[Introduction 1/32]
In this activity we'll examine two aspects of organic chemistry. Firstly we'll examine the shapes of molecules. For example, this ball and stick model is a representation of vitamin C. It exists in three dimensions and has a precise shape. Molecules such as vitamin C undergo a particular set of reactions. We can predict these reactions by looking at the structure of the molecule and identifying key groups of atoms. So, in the second part of this activity we explore this strategy, known as the functional group approach.

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In this part of the activity we'll look at the three dimensional shapes of molecules. We'll start by examining the structural formulas of some simple hydrocarbons. Methane molecules contain one carbon atom. Carbon has a valency of four, so it has four covalent bonds attached to it. Hydrogen has a valency of one, which means that four hydrogen atoms can be attached to the carbon atom. You can use the drawing tool on the right of the screen to draw out structural formulas. If this is your first time using the drawing tool, click the Demonstration button for a brief overview of how to use it.

When you’re ready have a go at duplicating the structure of methane shown on the left.[Demonstration]
If the Carbon atom button is pressed then clicking in the white area will create a new carbon atom. You can create more carbon atoms by clicking again in the white area. To create hydrogen atoms, click on the Hydrogen button. Again, clicking in the white area generates hydrogen atoms. You can move an atom around the drawing area by clicking on the Select button, and then clicking on the atom you want to move. By keeping the mouse button depressed, you will be able to drag the atom to a new position. Releasing the mouse drops the atom. To form a bond between two atoms, first select the bond button then click on one of the atoms. This will start a new bond. Whilst you are holding the mouse button down, move the arrow to select the other atom and then release the button. A bond will appear between the two atoms. You can only form one bond at a time. When an atom has enough bonds to satisfy its valency it will change colour from red to black. With the Delete button selected you can click on an atom or bond to remove it from the drawing area. When an atom is deleted, bonds attached to it are also removed.

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What is the molecular formula of methane?

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Ethane molecules contain two carbon atoms joined together by a single bond. Use the drawing tool to draw just these two carbon atoms connected by a single bond. Don't bother with the hydrogen atoms for the moment.

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Now connect sufficient hydrogen atoms such that the valencies of the carbon atoms are satisfied.

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Each carbon has a valency of four. The carbon atoms are attached to each other by one bond, leaving three bonds on each carbon to be joined to hydrogen atoms. What is the molecular formula of ethane?

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The structural formula shows that the molecular formula of ethane is C2H6.

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The next hydrocarbon in the series is propane. Molecules of propane contain three carbon atoms. Using the drawing tool, draw the three carbon framework, again without the hydrogen atoms.

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Now connect sufficient hydrogen atoms such that the valency of each carbon atom is satisfied.

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Each carbon has a valency of four. The carbon atoms on the ends are attached to the central carbon by one bond, leaving three bonds on each end carbon to be joined to hydrogen atoms. The central carbon has two bonds to other carbons leaving only two bonds to hydrogen atoms. Type the molecular formula of propane in the box below. Any numbers will automatically appear as subscripts.

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The structural formula shows that the molecular formula of propane is C3H8.

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A molecule of butane contains a linear chain of four carbon atoms with sufficient hydrogen atoms to satisfy the valency of each carbon atom. Use the drawing tool to construct a molecule of butane.

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Each carbon has a valency of four. The carbon atoms on the ends are attached to the central carbon atoms by one bond, leaving three bonds on each end carbon to be joined to hydrogen atoms. The two central carbon atoms each have two bonds to other carbon atoms, leaving only two bonds to the hydrogen atoms. What is the molecular formula of butane?

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This structural formula shows that the molecular formula of butane is C4H10.

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Have a look at this lower carbon backbone. Using the drawing tool, connect sufficient hydrogen atoms such that the valency of each carbon is satisfied.

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What is the molecular formula corresponding to this lower structural formula?

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Both these structural formulas lead to the same molecular formula. Although these two representations may not look alike, they are just different ways of drawing the same structural formula. A structural formula only shows which atoms are directly bonded to each other. Both drawings show a chain of four atoms. The carbon atoms on the ends are attached to the central carbon atoms by one bond, leaving three bonds on each end carbon to be joined to hydrogen atoms. The two central carbons have two bonds to other carbon atoms leaving only two bonds to hydrogen atoms. Have a look at this backbone of carbons. When we connect sufficient hydrogen atoms, does it correspond to the same structural formula? It does, and in fact we can draw the structural formula of butane in many different ways. A structural formula only tells us which atoms are connected to each other. It tells us nothing of how they are arranged in space. To get a better idea of what molecules actually look like, we need to use a ball and stick model in three dimensions.

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Let's go back and look at the simplest hydrocarbon, methane. We saw that it had the molecular formula CH4. If the shape of the molecule matched that of the structural formula drawn on paper, the molecule would be flat. Try rotating this ball and stick model of the structural formula, using the arrow buttons below the model.

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However, this ball and stick model is wrong. Experiments have shown that in reality carbon forms four bonds, each pointing to the corner of a tetrahedron. This arrangement of four single bonds is the same for carbon irrespective of the atoms at the other end of the bond. So, methane looks like this. Rotate the structure, using the buttons to get a feel for its three dimensional shape.

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Each hydrogen atom in a methane molecule is identical to the other three. We can show this by marking one hydrogen atom and then rotating the molecule so the labelled hydrogen takes up the position of one of the other hydrogen atoms. Use the arrow buttons to do this: that is, rotate the molecule so the labelled hydrogen atom takes up the position of one of the other hydrogen atoms. Every time we do this the molecule looks the same.

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The representation we have used is known as the ball and stick model. The balls represent atoms. They are colour-coded black or dark grey for carbon, white for hydrogen and red for oxygen. You can find a key to the colours by clicking on the Help menu and choosing 'key'. Each stick represents a chemical bond between two atoms. It identifies which atom is connected to which. For example there are no bonds between hydrogen atoms in methane. There are also other ways of showing the three-dimensional form of molecules: space filling, cylinder and wire frame. The buttons on the top right have labels that describe these different representations. Please try them out and rotate the molecules.

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We saw that ethane contains two carbons joined together by a bond. Each carbon has four bonds that point to the corners of tetrahedra. Adding six hydrogen atoms gives us a molecule of ethane. Once again, rotate the structure, using the arrow buttons to get a feel for its three dimensional shape.

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Rotation about a single bond between two carbon atoms occurs very easily and in reality one end of the ethane molecule is continuously spinning relative to the other end. So although we can show the molecule in a number of different ways, they are not different molecules because they can be readily converted into each other by rotation. Rotate the following representation about the carbon-carbon bond to give molecules that are identical to those on the left. You can rotate each half of the molecule independently by using the two sets of arrow buttons below the model.

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If you look at the two dimensional structural formula of ethane, it looks as if the hydrogen atoms pointing out on the left and right might be different in some way from those pointing up and down, because they are in different types of position. In fact this is wrong; the structural formula only shows which atoms are connected to which, not how they are arranged in space. Our three dimensional model shows that all the hydrogen atoms are identical. You can again show this by marking one hydrogen atom and rotating about the carbon-carbon bond so that the labelled hydrogen takes up the position of one of the other hydrogen atoms. Every time we do this the molecule looks the same.

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We saw that propane contains three carbon atoms joined together. Each carbon atom has four bonds that point to the corners of tetrahedra. Connecting eight hydrogen atoms gives us a molecule of propane. Rotate the structure for yourself.

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As we saw earlier, rotation about carbon-carbon single bonds occurs very easily. Rotate the following representations about either carbon-carbon bond to give models that are identical to those on the left. The left hand pair of arrow buttons rotate the left-hand bond and the right hand pair the right-hand bond.

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Are the hydrogen atoms in propane all equivalent? Again the structural formula doesn't give the full story. Our three-dimensional model shows that all the hydrogen atoms on the end carbons are identical. We can again show this by marking one hydrogen atom and rotating about a carbon-carbon bond so that it takes up the position of one of the other hydrogen atoms; the molecule still looks the same.

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However, the carbon in the middle is not equivalent to the carbon atoms at the end because it is attached to two other carbon atoms, whereas those at the end are only attached to one. So in the propane molecule the carbons on the ends are not equivalent to the carbon in the middle; also the hydrogen atoms attached to the carbon in the middle are not equivalent to the hydrogen atoms attached to the carbons at the end. We could draw the structural formula of propane in different ways. Although they look different they are not; they all convey the same information: that is the order in which the atoms are bonded together.

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Butane contains four carbon atoms in a chain. Connecting ten hydrogen atoms gives us the complete molecule. Rotate the structure for yourself.

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Are all the hydrogen atoms in butane equivalent?

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There are two different types of hydrogen atom: those on the end carbons and those on the middle two carbons. You can again show which ones are equivalent by marking one hydrogen atom and rotating it so that it takes up the position of one of the others; the molecule looks identical.

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If we rotate the molecule by 180 degrees we see the six hydrogen atoms on the carbon atoms at each end are all equivalent to each other.

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The second type of hydrogen atom is bonded to the middle two carbons. Again, rotation of the molecule by 180 degrees shows that the four hydrogen atoms on the two central carbon atoms are all equivalent.

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The structural formula of butane can be drawn in a number of different ways. Although they look different, because the structural formula only tells us which atoms are connected to which, and tells us nothing of the shape of the molecule, these representations all provide the same information about the molecule. Try manipulating the ball and stick models using bond rotations to give a structure that roughly matches each of the representations on the left. Again you can rotate the two halves independently.

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Sometimes you might be asked to compare two structural formulas and decide whether they refer to the same compound. You need to focus on the order in which the atoms are joined. In each case we have looked at so far the carbon atoms are joined one after the other. Secondly, in all the structures you will meet, all the hydrogen atoms attached to a particular carbon are identical, no matter how they are drawn in a structural formula.

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Have a look at these two structural formulas. Do they correspond to the same molecule? Before you answer, click on the Butane and Isomer buttons to see the structures in three dimensions.

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They are not identical because the carbon atoms are joined in a different order. In the first structure the four carbon atoms are joined one after the other. The end carbons are each attached to one carbon and the middle carbons are each attached to two carbons. In the second structure three carbon atoms are joined in a row and the middle carbon has an extra carbon attached. So, the three carbons on the outside each have only one carbon attached to them, whereas the carbon atom in the middle has three carbons attached. We can see this more clearly if we look at the three dimensional structures. There is no way we can rotate either molecule around single bonds and make it identical with the other one. Compounds which have the same molecular formula, C4H10 in this case, but which have different structural formulas are called isomers.

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Pentane has the structural formula shown on the left. What is its molecular formula?

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How many isomers are there of pentane? To answer this question you need to think about how many different ways there are of joining together 5 carbon atoms to give a different backbone each time. Watch out for identical structures just written back to front or upside down and don't include rings of carbon atoms since these will not accommodate twelve hydrogen atoms. Once you have identified the different backbones, add the twelve hydrogen atoms to give the full structural formulas. If you like, you can use the drawing tool on the right to help you. Clicking on the Check button will tell you if the structure you have built is pentane itself or one of its other isomers.

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In addition to pentane itself, there are two other isomers with the formula C5H12. These compounds have the same molecular formula but different structural formulas. Other structural formulas of C5H12 that you may have come up with are probably identical to these but drawn out differently.

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Drag any structure that is an isomer of pentane into the box on the left and leave any structural formulas of pentane itself where they are.

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That concludes the first part of this activity. To summarise:
Structural formulas only show the order in which atoms are connected and tell us nothing about the shape of the molecule. When considering whether structural formulas are identical or isomers, we must concentrate on the order in which the atoms are joined and not the shape of the representation on the paper. The four bonds attached to carbon atoms do not all lie in the same plane, but point to the four corners of a tetrahedron. Rotation about single bonds is easy. When examining whether two molecules are identical or isomers we must always consider rotations about a single bond, which may show them to be identical. You may now wish to proceed to the second part of the activity, which concerns functional groups. Alternatively, you may wish to end your study session now.

[Functional Groups 21/32]
In the first part of this activity, we examined the structure of hydrocarbons. In this part we shall look at other classes of organic compounds using the functional group approach. For example, this is a hydrocarbon but because it contains a carbon-carbon double bond it is an alkene not an alkane. Similarly, this is a member of a group known as carboxylic acids. The red atoms are oxygen atoms. There are two bonds to each oxygen atom because oxygen has a valency of two. The functional group approach is based on the fact that saturated hydrocarbons are fairly unreactive whereas groups containing double bonds, or atoms other than hydrogen and carbon, are fairly reactive. This means we can imagine breaking molecules up into the reactive functional group and the inert saturated hydrocarbon part. For example, this molecule contains an alkene functional group - a carbon-carbon double bond. The inert saturated hydrocarbon part is shown in blue. This means that when this molecule reacts, it is its alkene functional group that takes part in the reaction and not the saturated hydrocarbon chain. For example, in this reaction bromine reacts only at the double bond.

[Functional Groups 22/32]
Identify the alkene functional group in the following molecules. You can do this by clicking on the atoms which you think are part of the functional group in the molecules displayed in the work area on the right of the screen. This will highlight the atom you have selected in red. If you think you have selected an atom in error, you can remove the highlight by clicking on the atom again. Once you have selected the functional group, click on 'Done' to check your answer and then move to the next molecule.

[Functional Groups 23/32]
A carbon which is bonded to an oxygen atom by a double bond and also to an OH group forms a carboxylic acid functional group. As before, we can divide the molecule up into the reactive carboxylic acid group and the inert hydrocarbon portion. Identify the carboxylic acid functional group in the following molecules.

[Functional Groups 24/32]
Another functional group is the alcohol functional group, which involves an oxygen atom bonded to a hydrogen atom. Note that whilst both alcohols and carboxylic acids contain an OH group, alcohols do not contain a carbon-oxygen double bond As before, we can divide the molecule up into the reactive alcohol group and the inert hydrocarbon portion. Identify the alcohol functional group in the following molecules.

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Identify the functional groups in the molecules shown and then drag each of them to the appropriately labelled area of the screen. Click 'Done' when you think you've sorted them all.

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These two molecules are both carboxylic acids. The right hand structure is written using the abbreviated structural formula COOH. Since the hydrocarbon part does not change during a reaction we can simplify all the carboxylic acids to the formula R-COOH. In the first case R represents a CH3 group and in the second case a CH3-CH2-CH2 group. What does R stand for in the following molecule?

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The R notation can be used with other functional groups. What does R stand for in this molecule?

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A superscript is used when there may be more than one hydrocarbon chain present in a molecule. What do R1 and R2 stand for in this molecule?

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The strength of the functional group approach is that it enables us to identify the functional group in a molecule and thereby identify the reactions the molecule will undergo. For example, alkenes undergo addition reactions. In this addition reaction bromine adds across a double bond, the double bond is broken and a bromine atom ends up on each carbon. This reaction occurs for all alkenes. We can simplify this reaction using the R notation. For example, in this reaction R1 is CH3 and R2 is CH3-CH2.

[Functional Groups 28/32]
What will be the products of the following reaction? One simple way of answering this question is to refer back to the general reaction. In the reactants R1 is CH3-CH2 and R2 is CH3-CH2-CH2. So we can predict the product by rewriting the equation with the appropriate R groups.

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You can add water across a double bond. Predict the products of the following reaction.

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In the reactants R1 is CH3 and R2 is CH3. So we can predict the product by rewriting the equation for the addition of water with the appropriate R groups. This shows the true power of the functional group approach. You have been able to predict the outcome of a reaction by noticing which functional group is present and then, based on your knowledge of the reactions of this functional group, to write out the reaction.

[Functional Groups 30/32]
Let's test out the principles you have learnt using the following general equation - the reaction between a carboxylic acid, R1-COOH and an alcohol, R2-OH. To make it easier for you to see what's going on we shall turn the alcohol round. The product is an ester - another functional group. Have a look at these esters. Identify R1 and R2 in each of these molecules.

[Functional Groups 30/32b]
The formation of an ester from a carboxylic acid and an alcohol is known as a condensation reaction. It is called a condensation reaction because a small molecule, water in this instance, is formed when the two reactants combine. Identify R1 and R2 in the following reaction.

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This is the reaction between acetic acid and ethanol, although in this case the ethanol is written back to front. What are the two products of this reaction?

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Identify the R groups or the products in the following reactions. If you need to remind yourself of the general reactions, you can find them by clicking on the Help menu and choosing 'key'.

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That concludes the second part of this activity. To summarise:
Organic molecules can be classified using the functional group approach. The approach involves the imaginary division of the molecule into parts - the reactive functional group and the unreactive hydrocarbon fragment. To simplify structures we use the R notation to represent the hydrocarbon part of the molecule. Only the functional group undergoes reactions and this is one way of predicting the properties of an organic compound. We can write generalised forms of such reactions using R notation to represent the hydrocarbon group that does not change.