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Reactions and Stoichiometry Tables in the ELN

CDD Vault gives you the ability to insert interactive and editable reactions and stoichiometric tables into your ELN entries with seamless integration to the registration module of your CDD Vault. Draw or import your chemical reactions and provide your known masses, purity and density to determine product yield. Register molecules and reagents directly from the stoichiometry table within your ELN entry. Registered molecules in your table are automatically linked to its registered Molecule ID.

Please contact CDD support to activate the stoichiometry table function in your ELN.

Getting started

From the Explore Data dashboard, create a new ELN entry. For help and details on how to create an ELN entry, please see Creating an ELN entry.

  • Click on the Insert Molecule or Reaction icon in the header of the ELN entry to insert your reaction - this will open the Marvin JS structure editor.
  • Create your chemical reaction via importing a file, drawing the components individually, or inserting already-registered molecules directly from your CDD Vault.
  • Once your reaction is drawn, click on the green “Use this structure” button.  The reaction will be inserted into your ELN entry and the stoichiometry table is automatically generated.

This video provides a brief overview of inserting a reaction and interacting with the resulting stoichiometry table. 

 

Stoichiometry Table Columns

Name – the list of reactants and products contained within your chemical reaction. Any molecules that are already registered in your CDD Vault will automatically be cross-referenced and the corresponding Molecule ID will be shown.

Properties – lists the Molecular Weight (MW) of the parent molecule and the Formula Weight (FW) of the specific Batch. Concentration and density are optional fields which can be edited.

Amounts – lists the mass or volume (including ratio values) which are required to perform stoichiometric calculations. Also contains the purity value. NOTE: clicking on volume allows you to designate a solvent used for any solutions.

Calculation – provides a radio button to indicate the limiting reagent. Molar equivalents and product yield are also listed, and are calculated from values that are entered for the reactants and products.

Comment - an optional field available for observations, references and additional measurements pertaining to a specific component.

 

Seamless integration with the CDD Vault Registration system

Molecule IDs for any Molecules that are already registered in your CDD Vault are automatically populated.  For your convenience, IUPAC names and CAS numbers are displayed when available. 

If molecules are used in a reaction that are not already registered in your CDD Vault, you can register new Molecules, or new Batches of an existing Molecule directly from the stoichiometry table by hovering your cursor within the Name column of the stoichiometry table. Then click the “Register” button.

To specify a specific Batch of a Molecule that was used in a reaction, click on the molecule name and select the appropriate Batch from the list.

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Interact and edit

Reactant masses are required to enable calculations of molar equivalents and expected theoretical product yields. When you click to update any of these numerical fields, a pop-up window will appear. Note the default unit in brackets [ ]. It is not necessary to enter units with your numerical entry when updating these fields unless it is different than the default unit given. Note that numbers <1 will have to be entered with a leading zero (i.e. 0.6 instead of .6).

 

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Once the measured mass of the product is entered, the percent yield will be calculated. If necessary, you can edit any input and the calculations will update. Structures can be modified as well. Click the reaction preview and update any of the components. Click on the green “Use this structure” button and the resulting stoichiometry table will be updated, preserving as many of the existing values as possible.

You may also add reagents to your stoichiometry table even if they are not included in your reaction drawing. Below the last reactant in a new row, there is an option to “add a reagent”. Click and enter the name of the reagent and it will be added to your table. This feature will also perform a lookup for reagents based on CAS, Common Names, and CDD Vault Molecule IDs and synonyms (from all of your Vaults if search across Vaults is enabled).

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Example 1 - generating a Stoichiometry Table for a reaction

  • Create a new ELN entry.
    • Select the + Create a new button and create a new ELN entry.
    • Select the appropriate project.
    • Click begin editing.
  • Click on the Insert Molecule or Reaction icon in the header of the ELN entry to insert a reaction - this will open the Marvin JS structure editor.
  • Draw your reaction.
    • In this example, we will be synthesizing acetophenone.
    • Draw benzene.
    • Click +/-> in the left tool panel and click once to place a + to the right of the benzene.
    • Add acetyl chloride to the right of the +.
    • Click the +/-> and draw an arrow by dragging your cursor to the right, following acetyl chloride, to indicate the resulting product.
    • Draw 1-phenylethan-1-one as the yielded product.
    • OR should you choose to draw the reaction in ChemDraw, you may import your ChemDraw (.cdx) reaction into the Marvin JS editor.
    • Click on the green “Use this structure” button to insert the stoichiometry table into your ELN entry.
  • In the row corresponding to benzene, update the amount to 1g, purity to 95% and density to 0.88.
    • Remember the default units in brackets will be used unless you specify a different unit.
    • Click enter after updating each of the above required fields to record the value.
  • In the row corresponding to acetyl chloride, update the amount to 1.5g.
  • You may add reagents to your reactions.
    • Click add reagent in the row below Acetyl chloride and then click the "required" field under Name.
    • Type Aluminum Chloride or AlCl3. Press enter.
  • Update the product mass to 1.1 g. Once you press enter, you will see the yield calculated:

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Example 2 - editing a reaction and the Stoichiometry Table

  • Create a new ELN entry.
    • Select the + Create a new button and create a new ELN entry.
    • Select the appropriate project.
    • Click begin editing.
  • Click on the Insert Molecule or Reaction icon in the header of the ELN entry to insert a molecule or reaction - this will open the Marvin JS structure editor.
  • Draw your reaction.
    • In this example, we will be synthesizing aspirin.
    • Click the blue CDD icon to Insert structure, search for 2,6-Dihydroxybenzoic acid and click enter.
    • Drag the inserted structure to the left by clicking-and-holding an atom. Release when you reach the side.
    • Click the blue Insert structure icon again, search for acetyl acetate and click enter.
    • Reposition acetyl acetate so there is a small gap between your reactants.
    • Click +/-> and insert a + between your reactants by clicking once. Then drag your cursor to the right, following acetyl acetate, to insert an arrow to indicate the resulting product.
    • Click Insert structure and search for aspirin (also known as 2-Acetoxybenzoic acid). Click enter and position the structure to the right of the arrow.
    • Draw or use the Insert structure workflow to add acetic acid as an additional product.
    • Click the 2D Clean button.
    • Should you choose to draw the reaction in ChemDraw, you may import your ChemDraw (.cdx) reaction into the Marvin JS editor.
    • Click on the green “Use this structure” button to insert the stoichiometry table into your ELN entry.
  • In the row corresponding to the first reactant, 2,6-Dihydroxybenzoic acid, update the amount to 1g, purity to 95% and select the radio button to indicate it is the limiting reagent.
    • Remember the default units in brackets will be used unless you specify a different unit.
    • Click enter after updating each of the above required fields to record the value.
  • In the row corresponding to acetyl acetate (also known as acetic anhydride), update the amount to 1g.
  • Update the product mass of Aspirin to 1.5 g. Once you press enter, you will see the yield calculated

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In order to demonstrate the editing capabilities of the stoichiometry table, click on the reaction preview and remove one of the OH groups from the first reactant. Remove the acetic acid from the products. Click on the green “Use this structure” button. Note that the stoichiometry table is automatically updated based on the updated molecules in the reaction.

  

Duplicating a Stoichiometry Table with Reactants and Products

In your workflow, you may wish to duplicate a stoichiometry table in your current ELN entry or into another ELN entry. Point your cursor towards the border of your stoichiometry table until the border turns blue. Click on this area and then copy it (Ctrl + C). You may now paste (Ctrl + P) this stoichiometry table along with its reactants, products and updated masses within the same ELN entry or into another ELN entry. 

Helpful Hint: If you are not able to achieve the expected result of duplicating the stoichiometry table using the method above, include a line of text above and below the stoichiometry table to highlight and copy. Select the text and the stoichiometry table. Copy and then paste both lines of text and the stoichiometry table to your desired location. Edit your pasted text and stoichiometry table as you wish.

 

Other Noteworthy Features

  • Molecule IDs from your CDD Vault are automatically displayed in the stoichiometry table for any reaction components that already exist in your CDD Vault registration system.
  • While editing a stoichiometry table, click on a Molecule ID to associate the reaction component to a specific Batch of that Molecule.
  • Hovering over a reaction component within the stoichiometry table will allow you to register that structure into your CDD Vault registration system. The resulting Batch is automatically associated to that reaction component.
  • When adding a reagent, you can use the look-up feature to find reagents by searching for their CDD IDs, CAS Numbers, IUPAC Names or even a common name. 
  • To edit a reaction, click on the reaction preview and update the structures in the Marvin JS structure editor. Values already entered in the stoichiometry table will be preserved for the remaining components.
  • To edit an existing value in the stoichiometry table, click anywhere within the stoichiometry table to switch to edit mode, then make the necessary changes.
  • When entering a Volume of a reaction component, you may select the Solvent used from a drop-down list of common solvents.
  • Percent weight per volume (%w/v) can be entered as concentration for a given component as long as the MW is known.