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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.

The account of matter in terms of chemical atoms. Whole-number combinations of chemical atoms explain the law of definite proportions and law of multiple proportions for suitable pure chemical compounds.

A family of calcium–silicon–oxygen chemical compounds. The metasilicate $\mathrm{CaSi}{\mathrm{O}}_3$ is a simple model for one reaction in slag formation.

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 compound contains atoms of at least two chemical elements joined in a characteristic chemical structure. Molecular water has composition ${\mathrm{H}}_2\mathrm{O}$, while sodium chloride is an ionic solid with a one-to-one ratio of sodium and chloride ions rather than isolated NaCl molecules.

A compound differs from a mixture: separating its constituent elements generally requires a chemical transformation. A formula records composition but may not uniquely determine connectivity or stereochemistry, so different isomers can share a molecular formula.

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.

A chemical substance is matter identified by a characteristic chemical composition and set of chemical properties. It can be an elemental substance, such as molecular nitrogen, or a chemical compound, such as water. A mixture instead contains components whose proportions can vary without requiring a different compound identity.

Composition alone may not specify the physical form. Diamond and graphite are elemental carbon with different bonding networks, and a single compound can have several crystalline phases. Describing a sample therefore calls for both chemical identity and, when relevant, its phase, structure, and purity.

A diazine is an aromatic six-membered heterocyclic compound whose parent ring contains four carbon atoms and two nitrogen atoms. The three unsubstituted parent arrangements share formula ${\mathrm{C}}_4{\mathrm{H}}_4{\mathrm{N}}_2$ but differ in connectivity: pyridazine is the $1,2$ arrangement, pyrimidine the $1,3$ arrangement, and pyrazine the $1,4$ arrangement.^[ref]

Why only three? Fix one nitrogen at position $1$ on a six-membered ring. The other can be adjacent, separated by one intervening ring atom, or opposite. Reflection identifies the remaining apparent alternatives: positions $6$ and $2$ describe the same adjacent arrangement, while $5$ and $3$ describe the same next-nearest arrangement. Thus the distinct shortest ring separations are one, two and three bonds.

The three diazines are constitutional isomers, not different orientations of one molecule. Rotating a drawing changes its appearance without changing its atom-to-atom connections. Moving a ring nitrogen to another connectivity position instead changes which chemical compound the drawing represents. This makes the diazine family a compact example of why a molecular formula alone does not specify chemical identity.

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.

A homogeneous mixture has the same macroscopic composition throughout the region being described, at the scale of representative sampling. It contains more than one substance, unlike a pure chemical compound. A well-mixed chemical solution is a familiar example. The IUPAC definition of a chemical solution describes a liquid or solid thermodynamic phase containing more than one substance, with the solvent and solute assigned different roles.^[ref]

For an invented sampling example, dissolve 10 millimoles of a conserved solute and bring the final volume to 100 millilitres. After complete mixing, a representative 10-millilitre aliquot contains 1 millimole: $n_{\mathrm{aliquot}}=n_{\mathrm{total}}{V}_{\mathrm{aliquot}}/V_{\mathrm{total}}$. Its molar concentration equals that of the whole chemical solution, although its total amount of substance is smaller. Sampling from different heights provides a practical test for incomplete mixing.

Uniformity refers to the chosen physical description. A tiny region containing only a few molecules can fluctuate in composition; this does not contradict macroscopic homogeneity. Conversely, a vessel containing clear salt chemical solution above undissolved sodium chloride is heterogeneous as a whole, even if the liquid alone is homogeneous. The boundary of the described sample matters as much as its appearance.

A chemical compound whose solid composition includes water of crystallization.

Indium oxide usually denotes indium(III) oxide, $\mathrm{I}{\mathrm{n}}_2{\mathrm{O}}_3$, a solid chemical compound of indium and oxygen. Formal oxidation states of $+3$ for indium and $-2$ for oxygen give charge balance: $2(3)+3(-2)=0$. The formula expresses the elemental ratio; it does not imply discrete molecules in the solid.^[ref]

Doping this oxide with tin produces the material family indium tin oxide, used for transparent conducting layers. Electrical and optical performance depend on charge-carrier density and preparation, so knowing the host compound's formula alone does not specify a film's conductivity.^[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.

A class of iron–oxygen chemical compounds, including oxides with different iron oxidation states.

A pure stoichiometric chemical compound has fixed elemental mass ratios when isotopic composition is specified.

For simple chemical compounds of two chemical elements, the masses of one combining with a fixed mass of the other occur in ratios of small integers.

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.