Macromolecular soft materials offer tremendous versatility and design possibility to achieve novel functionalities for sustainability goals. They can be engineered to sequester ions from wastewater to combat pollution and recover elemental resources, or to transport ions for use as electrolytes in rechargeable batteries. Within these materials, the intricate interplay between chemically specific interactions and macromolecular entropy poses design challenges across various length scales. In this dissertation, diverse molecular simulation tools are employed to gain structural and dynamical insights. Supported by experimental evidence, these insights help advance the design of these materials. In the first past of this dissertation, atomistic molecular dynamic simulations are combined with various free energy methods to investigate self-assembled peptide amphiphile micelles that selectively capture and reclaim phosphate ions from water. Chapter 2 reports a prototype material that selectively captures and releases phosphate controlled by a pH trigger. Simulations identified the significance of chain flexibility and binding entropy as design factors. In Chapter 3, we examine these design elements using multi-component micelles and apply them to propose a de novo micelle design. In the second part, we focus on uncovering fundamental lithium-ion transport behavior in nonhomogeneous solid polymer electrolytes, using multiscale molecular dynamics simulations combined with network analysis. Chapter 4 focuses on graft solid polymer electrolytes to elucidate the role of polymer architecture on lithium-ion transport. The investigation reveals heterogenous dynamical and ion solvation behaviors along the grafted side chains. Chapter 5 examines the impact of monomeric mixing on lithium-ion transport by comparing a blend polymer electrolyte with a block copolymer counterpart. A graph-based transport model is proposed to quantify this effect. Chapter 6 builds upon our knowledge about graft architecture and monomeric mixing to characterize polymer electrolytes grafted with mixed polarity side chains, where entropic penalty, rather than polarity, dictates the solvation behavior of lithium ions. In Chapter 7, we summarize our findings and discuss a few interesting directions for future research.