Chemical tools, which enable highly specific, selective observation of chemical orbiological processes at a molecular level, are extremely powerful resources for the building of knowledge across interconnected research fields. A synthetic approach enables fine-tuning of a probe’s activity and allows visualization of a mechanism or interaction at a molecular level. These tools can be used as complements to analytical techniques such as microscopy and spectroscopy to gain information regarding a chemical process, interaction, or material. The best-known application of these tools is to chemical biology, but fields outside of the traditional academic environment, such as museum conservation science, benefit from a creative synthetic approach as well. This thesis will explore several applications of novel chemical tools, from fluorescent dyes, to tools for controlling protein-protein interactions, to complex metal substrates for surfaceenhanced Raman spectroscopy (SERS). The first part of this thesis will discuss the synthesis of tools for chemically induced dimerization (CID) of proteins and the development of a quantitative, microscopy-based assay for the evaluation and optimization of linker structure for heterobifunctional chemical tools. Next, the synthesis of fluorogenic, pH sensing dyes and preliminary work developing a photocleavable protecting group (PPG) based on the dimethylamino quinoline scaffold will be presented. Finally, pivoting from chemical biology to conservation science, the use of gold raspberry metamolecules (RMMs) for on-fiber SERS analysis of organic dyes will be discussed.