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Date of Award


Document Type

Thesis - Pacific Access Restricted

Degree Name

Master of Science (M.S.)


Pharmaceutical and Chemical Sciences

First Advisor

Jianhua Ren

First Committee Member

Liang Xue

Second Committee Member

Ryan Moffet

Third Committee Member

William Stringfellow


This thesis discusses two major projects. The first project focuses on understanding the effect of chirality on intrinsic acidity of oligopeptides. Gas-phase acidity (ΔacidG) and related thermochemical parameters (ΔacidH, and ΔacidS), of model N- and C-terminal cysteine polyalanine peptides in which one L-alanine was substituted by a D-alanine viz. CAADA and AADAC, were measured by the extended Cooks kinetic method. Gas-phase acidities of CAADA and AADAC were measured to be about 318 kcal/mol and 322 kcal/mol, respectively. These values are different from the gas-phase acidities of the all L-amino acid containing analogues of the above peptides, but suggest that D-alanine containing peptides show the same trend as their all L-amino acid analogues with the N-terminal cysteine peptide being more acidic than the C-terminal cysteine peptide. However, the difference in the acidities of CAADA and AADAC is about 4 kcal/mol which is about half of the difference between their all L-amino acid analogues. These results also suggest that, presumably, a single L-alanine to D-alanine substitution has a moderate effect on the conformation of the respective peptides.

The aim of the second project is to understand how acidic amino acids influence peptide fragmentation during tandem mass spectrometric analysis. A series of model N- and C- terminal glutamic acid polyalanine and polyglycine (EAn, AnE (n=2,3); EGn (n=2,3), GnE (n=2-4)) and cysteine polyalanine (CAn, AnC (n=4-6)) peptides were studied. Primarily, EAn and EGn peptides formed bn ions. In contrast, while EOn peptides formed all yn ions, EAn peptides formed fewer yn ions. Similarly, AnE and GnE peptides also formed bn ions. No major differences were observed in yn ion formation. For both sets of peptides, water loss seemed to trend with the position of glutamic acid. CAn and AnC peptides also formed bn ions, just like their glutamic acid counterparts. However, yn ions were observed only for AnC peptides. For all sets of peptides, ions related to bn and yn ions were also observed.



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