Jean-Yves Salpin

A relationship between the kinetics and thermochemistry of proton transfer reactions in the gas phase

Abstract For the proton transfer reaction [MH]+ + B → M + [BH]+ (I) a correlation is observed between the experimental reaction rate kexp and the standard free energy variation ΔG°. This correlation may be described by a relationship of the type k exp /k coll = 1 [1 + exp (ΔG° + G a °)/RT] where kcoll is the collision rate constant and ΔGa° an apparent energy barrier for reaction (I). It is found that ΔGa° is of the same order as RT and thus the preceding relationship allows the determination of unknown gas-phase basicities. Implications for the use of the “bracketing” and the “kinetic” methods are discussed.

Tautomerism of Uracil Probed via Infrared Spectroscopy of Singly Hydrated Protonated Uracil

Tautomerism of the nucleobase uracil is characterized in the gas phase through IR photodissociation spectroscopy of singly hydrated protonated uracil created with tandem mass spectrometric methods in a commercially available Fourier transform ion cyclotron resonance mass spectrometer. Protonated uracil ions generated by electrospray ionization are re-solvated in a low-pressure collision cell filled with a mixture of water vapor seeded in argon. Their structure is investigated by IR photodissociation spectroscopy in the NH and OH stretching region (2500-3800 cm(-1)) with a tabletop IR laser source and in the 1000-2000 cm(-1) range with a free-electron laser. In both regions the IR photodissociation spectrum exhibits well-resolved spectral signatures that point to the presence of two different types of structure for monohydrated protonated uracil, which result from the two lowest-energy tautomers of uracil. Ab initio calculations confirm that no water-catalyzed tautomerization occurs during the re-solvation process, indicating that the two protonated forms of uracil directly originate from the electrospray process.

Interaction of cisplatin with adenine and guanine: a combined IRMPD, MS/MS, and theoretical study.

Infrared multiple photon dissociation (IRMPD) spectroscopy of cis-[Pt(NH(3))(2)(G)Cl](+) and cis-[Pt(NH(3))(2)(A)Cl](+) ions (where A is adenine and G is guanine) has been performed in two spectral regions, 950-1900 and 2900-3700 cm(-1). Quantum chemical calculations at the B3LYP/LACV3P/6-311G** level yield the optimized geometries and IR spectra for the conceivable isomers of cis-[Pt(NH(3))(2)(G)Cl](+) and cis-[Pt(NH(3))(2)(A)Cl](+), whereby the cisplatin residue is attached to the N7, N3, or carbonyl oxygen atom, (O6), of guanine and to the N7, N3, or N1 position of adenine, respectively. In addition to the conventional binding sites of native adenine, complexes with N7-H tautomers have also been considered. In agreement with computational results, the IR characterization of cis-[Pt(NH(3))(2)(G)Cl](+) points to a covalent structure where Pt is bound to the N7 atom of guanine. The characterized conformer has a hydrogen-bonding interaction between a hydrogen atom of one NH(3) ligand and the carbonyl group of guanine. The experimental C═O stretching feature of cis-[Pt(NH(3))(2)(G)Cl](+) at 1718 cm(-1), remarkably red-shifted with respect to an unperturbed C═O stretching mode, is indicative of a lengthened CO bond in guanine, a signature that this group is involved in hydrogen bonding. The IRMPD spectra of cis-[Pt(NH(3))(2)(A)Cl](+) are consistent with the presence of two major isomers, PtAN3 and PtAN1, where Pt is bound to the N3 and N1 positions of native adenine, respectively.

Protonated Urea Collision-Induced Dissociation. Comparison of Experiments and Chemical Dynamics Simulations

Quantum mechanical plus molecular mechanical direct chemical dynamics were used, with electrospray tandem mass spectrometry experiments, potential energy surface calculations, and RRKM analyses, to study the gas-phase collision-induced dissociation (CID) of protonated urea. The direct dynamics were able to reproduce some of the experimental observations, in particular the presence of two fragmentation pathways, and, thus, to explain the dynamical origin of the two fragmentation ions observed in the CID spectra. A shattering dissociation mechanism takes place during the collision, and it becomes more important as the collision energy increases, thus explaining the linear increase of the high-energy reaction path (loss of ammonia) versus collision energy. By combining the different theoretical and experimental findings, a complete dynamical picture leading to the fragmentation was identified: (i) Oxygen-protonated urea, the most stable structure in the gas phase, must first isomerize to the nitrogen-protonated form. This can happen by multiple CID collisions or in the electrospray ionization process. (ii) Once the nitrogen-protonated isomer is formed, it can dissociate via two mechanisms: i.e, a slow, almost statistical, process forming a NH(4)(+)--NHCO intermediate that rapidly dissociates or a fast nonstatistical process which may lead to the high-energy products.

Interaction of Ca2+ with uracil and its thio derivatives in the gas phase

The structures and relative stabilities of the complexes formed by uracil and its sulfur derivatives, namely, 2-thio-, 4-thio, and 2,4-dithio-uracil when interacting with Ca(2+) in the gas phase have been analyzed by means of density functional theory (DFT) calculations carried out at the B3LYP/6-311++G(3df,2p)//B3LYP/6-31+G(d,p) level. For uracil and 2,4-dithiouracil, where the two basic sites are the same, Ca(2+) attachment to the heteroatom at position 4 is preferred. However, for the systems where both types of basic centers, a carbonyl or a thiocarbonyl group, are present, Ca(2+)-oxygen association is favored. The most stable complexes correspond to structures with Ca(2+) bridging between the heteroatom at position 2 of the 4-enol (or the 4-enethiol) tautomer and the dehydrogenated ring nitrogen, N3. The enhanced stability of these enolic forms is two-fold, on the one hand Ca(2+) interacts with two basic sites and on the other triggers a significant aromatization of the ring. Besides, Ca(2+) association has a clear catalytic effect on the tautomerization processes which connect the oxo-thione forms with the enol-enethiol tautomers. Hence, although the enol-enethiol tautomers of uracil and its thio derivatives should not be observed in the gas phase, the corresponding Ca(2+) complexes are the most stable species and should be accessible, because the tautomerization barriers are smaller than the Ca(2+) binding energies.

Gas-phase basicity of glycine, alanine, proline, serine, lysine, histidine and some of their peptides by the thermokinetic method.

The thermokinetic method is applied to a set of six amino acids (glycine, alanine, proline, serine, lysine, histidine) and 30 of their di-and tri-peptides for which experimental proton transfer rate constants were available. The comparison between the presently determined gas-phase basicities, GBs, of the amino acids with values obtained from equilibrium constant determination is generally good (a mean deviation of ∼3 kJ mol−1 is observed). Derived proton affinities values are discussed. The gas-phase basicities of peptides provided by the present study correct several previously estimated values thus offering a more firm basis for structural discussion. Composite reaction efficiency curves indicate the existence, for several peptides, of at least two non-interconverting populations of protonated forms.

Selenourea−Ca2+ Reactions in Gas Phase. Similarities and Dissimilarities with Urea and Thiourea

The gas-phase reactions between Ca(2+) and selenourea were investigated by means of electrospray/tandem mass spectrometry techniques. The MS/MS spectra of [Ca(selenourea)](2+) complexes show intense peaks at m/z 43, 121, 124, and 146 and assigned to monocations produced in different coulomb explosion processes. The structures and bonding characteristics of the stationary points of the [Ca(selenourea)](2+) potential energy surface (PES) were theoretically studied by DFT calculations carried out at the B3LYP/6-311+G(3df,2p)//B3LYP/6-311+G(d,p) level. The analysis of the topology of this PES allows identification of H(2)NCNH(+), CaSeH(+), selenourea(+). and CaNCSe(+) ion peaks at m/z 43, 121, 124, and 146, respectively. The reactivity of selenourea and the topology of the corresponding potential energy surface mimic that of thiourea. However, significant dissimilarities are found with respect to urea. The dissociative electron-transfer processes, not observed for urea, is one of the dominant fragmentations for selenourea, reflecting its much lower ionization energy. Similarly, the coulomb explosions yielding CaXH(+) + H(2)NCNH(+) (X = O or Se), which for urea are not observed, are very favorable for selenourea. Finally, while in urea the loss of NH(3) competes with the formation of NH(4+), for selenourea the latter process is clearly dominant.

Re-evaluated gas phase basicity and proton affinity data from the thermokinetic method

Gas phase basicities (GB) and proton affinities (PA) of molecules are still the subject of active experimental and theoretical investigations. Recently, a formidable compilation of evaluated GB and PA values of ca. 1700 neutrals has appeared (the Hunter and Lias compilation, 1 which will be abreviated HL hereafter), expanding and correcting the previous review established by the same laboratory. 2 Reevaluation of the GB/PA values derived from gas phase equilibrium experiments or from the ‘kinetic method’ has been made in a more or less straightforward manner. 1 For the values obtained by the ‘thermokinetic method’ the corrections have been made by using a bracketing estimate from the original data. The goal of the present note is to examine, in a more elaborate way, the impact of the new standard values on the GB and PA values obtained in the first applications of the thermokinetic method. It may be briefly recalled that the ‘thermokinetic’ method of determination of gas basicity and proton affinity values uses a correlation between the reaction efficiency (RE) and the standard free energy change, DG o , or the standard enthalpy variation, DH o , of a proton transfer process. 3 For a

Gas-phase interactions between lead(II) ions and thiouracil nucleobases: A combined experimental and theoretical study

The gas-phase interactions between lead(II) ions and 2-thiouracil, 4-thiouracil, and 2,4-dithiouracil have been investigated by combining mass spectrometry and theoretical calculations. The most abundant complexes observed, namely [Pb(thiouracil) − H]+, have been studied by MS/MS experiments. Cationization by the metal allows an unambiguous characterization of the sulfur position, several fragment ions being specific of each isomer. Moreover, compared with the uracil fragmentation, new fragmentation channels are observed: elimination of PbS or total reduction of the metal. Calculations performed on the different structures, including tautomers, show that sulfur is the preferred complexation site, suggesting the greater affinity of lead for sulfur. The most stable structures are always preferentially bidentate. Natural population analysis indicates a charge transfer from the base to the metal with a more pronounced covalent character for sulfur compared to oxygen. Energetic profiles associated with the main fragmentations have been described.

Collision induced dissociation of doubly-charged ions: Coulomb explosion vs. neutral loss in [Ca(urea)]2+ gas phase unimolecular reactivity via chemical dynamics simulations

In this paper we report different theoretical approaches to study the gas-phase unimolecular dissociation of the doubly-charged cation [Ca(urea)](2+), in order to rationalize recent experimental findings. Quantum mechanical plus molecular mechanical (QM/MM) direct chemical dynamics simulations were used to investigate collision induced dissociation (CID) and rotational-vibrational energy transfer for Ar + [Ca(urea)](2+) collisions. For the picosecond time-domain of the simulations, both neutral loss and Coulomb explosion reactions were found and the differences in their mechanisms elucidated. The loss of neutral urea subsequent to collision with Ar occurs via a shattering mechanism, while the formation of two singly-charged cations follows statistical (or almost statistical) dynamics. Vibrational-rotational energy transfer efficiencies obtained for trajectories that do not dissociate during the trajectory integration were used in conjunction with RRKM rate constants to approximate dissociation pathways assuming complete intramolecular vibrational energy redistribution (IVR) and statistical dynamics. This statistical limit predicts, as expected, that at long time the most stable species on the potential energy surface (PES) dominate. These results, coupled with experimental CID from which both neutral loss and Coulomb explosion products were obtained, show that the gas phase dissociation of this ion occurs by multiple mechanisms leading to different products and that reactivity on the complicated PES is dynamically complex.