Skip to main content

Molecule Editors/Sketchers

Caution

This page is still being edited.

Ketcher

The main way to enter chemical structures into the Chemotion ELN is the Ketcher Editor. The editor is available via the sample detail modal and can be opened by clicking on the area framed in light blue. The Ketcher Editor is not a product of the Chemotion programming group, but it has been modified so that it can be used flexibly for a wide variety of applications. After the additions made, the structure editor integrated within the Chemotion ELN is now unique in its functionality and, in addition to the input of small chemical molecules, it also enables the illustration of polymeric carrier materials (beads). The editor will also be supplemented by further developments in the future.

Basic functions#

The Ketcher structure editor offers all the basic functions that are necessary for chemical work and the input of structures. Drawn molecules can be rotated, optimized, copied and pasted again. The size of the displayed molecules can be changed by adjusting the zoom factor.

In the left side of the image above, some functions have a small balck arrow in the lower right corner. This arrow indicates the possibility to change to other similar function e.g. single bond to double bond. This will become clear later in this page.

Atoms#

Ketcher bonds

Atoms can be added to the structure from the column in the right side of the above image. The most frequently used atoms are already displayed in the column using their symbols, while less frequently used ones can be accessed from the icon, which displays the Periodic table to pick from. The user can either pick a Single atom, a List, or Not List. The user can also use Generics Groups to add one of Reaxys Generics. For more details about Reaxys Generics, please follow this link. When an atom is added, it is assumed to be attached with a number of Hydrogen atoms based on its valency, which can be manually modified (see Select), so if you add a Carbon atom C, you get CH4 unless .

Bonds#

Bonds

The bonds menu can be usually opened using this icon Single from Ketcher's left column. However, if another type of bonds is selected, the main icon changes to that type. Alongside the usual Single, Double, Triple bonds, Ketcher editor offers a variety of bonds to express coordination, stereochemistry, and aromaticity. All bonds types can be seen in the image above. If you draw a separate bond (not starting from an atom), it will be assumed to be between two Carbon atoms., so with a Single bond you will get Ch3-Ch3. If it starts from an atom, the end is assumed to be a Carbon atom. However those Carbon atoms can be replaced with the right ones from the atoms column. A bond can also be used to connect two atoms or to change the type of an already existing bond to another one. If the bond is asymmetric, such as with stereochemistry bonds, you can change its direction by re-clicking on the bond. Make sure that the right bond type is selected, otherwise you will change the bond type instead of changing its direction.

Chain Tool#

This tool Chain can be used to build chains of Carbon (methylene group) instead of taking time to add the groups one by one. If other atoms rather than Carbon are needed, or if bonds rather than Single one to be used, the used can always modify these details later on one by one.

Rings#

The rings menu can be usually opened using the Benzene icon Benzene from Ketcher's left column. A variety of rings is available where some of them are aromatic, saturated or unsaturated, but all of them are #TODO. The rings sizes vary between 3 and 8 atoms. If the user picks a ring rather than the Benzene one, the icon changes in the left column. The rings contain Carbon atoms only, but the user can modify the single atoms later on from the atoms column, and change the order of bonds from the bonds menu. If a ring of a larger size is needed, the user can open the available ring, add new atoms, and close it again with a bond. Another option is to build a ring from scratch.

Charge#

The user can modify the charge of an atom by increasing the positivity with the icon ChargeP, or increasing the negativity /with the icon ChargeM. The user has to click on the desired icon and then click on the desired atom. The change in charge is accompanied with change in the number of attached Hydrogen atoms.

Select#

The selection tool icon is Select by default, which corresponds to Lasso Selection Tool for free shape selection. There is also the Rectangle Selection Tool, and the Fragment Selection Tool which selects a connected fragment (all the atoms connected to the atom clicked on with bonds among them, non-atomic elements such as Reaction Arrows etc.).

Atoms properties

By using any selection tool, and when double click on an existing atom, a window Atoms Properties pops up, where you can modify properties of your atoms. When pressing OK, those changes appear on the atom.

Bond properties

Double-clicking on a bond opens Bond Properties window.

Many tools in the structure editor require selection first. However, those tools have the selection function included in them most of the time, such as with Erase and Rotate Tool. Others, such as Copy and Cut, need the selection tool.

Erase#

The Erase tool Erase can be used to erase atoms, bonds, or other elements. It works either by clicking on a single element to be erased (e.g. an atom), or using the tool directly to select a set of elements in a rectangle so those elements are deleted, or by using selection tool first, and then delete the selected elements.

When an atom is erased, all its bonds are erased too. However, when a bond is erased, the attached atoms are not erased unless they have no other bonds.

Rotate#

You can either rotate elements in a circular manner ( Rotate Tool Rotate ), flip them horizontally (Horizontal Flip Horizontal ), or vertically (Vertical Flip vertical). Rotation needs selection first, either directly by the rotation tools, or using the selection tools.

Polymer#

For solid-phase syntheses, the symbol Bead Polymer was introduced which, similar to the symbolism of the ChemDraw editor, depicts beads of the polymeric carrier material. Please use this symbol for the drawing of a solid phase material, because the ELN recognizes the bead and sets up the layout of the input module accordingly. The definition of the load is defined within the input model for the sample.

Clear Canvas#

The tool Clear deletes everything there is in the current canvas.

Open#

The user can use the tool Open to open files, either by inserting the content of a Molfile directly as input in the window Open File, or by browsing for a File (the later one is not available right now). In both cases, the user can also load the file as a fragment and copy it to the clipboard

Save As#

The user can use the tool Save As Save As to save their provided structures in one of three Formats: MDL/Symyx Molfile, Daylight SMILES, and InChI String (The latest is not ready right now). The chosen format is then displayed so that the user can copy it to a file.

Undo/Redo#

Any action done in the editor can be undone with Undo Undo, and the undone action can be redone with Redo Redo

Cut/Copy/Paste#

Any structure (or substructure) can be cut Cut, copied Copy, and pasted Paste somewhere else in the editor.

Zoom In/Out#

The user can use the tools Zoom In ZoomIn and Zoom Out ZoomOut to adjust the view, or they could set their preferred zoom directly as a percentage

Clean#

The tool Clean Clean provides a better view of the provided elements by aligning them, adjusting the distances among them, adjusting the rotations, and adjusting the bonds’ lengthes.

Show Molecule Info#

sMolecule Infohow_molecule_info

This tool Show Info shows information about all the provided molecules, e.g. the displayed molecular weight is the sum of the molecular weight of all the molecules. However, the user can select desired elements to get their details.

Standard templates#

The specified standard templates are given and cannot be changed. If you have suggestions or guidelines for additional templates or even a new template category, send a MolFile or a ChemDraw drawing to nicole.jung@kit.edu. We will review your structure and add it to the standard templates. The standard templates can be found in the lower bar of the editor and are arranged according to the categories Amino Acids, Aromatics, Bicyclics, Conformers, Cycloalkanes, Functional Groups, Nucleic Acids, Paracyclophanes, Schlegel-diagrams and Solid Supports. Press on a category to open its the template list, press again to close it.

Caution

When creating chiral compounds, the configuration of the unique structure is observed and registered accordingly. Planar chiral compounds are unfortunately not recognized as such yet, and therefore, they are not differentiated in lists and names, even if they were drawn accordingly by the Ketcher editor. An example is the Paracyclophanes. Please note the chirality of your samples in the Description field.

Last updated on by Jan C. Brammer