Chapter one and two introduce the raison d'etre for the research conducted and a background for the methods employed herein. Chapters three and four focus on the study of alanine, and the effects of solvation. Chapters five and six explore fragmentation models from development to general use. Chapter seven focuses on the use of molecular dynamics for solution phase chemical phenomena using the effective fragment potential. Chapter eight provides a general overview and summary of the projects explored in the dissertation.