The changes in molecular structure associated with the crystallization of the donor-acceptor complex HCN-BF3 are studied using density functional theory. Short-range dipole-dipole interactions have been attributed to be one of the main causes of the 0.84 Angstrom shortening of the B-N bond in the crystal phase compared to the gas phase. Natural bond orbital analysis is used to obtain information regarding the electron distribution and possible delocalization effects. The lone pair on the fluorine atoms shows significant delocalization toward the boron-nitrogen antibonding orbital, leading to substantial structural changes occurring that can be manipulated by increasing or decreasing the degree of overlap. Because the overlap is dependent on the position of the fluorine atom, the steric and electronic influences created by the surroundings of a molecular unit in the crystal are of considerable importance when the experimentally observed changes are explained.