Infrared spectroscopy of isolated nucleotides. 1. The cyclic 3′,5′-adenosine monophosphate anion

The intracellular second messenger deprotonated adenosine 3′,5′-cyclic monophosphate anion (cAMP-H)⁻, generated as gaseous species by electrospray ionization (ESI) and stored in a Paul ion-trap mass spectrometer, has been investigated by mass-resolved infrared multiple photon dissociation (IRMPD) spectroscopy in the 900–1800 cm⁻¹ fingerprint wavenumber range, exploiting the powerful and continuously tunable radiation from a free electron laser (FEL) at the Centre Laser Infrarouge d’Orsay (CLIO). The IRMPD features are interpreted by comparison with the IR spectra obtained by quantum chemical calculations for different low-lying conformers, allowing an assignment for the observed IRMPD bands. It is to be noted that the calculated IR spectra for the most stable conformers look all rather similar and do not allow an unambiguous structural assignment, based exclusively on the IRMPD spectrum. However, the positions and intensities of the IRMPD features of isolated (cAMP-H)⁻ ions are consistent with a species deprotonated at the phosphate group and compatible with the main equilibrium structures lying within 18 kJ mol⁻¹ from the lowest lying conformation, the anti-chair form with a C3′-endo sugar twist.     

An Investigation of Protonation Sites and Conformations of Protonated Amino Acids by IRMPD Spectroscopy

The protonation sites and structures of a series of protonated amino acids (Gly, Ala, Pro, Phe, Lys and Ser) are investigated by means of infrared multiple‐photon dissociation (IRMPD) spectroscopy and electronic‐structure calculations. The IRMPD spectra of the protonated species are recorded using the combination of a free‐electron laser (FEL) and an electrospray‐ion‐trap mass spectrometer. The structures of different possible isomers of these protonated species are optimized at the B3LYP/6‐311+G(d, p) level of theory and the IR spectra calculated using the same computational method. For every amino acid studied herein, the current results indicate that a proton is bound to the α‐amino nitrogen, except for lysine, in which the protonation site is the amino nitrogen in the side chain. According to the calculated and experimental IRMPD results, the structures of the protonated amino acids may be assigned unambiguously. For Gly, Ala, and Pro, in each of the most stable isomers the protonated amino group forms an intramolecular hydrogen bond with the adjacent carbonyl oxygen. In the case of Gly, the isomer containing a proton bound to the carbonyl oxygen is theoretically possible. However, it does not exist under the experimental conditions because it has a significantly higher energy (i.e. 26.6 kcal mol^?1) relative to the most stable isomer. For Ser and Phe, the protonated amino group forms two intramolecular hydrogen bonds with both the adjacent carbonyl oxygen and the side‐chain group in each of the most stable isomers. In protonated lysine, the protonated amino group in the side chain forms two hydrogen bonds with the α‐amino nitrogen and the carbonyl oxygen, which is a cyclic structure. Interestingly, for protonated lysine the zwitterionic structure is a local minimum energy isomer, but the experimental spectrum indicates that it does not exist under the experimental conditions. This is consistent with the fact that the zwitterionic isomer is 9.2 kcal mol^?1 higher in free energy at 298 K than the most stable isomer. The carbonyl stretching vibration in the range of 1760–1800 cm^?1 is especially sensitive to the structural change. In addition, IRMPD mechanisms for the protonated amino acids are also investigated.     

Cation-π Interactions between a Noble Metal and a Polyfunctional Aromatic Ligand: Ag+(benzylamine)

The structure of an isolated Ag⁺(benzylamine) complex is investigated by infrared multiple photon dissociation (IRMPD) spectroscopy complemented with quantum chemical calculations of candidate geometries and their vibrational spectra, aiming to ascertain the role of competing cation-N and cation-π interactions potentially offered by the polyfunctional ligand. The IRMPD spectrum has been recorded in the 800–1800 cm⁻¹ fingerprint range using the IR free electron laser beamline coupled with an FT-ICR mass spectrometer at the Centre Laser Infrarouge d'Orsay (CLIO). The resulting IRMPD pattern points toward a chelate coordination (N-Ag⁺-π) involving both the amino nitrogen atom and the aromatic π-system of the phenyl ring. The gas-phase reactivity of Ag⁺(benzylamine) with a neutral molecular ligand (L) possessing either an amino/aza functionality or an aryl group confirms N- and π-binding affinity and suggests an augmented silver coordination in the product adduct ion .     

Coupling infrared multiphoton dissociation spectroscopy, mass-spectrometry and ion mobility spectrometry for the determination of structures of angiotensin II cations

Gas-phase structures of mass-selected singly- and doubly charged angiotensin ions have been determined by means of infrared multiple photon dissociation (IRMPD) spectroscopy and ion mobility spectrometry. Simulation of IRMPD spectra at the DFT level provides the location of the proton on the Arg side-chain in the case of the singly charged species. Interpretation of the ion mobility data suggests that the structures of singly- and doubly charged species are rather similar except for an internal proton transfer.     

Dynamics of Electrons in Ammonia Cages: The Discovery System of Solvation

Two centuries ago solvated electrons were discovered in liquid ammonia and a century later the concept of the solvent cage was introduced. Here, we report a real time study of the dynamics of size‐selected clusters, n=20 to 60, of electrons in ammonia, and, for comparison, that of electrons in water cages. Unlike the water case, the observed dynamics for ammonia indicates the formation, through a 100 fs temperature jump, of a solvent collective motion in a 500 fs relaxation process. The agreement of the experimental results—obtained for a well‐defined n, gated electron kinetic energy, and time delay—with molecular dynamics theory suggests the critical and different role of the kinetic energy and the librational motions involved in solvation.     

The hydrated electron: a seemingly familiar chemical and biological transient

Since the discovery of the hydrated electron in bulk water in 1962, the species has been the subject of intense research and speculation. For many decades even the basic features of the simplest of all chemical and biological transients and reactants--such as its structure, binding motifs, lifetimes, and binding energies--remained elusive. Recently, another milestone in the research of the hydrated electron was the determination of its vertical binding energy (VBE). Also a long-lived hydrated electron near the surface of liquid water has been discovered. The present Minireview discusses the implications and consequences of this and other new findings in addition to the emerging complex picture of a solvated electron in water.     

Can an Elusive Platinum(III) Oxidation State be Exposed in an Isolated Complex?

Platinum(IV) complexes are extensively studied for their activity against cancer cells as potential substitutes for the widely used platinum(II) drugs. Pt^IV complexes are kinetically inert and need to be reduced to Pt^II species to play their pharmacological action, thus acting as prodrugs. The mechanism of the reduction step inside the cell is however still largely unknown. Gas‐phase activation of deprotonated platinum(IV) prodrugs was found to generate products in which platinum has a formal +3 oxidation state. IR multiple photon dissociation spectroscopy is thus used to obtain structural information helping to define the nature of both the platinum atom and the ligands. In particular, comparison of calculations at DFT, MP2 and CCSD levels with experimental results demonstrates that the localization of the radical is about equally shared between the d_xz orbital of platinum and the p_z of nitrogen on the amino group, the latter acting as a non‐innocent ligand.     

Thermochemistry of aqueous solutions of alkylated nucleic acid bases. VIII. Enthalpies of hydration of 6-alkyluracils

Enthalpies of solution in water H _sol ^o and enthalpies of sublimation H _sub ^o were determined for a number of crystalline derivatives of uracil: 1,6-dimethyluracil (m ₂ ^1,6 Ura), 1,3,6-trimethyluracil (m ₃ ^1,3,6 Ura), 6-ethyl-1,3-dimethyluracil (e⁶m ₂ ^1,3 Ura), 6-propyl-1,3-dimethyluracil (pr⁶m ₂ ^1,3 Ura) and 6-butyl-1,3-dimethyluracil (but⁶m ₂ ^1,3 Ura). Standard enthalpies of hydration H _hydr ^o and standard enthalpies of interaction H _int ^o of the solutes with their hydration shells were calculated. The data obtained show that dependence of H _int ^o on the number of-CH₂- groups of n-alkyl chain added upon substitution of diketopyrimidine ring is nonlinear. This finding is discussed in connection with results of X-ray diffraction structure determinations for the crystalline compounds.     

Gas‐Phase Interactions between Lead(II) Ions and Cytosine: Tandem Mass Spectrometry and Infrared Multiple‐Photon Dissociation Spectroscopy Study

Gas‐phase interactions between Pb²⁺ ions and cytosine (C) were studied by combining tandem mass spectrometry, infrared multiple photon dissociation spectroscopy, and density functional theory (DFT) calculations. Both singly and doubly charged complexes were generated by electrospray. The [Pb(C)?H]⁺ complex was extensively studied, and this study shows that two structures, involving the interaction of the metal with the deprotonated canonical keto‐amino tautomer of cytosine, are generated in the gas phase; the prominent structure is the bidentate form involving both the N1 and O2 electronegative centers. The DFT study also points out a significant charge transfer from the nucleobase to the low‐lying p orbitals of the metal and a strong polarization of the base upon complexation. The various potential energy surfaces explored to account for the fragmentation observed are consistent with the high abundance of the [PbNH₂]⁺ fragment ion.