Chemical ionization and Atmospheric-pressure chemical ionization (APCI)

Chemical ionization and  APCI

Chemical ionization (CI) [1] [2] is a complementary method of electron ionization (IE). Since the ion source electron ionization is too energetic, causing too much fragmentation of molecular ions, therefore, the information of the molecular weight may be missing. The basic principle of chemical ionization is to ionize neutral molecules (methane, butane, ammonia …) by electron impact ionization. Once the molecules are ionized, they exchange the charge with the analytes. In this way, the analytes are protected from the electron beam, so chemical ionization is a gentle method compared to the electron ionization. CI ion sources are very similar to IE source, in fact, modern ion sources are built by combining EI/CI and can switch easily.

Positive ion formation

Positive mode charge exchanges produced in the chemical ionization source are generally :

Proton transfer ; M + [B+H]+  [M+H]+  +  B

Adduct formation ; M +X+ → [M+X]+

Echange de charge ; M + X+X + M+

Energy of protonation

Chemical ionization is an acid-base reaction, in this reaction a molecule is a proton donor and the other one is a proton receptor. The ability of a B molecule to accept a proton is quantitatively described by its proton affinity (PA). The protonation process can be described as follows:

Bg + Hg+ → [BH]g+ ; – ΔHro = PA(B)

The proton affinity of the molecule B is the amount of energy produced by proton capture, it is expressed in joules / mol.

The collision of the molecule B with the protonated reactant gas makes it possible to approach the molecules and instantly forms an adduct.


Three situations can occur, either PA (B)> PA (G), molecule B carries the charge (the proton) after the degradation of the adduct, or PA (B) <PA (G), the molecule B is not protonated and it will not be observed in the mass spectrum. The last situation, the adduct is sufficiently stable until detection and it will be observed on the mass spectrum. The stability of the adduct is ensured by the hydrogen bonds and the proton which creates induced moments on the two molecules, this situation is generally observed, when the difference in the proton affinity of the molecules is not high.

In the first situation, molecule B is protonated and acquired the internal energy which is calculated from equation 2.

Eint(M+H) = PA(m) – PA(B)

According to this equation, the internal energy of the protonated molecular ion can be controlled by selecting the appropriate reactant gas according to their proton affinity (Table 1).

Table 1 : Proton affinity
Molecules PA Molecules PA
H2 424 CH4 552
i-C4H10 820 NH3 854
Methanol 757 Méthylamide 896
n-propanol 798 Diéthylamide 945
Diethylether 838 Triéthylamide 972
Formaldehyde 718 Diméthylsulfide 839
Butyraldehyde 806 Méthylnitrile 787
Acetone 823 Ethanethiol 858
Formic Acid 707 m-chloroaniline 867
Acetic Acid 796 n-méthylaniline 912
Acétate d’éthyle 840 3-méthylpyridine 937

Table 1 shows the proton affinity of the most used reactant gases in CI, in which hydrogen is the most exothermic of all the reactant gases, leading to considerable fragmentation. The use of hydrogen as a reactant gas is complicated by hydrogenation processes, which makes IC spectra less predictable, however, H2-CI has proven to be practical in special cases, especially for molecules that are very difficult to ionize. Methane is the gas widely used in CI, it allows to ionize most molecules because its proton affinity is low (Table 1), however the methane-CI spectra show a lot of fragment ions, and sometimes the molecular ions are not observed. The use of gases with high proton affinity significantly reduces fragmentation, such as ammonia or isobutane. Using the gases which have the high proton affinity, adduct ions are also observed, as is the case of ammonia because its proton affinity is high and it can easily form hydrogen bonds (Figure 1).


ionisation chimique masse

Figure 1: The IC spectra of allethrin with the different reactant gases, a) methane, b) isobutane, c) ammonia.

Negative ion formation

Generally all compounds can be ionized in positive mode, but the situation is not the same in the case of negative ions, all compounds do not produce negative ions in chemical ionization. However, many important compounds of environmental or biological interest can produce negative ions under good conditions. For such compounds, the negative mode is sometimes more efficient, more sensitive and selective. Negative ions can be formed by electron capture or by proton exchange with a charged species present in the plasma. In negative mode, a buffer gas is used (usually a common CI gas such as methane) to slow the electrons of the electron beam, until some electrons have just the right energy to be captured by the molecules of the electron beam analyte. The captured electron has very little kinetic energy of the order 1 eV to a few eV, the kinetic energy of the captured electrons does not bring any energy to the molecules, but the electron capture process is an endothermic one that brings about 2-5 eV which is enough to cleavage a covalent bonds. For electrons within too high kinetic energy, they are not captured by the molecule, but they can disrupt the electron cloud of the molecules. If the energy is too high, the disturbance can cause the fragmentation or even the loss of an electron (see also electron ionization), and the analytes are directly ionized by loss of the electron, these reactions are produced in the source CI which are the unwanted reactions.

Main reactions in negative mode.

(1) Proton transfer M + X = (M-H) + XH

(2) Charge exchange M + X = M + X

(3) Nucleophile addition M + X = MX

(4) Nucleophile replacement AB + X = BX + A

Primary ions produced by the reactant gas

The chemical ionization source is being used less and less in mass spectrometry compared to new modern ionization techniques such as MALDI or electrospray [3]. The reactions produced in the CI source are numerous and complicated, but the CI source offers a good understanding of the chemical reactions in the gas phase that do not occur in solution. Because the interactions in the solution such as hydrophobicity, coulomb forces, π-π interactions, van der Waals forces … are strongly reduced or non-existent in the gas phase.

Let’s examine the case of methane used as a reactant gas. The reactions produced under the effect of electron bombardment are:

CH4 → CH4+, CH3+, CH2+, CH+, C+, H2+, H+

Then the chemical reactions that have been systematically studied.

CH4+. + CH4 → CH5+ + CH3

CH3+ CH4 → C2H7+ → C2H5+ + H2

CH2+● + CH4 → C2H4+● +H2

CH2+● + CH4 → C2H3+ + H2 + H

C2H3+ + CH4 → C3H5+ + H2

C2H5+ + CH4 → C3H7+ + H2

Atmospheric-pressure chemical ionization (APCI)

The abundance of ions produced in the CI source is strongly influenced by the temperature and pressure in the source. These reactions produce molecules that contribute to increasing the pressure of the source, but their pressure contributions are low and do not affect the reproductivity of the IC spectra. Chemical ionization at atmospheric pressure (APCI) [4] [5] is a complementary method to electrospray. APCI does not generate multicharged ions, and operates at higher temperatures; it is commonly used to analyze polar and nonpolar compounds of low molecular weight (<1000 Da) and thermostable. APCI is a soft ionization method, it does not produce (or very little) fragmentation, and the ions produced are monocharged. The principle of APCI is to ionize the primary ions and then these ions exchange the charge with solvent molecules that exchange the charge in turn with the analytes (Figure 2), so it is based on the same principle of the chemical ionization but the reactions are carried out at atmospheric pressure. In the APCI source, the electron cloud is emitted by a corona discharge, the primary ions are produced from the gas in the atmosphere such as nitrogen, and oxygen.


Chemical ionization and Atmospheric-pressure chemical ionization (APCI)

Chemical ionization and Atmospheric-pressure chemical ionization (APCI)

Figure 2: Diagram of the APCI source

Figure 2 shows the operation of the APCI source, the analyte is introduced into the source at a flow rate of about 1.5 ml/min. The capillary is heated by a nitrogen gas nebulizer, at the outlet of the capillary, the liquid forms small gullets which will be heated to the temperature of 300-500°C which are transformed into steam. The steam passes through a stream of electrons emitted by the corona discharge brought to a potential of 5-10 kV, then the exchanges of charge will be carried out in the atmospheric pressure. In APCI the primary ions are ions formed from the discharge of the molecules present in the atmosphere such that N2 and O2 which form N2 + ions, N2+, N2+, O2+… then they exchange their charge with the molecules of the solvent. The APCI source can be used in positive and negative mode, in negative mode, the ions are produced by electron capture or by proton subtraction. The APCI source makes it easier to couple with liquid chromatography with respect to the source CI. It is less sensitive compared to electrospray, but for polar compounds such as lipids, it may offer some advantages over electrospray.

[1] Chemical ionization of amino acids C. W. Tsang, A. G. Harrison J. Am. Chem. Soc., 1976, 98 (6), pp 1301–1308

DOI: 10.1021/ja00422a001

[2] Herman,  J.A.;  Harrison,  A.G.  Effect  of Protonation Exothermicity on the CI Mass Spectra   of   Some   Alkylbenzenes.   Org. Mass Spectrom. 1981,16, 423-427.

[3] Yamashita, M. and J.B. Fenn. 1984. Electrospray ion-source—another variation on the free-jet theme. J. Phys. Chem. 88:4451-4459.

[4] Atmospheric pressure ionization (API) mass spectrometry. Solvent-mediated ionization of samples introduced in solution and in a liquid chromatograph effluent stream. Horning EC, Carroll DI, Dzidic I, Haegele KD, Horning MG, Stillwell RN. J Chromatogr Sci. 1974 Nov;12(11):725-9.

[5] ATMOSPHERIC PRESSURE IONIZATION MASS SPECTROMETRY Eric C. Huang Timothy Wachs James J. Conboy Jack D. Henion Anal. Chem., 1990, 62 (13), pp 713A–725A

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