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A chemical structure specifies how chemical atoms are connected and, where relevant, how they are arranged in space. A molecular formula counts atoms; a structural formula supplies connectivity information. Molecular geometry and stereochemistry add spatial distinctions that cannot generally be recovered from the atom inventory alone.^[ref]

For a concrete comparison, ethanol and dimethyl ether both have molecular formula ${\mathrm{C}}_2{\mathrm{H}}_6\mathrm{O}$. Their condensed structural formulas arerespectively. In ethanol, the oxygen is bonded to one carbon and one hydrogen; in dimethyl ether, it is bonded to two carbon atoms. The same atom counts therefore describe different connectivities.

A drawing is a representation of a chemical structure, not necessarily a frozen picture of every atom's position. Rotating around a bond can change a molecule's spatial arrangement while preserving its connectivity. Conversely, two drawings that look different on the page can represent the same chemical structure. Establishing identity requires interpreting bonds and spatial conventions, not comparing the appearance of the diagrams alone.

Dimethyl ether, also called methoxymethane, is an ether with an oxygen atom bonded to two methyl groups. Its structural formula is $\mathrm{C}{\mathrm{H}}_3-\mathrm{O}-\mathrm{C}{\mathrm{H}}_3$ and its molecular formula is ${\mathrm{C}}_2{\mathrm{H}}_6\mathrm{O}$. It is a constitutional isomer of ethanol: the atoms have the same inventory but different connectivity.^[ref]

The oxygen connectivity gives a useful molecular comparison. Ethanol contains an oxygen–hydrogen bond; dimethyl ether does not. Thus the two chemical structures present different possibilities for hydrogen bonding, even though weighing equal numbers of their molecules would not distinguish their common elemental formula.

Their physical identity can be tested by measurements beyond composition. NIST tabulates a normal boiling point near $248.3\mathrm{K}$, approximately $-24.9{}^{\circ }\mathrm{C}$, for dimethyl ether. This illustrates why a small carbon-containing molecule can be a gas under ordinary room conditions: phase behavior follows its interactions and external conditions, rather than molecular formula alone.^[ref]

A structural formula represents how chemical atoms in a molecule are connected. It adds information that a molecular formula alone does not provide. Depending on the notation, bonds and grouped atoms may be drawn explicitly or represented in a condensed structural formula.^[ref]

For ethanol, $\mathrm{C}{\mathrm{H}}_3\mathrm{C}{\mathrm{H}}_2\mathrm{OH}$ can be unpacked as a carbon with three hydrogens, joined to a carbon with two hydrogens, joined to oxygen, joined to hydrogen. Counting the groups recovers ${\mathrm{C}}_2{\mathrm{H}}_6\mathrm{O}$, since $3+2+1=6$. That count is a useful check, but it discards the connectivity information that distinguishes ethanol from dimethyl ether, $\mathrm{C}{\mathrm{H}}_3\mathrm{OC}{\mathrm{H}}_3$.

A structural drawing also needs a clear convention about spatial meaning. A plain line usually represents a chemical bond, rather than a measured length on the page. Rotating the paper does not change the represented molecule. If a drawing is intended to specify a three-dimensional configuration, the additional conventions belong to stereochemistry; a connectivity formula should not silently be treated as complete molecular geometry.