Hydrogen Bond Donors (HBD)

Hydrogen bond donors (HBD)

The count of hydrogen bond donors — atoms that can donate a hydrogen bond (commonly OH and NH groups). A hydrogen bond donor (HBD) is a molecule containing a hydrogen atom that is covalently bonded to an electronegative atom, such as nitrogen (N) or oxygen (O).

NumHDonors() is the function that is used to calculate the molecular weight of a compound.

1. Calculate the HBD of Butane (Figure 1).

Code:

butane_smiles = "CCCC"

butane_mol = Chem.MolFromSmiles(butane_smiles)

# HBD

butane_mw = Descriptors.NumHDonors(butane_mol)

print(f"Number of Hydrogen bond donors of Butane: {butane_mw:.2f}")

2. Calculate the HBD of Benzene (Figure 2).

Code:

benzene_smiles = "c1ccccc1"

benzene_mol = Chem.MolFromSmiles(benzene_smiles)

# HBD

benzene_mw = Descriptors.NumHDonors(benzene_mol)

print(f"Number of Hydrogen bond donors of Benzene: {benzene_mw:.2f}")

3. Calculate the HBD of Aspirin (Figure 3).

Code:

aspirin_smiles = "CC(=O)OC1=CC=CC=C1C(=O)O"

aspirin_mol = Chem.MolFromSmiles(aspirin_smiles)

# HBA

aspirin_mw = Descriptors.NumHDonors(aspirin_mol)

print(f"Number of Hydrogen bond donors of Benzene: {aspirin_mw:.2f}")

4. Calculate the HBD of Butanol (Figure 4).

Code:

#Butanol

butanol_smiles = "CCCCO"

butanol_mol = Chem.MolFromSmiles(butanol_smiles)

# Calculate Log P

butanol_mw = Descriptors.NumHDonors(butanol_mol)

print(f"Number of Hydrogen bond donors of Butanol: {butanol_mw:.2f}")

5. Calculate the HBA of Sodium Propionate (Figure 5).

Code:

sodiumpropionate_smiles = "CCC(=O)[O-].[Na+]"

sodiumpropionate_mol = Chem.MolFromSmiles(sodiumpropionate_smiles)

# Calculate LogP

sodiumpropionate_mw = Descriptors.NumHDonors(sodiumpropionate_mol)

print(f"Number of Hydrogen bond donors of Sodium propionate:{sodiumpropionate_mw:.2f}")

The following codes will calculate the Molecular weight, LogP, HBA, and HBD for the four compounds (Butane, Benzene, Aspirin, Butanol, and Sodium Propionate). (Figure 6). 

Code:

from rdkit import Chem

from rdkit.Chem import Descriptors

def calculate_molecular_properties(molecules):

    """

    Calculates and prints a table of molecular properties for a given

    dictionary of molecules.

    Args:

        molecules (dict): A dictionary where keys are molecule names (str)

                          and values are their SMILES strings (str).

    """

    # Print table header

    print(f"{'Molecule':<20} | {'Mol Weight':<12} | {'LogP':<8} | {'H Acceptors':<12} | {'H Donors':<10}")

    print("-" * 80)

    # Iterate through each molecule, calculate properties, and print the row

    for name, smiles in molecules.items():

        # Create a molecule object from the SMILES string

        mol = Chem.MolFromSmiles(smiles)

        # It's good practice to check if the molecule was created successfully

        if mol:

            # Calculate the descriptors

            mol_weight = Descriptors.MolWt(mol)

            mol_logp = Descriptors.MolLogP(mol)

            h_acceptors = Descriptors.NumHAcceptors(mol)

            h_donors = Descriptors.NumHDonors(mol)

            # Print the formatted results for the current molecule

            print(f"{name:<20} | {mol_weight:<12.2f} | {mol_logp:<8.2f} | {h_acceptors:<12} | {h_donors:<10}")

        else:

            print(f"Could not process molecule: {name} with SMILES: {smiles}")

if __name__ == '__main__':

    # Dictionary of molecules with their names and SMILES strings

    molecule_dict = {

        "Butane": "CCCC",

        "Benzene": "c1ccccc1",

        "Aspirin": "CC(=O)OC1=CC=CC=C1C(=O)O",

        "Butanol": "CCCCO",

        "Sodium Propionate": "CCC(=O)[O-].[Na+]"

    }

    calculate_molecular_properties(molecule_dict)