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How to Read Structural Formulas

In the remainder of this book, the descriptions of each ingredient include the chemical formula for the ingredient. This is often quite useful in comparing the ingredient to others, or in understanding how it performs its function, or how it interacts with other ingredients.

Some of the formulas might look intimidating at first, but you can actually learn to read them in a few minutes, as the following text will show.

Simple Formulas

Some formulas, such as the formula for table salt, are very simple. We don't need a picture, just a description of the two elements that make it up, sodium and chlorine. The formula is:

                NaCl

Other compounds are also fairly simple, although they may contain more elements. For example, phosphoric acid, a common ingredient in soft drinks (used to provide tartness) is:

                H3PO4

This says it is made up of three hydrogen atoms, one atom of phosphorus, and four atoms of oxygen.

A molecule you probably already know is water:

                H2O

Full Structural Formulas

For some compounds, it is especially useful to know the shape of the molecule. While this is critically important in large molecules made with a backbone of carbon, called organic molecules, it is often interesting in simpler molecules. The formula given above for water might cause someone to think that a hydrogen atom was attached to another hydrogen atom, and then an oxygen atom was attached to them:

That would be wrong, however, since a hydrogen atom can only form a bond with one other atom. Moreover, oxygen can bond with two other atoms, so a better picture would look like this:

As it turns out, however, the angle between the bonds is not 180 as that picture would make it seem, but 105, which is important in understanding some curious facts about water:

The electrons that the hydrogens share with the oxygen are located between the hydrogens and the oxygen. This leaves the hydrogens with a little bit of a positive charge, and the oxygen with a little bit of a negative charge. This polar arrangement means that the molecules prefer to align in certain ways, because the positive sides attract the negative sides. This gives water its surface tension, and explains why ice crystals arrange in hexagons, and take up more space than liquid water, making ice less dense than water, so it floats. It also explains how water molecules can dissolve other polar molecules like table salt. The water molecules surround the positive sodium ions and the negative chlorine ions, and prevent them from getting back together.

Simplified Structural Formulas

Earlier, we said that hydrogen atoms can only bond with one other atom. This is because they only have one electron to share. The element carbon has four electrons it can share easily, and so it can bond to four different atoms at a time. Because carbon is so versatile, it can form very complex molecules. These complex molecules are what led to life on this planet, and living things are primarily made of large molecules with a backbone of carbon.

Simple carbon compounds such as methane are often written using non-structural formulas, such as:

                CH4

or the structural formulas we have just discussed:

But when the molecules start getting larger, all those letters for carbon and hydrogen start to clutter up the page, making it hard to see detail.

Since we know that carbon has four bonds to fill, and that hydrogen is the most likely atom to be attached to carbon in an organic molecule, we can invent a shorthand notation that is easier to read and draw.

In our shorthand, we will assume that any vertex between two lines contains a carbon atom, unless we specify otherwise. If there are several carbons in a row, we will not just draw a long line, but we will make the lines join at angles, so we can count the carbons if need be.

We also will say that any carbon that has fewer than four lines from it will be assumed to have a hydrogen atom filling all the remaining bonds.

Thus the molecule propane (C3H8), which has three carbons in a row, and all of the remaining bonds filled with hydrogen:

becomes the much simpler looking picture:

There is a carbon at each end, and one in the middle. The carbons at each end have three remaining bonds, which are filled with three hydrogens. The carbon in the middle has only two bonds left, so there are two hydrogens there.

Now for simple molecules like propane, this is not much of an improvement. It is easier to draw, but the reader has to do some thinking to do to figure out at first what the molecule is.

However, with larger molecules, the simplification really helps to keep the picture uncluttered. Consider the molecule for aspartame, which would look like this:

but simplifies to this:

Three dimensional Structural Formulas

Sometimes it is important to know the three dimensional structure of a molecule. In glucose for example,

it is important to know which side of the molecule the various hydroxyl groups (the OH sub-units) are. Flipping one of them from the bottom to the top changes the sugar from glucose to galactose:

which is much less sweet than glucose.

We indicate that some parts of the molecule are closer to the reader by making the lines darker.


By Simon Quellen Field

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