We present a theoretical study of the elongation process of molecular junctions formed by octanedithiol molecule and Au electrodes. Five types of junctions that have different molecule-electrode coupling geometries are considered. It is found that the behavior of the H atom in the -SH group plays a crucial role in the system structure variation. The variation of the total energy and the average force needed to break the molecular junction are calculated, and each type of molecular junctions is found to have a characteristic breaking force. Comparing our theoretical results with those from experiment shows that the most probable coupling geometry was neglected in almost all the previous work. A dynamic analysis of the electronic structure of the molecular junctions is used to understand the variation of the system configuration.