drawing 3d structures of molecules
2.two.2. Cartoon three-Dimensional Molecules
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This page explains the various ways that organic molecules can be 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 cantlet present in the molecule, but tells you nothing about the style they are joined together. For example, 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 requite useful information about the bonding in the molecule. About the only place where yous 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 like this, the bonding in the organic molecule isn't important.
Structural formulae
A structural formula shows how the various atoms are bonded. There are various ways of drawing this and you lot will demand to be familiar with all of them.
Displayed formulae
A displayed formula shows all the bonds in the molecule as individual lines. You demand to remember that each line represents a pair of shared electrons. For example, this is a model of methyl hydride together with its displayed formula:
Observe that the mode the methane is fatigued bears no resemblance to the actual shape of the molecule. Methane isn't flat with 90° bond angles. This mismatch between what you draw and what the molecule really looks like can lead to problems if you aren't conscientious. For example, consider the simple molecule with the molecular formula CH2Cltwo. You might call back that there were 2 different ways of arranging these atoms if you drew a displayed formula.
The chlorines could be opposite each other or at right angles to each other. But these two structures are actually exactly the aforementioned. Wait at how they announced as models.
Ane structure is in reality a simple rotation of the other one. Consider a slightly more complicated molecule, C2H5Cl. The displayed formula could be written as either of these:
But, again these are exactly the same. Look at the models.
The commonest way to describe structural formulae
For anything other than the most simple molecules, drawing a fully displayed formula is a bit of a carp - particularly all the carbon-hydrogen bonds. Yous 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 form and a simplified class as:
You could fifty-fifty condense it farther to CH3COOH, and would probably exercise this if you had to write a simple chemic equation involving ethanoic acid. You lot do, however, lose something past condensing the acid group in this fashion, considering you can't immediately see how the bonding works. You still have to be careful in drawing structures in this manner. Call back from above that these two structures both represent the same molecule:
The adjacent iii structures all stand for butane.
All of these are just versions of iv carbon atoms joined up in a line. The only difference is that there has been some rotation about some of the carbon-carbon bonds. You tin see this in a couple of models.
Non one of the structural formulae accurately represents the shape of butane. The convention is that nosotros depict it with all the carbon atoms in a directly line - as in the first of the structures above. This is even more important when you lot commencement to have branched bondage of carbon atoms. The following structures again all stand for the same molecule - 2-methylbutane.
The 2 structures on the left are fairly obviously the aforementioned - all we've washed is flip the molecule over. The other one isn't so obvious until you look at the structure in detail. There are four carbons joined up in a row, with a CHiii group attached to the next-to-end one. That'due south exactly the same equally the other two structures. If you lot had a model, the but difference between these three diagrams is that you have rotated some of the bonds and turned the model around a bit.
To overcome this possible confusion, the convention is that you always look for the longest possible chain of carbon atoms, and so depict it horizontally. Annihilation else is simply hung off that concatenation. It does non affair in the least whether you draw any side groups pointing up or downwards. All of the following represent exactly the same molecule.
If you made a model of i of them, you could turn it into any other one simply by rotating one or more of the carbon-carbon bonds.
How to draw structural formulae in 3-dimensions
At that place are occasions when it is of import to be able to evidence the precise 3-D arrangement in parts of some molecules. To practise this, the bonds are shown using conventional symbols:
For instance, you might want to show the 3-D organization of the groups around the carbon which has the -OH group in butan-2-ol.
| Example one: butan-ii-ol |
|---|
| Butan-2-ol has the structural formula: Using conventional bail notation, you could draw it as, for example: The just difference between these is a slight rotation of the bail between the eye two carbon atoms. This is shown in the two models below. Expect carefully at them - peculiarly at what has happened to the lone hydrogen atom. In the left-manus model, it is tucked behind the carbon atom. In the right-paw model, it is in the same plane. The change is very slight. Information technology doesn't affair in the least which of the two arrangements y'all depict. You lot could hands invent other ones besides. Choose one of them and get into the habit of drawing 3-dimensional structures that way. My own habit (used elsewhere on this site) is to draw 2 bonds going back into the paper and one coming out - equally in the left-hand diagram above. Notice that no attempt was fabricated to bear witness the whole molecule in 3-dimensions in the structural formula diagrams. The CHiiCH3 grouping was left in a simple form. Continue diagrams elementary - trying to show as well much detail makes the whole thing amazingly difficult to understand! |
Skeletal formulae
In a skeletal formula, all the hydrogen atoms are removed from carbon chains, leaving just a carbon skeleton with functional groups fastened to it. For instance, we've just been talking about butan-2-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 atom at each junction betwixt bonds in a chain and at the stop of each bail (unless there is something else there already - like the -OH group in the example);
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in that location are enough hydrogen atoms attached to each carbon to make the total number of bonds on that carbon upward to 4.
Beware! Diagrams of this sort accept practice to interpret correctly - and may well not be acceptable to your examiners (run into 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 band of carbon atoms each with two hydrogens attached. This is what it looks similar in both a structural formula and a skeletal formula.
And this is cyclohexene, which is like but contains a double bail:
But the commonest of all is the benzene ring, C6H6, which has a special symbol of its ain.
Deciding which sort of formula to use
In that location'southward no easy, all-embracing answer to this problem. It depends more than than anything else on feel - a feeling that a item way of writing a formula is best for the situation you lot are dealing with.
Don't worry about this - as you do more than and more organic chemistry, yous will probably find it will come naturally. You lot'll get so used to writing formulae in reaction mechanisms, or for the structures for isomers, or in simple chemical equations, that you won't fifty-fifty think nigh it.
Source: https://chem.libretexts.org/Courses/Purdue/Purdue_Chem_26100:_Organic_Chemistry_I_%28Wenthold%29/Chapter_02._Structures_and_Properties_of_Organic_Molecules/2.2_Molecular_Shapes_and_Hybridization/2.2.2._Drawing_3-Dimensional_Molecules
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