This is an exciting time for studying thiolated ld nanoclusters. Single crystal structures of Au₁₀₂(SR)₄₄ and Au₂₅(SR)₁₈^- (—SR being an organothiolate group) bring both surprises and excitement in this field. First principles density functional theory (DFT) simulations turn out to be an important tool to understand and predict thiolated ld nanoclusters. In this review, I summarize the progresses made by us and others in applying first principles DFT to thiolated ld nanoclusters, as inspired by the recent experiments. First, I will give some experimental background on synthesis of thiolated ld nanoclusters, followed by a description of the recent experimental breakthroughs. Then I will introduce the superatom complex concept as a way to understand the electronic structure of thiolated ld nanoclusters or smaller nanoparticles. Next, I will describe in detail how first principles DFT is used to understand the Au-thiolate interface, predict structures for Au₃₈(SR)₂₄, screen od dopants for the Au₂₅(SR)₁₈^- cluster, design the smallest magic thiolated ld cluster, and demonstrate the need for the trimer protecting motif. I will conclude with a grand challenge: the real time monitoring of nucleation of thiolated ld nanoclusters.