Getting Started

Not all Beilstein and Gmelin substance records include structures. A structure search will eliminate such records.

1. Launch DiscoveryGate: http://www.discoverygate.com
2. Click on SEARCH DATABASES.
   
3. Select database in the MDL Database Browser window.
   
   
   • MDL Compound Index provides one-query access to several databases. Contact askchem for information about licensed access to databases included in the MDL Compound Index.
   • The MDL Compound Index DOES NOT include Gmelin.
   • It is not possible to search Beilstein and Gmelin simultaneously.
4. Click on RESET to delete a previous structure.
5. Delete previous PROPERTY search.
6. Double-click in the Structure box to launch MDL Draw.
   
   

Basic Procedure

1. Click on All-Purpose Drawing tool to draw an entire structure without switching tools.
2. Use templates on the Template Bar to add simple structural fragments.
3. Click on DONE to return structure query to MDL DATBASE BROWSER.
4. Select STRUCTURE QUERY OPTIONS. Options will vary depending on database choice. The following options apply to Beilstein:
   
5. Click on START SEARCH.

Drawing Atoms and Bonds

The default atom view is set to view structures without displaying Carbon or Hydrogen. To change this display:

1. Click on Edit, then Preferences.
   

Atoms

1. Click on All-Purpose Drawing tool to draw structure(s) and bond(s).
2. Click on either the All-Purpose Tool or the Change Atom Tool.
3. Right-click on an existing atom to display the Atom Property window.
4. Click on Atom Symbol.
5. Select desired atom from display or click on ... to open the Symbol window .
6. Choose Change atom type, Allow selected atoms, or Prohibit selected atoms.
7. Select atom(s) from the periodic table.
8. (Optional) Right-click on an existing atom to display the Atom Property window again to set Charge, Valence or other attributes.
9. Click on OK.

Bonds

1. Click on either the All-Purpose Tool or the Bond Tool.
2. Right-click on an existing bond to display Bond Property window.
3. If the bond is unknown, select ANY from Query Bond Type.
4. Click on OK.
   

Merging Atoms and Bonds

1. Click on LASSO.
2. Select the structure to be merged.
3. Drag the selected fragment to the target bond or target atom.
   

Predefined Atom Lists and Generic Groups

A substituent can be defined using predefined atoms, predefined groups, user defined atoms, or user defined groups.

1. Click on either the All-Purpose Tool or the Change Atom Tool.
2. Right-click on an existing atom to open the Change Atom Type window.
3. Select a predefined group in Allow these Atoms or Beilstein Generic Group listings.
   

User Defined Atom Lists

Create user defined atom lists to define specific atom substitutions.

1. Click on either the All-Purpose Tool or the Change Atom Tool.
2. Right-click on an existing atom to display the Atom Property window.
3. Click on Allow these atoms.
4. Click on Atom List... .
5. Select atom(s) from the periodic table.
6. Click on OK.

User Defined R-Groups

Create generic groups to define structure/substructure fragment substituents.

1. Draw the root structure.
2. Click on (R-Group tool), then click on the desired atom to label.
3. Choose a label from the label palette (e. g. R1) .
4. Draw R-group fragments using other drawing tools.
5. Click the R-Group tool, click the fragment you want to add, and drag the fragment onto the R-group definition (Rn=).
   
6. (Optional) To move the attachment point, click the R-Group tool, click the asterisk of the attachment, then drag the asterisk onto the desired atom.
   

Template Files

Group template files are available. Personal User template files may be created by drawing structures and saving the files with a .mol extension in your local MDL\Template directory.

To access Group or User template files:

1. Click on Template Selector in the Template bar.
2. Scroll down the list to find User template files.
3. Select the appropriate directory to view a list of files.
4. Double-click the desired template file to view contents of files.
5. Double-click on the desired structure to place it in the Structure Editor window.

To create a User Template file:

1. Draw desired structure in the Structure Editor.
2. Click on FILE.
3. Click on SAVE AS.
4. Select C:\documents and settings\your profile name\MDLDraw\templates.
   (Note: MAC users: Save the file in \your profile name\MDLDraw\templates.)
5. Name the file with a ".mol" extension and click on SAVE.

To add a custom template to the Template Toolbar:

1. Draw the structure.
2. Select the structure.
3. Drag the structure to an empty position in the horizontal Template Bar. You may need to double-click the structure to have it appear in the Template Bar.
   Caution: If you drag the structure over an exiting template, the former tool is overwritten.

Query Options

1. Select query options in the MDL Database Browser window.