This book focuses on the latest developments in molecular mechanics and modeling research. Included in this book are chapters reviewing the progress of the bridging cell method (BCM) in its formulation and its nanostructure and material modeling applications; an analysis of the reaction selectivity of alanine racemase mutants; and a step-wise process for inferring the stereo structure of proteins constructed using related stereo structures. Lastly, molecular mechanics based models have proven to provide a representation of average carbon porosity and enable computational estimates of molecule-surface interaction energies. In the last chapter, the authors focus on graphene layer pore models for molecule-surface binding energies.