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*   Base Page
Use the Base page to specify the type of knowledge base the system uses for predicting fragmentation pathways. See Base page of the Reaction Restrictions dialog box.
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To minimize the generation of useless fragments
Some mechanisms of small fragments can fit virtually every structure and can generate an immense number of useless fragments.
1.
In the Spreadsheet view for the library, clear the Active check box for these structures in the Fragmentation Library.
For additional information about active records, see Spreadsheet View.
2.
The fragment generation ignores the inactive records in the Fragmentation Library.
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To disable automatic simulation
Select the Library Ionization Only check box and add an ionization mechanism to the library.
Note  When a neutral molecule is provided, the application automatically simulates the ionization process according to the selected ionization mode on the Ionization & Cleavage page. You must first disable this automatic simulation feature to use a different ionization site. For additional information, see Ionization and Cleavage Page.
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To speed up fragment generation
1.
Select the General Fragmentation Rules option in the Knowledge Base area.
The fragmentation library mechanisms must follow general fragmentation rules.
2.
Clear the Ignore General Frag. Rules in Library Reactions check box in the Fragmentation Library Options area.
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To exclude mechanisms with unspecified charge sites
Select the Charge Localization Concept Only check box in the Fragmentation Library Options area.
This option excludes mechanisms in the fragmentation library that contain unspecified charge sites from the generation process.
Note  Structures with an unspecified charge site in the fragmentation library or in the starting structure slow the generation process. When you use an unspecified charge site, the system must consider a large number of combinations for each step. When possible, avoid using unspecified charge sites in the fragmentation library.
Base page of the Reaction Restrictions dialog box
Activates the Selected Fragmentation Library and the Fragmentation Library Options areas where you can choose the libraries and options to use for generating fragments and mechanisms.
The HighChem Fragmentation Library contains approximately 19 000 mechanisms, so calculation times are significantly longer when you choose this library.
Ignores records in the Fragmentation Library that are not marked as Active. When this option is not selected, the fragmentation generation function considers all mechanisms from the selected libraries.
Ignore General Frag. Rules in Library Reactions
Excludes mechanisms in the fragmentation library that contain unspecified charge sites from the generation process.
Display This Window Every Time Generation of Fragments & Mechanisms Is Started
Opens the Reaction Restrictions dialog box each time you start fragment generation. Clear this check box if you want to use the same parameter settings for subsequent fragment generations and do not want to see this dialog box each time.
If you clear this option and want to return to displaying the Reaction Restrictions dialog box each time you start fragment generation, follow the instructions To restore the Reaction Restrictions dialog box each time you start fragment generation.
Restores all default values in the Reaction Restrictions dialog box. These values take effect after the regeneration of fragments and mechanisms and affect all subsequent generations. The current Fragments & Mechanisms windows are not affected.


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Related Topics:
  Ionization and Cleavage Page
  H-Rearrangements Page
  Resonance Page
  Additional Page
  Sizes Page
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