how to draw a molecule in 3d
two.2.2. Cartoon 3-Dimensional Molecules
- Page ID
- 32659
This page explains the various ways that organic molecules tin be 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, simply tells you nothing about the fashion they are joined together. For example, the molecular formula of butane is \(C_4H_{ten}\), 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 most the bonding in the molecule. About the only 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 like this, the bonding in the organic molecule isn't important.
Structural formulae
A structural formula shows how the diverse atoms are bonded. There are various means of cartoon this and you will need to be familiar with all of them.
Displayed formulae
A displayed formula shows all the bonds in the molecule equally individual lines. You lot 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:
Notice that the way the methane is drawn bears no resemblance to the actual shape of the molecule. Marsh gas isn't apartment with 90° bond angles. This mismatch between what you draw and what the molecule actually looks like can lead to problems if you lot aren't careful. For example, consider the simple molecule with the molecular formula CHiiCl2. You might call up that there were two different means of arranging these atoms if you drew a displayed formula.
The chlorines could be opposite each other or at right angles to each other. Simply these two structures are actually exactly the same. Look at how they appear equally models.
One structure is in reality a unproblematic 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 aforementioned. Wait at the models.
The commonest mode to draw structural formulae
For annihilation other than the most simple molecules, drawing a fully displayed formula is a bit of a carp - peculiarly all the carbon-hydrogen bonds. You can simplify the formula past writing, for example, CH3 or CH2 instead of showing all these bonds. For example, ethanoic acrid would exist shown in a fully displayed course and a simplified course as:
You could even condense it further to CH3COOH, and would probably do this if you lot had to write a unproblematic chemic equation involving ethanoic acid. Yous do, however, lose something past condensing the acid group in this style, considering you can't immediately see how the bonding works. You still accept to exist conscientious in drawing structures in this way. Remember from above that these two structures both represent the same molecule:
The side by side three structures all represent butane.
All of these are just versions of four carbon atoms joined upwards in a line. The just difference is that there has been some rotation about some of the carbon-carbon bonds. Yous tin encounter this in a couple of models.
Not one of the structural formulae accurately represents the shape of butane. The convention is that we draw it with all the carbon atoms in a straight line - every bit in the starting time of the structures above. This is fifty-fifty more important when y'all start to take branched chains of carbon atoms. The following structures again all represent the same molecule - 2-methylbutane.
The two structures on the left are fairly obviously the aforementioned - all we've done is flip the molecule over. The other 1 isn't so obvious until you look at the structure in detail. In that location are four carbons joined upward in a row, with a CHthree grouping attached to the adjacent-to-cease 1. That'due south exactly the same every bit the other two structures. If you had a model, the only difference between these iii diagrams is that yous have rotated some of the bonds and turned the model around a bit.
To overcome this possible confusion, the convention is that you always wait for the longest possible concatenation of carbon atoms, and then draw it horizontally. Anything else is simply hung off that concatenation. Information technology does non matter in the to the lowest degree whether you describe whatsoever side groups pointing up or downwardly. All of the post-obit represent exactly the aforementioned molecule.
If yous made a model of ane of them, you could turn it into whatsoever other one simply by rotating i or more of the carbon-carbon bonds.
How to draw structural formulae in three-dimensions
There are occasions when it is important to exist able to show the precise 3-D arrangement in parts of some molecules. To practice this, the bonds are shown using conventional symbols:
For example, you might want to testify the iii-D organisation of the groups effectually the carbon which has the -OH group in butan-two-ol.
| Case 1: butan-2-ol |
|---|
| Butan-2-ol has the structural formula: Using conventional bond notation, y'all could depict it as, for case: The only divergence between these is a slight rotation of the bond betwixt the centre ii carbon atoms. This is shown in the ii models below. Look carefully at them - particularly at what has happened to the lone hydrogen atom. In the left-hand model, information technology is tucked behind the carbon atom. In the right-hand model, it is in the same plane. The alter is very slight. It doesn't matter in the least which of the 2 arrangements you lot draw. You could easily invent other ones besides. Choose one of them and get into the habit of drawing 3-dimensional structures that style. My own habit (used elsewhere on this site) is to draw 2 bonds going dorsum into the paper and 1 coming out - as in the left-paw diagram higher up. Observe that no try was made to testify the whole molecule in 3-dimensions in the structural formula diagrams. The CH2CH3 grouping was left in a uncomplicated form. Go on diagrams unproblematic - trying to show as well much detail makes the whole matter amazingly hard to empathise! |
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 information technology. For example, we've just been talking about butan-two-ol. The normal structural formula and the skeletal formula look like this:
In a skeletal diagram of this sort
-
there is a carbon atom at each junction between bonds in a chain and at the finish of each bail (unless there is something else in that location already - similar the -OH group in the example);
-
there 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 have practice to translate correctly - and may well non be acceptable to your examiners (encounter below).
There are, still, some very common 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, CviH12, is a ring of carbon atoms each with two hydrogens attached. This is what it looks like in both a structural formula and a skeletal formula.
And this is cyclohexene, which is similar but contains a double bond:
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's no like shooting fish in a barrel, all-embracing answer to this problem. Information technology depends more than anything else on experience - a feeling that a detail fashion of writing a formula is best for the situation you lot are dealing with.
Don't worry about this - every bit you do more and more organic chemistry, you will probably observe it will come naturally. You'll become and then used to writing formulae in reaction mechanisms, or for the structures for isomers, or in simple chemic equations, that y'all won't fifty-fifty recall almost 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
0 Response to "how to draw a molecule in 3d"
Publicar un comentario