Proton affinity of proline and modified prolines using the kinetic method: role of the conformation investigated by ab initio calculations

Fragmentation pattern of amides by EI and HRESI: study of protonation sites using DFT-3LYP data

Amides are important natural products which occur in a few plant families. Piplartine and piperine, major amides in Piper tuberculatum and P. nigrum, respectively, have shown a typical N–CO cleavage when analyzed by EI-MS or HRESI-MS. In this study several synthetic analogs of piplartine and piperine were subjected to both types of mass spectrometric analysis in order to identify structural features influencing fragmentation. Most of the amides showed an intense signal of the protonated molecule [M + H]⁺ when subjected to both HRESI-MS and EI-MS conditions, with a common outcome being the cleavage of the amide bond (N–CO). This results in the loss of the neutral amine or lactam and the formation of aryl acylium cations. The mechanism of N–CO bond cleavage persists in α,β-unsaturated amides because of the stability caused by extended conjugation. Computational methods determined that the protonation of the piperamides and their derivatives takes place preferentially at the amide nitrogen supporting the dominant the N–CO bond cleavage.

The N–CO cleavage of α,β-unsaturated piperamides under EI and ESI is supported by computational studies.

Kinetic Method Analysis of the Effect of cis- and trans-Hydroxylation on the Proton Affinity of Proline

Proton affinities of proline and hydroxyproline were measured using the Cooks’ kinetic method. The measurements show that hydroxylation increases the proton affinity, which is consistent with X3LYP computation results. This work supports findings from a previous study (S. Mezzache et al., Rapid Commun. Mass Spectrom. 2005, 19, 2279) that modification of proline increases its proton affinity, but it does not provide compelling evidence for the prediction in the same study that proton affinity of the molecule is substantially influenced by intramolecular interactions involving the proton. PBE1PBE calculations suggest that isotropic polarizability rather than intramolecular hydrogen-bonding interactions provides a more suitable diagnosis for trends in proton affinity changes associated with modifications.

Electronic effects of 11β substituted 17β-estradiol derivatives and instrumental effects on the relative gas phase acidity

Numerous studies have highlighted the role of the proton donor characteristics of the phenol group of 17β-estradiol (E(2)) in its association with the estrogen receptor alpha (ERα). Since the substitutions at position C((11)) have been reported to modulate this association, we hypothesized that such substitutions may modify the phenol acidity. Hence, phenol gas-phase acidity of nine C((11))-substituted E(2)-derivatives were evaluated using the extended Cooks' kinetic method, which is a method widely used to determine thermochemical properties by mass spectrometry. To enhance accuracy in data collection we recorded data from several instruments, including quadrupole ion trap, triple quadrupole, and hybrid QqTOF. Indeed, we report for the first time the use of the QqTOF instrument to provide a novel means to improve data accuracy by giving access to an intermediate effective temperature range. All experimental gas-phase acidity values were supported by theoretical calculations. Our results confirmed the ability of distant substituents at C((11)) to modulate the phenol acidity through electrostatic interactions, electron withdrawing inductive effects, and mesomeric effects. However, no relationship was found between the phenol gas-phase acidity of investigated steroids and their binding affinity for ERα assessed in solution. Thus, our results highlight that the intrinsic properties of the hormone do not influence sufficiently the stabilization of the hormone/ERα complex. It is more likely that such stabilization would be more related to factors depending on the environment within the binding pocket such as hydrophobic, steric as well as direct intermolecular electrostatic effects between ERα residues and the substituted steroidal estrogens.

Gas phase basicities of polyfunctional molecules. Part 3: Amino acids

The present article is the third part of a general overview of the gas-phase protonation thermochemistry of polyfunctional molecules (first part: Mass Spectrom. Rev., 2007, 26:775-835, second part: Mass Spectrom. Rev., 2011, in press). This review is devoted to the 20 proteinogenic amino acids and is divided in two parts. In the first one, the experimental data obtained during the last 30 years using the equilibrium, thermokinetic and kinetic methods are presented. A general re-assignment of the values originating from these various experiments has been done on the basis of the commonly accepted Hunter & Lias 1998 gas-phase basicity scale in order to provide an homogeneous set of data. In the second part, theoretical investigations on gaseous neutral and protonated amino acids are reviewed. Conformational landscapes of both types of species were examined in order to provide theoretical protonation thermochemistry based on the truly identified most stable conformers. Proton affinities computed at the presently highest levels of theory (i.e. composite methods such as Gn procedures) are presented. Estimates of thermochemical parameters calculated using a Boltzmann distribution of conformers at 298K are also included. Finally, comparison between experiment and theory is discussed and a set of evaluated proton affinities, gas-phase basicities and protonation entropies is proposed.

Isomeric discrimination and quantification of thyroid hormones, T3 and rT3, by the single ratio kinetic method using electrospray ionization mass spectrometry

The single ratio kinetic method is applied to the discrimination and quantification of the thyroid hormone isomers, 3,5,3'-triiodothyronine and 3,3',5'-triiodothyronine, in the gas phase, based on the kinetics of the competitive unimolecular dissociations of singly charged transition-metal ion-bound trimeric complexes [M(II)(A)(ref*)(2)-H](+) (M(II) = divalent transition-metal ion; A = T(3) or rT(3); ref* = reference ligand). The trimeric complex ions are generated using electrospray ionization mass spectrometry and the ions undergo collisional activation to realize isomeric discrimination from the branching ratio of the two fragment pathways that form the dimeric complexes [M(II)(A)(ref*)-H](+) and [M(II)(ref*)(2)-H](+). The ratio of the individual branching ratios for the two isomers R(iso) is found strongly dependent on the references and the metal ions. Various sets are tried by choosing the reference from amino acids, substituted amino acids, and dipeptides in combination with the central metal ion chosen from five transition-metal ions (Co(II), Cu(II), Mn(II), Ni(II), and Zn(II)) for the complexes in this experiment. The results are compared in terms of the isomeric discrimination for the T(3)/rT(3) pair. Calibration curves are constructed by relating the ratio of the branching ratios against the isomeric composition of their mixture to allow rapid quantitative isomer analysis of the sample pair. Furthermore, the instrument-dependence of this method is investigated by comparing the two sets of results, one obtained from a quadrupole ion trap mass spectrometer and the other from a quadrupole time-of-flight mass spectrometer.

A reevaluation of computed proton affinities for the common alpha-amino acids

The proton affinities of the 20 common amino acids have been computed at the G3MP2 level using structures derived from broad conformational searches at a variety of levels including G3MP2. In some cases, the conformational surveys identified more stable species than had been used in previous studies of proton affinities, though the differences in energy are sometimes rather small. The present values are likely the most reliable measure of amino acid proton affinities in the gas phase. An analysis of differences between these values and those obtained experimentally via the kinetic method indicates that the extraction of proton affinities from kinetic method data can potentially lead to large errors linked to the estimation of relative protonation entropies.

Improved proton affinity measurements for proline and modified prolines using triple quadrupole and ion trap mass spectrometers

Proton affinity (PA) of compounds such as proline, cis-3-methylproline, cis-3-ethylproline, cis-3-isopropylproline and cis-3-isopentanylproline was determined by kinetic method with amines as the reference bases. The effective temperatures determined using ion trap and triple quadrupole mass spectrometers were found to be significantly different. In the case of the triple quadrupole instruments, the effective temperature depends significantly on the collision energy. The influence of the apparent basicity (GBapp) on the effective temperature may be used to estimate the difference in protonation entropy (DeltaDeltaS degrees) between the sample and reference compounds. In case of the ion trap mass spectrometer, the variation of the effective temperature as a function of the excitation amplitude is small, so it is difficult to account for the contribution of the entropy effects to the proton affinity value. A better estimation of the PA and DeltaDeltaS degrees values for the investigated molecules is obtained by combining the GBapp and Teff data pairs that are obtained from both the mass spectrometers.

Proton affinity ladder for uridine and analogs: influence of the hydroxyl group on the sugar ring conformation

A ladder of relative proton affinities (PA) for a series of modified uridines (e.g. araU, ddU, 5BrU, 5BrdU and 5IU) was established from competitive dissociations of proton-bound heterodimers using Cooks and co-workers' kinetic method. The studied heterodimers are constituted of a modified nucleoside and either an amino acid or a nucleoside with known PA value. These non-covalent heterodimers were prepared under electrospray conditions to be selected and dissociated into the ion-trap analyzer. These results allowed our PA ladder of uridine and deoxyuridine analogs substituted at the C-5 position in the uracil ring to be extended. From this scale, it was showed that the substitution of hydrogen atom at the C-2' position in the sugar ring by a hydroxyl group involves a decrease of about 7 kJ mol(-1). The experimental values for U, 5MeU, dU, 5MedU, ddU and araU are consistent with those obtained by DFT calculations (B3P86/6-31+G//B3LYP/6-31G(.)). Several neutral and protonated conformations of these compounds were considered, in particular the ring conformation of furanose and the orientation of the base with respect to the sugar ring. These calculated results showed the influence of sugar substituent on the conformation of the neutral form of theses nucleosides. However, the most stable protonated structure is the same for all the studied nucleosides except for araU, where the position of the anti 2'-OH group imposes a specific conformation.

Structures of Cationized Proline Analogues: Evidence for the Zwitterionic Form

The structures of lithiated and sodiated alpha-methyl-proline (alpha-Me-Pro) and structural isomers, both with and without a water molecule, are investigated using blackbody infrared radiative dissociation (BIRD) and density functional theory. From the BIRD kinetic data measured as a function of temperature, combined with master equation modeling of these data, threshold dissociation energies for the loss of a water molecule from these clusters are obtained. These energies are 77.5 +/- 0.5 and 53 +/- 1 kJ/mol for lithiated and sodiated alpha-Me-Pro, respectively. For the nonzwitterionic isomer, proline methyl ester, these values are 3.0-4.5 kJ/mol higher. These results provide compelling experimental evidence that alpha-Me-Pro is zwitterionic in these clusters. Theory at the temperature corrected B3LYP/6-311++G**//B3LYP/6-31++G** level indicates that the salt-bridge or zwitterionic forms of lithiated and sodiated alpha-Me-Pro are between 17 and 23 kJ/mol lower in energy than the nonzwitterionic or charge-solvated forms and that attachment of a single water molecule does not significantly change the structure or the relative energies of these clusters. The proton affinity of proline is 8 kJ/mol higher than that of alpha-Me-Pro, indicating that lithiated and sodiated singly hydrated proline should also be zwitterionic.

Proton affinity of diastereoisomers of modified prolines using the kinetic method and density functional theory calculations: role of the cis/trans substituent on the endo/exo ring conformation

The proton affinity (PA) of cis/trans-3-prolinoleucines and cis/trans-3-prolinoglutamic acids have been studied by the kinetic method and density functional theory (DFT) calculations. Several conformations of the neutral and the protonated modified prolines, in particular the endo and exo ring conformations, were analyzed with respect to their contribution to the PA values. When the substituent is an alkyl, both the diastereoisomers have the same PA value. However, the PA values for the diastereoisomers are different when the substituted chain contains functional groups (e.g. a carboxyl group). This variation in PA values could be attributed to the existence of intramolecular hydrogen bonds.

Isomeric discrimination of arginine-containing dipeptides using electrospray ionization-ion trap mass spectrometry and the kinetic method

The Kinetic Method (KM), applied commonly for thermochemical determinations, is used here for sterically-controlled isomeric determination of N- versus C-terminal Arg-containing dipeptide isomers (ArgX versus XArg; where X = His, Leu, Lys, Pro, Ser, Phe, and Tyr). The KM is offered as an alternate approach to direct collision-induced dissociation (CID) procedures. Through formation, isolation, and dissociation of a sterically-encumbered, metal-centered complex with electrospray ionization ion trap mass spectrometry technology, reference dipeptide molecules are screened to quantitatively differentiate a mixture of isomers based on their arrangement about the metal center. Arg-containing dipeptide molecules are chosen because of their contribution in a wide array of protein and peptide functions. Additionally, problems cited previously for evaluation of systems containing Arg residues (due to the incorporation of the guanidinium moiety) by the KM are addressed. The method is shown to be successful for highlighting favorable reference analytes (e.g., ArgPhe, ArgLeu, ProArg, PheArg, among others) for exceptional discrimination (R(iso) > 2.0) of the majority of N- and C-terminal Arg-containing peptides tested.