The Chemistry Tools let you do a multitude of things very easily. Whether you're working on an experiment or customising your Inventory, your molecule or reaction will automatically be added to your content once you've finished editing it. Need to work out the stoichiometry or record the hazards of a molecule? No worries, the Chemistry Tools can do it for you!

Click on 'Fetch from PubChem' to obtain metadata such as IUPAC Name or Molecular Weight.

Click on 'Generate Stoichiometry Table' to allow for quick and easy calculation of relative mass, volumes and molar amounts required for a reaction. Additionally, you can edit the tale to carry out custom calculations. Please note if you refresh the table, the custom fields will disappear.

Labstep team tip: You can search for chemicals by name or CAS number to add to the canvas using the search bar.

Labstep team tip: If the chemistry metadata is at the top, this will be the data shown in the preview. If you'd prefer different metadata to be displayed, simply move up or down the relevant metadata.

Using the Tool palette, you can:

To select one atom or bond, click Lasso (1) or Rectangle Selection tool (2) and click the atom or bond.

To select the entire structure:

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

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

You can use the buttons of the main toolbar:

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

You can perform the following actions:

"Lines" drawing method, "Bright" atom name colouring method and "Light" background colouring are default.

To draw/edit atoms, you can:

To draw/edit bonds you can:

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

For the full-screen format, the Bond tool from the Tool palette splits into four: Single Bond, Single Up Bond, Any Bond and Dative Bond, which include the corresponding bond types:

Select a bond type from the drop-down list and click inside the drawing area; a bond of the selected type will be drawn

Use the R-Group toolbox

to draw R-groups in Markush structures:

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

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

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

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:

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 dialogue that appears after clicking on the atom:

If there are two attachment points on an R-Group member, there must be two corresponding attachments (bonds) to the R-Group atom with the same R-Group label. Clicking on OK in the above dialogue creates the attachment point.

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

To access the R-Group logic:

To mark S-Groups, use the S-Group tool

and the following dialogue that appears after selecting a fragment with this tool:

Available S-Group types:

The Data S-Groups Tool

is a separate tool for comfortable use with the accustomed set of descriptors (like Attached Data in Marvin Editor).

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 element:

Use the Rotate tool

to change the structure display:

For the full-screen format, the Rotate tool is split into separate buttons:

Rotate Tool (1)

This tool allows rotating objects.

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.

Flip Tool (2, 3)

This tool flips the objects horizontally or vertically.

To draw/edit reactions you can:

1 – Reaction Arrow Tool

2 – Reaction Arrow Equilibrium Tool

3 – Reaction Plus Tool

4 – Reaction Auto-Mapping Tool

5 – Reaction Mapping Tool

6 – Reaction Unmapping Tool

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 tools:

Shape Ellipse (1), Shape Rectangle (2), and Shape Line (3).

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:

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:

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

Rules of using templates:

The bond in the initial structure is replaced with the bond in the template.

This procedure doesn't 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 program's default attachment atom or bond preset.

Note: The user can define the attachment atom and bond by clicking the Edit button for template structure in the Template Library.

The Custom Templates button

invokes the scrolling list of templates available in the program; both built-in and created by the user:

To create a user template:

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

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 dialogue enables one to either browse for a file or manually input, e.g. the Molfile table for the molecule to be imported:

The Save Structure dialogue enables one to save the molecular file:

You can also save a structure as an image, but you risk losing the chemical information within the file. Supported graphics file formats are: Portable Network Graphics (.png) and Scalable Vector Graphics (.svg).

When the structure with the correct tetrahedral stereochemistry is created on the canvas, you can open the 'Enhanced Stereochemistry' window by clicking the Stereochemistry button

and assign stereo marks:

In the Stereochemistry tab in Settings, you can:

You can use keyboard hotkeys (including Numeric keypad) for some features/commands of the Editor. To display the hotkeys, 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.

Note: Please, use Ctrl+V to paste the selected object in Google Chrome and Mozilla Firefox browsers.

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