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2-Mercaptoethanol is the chemical compound ${\mathrm{HOCH}}_2{\mathrm{CH}}_2\mathrm{SH}$; see the NIST Chemistry WebBook, 2-mercaptoethanol: structure and names. In the ribonuclease A refolding experiment, it breaks protein disulfide bonds, while the peptide bonds of the protein backbone remain intact. This separates a change in crosslinks from cutting the polypeptide chain.

A chemical compound used as a fluorescence screen in the Röntgen X-ray discovery experiment.

Carbon fixation incorporates carbon from carbon dioxide into organic chemical compounds. It identifies a material transformation, rather than a particular source of energy: carbon fixation can be supported by photosynthesis or by other metabolism. The Calvin cycle is one pathway, not the definition of all carbon fixation.

A ceramic is an inorganic, nonmetallic solid, often formed by heating and cooling. Ceramics may contain several chemical compounds and need not have a single crystal structure.

A chemical element is an identity shared by all chemical atoms whose atomic nuclei contain the same number of protons. That number is its atomic number, $Z$: six means carbon, eleven means sodium. The identity survives differences in neutron count, which distinguish isotopes, and differences in electron count, which distinguish neutral chemical atoms from ions. See the IUPAC Gold Book, chemical element.

The same name can also denote a pure chemical substance containing only that chemical element. These two uses answer different questions. Molecular oxygen, ${\mathrm{O}}_2$, is a chemical substance made entirely of oxygen; water, ${\mathrm{H}}_2\mathrm{O}$, is a chemical compound containing both hydrogen and oxygen. A water molecule contains three chemical atoms but only two chemical elements. Joining chemical atoms through chemical bonds changes their arrangement without changing their atomic numbers.

This distinction makes stoichiometry possible: ordinary chemical reactions rearrange chemical atoms, so one can count each chemical element before and after a transformation. Changing the proton count instead changes the chemical element and requires a nuclear reaction. The periodic table organizes these identities into a useful map, while atomic number bookkeeping keeps identity, isotope, and electric charge separate.

An ecosystem is a system of interacting organisms and their nonliving surroundings. A pond study might include algae, fish, bacteria, water, dissolved chemical compounds and incoming light. The useful step is to state the boundary and time interval: the pond surface, bottom and shoreline might enclose the study region, but water, organisms and energy can cross them. The chosen boundary specifies what counts as internal storage, input or output; it does not make the ecosystem sealed. See Clark, Douglas and Choi, Biology 2e, 46.1: ecosystems and their components.

For a toy pond water budget over one day, begin with $1000{\mathrm{m}}^3$, add $120{\mathrm{m}}^3$ crossing inward, and remove $90{\mathrm{m}}^3$ crossing outward. With all other transfers omitted by assumption, the final amount is $1000+120-90=1030{\mathrm{m}}^3$. The same bookkeeping asks whether a change inside an ecosystem came from internal processes or exchanges with its surroundings. Changing the boundary to include an upstream reservoir changes which transfers are internal, while preserving the accounting.

Ethanol is the chemical compound produced by the alcoholic fermentation described under Saccharomyces cerevisiae. Its two carbon chemical atoms explain the product bookkeeping there. See NIST Chemistry WebBook: ethanol formula and identity; the Biology 2e section cited under Saccharomyces cerevisiae identifies ethanol as the alcohol product.

The hydrated chemical compound used in the Giauque-MacDougall magnetic cooling experiment.

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.

The chemical compound $\mathrm{HgO}$. Thermal decomposition can release oxygen and produce mercury; historical preparations of the red oxide featured in Joseph Priestley's and Antoine Lavoisier's investigations.

A meso compound is an achiral molecule despite having stereocenters. Tartaric acid, $\mathrm{HOOC}-\mathrm{CH}(\mathrm{OH})-\mathrm{CH}(\mathrm{OH})-\mathrm{COOH}$, has two tetrahedral carbon stereocenters. Its $(2R,3R)$ and $(2S,3S)$ forms are enantiomers, but $(2R,3S)$ and $(2S,3R)$ name the same meso form after equivalent ends are identified. A symmetric spatial arrangement has a mirror plane exchanging its two halves. Thus there are three stereoisomers, not four.^[ref]

Opposite R and S configurations alone do not guarantee a meso compound: the rest of the molecule must permit mirror superposition. Likewise, a meso compound is one achiral chemical compound, whereas a racemate is a mixture of two chiral molecule populations. Both can give zero optical rotation for different reasons.

A mixture contains two or more chemical substances combined in proportions that need not be fixed. A chemical compound instead has a definite composition: water has two hydrogen chemical atoms per oxygen chemical atom, whereas a sucrose and water mixture can contain different sugar proportions. A homogeneous mixture has uniform composition on the scale of representative samples; a heterogeneous mixture has distinguishable regions of different composition. A chemical solution is homogeneous, whereas sand dispersed in water is a particle suspension.^[ref]

The distinction concerns the sample, not merely its ingredient list. A vessel with dissolved sodium chloride and excess undissolved sodium chloride contains a chemical solution and an ionic crystal thermodynamic phase. The liquid portion can be homogeneous while the whole vessel is heterogeneous. Similarly, molecular oxygen dissolved in water is part of a chemical solution; visible gas bubbles introduce a separate gas thermodynamic phase.

A molecule, using the International Union of Pure and Applied Chemistry (IUPAC) convention, is an electrically neutral entity containing two or more chemical atoms. Its constituents form a bound unit through chemical bonds; merely drawing a boundary around neighboring particles does not make a molecule. The neutrality requirement concerns total electric charge, not the absence of internal charge separation: water is a polar molecule with zero total electric charge.^[ref]

One water molecule, ${\mathrm{H}}_2\mathrm{O}$, contains two hydrogen and one oxygen chemical atom. One molecular oxygen molecule, ${\mathrm{O}}_2$, contains two oxygen chemical atoms; a molecule need not contain different chemical elements. One carbon dioxide molecule, $\mathrm{C}{\mathrm{O}}_2$, contains one carbon and two oxygen chemical atoms. The molecular formula records these inventories, while molecular geometry describes their arrangement. Water and carbon dioxide are chemical compounds; molecular oxygen is a form of one chemical element.

Ordinary crystalline sodium chloride, $\mathrm{NaCl}$, contains an extended arrangement of sodium cations $\mathrm{N}{\mathrm{a}}^{+}$ and chlorine anions $\mathrm{C}{\mathrm{l}}^{-}$. Its formula unit specifies one of each for compositional accounting, without selecting a unique isolated pair. Bulk neutrality therefore does not imply a material consists of neutral molecules. This statement concerns the ionic crystal; the physical state and conditions matter when deciding what particles a chemical formula represents.^[ref]

A polyatomic ion is a charged bound group of chemical atoms, such as hydronium, ${\mathrm{H}}_3{\mathrm{O}}^{+}$. A molecular ion formed by removing an electron from intact water, ${\mathrm{H}}_2{\mathrm{O}}^{\bullet +}$, retains the same atom inventory but has net electric charge $+e$. Neither satisfies the neutral-molecule definition. Distinguishing these entities makes molecular count and amount of substance and mass spectrometry interpretable: say whether the count is of chemical atoms, neutral molecules, ions, or formula units.

The useful surprise is that a molecule can be treated as one particle for motion and counting while retaining internal structure. Its molar mass connects a particle inventory to bulk mass; molecular rotation and molecular vibration reveal internal organization. The continuum approximation uses bulk fields in place of individual molecular positions and motions.

The octet rule is a useful empirical guide: many Lewis structures of chemical compounds containing carbon, nitrogen, and oxygen give each of those chemical atoms eight electrons when nonbonding electrons and all incident bonding electrons are counted. Hydrogen instead normally counts two electrons. These are local counts, not independent budgets: a shared bond pair counts at both endpoints but only once in the molecule's valence electron total.

In water, oxygen counts $4+4=8$ electrons; in ammonia, nitrogen counts $2+6=8$; in $\mathrm{O}=\mathrm{C}=\mathrm{O}$, carbon counts $0+8=8$ and each oxygen counts $4+4=8$. The charge-separated carbon dioxide drawing also satisfies the octet rule, so the octet rule alone cannot select the dominant contributor. Formal charge provides another check.

The octet rule is a heuristic rather than a theorem about every chemical bond. Odd valence electron totals cannot be partitioned entirely into electron pairs, and some valid Lewis structures have fewer or more than eight electrons around a chemical atom. See Chemistry 2e, 7.3: exceptions to the octet rule. The capacity of the $s$ and $p$ electron subshells, $2+6=8$, helps motivate the guide for these chemical elements, but does not prove universal compliance. Lewis discussed a stable outer group of eight, together with a two-electron arrangement for hydrogen, in The Atom and the Molecule (1916), pp. 768 and 774.

Photosynthesis captures light energy and transforms it into chemical forms that a biological cell can use. In plants, algae and cyanobacteria, this supports carbon fixation: incorporation of carbon from carbon dioxide into chemical compounds used to build living material. Capturing light and incorporating carbon are distinct processes coupled through metabolism. See OpenStax Biology 2e, 8.1: overview of photosynthesis.

For oxygenic photosynthesis, a simplified net equation writes a six-carbon sugar, glucose, as the representative product:This is net stoichiometry, not a one-step mechanism. A worked bookkeeping check counts six carbon chemical atoms, twelve hydrogen chemical atoms, and eighteen oxygen chemical atoms on each side: the product side has six oxygen chemical atoms in the sugar and twelve in molecular oxygen. The light label supplies energy, not additional chemical atoms.

Crucially, the released molecular oxygen comes from water, not carbon dioxide. Cancelling water made and consumed in different steps hides this distinction in the net equation. The Calvin cycle supplies a net three-carbon triose phosphate, such as glyceraldehyde 3-phosphate, for subsequent sugar synthesis; it does not directly export glucose. See OpenStax Biology 2e, 8.2: light-dependent reactions and OpenStax Biology 2e, 8.3: using light energy to make organic molecules.

The useful achievement is connecting incoming light to both usable energy and new biological material. ATP is an immediate energy currency; NADPH supplies electrons for synthesis; carbon dioxide supplies the carbon incorporated into carbohydrates. These roles are complementary. Conservation of energy still holds: photosynthesis transforms energy, never creates it, and some absorbed energy is dissipated as heat. A plant also carries out cellular respiration, including in biological cells that perform photosynthesis. Gas exchange reflects both processes. Oxygenic photosynthesis remains central to interpreting terrestrial molecular oxygen as an atmospheric biosignature gas. See OpenStax Biology 2e, 8.3: photosynthesis and respiration.

A primary producer builds organic chemical compounds from inorganic sources. Photosynthetic algae, plants and cyanobacteria use light energy for this role through photosynthesis and carbon fixation. The role supplies new living material to a food web; it does not mean that the organism creates energy.

Let $m$ be the transferred sample mass, $p$ the known mass fraction of the intended chemical compound, and $M$ its molar mass. In a model with complete dissolution and chemically inactive impurities,The purity fraction is dimensionless: $99.95\%$ would mean $p=0.9995$, not $99.95$. These equations assume that the impurity contributes no titrant demand; an impurity that also reacts needs its own inventory equation. The value of $p$ must refer to the same preparation state as $m$, for example the specified dry material. A mass fraction assigned before unaccounted uptake of water cannot simply be used after it.

For an original worked example, stipulate pure potassium hydrogen phthalate, abbreviated KHP, so $p=1$, a selected mass $m=0.51055\mathrm{g}$, and rounded molar mass $M=204.22\mathrm{g}\mathrm{mo}{\mathrm{l}}^{-1}$. The NIST Chemistry WebBook lists formula ${\mathrm{C}}_8{\mathrm{H}}_5\mathrm{K}{\mathrm{O}}_4$ and molecular weight $204.2212$, consistent with the rounded molar mass used here.^[ref] The selected mass, purity assumption and volumes in this example are chosen inputs, not measured results or a claim about a real batch's purity.

The acid-bearing anion of potassium hydrogen phthalate loses one proton to hydroxide. The net chemical equation isThus sodium hydroxide has one-to-one stoichiometry with potassium hydrogen phthalate in this neutralization, givingChoose a delivered endpoint titre of $24.85\mathrm{mL}$ and matched titration blank of $0.05\mathrm{mL}$. ThenThe extra displayed digits show the arithmetic of the stipulated model; they do not establish experimental accuracy. A compact rounded result is $0.1008\mathrm{mol}{\mathrm{L}}^{-1}$.

When the entire weighed portion is titrated, added water changes concentration and the pH path but preserves the initial acid inventory. The dissolution volume therefore does not appear in $n_s=mp/M$. If instead a volumetric flask prepares a stock and a volumetric pipette selects an aliquot, the selected inventory is $n_s{V}_a/V_f$ for homogeneous stock, with delivered aliquot volume $V_a$ and final stock volume $V_f$. The same bookkeeping explains why complete transfer matters even when the amount of dissolution water is approximate.

Silver chloride is a chemical compound with formula $\mathrm{AgCl}$. Its darkening under illumination supplied the chemical readout in the historical ultraviolet discovery described above. That response depends on the incident optical spectrum and the sample's condition; it does not provide an uncalibrated direct measurement of incident power. ^[ref].

The chemical compound used in the conductometric determination of activation energy. Its chemical formula and alternative name 2-Bromo-2-methylbutane are listed by the ^[ref].

A thiol is a chemical compound of the form $\mathrm{R}-\mathrm{SH}$, with an organic group $R$ attached to sulfur. The conjugate base is $\mathrm{R}-{\mathrm{S}}^{-}$; cysteine and mercaptoethanol supply examples of thiol groups. Two thiol groups can undergo oxidation to form a disulfide bond. ^[ref]