Increases in the molecular length of narrow band gap conjugated chromophores reveal potentially beneficial optical and electronic properties, thermal stabilities, and high power conversion efficiencies when integrated into optoelectronic devices, such as bulk heterojunction organic solar cells. With the objective of providing useful information for understanding the transition from small-sized molecules to polymers, as well as providing a general chemical design platform for extracting relationships between molecular structure and bulk properties, we set out to vary the electron affinity of the molecular backbone. Therefore, a series of donor (D) acceptor (A) alternating narrow band gap conjugated chromophores were synthesized based on the general molecular frameworks: D-1-A(1)-D-2-A(2)-D-2-A(1)-D-1 and D-1-A(1)-D-2-A(2)-D-2-A(2)-D-2-A(1)-D-1. When the central electron-accepting moiety (A(2)) was varied or modified, two classes of molecules could be compared. First, we showed that the alteration of one single electron-accepting group, while maintaining the shape of the molecular framework, can effectively impact the optical properties and energy levels of the molecules. DFT ground state structure optimizations show similar "U" shape conformations among these molecules. Second, we examined how the site-specific introduction of fluorine atom(s) modifies the thermal properties in the solid state, while maintaining relatively similar optical and electrochemical features of interest. Structure property relationship of such molecular systems could be rationally evaluated in the aspects of thermal-responsive molecular organizations in the solid state and dipole moments both in the ground and excited states. The impact of molecular structure on charge carrier mobilities in field effect transistors and the performance of photovoltaic devices were also studied.