Fundamental studies of the structures, energetics and collision dynamics of large molecules in the gas phase

Citation

Marzluff, Elaine M. (1995) Fundamental studies of the structures, energetics and collision dynamics of large molecules in the gas phase. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/ecqj-my65. https://resolver.caltech.edu/CaltechETD:etd-10172007-112712

Abstract

The construction and application of an external source Fourier transform ion cyclotron resonance mass spectrometer equipped with a fast atom bombardment source for studies of biological molecules is described. The instrument features an octopole ion guide, Shulz-Phelps ionization gauge and 7-Tesla superconducting magnet and has been specifically designed for quantitative studies of biological molecules. The primary focus of the work described here has been the development of chemical and physical probes to examine the properties and structures of biomolecules in the gas phase.

The results of a complete study of the low energy dissociation pathways using off resonance collisional activation of deprotonated peptides is presented. The dissociation pathways are governed by the site of charge and yield partial C-terminus sequence information in favorable cases. Application of statistical RRKM calculations to these systems allows a qualitative understanding of the energetic changes associated with the observed dissociation processes. The bimolecular reactivity of these species was investigated. Several reactions taking advantage of the nucleophilicity of the deprotonated carboxylic group were observed. This is particularly noteworthy as there are few previously reported instances of bimolecular reactions (other than proton transfer) involving biological species in the gas phase.

The results of the above study identified a homologous system of deprotonated peptides which dissociate with similar activation parameters. This was used as a model system to investigate the effect of molecular size on the collisional activation process. Contrary to the common belief that it is inherently harder to activate large molecules and induce dissociation, it was discovered that molecules with many degrees of freedom dissociate more readily than molecules with fewer degrees of freedom. This is attributed to the ability of these molecules to easily deform and efficiently convert translational energy into internal excitation.

The mechanism of the collisional energy transfer was investigated using trajectory calculations with a molecular mechanics force field. The collisions appear to be impulsive in nature and energy transfer occurs on a timescale similar to a vibrational period. Large molecules have the ability to undergo several encounters with the collision gas in a single collision event, each encounter resulting in a significant amount of internal energy being transferred into internal modes.

A master equation analysis was applied to the off resonance collisional activation process in an attempt to obtain a more quantitative understanding of the dissociation energetics of large molecules. This analysis takes into account all processes contributing to the change in ion internal energy. The primary result of this analysis was the observation that a significant fraction of the ions formed in the collisional activation process have a large internal energy and are slow to collisionally relax under conditions employed in our experiments. A more thorough knowledge of this energy distribution is required before an analysis such as this can be used.

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