Annotations are bits of text that are closely associated with the atoms and bonds of a structure but not chemically meaningful themselves. They may describe something about the structure, or they may simply provide a convenient label. In either case, they should be close enough to the subject of interest that they are clearly associated, and far enough from other objects that the nature of the association is not confused.
Some software may have special ways to create annotations so that they remain associated with their target objects, or so that they may be indicated as having a specific meaning. If you are using annotations in an electronic environment (as opposed to a printed one), you may want to take advantage of the features that your chemical drawing software offers in this area.
Annotations that describe a specific atom should be positioned close to that atom. Some common atom-based annotations include atom numbering and stereochemistry indicators.
Atom-based annotation is generally positioned in the largest open space near the atom, since there is less chance that the annotation will be interpreted as referring to another object if there are fewer objects nearby. When annotating several atoms in a ring system, it is also common to place the annotations within the ring. Annotations describing the stereochemical configuration of an atom will generally be placed opposite one of the atom's wedged or hashed bonds.
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Annotations should be clearly separated from the atom in question, whether it has a label or represents an unlabeled carbon. However, they should also be closer to the atom in question than to any other atom. Typically, atom-based annotations will be separated from the atom by a distance on the order of half the height of a "C" or an "H" in the font used for atom labels, but that distance may vary according to the aesthetics of the chemist. As a practical matter, the indicator will rarely be separated from its atom by as much as the full height of a "C" or an "H" in the font used for atom labels.
Annotations should also be visually different from regular atom labels. Typically, they will be drawn smaller. They may also be drawn in a different font, style, or color. If numeric indicators are drawn smaller than regular atom labels, then care should be taken when positioning them to the right or left of an existing atom label, lest they be mistaken for element repeat counts or isotopic labels.
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An asterisk is traditionally reserved as the indicator of a chiral center and should not be used for other purposes. As with all annotation, the asterisk should not be used capriciously. While it is certainly possible to label every chiral center in every structure with an asterisk, it it much more useful to restrict such labeling to those centers that need to be highlighted, for example if they are referenced as being chiral in associated descriptive text.
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Many of the issues relating to atom-based annotation also apply to bond-based annotation. Stereochemistry indicators are a common example of bond-based annotation. Annotations associated with a bond are generally positioned near the midpoint of the bond.
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Annotations describing an entire structure are probably the most common sort of annotations. Nearly every structure depicted in a journal article will be identified by a letter or number nearby.
Structure-based annotation should be clearly associated with a specific structure. It should be positioned so that it is closer to the target structure than to any other structure, but it should also be positioned far enough away from the structure that it is not likely to be interpreted as an annotation of a single atom or bond within the structure. Typically, that means that it will be separated from the closest part of the structure by a distance at least equal to half of the bond length used in the structure, and no further than twice as far as the structure's bond length.
These annotations should be visually different both from atom labels and from atom- and bond-based annotation (if present). Typically, structure-based annotation will be drawn in a font that is the same size as or larger than the structure's atom labels. The font, style, or color may also be different.
Structure-based annotations will usually be placed below the structure. They will often appear to the left or right instead, but that positioning should be avoided in reaction schemes where there are other structures to the left or right.
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