1. ‘Tertiary’ Structure in Gaseous Ions
Recently, we carried out a study of gas phase acidities of carboxylic acids in which the effects of alkyl chain length were examined [J.Phys.Chem.A., 103, 7008 (1999)]. This investigation showed that deprotonation of long chain carboxylic acids was remarkably favourable, in terms of enthalpy, but that the entropy changes associated with deprotonation could be extremely unfavourable. This was suspected to be due to a certain amount of coiling of the alkyl chain around the carboxylate anion moiety and this speculation was then verified by ab initio calculation. These observations have spurred us to undertake a general investigation of ions in which such ‘tertiary’ structural effects might be observed where, by analogy to structure in biopolymers, groups may be proximal in space which are not proximal in sequence. For example, the interactions of Cl- with a series of n-alkanes and cyclo-alkanes have been investigated using HPMS methods. To our initial surprise, no unusual entropic effects were observed for association of Cl- with the n-alkanes, indicating that no coiling of the alkyl chain was occurring about the Cl-. Ab initio calculations then revealed that the Cl- was in fact consistently localized near the center of the chain, resulting in several short Cl-H contacts, but with no serious restriction of rotations about more than 2 C-C bonds. We have now designed experiments in which we will attempt to ‘force’ a Cl- to be localized near one end of a long chain molecule in order to observe whether the chain will subsequently wrap around the Cl- to achieve additional stabilization due to this type of intramolecular solvation. The first series to be attempted will be methyl n-alkyl ethers where the length of the n-alkyl chain is allowed to systematically increase. Two bonding modes can be envisioned for the initial contact with Cl-: one in which a SN2 like back side attack occurs at the methyl group adjacent to the ether oxygen and a second involving a hydrogen bond like interaction with one or more C-H bonds. The first would be driven by the weak, but non-negligible, ion-local dipole, interaction, while the second would mimic the situation observed for the n-alkanes. A second, presumably stronger, driving force to localize the Cl- near one end would be to use methyl n- alkyl ketones where the larger carbonyl local dipole as well as the acidity of the hydrogens would dominate the directing force. Preliminary experiments with a series of fluorinated ethers have given us some initial indications of the relative importance of dipolar and hydrogen bonding effects. For example, entropy measurements suggest that Cl- associates with CF3OCH3 in a SN2 like complex while it interacts with CF2HOCF2H via a double hydrogen bond interaction which results in restriction of both CF2H- rotors. Following completion of these series of experiments involving Cl- interactions, a similar series of experiments will be initiated using a probe, spherical positive ion, such as Na+. Once such experiments are complete we would hope to have a much better understanding of the forces driving intramolecular interactions in large molecular complexes with charge centers. All studies will be accompanied by ab initio calculations to the extent that our computing resources are compatible with the size of the species involved.
2. Experimental Location of Transition States on Potential Energy Surfaces
In the course of developing the computational resources to carry out master equation modeling of black-body radiation induced dissociation it became apparent that our FTICR experiment and the associated computational packages could equally well be applied to the study of slow bimolecular ion-molecule reactions. For example, while exothermic proton transfer reactions are most frequently very rapid, analogous exothermic methyl cation transfer reactions are almost invariably slow. This is due to the fact that the former reactions are barrierless whereas the latter have a significant barrier, most often near the energy of the separated ion-molecule pair. A classic example is the reaction of protonated methanol with methanol to yield protonated dimethyl ether and water. We have studied the temperature dependence of the rate constant for this reaction in our FTICR system and obtained a barrier to methyl cation transfer which lies ~4 kcal mol-1 below the energy of separated reactants, in excellent agreement with the best available ab initio calculations. Further, when our RRKM modeling of some analogous reactions, such as protonated dimethyl ether plus dimethyl ether to yield trimethyloxomium and methanol, is used, we have observed that there is very poor agreement between calculated and observed rate data. We have exploited this observation to deduce that the potential energy surface is considerably more complex than our initial simple model and, in conjunction with ab initio calculation have been able to propose a more complicated surface with which we can model the rate data much more precisely. We now propose to apply this combined FTICR/ab initio/RRKM approach to a variety of other slow ion-molecule reactions in order to locate experimentally the transition states on complex potential energy surfaces with high intermediate barriers. This, combined with HPMS investigations of clustering energetics to locate the stable minima should allow us to generate complete, or nearly complete, potential energy surfaces for interesting reactions.
3. Protein Folding
Mass spectrometry cannot be limited to only physical chemistry, we must venture into a new era of the advancing trends in biochemistry. Recently, we have obtained a new Micromass Q-TOF Ultima Global for theses studies of proteins, particularly their rates and types of populations of folding and unfolding. The Q-TOF is fitted with a Z-spray, dual orthogonal sampling ESI source. The purpose of venturing into this relatively new field of research is to further a comprehensive and predictive understanding of proteins at a structural level has not been achieved. Complete characterization of a protein would require the interplay of three features: function, structure and dynamics. The extensive use of isotope hydrogen exchange is used for the purpose of studying protein structure and dynamics. Hydrogen exchange within proteins is measured for many reasons: detection of structural changes, dynamic or stability due to mutation, probing protein-protein interactions, and elucidation of protein folding. Furthermore, this technique has been used to explore folding or unfolding, conformational changes, structural heterogeneity, and effects of binding or aggregation of proteins. The research involves investigation of the protein, hisactophilin, which is a histidine-rich, actin-binding protein from the slime mold, Dictyostelium discoideum. This organism is a simple, unicellular organism whose cytoskeleton has many similarities to the cytoskeleton of higher organisms. As a result, this organism has developed into a model system for studying cytoskeleton structure and dynamics. The microfilament system of amoeboid Dictyostelium discoideum cells is associated with movement, chemotactic orientation during aggregation, and endocytosis during growth. Actin, which is the key constituent of this system, is interrelated with proteins that direct its polymerization, cross-linkage and membrane association. A number of actin-binding proteins including hisactophilin are correlated in structure and function to proteins of different species, including proteins that originate in vertebrate non-muscle and muscle cells. Scientists have conducted many different types of study on amide exchange in an effort to better understand the mechanisms involved in structural fluctuations or dynamics in proteins. It has been assumed by hydrogen/deuterium exchange that the slow exchanging amides do so via an EX2 mechanism. This concept of exchange has not been studied in depth, although many studies have been based on this assumption. The goal of this research is to complete a systematic study of protein folding of the protein hisactophilin using mass spectrometric hydrogen/deuterium exchange measurements. In particular, the slow exchangeable amides will be closely examined to determine and understand the mechanistic reaction underlying native exchange of these amides.
4. Radiative Activation and Deactivation of Gas-Phase Ions at Low Pressures