Chemical graph theory provides useful tools such as molecular descriptors to develop strong intrinsic relationship between the physicochemical features of chemical compounds and their molecular graphs. The study of molecular descriptors provides a theoretical basis for the fabrication of chemical materials and is helpful in making up for the lack of chemical experiments. There are two prominent types of molecular descriptors; the topological indices and counting polynomials. Further, topological indices can be categorized in two major classes: one class is based on degree and the other class is based on distance. In this thesis, we present the study of certain topological indices belonging to degree- and distance-based classes and counting polynomials for some well-known nanostructures. We also present a comparative study between different topological indices belonging to degree- and distance-based classes for general graphs. In addition, we study the para-line transformation of graphs and obtain the general expressions of certain topological indices for this transformation. We achieve the lower and upper bounds of certain distance-based topological indices for the para-line transformation of graphs.