Molecule Editors/Sketchers

Caution

This page is still being edited.

Ketcher

The main way to enter chemical structures into the 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 ELN is now unique in its functionality and, in addition to the input of small chemical molecules, it also enables the mapping 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 minimum covalency, so if you add a Carbon atom C, you get CH4.

Bonds#

Bonds

The bonds menu can be usually opened using this icon Single from Ketcher's left column. Hoxever, 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 . 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.