Once reaction-generating process has finished, a Fragments & Mechanisms window is displayed.

A Fragments & Mechanism window allows the display of either complete mechanisms of ion-decomposition reactions, or of resulting fragments only. To display the desired mechanism, or fragment for a particular m/z value, choose the appropriate m/z tab. If you do not like the tab control you can replace it with a combo box in the Options | Mechanism Layout dialog window.

A Fragments & Mechanism window contains two Copy buttons. The first one is designed for the copying of mechanisms in graphic format (Enhanced Windows Metafile). The second one is for the copying of a selected fragment. If you copy a fragment, this can be pasted to Structure Editor, Database Manager in Mass Frontier or to any Windows application.

Several possible isobaric fragments can be generated for a particular m/z value. If more then one fragment is generated for a m/z value, a hand pointer with the caption “Select possible fragments with m/z xy” will move from right to left to draw your attention to this fact. The isobaric fragments, with their corresponding mechanisms, can be displayed by clicking the numbered buttons next to the hand pointer.

The fragments are sorted according to the simplicity of their production mechanism. So, fragment No.1 is produced by the simplest (shortest) mechanism. The isobaric fragments are usually isomers of the same fragments with a different charge, radical or, p-bond location.

The Fragments & Mechanisms module is based on an expert system, which uses a mathematical approach for the simulation of unimolecular ion-decomposition reactions. So, it is important to understand what the system is, and is not capable of, and what the user can, and cannot, expect from this module.

The expert system, which generates possible fragmentation and rearrangement pathways, is based on the following assumptions:

• General Fragmentation and Rearrangement Rules - The system optionally predicts reaction pathways that are based on general fragmentation and rearrangement rules. Compound specific mechanisms that cannot be applied generally are not included in this feature. Although this might initially seem a disadvantage, this feature can be used in combination with a substructure search for the identification of specific compound classes.

• Fragmentation Library Mechanisms - The system optionally accesses an intelligent fragmentation mechanism knowledge base for the prediction of unimolecular decomposition reactions. HighChem Fragmentation Library™ currently contains around 19,000 individual mechanisms. User mechanisms can be included in fragmentation prediction, as well.

• Charge Localization Concept - Every ion-decomposition reaction that is generated is based on the charge localization concept. The location of the charge site in all precursor and product ions is exactly determined by the program. Mass Frontier internally generates resonance reactions, which are not displayed by default. Please note that charge sites can be moved to distant locations by these reactions and in some complicated structures it may appear that the charge localization concept has been violated. If a reaction step is not clear, you can instruct the program to display mechanisms along with resonance reactions. It is, however, possible to use an unspecified charge location that is internally transformed to all combinatorial structures with a localized charge.

• Unimolecular Linear Reaction Mechanisms - Mass Frontier only generates unimolecular reactions. The reaction pathways are displayed as linear reaction mechanisms, which incorporate one intermediate left-hand site and one intermediate right-hand site for each reaction step. So, only ionic products are included in reaction pathways and neutral fragments are not displayed.

• Even-Electron Rule - Reactions mechanisms are generated in accordance with the Even-Electron rule. The Even-Electron rule says that the homolytic bond cleavages of an even electron ion are energetically unfavorable. Therefore, Mass Frontier never generates radical cations from an even-electron ion.

• Bond Cleavages Only - Using the General Fragmentation and Rearrangement Rules option fragments can only be generated from bond cleavages. Bond creation is not supported, with the exception of the creation of an H-X bond (X=any element) in hydrogen rearrangements. Thus, for this option the expert system does not include ring contractions, cyclizations, or skeletal and non-hydrogen rearrangements. The Fragmentation Library option supports bond creation with all rearrangements and ring transformations.

• Ionization Methods - Mass Frontier supports Electron Impact , protonation , deprotonation, cluster ion formation, alkali metal adducts, and chemical ionization methods.

• Formally Possible Solutions - The mechanisms generated by Mass Frontier contain formally possible reaction steps. The determination of the stability of product ions from thermodynamic data or rates of reaction is not performed. When evaluating generated mechanisms, a simple rule should be kept in mind: Short and uncomplicated reaction pathways are more favorable than complex mechanisms involving complicated, multi-step hydrogen rearrangements.

HighChem Fragmentation Library™ and Fragmentation Library™ are trademarks of HighChem, Ltd., Slovak Republic

Mass Frontier utilizes general unimolecular reactions for prediction of fragmentation, rearrangement and resonance mechanisms.

To preview unimolecular reactions employed by the program:

• Click on the Reaction Mechanisms Overview button in any Fragments & Mechanisms window.

Reaction formalism used in Mass Frontier: