Honors Program

Honors in Physics and Astronomy

Date of Award


Thesis Professor(s)

David Close

Thesis Professor Department

Physics and Astronomy

Thesis Reader(s)

Frank Hagelberg, Scott Kirkby


Previous density functional theory (DFT) calculations of hyperfine coupling constants (HFCC) on single nucleic acid base radicals agree well with the EPR/ENDOR experiments’ values on radiation induced nucleic acid constituents radicals, except for four problem cases,1 namely the N1-deprotonated cytosine cation radical, the native guanine cation radical, the N3-deprotonated 5’-dCMP cation radical and the N7-H, O6-H protonated 5’-GMP anion. The main effort of the present work is to address these four discrepancies by using the highly parameterized density functional M05/6-2X and by including the crystalline environment’s H-bonding effects in the calculations. The geometries of the four model radicals are optimized within their single crystal environment using ONIOM technique. Then the spin density distributions and HFCCs of the radicals are examined within various scales of cluster models. The results obtained by including H-bonding environment are in strong agreement with the experimental values. The calculations show advantages of using the M05/62X functional rather than the B3LYP functional in obtaining more satisfactory HFCC results. However, the delocalization errors are encountered with both M05/6-2X and B3LYP functionals. Further development in eliminating delocalization errors in practical DFT approximations is suggested.

Document Type

Honors Thesis - Open Access

Creative Commons License

Creative Commons License
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