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== Advantages and limitations == One of the main advantages of CI over EI is the reduced fragmentation as noted above, which for more fragile molecules, results in a peak in the mass spectrum indicative of the molecular weight of the analyte. This proves to be a particular advantage for biological applications where EI often does not yield useful molecular ions in the spectrum. The spectra given by CI are simpler than EI spectra and CI can be more sensitive than other ionization methods, at least in part to the reduced fragmentation which concentrates the ion signal in fewer and therefore more intense peaks. The extent of fragmentation can be somewhat controlled by proper selection of reagent gases. Moreover, CI is often coupled to chromatographic separation techniques, thereby improving its usefulness in identification of compounds. As with EI, the method is limited to compounds that can be vapourized in the ion source. The lower degree of fragmentation can be a disadvantage in that less structural information is provided. Additionally, the degree of fragmentation and therefore the mass spectrum, can be sensitive to source conditions such as pressure, temperature, and the presence of impurities (such as water vapour) in the source. Because of this lack of reproducibility, libraries of CI spectra have not been generated for compound identification.

== Applications ==

CI mass spectrometry is a useful tool in structure elucidation of organic compounds. This is possible with CI, because formation of [M+1]+ eliminates a stable molecule, which can be used to guess the functional groups present. Besides that, CI facilitates the ability to detect the molecular ion peak, due to less extensive fragmentation. Chemical ionization can also be used to identify and quantify an analyte present in a sample, by coupling chromatographic separation techniques to CI such as gas chromatography (GC), high performance liquid chromatography (HPLC) and capillary electrophoresis (CE). This allows selective ionization of an analyte from a mixture of compounds, where accurate and precised results can be obtained.

== Variants ==

=== Negative chemical ionization === Chemical ionization for gas phase analysis is either positive or negative. Almost all neutral analytes can form positive ions through the reactions described above. In order to see a response by negative chemical ionization (NCI, also NICI), the analyte must be capable of producing a negative ion (stabilize a negative charge) for example by electron capture ionization. Because not all analytes can do this, using NCI provides a certain degree of selectivity that is not available with other, more universal ionization techniques (EI, PCI). NCI can be used for the analysis of compounds containing acidic groups or electronegative elements (especially halogens).Moreover, negative chemical ionization is more selective and demonstrates a higher sensitivity toward oxidizing agents and alkylating agents. Because of the high electronegativity of halogen atoms, NCI is a common choice for their analysis. This includes many groups of compounds, such as PCBs, pesticides, and fire retardants. Most of these compounds are environmental contaminants, thus much of the NCI analysis that takes place is done under the auspices of environmental analysis. In cases where very low limits of detection are needed, environmental toxic substances such as halogenated species, oxidizing and alkylating agents are frequently analyzed using an electron capture detector coupled to a gas chromatograph. Negative ions are formed by resonance capture of a near-thermal energy electron, dissociative capture of a low energy electron and via ion-molecular interactions such as proton transfer, charge transfer and hydride transfer. Compared to the other methods involving negative ion techniques, NCI is quite advantageous, as the reactivity of anions can be monitored in the absence of a solvent. Electron affinities and energies of low-lying valencies can be determined by this technique as well.

=== Charge-exchange chemical ionization === This is also similar to CI and the difference lies in the production of a radical cation with an odd number of electrons. The reagent gas molecules are bombarded with high energy electrons and the product reagent gas ions abstract electrons from the analyte to form radical cations. The common reagent gases used for this technique are toluene, benzene, NO, Xe, Ar and He. Careful control over the selection of reagent gases and the consideration toward the difference between the resonance energy of the reagent gas radical cation and the ionization energy of the analyte can be used to control fragmentation. The reactions for charge-exchange chemical ionization are as follows.

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{\displaystyle {\ce {He{}+e^{-}->He^{+\bullet }{}+2e^{-}}}}




  
    
      
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{\displaystyle {\ce {He^{+\bullet }{}+M->M^{+\bullet }}}}

=== Atmospheric-pressure chemical ionization === Chemical ionization in an atmospheric pressure electric discharge is called atmospheric pressure chemical ionization (APCI), which usually uses water as the reagent gas. An APCI source is composed of a liquid chromatography outlet, nebulizing the eluent, a heated vaporizer tube, a corona discharge needle and a pinhole entrance to 103 torr vacuum. The analyte is a gas or liquid spray and ionization is accomplished using an atmospheric pressure corona discharge. This ionization method is often coupled with high performance liquid chromatography where the mobile phase containing eluting analyte sprayed with high flow rates of nitrogen or helium and the aerosol spray is subjected to a corona discharge to create ions. It is applicable to relatively less polar and thermally less stable compounds. The difference between APCI and CI is that APCI functions under atmospheric pressure, where the frequency of collisions is higher. This enables the improvement in sensitivity and ionization efficiency.

== See also == Electrospray ionization Proton-transfer-reaction mass spectrometry

== References ==

== Bibliography == Harrison, Alex. G. (1992). Chemical ionization mass spectrometry (2. ed.). Boca Raton, Fla. [u.a.]: CRC Press. ISBN 9780849342547. Hunt, Donald F.; McEwen, Charles N.; Harvey, T. Michael. (2002). "Positive and negative chemical ionization mass spectrometry using a Townsend discharge ion source". Analytical Chemistry. 47 (11): 17301734. doi:10.1021/ac60361a011. Dass, Chhabil (2007). Fundamentals of contemporary mass spectrometry ([Online-Ausg.]. ed.). Hoboken, N.J.: Wiley-Interscience. ISBN 9780470118498.

== External links == Using Amines as Chemical Ionization Reagents and Building Custom Manifold