Hydrogen_bond - Wikiparency

# Hydrogen bond  ## Microsims — three.js ### Hydrogen bond (three.js) <div class="microsim-player"> <iframe src="https://wikitube-3d-microsims.netlify.app/Hydrogen_bond.html" width="100%" height="620" frameborder="0" loading="lazy" sandbox="allow-scripts allow-same-origin" title="Hydrogen bond — three.js microsim"></iframe> </div> **Open it full-screen:** [Hydrogen_bond.html](https://wikitube-3d-microsims.netlify.app/Hydrogen_bond.html) · library `threejs` · route `microsim/threejs/` ### Related microsims Live sims on neighbouring articles: - [[Allotropes_of_oxygen]] - [[Atomic_orbital]] - [[Hemoglobin]] - [[Molecular_orbital]] - [[Ozone_layer]] - [[Silicon_dioxide]] *Sim hosted off-article; the article owns the reference, not the runtime (WIKI_RULES §10.4). Placed by `g08_place_microsims.py`.*  ## Overview A hydrogen bond is the attraction between a hydrogen atom already covalently bound to a strongly electronegative atom -- most often oxygen, nitrogen or fluorine -- and a lone pair on another such atom. It is far weaker than a covalent bond and far stronger than ordinary dispersion forces, and that intermediate strength is precisely what makes it useful: strong enough to organise matter, weak enough to break and reform at ordinary temperatures. Oxygen's electronegativity is what puts water at the centre of this story. In water the hydrogen bond is responsible for essentially every property that makes the substance anomalous: a boiling point roughly 160 degrees higher than its molecular mass would suggest, an unusually high heat capacity and surface tension, a density maximum at 3.98 degrees C, and solid ice that floats on its own liquid. ## The physics A water molecule is bent, with an H-O-H angle of 104.5 degrees and O-H covalent bonds of 95.8 pm. Oxygen carries a partial negative charge and each hydrogen a partial positive one. Each molecule can donate two hydrogen bonds (one per hydrogen) and accept two (one per lone pair), giving tetrahedral coordination -- four neighbours. That single structural fact generates the rest. In ice Ih the tetrahedral network is fully satisfied and periodic, which forces an open hexagonal lattice with a good deal of empty space. Because the lattice is open, ice has a density of about 0.917 g/cm3 against liquid water's 1.000, so it floats. Melting partially collapses the network: molecules pack closer even as thermal motion increases, and the competition between those two effects produces the density maximum a few degrees above freezing. Energetically the hydrogen bond is around 20 kJ/mol, against roughly 460 to 490 kJ/mol for the O-H covalent bond -- a ratio of about one to twenty. Reference geometries are usually quoted as H...O about 197 pm and O...O about 280 pm. Note that those three reference numbers are not mutually consistent for a perfectly linear bond, since 95.8 + 197 = 292.8 rather than 280; they come from different measurements of different phases, and a lattice built on an exact O...O spacing of 280 pm gives a rendered H...O nearer 184 pm. ## Controls -> what each maps to | Control | Maps to | Range / values | Physical meaning | |---|---|---|---| | Temperature | T | -40 to +80 C | Drives procedural disordering of the network; the count of intact bonds falls as T rises | | Lattice size | N unit cells | small - large | How much of the ice Ih lattice is built | | Show hydrogen bonds | -- | on / off | Distinguishes dashed hydrogen bonds from solid covalent O-H bonds | | Highlight one molecule | -- | on / off | Picks out one molecule and its four tetrahedral neighbours from the crowd | | Spin the view | -- | on / off | Rotation only; disabled under prefers-reduced-motion | ## Learning objective After playing, a learner can explain why ice floats in terms of tetrahedral coordination and an open lattice, distinguish a hydrogen bond from a covalent bond by both geometry and energy, and connect oxygen's electronegativity to water's anomalous properties. ## Limits and connections The liquid here is a procedural disordering of the ice lattice driven by the temperature control, not a molecular dynamics simulation: there is no force field, no thermostat, and no real diffusion. Mean bond counts are measured from the rendered geometry using a distance and angle criterion, so they depend on that criterion. The mean is reported over bulk molecules only, since surface molecules genuinely have fewer neighbours and would otherwise drag the ice figure below four. Hydrogen bonding also underpins protein and nucleic-acid structure, which is the route from here to [[Hemoglobin]].  **Part of the [[WT!Thury_Hydrodynamics_Compendium|Thury Hydrodynamics Compendium]]** — main article for section 8, *The hydrogen bond*. Related sections: [[Properties_of_water]] · [[Liquid–liquid_critical_point]] · [[Fuel_cell]].   **Microsim — three.js (Wikitube framework):** *Hydrogen bond* <div class="wt-sim" data-src="https://wikitube-3d-microsims.netlify.app/thury/Hydrogen_bond.html" data-title="Hydrogen bond"></div> *Built from `MICROSIM_GUIDE/specs/sims/Hydrogen_bond.json`; part of the [[WT!Thury_Hydrodynamics_Compendium|Thury Hydrodynamics Compendium]] set.*  ## Wikipedia : Wikitube **Strict pair:** [Wikipedia](https://en.wikipedia.org/wiki/Hydrogen_bond) : [Wikitube](https://en.wikitube.io/wiki/Hydrogen_bond) ## Previous hub tags Tree parent: [[Oxygen]]. Legacy hubs: `REACTION`. --- *Created 2026-08-05 - append-only - hand-authored to WIKI_REPOPULATION_PROTOCOL v1.0 section 5 - 0 deletions*