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The Hill reaction couples light-driven electron transfer from water to an added electron acceptor with molecular oxygen release in an isolated photosynthetic preparation. The chloroplast dye-reduction experiment uses DCPIP.^[ref]

In 1937, Robin Hill's Oxygen Evolved by Isolated Chloroplasts described a spectroscopic molecular oxygen measurement in illuminated isolated chloroplasts: oxygenation of muscle hemoglobin provided the indicator. This was an oxygen-binding readout. The publicly accessible first paragraph establishes that method; it does not specify enough preparation or control details to reconstruct the entire historical experiment here.^[ref]

The experimental idea is powerful because isolation asks how much of photosynthesis remains functional outside an intact biological cell. Breaking a chloroplast envelope does not logically imply destroying every internal thylakoid membrane. Conversely, finding an active preparation cannot establish that its chloroplast envelope remains intact. Activity and structural integrity require different evidence.

In homogeneous catalysis, the catalyst and reactants occupy the same thermodynamic phase.

For a liquid example, specify hydrogen peroxide as the reactant, dissolved iodide as the catalyst, and water as the solvent. If both reacting chemical species remain dissolved in that one liquid thermodynamic phase, this is homogeneous catalysis. The University of Wisconsin–Madison's The Rate of a Reaction identifies iodide-catalysed hydrogen peroxide decomposition in its final example; the aqueous setting here makes the phase roles explicit.^[ref] Its net chemical equation isThe molecular oxygen is a reaction product: its bubbles do not make the dissolved catalytic route heterogeneous catalysis. The classification compares the participating catalyst and reactants, rather than demanding that everything in the vessel share a phase.^[ref]

Being in the same thermodynamic phase describes where the chemical species are; it does not specify their reaction mechanism. A uniform-looking liquid can contain unresolved solid particles, so appearance alone is insufficient. Conversely, suspended solid particles do not establish that their surfaces supply the observed catalysis: dissolved material released from them could contribute. Phase identification and catalytic participation need separate evidence.

The bookkeeping of a catalyst in homogeneous catalysis is particularly transparent in the schematic catalytic cycle A plus C forming AC, followed by AC releasing B plus C. This is the generic model in catalyst, not an asserted iodide reaction mechanism. Suppose a fixed volume initially contains $1.00\mathrm{mmol}$ of A and $0.20\mathrm{mmol}$ of C. At a chosen snapshot, let $0.60\mathrm{mmol}$ of B and $0.12\mathrm{mmol}$ of AC be present, with no other chemical reactions. Each AC contains one A unit and one C unit, soThus free A is $0.28\mathrm{mmol}$ and free C is $0.08\mathrm{mmol}$. B formation already exceeds the initial amount of substance of C by a factor of three, while the total C inventory remains $0.20\mathrm{mmol}$. Adding the two steps cancels C and AC, giving the net A-to-B chemical reaction; counting their constituents proves these balances. Conserved total catalyst does not mean constant free catalyst concentration.

Dissolved contact is useful because reactants can encounter the catalytic chemical species throughout the mixed liquid, without first reaching a macroscopic solid surface. Recovering a dissolved catalyst from the same chemical solution can instead require a separation. Neither ease of contact nor phase classification determines an activation energy or an equilibrium constant; those depend on the relevant chemical kinetics and endpoint thermodynamics.

In the usual atmospheric convention, hydroxyl radical and HO2 form a rapidly interconverting hydrogen-oxide radical family. Some budgets also explicitly include H; state the counting convention. Radical production, recycling and termination differ from the abundance of the water reservoir.

Hydration of ions is solvation by water. The polar water molecules orient preferentially around cations and anions, though the surrounding arrangement fluctuates rather than forming a permanently fixed cage.^[ref]

A hydration shell is a solvation shell in water. The existing hydration of ions discussion describes preferential orientations around cations and anions.

Hydraulic head is the sum of elevation and pressure head, measured in metres relative to a chosen height datum. For constant mass density $\rho$ and gravitational acceleration magnitude $g$, the pressure head $p/(\rho g)$ is the height of a column of the same fluid supported by fluid pressure $p$. A water-filled open measuring tube records hydraulic head as the elevation of its water level when $p$ is gauge fluid pressure. Changing the common pressure reference or height datum adds a constant to hydraulic head and leaves its driving gradient unchanged.

For water with $\rho =1000\mathrm{kg}{\mathrm{m}}^{-3}$ and $g=9.81\mathrm{m}{\mathrm{s}}^{-2}$, a point at $z=2\mathrm{m}$ with gauge fluid pressure $p=9810\mathrm{Pa}$ has $h=3\mathrm{m}$. A second point at $z=0$ with gauge fluid pressure $29430\mathrm{Pa}$ also has $h=3\mathrm{m}$: these values are compatible with a stationary column under hydrostatic pressure. It is a difference in hydraulic head, rather than a difference in fluid pressure alone, that drives saturated Darcy flow. This form uses constant mass density; one cannot generally pull spatially varying $\rho$ through the gradient.^[ref]

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.

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”.

In acid-base chemistry, hydrogen ion usually refers to positively charged hydrogen, represented by ${\mathrm{H}}^{+}$. In water, this notation describes solvated species, commonly represented by hydronium, rather than an isolated bare proton. The hydrogen ion thermodynamic activity defines pH.

Hydrolysis is a chemical reaction involving water that breaks a chemical bond. The free energy released by suitably coupled ATP hydrolysis can drive active transport; the available free energy depends on the actual composition and conditions.

Hydrolytic deamination replaces an amino group using water, releasing ammonia or ammonium according to pH. Adenosine deaminase introduces solvent oxygen at the C6 position of adenosine.

Hydronium is the ion formed when a water molecule accepts a proton. It provides the usual aqueous shorthand for the hydrogen ion used in pH calculations.

Hydrophilicity describes affinity for water. Regions with chemical polarity or electric charge can interact favorably with water, including through hydrogen bonds where suitable groups are present. Hydrophilic regions of membrane-forming phospholipids face the water on either side of a lipid bilayer. Such affinity does not mean forming covalent bonds with every neighboring substance, nor does it require a net negative electric charge. See Alberts et al.: the chemical components of a cell.

The hydrophobic effect is the solvent-mediated tendency of nonpolar regions to associate in water. Exposing a hydrocarbon region changes how surrounding water molecules can arrange and interact; reducing that exposure can lower the total free energy. Both water and lipids enter the accounting. The effect is not an additional covalent bond between chains. See IUPAC Gold Book: hydrophobic interaction.

At fixed temperature and pressure, compare two candidate organizations by the change in Gibbs free energy, $\Delta G=\Delta H-T\Delta S$, where $H$ is enthalpy, $T$ is absolute temperature, and $S$ is entropy. An organization with lower $G$ is favored in this comparison. Reducing exposed hydrocarbon area is one contribution; changes in chain packing and the entropy of the lipids also matter. This explains why hydrophobicity alone cannot predict every aggregate shape. See 16.4 Free Energy.

Hydrophobicity describes unfavorable mixing with water, as illustrated by long hydrocarbon regions. The hydrophobic regions of membrane-forming phospholipids face the interior of a lipid bilayer. This organization is explained by the hydrophobic effect, rather than by imagining that chains actively repel water. See IUPAC Gold Book: hydrophobic interaction.

Hydrostatic pressure is the pressure distribution in a resting fluid, balancing its body force from gravity. Take $z$ upward and a uniform downward gravitational field $\mathbf{g}=-g{\mathbf{e}}_z$, where $g>0$. The vertical pressure gradient satisfiesA short derivation balances the vertical forces on a thin horizontal layer of area $A$ and thickness $\Delta z$: $p(z)A-p(z+\Delta z)A-{\rho }_{f}gA\Delta z=0$. Dividing by $A\Delta z$ and taking the derivative gives the equation above. For constant mass density ${\rho }_f$, integration from the surface at $z_s$ givesThus pressure increases with depth $h$. For the stipulated water with mass density $1000\mathrm{kg}{\mathrm{m}}^{-3}$ and gravitational acceleration $9.81\mathrm{m}{\mathrm{s}}^{-2}$, depths $0.20\mathrm{m}$ and $0.30\mathrm{m}$ give gauge pressures $1962\mathrm{Pa}$ and $2943\mathrm{Pa}$. Their difference produces the buoyancy of the example cube. ^[ref]

Circulation of heated water-rich fluids through rock, transporting heat and dissolved components.

A hydroxo ligand is coordinated $\mathrm{O}{\mathrm{H}}^{-}$. Deprotonation of coordinated water can make it without first breaking the metal–oxygen bond.

A hypertonic solution favors initial net water loss under the reference conditions above. In a walled plant cell, enough loss can produce plasmolysis.