How to learn to Read Structural Formulas
Some of the Structural formulas may look intimidating at 1st, but you could actually learn to read them in a several minutes, as the following text will show.
Simple Structural Formulas
Some Structural formulas, such as the formula for table salt, are very simple. We don't need a picture, just a description of the 2 elements that make it up, sodium and chlorine. The Structural formula is:
NaCl
Other ingredients are also fairly simple, although they might contain more elements. For example, phosphoric acid, a common ingredient in soft drinks (used to provide tartness) is:
H3PO4
This tells 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 ingredients, it's 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 Structural 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: H-H-O
That would be wrong, however, since a hydrogen atom could only form a bond with one other atom. Moreover, oxygen can bond with two other atoms, so a better would look like this: H-O-H
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 could 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 told that hydrogen atoms could 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 4 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 2 lines contains a carbon atom, unless we specify otherwise. If there are few carbons in a row, we willn't 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 tell 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:
There is a carbon at each end, and one in the middle. The carbons at each end have 3 remaining bonds, which are filled with three hydrogens. The carbon in the middle has only 2 bonds left, so there are 2 hydrogens there.
Now for simple molecules like propane, this is not much of an improvement. It's easier to draw, but the reader has to do some thinking to do to figure out at first what the molecule is.
But with larger molecules, the simplification really helps to keep the picture uncluttered. Consider the molecule for aspartame, which would look like this:
Three dimensional Structural Formulas
Sometimes it's important to know the 3d structure of a molecule. It's 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:
We indicate that some parts of the molecule are closer to the reader by making the lines darker.
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