrations leading to the formation of novel nanostructured supramolecular alcogels. The gels responded to thermal, mechanical, optical and chemical stimuli. Solubility studies, gelation ability tests and computer modeling of a series of structurally related squaramides proved the existence of a unique combination of non-covalent molecular interactions and favorable hydrophobic/hydrophilic balance in that drive the anisotropic growth of alcogel networks. The results have also revealed a remarkable effect of ultrasound on both the gelation kinetics and the properties of the alcogels.

Self-Assembly of Tetraphenylalanine Peptides.

Three different tetraphenylalanine (FFFF) based peptides that differ at the N- and C-termini have been synthesized by using standard procedures to study their ability to form different nanoassemblies under a variety of conditions. The FFFF peptide assembles into nanotubes that show more structural imperfections at the surface than those formed by the diphenylalanine (FF) peptide under the same conditions. Periodic DFT calculations (M06L functional) were used to propose a model that consists of three FFFF molecules defining a ring through head-to-tail NH3(+)⋅⋅⋅(-)OOC interactions, which in turn stack to produce deformed channels with internal diameters between 12 and 16 Å. Depending on the experimental conditions used for the peptide incubation, N-fluorenylmethoxycarbonyl (Fmoc) protected FFFF self-assembles into a variety of polymorphs: ultra-thin nanoplates, fibrils, and star-like submicrometric aggregates. DFT calculations indicate that Fmoc-FFFF prefers a parallel rather than an antiparallel ß-sheet assembly. Finally, coexisting multiple assemblies (up to three) were observed for Fmoc-FFFF-OBzl (OBzl = benzyl ester), which incorporates aromatic protecting groups at the two peptide terminals. This unusual and noticeable feature is attributed to the fact that the assemblies obtained by combining the Fmoc and OBzl groups contained in the peptide are isoenergetic.

An experimental-computer modeling study of inorganic phosphates surface adsorption on hydroxyapatite particles.

The adsorption of orthophosphate, pyrophosphate, triphosphate and a trisphosphonate onto hydroxyapatite has been examined using experiments and quantum mechanical calculations. Adsorption studies with FTIR and X-ray photoelectron spectroscopies have been performed considering both crystalline hydroxyapatite (HAp) and amorphous calcium phosphate particles, which were specifically prepared and characterized for this purpose. Density functional theory (DFT) calculations have been carried out considering the (100) and (001) surfaces of HAp, which were represented using 1 × 2 × 2 and 3 × 3 × 1 slab models, respectively. The adsorption of phosphate onto the two crystallographic surfaces is very much favored from an energetic point of view, which is fully consistent with current interpretations of the HAp growing process. The structures calculated for the adsorption of pyrophosphate and triphosphate evidence that this process is easier for the latter than for the former. Thus, the adsorption of pyrophosphate is severely limited by the surface geometry while the flexibility of triphosphate allows transforming repulsive electrostatic interactions into molecular strain. On the other hand, calculations predict that the trisphosphonate only adsorbs onto the (001) surface of HAp. Theoretical predictions are fully consistent with experimental data. Thus, comparison of DFT results and spectroscopic data suggests that the experimental conditions used to prepare HAp particles promote the predominance of the (100) surface. Accordingly, experimental identification of the adsorption of trisphosphonate onto such crystalline particles is unclear while the adsorption of pyrophosphate and triphosphate is clearly observed.

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 mineral's 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.

A rational design for the selective detection of dopamine using conducting polymers.

Poly(N-methylpyrrole) (PNMPy), poly(N-cyanoethylpyrrole) (PNCPy) and poly(3,4-ethylenedioxythiophene) (PEDOT) films have been prepared using both single and two polymerization steps for the selective determination of low concentrations of dopamine, ascorbic acid and uric acid in tertiary mixtures. Analysis of the sensitivity and resolution parameters derived from the electrochemical response of such films indicates that PEDOT is the most appropriate for the unambiguous detection of the three species. Indeed, the performance of PEDOT is practically independent of the presence of both gold nanoparticles at the surface of the film and interphases inside the film, even though these two factors are known to improve the electroactivity of conducting polymers. Quantum mechanical calculations on model complexes have been used to examine the intermolecular interaction involved in complexes formed by PEDOT chains and oxidized dopamine, ascorbic acid and uric acid. Results show that such complexes are mainly stabilized by C-HO interactions rather than by conventional hydrogen bonds. In order to improve the sensitivity of PEDOT through the formation of specific hydrogen bonds, a derivative bearing a hydroxymethyl group attached to the dioxane ring of each repeat unit has been designed. Poly(hydroxymethyl-3,4-ethylenedioxythiophene) (PHMeDOT) has been prepared and characterized by FTIR, UV-vis spectroscopy, cyclic voltammetry, scanning electron microscopy and atomic force microscopy. Finally, the performance of PHMeDOT and PEDOT for the selective detection of the species mentioned above has been compared.

Mineralization of DNA into nanoparticles of hydroxyapatite.

Encapsulation of DNA into hydroxyapatite (HAp) has been investigated using a rational approach that involves computer simulation and experimental techniques. The temporal evolution of the radial distribution functions derived from atomistic molecular dynamics simulations of Ca(2+), PO4(3-) and OH(-)-containing aqueous solutions in the presence and absence of B-DNA has been used to conclude that the backbone of the double helix acts as a template for HAp growth. More specifically, results reveal the formation of calcium phosphate clusters at the first stages of the simulations, which subsequently re-organize to nucleate HAp. This effect is produced in the absence and, especially, presence, of DNA indicating that the biomolecules do not inhibit but even promote mineral growth. Furthermore, computer simulations suggest that the diffusion of the OH(-) anions through the inorganic solution is the limiting step for the nucleation of the biomineral. Nanocapsules and crystalline nanorods of HAp containing DNA molecules inside have been prepared by mixing solutions containing Ca(2+) and PO4(3-) ions with fish sperm DNA at high pH. The dimensions and morphology of such nanostructures have been examined by transmission electron microscopy, while the characterization of the biomineral has been focused on the identification of DNA inside HAp using infrared, X-ray photoelectron and UV-vis spectroscopies, as well as gel electrophoresis. The biominerals reported in this work are important for biomedical applications requiring the protection of DNA from aggressive environmental conditions.

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.

Use of proton pump inhibitors and risk of fragility hip fracture in a Mediterranean region.

OBJECTIVE: To determine whether there is an increased risk of hip fracture associated with the use of proton pump inhibitors in a Mediterranean area after adjusting for other potential risk factors. METHODS: Retrospective multicenter case-control study carried out in 6 primary health care centers in Catalonia, Spain. Cases were patients aged 50years and over with a fragility hip fracture registered between January 2007 and December 2010, matched with 2 controls by sex and age. DATA COLLECTED: use of proton pump inhibitors (type, dosage) in the 5years previous to the hip fracture, socio-demographic data, body mass index, alcohol and tobacco consumption as well as health conditions and drugs associated with an increase risk of fragility hip fracture. RESULTS: 358 cases were matched with 698 controls. The mean age was 82years old in both groups. Women represented 77.1% in the case group and 76.9% in the control group. Crude association between proton pump inhibitors and hip fracture was 1.44 (95% CI, 1.09-1.89) and adjusted OR was 1.24 (95% CI, 0.93-1.65). No association was found with the continuous or discontinuous use of proton pump inhibitors, OR 1.17 (95% CI, 0.77-1.79), and OR of 1.16 (95% CI, 0.85-1.60) respectively. No association was found when restricting the analysis by sex, OR of 1.19 (95% CI, 0.27-5.14) or by age, younger or older than 80years, OR of 0.72 (95% CI, 0.24-2.15). CONCLUSION: The use of proton pump inhibitors was not associated with an increased risk of hip fracture after adjusting for other risk factors in a Mediterranean area. This result suggests the existence of protective environmental factors linked to this southern area of Europe that eventually could compensate for the potential harm produced by proton pump inhibitors.

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 Ca(2+) have been found to essential for the formation of stable ion complexes, which were the starting point of calcium phosphate clusters by incorporating PO3(4) from the solution.