This chapter deals with studies of the structural, electronic, optic, and catalytic properties of transition metal nanoclusters using molecular modeling techniques, often denoted as Computational Chemistry. Over the past two decades, in silico (performed on a computer or via computer simulation) study of materials has become an important tool in both university and industrial R & D laboratories in the development of new or improved materials ranging from catalysts to electronic and optic materials. The chapter begins with a brief description of in silico synthesis and characterization of transition metal nanoclusters followed by presentation of in silico studies of a few functionalities of transition metal nanoclusters: nanocatalysts for O₂ reduction, CH₄ dehydrogenation, as well as sinter-resistant Ir nanoclusters. Also, this chapter covers the in silico studies of Au nanoclusters as regulator for chiral separation, Pd nanoclusters as CH₄ sensors, and Ag nanoclusters as conductive ink.