Structures of Organic Compounds

The structures of organic compounds should be drawn so as to represent one, and only one, structure. Specialized drawings are sometimes needed to show certain structural details such as three dimensions.

Definitions

• Molecular formula - gives the elemental composition of a compound and the number of atoms of each element that are present in one molecule of the compound

• Structural formula - shows which atoms are bonded to which

• Isomers - two or more compounds that have the same formula but different structures

• Conformations - two or more forms of the same compound that are related by twisting and/or bending bonds

General Assumptions and Useful Information

Only valence electrons are used in chemical bonding in organic molecules.

Carbon typically engages in a total of four bonds in a compound. These bonds can be distributed in several ways: four single bonds, one double bond and two single bonds, two double bonds or one triple bond and one single bond.

Normal valences of other elements commonly found in organic compounds are as follows–hydrogen and halogens -one, oxygen and sulfur - two, nitrogen - three.

Carbon will not have a lone pair of electrons in a structure unless there is a formal charge of -1 on that carbon.

The spacial relationship ("geometry") of the atoms around carbon will typically be tetrahedral (four single bonds), trigonal planar (one double and two single bonds) or linear (one triple and one single bond).

Drawing Organic Structures

Representing three-dimensional organic structures on a two-dimensional surface (such as a piece of paper) presents some challenges.

Tetrahedral carbons are often shown, for the sake of convenience, with 90° bond angles in Lewis and Kekule structures as shown in two of the structures of dimethyl ether and ethanol below. Condensed structures (and partially condensed structures) convey all the information about which atom is attached to which, but are less cumbersome to draw. It is understood that hydrogens in condensed structures are directly attached to the atom that they follow. Note that the condensed structures of the two molecules below clearly show that they are different.

 

The three-dimensional aspect of a molecule can be shown through the use of wedged and dashed bonds. Wedged bonds are understood to be coming out of the plane of the paper toward the reader, whereas dashed bonds are understood to be going away from the reader. Bonds that drawn as plain lines in one of these structures are in the plane of the paper. This is shown for ethanol below.

Fischer projections are also used to show three-dimensions. These structures are drawn with the longest carbon chain vertically and it is understood that all horizontal bonds are coming towards the reader, all vertical bonds are going away from the reader and that there is a carbon atom at the intersection of four bonds. This type of drawing is commonly used for carbohydrates.

Compounds with double bonds are most accurately drawn with the correct 120° bond angles. The doubly-bonded and adjacent atoms all lie in the same plane. These molecules may be drawn using condensed and partially condensed structures. All carbon-carbon double and triple bonds must be explicitly shown in condensed structures and it isn't a bad idea to show carbon-oxygen double bonds until you are familiar with these structures.

Line structures are used for both linear and cyclic structures. In these structures it is understood that there is a carbon atom at each "bend" and that each carbon atom is attached to as many hydrogen atoms as are needed to complete its valence of four. A zig-zag structure is used for linear compounds. The carbon atoms that make up a cyclic compound are represented with a polygon.

Isomers

Two (or more) compounds that have the same molecular formula but different structures are called isomers. Isomers can be interconverted only by breaking bonds and reforming them in a different way. They are distinct compounds with different physical properties and can be separated from each other. There are several categories of isomers.

Structural Isomers have different structural formulas (and different names. Differences in structure can be manifested as different carbon skeletons, different functional groups, different location of a functional group, or some combination of these. The two compounds in the first set of drawings are examples of isomers with different functional groups. The compounds CH3CH=CHCH3 and CH3CH2CH=CH2 are an example of two compounds with the same functional group (the carbon-carbon double bond) in a different position. The compounds CH3CH2CH2CH3 and CH3CH(CH3)CH3 are two compounds that differ only in their carbon skeleton.

Stereoisomers have the same basic structural formula ("order of attachment of atoms"), but a different arrangement of the atoms in space. Two compounds cannot be both structural isomers and stereoisomers of each other; if their structural formulas are different, then they are structural isomers. Two types of stereoisomers are cis-trans isomers and optical isomers.

Cis-trans isomers have different arrangements of atoms or groups around a carbon-carbon double bond or with respect to the plane of a cyclic structure. Trans refers to groups or atoms which are on opposite sides (think about the definition of transcontinental), whereas cis refers to groups or atoms which are on the same side. For alkenes you must look at the arrangement of the longest carbon chain with respect to the double bond. The spacial arrangement of the groups directly attached to the double bond or ring must be clearly shown in the drawing of the molecule in order to show a cis-trans relationship correctly.

The most commonly encountered type of optical isomers have different arrangements of atoms or groups around a chiral carbon (a carbon with four different groups or atoms attached to it). The pair of compounds below are one type of optical isomers, enantiomers (non-identical mirror images). This type of isomerism is very important in biological compounds; often one enantiomer will be biologically active and the other one won't. If you dont believe that the two enantiomers below are different compounds, make models of each one and compare them.

Conformations

These are not different molecules; instead they are different forms of the same molecule that can be interconverted by rotation around bonds. Remember that molecules are not frozen in one form. Special structures are used to show this type of relationship.

Rotation around a bond in a linear structure is shown through the use of sawhorse structures or Newman projections. The structures below show only two of the many possible conformations. In each pair of structures below, the conformation on the left is referred to as staggered and the conformation on the right is referred to as eclipsed. The front and back groups are drawn slightly offset in the Newman projection of the eclipsed structure so that they don't overlap.

Sawhorse structures are drawn as follows:

• Draw three lines that intersect at their ends and are at 120° angles to each other. The intersection represents the carbon atom at one end of the bond around which the rotation is being shown.

• Draw a slanted line from the intersection of the three original lines to a second set of three lines.

• Place the groups or atoms that are attached to each of the carbon atoms that make up the bond whose rotation is being shown on the appropriate carbon.

Newman projections (think of them as a head-on views of sawhorse structures) are drawn as follows:

• Draw a circle.

• Draw three lines that intersect at their ends and are at 120° angles to each other so that the intersection is in the middle of the circle.

• Draw a second set of intersecting three lines "behind the circle."

• Place the groups or atoms that are attached to each of the carbon atoms that make up the bond whose rotation is being shown on the appropriate carbon.

 

Cyclic compounds also exist in different conformations. For example, cyclohexane can exist in a variety of forms which include the "boat" and the "chair." You can differentiate two chair forms in substituted cyclohexane molecules, as shown below. The CH3 in the chair on the left is said to be axial whereas that in the other chair is equatorial.

In a correctly drawn chair structure the two bonds on opposite sides of the ring are parallel to each other (see drawing "B" below). One method that can be used to generate chair structures is the following:

Start out by drawing the lines for a sawhorse structure in the staggered conformation (structure "A" below).

Complete the ring by adding the remaining three bonds (structure "B"). The bonds on opposite sides of the ring are parallel (the two x's are parallel, as are the two y's and the two z's).

Add the bonds from the ring. Each ring carbon has one axial (a) and equatorial (e) bond, one of which will be pointing up and one of which will be pointing down. The axial bonds alternate up-down-up-down… around the ring. Each equatorial bond will be parallel to the carbon-carbon ring bond once removed from it (structure "C"). On the "y" set of bonds is shown in structure C.



Dr. Peggy Kline | Physical Science Department | Santa Monica College | last updated 9/8/04