3d drawing of molecular shapes
2.2.ii. Cartoon 3-Dimensional Molecules
- Folio ID
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This page 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 only counts the numbers of each sort of atom present in the molecule, but tells you nothing about the manner 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, considering they do not give useful data about the bonding in the molecule. About the only place where you lot might come up 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 need to be familiar with all of them.
Displayed formulae
A displayed formula shows all the bonds in the molecule as individual lines. You need to remember that each line represents a pair of shared electrons. For instance, this is a model of methyl hydride together with its displayed formula:
Observe that the way the methane is drawn bears no resemblance to the actual shape of the molecule. Methane isn't apartment with 90° bond angles. This mismatch between what yous draw and what the molecule actually looks like tin can lead to bug if you aren't careful. For example, consider the uncomplicated molecule with the molecular formula CHtwoCl2. You might think that there were two 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. Look at how they appear every bit models.
One structure is in reality a elementary rotation of the other one. Consider a slightly more complicated molecule, CiiH5Cl. The displayed formula could exist written as either of these:
But, once again these are exactly the same. Look at the models.
The commonest way to depict structural formulae
For anything other than the most uncomplicated molecules, drawing a fully displayed formula is a bit of a bother - especially all the carbon-hydrogen bonds. You can simplify the formula by writing, for instance, CH3 or CHtwo instead of showing all these bonds. For example, ethanoic acid would be shown in a fully displayed form and a simplified grade equally:
Yous could even condense it farther to CH3COOH, and would probably do this if you had to write a simple chemical equation involving ethanoic acid. Y'all do, even so, lose something past condensing the acrid group in this way, because yous can't immediately see how the bonding works. Y'all all the same have to be careful in drawing structures in this way. Call back from above that these two structures both represent the same molecule:
The adjacent three structures all stand for butane.
All of these are just versions of four carbon atoms joined upward in a line. The but difference is that there has been some rotation about some of the carbon-carbon bonds. You lot can see this in a couple of models.
Not one of the structural formulae accurately represents the shape of butane. The convention is that nosotros draw information technology with all the carbon atoms in a straight line - as in the first of the structures above. This is even more than important when you beginning to have branched chains of carbon atoms. The following structures once more all represent the same molecule - 2-methylbutane.
The two structures on the left are fairly obviously the aforementioned - all nosotros've washed is flip the molecule over. The other ane isn't so obvious until you look at the structure in detail. There are four carbons joined up in a row, with a CH3 group attached to the next-to-finish one. That's exactly the same as the other two structures. If you had a model, the just difference betwixt these three diagrams is that you have rotated some of the bonds and turned the model around a bit.
To overcome this possible defoliation, the convention is that you always await for the longest possible chain of carbon atoms, and and so draw it horizontally. Anything else is simply hung off that chain. It does not matter in the least whether yous draw whatsoever side groups pointing upward or down. All of the following correspond exactly the same molecule.
If y'all made a model of one of them, you could turn it into whatever other one simply by rotating one or more of the carbon-carbon bonds.
How to depict structural formulae in 3-dimensions
There are occasions when it is important to be able to prove the precise iii-D arrangement in parts of some molecules. To do this, the bonds are shown using conventional symbols:
For example, you lot might want to show the 3-D arrangement of the groups effectually the carbon which has the -OH group in butan-2-ol.
| Case 1: butan-ii-ol |
|---|
| Butan-2-ol has the structural formula: Using conventional bail notation, you could draw it equally, for example: The but divergence between these is a slight rotation of the bond between the centre two carbon atoms. This is shown in the two models below. Await carefully at them - particularly at what has happened to the lone hydrogen atom. In the left-hand model, it is tucked backside the carbon atom. In the right-hand model, it is in the aforementioned plane. The modify is very slight. It doesn't matter in the least which of the two arrangements you describe. Y'all could easily invent other ones also. Choose ane of them and become into the habit of drawing 3-dimensional structures that way. My own addiction (used elsewhere on this site) is to draw 2 bonds going back into the newspaper and one coming out - as in the left-hand diagram higher up. Notice that no attempt was made to show 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 evidence too 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 attached to it. For example, we've just been talking about butan-2-ol. The normal structural formula and the skeletal formula wait 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 bail (unless there is something else there already - like the -OH grouping in the example);
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at that place are enough hydrogen atoms attached to each carbon to make the total number of bonds on that carbon up to 4.
Beware! Diagrams of this sort take practice to interpret correctly - and may well not exist acceptable to your examiners (see below).
In that location are, however, some very mutual cases where they are frequently 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 ii hydrogens attached. This is what information technology looks like in both a structural formula and a skeletal formula.
And this is cyclohexene, which is similar just contains a double bond:
Simply the commonest of all is the benzene ring, C6H6, which has a special symbol of its own.
Deciding which sort of formula to utilise
At that place's no easy, all-embracing respond to this problem. It depends more than than anything else on experience - a feeling that a particular way of writing a formula is best for the state of affairs you are dealing with.
Don't worry virtually this - every bit you lot do more and more than organic chemistry, you lot will probably find information technology will come up naturally. You'll get and then used to writing formulae in reaction mechanisms, or for the structures for isomers, or in simple chemical equations, that you lot won't even recollect about it.
Source: https://chem.libretexts.org/Courses/Purdue/Purdue_Chem_26100%3A_Organic_Chemistry_I_(Wenthold)/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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