Ligand-protected noble metal nanoclusters are of interest for their potential applications in areas such as bioimaging, catalysis, photocatalysis, and solar energy harvesting. These nanoclusters can be prepared with atomic precision, which means that their stoichiometries can be ascertained; the properties of these nanoclusters can vary significantly depending on the exact stoichiometry and geometric structure of the system. This leads to important questions such as: What are the general principles that underlie the physical properties of these nanoclusters? Do these principles hold for all systems? What properties can be "tuned" by varying the size and composition of the system? In this Account, we describe research that has been performed to analyze the electronic structure, linear optical absorption, and excited state dynamics of thiolate-stabilized noble metal nanoclusters. We focus primarily on two systems, Au(SR) and Au(SR), as models for understanding the principles underlying the electronic structure, optical properties, luminescence, and transient absorption in these systems. In these nanoclusters, the orbitals near the HOMO-LUMO gap primarily arise from atomic 6sp orbitals located on Au atoms in the gold core. The resulting nanocluster orbitals are delocalized throughout the core of these systems. Below the core-based orbitals lies a set of orbitals that are primarily composed of Au 5d and S 3p atomic orbitals from atoms located around the exterior gold-thiolate oligomer motifs. This set of orbitals has a higher density of states than the set arising from the core 6sp orbitals. Optical absorption peaks in the near-infrared and visible regions of the absorption spectrum arise from excitations between core orbitals (lowest energy peaks) and excitations from oligomer-based orbitals to core-based orbitals (higher energy peaks). Nanoclusters with different stoichiometries have varying gaps between the core orbitals themselves as well as between the band of oligomer-based orbitals and the band of core orbitals. These gaps can slow down nonradiative electron transfer between excited states that have different character; the excited state electron and hole dynamics depend on these gaps. Nanoclusters with different stoichiometries also exhibit different luminescence properties. Depending on factors that may include the symmetry of the system and the rigidity of the core, the nanocluster can undergo large or small nuclear changes upon photoexcitation, which affects the observed Stokes shift in these systems. This dependence on stoichiometry and composition suggests that the size and the corresponding geometry of the nanocluster is an important variable that can be used to tune the properties of interest. How does doping affect these principles? Replacement of gold atoms with silver atoms changes the energetics of the sp and d atomic orbitals that make up the nanocluster orbitals. Silver atoms have higher energy sp orbitals, and the resulting nanocluster orbitals are shifted in energy as well. This affects the HOMO-LUMO gap, the oscillator strength for transitions, the spacings between the different bands of orbitals, and, as a consequence, the Stokes shift and excited state dynamics of these systems. This suggests that nanocluster doping is one way to control and tune properties for use in potential applications.