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International audience; Six-membered-diaza ring of Cinnoline has been fused on Naphthalimide dye to give a donor-acceptor system called CinNapht. This red shifted fluorophore, that can be synthetised in gram scale, exhibits a large Stoke Shift and a fluorescence quantum yield up to 0.33. It is also characterized by a strong solvatochromic effect from green to red emission as well and can be used for bioimaging.

The 2'-substituents distinguish DNA from RNA nucleosides. 2'-O-methylation occurs naturally in RNA and plays important roles in biological processes. Such 2'-modifications may alter the hydrogen-bonding interactions of the nucleoside and thus may affect the conformations of the nucleoside in an RNA chain. Structures of the protonated 2'-O-methylated pyrimidine nucleosides were examined by infrared multiple photon dissociation (IRMPD) action spectroscopy, assisted by electronic structure calculations. The glycosidic bond stabilities of the protonated 2'-O-methylated pyrimidine nucleosides, [Nuom+H]+, were also examined and compared to their DNA and RNA nucleoside analogues via energy-resolved collision-induced dissociation (ER-CID). The preferred sites of protonation of the 2'-O-methylated pyrimidine nucleosides parallel their canonical DNA and RNA nucleoside analogues, [dNuo+H]+ and [Nuo+H]+, yet their nucleobase orientation and sugar puckering differ. The glycosidic bond stabilities of the protonated pyrimidine nucleosides follow the order: [dNuo+H]+ < [Nuo+H]+ < [Nuom+H]+. The slightly altered structures help explain the stabilization induced by 2'-O-methylation of the pyrimidine nucleosides.

International audience; The gas-phase structure of the protonated isomeric methyl uracils (1-Me-, 3-Me- and 6-Me-) was examined using mid‐infrared multiple photon dissociation (IRMPD) spectroscopy performed at CLIO, the Orsay (France) free electron laser facility. Experimental infrared spectra were recorded for protonated species generated by electrospray ionization, isolated and irradiated in a quadrupole ion trap, and compared to calculated infrared absorption spectra of the different low-lying isomers computed at the B3LYP/6-31++G(d,p) level of theory. For both protonated 1-Me-uracil and 6-Me-uracil, the global energy minima correspond to enolic tautomers, whose infrared absorption spectra were found to match very well with the experimental IRMPD spectra. A small fraction of another low energy lying keto tautomer is also present under electrospray conditions. Protonation of 3-Me-uracil by electrospray results exclusively in the formation of a keto form. 3-Me-uracil therefore constitutes a particular case in the series of pyrimidine nucleobases studied so far. Methylation of the N3 position of uracil prevents the interconversion between the keto and enol forms, as encountered for uracil and uracil methylated on N1, C5, or C6. These data also give new insights about the unimolecular reactivity of protonated uracils.

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 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 multiple photon dissociation spectra of the proton-bound heterodimers of phenylalanine/glycine (Phe·H + ·Gly) and pentafluorophenylalanine/glycine (F 5 -Phe·H + ·Gly) have been acquired in the 975–1975 cm −1 region. Exhaustive basin hopping molecular dynamics searches and subsequent DFT calculations predict four low energy intermolecular binding motifs. The spectrum of F 5 -Phe·H + ·Gly is assigned predominantly to isomers exhibiting a N H + ⋯O intermolecular interaction between nitrogen-protonated Gly and the carbonyl oxygen atom of F 5 -Phe. In contrast, the spectrum Phe·H + ·Gly is found to consist of a mixture of isomers exhibiting the N H + ⋯O between nitrogen-protonated Gly and the carbonyl oxygen of neutral Phe, and isomers exhibiting a N H + ⋯N interaction between nitrogen-protonated Phe and the neutral Gly moiety. Cation-π effects also seem to influence the cluster geometries, especially in the case of the Phe·H + ·Gly global minimum structure where the phenyl ring orients with the site of protonation so as to maximize charge-quadrupole interactions.

The formation and investigation of sulfur-based cysteine radicals cationized by a group 1A metal ion or Ag+ in the gas phase are reported. Gas-phase ion-molecule reactions (IMR) and infrared multiple-photon dissociation (IRMPD) spectroscopy revealed that the Li+ , Na+ , and K+ adducts of the cysteine radical remain S-based radicals as initially formed. Theoretical calculations for the three alkali metal ions found that the lowest-energy isomers are Cα -based radicals, but they are not observed experimentally owing to the barriers associated with the hydrogen-atom transfer. A mechanism for the S-to-Cα radical rearrangement in the metal ion complexes was proposed, and the relative energies of the associated energy barriers were found to be Li+ >Na+ >K+ at all levels of theory. Relative to the B3LYP functional, other levels of calculation gave significantly higher barriers (by 35-40 kJ mol-1 at MP2 and 44-47 kJ mol-1 at the CCSD level) using the same basis set. Unlike the alkali metal adducts, the cysteine radical/Ag+ complex rearranged from the S-based radical to an unreactive species as indicated by IMRs and IRMPD spectroscopy. This is consistent with the Ag+ /cysteine radical complex having a lower S-to-Cα radical conversion barrier, as predicted by the MP2 and CCSD levels of theory.

Intrinsic properties of pantothenic acid, an essential nutraceutical, are examined. The effect of protonation on the energetic and geometric features of pantothenic acid, generated as gaseous protonated species, are investigated by infrared multiple photon dissociation (IRMPD) spectroscopy over an extended frequency range (800–2000 cm−1 and 2800–3700 cm−1). DFT calculations are exploited to identify the possible structures and predict the absorption spectra at the B3LYP/6-311++G(d,p) level. Two amide-protonated structures, characterized by the most stable binding motifs, account well for the experimental spectrum, thus revealing structurally diagnostic features of potential benefit for the development of highly sensitive and selective nutrient screening.

A combination of infrared multiple photon dissociation (IRMPD) spectroscopy and density functional theory calculations is used to investigate the structures and charge-transfer properties of clusters containing transition metals (TM = Co(II), Ni(II), Cu(I), Zn(II), Rh(III), Pd(II), Ag(I), Cd(II)) and the dodecafluorododecaboron dianion, B12F122–. In all cases, IRMPD resulted in transfer of electron density to the metal center and production of B12F12–. Metals that exhibit the highest degree of charge transfer are found to induce reaction among the B12F12 cages, leading to production of BnFm (up to n = m = 24).

The structure of a protonated diketopiperazine dipeptide, cyclo-diphenylalanine, is studied by means of infrared multiple photon dissociation spectroscopy combined with quantum chemical calculations. Protonation exclusively occurs on the oxygen site and, in the most stable conformer, results to an intramolecular OH···π interaction, accompanied by a CH···π interaction. Higher-energy conformers with free OH and NH···π interactions are observed as well, due to kinetic trapping. Optimization of the intramolecular interactions involving the aromatic ring dictates the geometry of the benzyl substituents. Changing the chirality of one of the residues has consequences on the CH···π interaction, which is of CαH···π nature for LD, while LL shows a CβH···π interaction. Higher-energy conformers also display some differences in the nature of the intramolecular interactions.

International audience; This work aims to improve the computation of infrared spectra of gas-phase cations using DFT methods. Experimental IRMPD spectra for ten Zn and Ru organometallic complexes have been used to provide reference data for 64 vibrational modes in the 900-2000 cm-1 range. The accuracy of the IR vibrational frequencies predicted for these bands has been assessed over five DFT functionals and three basis sets. The functionals include the popular B3LYP and M06-2X hydrids and the range-separated hybrids (RSH) CAM-B3LYP, LC-BLYP and B97X-D. B3LYP gives the best mean absolute error (MAE) and root-mean-square error (RMSE) values of 7.1 and 9.6 cm-1 , whilst the best RSH functional, B97X-D, gives 12.8 and 16.6 cm-1 respectively. Using linear correlations instead of scaling factors improves the prediction accuracy significantly for all functionals. Experimental and computed spectra for a single complex can show significant differences even when the molecular structure is calculated correctly, and a means of defining confidence limits for any given computed structure is also provided.

The monitoring by UV spectroscopy of the Pd-catalyzed hydrogenolysis in acetonitrile of 2-methyl-2-benzyloxycarbonyl-1-indanone and 2-methyl-2-benzyloxycarbonyl-1-tetralone showed the successive formation of corresponding beta-ketoacids and enols to deliver finally the ketones. Some factors which influence the stability of the intermediates are determined. In contrast to the above benzyl beta-ketoesters, the enol was not detected from benzyl (2-methylinden-3-yl) carbonate.

Oxidative damage to DNA yields guanine radical cations. Their gas-phase IR spectroscopic signature and acidity have been modelled by the radical cation of 9-methylguanine. Comparisons with quantum chemistry calculations suggest that radical cation formation produces the ground-state keto tautomer, which has an N-H acidity enhanced by ~470 kJ mol(-1).

A novel type of hemispherical cage was synthesized in a one-pot procedure, which displayed good binding properties towards nickel(II).