Li+ and Na+ attachment to some dipeptides via LDI-TOF mass spectrometry: Fragmentation patterns.

Laser desorption ionization-time of flight (LDI-TOF) mass spectrometry is used for studying the attachment of Na+ and Li+ ions to four dipeptides including phenylalanyl-alanine (Phe-Ala), tyrosyl-alanine (Tyr-Ala), L-Phenylalanyl-L-Phenylalanine (Phe-Phe), and alanyl-glutamine (Ala-Gln) dipeptides. The LiCl, NaOH, and NaF salts are used as the source of Li+ and Na+ ions in the LDI of the dipeptides. Our aim is the investigation of the difference between the fragmentation patterns of the selected dipeptides in the presence of Na+ and Li+ ions due to the laser radiation and providing information for the fragmentation of larger peptides in the same conditions. The characteristic peak, related to [dipeptide-H + 2Na]+ species, is observed in the mass spectrum of Phe-Ala and Tyr-Ala dipeptides in the presence of NaF, while the breaking of the peptide bond (OC-NH) occurs for the Phe-Phe in the presence of the aforementioned salts. The characteristic peak of Ala-Gln dipeptide ([(Ala-Gln)-H + 2Na]+) is observed in the absence of any salt. The mass spectra of the dipeptides, recorded in the presence of LiCl, are crowded compared to those recorded in the presence of NaF and NaOH showing the effect of the type of alkali salt on the dipeptide fragmentation. The theoretical calculations are employed to investigate the ability of the interaction sites of dipeptides for the attachment of one and two Na+ and determine the most stable structure of the [dipeptide-H + 2Na]+ species for each dipeptide.

A TD-DFT study of the excited dissociative electronic states of the DNA nucleobases bound to Li.

In this work, the first and second dissociative potential curves of adenineLi+ (ADLi+), guanineLi+ (GUALi+), cytosineLi+(CYTLi+), and thymineLi+ (THYLi+) complexes, related to the dissociation of their LiO and LiN bonds, have been calculated in the gas phase and water, separately. For this purpose, the fifteen excited potential curves, in order of increasing energy, were calculated for each complex and the dissociative potential curves were distinguished from them considering the conical intersection points. The time-dependent density functional theory (TD-DFT) method employing the M06-2X functional was used for the calculations. It was observed that the electron transfer from the DNA base to the Li+ took place during the dissociation of complexes in the gas phase. The electrostatic field of water blocked this charge transfer and led to the excited DNA base and Li+ in its ground state. The vertical excitation energy for the desorption of the Li fragment as a neutral and cation species from the DNA bases was determined. The effect of the interaction site of Li+ on the dissociative potential curves was also investigated.

Effect of helium nanoclusters on the spectroscopic properties of embedded SF6: Ionization, excitation and vibration.

Ionization and excitation energies, IR and Raman spectra of sulfur hexafluoride (SF6), located inside helium (He) nanoclusters with different sizes (SF6@Hen; n=20, 40, 60), were calculated. The effect of the cluster size on the spectroscopic properties of the SF6 was investigated and found that the Hen-SF6 interaction in the He clusters with large number of atoms is small so that the ionization and absorption energies of SF6 are not affected while for small He nanoclusters the Hen-SF6 interaction is more important. The effect of Hen-SF6 interaction and deformation of the fragments on the photoelectron and absorption spectra of SF6@Hen were separated theoretically and discussed in details. It was deduced that the effect of the cluster size on the IR and Raman vibrational frequencies of the SF6 is negligible for the cluster size range considered in this work. Density functional theory (DFT) employing M06-2X functional and 6-31+G(df) basis set were used for optimizing the structures of SF6@Hen. Symmetry adapted cluster-configuration interaction (SAC-CI) methodology, with the same basis set, were used to calculate the ionization and excitation energies of the SF6@Hen structures. Using the calculated ionization and absorption energies and their intensities, the photoelectron and absorption spectra of the considered SF6@Hen structures were simulated and compared with the experiment.

Theoretical Modeling of the Chirality Discrimination of Enantiomers by Nanotubular Cyclic Peptides using Gas-Phase Photoelectron Spectroscopy: An ONIOM Spectroscopic Calculations.

In the present work, the chirality recognition of the enantiomers of a chiral molecule (1-phenyl-1-propanol) interacting with a nanotubular cyclic peptide (E-type cyclic decapeptide) was investigated by their ionization in the gas phase, theoretically. The absolute energy difference between the interaction of the S- and R-enantiomer with the cyclic peptide, calculated at the M06-2X/6-311++G(d, p) level of theory, was 4.70 kcal·mol(-1). Two different schemes of "Our own N-layered Integrated molecular Orbital and molecular Mechanics (ONIOM)" method such as (quantum mechanics (QM):molecular mechanics (MM)) and (QM:QM) were employed to study the effect of the interaction on the gas-phase ionization energies of the enantiomers and cyclic peptide, separately. The symmetry-adapted cluster/configuration interaction (SAC-CI) methodology was used for the calculation of the ionization energies. It was found that the difference between the interactions of R- and S-enantiomer with the cyclic peptide caused different changes in the photoelectron spectrum of each enantiomer so that these changes could be used for the chirality discrimination of the enantiomers in the gas phase. Similarly, the photoelectron spectrum of the cyclic peptide interacting with the R and S-enantiomer were calculated, separately, and it was observed that the difference in the interaction with the R- and S-enantiomer created different changes in the spectrum of cyclic peptide. Finally, it was shown that the difference in the interaction of cyclic peptide with the enantiomers of a chiral molecule in the gas phase can be used for the identification of enantiomers in the gas phase by the direct ionization.

Corona discharge ionization of paracetamol molecule: peak assignment.

Ionization of paracetamol was investigated using ion mobility spectrometry equipped with a corona discharge ionization source. The measurements were performed in the positive ion mode and three peaks were observed in the ion mobility spectrum. Experimental evidence and theoretical calculations were used to correlate the peaks to related ionic species of paracetamol. Two peaks were attributed to protonated isomers of paracetamol and the other peak was attributed to paracetamol fragment ions formed by dissociation of the N-C bond after protonation of the nitrogen atom. It was observed that three sites of paracetamol compete for protonation and their relative intensities, depending on the sample concentration. The ratio of ion products could be predicted from the internal proton affinity of the protonation sites at each concentration.

Theoretical and experimental study of valence photoelectron spectrum of D,L-alanine amino acid.

In this work, the He-I (21.218 eV) photoelectron spectrum of D,L-alanine in the gas phase is revisited experimentally and theoretically. To support the experiment, the high level ab initio calculations were used to calculate and assign the photoelectron spectra of the four most stable conformers of gaseous alanine, carefully. The symmetry adapted cluster/configuration interaction (SAC-CI) method based on single and double excitation operators (SD-R) and its more accurate version, termed general-R, was used to separately calculate the energies and intensities of the ionization bands of the L- and D-alanine conformers. The intensities of ionization bands were calculated based on the monopole approximation. Also, natural bonding orbital (NBO) calculations were employed for better spectral band assignment. The relative electronic energy, Gibbs free energy, and Boltzmann population ratio of the conformers were calculated at the experimental temperature (403 K) using several theoretical methods. The theoretical photoelectron spectrum of alanine was calculated by summing over the spectra of individual D and L conformers weighted by different population ratios. Finally, the population ratio of the four most stable conformers of alanine was estimated from the experimental photoelectron spectrum using theoretical calculations for the first time.

Excitation of 1S and 3S metastable helium atoms to doubly excited states.

We present spectra of triplet and singlet metastable helium atoms resonantly photoexcited to doubly excited states. The first members of three dipole-allowed ;{1,3}P;{o} series have been observed and their relative photoionization cross sections determined, both in the triplet (from 1s2s ;{3}S;{e}) and singlet (from 1s2s ;{1}S;{e}) manifolds. The intensity ratios are drastically different with respect to transitions from the ground state. When radiation damping is included the results for the singlets are in agreement with theory, while for triplets spin-orbit interaction must also be taken into account.