A fundamental study of the mechanics at the molecular scale and bridging it to the continuum level through multiscale modeling is the focus of this work. This work investigates how the material properties of nanoscale systems are influenced by the nonbonded interactions and molecular conformations. The molecular model is then bridged with the finite element model to link mechanics at nanoscale with the continuum scale. This work provides an unprecedented insight into how the interactions at the molecular scale influence mechanical properties at higher scales. Two materials are considered for the molecular modeling study: bone and Na-montmorillonite swelling clay. Bone is composed of composed of collagen molecules and hydroxyapatite in the molecular scale, which are organized into collagen fibril. The molecular dynamics study is carried out to study the nature of collagen-hydroxyapatite interface and the mechanics of collagen in bone. Furthermore, the molecular model of full-length collagen is built for the first time to show the differences in its conformation and deformation mechanism during pulling as compared to the short molecules, upon which the current understanding of is based. The mechanics of collagen is explained with the help of three-tier helical hierarchy not seen in short molecules. Two mechanisms of deformation and conformational stability of collagen are proposed: (i) interlocking gear analogy, and (ii) interplay between level-1 and level-2 hierarchies, the hydrogen bonds acting as an intermediary. The multiscale model of collagen fibril is developed by bridging nanomechanical molecular properties of collagen into the finite element model. This model shows that the molecular interactions between collagen and mineral significantly affect the mechanical response of collagen fibril. The deformation mechanism of collagen fibril and the effect of collagen crosslinks are also elucidated in this study. In recent years Na-montmorillonite has been proposed for bone regenerative medicine, besides other existing engineering applications. The molecular dynamics study of Na-montmorillonite at different levels of hydration is carried out to understand the role played by molecular interactions in the swelling behavior of Na-montmorillonite. This study greatly adds to our understanding of clay swelling, and provides important insights for modeling exfoliation and particle breakdown in clay.