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The ground-state dissociation energy starts at the lowest vibrational quantum state, with the lowest allowed rotational quantum state and the fragment states explicitly specified. For a diatomic molecule whose fragments are ground-state chemical atoms, omitting any additional rotational correction,where $E_{\mathrm{ZP}}$ is the vibrational zero-point energy measured upward from the well minimum. The initial molecule already has this energy, so less additional energy is needed to reach the same final limit.^[ref]

For fragments that are themselves molecules, include their zero-point energies too. Define $D_e$ as the electronic energy difference between separately relaxed products and reactant; then, with consistent rotational conventions,Thus “subtract the parent's zero-point energy” is sufficient for atomic products but generally incomplete for molecular products. An excited final quantum state raises its channel threshold by its excitation energy; that threshold does not become the ground-product $D_0$ just because a detector selects it.

Heterolysis assigns both bonding Electrons to one fragment. For an initially neutral molecule, the resulting cation and anion define a different dissociation channel from homolysis; their isolated gas-phase energy differs from that of solvated ions.

Homolysis splits a covalent bond with one bonding Electron assigned to each fragment. A neutral closed-shell molecule thereby produces fragments with unpaired Electrons, each a radical. The usual bond-dissociation enthalpy uses this product convention.

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”.

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.

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.

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 ideal gas obeys $pV=N{k}_{B}T$ and neglects intermolecular interactions except during elastic collisions.

Infrared is electromagnetic radiation with wavelengths longer than the red end of ordinarily visible light. A useful named convention is the CIE range $780\mathrm{nm}$ to $1\mathrm{mm}$; the approximate visible range $400$–$700\mathrm{nm}$ used in some teaching texts puts the boundary nearer $700\mathrm{nm}$. ^[ref]. Neither number is a sharp physical cutoff of human vision. The CIE divisions IR-A, IR-B and IR-C are respectively $0.78$–$1.4\mu \mathrm{m}$, $1.4$–$3\mu \mathrm{m}$ and $3$–$1000\mu \mathrm{m}$; the boundaries of near-, middle- and far-infrared vary between applications. ^[ref].

Use vacuum wavelength $\lambda$ when comparing these ranges. With frequency $\nu$, speed of light $c$, Planck constant $h$ and photon energy $E$,Thus the CIE infrared interval corresponds approximately to $3.00\times 10^{11}$–$3.84\times 10^{14}\mathrm{Hz}$ and $1.99\times 10^{-22}$–$2.55\times 10^{-19}\mathrm{J}$ per photon, with the smaller energy at the longer wavelength. A $940\mathrm{nm}$ infrared photon has $E\simeq 2.11\times 10^{-19}\mathrm{J}$, whereas a $254\mathrm{nm}$ ultraviolet photon has $E\simeq 7.82\times 10^{-19}\mathrm{J}$. These are calculations from $hc/\lambda$, not measurements of a particular source. A television remote is a familiar approximately $940\mathrm{nm}$ source; its information is carried by variations in the emitted radiant flux. ^[ref].

Detection and visual perception answer different questions. A photodetector can respond to infrared even when an observer perceives no light; a thermometer detects an increase in temperature after photon absorption. Conversely, a small readout can reflect a small spectral responsivity, rather than absence of incident electromagnetic radiation. Images made from infrared readouts use display colors chosen by the imaging system; those colors are not the colors of the incoming infrared.

The important microscopic mechanisms also differ. In infrared spectroscopy, photon absorption often increases the energy of a normal mode in which chemical bonds stretch or bend. The corresponding optical spectrum helps distinguish molecules by their motions. For the usual electric dipole mechanism, the motion must change the electric dipole moment; matching the frequency alone is not sufficient. ^[ref]. Electronic processes can also emit or absorb infrared, so it is not exclusively radiation from molecular motion. ^[ref]; ^[ref].

Infrared is especially useful for observing thermal radiation from objects near everyday temperatures. For an ideal $300\mathrm{K}$ blackbody, Wien's displacement law gives a wavelength peak near $9.66\mu \mathrm{m}$. A thermal camera's readout nevertheless depends on emissivity, reflected surroundings and transmission along the path, as well as temperature. ^[ref]. A source emitting infrared need not be hot: an infrared remote is useful precisely because a photodetector can distinguish its signal from a background. Visible light and ultraviolet can also cause heating when absorbed; “infrared” names a wavelength range, not a unique form of heat.

Herschel's 1800 discovery made the distinction between sight and detection experimentally concrete. His report describes a optical prism spreading sunlight across a white, ruled receiving surface, with three thermometers at different positions near the end of the visible optical spectrum. He observed heating beyond the red edge where no visible color appeared. The result established that sunlight contained invisible radiation less strongly refracted by that optical prism than the visible red; it did not measure a photon energy or establish today's infrared boundaries. ^[ref]; ^[ref].

A documented modern version by Caltech/IPAC uses a glass optical prism, white paper in a shaded box and three blackened liquid-filled thermometers. Initial readings in shade provide each thermometer's baseline; subsequent readings compare blue, yellow and just beyond red after the bulbs have had time to warm. The measured quantity is the rise in temperature, not a “temperature of a color”. The lesson reports the expected largest rise beyond visible red and specifically discusses matching the bulb coatings and thermometer calibration. Clouds and changes in the projected optical spectrum affect the comparison. ^[ref].

For a stronger modern interpretation, an additional shaded thermometer would monitor ambient drift, exchanging bulbs between positions would test differences between thermometers, and blocking the incident beam would distinguish beam-dependent heating from warmed supports or air. These are suggested controls, not claims about Herschel's historical procedure. Thermal conduction through the mounting and convection can change the readout. A broad bulb also samples a range of wavelengths; the optical prism's transmission and optical dispersion, the bulb's absorption and heat loss all affect the position of the largest rise. In particular, the result does not show that an infrared photon carries more energy than a visible photon.

A simple analytical illustration makes those limitations explicit. Let $\theta =T-T_{\mathrm{amb}}$ be the bulb's excess temperature, $C$ its heat capacity, $G$ its effective heat-loss coefficient in $\mathrm{W}{\mathrm{K}}^{-1}$, and $P_{\mathrm{abs}}$ the absorbed power. Assume one uniform bulb temperature, constant ambient temperature, constant $C,G$, and losses linear in $\theta$. Thenfor a beam switched on at $t=0$ with $\theta (0)=0$. After switching the beam off at $t=t_s$, $\theta (t)=\theta (t_s)e^{-(t-t_s)/\tau }$. The exponential function follows by solving this linear differential equation. The steady excess temperature measures $P_{\mathrm{abs}}/G$; it is not a direct measurement of the optical spectrum. With illustrative $C=0.020\mathrm{J}{\mathrm{K}}^{-1}$ and $G=0.0010\mathrm{W}{\mathrm{K}}^{-1}$, $\tau =20\mathrm{s}$. Absorbed powers of $1.0$ and $0.5\mathrm{mW}$ give steady rises of $1.0$ and $0.5\mathrm{K}$, regardless of which wavelengths supplied that absorbed power.

The upper schematic represents the logic of the optical prism experiment; its light ray positions are not a calibrated wavelength scale. The lower curves use the illustrative heat-balance model, with the beam blocked at $60\mathrm{s}$; they are not historical or modern measured data. The beauty of the experiment is that a simple change of detector extends observation beyond what the eye can perceive.

Internal energy is the energy stored in the microscopic degrees of freedom of a system.

For a fixed amount of ideal gas, internal energy depends only on temperature. If $C_V$ is constant, $dE=C_{V}dT$ and hence $E=C_{V}T$ after a choice of energy zero.