Microhydration of Dibenzo-18-Crown‑6 Complexes with K⁺, Rb⁺, and Cs⁺ Investigated by Cold UV and IR Spectroscopy in the Gas Phase

In this Article, we examine the hydration structure of dibenzo-18-crown-6 (DB18C6) complexes with K⁺, Rb⁺, and Cs⁺ ion in the gas phase. We measure well-resolved UV photodissociation (UVPD) spectra of K⁺·DB18C6·(H₂O)_<i>n</i>, Rb⁺·DB18C6·(H₂O)_<i>n</i>, and Cs⁺·DB18C6·(H₂O)_<i>n</i> (<i>n</i> = 1–8) complexes in a cold, 22-pole ion trap. We also measure IR-UV double-resonance spectra of the Rb⁺·DB18C6·(H₂O)_1–5 and the Cs⁺·DB18C6·(H₂O)₃ complexes. The structure of the hydrated complexes is determined or tentatively proposed on the basis of the UV and IR spectra with the aid of quantum chemical calculations. Bare complexes (K⁺·DB18C6, Rb⁺·DB18C6, and Cs⁺·DB18C6) have a similar boat-type conformation, but the distance between the metal ions and the DB18C6 cavity increases with increasing ion size from K⁺ to Cs⁺. Although the structural difference of the bare complexes is small, it highly affects the manner in which each is hydrated. For the hydrated K⁺·DB18C6 complexes, water molecules bind on both sides (top and bottom) of the boat-type K⁺·DB18C6 conformer, while hydration occurs only on top of the Rb⁺·DB18C6 and Cs⁺·DB18C6 complexes. On the basis of our analysis of the hydration manner of the gas-phase complexes, we propose that, for Rb⁺·DB18C6 and Cs⁺·DB18C6 complexes in aqueous solution, water molecules will preferentially bind on top of the boat conformers because of the displaced position of the metal ions relative to DB18C6. In contrast, the K⁺·DB18C6 complex can accept H₂O molecules on both sides of the boat conformation. We also propose that the characteristic solvation manner of the K⁺·DB18C6 complex will contribute entropically to its high stability and thus to preferential capture of K⁺ ion by DB18C6 in solution

Franck–Condon-like Progressions in Infrared Spectra of Biological Molecules

Infrared spectra in the NH stretch region are often used for structure determination of gas-phase biological molecules. Vibrational couplings complicate the structure determination process by giving rise to additional vibrational bands along with the expected fundamental transitions. We present an example of a strong anharmonic coupling in a biological molecule, Ac-Phe-Ala-LysH⁺, which causes the appearance of long vibrational progressions in the infrared spectrum. By analyzing the spectra of the ground and the electronically excited state, we determined that the coupling occurs between the NH stretch (ω_NH) and a low-frequency torsion of the phenyl ring (ω_τ). We describe the vibrational progressions using a Born–Oppenheimer-like separation of the high-frequency stretch and low-frequency torsion with a quartic Taylor expansion for the potential energy surface that accounts for the equilibrium distance and frequency change of the torsional vibration upon the NH stretch excitation. We also demonstrate that small conformational changes in the peptide are sufficient to break this coupling

Cryogenic Spectroscopy and Quantum Molecular Dynamics Determine the Structure of Cyclic Intermediates Involved in Peptide Sequence Scrambling

Collision-induced dissociation (CID) is a key technique used in mass spectrometry-based peptide sequencing. Collisionally activated peptides undergo statistical dissociation, forming a series of backbone fragment ions that reflect their amino acid (AA) sequence. Some of these fragments may experience a “head-to-tail” cyclization, which after proton migration, can lead to the cyclic structure opening in a different place than the initially formed bond. This process leads to AA sequence scrambling that may hinder sequencing of the initial peptide. Here we combine cryogenic ion spectroscopy and <i>ab initio</i> molecular dynamics simulations to isolate and characterize the precise structures of key intermediates in the scrambling process. The most stable peptide fragments show intriguing symmetric cyclic structures in which the proton is situated on a <i>C</i>₂ symmetry axis and forms exceptionally short H-bonds (1.20 Å) with two backbone oxygens. Other nonsymmetric cyclic structures also exist, one of which is protonated on the amide nitrogen, where ring opening is likely to occur

Infrared Spectroscopy as a Probe of Electronic Energy Transfer

We have combined electronic and vibrational spectroscopy in a cryogenic ion trap to produce highly resolved, conformer-selective spectra for the ground and excited states of a peptide containing two chromophores. These spectra permit us to determine the precise three-dimensional structure of the peptide and give insight into the migration of the electronic excitation from phenylalanine to tyrosine because changes in the excited-state infrared spectra are sensitive to localization of the electronic energy in each chromophore. The well-controlled experimental conditions make this result a stringent test for theoretical methods dealing with electronic energy transfer

New Approach for the Identification of Isobaric and Isomeric Metabolites

The structural elucidation of metabolite molecules is important in many branches of the life sciences. However, the isomeric and isobaric complexity of metabolites makes their identification extremely challenging, and analytical standards are often required to confirm the presence of a particular compound in a sample. We present here an approach to overcome these challenges using high-resolution ion mobility spectrometry in combination with cryogenic vibrational spectroscopy for the rapid separation and identification of metabolite isomers and isobars. Ion mobility can separate isomeric metabolites in tens of milliseconds, and cryogenic IR spectroscopy provides highly structured IR fingerprints for unambiguous molecular identification. Moreover, our approach allows one to identify metabolite isomers automatically by comparing their IR fingerprints with those previously recorded in a database, obviating the need for a recurrent introduction of analytical standards. We demonstrate the principle of this approach by constructing a database composed of IR fingerprints of eight isomeric/isobaric metabolites and use it for the identification of these isomers present in mixtures. Moreover, we show how our fast IR fingerprinting technology allows to probe the IR fingerprints of molecules within just a few seconds as they elute from an LC column. This approach has the potential to greatly improve metabolomics workflows in terms of accuracy, speed, and cost

UV and IR Spectroscopy of Cryogenically Cooled, Lanthanide-Containing Ions in the Gas Phase

We measure UV and IR spectra in the gas phase for EuOH⁺, EuCl⁺, and TbO⁺ ions, which are produced by an electrospray ionization source and cooled to ∼10 K in a cold, 22-pole ion trap. The UV photodissociation (UVPD) spectra of these ions show a number of sharp, well-resolved bands in the 30000–38000 cm^–1 region, although a definite assignment of the spectra is difficult because of a high degree of congestion. We also measure an IR spectrum of the EuOH⁺ ion in the 3500–3800 cm^–1 region by IR–UV double-resonance spectroscopy, which reveals an OH stretching band at 3732 cm^–1. We perform density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations of these ions in order to examine the nature of the transitions. The DFT results indicate that the states of highest-spin multiplicity (octet for EuOH⁺ and EuCl⁺ and septet for TbO⁺) are substantially more stable than other states of lower-spin multiplicity. The TD-DFT calculations suggest that UV absorption of the EuOH⁺ and EuCl⁺ ions arises from Eu­(4f) → Eu­(5d,6p) transitions, whereas electronic transitions of the TbO⁺ ion are mainly due to the electron promotion of O­(2p) → Tb­(4f,6s). The UVPD results of the lanthanide-containing ions in this study suggest the possibility of using lanthanide ions as “conformation reporters” for gas-phase spectroscopy for large molecules

Ion Selectivity of Crown Ethers Investigated by UV and IR Spectroscopy in a Cold Ion Trap

Electronic and vibrational spectra of benzo-15-crown-5 (B15C5) and benzo-18-crown-6 (B18C6) complexes with alkali metal ions, M⁺•B15C5 and M⁺•B18C6 (M = Li, Na, K, Rb, and Cs), are measured using UV photodissociation (UVPD) and IR–UV double resonance spectroscopy in a cold, 22-pole ion trap. We determine the structure of conformers with the aid of density functional theory calculations. In the Na⁺•B15C5 and K⁺•B18C6 complexes, the crown ethers open the most and hold the metal ions at the center of the ether ring, demonstrating an optimum matching in size between the cavity of the crown ethers and the metal ions. For smaller ions, the crown ethers deform the ether ring to decrease the distance and increase the interaction between the metal ions and oxygen atoms; the metal ions are completely surrounded by the ether ring. In the case of larger ions, the metal ions are too large to enter the crown cavity and are positioned on it, leaving one of its sides open for further solvation. Thermochemistry data calculated on the basis of the stable conformers of the complexes suggest that the ion selectivity of crown ethers is controlled primarily by the enthalpy change for the complex formation in solution, which depends strongly on the complex structure

The Structure of the Protonated Serine Octamer

The amino acid serine has long been known to form a protonated “magic-number” cluster containing eight monomer units that shows an unusually high abundance in mass spectra and has a remarkable homochiral preference. Despite many experimental and theoretical studies, there is no consensus on a Ser₈H⁺ structure that is in agreement with all experimental observations. Here, we present the structure of Ser₈H⁺ determined by a combination of infrared spectroscopy and ab initio molecular dynamics simulations. The three-dimensional structure that we determine is ∼25 kcal mol^–1 more stable than the previous most stable published structure and explains both the homochiral preference and the experimentally observed facile replacement of two serine units