Polyelectrolytes are charged polymers used in a variety of applications spanning across many areas. The physical behaviour of polyelectrolytes in solution is influenced by several factors such as pH or ionic strength, charge density, concentration, chemical nature of the polymer, molecular weight, thermodynamic quality of solvent etc. We present atomistic modeling studies of a fundamental nature on the variation of hydrophobic structure and stereochemistry of polar polymers, polyelectrolytes and oppositely charged polyelectrolyte complexes in salt-free and aqueous salt solution. Studies were carried out using different force-fields. Simulations are able to capture the conformations of anionic polyelectrolytes of different stereochemical configurations in agreement with experimental observations. An analysis of intermolecular structure, chain conformations, dynamics of conformations and hydrogen bonds, polymer hydration, counter-ion condensation, and molecular thermodynamics, was carried out, as a function of molar composition and charge density of the polymers. The contributions of conformations, non-bonded dispersion and electrostatic intermolecular interactions to molecular thermodynamics was analyzed. The molecular mechanism for the formation of PEC was studied for uncharged as well as charged systems. PEC complex formation occurs in a two-step process by diffusion of chains in solution followed by conformational rearrangement. In the study of the PEC formation in oppositely charged polymers the MD simulations showed the formation of PEC coacervates of PAH and PMA in solutions. Thermodynamically and structurally, stronger complexes are formed at 1:1 molar ratio and at higher charge density. The formation and molecular characteristics of the non-ionic complex of PEO and PAA in the presence of NaCl (salt) was studied as a function of salt concentration. The PAA/PEO complex is thermodynamically more stable and becomes more spherical at higher salt concentration. The thermodynamic show a favorable result towards PAA/PEO complex formation with an increase in salt concentration that is in agreement with the experimental data.