Access Type

Open Access Dissertation

Date of Award

January 2012

Degree Type


Degree Name




First Advisor

Mary T. Rodgers


Absolute 18-crown-6 (18C6) binding affinities of the side chains of AAs in peptides and proteins were determined in a step by step fashion using guided ion beam tandem mass spectrometry techniques. Firstly, 18C6 binding affinities of several peptidomimetic bases (B) that serve as mimics of the side chains of Lys, Arg, and His and n-terminal amino group have been examined to provide initial estimates of the 18C6 binding affinities of the side chains of AAs. The Bs were extended to natural occurring AAs and further extended to acetylated AAs (AcAA) to determine the binding affinities of the side chains of AAs in peptides and proteins. The Bs examined here include isopropylamine (IPA), imidazole (IMID) and 4-methylimidazole (4MeIMID), 1 methylguanidine (MGD), methylamine (MA), ethylamine (EA), n-propylamine (NPA), n-butylamine (NBA), and 1,5-diamino pentane (DAP). The Bs were extended to five amino acids (AA), where AA = glycine (Gly), alanine (Ala), lysine (Lys), histidine (His), and arginine (Arg), and further extended to acetylated amino acids (AcAA), where AcAA = Nα-AcLys, Nβ-AcLys, Nα-AcArg, and Nα-AcHis.

Our measured 18C6 binding affinities of Bs, AAs, and AcAAs suggest that the side chains of Lys residues are the preferred binding site for 18C6 complexation in peptides and proteins. The n-terminal amino group provides another favorable binding site for 18C6. Trends in the 18C6 binding affinities exhibit an inverse correlation with the polarizability and proton affinity of the B and AA. Therefore, the ability of the n-terminal amino group to compete for 18C6 complexation is best for Gly and should become increasing less favorable as the size of the side chain substituent increases.

The proton affinity (PA) of 18C6 plays a critical role in the binding and CID behavior of proton-bound complexes between 18C6 and guest cations. Therefore, the PA of 18C6 is re-evaluated using competitive threshold collision-induced dissociation techniques. The PA determined here for 18C6 exhibits excellent agreement with M06 and B3LYP theories, and very good agreement with the value reported by Meot-Ner determined using high pressure mass spectrometry (HPMS) techniques, suggesting that the PA of 18C6 reported in the NIST Webbook and based on HPMS measurements by Kebarle and coworkers is overestimated.

The IRMPD action spectroscopy of (B)H+(18C6) complexes are examined using a FT-ICR MS coupled to a free electron laser. The structural information elucidated here supports the experimental measurements of the absolute 18C6 binding affinities of the basic amino acids and facilitates the understanding of the intrinsic factors that contribute to the strength and selectivity of binding and thus molecular recognition in SNAPP and related techniques.

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