A vibrational spectroscopic and computational study of gaseous protonated and alkali metal cationized G-C base pairs

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Structures and Unimolecular Reactivity of Gas-Phase [Zn(Proline-H)]⁺ and [Zn(Proline-H)(H₂O)]⁺

A combination of IRMPD spectroscopy, collision-induced dissociation, deuterium isotopic substitution, and computational chemistry was used to determine the structure and unimolecular chemistry of [Zn­(Pro-H)]⁺ and the singly hydrated complex in the gas phase. Five competing dissociation channels were observed: loss of H₂O, CO, CO₂, and HCOOH and the main fragmentation pathway, loss of neutral Zn. By comparing the IRMPD spectrum with the predicted IR spectra of the lowest energy structures, it was confirmed that [Zn­(Pro-H)]⁺ complex is deprotonated at the amine moiety, and a hydrogen from either C2 or C5 migrated to Zn²⁺. In this H-type complex, ZnH⁺ was chelated between the amine nitrogen and the carbonyl oxygen. Calculations of the potential energy surface revealed that the loss of neutral zinc is energetically more favorable than the loss of dehydrogenated proline leading to ZnH⁺ product. Furthermore, calculations on all five primary decomposition routes, all beginning with the lowest energy structure, revealed that loss of Zn has the lowest energy requirement, consistent with it being the most abundant product of unimolecular dissociation following collisional or IR multiphoton activation. For the singly hydrated complex, [Zn­(Pro-H)­(H₂O)]⁺, IRMPD spectroscopy confirms a structure with water added to the H-type structure and intramolecularly hydrogen bonded to the deprotonated amine site. This structure is not the lowest-energy [Zn­(Pro-H)­(H₂O)]⁺ isomer, but it is the one where water is added to the lowest energy [Zn­(Pro-H)]⁺ isomer

An IRMPD spectroscopic and computational study of protonated guanine-containing mismatched base pairs in the gas phase

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IRMPD Spectroscopic Study of Microsolvated [Na(GlyAla)]⁺ and [Ca(GlyAla–H)]⁺ and the Blue Shifting of the Hydrogen-Bonded Amide Stretch with Each Water Addition

In this study, the structures of [Na­(GlyAla)­(H₂O)]⁺ and [Ca­(GlyAla–H)­(H₂O)_<i>n</i>]⁺, (<i>n</i> = 1–3) solvated ion–molecule complexes (as well as the AlaGly isomers) were investigated using infrared multiple photon dissociation (IRMPD) spectroscopy and with computational methods. Calculations showed that in the calcium clusters, the lowest-energy complex is the one in which the peptide is deprotonated at the carboxylic acid end and that Ca²⁺ binds to both carboxylate oxygen atoms as well as the amide carbonyl oxygen. For the microsolvated structures, all three water molecules also bind directly to Ca²⁺. For the singly, doubly, and triply solvated complexes, these structures are supported by experimental IRMPD spectra. For the [Na­(GlyAla)­(H₂O)]⁺ complex, both carbonyl oxygen atoms, one from the intact carboxylic acid and one from the amide group, as well as the water molecule were found to be bound to the Na⁺. In all of the spectra, a strong band is observed between 3300 and 3400 cm^–1 and is assigned to the amide N–H stretch, which is red-shifted due to hydrogen bonding with the amine nitrogen. The position of the hydrogen-bonded amide N–H stretch is experimentally and theoretically found to be sensitive to the number of water molecules; it is shown to blue shift upon successive hydrations

Gas-Phase Structures of Pb²⁺-Cationized Phenylalanine and Glutamic Acid Determined by Infrared Multiple Photon Dissociation Spectroscopy and Computational Chemistry

Infrared multiple photon dissociation (IRMPD) spectroscopy in the 3200–3800 cm^–1 region was used to determine the gas-phase structures of bare and monohydrated [Pb­(Phe-H)]⁺ and [Pb­(Glu-H)]⁺. These experiments were supported by infrared spectra calculated at the B3LYP/6-31+G­(d,p) level of theory as well as 298 K enthalpies and Gibbs energies determined using the MP2­(full)/6-311++G­(2d,2p)//B3LYP/6-31+G­(d,p) method. The gas-phase structure of [Pb­(Phe-H)]⁺ has Pb²⁺ bound in a tridentate fashion between Phe’s amine nitrogen, one oxygen of the deprotonated carboxyl group, and the aromatic ring. The IRMPD spectrum of [Pb­(Glu-H)]⁺ can be assigned to a structure where the side chain carboxyl group is deprotonated. The structure of [Pb­(Phe-H)­H₂O]⁺ is simply the hydrated analogue of [Pb­(Phe-H)]⁺ where water attaches to Pb²⁺ in the same hemisphere as the ligated amino acid. The spectrum of [Pb­(Glu-H)­H₂O]⁺ could not be assigned a unique structure. The IRMPD spectrum shows features attributed to symmetric and antisymmetric O–H stretching of water and a broad band characteristic of a hydrogen bonded O–H stretching vibration. These features can only be explained by the presence of at least two isomers and agree with the computational results that predict the four lowest energy structures to be within 6 kJ mol^–1 of one another