This thesis demonstrates the application of single-walled carbon nanotubes (SWCNTs) as single-digit nanopores for molecular sieving and addresses a fundamental challenge pertaining to controlled synthesis of organic color-centers (OCCs) on the sp2 carbon lattice of SWCNTs. First, I describe a hyperspectral single-defect photoluminescence imager system that provides both hyperspectral imaging and super-resolution capabilities in the shortwave infrared. Second, I aim to understand the relationship between nanotube photoluminescence and encapsulated molecules. Using carbon nanotubes with sub-1 nm pores, I demonstrate molecular sieving of n-hexane from cyclohexane, which are nearly identical in size. Furthermore, I discovered a light irradiation method to drive structural transformation of OCCs which allow us to narrow the spectral distribution of defect emissions by 26%. Finally, I show that [2+2] cycloaddition can efficiently create OCCs. Remarkably, this novel defect chemistry reduces the number of OCC bonding configurations from six, which are commonly observed with monovalent defect chemistries, to just three. This work may have broad implications to the potential applications of SWCNTs and OCCs in chemical sensing, bioimaging, and quantum information science.