Nanoscience and nanotechnology present challenges beyond understanding the nanoscale systems. Challenges include designing, synthesizing, and interacting with the larger world, as well as achieving large-scale production. Large-scale manufacturing is important for making nanotechnology practical and applicable in society. Commercial enterprises require a full understanding of materials and precise control over the manufacturing process within specific limits before investing in large-scale production. While empirical knowledge gained from experimental characterization has traditionally been the foundation for understanding and producing larger-scale systems, the complexity and dependence on molecular composition and structures at the nanoscale make it impossible to rely solely on experimentation. That is where molecular modeling comes into play. Tools like electronic structure modeling, molecular simulation, and mesoscale modeling are becoming increasingly important in characterizing nanoscale systems. Nanoscience has the potential to revolutionize science and technology. Nanoscale structures often involve different materials, making experimental characterization difficult. Manipulation of nanoscale structures at the larger macroscale is necessary. Bridging the gap between nanoscale and larger scales requires new theories and methods. Device simulation, with a focus on quantum effects, plays a vital role in the success of the semiconductor industry. With the expanding design space in nanoelectronics and the abundance of material systems and design concepts, simulation tools are carefully selected to capture the appropriate quantum mechanical effects, ensuring accurate results. This chapter explores various modeling and simulation methods for functionalized nanomaterials in electronic and optoelectronic devices, highlighting the importance of precise quantum effects representation through appropriate simulation tool choices.