Predicting the Strength of Hydrogen-Bond Acceptors/Donors
Rowan's hydrogen-bond acceptor/donor strength workflow predicts pKBHX values of hydrogen-bond acceptors and pKα values of hydrogen-bond donors using neural network potentials and r2SCAN-3c. You can read more about how it works on our science page.
To create a new hydrogen-bond acceptor/donor strength workflow, find your way to this screen in Rowan:
Click on "Hydrogen-bond acceptor/donor strength" to create the workflow.
Add a molecule
The hydrogen-bond acceptor/donor strength workflow in Rowan is designed for individual molecules, and inputting multiple structures may not function as expected.
To add a molecule, you can use any of the following input formats:
- Draw a molecule using Rowan's 2D or 3D editors.
- Upload a file, using the "Upload files" button. (Rowan accepts .xyz, .gjf, .out, .mol2, .sdf, .cif, and .mae chemical file formats.)
- Paste XYZ coordinates, using the "Paste XYZ" button.
- Input a SMILES string, using the "Input SMILES" button.
- Input the name of the chemical, for its information to be fetched from PubChem.
- Drag and drop files anywhere on the page.
For small molecules, it's often easiest to start with a SMILES string. Many 2D molecule drawing programs, including ChemDraw and MarvinJS, will let you export/copy structures as SMILES.
Configure the workflow
The hydrogen-bond acceptor/donor strength workflow has only two settings.
If you would like to perform a conformer search on your input molecule to find the lowest energy conformer prior to predicting predicting the strength of its hydrogen-bond acceptors/donors, enable "Run conformer search?".
If you would like to reoptimize the inputted structure, enable "Optimize structure(s)?". Optimize structures will always be enabled if the conformer search is enabled.
Submit your workflow
Once you have configured your workflow, click "Submit HBA/HBD" to begin the calculation.