Configure Molecule schemas for Reactions

To enable your team to capture reactions in Benchling, a tenant admin needs to complete a one-time configuration. This article walks through setting up the Salt & Solvate library, the Molecule and Molecule Form schemas for molecule registration, a Molecule Fieldset to group them, and the Molecule Lot schema for tracking physical batches.

Follow the configuration order. The Molecule Form schema depends on the Molecule Compound schema, and the Molecule Lot schema depends on both.

1. Set up the Salt & Solvate library
2. Create the Molecule Fieldset
3. Create the Molecule schema
4. Create the Molecule Form schema
5. Create the Molecule Lot schema 

Set up the Salt & Solvate library

The Salt & Solvate library is a tenant-wide list of the salts and solvates your organization uses. Benchling references this library when registering salted or solvated molecules. Library management is restricted to users with the Tenant Admin role.

When adding entries, enter the neutral form of each salt or solvate where possible — for example, enter HCl rather than Cl-. However, enter the charged ion form in the following cases:

• Metal and similar cations such as Na⁺, K⁺, or Ca²⁺ — these have no meaningful neutral form
• Permanently charged species such as quaternary ammonium salts — there is no proton to add or remove to produce a neutral structure
• Zwitterions where the internal charge is intentional and should be preserved

Import salts and solvates in bulk

Benchling provides two CSV options for bulk import:

• A starter list of 78 commonly used salts and solvates — download it from the bottom of this article, remove entries your organization doesn’t use, and add any that are missing
• A blank CSV template to build your own list from scratch

1. Go to Feature Settings, then Chemistry Settings, then Salt & Solvate library
2. Click the CSV import button
3. Download the starter list — [benchling_bulk_import_saltsolvent.csv] — or the blank CSV template
4. Review or fill in the name, structure (as SMILES), and optional code for each entry
5. Upload your completed file and click Import

Add salts and solvates manually

1. Go to Feature Settings, then Chemistry Settings, then Salt & Solvate library
2. Click Add new salt or solvate a modal will open
3. Draw or paste the neutral, single-fragment structure
4. Enter a name for the salt or solvate
5. Optionally enter a short code (Molecule code is an available component of Molecule Form entity name templates) 
6. Click Create
7. Repeat for each salt and solvate your organization uses

Note: Each salt or solvate must be its own entry. Benchling validates that the structure is a single fragment, that the name and chemical structure are unique in your tenant, and that the code, if entered, is also unique. If your tenant already has entries in the Salt & Solvate library, check for duplicates before importing. Benchling will flag duplicate names, structures, or codes as errors. To resolve: either archive the existing entry from the library or remove the row from your CSV. Error messages reference the row number.

Note: Entries in the library can be archived when no longer needed but cannot be permanently deleted.

Create a Molecule Fieldset 

If your organization has both a Molecule and a Molecule Form schema, we recommend creating a fieldset to group them. This allows your Molecule Lot schema to link to both schema types, so chemists can create lots against either a Molecule or a Molecule Form.

1. Go to Registry Settings, then Fieldsets, and click Create
2. Enter a schema name 
3. Set the Fieldset type to Molecule entities
4. Optionally add fields, uniqueness constraints, or a naming template
5. Click Create

Note: This step is optional. If your organization only tracks lots against one schema type, you can skip this step and point the Molecule Lot parent link directly to that schema.

Create the Molecule Compound schema

The Molecule Compound schema stores the neutral parent structure of each molecule — the free base or free acid form, with no salts or solvates attached. Create the Molecule Compound schema before the Molecule Form schema — the Molecule Form schema must point to it.

1. Go to Registry Settings, then Entity Schemas, and click Create
2. Select Molecule as the entity type
3. Select Molecule Compound as the molecule component type
4. Enter a name (for example, Compound) and configure a registry ID prefix
5. If you created a Molecule Fieldset, assign it here
6. Add any custom fields your organization needs
7. Click Next
8. Configure access policies
9. Click Create

Create the Molecule Form schema

The Molecule Form schema stores salted or solvated versions of a Molecule Compound. Each Molecule Form links back to its parent Molecule Compound.

1. Go to Registry Settings, then Entity Schemas, and click Create
2. Select Molecule as the entity type
3. Select Molecule Form as the molecule component type
4. Enter a name and configure a registry ID prefix
5. If you created a Molecule Fieldset, assign it here
6. In the Molecule parent link field, select the Molecule Compound schema you created above and set it as required
7. Add any custom fields your organization needs
8. Optionally configure a name template. To include the salt or solvate in the entity name, reference {salt code} — for example, {parent registry ID}-{salt code} produces IDs like MOL-001-HCl. Salt codes are configured in the Salt & Solvate library.
9. Click Next
10. Configure access policies
11. Click Create

Note: A Form schema must have exactly one required parent link field pointing to a Molecule Compound schema. A Compound schema can only be referenced by one Form schema.

Create Molecule Lot schema

The Molecule Lot schema tracks physical batches of a molecule, including purity and concentration. Each lot links to a parent molecule — either a Molecule or a Molecule Form — so chemists can track exactly which physical batch was used in a reaction and reference it directly in the reaction table to auto-fill purity and concentration.

1. Go to Registry Settings, then Entity Schemas, and click Create
2. Select Custom Entity as the entity type
3. Enter a name (for example, Molecule Lot) and configure a registry ID prefix
4. Check Configure as a Molecule Lot — Benchling automatically adds four fields: Molecule (parent link), Purity, Concentration (molar), and Concentration (density)
5. In the Molecule parent link field, select the Molecule Fieldset if you created one, or select your Molecule schema directly if you only have one molecule schema
6. Review and update the concentration units for Concentration (molar) and Concentration (density) to match your organization’s preferences
7. Optionally configure a naming template — for example, {parent registry ID}-L{lot number} produces lot IDs like MOL-001-L1
8. Click Next
9. Configure access policies
10. Click Create

Note: If no matching unit type is found for Concentration (density), Benchling will display a warning. Configure the unit manually using the gear icon on that field

FAQ

Q: Can a Molecule schema link to more than one Molecule Form schema?
A: Yes. To use a salt or solvate in a reaction, create it as a Molecule Compound even if it already exists in the library.

Q: Do I need both a Molecule and a Molecule Form schema?
A: Only if your organization registers molecules in salt or solvate forms. If your organization only works with neutral parent structures, a Molecule schema alone is sufficient.

Q: Do I need a Molecule Fieldset?
A: A fieldset is recommended if you have both a Molecule and a Molecule Form schema. Without it, your Molecule Lot schema can only link to one schema type — meaning chemists could create lots against a Molecule but not a Molecule Form, or vice versa.

Q: Can a Molecule Lot schema’s parent link point to more than one schema without a fieldset?
A: No. A parent link field can only target one schema at a time. If your organization uses both a Molecule and a Molecule Form schema, point the Molecule Lot parent link to the Molecule Fieldset instead of a single schema — this allows chemists to create lots against either schema type.

Q: Is there a limit to how many salts or solvates I can attach to a single molecule?
A: Yes. Benchling supports up to 5 salt or solvate counterparts per molecule and up to 10 total fragments after normalization.

Q: What happens if I import a molecule with a salt or solvate fragment that isn’t in my Salt & Solvate library?
A: The import fails with an error for that row rather than silently dropping the fragment. Add the missing salt or solvate to the library and re-import.

Q: Can I add a salt or solvate to the library after schemas are already configured?
A: Yes. The Salt & Solvate library can be updated at any time. New entries are immediately available for molecule registration and bulk import.

Q: Can I edit a Molecule schema after it’s been created?
A: You can add custom fields and update access policies after creation. However, changing the molecule component type (Molecule Compound or Molecule Form) is not supported after the schema has been created and used to register molecules.

• benchling_bulk_import_saltsolvent.csv3 KB