Rearrangement of Proline Complexes with Zn2+: An Infrared Multiple Photon Dissociation and Theoretical Investigation

Complexes of proline (Pro) cationized with Zn2+ and Cd2+ were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy using light generated from a free electron laser. Complexes of intact Pro with CdCl+, CdCl+(Pro), a complex of (Zn+Pro-H)+ where a proton has been lost, as well as Zn+(Pro-H)(Pro) were formed by electrospray ionization. In order to identify the structures formed experimentally, the IRMPD spectra were compared to those calculated from optimized structures at the B3LYP/6-311+G(d,p) level for zinc complexes and B3LYP/def2-TZVP level with an effective core potential on cadmium for the CdCl+(Pro) system. For the latter complex, the main binding motif observed has a zwitterionic proline ligand structure, [CO2-]cc, where the metal binds to the two carboxylate oxygens. In contrast, for Zn+(Pro-H)(Pro), both ligands interact with zinc via a [N,CO-][N,CO] binding motif, where binding is observed at the carbonyl oxygens and nitrogens for both ligands, consistent with previous work. In both cases, contributions from different puckers of the proline ring may contribute. For (Zn+Pro-H)+, we identify that the structure is actually ZnH+(Pro-2H), in which the proline has been dehydrogenated and one of the hydrogens has migrated to form a covalent bond with Zn, which verifies a previous report relying on a single OH stretch band.

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

Infrared multiple photon dissociation spectroscopy has been used to probe the structures of the three protonated base-pair mismatches containing 9-ethylguanine (9eG) in the gas phase. Some of these protonated base-pairs have been identified in RNA.

Hydrogen bonding in alkali metal cation-bound i-motif-like dimers of 1-methyl cytosine: an IRMPD spectroscopic and computational study

The structures of alkali metal cation bound 1-methylcytosine (1-mCyt) dimers were explored using vibrational spectroscopy in the form of infrared multiple photon dissociation (IRMPD) spectroscopy and by computational methods. For the smaller alkali metal cations, Li⁺ and Na⁺, only non-hydrogen bonded symmetric anti-parallel structures were observed in agreement with the lowest energy computed structures. For K⁺, Rb⁺, and Cs⁺ the vibrational spectra in the N-H stretch region showed strong evidence for hydrogen bonding in agreement with the lowest energy structures which contained hydrogen bonding interactions between the amine group of one cytosine and the carbonyl oxygen of the other cytosine. The lowest energy structures for these complexes were compared to previously studied cytosine complexes [(Cyt)₂M]⁺ where M = Li, Na, and K. The calculations are in agreement that only the non-hydrogen bonded structures would be observed for these cytosine complexes.

Multistage dynamics of Hg2+-DNA interactions: a single-molecule study

The metal ion-DNA interaction is key to biochemical processes and has applications in areas such as metal ion sensors and DNA nanomachines. For example, the formation of the T-Hg2+-T structure has been used in technologies such as DNA-based mercuric ion sensors. Though the interaction is widely used for practical purposes, the underlying mechanism has not been fully understood. In the present study, we used magnetic tweezers to explore the interactions between λ-DNA and two metal ions, Hg2+ and Cd2+, at the single-molecule level. Both metal ions caused considerable DNA conformational changes. The resulting DNA compaction dynamics were related to the ion concentration and the exerted force. The increase in the ion concentration promoted DNA compaction, whereas exerting greater forces inhibited this process. Application of a high force generated two-stage dynamics of the Hg2+-DNA interaction. However, at a sufficiently high Hg2+ concentration, a lower force led to a three-stage process. In contrast, the curves of the binding of Cd2+ ions to DNA had a stepwise pattern. Both the AFM scanning results and the single-molecule measurements confirmed that Hg2+ influences the DNA conformation in a more pronounced manner than Cd2+. The multistage Hg2+-DNA interaction was considered to be a result of the different binding mechanisms, including the mismatched base-pair formation. A model was then proposed to explain the peculiar dynamics.

Infrared Multiple Photon Dissociation Spectroscopy of Cationized Canavanine: Side-Chain Substitution Influences Gas-Phase Zwitterion Formation†

Infrared multiple photon dissociation spectroscopy was performed on protonated and cationized canavanine (Cav), a non-protein amino acid oxy-analog of arginine. Infrared spectra in the XH stretching region (3000 - 4000 cm^-1) were obtained at the Centre Laser Infrarouge d'Orsay (CLIO) facility. Comparison of the experimental infrared spectra with scaled harmonic frequencies at the B3LYP/6-31+G(d,p) level of theory indicates that canavanine is in a canonical neutral form in CavH⁺, CavLi⁺, and CavNa⁺; therefore, these cations are charge-solvated structures. The infrared spectrum of CavK⁺ is consistent with a mixture of Cav in canonical and zwitterionic forms leading to both charge-solvated and salt-bridged cationic structures. The Cav moiety in CavCs⁺ is shown to be zwitterionic, forming a salt-bridged structure for the cation. Infrared spectra in the fingerprint region (1000 - 2000 cm^-1) obtained at the FELIX Laboratory in Nijmegen, Netherlands support these assignments. These results show that that a single oxygen atom substitution in the side chain reduces the stability of the zwitterion compared to that of the protein amino acid arginine (Arg), which has been shown previously to adopt a zwitterionic structure in ArgNa⁺ and ArgK⁺. This difference can be explained in part due to the decreased basicity of Cav (PA = 1001 kJ/mol) as compared to arginine (PA = 1051 kJ/mol), but not entirely, as lysine, which has nearly the same proton affinity as Cav, (~993 kJ/mol) forms only canonical structures with Na⁺, K⁺, and Cs⁺. A major difference between the zwitterionic forms of ArgM⁺ and CavM⁺ is that the protonation site is on the side chain for Arg and on the N-terminus for Cav. This results in systematically weaker salt bridges in the Cav zwitterions. In addition, the presence of another hydrogen-bonding acceptor atom in the side chain contributes to the stability of the canonical structures for the smaller alkali cations.

Infrared Multiphoton Dissociation Spectroscopy with Free-Electron Lasers: On the Road from Small Molecules to Biomolecules

Infrared multiphoton dissociation (IRMPD) spectroscopy is commonly used to determine the structure of isolated, mass-selected ions in the gas phase. This method has been widely used since it became available at free-electron laser (FEL) user facilities. Thus, in this Minireview, we examine the use of IRMPD/FEL spectroscopy for investigating ions derived from small molecules, metal complexes, organometallic compounds and biorelevant ions. Furthermore, we outline new applications of IRMPD spectroscopy to study biomolecules.