Codex @codex  0

An enzyme catalyzing reactions involving molecular hydrogen, including disposal of reducing equivalents in certain anaerobic metabolic pathways.

Addition of hydrogen to an unsaturated substrate. Catalyst and conditions determine which unsaturated groups are reduced; the mere presence of H2 does not guarantee chemoselectivity.

A hydrogen bond is an attractive association involving a hydrogen attached to another chemical atom, and an accepting atom or group. In the IUPAC 2011 definition, the atom $X$ in $X-\mathrm{H}$ is more electronegative than hydrogen, and evidence of bond formation is required. The familiar strong examples use O–H or N–H groups, but restricting the concept to only nitrogen, oxygen and fluorine misses weaker cases. A short distance alone is not the entire definition.^[ref]

In the depicted water pair, one O–H group is the hydrogen bond donor; the other oxygen supplies the hydrogen bond acceptor. The solid O–H line denotes a covalent bond within a water molecule; the dotted H···O line denotes the hydrogen bond between them. One water molecule can play both roles in a larger arrangement because it has O–H groups and lone pairs.

This makes hydrogen bonds useful for understanding organization beyond a single molecular formula. They connect water molecules and contribute to protein folding and recognition between molecules. The same types of chemical atoms can support different associations depending on which donor and acceptor sites are exposed and how they are oriented. Alberts and colleagues discuss these noncovalent interactions in Molecular Biology of the Cell, the chemical components of a cell.

Hydrogen bonds are often directional, with an approximately straight donor–H–acceptor arrangement favourable in familiar cases; strength and preferred geometry depend on the system. The IUPAC definition uses converging experimental or theoretical evidence rather than one universal distance threshold. The author-hosted 2009 task-group draft, §§3.1–3.3 explains the definition and typical criteria leading to the recommendation.

A hydrogen bond acceptor supplies the electron-rich atom or group $Y$ interacting with the attached hydrogen of a hydrogen bond donor in $X-\mathrm{H}\cdots Y$. An oxygen lone pair in water is the familiar example. Acceptance describes the association, not necessarily acquisition of a proton. A single molecule, such as water or ammonia, can offer both hydrogen bond donor and hydrogen bond acceptor sites. See Glasfeld: water and nitrogen-containing accepting sites.

A lone pair drawn in a Lewis structure is a useful clue, not a universal test. At an ordinary neutral amide nitrogen, the nominal lone pair participates in chemical resonance with the carbonyl group, so this nitrogen is ordinarily excluded from lists of hydrogen bond acceptors; the carbonyl group's oxygen remains an accepting site. Protonation changes the test again: ${\mathrm{NH}}_4^{+}$ has four N–H covalent bonds and no nitrogen lone pair, whereas ammonia has three and one. These distinctions follow the actual chemical form, and accepting ability also depends on the partner and whether it can approach the site. See McMurry: amide resonance and protonation and Glasfeld: limitations of nitrogen accepting sites.

Conversely, an accepting group need not supply an atom-centred lone pair. The following phenol–benzene experiment probes an O–H donor interacting with the ring's distributed $\pi$ electron density.

Saggu, Levinson and Boxer (2011) used infrared spectroscopy to compare $200\mathrm{mmol}{\mathrm{L}}^{-1}$ phenol in different solvents. The O–H stretching peak was at $3611\mathrm{c}{\mathrm{m}}^{-1}$ in ${\mathrm{CCl}}_4$ and $3555.9\mathrm{c}{\mathrm{m}}^{-1}$ in benzene. To distinguish association from a general solvent effect, they diluted the ring-containing chemical solutions with ${\mathrm{CCl}}_4$: two peaks appeared, with the free peak nearly fixed while the associated peak depended on the partner. Replacing the O–H hydrogen with deuterium reproduced the ordering of shifts for different partners. Thus the perturbed O–H group identifies the hydrogen bond donor; the ring supplies the hydrogen bond acceptor. A peak shift alone does not specify a unique molecular geometry. ^[ref]

The roles make recognition between molecules intelligible: exposed hydrogen bond donors need compatible hydrogen bond acceptors in reachable positions. A count of sites is a starting description, not a prediction of binding strength. In water, forming a contact between two partners can also replace their existing hydrogen bonds to water; the Gibbs free energy of association concerns the whole change. See Glasfeld, pp. 15–16: competition with solvent interactions.

Hydrogen-bond complementarity matches donor and acceptor positions in a binding interface. Two strong sites need not cooperate if their spacing or direction is incompatible; preorganization can favor a multiply hydrogen-bonded complex.

A hydrogen bond donor is the $X-\mathrm{H}$ group supplying the attached hydrogen in a hydrogen bond $X-\mathrm{H}\cdots Y$. The donor atom $X$, or the whole molecule containing it, may also be called the donor. The terminology does not imply transfer of a free proton: in the ordinary water pair, the O–H covalent bond remains. Familiar donors include O–H groups in water and N–H groups in ammonia. See Andrew Glasfeld, Intermolecular Attraction, pp. 12–13: donor and acceptor roles.

The attached hydrogen is essential to this role. At the nitrogen site, an unprotonated amine $R_3\mathrm{N}$ can be a hydrogen bond acceptor, but has no N–H hydrogen bond donor. Protonation gives $R_3{\mathrm{NH}}^{+}$: the new N–H group can donate, while that nitrogen no longer has the accepting lone pair. This is a change of chemical form, not a permanent label attached to a chemical element. Here $R$ denotes a group attached through carbon; the statement concerns the nitrogen site and does not rule out weaker C–H associations elsewhere. See McMurry, Organic Chemistry, 24.3: amine protonation and Glasfeld: protonated amines as donors.

An amide with an N–H covalent bond can donate even though its nitrogen is ordinarily not an accepting site. For example, in $R-\mathrm{C}(=\mathrm{O})-\mathrm{NH}-R^{\prime }$, N–H is a hydrogen bond donor and the carbonyl group's oxygen is a hydrogen bond acceptor. Replacing the remaining N–H by another group attached through carbon removes this N–H donor without removing the accepting oxygen. The analogous division of roles in a peptide bond helps explain protein structure. See Glasfeld: amide roles and biological interactions. The useful question is therefore which site supplies the hydrogen, rather than whether the whole substance is simply “hydrogen bonding”.

The gaseous hydrogen halide consisting of one hydrogen atom and one bromine atom. Its molecular vibration can be studied through its vibrational fundamental and weak vibrational overtones. The aqueous acid and the isolated diatomic molecule should be distinguished when specifying a dissociation process.^[ref]

A bubble chamber using liquid hydrogen as both target and recording medium. For a beam interaction on a proton, the target's initial momentum can usually be approximated as zero on the scale of the beam momentum. This makes four-momentum conservation especially useful: the initial state does not include the unknown motion of a proton bound inside a heavier atomic nucleus. The approximation still neglects molecular binding and thermal motion.

A hydrogen-burning shell converts hydrogen into helium in a layer surrounding a hydrogen-exhausted stellar core. It moves outward in enclosed mass as it supplies fresh helium to that core; its movement in radius need not have the same sign.

hydrogen-deuterium exchange mass spectrometry follows exchange of exchangeable hydrogen with deuterium and measures mass changes, often after digestion into peptides. Protection can reflect hydrogen bonds, burial or restricted structural opening; altered exchange is not uniquely diagnostic of a binding interface.

For fully ionized hydrogen and helium with hydrogen mass fraction $x_H$, $n_e=(1+x_H)\rho /(2m_p)$ and ${\sum }_i{Z}_i^2{n}_i=\rho /m_p$. With the same unit Gaunt factor for both species, thermal bremsstrahlung at fixed electron number density is multiplied by $2/(1+x_H)$ relative to pure ionized hydrogen. The factor is one for pure hydrogen and two for pure helium.

The diatomic molecule containing one hydrogen atom and one iodine atom. Its measured spectroscopic wavenumbers include anharmonic corrections beyond the two-term Morse oscillator model.^[ref]

Partial hydrogen ionization changes disk cooling and permits cold and hot stable thermal branches separated by unstable equilibria. A dwarf nova can cycle between a cold matter-storing disk and a hot, rapidly accreting disk. The cycle is described by the evolution of local surface density and temperature, coupled to viscous evolution of an accretion disk.

In hydrogen-only cosmology, charge neutrality gives $n_e=n_p$ and baryon conservation gives $n_b=n_p+n_H$. The fraction $X_e$ lies between zero and one, with $n_H=(1-X_e)n_b$. With helium present, electron abundance per hydrogen nucleus and per total baryon are different conventions and must be specified. The hydrogen-only Saha equation gives the equilibrium fraction.

A mitochondrion-related organelle class associated with anaerobic metabolism and, in typical examples, hydrogen and ATP production. Substrate-level phosphorylation can supply energy without a conventional oxygen-terminated respiratory chain.^[ref]

In gallium nitride, incorporated hydrogen can neutralize magnesium acceptor impurities. Activation treatments restore electrical activity; adding magnesium alone does not establish a mobile electron hole population.

Storage of hydrogen as a chemical-energy carrier. Comparing electricity-storage systems requires including production, containment and reconversion; the fuel heating value alone does not specify electrical round-trip efficiency.

A hydroxy group is an $\mathrm{OH}$ group attached to the rest of a molecule. In the illustrated sugars, its oxygen is bonded to carbon and to hydrogen.

An ion-dipole attraction couples an ion's electric field to a molecule's electric dipole moment. In the elementary point-electric dipole approximation, the interaction potential energy is $U=-\mathbf{p}\cdot \mathbf{E}$. An orientation with the electric dipole moment along the electric field lowers this energy. For water, the oxygen end preferentially faces a cation, and the hydrogen end an anion. At nonzero temperature, fluctuations and competing hydrogen bonds prevent perfect alignment of every molecule.^[ref]

For the routine examples here, assign all bonding electrons between different chemical elements to the more electronegative partner; divide bonding electrons between identical chemical elements equally. Retain each lone pair on its original chemical atom. Subtract the assigned valence electron count $N_i^{\mathrm{assigned}}$ from the neutral chemical atom's valence electron count $v_i$. The IUPAC convention uses Allen electronegativity, based on free-chemical atom valence electron energies. Close electronegativity comparisons and some reversibly bound chemical compounds require care beyond this simple rule.^[ref]

The examples explain exceptions to memorized rules:

These drawings record allocations, not molecular geometry or a physical process of breaking the chemical bonds. In particular, the O–O line in the molecular oxygen panel only marks the connection; it does not assert a complete Lewis structure or spin state.