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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.

The LCAO approximation builds a molecular orbital as a linear combination of single-centre atomic orbitals. For two equivalent normalized real $1s$ functions ${\varphi }_A$ and ${\varphi }_B$, choose their signs positive and define their orbital overlap $S$. At nonzero separation, $0<S<1$, and the normalized combinations areHere ${\sigma }_{+}={\sigma }_g$ and ${\sigma }_{-}={\sigma }_u^{\ast }$. Equal coefficients use the equivalence of the two centres; a general LCAO need not have equal coefficients. See Field, MIT 5.61, lecture 24, pp. 3–6: LCAO coefficients and overlap integrals.

For the Gaussian function toy's $a=1$, the two denominators are $\sqrt{2(1+S)}\approx 1.654013$ and $\sqrt{2(1-S)}\approx 1.124385$. To check wavefunction normalization, expand the square: $\int ({\varphi }_A\pm {\varphi }_B{)}^2=1+1\pm 2S$. Dividing by $2(1\pm S)$ gives one. The local probability density isThe cross term is the interference; adding the separate densities first would lose it. These formulas normalize the chosen linear combination exactly, while the restricted choice of atomic orbitals remains an approximation to an actual molecular orbital.

Molecular orbital theory describes the electronic arrangement of a molecule using molecular orbitals: one-Electron spatial wavefunctions extending over the combined atomic nuclei. Filling bonding molecular orbitals can stabilize a chemical bond; filling antibonding molecular orbitals opposes that stabilization. A molecular orbital is a building block of a many-Electron description, rather than the entire many-Electron wavefunction. See Robert W. Field, MIT 5.61, lecture 24, pp. 1–4: molecular orbitals and the LCAO approximation.

First make the interference visible with an exactly normalized one-dimensional toy. Replace the three-dimensional $1s$ atomic orbitals of the hydrogen atom by two Gaussian functions centred at $x=\pm a$, with dimensionless $x$ and $a>0$:The normalized sum and difference are ${\psi }_{\pm }=({\varphi }_A\pm {\varphi }_B)/\sqrt{2(1\pm S)}$, following the same linear combination of atomic orbitals algebra. At $a=1$, the orbital overlap is $S=e^{-1}\approx 0.367879$. At the midpoint, ${\varphi }_A(0)={\varphi }_B(0)\approx 0.455581$, givingBoth probability densities have total integral one: interference redistributes probability, rather than creating an extra Electron. These are toy wavefunctions, not actual hydrogen atom orbitals or predictions of molecular hydrogen energies.

Now fill the two $1s$-derived molecular orbitals in the minimal model. The lower bonding molecular orbital is labelled ${\sigma }_g$; the upper antibonding molecular orbital is ${\sigma }_u^{\ast }$. The Pauli exclusion principle permits at most two Electrons in each spatial molecular orbital, with opposite spin projections along a chosen axis. For the lowest electron configuration in this model, fill ${\sigma }_g$ first. The subscripts $g$ and $u$ denote even and odd behaviour under inversion through the midpoint; the star marks an antibonding molecular orbital. See Flowers et al., Chemistry 2e, 8.4: occupancy and bond order and Field, MIT 5.61, lecture 25, pp. 1–3: bonding, antibonding, and symmetry labels.

With $N_b$ Electrons in bonding molecular orbitals and $N_a$ in antibonding molecular orbitals, the model's bond order is $b=(N_b-N_a)/2$. The three elementary counts are:

The zero bond order says this minimal model gives no net covalent bond for ${\mathrm{He}}_2$. It does not rule out every bound pair of helium chemical atoms: a very weak Van der Waals force can bind a neutral helium dimer, which has been observed experimentally. See Zeller et al., Imaging the He2 quantum halo state using a free electron laser, PNAS 113, 14651–14655 (2016), p. 14651: van der Waals binding and Luo et al., The weakest bond: Experimental observation of helium dimer, Journal of Chemical Physics 98, 3564–3567 (1993). The bond order count does not include that weak binding mechanism.

The useful surprise is that sharing alone does not determine a chemical bond: the relative quantum phase and the occupancy matter together. The same two shapes explain why adding an Electron to a bonding molecular orbital increases the model's bond order, while adding one to an antibonding molecular orbital decreases it. Molecular orbital theory also accounts for the unpaired Electrons and paramagnetism of molecular oxygen, which its all-paired Lewis structure misses. See Chemistry 2e, 8.4: the molecular orbital description of oxygen.

A radical has one or more unpaired Electrons. In a simple atomic orbital or molecular orbital occupancy picture, an unpaired Electron occupies a spatial orbital without an opposite-spin partner in that orbital. A dot such as ${\mathrm{H}}^{\bullet }$ marks this electronic property; it does not mean a missing Electron or positive electric charge. Free radicals can be neutral or charged. Terminology also has a boundary: metal ions exhibiting paramagnetism are not normally called free radicals just because they have unpaired Electrons.^[ref]

Compare three species containing the same single proton. The hydrogen atom ${\mathrm{H}}^{\bullet }$ has one Electron in its $1s$ atomic orbital, and is a neutral radical. The hydrogen cation ${\mathrm{H}}^{+}$ has no Electrons, so no unpaired Electron. The hydrogen anion ${\mathrm{H}}^{-}$ has two Electrons paired in its $1s$ atomic orbital. It is charged but is not a radical in its ground state. With $N_p$ protons, $N_e$ Electrons, and positive elementary charge $e$, the independent electric charge count isThe electron pair and electric charge questions require different information. An odd $N_e$ ensures that not all Electrons can be paired; an even $N_e$ alone does not ensure pairing, as the molecular orbital description of molecular oxygen illustrates.

The distinction matters whenever a chemical reaction mechanism uses dots and charge signs together. Homolysis gives one bonding Electron to each fragment, while heterolysis assigns both to one fragment. A radical chain reaction can pass an unpaired Electron from one species to another without generating net electric charge. Detection then exploits the unpaired Electron's spin and magnetic moment, rather than merely measuring whether the sample carries an electric charge.