Date of Award


Document Type

Union College Only

Degree Name

Bachelor of Science






Old Yellow Enzyme is an interesting protein clue to its involvement in many biochemical systems, such as bioluminescence and degradation of variety of substrates. The flavin mononucleotide (FMN) is the active site of the protein. The FMN is an isoalloxazine ring with a phospholipid tail, which attaches to the protein through a phosphate group and hydrogen bonding in the hydrophilic section of the ring system. My research is a theoretical, computational calculation, which uses Spartan, a quantum mechanical calculation program, to determine how the dipole moment and electrostatic charges change upon the substitution of the FMN and within the protein environment. The geometry optimization of flavin used AM l and MNDO which are both semi-empirical quantum mechanical programs. After optimization, the dipole moment and the electrostatic charges were calculated. The same steps were executed for the flavin within the protein environment. 8-azido-FMN and 6-sulfoxo-FMN were also studied to determine the effect of ring substitution on charge distribution. Before the calculations could be performed, the flavin and the protein environment had to be modified. The phospholipid tail of the Flavin was replace by a methyl group. The protein itself was modeled by "overlay" protein molecules which are close to flavin in the crystal structure. These overlay molecules were placed in the same orientation as found in the real protein and constrained to known distances from the ring system. All of these modifications are presumed not to affect the calculations since no π electrons were removed from the flavin or the protein. The evidence collected showed that the dipole moment of flavin significantly changed when placed in a "protein" environment. The electrostatic charges also changed upon placement into the "protein" environment. Upon comparing the changes in the electrostatic charge to the resonance structures of the flavin, the positive and negative charges occurred on the same atoms that have a positive or negative charge in the resonance structures. This pattern support the theory that the flavin is stabilized by two or more resonance structures within the protein.