Molecules bond-line drawings

Bond-line drawings show the carbon skeleton (the connections of all the carbon atoms that build up the backbone, or skeleton, of the molecule) with any functional groups that are attached, such as - OH or -Br. Lines are drawn in a zigzag format, where each comer or endpoint represents a carbon atom. For example, the following compound has 7 carbon atoms ... 

Now that we know how to count carbon atoms, we must learn how to count the hydrogen atoms in a bond-line drawing of a molecule. Most hydrogen atoms are not shown, so bond-line drawings can be drawn very quickly. Hydrogen atoms connected to atoms other carbon (such as nitrogen or oxygen) must be drawn ... 

When drawing a molecule, you should either show aU of the H s and all of the C s, or draw a bond-line drawing where the C s and H s are not drawn. You cannot draw the C s without also drawing the H s ... 

In Chapter 1, we introduced one of the best ways of drawing molecules, bond-line structures. They are fast to draw and easy to read, but they have one major deficiency they do not describe molecules perfectly. In fact, no drawing method can completely describe a molecule using only a single drawing. Here is the problem. 

There is an entirely different way to draw stereocenters (instead of using regular bond-line drawings with dashes and wedges). Fischer projections are helpful for drawing molecules that have many stereocenters, one after another. These drawings look like this ... 

Many molecules have double or triple bonds, often called unsaturation because a compound with a double or triple bond has less hydrogen than it would have without the double or triple bond. These double and triple bonds are very easy to see in bond-line drawings ... 

ChemSketch has some special-purpose building functions. The peptide builder creates a line structure from the protein sequence defined with the typical three-letter abbreviations. The carbohydrate builder creates a structure from a text string description of the molecule. The nucleic acid builder creates a structure from the typical one-letter abbreviations. There is a function to clean up the shape of the structure (i.e., make bond lengths equivalent). There is also a three-dimensional optimization routine, which uses a proprietary modification of the CHARMM force field. It is possible to set the molecule line drawing mode to obey the conventions of several different publishers. 

Note how we have resorted to another form of representation of the ethane, ethylene, and acetylene molecules here, representations that are probably familiar to you (see Section 1.1). These line drawings are simpler, much easier to draw, and clearly show how the atoms are bonded - we use a line to indicate the bonding molecular orbital. They do not show the difference between a and rr bonds, however. We also introduce here the way in which we can represent the tetrahedral array of bonds around carbon in a two-dimensional drawing. This is to use wedges and dots for bonds instead of lines. By convention, the wedge means the bond is coming towards you, out of the plane of the paper. The dotted bond means it is going away from you, behind the plane of the paper. We shall discuss stereochemical representations in more detail later (see Section 3.1). 

Each carbon-hydrogen bond on one carbon of the eclipsed conformation of ethane is directly in line with a carbon-hydrogen bond on the other carbon. This is easier to see if we view the molecule end-on—that is. down the carbon-carbon bond. A drawing of such a view, called a Newman projection, is as follows ... 

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