In this paper, we study the implementation of the Berry approach as expressed in his seminal publication (1984 Proc. R. Soc. Lond. A 392 45) within Born-Oppenheimer molecular systems (1927 Ann. Phys., Lpz. 84 457). This was done with the purpose of revealing the relation between the various timedependent magnitudes in the adiabatic limit and their time-independent counterparts. The two main results are: (1) in the adiabatic limit, a single Born-Oppenheimer state becomes an eigenstate of the system during the excursion of a system along a given contour, and (2) at the end of a closed contour, the topological phases associated with the states that moved adiabatically along a closed contour are well presented by the diagonal D-matrix as obtained from the time-independent treatment. The theoretical study is supported by a detailed numerical study carried out for two ab initio molecular systems, namely the (Na, H 2 ) and the (H, H 2 ) systems.