Molecular modeling of polymers and development of an octanol continuum solvation model

The content of this thesis can be broken into essentially two parts. The first half of the thesis is concerned with the study of organic and inorganic polymers using a variety of molecular modeling techniques. The second portion of the thesis pertains to the development of an octanol continuum solvation model and an investigation into the solvation properties of solutes in water-saturated 1-octanol. An examination of polycarbyne network backbone polymers using both experimental and theoretical methods is described in the first section in order to predict possible macroscopic structures for this class of polymer. Both quantum mechanical (semiempirical) and force field calculations of oligomers of these polymers indicated elongated bond lengths in the polymer backbone. This bond elongation is theorized to result in biradical formation within the polymer backbone, and is supported experimentally through spectroscopic analyses.; A second study in this thesis pertains to an investigation of the mechanism of ionic conduction in polyphosphazene polymers using molecular dynamics (MD) simulations. Structural properties of various polymer/salt complexes were examined and were found to be in support experimental NMR data. The theoretical results predict selective binding of ions to the polymers which lends information to the mechanism of ion conduction in this polymer electrolyte media.; The development of a continuum model for 1-octanol on the basis of the generalized Born/surface area (GB/SA) formalism is shown in the next section. The model was fit to reproduce experimental free energies of solvation for a training set of 66 diverse organic solutes, resulting in a 0.50 kcal/mol averaged unsigned error for the model. This model was used in conjunction with aqueous free energies of solvation to accurately calculate octanol/water partition coefficients, log P{dollar}sb{lcub}rm ow{rcub}.{dollar} In the final portion of the thesis, a solution phase study was undertaken in which water-saturated 1-octanol was the solvent. Free energies of solvation for a series of small organic solutes were calculated in this solvent mixture utilizing MD and free energy perturbation (FEP) methodologies. The results of these simulations compares well with experimental results and to those calculated using the GB/SA methodology.