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.
It is worth noting that the linear drawing style has very different rules for drawing bonds, and is considered separately.
Most atoms connected to two single bonds (or connected to one single bond and one double bond) should be drawn with a 120° angle separating the bonds. The relative orientation of adjacent bonds around a double bond should preserve the cis/trans configuration of that double bond. For a series of single bonds, an s-trans configuration is strongly preferred and arbitrary "bends" in the chain should be avoided without specific reason.
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A single bond connected to a double bond by a 180° angle indicates that the cis/trans configuration is unknown in the corresponding structure. It is only necessary to have this straight connection at one end of the double bond, although it is certainly acceptable to have it on both ends.
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There are some cases where an atom connected to two single bonds should be drawn with a 180° angle separating the bonds. Such cases are restricted to elements that fail to obey the octet rule, and are generally limited to metals or noble gases that have a deficit or surplus of electrons compared to the more-usual eight. Atoms such as these are colinear in three dimensions as well, and that colinearity should be preserved when representing the structure in two dimensions:
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Atoms in the carbon and nitrogen groups connected to two double bonds (or connected to one single bond and one triple bond) should be drawn with a 180° angle separating the bonds. Any carbon connected to two double bonds should always be explicitly labeled, to remove the possibility of the two bonds being misinterpreted as a single long bond. The use of a dot in place of an explicit carbon label is discouraged.
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Again, some rare cases exist, but limited to atoms other than in the carbon and nitrogen groups
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Atoms connected to three bonds should almost always be drawn with three equal 120° angles separating the bonds.
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Again, some rare cases exist, principally limited to cases of T-shaped configuration where the central atom has two lone pairs in addition to the three bonds. Such structures should be drawn with two of the bonds extending vertically above and below the central atom, and the third bond extending to the left.
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There are further restrictions for depicting tetrahedral stereochemistry for atoms with three bonds drawn. Those are discussed in the section on tetrahedral stereochemistry recommendations.
Atoms connected to four bonds may be drawn in several different ways, with a preference among these ways occasionally determined by context.
One style is drawn with the four bonds separated by four equal 90° angles separating the bonds. This style is most commonly used when at least three of the four substituents are small. If two of the bonds in the style are double bonds (as in sulfonyl groups), those two bonds should always be drawn opposing each other, with 180° separating them around the central atom. This style should not be depicted with the bonds drawn at a 45° angle from the x-axis; structures drawn in that orientation should be limited to square planar complexes.
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A second style has the four bonds separated by one 60° angle, an opposing 120° angle, and two 90° angles. Because of the 120° angle, this style will not disrupt the orientation of a chain in which it appears. This style is also commonly used when depicting chiral centers; the two bonds separated by the 60° angle are marked with a wedge and a hash. If the substituents connected to the two bonds separated by the 60° angle are not identical, the graphically larger substituent should be on the right for aesthetic purposes. In this context, "graphically larger" refers to the size of the substituent within the drawing itself: An "OH" atom label is graphically larger than an "I" atom label because it consists of two characters rather than one, even though the iodine atom might be physically larger than the hydroxy group in terms of van der Waals radius.
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A third style has the four bonds separated by two 60° angles, and two 120° angles. This style is may be preferred in sterically congested structures. It is also commonly used when depicting chiral centers; the bond adjacent to the two 60° angles is usually the one marked with a wedge or a hash. The use of this style should be limited to cases where that fourth bond (the one separated by two 60° angles) is smaller than the other three bonds, or when that bond and the two adjacent bonds are all significantly smaller than the fourth. In other cases, especially with two small substituents and two large ones, one of the previous two drawing style would be preferred.
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A fourth style has the four bonds separated by one 30° angle, two 105° angles and one 120° angle. This style is occasionally used to emphasize the tetrahedrality of phosphates and phosphate esters (and their arsenic and antimony analogs). The style can also be used in other cases where the tetrahedral geometry is to be emphasized, but it should only be used when two of the substituents are relatively small, and those substitutents should be placed on the bonds separated by the 30° angle. This style should always be drawn with one of the other bonds exactly vertical or horizontal.
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The style with four bonds separated by equal 90° angles and with a 45° angle between those bonds and the x-axis should be restricted to square planar complexes.
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There are further restrictions for depicting tetrahedral stereochemistry for atoms with four bonds drawn. Those are discussed in the section on tetrahedral stereochemistry recommendations.
Atoms connected to more than four bonds 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 one of the bonds directed vertically and the remainder separated by equal angles. If stereochemistry is a concern, the bonds should be drawn in one of the recommended styles for non-tetrahedral stereochemistry.
In addition to the styles shown above, there is an additional style that may be used when drawing double bonds in long chains, where the double bonds are in a cis configuration relative to the chain. In this style, the double bond is drawn with 150° angles between it and its attached chain bonds rather than the usual 120°. Any further substitution on the double bond should preserve the usual 120° angle between those substituents and the double bond, or a 90° angle between them and the chain bonds. This style serves to preserve the linearity of the chain, and should only be used when that is desired.
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