Four acceptor-donor organic conjugated molecules based on thieno[3,4-b]pyrazine-terthienyls were analyzed in order to explore the effect of the donor substituent on their molecular structures, electronic and optical properties. Density Functional Theory (DFT) and Time-Dependent Density Functional Theory (TD/DFT) calculations were carried out employing the B3LYP hybrid functional in combination with the 6-31G(d,p) basis set. The results suggests that the addition of electron-donating substituents to the conjugated molecules can diminish their energy gap value, which is beneficial to the photon harvesting. The lowest-lying absorption spectra of compounds substituted with electron donor groups exhibited a red-shift and a high oscillation factor compared with the unsubstituted molecule. Additionally, the ionization potential (IP), electron affinity (EA), reorganization energy (λ) and open-circuit voltage (Voc) of the molecules were evaluated. According to these values, the molecules show good photovoltaic properties, and efficient charge transfer for hole and electron and balanced charges.