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A chemical equation represents a chemical reaction using chemical formulas, with reactants on the left and reaction products on the right. A balanced chemical equation has the same number of chemical atoms of each chemical element on both sides. For molecular hydrogen and molecular oxygen forming water,The coefficients $2,1,2$ give the relative numbers of molecules; the coefficient $1$ is normally omitted. Count hydrogen as $2\times 2=4$ on the left and $2\times 2=4$ on the right, and oxygen as $1\times 2=2$ on the left and $2\times 1=2$ on the right. See Flowers et al., Chemistry 2e, §4.1: writing and balancing chemical equations.

To balance the initial expression ${\mathrm{H}}_2+{\mathrm{O}}_2⟶{\mathrm{H}}_2\mathrm{O}$, first put $2$ before water to match the two oxygen chemical atoms. This creates four hydrogen chemical atoms on the right, so put $2$ before molecular hydrogen. Changing a coefficient multiplies the entire chemical formula. Changing a subscript changes composition and usually the chemical substance: $2{\mathrm{H}}_2\mathrm{O}$ is two water molecules, whereas ${\mathrm{H}}_2{\mathrm{O}}_2$ is one hydrogen peroxide molecule. Never balance a chemical equation by changing its subscripts.

The bookkeeping follows from conservation of the atomic nuclei in ordinary, non-nuclear chemical reactions; chemical bonds and the distribution of electrons can change. For a chemical equation involving ions, total electric charge must also match. For example, the existing self-ionization of water equation has zero total electric charge on each side, since the $+1$ of hydronium cancels the $-1$ of hydroxide. See 2.6 Ionic and Molecular Compounds (§2.6: nuclei and ions).

The same $2:1:2$ ratio relates changes in amount of substance: two moles of molecular hydrogen consumed per mole of molecular oxygen correspond to two moles of water formed. A mole is a defined unit, not one molecule; the little whole-number picture is an abstract counting model, not a claim that a macroscopic sample contains just five molecules. See molecular count and amount of substance for the exact conversion and SI base unit: mole by Bureau International des Poids et Mesures for the definition.

This is why a balanced chemical equation is useful: stoichiometry turns the same atom accounting into relations between measurable quantities. It does not determine reaction rate, the final conversion set by chemical equilibrium, or the actual yield of recovered reaction products. The limiting reagent gives an upper bound under the specified chemical reaction.

A chemical formula uses symbols of chemical elements and numerical subscripts to record composition. In the molecular formula ${\mathrm{H}}_2\mathrm{O}$ of water, the subscript $2$ counts two hydrogen chemical atoms, and the omitted subscript after $\mathrm{O}$ means one oxygen chemical atom. A molecular formula describes one molecule; a chemical formula need not describe a discrete molecule.

Read a preceding coefficient separately from the subscripts. One ${\mathrm{H}}_2\mathrm{O}$ contains two hydrogen and one oxygen chemical atom; $2{\mathrm{H}}_2\mathrm{O}$ contains four hydrogen and two oxygen chemical atoms distributed between two water molecules. In ${\mathrm{H}}_2{\mathrm{O}}_2$, the second subscript instead puts two oxygen chemical atoms into each hydrogen peroxide molecule. Thus $2{\mathrm{H}}_2\mathrm{O}\ne {\mathrm{H}}_2{\mathrm{O}}_2$: the coefficient scales the whole chemical formula, while a subscript specifies its composition. See Flowers et al., Chemistry 2e, §2.4: chemical formulas.

For crystalline $\mathrm{NaCl}$, the chemical formula specifies a $1:1$ ratio of sodium ions ${\mathrm{Na}}^{+}$ to chlorine ions ${\mathrm{Cl}}^{-}$. Its formula unit is the accounting entity; the ordinary crystal is an extended arrangement of ions, rather than a collection of discrete $\mathrm{NaCl}$ molecules. Specifying the entity matters when assigning an amount of substance. See formula unit and 2.6 Ionic and Molecular Compounds (§2.6: ionic and molecular compounds).

A molecular formula gives an atom inventory, not the full arrangement of chemical bonds or the molecular geometry. For example, ${\mathrm{C}}_6{\mathrm{H}}_{12}{\mathrm{O}}_6$ counts six carbon, twelve hydrogen, and six oxygen chemical atoms in a glucose molecule, but does not specify the pattern shown by its Fischer projection. Different structures can share a molecular formula. This compact inventory is useful for chemical equation accounting precisely because it leaves the structural detail to other representations.

The choice of letters has an early explanation in Jöns Jacob Berzelius, Essay on the Cause of Chemical Proportions (1813–1814), §III, transcribed by Carmen Giunta: letters made chemical signs easier to write and print, and formulas compressed information about composition. His numerical notation differed from modern subscripts; the lasting idea was to make proportions readable in ordinary text.

An ion is a chemical atom or a group of chemical atoms with a nonzero net electric charge. A positive ion is a cation; a negative ion is an anion. The whole entity carries the electric charge: a hydronium ion is a group of four chemical atoms with net charge $+e$. This definition agrees with ^[ref].

For an ordinary ion containing only atomic nuclei and electrons, let $N_p$ count all its protons and $N_e$ all its electrons. Each proton contributes the elementary charge $+e$, each electron contributes $-e$, and neutrons contribute zero. ThereforeThe signed integer $z$ is the net electric charge number. Removing an electron increases $z$ by one; adding an electron decreases $z$ by one. Changing the electron count leaves the atomic number, and therefore the identity of the chemical element, unchanged.

For example, a neutral sodium chemical atom has $11$ protons and $11$ electrons. Its cation ${\mathrm{Na}}^{+}$ still has $11$ protons, but only $10$ electrons, so $q=(11-10)e=+e$. A neutral chlorine chemical atom has $17$ protons and $17$ electrons; its anion ${\mathrm{Cl}}^{-}$ has $17$ protons and $18$ electrons, so $q=(17-18)e=-e$. These are particle inventories, not pictures of atomic orbitals. See 2.6 Ionic and Molecular Compounds (§2.6: ions and ionic compounds).

One sodium chloride formula unit accounts for one ${\mathrm{Na}}^{+}$ cation and one ${\mathrm{Cl}}^{-}$ anion, whose net electric charges sum to zero. Ordinary solid sodium chloride is an extended arrangement of ions, rather than discrete $\mathrm{NaCl}$ molecules. This is a useful distinction: a neutral material can contain charged constituents, and its chemical formula tells us their ratio without claiming that each pair is a separate molecule.

Ion bookkeeping connects chemistry to electric current: moving ions can transport electric charge, while stationary ions cannot supply a transport current density. In electrochemistry, both signs of ions can contribute to the same conventional current. An ion opposing a fixed electric charge is called a counterion.

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.

A polyatomic ion consists of a bound group of two or more chemical atoms with nonzero total electric charge. Hydronium, ${\mathrm{H}}_3{\mathrm{O}}^{+}$, contains three hydrogen and one oxygen chemical atom; its net electric charge is $+e$, where $e$ is the elementary charge. This is a discrete charged group, while an ionic crystal can contain an extended arrangement of ions.^[ref]