When chemical structures are depicted in two dimensions, they should be drawn in a way that accurately represents the true three-dimensional structures. The key word in the previous sentence is "represents". A two-dimensional structure is still a schematic representation, and some liberties may be taken with bond lengths, angles, etc, to produce a drawing that is most easily recognized. Still, because the two-dimensional drawing represents the more accurate three-dimensional model, it should not imply bonding patterns or geometries that are completely inaccurate. To phrase things more simply: bonds should be drawn at an angle in two dimensions if and only if they connect at an angle in three dimensions, and they should be drawn colinearly in two dimensions if and only if they connect colinearly in three dimensions.
The issues related to bond angles between ring systems and their substituents are very similar to the issues related to acyclic bond angles. In many cases bonds from rings to their substituents may be positioned as if the two neighboring ring bonds described a very short chain, with the substituents being placed as if they were substituents of that chain. There are a few other issues to consider, but they are generally fairly minor.
In most cases, exterior (non-fusion, non-spiro) ring atoms with a single substituent should be drawn so that the substituent bisects the larger angle formed by that atom's two ring bonds. This is true regardless of the size of the ring or the order of the bond, and also true for non-convex rings
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Ring fusion atoms already have three bonds within the ring system. Since those three bonds are most often separated by equal 120° angles, there is no obvious "largest" side on which to place another substituent. For external ring fusion atoms, the substituent should preferentially be positioned outside the ring system and oriented so that it bisects the angle between the adjacent bonds. In cases where bisecting the adjacent bonds would result in a substituent that is nearly (but not quite) horizontal or vertical, it is also acceptable to adjust the substituent so that it is exactly horizontal or vertical (this most commonly happens at fusions between 6-member and 5-member rings).
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In some cases, placing a ring fusion substituent outside the ring system would cause it to overlap with another substituent. In those cases, it is acceptable to draw the substituent within the ring system. A substituent drawn in this way should preferentially be drawn exactly vertically or horizontally, whichever direction would minimize overlap with other atoms and bonds. Small substituents on the C-9 and C-10 atoms of steroids should be drawn within the ring system in this fashion even if they would not overlap with other atoms when placed external to the ring system. Certain other natural products also preferred orientations that place substituents within the ring system.
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Substituents on interior fusion atoms have no option other than being drawn within the ring system. As above, such substituents should preferentially be drawn exactly vertically or horizontally, whichever direction would minimize overlap with other atoms and bonds.
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If a substituent consists of a long chain, it is also acceptable to rotate the chain slightly so that it is more exactly horizontal or vertical.
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Atoms connected to two external substituents should normally be drawn with a 60° angle between the substituents. This is true regardless of the bond order of the substituents. For substituents on four-membered rings only, it is also acceptable to separate the substituents by a 90° angle.
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Atoms that form a spiro fusion between two ring systems should normally be drawn so that the bisector of the angle between the two bonds in one ring is parallel with the similar bisector in the other ring. As always, that recommendation may be overriden by other considerations. With spiro-fused compounds, for example, it is common for structures to be very crowded. It is far better to distort the spiro fusion angle than it is to have overlapping atoms and bonds in the other parts of the structure.
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Atoms connected to more than two external substituents are rare in organic chemistry but more common when dealing with inorganic complexes. If no stereochemical significance is assigned to the bonds, they should most commonly be drawn with substituents separated from each other and from the ring bonds by equal angles. If stereochemistry is a concern, the bonds should be drawn in one of the recommended styles for non-tetrahedral stereochemistry.
Substituents on rings that have been drawn in perspective should preserve the perspective of those rings. This generally means that such substituents would not be drawn to bisect the angles of the ring bonds. Some examples of substituents on rings drawn in perspective are shown.
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While rings of eight or fewer members are most commonly drawn as convex polygons, larger rings are more often drawn with some reentrant (non-convex) bond angles. Whenever possible, the ring should be depicted so that any substituents are positioned on outward-pointing atoms, so that the substituents themselves point outward according to the recommendations above.
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Special care should be taken when representing stereochemistry on reentrant bond angles. As discussed in the tetrahedral stereochemistry recommendations, it can be extremely difficult and confusing to interpret hashed and wedged bonds in non-standard configurations. When such stereobonds are placed so that they point outward from a reentrant atom, their proper interpretation can be very difficult indeed. In the example below, the third structure is the actual diagram as published in J. Nat. Prod 2001, 64, 1093-1094. The second structure shows a correct representation of the (R,R,R,R) form, which was the intended form as described in the text of the paper. The first structure is preferred, since it has all of the substituents atoms that are naturally pointing outward.
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A second diagram, to help clarify this important point even further:
