Reaction products in mass spectrometry elucidated with infrared spectroscopy

Infrared multiple photon dissociation spectroscopy of sodium and potassium chlorate anions

The structures of gas-phase, metal chlorate anions with the formula [M(ClO(3))(2)](-), M = Na and K, were determined using tandem mass spectrometry and infrared multiple photon dissociation (IRMPD) spectroscopy. Structural assignments for both anions are based on comparisons of the experimental vibrational spectra for the two species with those predicted by density functional theory (DFT) and involve conformations that feature either bidentate or tridentate coordination of the cation by chlorate. Our results strongly suggest that a structure in which both chlorate anions are bidentate ligands is preferred for [Na(ClO(3))(2)](-). However, for [K(ClO(3))(2)](-) the best agreement between experimental and theoretical spectra is obtained from a composite of predicted spectra for which the chlorate anions are either both bidentate or both tridentate ligands. In general, we find that the overall accuracy of DFT calculations for prediction of IR spectra is dependent on both functional and basis set, with best agreement achieved using frequencies generated at the B3LYP/6-311+g(3df) level of theory.

Evidence of diketopiperazine and oxazolone structures for HA b2+ ion

Peptide fragmentation can lead to an oxazolone or diketopiperazine b(2)(+) ion structure. IRMPD spectroscopy combined with computational modeling and gas-phase H/D exchange was used to study the structure of the b(2)(+) ion from protonated HAAAA. The experimental spectrum of the b(2)(+) ion matches both the experimental spectrum for the protonated cyclic dipeptide HA (a commercial diketopiperazine) and the theoretical spectrum for a diketopiperazine protonated at the imidazole pi nitrogen. A characteristic band at 1875 cm(-1) and increased abundance of the peaks at 1619 and 1683 cm(-1) indicate a second population corresponding to an oxazolone species. H/D exchange also shows a mixture of two populations consistent with a mixture of b(2)(+) ion diketopiperazine and oxazolone structures.

Spectroscopic evidence for mobilization of amide position protons during CID of model peptide ions

Infrared multiple photon dissociation (IRMPD) spectroscopy was used to study formation of b2+ from nicotinyl-glycine-glycine-methyl ester (NicGGOMe). IRMPD shows that NicGGOMe is protonated at the pyridine ring of the nicotinyl group, and more importantly, that b2+ from NicGGOMe is not protonated at the oxazolone ring, as would be expected if the species were generated on the conventional bn+/yn+ oxazolone pathway, but at the pyridine ring instead. IRMPD data support a hypothesis that formation of b2+ from NicGGOMe involves mobilization and transfer of an amide position proton during the fragmentation reaction.

Infrared consequence spectroscopy of gaseous protonated and metal ion cationized complexes

In this article, the new and exciting techniques of infrared consequence spectroscopy (sometimes called action spectroscopy) of gaseous ions are reviewed. These techniques include vibrational predissociation spectroscopy and infrared multiple photon dissociation spectroscopy and they typically complement one another in the systems studied and the information gained. In recent years infrared consequence spectroscopy has provided long-awaited direct evidence into the structures of gaseous ions from organometallic species to strong ionic hydrogen bonded structures to large biomolecules. Much is being learned with respect to the structures of ions without their stabilizing solvent which can be used to better understand the effect of solvent on their structures. This review mainly covers the topics with which the author has been directly involved in research: structures of proton-bound dimers, protonated amino acids and DNA bases, amino acid and DNA bases bound to metal ions and, more recently, solvated ionic complexes. It is hoped that this review reveals the impact that infrared consequence spectroscopy has had on the field of gaseous ion chemistry.

Vibrational spectroscopy of bare and solvated ionic complexes of biological relevance

The low density of ions in mass spectrometers generally precludes direct infrared (IR) absorption measurements. The IR spectrum of an ion can nonetheless be obtained by inducing photodissociation of the ion using a high-intensity tunable laser. The emergence of free electron lasers (FELs) and recent breakthroughs in bench-top lasers based on nonlinear optics have now made it possible to routinely record IR spectra of gas-phase ions. As the energy of one IR photon is insufficient to cause dissociation of molecules and strongly bound complexes, two main experimental strategies have been developed to effect photodissociation. In infrared multiple-photon dissociation (IR-MPD) many photons are absorbed resonantly and their energy is stored in the bath of vibrational modes, leading to dissociation. In the "messenger" technique a weakly bound van der Waals atom is detached upon absorption of a single photon. Fundamental, historical, and practical aspects of these methods will be presented. Both of these approaches make use of very different methods of ion preparation and manipulation. While in IR-MPD ions are irradiated in trapping mass spectrometers, the "messenger" technique is generally carried out in molecular beam instruments. The main focus of this review is the application of IR spectroscopy to biologically relevant molecular systems (amino acids, peptides, proteins). Particular issues that will be addressed here include gas-phase zwitterions, the (chemical) structures of peptides and their collision-induced dissociation (CID) products, IR spectra of gas-phase proteins, and the chelation of metal-ligand complexes. Another growing area of research is IR spectroscopy on solvated clusters, which offer a bridge between the gas-phase and solution environments. The development of state-of-the-art computational approaches has gone hand-in-hand with advances in experimental techniques. The main advantage of gas-phase cluster research, as opposed to condensed-phase experiments, is that the systems of interest can be understood in detail and structural effects can be studied in isolation. It will be shown that IR spectroscopy of mass-selected (bio)molecular systems is now well-placed to address specific questions on the individual effect of charge carriers (protons and metal ions), as well as solvent molecules on the overall structure.

Spectroscopic evidence for an oxazolone structure of the b(2) fragment ion from protonated tri-alanine

Infrared multiple photon dissociation (IRMPD) spectroscopy is used to identify the structure of the b(2)(+) ion generated from protonated tri-alanine by collision induced dissociation (CID). The IRMPD spectrum of b(2)(+) differs markedly from that of protonated cyclo-alanine-alanine, demonstrating that the product is not a diketopiperazine. Instead, comparison of the IRMPD spectrum of b(2)(+) to spectra predicted by density functional theory provides compelling evidence for an oxazolone structure protonated at the oxazolone N-atom.

Structure, vibrational spectra, and unimolecular dissociation of gaseous 1-fluoro-1-phenethyl cations

The multiple CF bond character of PhCFMe (+) ions has been examined by means of theory, vibrational spectroscopy of the gaseous ions, and unimolecular decomposition chemistry. Atoms in Molecules analysis of DFT wave functions gives a CF bond order of n = 1.25 (as compared with n = 1.38 for Me 2CF (+), relative to n = 1 for fluoromethane and n = 2 for diatomic CF (+)), which is consistent with calculations of adiabatic CF stretching frequencies (nu CF). Experimental gas phase IR spectra, recorded by means of resonant multiphoton dissociation (IRMPD) using a free-electron laser connected to an FTICR mass spectrometer, show good agreement with predicted band positions for five deuterated isotopomers of PhCFMe (+). Metastable ion decompositions of deuterated analogues of PhCFMe (+) show the same HF/DF loss patterns as those produced by IRMPD. The evidence supports the conclusion that PhCFMe ions retain structural integrity until they become sufficiently excited to dissociate, whereupon they undergo intramolecular hydrogen scrambling that is competitive with HF/DF expulsion. Relative rates of hydrogen transposition and unimolecular dissociation are extracted from relative experimental fragment ion abundances. The predominant decomposition pathway is inferred to operate via a five-center transition state, as opposed to a four-center transition state for HF loss from gaseous Me 2CF (+).

The C-O stretch as an unprecedently large spectral marker for the electron transfer between Copper(II) and a phenolate anion

An unprecedented red shift of more than 200 cm(-1) in the vibrational frequency of the C-O bond in the [Cu(PhO)Ln]+ complex (PhO = phenoxy), dependent on the number n of additional ligands L, is reported. Upon change of n from 1 to 2, the spin density is shifted from the aromatic ring to the oxygen and copper atoms, which is reflected in the bond order and thus vibrational frequency of the C-O bond.