Hydrogen Bonding Calculator

A hydrogen bond is the strongest type of intermolecular force, much weaker than a covalent bond but much stronger than typical van der Waals attractions. It forms when a hydrogen atom covalently bonded to a strongly electronegative atom (nitrogen, oxygen, or fluorine) is attracted to another N, O, or F atom that has a lone pair of electrons.

Two roles a molecule can play in hydrogen bonding:

Donor: provides the hydrogen. Each H atom directly bonded to N, O, or F counts as one donor site. Water has 2 (both H atoms attached to oxygen). Ammonia has 3 (all three H atoms on nitrogen).

Acceptor: provides the lone pair. Each non-bonding electron pair on an N, O, or F atom can accept one hydrogen bond. Water has 2 (oxygen has two lone pairs). Ammonia has 1 (nitrogen has only one lone pair).

The maximum number of hydrogen bonds a single molecule can simultaneously participate in is donors + acceptors.
Water at 2 + 2 = 4 is why ice has a tetrahedral structure: each water molecule connects to four neighbors. Ammonia at 3 + 1 = 4 also caps at four, but the 3:1 donor-acceptor ratio is lopsided, which is why ammonia boils so much lower than water despite the same total capacity.

How the presets count. Every preset applies the rule above mechanically: donors are H atoms bonded to N, O or F, and acceptors are lone pairs on N, O or F. Picking one fills both boxes so you can see the numbers that produced the answer, and edit them if you disagree. Two counts are worth spelling out because they are easy to get wrong:

• Glucose has 5 hydroxyl hydrogens, so 5 donors. For acceptors it has 6 oxygens with 2 lone pairs each, giving 12. That includes the ring oxygen, which is a weaker acceptor than a hydroxyl but does accept.
• Guanine, as it sits in DNA with N9 bonded to the sugar, has 3 donor hydrogens (N1-H and the two on N2). Its acceptors are the two lone pairs on the O6 carbonyl plus one each on N3 and N7, so 4. Note that only three of those seven sites face cytosine, which is why the G-C pair uses 3 hydrogen bonds and not 7.

Why hydrogen bonding matters:

• Water’s anomalously high boiling point and surface tension
• DNA’s double-helix base pairing (A-T uses 2 H-bonds, G-C uses 3)
• Protein secondary structure (alpha helices and beta sheets)
• Why alcohols mix with water and hydrocarbons do not
• The unusually low density of ice compared to liquid water

Typical hydrogen bond strengths range from 5 to 30 kJ/mol, about a tenth to a twentieth of a single covalent bond. Strong enough to hold biological structures together, weak enough that thermal energy at body temperature constantly breaks and reforms them.

Use the preset list to fill in known molecules, or “Custom” to enter values yourself.