Understanding Organic Structures

Organic structures can be quite complicated and pose serious challenges for 2-dimensional representations. In order to meet these challenges, organic chemists have, over the past 200 years, developed drawing conventions for representing these structures. There are a number of shorthand rules that are employed, but there are also several styles of drawings depending on what wants to emphasize in a a particular structure. In some cases part of the molecule may be drawn using a different style from the rest of the molecule precisely for that reason. These shorthand drawing methods make it much easier for chemists to draw and talk about structures in classroom presentations as well as in published articles. But this practice places a burden on the viewer to develop an understanding of the structures. The benefit is that this information is widely useful in everyday life. These structures are routinely included in the information on pharmaceuticals, food supplements and food additives, so understanding what the drawings represent can be very helpful. You might even want to look up online the structures of such substances as Vitamin B12, zinc picolinate, testosterone, etc. to see if you understand them better after reading this page.

The hope is that in working with these structures, a student will develop an understanding not only of how things are connected but also what the 3-dimensional structure of the molecule is. The 3-dimensional structures are critical to how molecules react and interact with other molecules, but it does take practice to be able to visualize the 3-dimensional structures from 2-dimensional drawings. Fortunately, modern computer programs for creating images, both 2- and 3-dimensional, of molecules and compounds are quite good and allow for very good pictorial representations. Additionally, as will be seen on these web pages, it is possible to have interactive views of the 3-dimensional molecular and compound structures so that they can be rotated and enlarged to make it easier to get an understanding of what the structures are. Comparing the line drawings with the 3-dimensional interactive images can be helpful in understanding the structures of organic molecules.

The Lewis structures of methane, ammonia, water and hydrogen fluoride.

The simplest of the drawings are known as Lewis structures and they were developed to show where the electrons are in bonds between atoms. those for organic molecules generally follow the octet rule which seeks to place eight electrons around each atom, except for hydrogen which has only two. This rule is applies to carbon, nitrogen, oxygen and fluorine for all structures of stable molecules. Some atoms like boron and aluminum may be 'happy' with only six electrons. These molecules are commonly called electron deficient molecules, although the molecules themselves have no particular sense of inadequacy. Similarly, heavier atoms may exhibit octet expansion, which means that those atoms may have 10 or 12 electrons rather than the normal 8. Another term applied to these molecules is hypervalent. Examples of this are sulfur tetrafluoride (SF4), sulfur hexafluoride (SF6) and the hexafluorophosphate ion (PF6-). The figure shows the Lewis structures of methane, ammonia, water and hydrogen fluoride. It is common in Lewis structures to replace a pair of electrons in a bond with a simple line as shown to the right of each Lewis structure. These drawings are then referred to as line drawings.

a wedge-bond representation for methaneTwo different ways of representing methane with wedge-shaped bonds to emphasize its tetrahedral shape.

It is important to realize that Lewis structures are not necessarily drawn to represent the actual shape of the molecule, only the atom connectivity. Methane is a tetrahedral molecule with all H-C-H bond angles equal to 109.5°, not a square planar flat molecule with 90° angles. Ammonia is trigonal pyramidal with H-N-H bond angles of about 107°, and water is bent with a an H-O-H bond angle close to 105°. While we are not obligated to indicate the actual geometry for a structure, drawings will often do this where it is easy to do. For example, the Lewis structure of water in the figure has the H's 90° apart but the line drawing shows a more conventional bent water molecule.

Another way to emphasize 3-dimensional structures in 2-dimensional pictures is to add wedges for bonds. In these depictions, bonds that are in the plane of the paper are the unusual lines, but atoms coming out of the plane have bonds that are solid wedges, while those going back behind the plane are shown as dashed wedges as illustrated for methane in the figure.

Line drawings for some simple hydrocarbons.

We can further simplify our pictures in complex structures. The figure shows the line drawings for methane, ethane, propane, ethene and ethyne. The first line drawings do not necessarily indicate the geometry about the carbon atoms, although it is common for do so for double bonds such as found in ethene, where the actual H-C-H and H-C-C bond angles are close to 120°. But two important ways that these structures are simplified is to omit the labels on the carbon atoms as well as the hydrogen atoms. For example, propane can be represented by a simple bent line, and the viewer needs to understand that a carbon atom occurs are every bend and at the end of each line segment. If hydrogens are omitted, no lines are drawn to where they would be, rather one must understand that any missing bonds on carbon are occupied by hydrogen atoms. This is not too difficult for carbon because it will always have four bonds attached, so if there are fewer bonds drawn to a carbon atom, then the balance must be occupied by hydrogen atoms. For carbon, these can include single, double and triple bonds but the total number of bonds cannot exceed four (e.g., one single bond plus one triple bond). Ethene, also known commonly as ethylene, can be represented by a simple double line. This means that there are two bonds connecting the two carbons, one at each end, and that there must be two hydrogens to attached to each of those carbon atoms. Similarly, ethyne is simmply a set of three parallel lines.

isomers of C4H8Isomers with the formula C4H8.

Unlike single bonds, the double bond in ethane is restrained from twisting. The rigidness of this bond means that we can form isomers when we add groups to the carbons involved in a double bond. The figure shows the different possible isomers of the formula C4H8. When two groups line on the same side of the double bond, the molecule is referred to as cis, while groups on opposite sides of a double bond are called trans in order to distinguish the two possible arrangements.

organic ring structuresSome six-membered organic rings.

Many of the organic molecules encountered in artist materials have rings of carbon atoms, and these rings may include single or double bonds. Cyclohexane is the simplest of the six-membered rings with a formula of C6H12. It can be drawn as a simple hexagon, but in many cases it is drawn to show the 3-dimensional structure. Because a carbon atom with four bonds to it is tetrahedral, the ring will not be flat. The bonds have the flexibility to twist and flex, giving rise to two conformers which interchange dynamically when the molecules are in solution. The two end points of this twisting motion are called the boat and chair configurations based on the objects their stylized drawings appear to resemble. The chair form is usually more stable because it most often minimizes the steric repulsions between other groups of atoms attached to the ring. Even though the rings are not flat, they do have 'sides' and if we put more than one group on the ring in place of hydrogen, the groups can either be on the same side of the ring (cis) or on opposite sides of the ring (trans). Incorporation of one (cyclohexene) or two(cyclohexadiene) double bonds in the ring still allows the rings to twist slightly, but their ability to do so is much more restricted than for cyclohexane.

But if there are three double bonds in the ring, the motion is entirely restricted and the molecule is flat. This molecule is benzene, C6H6. When we draw the Lewis structure of benzene and include the double bonds, we end up having two equal possibile ways of arranging the double bonds as shown in the figure. As a consequence, there is no way to determine which of these is better, and in fact neither is a good representation of the actual structure of benzene. Years ago when bonding theories were in their infancy, chemists decided that the actual structure is best represented as a hybrid of these two structures, and they did so because they knew from the characterization of benzene that all of the C-C bonds were equal in length and that they were intermediate between single and double bonds. To make the Lewis structures fit reality, they concluded that the best picture was an average of these two possible drawings, and the situation is called resonance. If we average the bond orders from the two structures, we get that each C-C bond has a bond order of 1.5, and the distances fit this: C-C single bond = ca. 1.54Å C=C = ca. 1.34Å and the C-C bond in benzene = 1.45Å. Ring systems with resonance fornms are also called aromatic rings. If more advanced molecular orbital theory is used, this approximation is not necessary; however, and averaging Lewis resonance structures is easy (much easier than molecular orbital theory for beginning organic chemistry students!), and so they are still widely used because the resulting answer is usually close to reality. In depicting rings in which resonance is possible, drawings will often replace the individual double bonds with a circle as seen on the far right of the figure.

Additional organic structures Structures of more organic molecules.

When atoms other than carbon are included in the structures there aren't many shortcuts. These atoms are always included explicitly and hydrogens attached to them are always included, either in the name of the atom or with drawn bonds. Some examples show common ways of handling the inclusion of nitrogen and oxygen atoms. The hydrogens can be included in the label of the atom, or they can be explicitly drawn with bonds to them. Just remember that if you draw a line with no labels attached to it, the atoms assumed to be at the ends are carbon atoms, as illustrated for dimethyl aniline, C6H5N(CH3)2.

A good way to get practice understanding these structures is to figure out the chemical formula based on the line diagrams for structures on the various pages of this web site. The page on Organic Pigments in particular shows a number of organic molecules of varying degress of complexity and, in most cases, the chemical formula is also included. These can provide excellent practice is testing your understanding of the drawings.

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