Protonated molecular cations

Some of the target molecules gain so much excess internal energy in a short space of time that they lose an electron and become ions. These are the molecular cation-radicals found in mass spectrometry by the direct absorption of radiation. However, these initial ions may react with accompanying neutral molecules, as in chemical ionization, to produce protonated molecules. 

To gain insight into the structure of these biomarkers, ESI MS/MS analyses were carried out by selecting the protonated molecular ions of the compounds of interest in the first quadmpole of the mass spectrometer. This cation was then collided with argon at a chosen energy in the second quadmpole and analysed in the third quadmpole (Gamier... 

A little recognized systematic error in the calculation of accurate masses of, for example, small radical cation molecular ions (as in electron ionization (El)) or protonated molecular ions (as seen in the soft ionization methods) is the fact that the electron has a small, but finite mass. The accurate masses of radical cations, in which a valence electron has been removed, of anions that have been created by capture of an electron, and of protonated species produced by soft ionization processes, should take into consideration this small mass difference [19]. For example, there is a small difference between the relative atomic mass of a neutral hydrogen atom and a proton. The accepted accurate mass of 1H° is 1.007825 Da. The accurate mass of 1H+ is 1.007276 Da. To be completely correct, expected accurate masses of protonated molecular ions, [M+H]+, produced by electrospray should be calculated using the mass of one H+, rather than all of neutral hydrogen atoms. Mamer and Lesimple do acknowledge, however, that, for large molecules, the error is of little consequence. 

Analytes of very high polarity are not anymore ionized by field ionization. Here, the prevailing pathways are protonation or cationization, i.e., the attachment of alkali ions to molecules. [78] The subsequent desorption of the ions from the surface is effected by the action of the electric field. As [M-t-Na]" and [M-i-K] quasi-molecular ions are already present in the condensed phase, the field strength required for their desorption is lower than that for field ionization or field-induced [Mh-H]" ion formation. [37,79] The desorption of ions is also effective in case of ionic analytes. 

Protonated and cationized species are the most commonly detected ions using the ES process if a positive ionization mode is selected. Protonation is a result of the addition of proton(s) to a neutral molecule for every proton added, a net charge of +1 will result. Similarly, canonization is due to the addition of cation(s) to a neutral molecule. Detection of cationized ions can be useful in the determination of molecular mass of unknown analytes.If ESI is operated under negative ion mode, deprotonated ions will usually be the most dominant ions. Eor either operation mode, solvent adducts of the protonated/deprotonated ions are frequently detected in ESI/MS mass spectra. 

The FAB matrix is essentially a nonvolatile liquid material, such as those illustrated in Scheme 1, that serves to constantly replenish the surface with new sample as the incident ion beam bombards the surface. The matrix also serves to minimize sample damage from the high-energy particle beam by absorbing most of the incident energy and is believed to facilitate the ionization process. The spectrum produced often includes matrix peaks along with some fragments and a peak for the protonated or cationized (i.e., M + Na+) molecular ion. 

These interactions may usefully be described as an acid-base type interaction, in which the cyclopropane ring acts as a base (electron donor) and the proton or cationic center acts as the acid (electron acceptor). One of the factors that controls the basicity of a hydrocarbon is the energy of the highest occupied molecular orbital (HOMO).60 The 6-31 G HOMO energies of some cycloalkanes and cycloalkenes are given in Table 4.61... 

The second process involves the formation of protonated or cationized molecular ions, i.e., [M+H]+ or [M+C]+, where the cationizing species C is usually a metal ion from the substrate, matrix, or an impurity. The basic fragmentation process... 

The LD spectrum of the tridecapeptlde neurotensin (Figure 4), shows several differences. Here fragmentation results almost exclusively from small neutral losses. A protonated molecular ion is still one of the major ions observed (m/z = 1673) and some cationized (K+) fragment species are apparent as well as a small amount of cationized molecular ion (<5%). Resolution has begun to be degraded to some extent, partially due to the decrease in overall ion signal which necessitates transformation of fewer data points to maximize signal to noise ratio. 

Under LD conditions, alkali metal cation attachment is the dominant ionization process. Protonated molecular and fragment ions are generally not... 

In MALDI, the sample is deposited on a target and co-ciystallized with a solid matrix [14-15]. The target is transferred to vacuum and bombarded by photon pulses from a laser, in most cases a nitrogen laser (337 nm) nowadays. The ionization results from efficient electronic excitation of the matrix and subsequent transfer of the energy to the dissolved analyte molecules, which are desorbed and analysed as protonated or cationized molecules [7]. The ionization process is not fully understood. Extremely high molecular-mass compounds, e.g., in excess of 200 kDa, can be analysed using the MALDI, if performed on a time-of-flight mass spectrometer (Ch. 2.4.3). 

The term "molecular ion" by definition refers to a radical cation or anion of an intact molecule. Molecular ions are odd-electron ions, which may thus be generated by El. Unfortimately, the term molecular ion is also frequently used to indicate the even-electron ionic species produced by electrospray and APCl. This obviously is not correct. In the soft ionization techniques, predominantly even-electron protonated molecules are generated in positive-ion mode, and deprotonated molecules in negative ions. In addition, various adduct ions may be generated (Table 2.2). These all are even-electron ions, and should therefore not be referred to as molecular ions. Alternatively, the term protonated molecular ions is used, which again is incorrect one cannot protonate a radical cation ... 

Finally, the desorption chemical ionization (DCI) mass spectra of several synthetic nucleosides, mostly in the pyrimidine series, have been recorded. The potential application of protonated or cationized (NH4 ) molecular ions and bases for the detection of these nucleosides has been demonstrated. One of the important features of these spectra is the presence of [ B + H ] and/or [B -f- NHJ ions, which confirms the previously described general fragmentation scheme. In desorption chemical ionization studies (which describe in-beam experiments in a Cl source), the desorption of intact molecules, followed by ionization, is often confused with the desorption of preformed ions. Slow hydrolysis within a Cl source leads to intense ions (e.g., [BH]" ) such as those observed for nucleosides, as well as for intact DNA. ... 

Within the time scale of the electron hydration process, the primary water molecular cation (H20 ) reacts with surrounding water molecules (ion-molecule reaction, equation 5). This ultrafast proton transfer is faster than a second electron stabilization channel for which a concerted electron-proton transfer is under consideration (equation 7) (56, 72, 73). 

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