How to use chemistry editor? – LabCollector

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How to use chemistry editor?

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SUMMARY:

The molecular editor is present in both the Chemistry module and ELN.

Chemistry editor can be used to create a chemical structure and save it as a record. It also provides you the possibility to edit a chemical molecule structure that is already present in the chemistry module.

In the ELN (Electronic Lab Notebook) add-on, it can be used to make 2D chemical structures, that can be inserted easily ELN ‘content’ or it can also be saved as a chemistry template in ELN.

To use the chemistry molecule editor, please follow the steps below:

1. The chemistry editor

1.1. Chemistry module

1.2. ELN

2. Tools in chemistry editor

1. The chemistry editor

  • As described in the introduction, a chemistry editor can be found in both the chemistry modules and ELN add-on.
  • 1.1. Chemistry module

    • There are 2 ways to use the chemistry editor in the chemistry module.
      • First-way is go to a CHEMISTRY MODULE -> NEW RECORD -> MOLECULAR DATA -> STRUCTURE -> DRAW MOLECULE.
        – The chemistry editor will open the page below, which is described in section 2 in detail.

      • The second way is to go to a CHEMISTRY MODULE -> EDIT RECORD (already existing) -> MOLECULAR DATA -> DRAW MOLECULE.
        – The chemistry editor will open the page below, which is described in section 2 in detail.
  • 1.2. ELN

    • To check the default fields for each module go to HOME -> BOOK / EXPERIMENT OR PAGE(OF YOUR CHOICE) -> CONTENT -> EDIT.

    • Once you click on the “Add molecules & reactions” icon it will open a page will the options below.

    • You need to click on the “New” option to open the chemistry editor that is described below.

2. Tools in chemistry editor

  • Option A: Center Canvas

    • This is the canvas where you will see the molecule you are creating.
  • Option B: Top toolbar

  • The various options here are:
    • Undo & Redo options to retrace actions.
    • To bring/adjust your molecule in the center of the canvas.
    • Toggle R/S labels. (S & R are used to name the enantiomers of a chiral compound. It refers to left handedness-S or right handedness-R of a molecule.)
      – For example, imagine a carbon atom with a chiral center, attached to 4 atoms.
      – Each atom connected to the chiral atom C is given priority where 1 is the highest and 4 is the lowest.
      – Priority is given according to atomic number, the higher the atomic number the higher is the priority.

    • This option is to clear everything on the canvas.
    • This option creates the Mol and Smiles format for the molecules. You can copy and save it for future use.

      – The import button allows you to paste MOL, SMILES, or InChI files of a molecule. 
      – The export button allows you to copy the MOL or SMILES format of the molecule you generated.
      – InChI (International Chemical identifier); SMILES (Simplified Molecular Input Line Entry Specification is a linear notation of the molecule ); MOL (MDL Molfile holds information about the atoms, bonds, connectivity, and coordinates of a molecule.) For example, the image below shows the benzene molecule and the different formats in wich it can be represented.

    • This option tells you about the software and its version.
    • This 2D depiction/cleanup option allows you to change how your molecule is oriented.

    • This chemical dictionary search option helps you to import a molecule structure. 
      – You can also edit the structure you have imported.

  • Option C: Right toolbar

  • The different options here are:
    • Rectangular and Lasso selection. These are different types of select tools.
      Rectangle select: select atoms and bonds using a rectangular selection area
      Lasso select: select atoms and bonds by drawing a freehand selection area
    • You can delete the selection using the DEL key or using the eraser tool .
    •  This charge option allows the increment (+) or decrements (-) the charge of atoms.
    • It allows you to add isotope to your molecule structure.
    • The fragments allow you to have a pre-prepared structure of benzene , cyclopentane , cyclopropane , cyclobutane , cyclohexane , cycloheptane .
    • This allows creating a chain of carbon atoms.
  • Option D: Left toolbar

    • This toolbar also allows you to select from a number of elements that you can use to create a new element or modify an existing one.
    • The atoms that are present are Hydrogen, Sulphur, Phosphorus, Florine,  Oxygen, Nitrogen & Carbon.
    • You can add here a custom element. An element that is not defined, along with the hydrogen atoms, heavy atom count (D) or ring atom count (R).
      – Heavy atoms are, for example, C, N, O, S, F, Cl, Br, etc.
      – Ring atoms are those that constitute the part of the ring.
    • The toolbar offers different types of bonds single, double, triple, up.
  • Option E: Add

    • Once you have finished creating a compound, you can add it and include it in your reaction and insert it on your content in the ELN book, experiment or chemistry.
    • You can also save it as a template as shown in the video below.
      * To access chemistry templates in ELN you can go to ADMIN -> TEMPLATE -> VIEW/EDIT REACTION TEMPLATE.
      * Remember you can view and edit reaction template depending on the permissions the super admin or admin has given to you. Please check our KB to see more about ELN permissions.

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