1. Chemical Drawing Overview

Alchemy’s Chemical Drawing is a tool to draw molecular structures and chemical reactions. This enables you to quickly, accurately and easily draw molecules and reactions for future reference in our Lab Book. 

Chemical Drawing consists of the following elements:  

Figure 1.1 Chemical Drawing

1.1 Tool Palette

The tool palette allows you to:

• Draw and edit a molecule or reaction by clicking on and dragging atoms, bonds, and other elements provided with the buttons on the Atoms toolbar and Tool Palette.
• Delete any element of the drawing (atom or bond) by clicking on it with the Erase tool.
• Delete the entire molecule or its fragment using the lasso, rectangle, or fragment selection and the Erase tool.
• Draw special structures.
• Select the entire molecule or its fragment using the selection tools.

Key Benefits: This enables you to quickly, accurately and easily draw molecules and reactions for future reference in our ELN.

1.1.1 Selection Tools

Figure 1.2 Selection Tools - Lasso (1), Rectangle (2), Fragment (3)

To select a single atom or bond: 

• Click the Lasso (1) or Rectangle selection tool (2)
• Click the atom or bond in the drawing

To select an entire structure:

• Select the Fragment selection tool (3)
• Click the object

Alternatively, select the Lasso or Rectangle selection tool, and then drag the mouse over the object.

To select multiple atoms, bonds, structures, or other objects, do one of the following:

• Shift-click with the Lasso or Rectangle Selection tool selects some (connected or not) atoms/bonds.
• With the Lasso or Rectangle Selection tool click and drag the mouse around the atoms, bonds, or structures that you want to select.

Note: Ctrl+Shift-click each structure with the Lasso or Rectangle Selection tool selects several structures.

1.2 Main Toolbar

The Main Toolbar has the following features:

Figure 1.3 Main Toolbar

• Clear Canvas (1) - Clear the entire drawing area with a single click.
• Open (2) - Import a molecule from a molecular file.
• Save As (3) - Save a drawing to a supported molecular file format.
• Copy As (4)
• Paste (5)
• Cut (6)
• Undo (7)
• Redo (8) 
• Aromatize (9) - Mark aromatic structures
• Dearomatize (10) - Convert a structure to kekule presentation.
• Layout (11) - Change the position of the structure.
• Clean Up (12) - Improve the appearance of the structure by assigning uniform bond lengths and angles.
• Calculate CIP (13) - Determine R/S and E/Z configurations.
• Check Structure (14) - Check the following properties of the structure: 

Figure 1.4 Structure Check

• Calculated Values (15) - Displays properties of the structure:
  

Figure 1.5 Calculated Values

• 3D Viewer (16)
• Settings (17) - For molecular files:
  

Figure 1.6 Settings

• Help (18)
• About (19) - Displays version and copyright information of the tool.
• Zoom panel (21) - Displays the current zoom percentage. Click to expand the Zoom panel and use the following actions:
  • Zoom percentage (22) - Set the view manually
  • Zoom out (23) 
  • Zoom in (24) 
  • Zoom 100% (25)

Figure 1.7 Zoom Panel

1.2.1 3D Viewer

The structure appears in a modal window after clicking on the 3D Viewer button in the Main Toolbar:

Figure 1.8 3D View

You can perform the following actions:

• Rotate the structure holding the left mouse button
• Zoom In/Out on the structure

Users can also change the appearance of the structure and background coloring on the 3D Viewer tab from the default settings:

• Drawing Method: Lines
• Atom Name Coloring Method: Bright
• Background Coloring: Light

2. Drawing Atoms

To draw or edit atoms you can:

• Select an atom in the Atoms toolbar and click inside the drawing area
• If the desired atom is absent in the toolbar, click on the PT button to display the Periodic Table and select the desired atom
  

Figure 2.1 Periodic Table

• Add an atom to an existing molecule by selecting an atom in the Atoms toolbar, clicking on an atom in the molecule, and dragging the cursor. The atom will be added with a single bond. Vacant valences will be filled with the corresponding number of hydrogen atoms.
• Change an atom by selecting an atom in the Atoms toolbar and clicking on the atom to be changed. In the event a wrong valence appears, the atom will be underlined in red.
• Change an atom by clicking on an existing atom with the Selection tool and starting to enter text after that. Type another atom symbol in the text box:
  

Figure 2.2 Atom Label Edit

• Change the charge of an atom by selecting the Charge Plus or Charge Minus tool and clicking consecutively on an atom to increase/decrease its charge:
  

Figure 2.3 Atom Charge Tool

• Change an atom or its properties by double-clicking on the atom to invoke the Atom Properties modal:
  

Figure 2.4 Atom Properties

• Click on the ET button to use the Extended table and select a corresponding Generic group or Special Node:
  

Figure 2.5 Extended Table

3. Drawing Bonds

To draw or edit bonds you can:

• Click an arrow on the Bond tool in the Tool palette to open the drop-down list with the following bond types:

Figure 3.1 Bond Tools

• Select a bond type from the list and click inside the drawing area. A bond of the selected type will be displayed.
• Click on an atom in the molecule and a bond of the selected type will be added to the atom at the angle of 120 degrees. 
• Add a bond to the existing molecule by clicking on an atom in the molecule and dragging the cursor. This allows you to set the angle manually. 
• Change the bond type by clicking on it.
• Use the Chain Tool, beneath the Bond tool, to draw consecutive single bonds.
• Change a bond or its properties by double-clicking on the bond to invoke the Bond Properties dialog:

Figure 3.2 Bond Properties

• Clicking on the drawn stereo and dative bonds change their direction.
• Clicking with the Single Bond tool or Chain tool switches the bond type cyclically: Single-Double-Triple-Single.

4. Drawing R-Groups

Use the R-Group toolbox to draw R-groups in Markush structures:

Figure 4.1 R-Group Toolbox

Selecting the R-Group Label Tool (1) and clicking on an atom in the structure invokes the modal to select the R-Group label for a current atom position in the structure:

Figure 4.2 R-Group Label Tool

Selecting the R-Group label and clicking OK converts the structure into a Markush structure with the selected R-Group label:

Figure 4.3a R-Group Label - Single

Note: You can choose several R-Group labels simultaneously:

Figure 4.3b R-Group Label - Multiple

Particular chemical fragments that may be substituted for a given R-Group form a set of R-Group members. R-Group members can be any structural fragment, including functional groups and single atoms or atom lists.

To create a set of R-Group members:

1. Draw a structure to become an R-Group member.
2. Select the structure using the R-Group Fragment Tool (2) to invoke the R-Group modal and select the label of the R-Group to assign the fragment to.
3. Click on Apply to convert the structure into an R-Group member.

Schematically, the entire process of the R-Group member creation can be presented as:

Figure 4.4 R-Group Member Creation

4.1 R-Group Attachment Point

An R-Group attachment point is the atom in an R-Group member fragment that attaches the fragment to the initial Markush structure.

Selecting the Attachment Point Tool (3) and clicking on an atom in the R-Group fragment converts this atom into an attachment point. If the R-Group contains more than one attachment point, you can specify one of them as primary and the other as secondary. You can select between either the primary or secondary attachment point using the dialog that appears after clicking on the atom: 

Figure 4.5 Attachment Points

Below is a resulting view of R-Group attachment points (IUPAC style):

Figure 4.6a R-Group Attachment Points

If there are two attachment points on an R-Group member, there must be two corresponding attachments (bonds) to the R-Group atom that has the same R-Group label. Clicking on Apply in the above dialog creates the attachment points. Below is a resulting view of R-Group attachment points both primary and secondary (IUPAC style):

Figure 4.6b R-Group Attachment Points - Primary and Secondary

5. R-Group Logic

Chemical Drawing enables you to add logic when using R-Groups. To access the R-Group logic:

1. Create an R-Group member fragment as described above.
2. Move the cursor over the entire fragment for the green frame to appear, then click inside the fragment. The following modal appears:
   

Figure 5.1 R-Group Logic Condition

3. Specify Occurrence to define how many of an R-Group occurs. If an R-Group atom appears several times in the initial structure, you will specify Occurrence">n", n being the number of occurrences. If it appears once, you see "R1 > 0".
4. Specify H at unoccupied R-Group sites (RestH): Check or clear the checkbox.
5. Specify the logical Condition. Use the R-Group condition If R(i) Then to specify whether the presence of an R-Group is dependent on the presence of another R-Group.

6. Marking S-Groups

To mark S-Groups, use the S-Group tool and the following modal that appears after selecting a fragment with the tool:

Figure 6.1 S-Group Properties

Available S-Group types include:

• Generic: A pair of brackets without any labels.
• Multiple group: Indicates a number of replications of a fragment, or a part of a structure, in contracted form.
• SRU Polymer: The Structural Repeating Unit (SRU) brackets enclose the structural repeating of a polymer. You have three available patterns:
  • Head-to-tail (default)
  • Head-to-head
  • Either/Unknown

6.1 Superatom S-Group

An abbreviated structure (abbreviation) is all or part of a structure (molecule or reaction component) that has been abbreviated to a text label. Structures that you abbreviate keep their chemical significance, but their underlying structure is hidden.

Figure 6.2 S-Group Properties - Superatom

After applying Superatom S-Group, there is the ability to contract the S-Group and remove the abbreviation, from the right-click menu on the S-Group:

Figure 6.3 S-Group Right-Click Menu

6.2 Data S-Groups

You can attach data to an atom, a fragment, a multi-fragment, a single bond, or a group. The defined set of Names and Values is introduced for each type of selected elements:

Figure 6.4 S-Group Properties - Data

• Select the appropriate S-Group Field Name.
• Select the appropriate Field Value.
• Labels can be specified as Absolute, Relative or Attached.

7. Changing Structure Display

After selecting the structure with the Selection tool, use the Rotate tool (1) to change the structure display:

Figure 7.1 Display Tools

This tool allows for the rotating of objects.

• If some objects are selected, the tool rotates the selected objects.
• If no objects are selected, or all objects are selected, the tool rotates the whole canvas.
• The default rotation step is 15 degrees.
• Press and hold the Ctrl key for more gradual continuous rotation with 1 degree rotation step.

Figure 7.2 Rotation Tool Scale

Select any bond on the structure and click Alt+H to rotate the structure so that the selected bond is placed horizontally. 

Select any bond on the structure and click Alt+V to rotate the structure so that the selected bond is placed vertically.

The Flip Tools flips the objects horizontally (2) or vertically (3).

• If some objects are selected, the Horizontal Flip tool flips the selected objects horizontally.
• If no objects are selected, or all objects are selected, the Horizontal Flip tool flips each structure horizontally.
• If some objects are selected, the Vertical Flip tool flips the selected objects vertically.
• If no objects are selected, or all objects are selected, the Vertical Flip tool flips each structure vertically.

8. Drawing Reactions

To draw or edit reactions you can:

• Draw reagents and products as described above.
• use options from the Reaction Arrow Tool to draw an arrow. Select the arrow needed from the list: 

Figure 8.1 Reaction Arrows

• Draw pluses in the reaction equation using the Reaction Plus Tool 
• Map the same atoms in reagents and products with the Reaction Mapping Tools. Explore the available reaction mapping tools below:

Figure 8.2 Reaction Mapping Tools

1 – Reaction Auto-Mapping Tool

2 – Reaction Mapping Tool

3 – Reaction Unmapping Tool

9. Drawing Graphical Objects

To draw graphical objects click the arrow on the Shape Ellipse tool  in the Tools palette to open the drop-down list with the following options:

Figure 9.1 Shape Ellipses

1 - Shape Ellipse

2 - Shape Rectangle

3 - Shape Line

10. Creating Text Objects on the Canvas

To add text to the canvas click the Add Text tool in the Tools palette and click the canvas to open the Text Editor window:

Figure 10.1 Text Editor

• To enter text, type in the Text editor field.
• To edit text, double click the text object on the canvas.
• Change the text style to bold and italic, make it subscript and superscript while typing or by selecting text and applying styles.

11. Templates Toolbar

You can add templates (rings or other predefined structures) to the structure using the Templates Toolbar together with the Custom Templates button located at the bottom of the chemical drawing window:

Figure 11.1 Templates Toolbar

To add a ring to the molecule, select a ring from the toolbar and click inside the drawing area, or click on an atom or a bond in the molecule.

Rules of using templates:

Note: Users are able to define the attachment atom and bond by clicking the Edit button for template structure in the Template Library.

• Selecting a template and clicking on an atom in the existing structure adds the template to the structure connected with a single bond:
  

Figure 11.2a Templates Toolbar - Single Bond

• Selecting a template and dragging the cursor from an atom in the existing structure adds the template directly to this atom resulting in the fused structure:
  

Figure 11.2b Templates Toolbar - Fused Structure

• Dragging the cursor from an atom in the existing structure results in the single bond attachment if the cursor is dragged to more than the bond length. Otherwise the fused structure is drawn.
• Selecting a template and clicking on a bond in the existing structure created a bond-to-bond fused structure:
  

Figure 11.2c Templates Toolbar: Bond-to-Bond Fused Structure

• The bond in the initial structure is replaced with the bond in the template.
• This procedure does not change the length of the bond in the initial structure.
• Dragging the cursor relative to the initial bond applies the template at the corresponding side of the bond.

Note: The added template will be fused by the default attachment atom or bond preset in the program.

The Custom Templates button allows to view the list of templates available, both built-in and created by the user:

Figure 11.3 Custom Templates

To create a user template:

• Draw a structure
• Click the Save As button
• Click the Save to Templates button. This displays a Template Edit form.

Figure 11.4 Template Edit Form

• Enter a name and define the attachment atom and bond by clicking on the structure preview. Click on the Apply button to save the template.

The saved template will be available in the User Templates tab in the list of templates.

12. Functional Groups

Alchemy’s Chemical Drawing allows you to select and use Functional Groups to properly represent your structure on the canvas. A set of functional groups available is predefined and cannot be changed.

Explore the list of the Functional Groups available in the Templates library. Open it using the icon in the bottom toolbar.

Navigate to the Functional Groups tab to explore the Functional Groups available:

• Filter Functional Groups by name.
• To add the Functional Group to the canvas and join it to the structure do the following:
  • Select the proper Functional Group in the menu and click Add to canvas.

Figure 12.1 Structure Library - Functional Groups

• Click on the atom the functional group should connect with on the canvas: the bond will be created automatically and and the functional group will be joined to the structure.
  

You can click on the canvas having the Functional Group selected. To connect it with other structure on the canvas do the following:

• Select the Simple Bond tool in the left Chemical Drawing toolbar.
• Drag the bond from the connection atom and drop it to the Functional Group on the canvas.

12.1 Contracted S-Group Tooltip

Hover mouse cursor over the contracted s-group, and you will see the preview of the s-group.

Figure 12.2 S-Group Preview

12.2 Expanding and Contracting S-Group

A Functional Group on the canvas can be expanded to view its internal structure. Expanded groups can also be contracted back to the compact presentation.

You can also Remove the Abbreviation on the group. It will allow you to work with the functional group atoms and bonds as with regular atoms and bonds on the canvas. To Expand, Contract and Remove Abbreviation:

1. Click on the functional group with right mouse button:
   

Figure 12.3 S-Group Options

2. Select the command from the context menu.

12.3 Disability to Change S-Group

Functional Groups can only be selected as a whole. It can also be deleted, moved, or rotated as a single entity.

Alchemy’s Chemical Drawing will let you know if the tool is not applicable for the functional group and will suggest to Remove the Abbreviation immediately:

Figure 12.4 Edit Abbreviation

Aromatize & Dearomatize operations will not be applied to the rings that are part of the functional group.

Functional Groups will be considered as super atoms when opening and saving .mol files.

13. Working with Files

Chemical Drawing supports the following molecular formats that can be entered either manually or from files:

Figure 13.1 Accepted File Formats

You can use the Open… and Save As… buttons of the Main toolbar to import a molecule from a molecular file or save it to a supported molecular file format.

The Open Structure modal enables you  to either browse for a file or manually input, for the molecule to be imported:

Figure 13.2 Open Structure

The text editor form is initiated for the text from the Clipboard and when the file is selected for opening. It allows a user to immediately edit the text representation before opening the structure:

Figure 13.3 Open Structure - Text Editor

Alchemy suggests 2 ways for structure to be opened:

Open as New Project will clear the canvas and position a new structure on it. Add to Canvas will save the structure in the clipboard. Click on the canvas to place it.

The Save Structure modal enables you to save the molecular file:

Figure 13.4 Save Structure

Select the format needed in the File Format drop down.
Check out the Warnings tab if it is represented. It provides the list of chemical information that cannot be saved properly to the format selected.

You can save a structure as an image (in Standalone mode and in Remote mode when the server is available) by selecting the SVG Document or PNG Image format. Please note that saving a structure to the image formats will result in chemical information loss in the file. You will not be able to open files in these formats in Chemical Drawing records. Supported graphics file formats include: Portable Network Graphics (.png) and Scalable Vector Graphics (.svg).

Figure 13.5 Save Structure - Preview

14. Stereochemistry

When the structure with the correct tetrahedral stereochemistry is created on the canvas you can open the Enhanced Stereochemistry modal by clicking the Stereochemistry button and assign stereo marks:

Figure 14.1 Enhanced Stereochemistry

In the Stereochemistry tab in Settings you can:

• Enable/disable the display of the Stereo flags
• Set the text of the Absolute/AND/OR/Mixed flags
• Change the style of the Label display at stereogenic centers
• Select the color of Absolute/AND/OR stereogenic centers
• Choose one of the four color display modes
• Enable/disable option when Chiral flag is ignored (false by default)

Figure 14.2 Settings - Stereochemistry

When the option Ignore the chiral flag is true it will affect opening and saving of MDL V2000 and MDL V3000 files, as well as the display of labels at stereogenic centers and stereo flags:

• Stereo flags are not displayed.

Figure 14.3 Stereo flags not displayed

• Labels at stereogenic centers are displayed only for non-absolute groups.

Figure 14.4 Stereogenic centers displayed

• MDL V2000 and MDL V3000 file formats will save stereo information according to the following table.

Figure 14.5 Accepted Stereo File Formats

15. Chemical Properties

You can pull certain chemical property values directly from a chemical drawing in your Lab Book. These added properties make the chemical drawing tool more powerful by allowing the user to pull information from their drawings automatically. 

Supported chemical properties include:

• Molecular Mass
• Molecular Formula
• Atom Count
• Hydrogen Bond Acceptor
• Donor Count
• SMILES

These properties can be configured by your system administrator in the Alchemy Configuration portal. For more information, see the Configuration Portal - System Admin Manual.

15. Hotkeys

You can use keyboard hotkeys (including Numeric keypad) for some features/commands of the Editor. To display the hotkeys just place the cursor over a toolbar button. If a hotkey is available for the button, it will appear in brackets after the description of the button.

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