ANNUAL REPORT 2011 - Instituto de Estructura de la Materia

Coarse-grained (CG) potentials to study polymer crystallization. The formation of polymer nuclei is the result ofthe folding back and forth into stems of the chain perpendicular to the lamellar surface. It is well accepted thatexperiments cannot track the evolution of the system from the motion of individual polymer chains in the time scalein which the order events may occur. In this line, computer simulations represent an alternative way to shed light onthe crystallization mechanisms of polymers. However, the study of polymer crystallization with atomistic computersimulations is a difficult task, since one needs huge computational resources. One way to construct models with lesscomputational effort is to average out the fast motions (an unimportant in the required time scale) removing some ofthe atomistic degrees of freedom. Thus, the hard atomistic potentials are replaced by mean-force potentials. Thesepotentials are derivated from atomistic simulations of small systems by using the iterative inverse Boltzmannmethod. We have performed studies of the crystallization processes of PVA and PE with different degree ofbranching. In general, the CG models reproduce the atomistic behaviors and, when possible, the simulationsreproduce the available experimental data, i.e. crystallization, density and molecular size as a function of thebranches.Simulation of the isothermal crystallization of polyethylene in presence of nanotubes.The main objective of thiswork consisted in the study of the carbon nanotube effect on the isothermal crystallization of polyethylene at 300K.This was accomplished by molecular dynamics simulations of pure polyethylene and ethylene/1-hexene copolymersin presence of a carbon nanotube. The nanotube presence offers a contact surface suitable to nucleation and wherethe crystal growth of the polymer chain is favoured. However, the polymer chain branching limits the crystalliteformation even in presence of the carbon nanotube. In general, these nanostructured models showed higher orderand crystallinity that can be reflected in an improvement on the mechanical properties of these materials.MOBILITY, ORDER AND NANOSTRUCTURE IN MACROMOLECULAR SYSTEMSThe study of the physical properties in the melt of molecular models of polyolefins, blends and nanocomposites hasallowed study the effects of the molecular architecture in emerging physical propeties. The specific properties areespecially interesting in the case of blends and nanocomposites, as emerging phenomena seem to be related tospecific interactions betweent the components of the systems. In what the nanostructure and solid state propertiesconcerns, an exhaustive study of the semicrystalline molecular models, blends and naocomposites has beenperformed using differential scanning calorimetry, wide angle X-ray scattering and dynamic-mechanical analysis.The results obtained allow getting a deeper understanding about the complex nature of the phase structure of thesystems and on the relationship between nanostructure and macroscopic physical properties. Additionally, thecrystalization process in dilute solution has been studied by transmision electron microscopy in polyolefin molecularmodels. This study stablishes the strong effect of branching in crystal size and habit, in agreement with our atomisticcomputer simulations.SIMULATION OF BIOMACROMOLECULAR SYSTEMSSimulation of dipeptide amino acids in aqueous solution. Dipeptide amino acids are important molecules becausethey are suitable models for the protein “bricks”. The study of the predominant conformations of all possibledipeptides is relevant to understand the secondary structural elements of proteins. We have combined umbrellasampling molecular dynamics simulations (USMD) and multiple Bennet acceptance ratio (MBAR) estimators tocalculate the intrinsic conformations for each of the 19 amino acids, except proline. Our results confirm thatdipeptide extended conformations (P II and β) are more populated than the helical α conformations, that in somecases is opposed to the simulation results in the literature. This difference has been attributed to the combination ofUSMD/MBAR methodology with OPLS-AA force field. Moreover, our results show a better agreement withrecently published propensities obtained by IR and Raman spectroscopy on the same amino acid dipeptides. Thehydrogen bonds between water and dipeptides have been widely discussed. We have found that extendedconformations have largest probabilities to form H bonds with water than helical ones. In the case of alanine, wehave performed high level ab-initio molecular dynamics simulations (Car-Parrinello) to study these nonbondedinteractions between solvent and dipeptide. The high level calculations are in good agreement with the results fromboth USMD/MBAR simulations and experiments. It is worth to point out that this scientific activity started througha publication with a high impact in the media (V. Cruz, J. Ramos and J. Martínez-Salazar, “Water-mediatedconformations of the alanine dipeptide as revealed by distributed umbrella sampling simulations, QuantumMechanics based-calculations and experimental data”, The Journal of Physical Chemistry B 115, 4880-4886,2011).ERBB receptors.The aberrant overexpression of some members of the Epithelial Growth Factor Receptor (EGFRor ERBB) family is associated to a poor prognosis in several cancer types, in particular, breast cancer. ERBB2 andERBB3 are two ERBB family members that are used as biomarkers correlated with more aggressive tumours. Thesetransmembrane proteins are associated to cellular proliferation and growth and are considered important targets foranti-cancer therapies.In our research group, molecular dynamics simulations at an atomistic scale are being done77