John K. Merle

N-Protonated Isomers as Gateways to Peptide Ion Fragmentation

According to the popular “mobile proton model” for peptide ion fragmentation in tandem mass spectrometry, peptide bond cleavage is typically preceded by intramolecular proton transfer from basic sites to an amide nitrogen in the backbone. If the intrinsic barrier to dissociation is the same for all backbone sites, the fragmentation propensity at each amide bond should reflect the stability of the corresponding N-protonated isomer. This hypothesis was tested by using ab initio and force-field computations on several polyalanines and Leu-enkephalin. The results agree acceptably with experimental reports, supporting the hypothesis. It was found that backbone N-protonation is most favorable near the C-terminus. The preference for C-terminal N-protonation, which is stronger for longer polyalanines, may be understood in terms of the well known “helix macrodipole” in the corresponding helical conformations. The opposite stability trend is found for peptides constrained to be linear, which is initially surprising but turns out to be consistent with the reversed direction of the macrodipole in the linear conformation.

The chemistry of reactive radical intermediates in combustion and the atmosphere

Publisher Summary This chapter describes the chemistry of reactive radical intermediates in combustion and the atmosphere. Combustion processes convert chemical energy into heat and work, playing several important roles in society. Oxidation processes provide power to beneficiaries ranging from automobiles to electrical generators and atmospheric oxidation reactions impact a wide range of environmental phenomena. At high temperatures, methane oxidation is initiated through hydrogen atom abstraction by hydroxyl radical, oxygen atom, or hydrogen atom. Peroxy radical chemistry plays a substantial role in low-temperature combustion as opposed to the alkoxy radical chemistry of high-temperature combustion.The peroxy radicals constitute an important class of reactive intermediates with significant implications for low temperature combustion and atmospheric reactions. Phenylperoxyradical, originally assumed to be a factor in low-temperature combustion only, has actually been shown to play a substantial role in dictating the overall combustion trends of benzene. The chapter suggests that both hydrogen atom and alkyl group loss can contribute to the combustion of coal in initiation reactions.

Volatilization of Organotin Species from Municipal Waste Deposits: Novel Species Identification and Modeling of Atmospheric Stability

Organotin compounds are used as pesticides and fungicides as well as additives in plastics. This study identifies the de novo generation of novel volatile organotins in municipal waste deposits and their release via landfill gas. Besides tetramethyltin (Me(4)Sn), a strong neurotoxin, and 5 previously reported organotins, 13 novel ethylated, propylated, and butylated tetraalkyltin compounds were identified. A concentration of 2-4 μg of Sn m(-3) landfill gas was estimated for two landfill sites in Scotland. The atmospheric stability of Me(4)Sn and methylated tin hydrides was determined empirically in a static atmosphere in the dark and under UV light to simulate night- and daytime conditions. Theoretical calculations were carried out to help predict the experimentally obtained stabilities and to estimate the relative stabilities of other alkylated species. Assuming first-order kinetics, the atmospheric half-life for Me(3)SnH was found to be 33 ± 16 and 1311 ± 111 h during day- and nighttime conditions, respectively. Polyalkylation and larger alkyl substitutes tend to reduce the atmospheric stability. These results show that substantial concentrations of neurotoxic organotin compounds can be released from landfill sites and are sufficiently stable in the atmosphere to travel over large distances in night- and daytime conditions to populated areas.

Tryptic y ++ Fragment Ion Distributions Are Guided by Coulombic Repulsion

Ideal tryptic peptides contain only a single basic residue, located at the C-terminus. Collisional fragmentation of their doubly- or triply-protonated ions generates doubly-charged y++ fragment ions with modest intensities. The size distribution of the y++ fragments, when averaged over many spectra, corresponds closely to the expectations from charge-directed backbone cleavage and a Coulomb-Boltzmann distribution of mobile protons. This observation should be helpful in developing mechanistic models for y++ formation.