How To Draw Molecules In Organic Chemistry
How to Describe Organic Molecules
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This folio explains the various ways that organic molecules can exist represented on paper or on screen - including molecular formulae, and various forms of structural formulae.
Molecular formulae
A molecular formula simply counts the numbers of each sort of atom present in the molecule, but tells you nothing about the way they are joined together. For instance, the molecular formula of butane is \(C_4H_{10}\), and the molecular formula of ethanol is \(C_2H_6O\).
Molecular formulae are very rarely used in organic chemistry, because they exercise not give useful information about the bonding in the molecule. Near the but place where you might come across them is in equations for the combustion of simple hydrocarbons, for example:
\[ C_5H_{12} + 8O_2 \rightarrow 5CO_2 + 6H_2O\]
In cases similar this, the bonding in the organic molecule isn't important.
Structural formulae
A structural formula shows how the various atoms are bonded. There are diverse ways of drawing this and y'all volition need to be familiar with all of them.
Displayed formulae
A displayed formula shows all the bonds in the molecule as individual lines. Yous need to remember that each line represents a pair of shared electrons. For example, this is a model of methane together with its displayed formula:
Notice that the way the methyl hydride is drawn bears no resemblance to the bodily shape of the molecule. Methane isn't apartment with 90° bond angles. This mismatch betwixt what you draw and what the molecule actually looks like tin can pb to bug if yous aren't careful. For example, consider the unproblematic molecule with the molecular formula CH2Cltwo. You lot might think that there were ii different ways of arranging these atoms if yous drew a displayed formula.
The chlorines could be opposite each other or at right angles to each other. But these two structures are really exactly the same. Look at how they announced as models.
1 structure is in reality a simple rotation of the other ane. Consider a slightly more complicated molecule, CtwoH5Cl. The displayed formula could be written as either of these:
But, again these are exactly the same. Wait at the models.
The commonest way to describe structural formulae
For annihilation other than the about simple molecules, drawing a fully displayed formula is a bit of a carp - especially all the carbon-hydrogen bonds. You can simplify the formula by writing, for example, CH3 or CH2 instead of showing all these bonds. For example, ethanoic acid would be shown in a fully displayed grade and a simplified form every bit:
You lot could even condense it farther to CH3COOH, and would probably do this if y'all had to write a simple chemical equation involving ethanoic acid. You lot practise, however, lose something by condensing the acid group in this mode, considering you tin can't immediately see how the bonding works. Yous still have to be conscientious in cartoon structures in this mode. Remember from in a higher place that these two structures both represent the aforementioned molecule:
The adjacent 3 structures all correspond butane.
All of these are merely versions of four carbon atoms joined up in a line. The simply difference is that at that place has been some rotation about some of the carbon-carbon bonds. You can see this in a couple of models.
Not ane of the structural formulae accurately represents the shape of butane. The convention is that nosotros draw it with all the carbon atoms in a straight line - as in the first of the structures higher up. This is fifty-fifty more of import when you get-go to have branched chains of carbon atoms. The following structures again all represent the same molecule - 2-methylbutane.
The ii structures on the left are fairly obviously the same - all we've done is flip the molecule over. The other 1 isn't and then obvious until yous expect at the construction in detail. At that place are four carbons joined up in a row, with a CH3 group fastened to the next-to-end one. That'due south exactly the aforementioned every bit the other ii structures. If you had a model, the only divergence betwixt these three diagrams is that yous have rotated some of the bonds and turned the model around a bit.
To overcome this possible defoliation, the convention is that you always look for the longest possible chain of carbon atoms, and then draw information technology horizontally. Annihilation else is just hung off that concatenation. Information technology does not matter in the least whether you describe whatsoever side groups pointing upwards or down. All of the following correspond exactly the aforementioned molecule.
If yous made a model of one of them, you lot could turn information technology into any other i simply past rotating one or more of the carbon-carbon bonds.
How to draw structural formulae in 3-dimensions
There are occasions when information technology is important to exist able to show the precise 3-D organisation in parts of some molecules. To do this, the bonds are shown using conventional symbols:
For example, you lot might want to prove the iii-D organization of the groups around the carbon which has the -OH grouping in butan-two-ol.
| Instance 1: butan-two-ol |
|---|
| Butan-ii-ol has the structural formula: Using conventional bond annotation, y'all could draw information technology as, for example: The only difference between these is a slight rotation of the bond between the eye ii carbon atoms. This is shown in the two models below. Expect carefully at them - particularly at what has happened to the lone hydrogen cantlet. In the left-manus model, it is tucked behind the carbon cantlet. In the right-hand model, it is in the aforementioned airplane. The change is very slight. It doesn't thing in the least which of the 2 arrangements you depict. You could easily invent other ones as well. Choose one of them and go into the addiction of cartoon three-dimensional structures that way. My ain habit (used elsewhere on this site) is to draw two bonds going back into the newspaper and 1 coming out - as in the left-mitt diagram in a higher place. Notice that no endeavour was made to prove the whole molecule in 3-dimensions in the structural formula diagrams. The CH2CH3 group was left in a uncomplicated form. Keep diagrams simple - trying to show too much detail makes the whole thing amazingly difficult to empathize! |
Skeletal formulae
In a skeletal formula, all the hydrogen atoms are removed from carbon bondage, leaving only a carbon skeleton with functional groups attached to it. For example, we've only been talking well-nigh butan-two-ol. The normal structural formula and the skeletal formula look like this:
In a skeletal diagram of this sort
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there is a carbon cantlet at each junction between bonds in a chain and at the end of each bond (unless in that location is something else in that location already - similar the -OH grouping in the example);
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in that location are enough hydrogen atoms attached to each carbon to brand the total number of bonds on that carbon up to 4.
Beware! Diagrams of this sort take exercise to translate correctly - and may well not be acceptable to your examiners (encounter below).
At that place are, however, some very common cases where they are ofttimes used. These cases involve rings of carbon atoms which are surprisingly awkward to draw tidily in a normal structural formula. Cyclohexane, C6H12, is a ring of carbon atoms each with 2 hydrogens attached. This is what it looks like in both a structural formula and a skeletal formula.
And this is cyclohexene, which is similar simply contains a double bond:
Just the commonest of all is the benzene ring, C6H6, which has a special symbol of its ain.
Deciding which sort of formula to use
There'southward no easy, across-the-board reply to this trouble. It depends more than than anything else on feel - a feeling that a particular mode of writing a formula is all-time for the state of affairs you are dealing with.
Don't worry almost this - as you do more than and more than organic chemistry, you volition probably find it will come naturally. You'll get then used to writing formulae in reaction mechanisms, or for the structures for isomers, or in simple chemical equations, that you won't fifty-fifty recollect about it.
Source: https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Supplemental_Modules_(Organic_Chemistry)/Fundamentals/How_to_Draw_Organic_Molecules
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