The interactions of alkali metal cations (M(+) = Li(+), Na(+), K(+), Rb(+)) with the amino acid cysteine (Cys) are examined in detail. Experimentally, bond energies are determined using threshold collision-induced dissociation of the M(+)(Cys) complexes with xenon in a guided ion beam mass spectrometer. Analyses of the energy dependent cross sections provide 0 K bond energies of 2.65 +/- 0.12, 1.83 +/- 0.05, 1.25 +/- 0.03, and 1.06 +/- 0.03 eV for complexes of Cys with Li(+), Na(+), K(+), and Rb(+), respectively. All bond energy determinations include consideration of unimolecular decay rates, internal energy of reactant ions, and multiple ion-molecule collisions. Ab initio calculations at the MP2(full)/6-311+G(2d,2p), B3LYP/6-311+G(2d,2p), and B3P86/6-311+G(2d,2p) levels with geometries and zero-point energies calculated at the B3LYP/6-311G(d,p) level for the lighter metals show good agreement with the experimental bond energies. For Rb(+)(Cys), similar calculations using the HW* basis set and ECP underestimate the experimental bond energies, whereas the Def2TZVP basis set yields results in good agreement. Ground state conformers are tridentate for Li(+) and Na(+), and subtle changes in the Cys side-chain orientation are found to cause noticeable changes in the alkali metal binding energy. For K(+) and Rb(+), tridentate and carboxylic acid bound (both charge-solvated and zwitterionic) structures are nearly isoenergetic, with different levels of theory predicting different ground conformers. The combination of this series of experiments and calculations allows the influence of the sulfur functional group of Cys on the overall binding strength to be explored. Comparison to previous results for serine elucidates the influence of sulfur for oxygen substitution.

Upon oxidation of the heterocyclic ring in 2′-deoxyguanosine (dG), the initial electrophilic intermediate displays a wide range of reactivities with nucleophiles leading to many downstream products. In the present study, the product profiles were mapped when aqueous solutions of dG were allowed to react with NH4Cl in the presence of the photooxidants riboflavin and Rose Bengal as well as the diffusible one-electron oxidant Na2IrCl6. Product characterization identified the 2′-deoxyribonucleosides of spiroiminodihydantoin, 5-guanidinohydantoin, and oxazolone resulting from H2O as the nucleophile. When NH3 was the nucleophile, a set of constitutional isomers that are diastereotopic were also observed, giving characteristic masses of dG + 31. ESI+-MS/MS of these NH3 adducts identified them to be spirocycles with substitution of either the C5 or C8 carbonyl with an amine. The NH3 adducts exhibit acid-catalyzed hydrolysis to spiroiminodihydantoin. Quantification of the NH3 and H2O adducts resulting from oxidation of dG in the nucleoside, single-stranded, and duplex oligodeoxynucleotide contexts were monitored allowing mechanisms for product formation to be proposed. These data also provide a cautionary note to those who purify their oligonucleotide samples with ammonium salts before oxidation because this will lead to unwanted side reactions in which ammonia participates in product formation.