Intermolecular hydrogen bonding is responsible for the high boiling point of water (100 °C). This is because of the strong hydrogen bond, as opposed to other group 16 hydrides. Intramolecular hydrogen bonding is partly responsible for the secondary, tertiary, and quaternary structures of proteins and nucleic acids.

Bonding

A hydrogen atom attached to a relatively electronegative atom is a hydrogen bond donor. This electronegative atom is usually fluorine, oxygen, or nitrogen. An electronegative atom such as fluorine, oxygen, or nitrogen is a hydrogen bond acceptor, regardless of whether it is bonded to a hydrogen atom or not. An example of a hydrogen bond donor is ethanol, which has a hydrogen bonded to oxygen; an example of a hydrogen bond acceptor which does not have a hydrogen atom bonded to it is the oxygen atom on diethyl ether.

The hydrogen bond is often described as an electrostatic dipole-dipole interaction. However, it also has some features of covalent bonding: it is directional, strong, produces interatomic distances shorter than sum of van der Waals radii, and usually involves a limited number of interaction partners, which can be interpreted as a kind of valence. These covalent features are more significant when acceptors bind hydrogens from more electronegative donors.

The partially covalent nature of a hydrogen bond raises the questions: "To which molecule or atom does the hydrogen nucleus belong?" and "Which should be labeled 'donor' and which 'acceptor'?" Usually, this is easy to determine simply based on interatomic distances in the X-H...Y system: X-H distance is typically ~1.1 Å, whereas H...Y distance is ~ 1.6 to 2.0 Å. Liquids that display hydrogen bonding are called associated liquids.

Hydrogen bonds can vary in strength from very weak (1-2 kJ mol⁻¹) to extremely strong (>155 kJ mol⁻¹), as in the ion HF₂⁻. Typical values include:

• F—H^...:F (155 kJ/mol or 40 kcal/mol)
• O—H^...:N (29 kJ/mol or 6.9 kcal/mol)
• O—H^...:O (21 kJ/mol or 5.0 kcal/mol)
• N—H^...:N (13 kJ/mol or 3.1 kcal/mol)
• N—H^...:O (8 kJ/mol or 1.9 kcal/mol)
• HO—H^...:OH₃⁺ (18 kJ/mol or 4.3 kcal/mol) {Data obtained using molecular dynamics as detailed in the reference and should be compared to 7.9 kJ/mol for bulk waters, obtained using the same molecular dynamics.}