A comparative study of 36 molecular descriptors derived from the topologicaldistance matrix and van der Waals space is carried out within this paper. They arepartitioned into 16 generalized topological distance matrix indices, 11 topologicaldistance indices known in the literature (seven obtained from eigenvalues/eigenvectors ofdistance matrix), and 9 van der Waals molecular descriptors. The generalized topologicaldistance indices, kδλ (λ = 1 – 3, k = 1 – 4), are introduced in this work on the basis ofreciprocical distance matrix. Intercorrelation analysis reveals that topological distanceindices mostly contain the same type of information, while van der Waals indices can bebound to the shape or the size of molecules. Furthermore, we found that topologicaldistance indices are good for describing molecular size, and they may be viewed as bulkparameters. The most accurate QSPR models for predicting boiling point of alkanes arebased on some of the generalized, eigenvalues/eigenvectors topological distance indicesand the van der Waals descriptors of molecular size.