05 Organic Compounds Ii

ORGANIC COMPOUNDS II RECALLING SOME FEATURES OF COVALENT BONDING Carbon bonds covalently to other atoms. Although carbon – metal bonds have a highly ionic character and there are compounds in which carbon forms stable cations, the tetracovalency of carbon still holds for 99.9 % of the cases. You should recall that “mixing” or hybridization of atomic orbitals lead to sp3, sp2 and sp combinations that are properly oriented to accomplish with the geometrically most stable distribution of the electron pairs (VEPReT). Single bonds are formed by frontal interpenetration of the orbitals of the atoms forming the bond: these are the σ (sigma) bonds. If there is a double or triple bond between two atoms, then the first bond that holds the atoms together will be of the σ type but the other (or others) will be formed by lateral overlapping of the orbitals located at right angles of the σ bond axis. These are the π bonds in which the molecular orbitals have two lobes lying above and below the plane that contains both nuclei.

The formation of σ bonds in ethane C2H6

The formation of a π bond in ethane C2H4 Sigma (σ) bonds • •

Unlike pi (π) bonds allow free rotation around the axis joining the nuclei Are stronger than pi (π) bonds

LCAO The mathematical approach to molecular orbitals uses an approximation called the Linear Combination of Atomic Orbitals (LCAO) theory. According to this theory the molecular orbitals can be fairly approximated as a new function that is obtained by linear combination of the atomic functions involved in the bond: Molecular orbital (MO) = Atomic Orbital (AO)1 ± Atomic Orbital (AO)2

Thus, the simplest combination of the AO’s gives two possible MO’s. Calculations show that addition gives a MO with lower energy than each of the individual AO’s: it is called a bonding MO and the electrons of the bond will occupy this level. On the other hand subtraction gives a MO that is more energetic than the original AO’s. This one is called the anti- bonding MO* and remains empty. If electrons were promoted to this anti – bonding orbital, the bond would be unstable and eventually break down (that happens when UV radiation is absorbed: DNA may break and tumours appear)

The hydrogen molecule

Forming bonding and anti – bonding σ and π orbitals

DELOCALISED BONDS An orbital model for the benzene structure Benzene is built from hydrogen atoms (1s1) and carbon atoms (1s22s22px12py1). Each carbon atom has to join to three other atoms (one hydrogen and two carbons) and doesn't have enough unpaired electrons to form the required number of bonds, so it needs to promote one of the 2s2 pair into the empty 2pz orbital. This is exactly the same as happens whenever carbon forms bonds whatever else it ends up joined to. Because each carbon is only joining to three other atoms, when the carbon atoms hybridise their outer orbitals before forming bonds, they only need to hybridise three of the orbitals rather than all four. They use the 2s electron and two of the 2p electrons, but leave the other 2p electron unchanged. The new orbitals formed are called sp2 hybrids, because they are made by an s orbital and two p orbitals reorganising themselves. The three sp2 hybrid orbitals arrange themselves as far apart as possible which is at 120° to each other in a plane. The remaining p orbital is at right angles to them. Each carbon atom now looks like the diagram on the right. This is all exactly the same as happens in ethene. The difference in benzene is that each carbon atom is joined to two other similar carbon atoms instead of just one. Each carbon atom uses the sp2 hybrids to form sigma bonds with two other carbons and one hydrogen atom. The next diagram shows the sigma bonds formed, but for the moment leaves the p orbitals alone (the two C atoms to the front are not shown).

Notice that the p electron on each carbon atom is overlapping with those on both sides of it. This extensive sideways overlap produces a system of pi bonds which are spread out over the whole carbon ring. Because the electrons are no longer held between just two carbon atoms, but are spread over

the whole ring, the electrons are said to be delocalised. The six delocalised electrons go into three bonding molecular orbitals - two in each. In common with the great majority of descriptions of the bonding in benzene, we are only going to show one of these delocalised molecular orbitals for simplicity. In the diagram, the sigma bonds have been shown as simple lines to make the diagram less confusing. The two rings above and below the plane of the molecule represent one molecular orbital. The two delocalised electrons can be found anywhere within those rings. The other four delocalised electrons are in two similar (but not identical) delocalised molecular orbitals. RELATING THE ORBITAL MODEL TO THE PROPERTIES OF BENZENE The shape of benzene Benzene is a regular hexagon because all the bonds are identical. The delocalisation of the electrons means that there aren't alternating double and single bonds. The energetic stability of benzene This is accounted for by the delocalisation. As a general principle, the more you can spread electrons around - in other words, the more they are delocalised - the more stable the molecule becomes. The extra stability of benzene is often referred to as "delocalisation energy". The reluctance of benzene to undergo addition reactions With the delocalised electrons in place, benzene is about 150 kJ mol-1 more stable than it would otherwise be. If you added other atoms to a benzene ring you would have to use some of the delocalised electrons to join the new atoms to the ring. That would disrupt the delocalisation and the system would become less stable. Since about 150 kJ per mole of benzene would have to be supplied to break up the delocalisation, this isn't going to be an easy thing to do. The symbol for benzene For most purposes we use the structure on the right. The hexagon shows the ring of six carbon atoms, each of which has one hydrogen attached. The circle represents the delocalised electrons. It is essential that you include the circle. AROMATICITY This special stabilisation of benzene and related organic substances is called aromaticity and the substances containing aromatic rings are called aromatic compounds. The chemistry of aromatic compounds is different to the chemistry of non – aromatic (called aliphatic) compounds. Aromatic compounds contain six membered rings with six

contiguous p electrons (there are other aromatic compounds beyond the scope of this paper). The following structures show some simple aromatic compounds

HOW TO DRAW STRUCTURAL FORMULAE IN 3-DIMENSIONS There are occasions when it is important to be able to show the precise 3-D arrangement in parts of some molecules. To do this, the bonds are shown using conventional symbols:

For example, you might want to show the 3-D arrangement of the groups around the carbon which has the -OH group in butan-2-ol. Butan-2-ol has the structural formula:

Using conventional bond notation, you could draw it as, for example:

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 look like this:

In a skeletal diagram of this sort •

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there is a carbon atom at each junction between bonds in a chain and at the end of each bond (unless there is something else there already - like 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 up to 4.

Cyclohexane, C6H12, 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 own as we have already seen. WHAT IS STEREOISOMERISM? You have learned what the terms “structural isomerism” means. Isomers are molecules that have the same molecular formula, but have a different structure. In stereoisomerism, the atoms making up the isomers are joined up in the same order, that is, the structure of the isomers is the same but have a different configuration Configuration of a structure is any of the different arrangements in space of its atoms that can be isolated.

UNRESTRICTED ROTATION Think about what happens in molecules where there is unrestricted rotation about carbon bonds - in other words where the carbon-carbon bonds are all single. The next diagram shows two possible space arrangements of 1,2-dichloroethane.

These two models represent exactly the same molecule. You can get from one to the other just by twisting around the carbon-carbon single bond and at room temperature the molecules have enough rotational energy to overcome low energy barriers. These molecules are not isomers but conformers. CONFORMATION Conformation of a molecule is any of the infinite spatial arrangements of its structure, obtained by rotation of any of its single (σ) bonds. Conformations are easily interconverted and actually a molecule generally exists in many of them simultaneously. Despite this apparent freedom, only two limiting conformations are important: eclipsed conformation and staggered conformation.

The case of butane is similar but somewhat different: the methyl groups can be eclipsed either with a hydrogen atom or with the other methyl. This last conformation is the less stable and of the staggered conformations the “anti” is more stable than any “gauche”

The energy barriers are low and do not hinder free rotation at room to moderately cold temperatures. But nevertheless, these species can be detected as different entities at temperatures below -100°C!! GEOMETRIC (CIS / TRANS) ISOMERISM How geometric isomers arise When you have restricted rotation somewhere in a molecule, at that point the conformers are no longer interchangeable at room temperature and appear as two distinctly different substances: these are called cis-trans or geometric isomers. Geometric isomerism is one form of stereoisomerism. If you draw a structural formula instead of using models, you have to bear in mind the possibility of this free rotation about single bonds. You must accept that these two structures represent the same molecule:

But what happens if you have a carbon-carbon double bond - as in 1,2-dichloroethene?

These two molecules aren't the same. The carbon-carbon double bond won't rotate (π bonds will break) and so you would have to take the models to pieces in order to convert one structure into the other one. That is a simple test for isomers. If you have to take a model to pieces to convert it into another one, then you've got isomers. If you merely have to twist it a bit, then you haven't! Drawing structural formulae for the last pair of models gives two possible isomers. In one of them the two chlorine atoms are locked on opposite sides of the double bond. This is known as the trans isomer. (trans: from Latin meaning "across"). In the other one the two chlorine atoms are locked on the same side of the double bond. This is known as the cis isomer. (cis: from Latin meaning "on this side")

Another example of geometric isomers is the but-2-enes: in one case, the CH3 groups are on opposite sides of the double bond, and in the other case they are on the same side.

How to recognise the possibility of geometric isomerism You obviously need to have restricted rotation somewhere in the molecule. Cycles and double bonds are commonest cases. If you have a carbon-carbon double bond, then think carefully about the possibility of geometric isomers. What needs to be attached to the carbon-carbon double bond? Think about this case:

Although we've swapped the right-hand groups around, these are still the same molecule. To get from one to the other, all you would have to do is to turn the whole model over. You won't have geometric isomers if there are two groups the same on one end of the bond - in this case, the two pink groups on the left-hand end. So there must be two different groups on the left-hand carbon and two different groups on the right-hand one. The cases we've been exploring earlier are like this:

PLANE POLARISED LIGHT A simple analogy - "plane polarised string" Imagine tying a piece of thick string to a hook in a wall, and then shaking the string vigorously. The string will be vibrating in all possible directions - up-and-down, sideto-side, and all the directions in-between - giving it a really complex overall motion.

Now, suppose you passed the string through a vertical slit. The only vibrations still happening on the other side of the slit will be vertical ones. All the others will have been prevented by the slit.

What emerges from the slit could be described as "plane polarised string", because the vibrations are only in a single (vertical) plane.

Now look at the possibility of putting a second slit on the string. If it is aligned the same way as the first one, the vibrations will still get through.

But if the second slit is at 90° to the first one, the string will stop vibrating entirely to the right of the second slit. The second slit will only let through horizontal vibrations and there aren't any.

Plane polarised light Light is also made up of vibrations - this time, electromagnetic ones. Some materials have the ability to screen out all the vibrations apart from those in one plane and so produce plane polarised light. The most familiar example of this is the material that Polaroid sunglasses are made of. If you wear one pair of Polaroid sunglasses and hold another pair up in front of them so that the glasses are held vertically rather than horizontally, you'll find that no light gets through - you will just see darkness. This is equivalent to the two slits at right angles in the string analogy. The polaroids are described as being "crossed". OPTICAL ISOMERISM Optical isomers are named like this because of their effect on plane polarised light An optically active substance is one which can rotate the plane of polarisation of plane polarised light. If you shine a beam of polarised monochromatic light (light of only a single frequency - in other words a single colour) through a solution of an optically active substance, when the light emerges, its plane of polarisation is found to have rotated. The rotation may be either clockwise or anti-clockwise. Assuming the original plane of polarisation was vertical, you might get either of these results. How can you tell that the plane of polarisation has been rotated? You use a polarimeter. The polariser and analyser are both made of polaroid material. The polarimeter is originally set up with water in the tube. Water isn't optically active - it has no effect on the plane of polarisation. The analyser is rotated until you can't see any light coming through the instrument. The polaroids are then "crossed". You will see no light. Now you put a solution of an optically active substance into the tube. It rotates the plane of polarisation of the light, and so the analyser won't be at right-angles to it any longer and some light will get through. You would have to rotate the analyser in order to cut the light off again. ENANTIOMERS Simple substances which show optical isomerism exist as two isomers known as enantiomers.

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A solution of one enantiomer rotates the plane of polarisation in a clockwise direction. This enantiomer is known as the (+) form.

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A solution of the other enantiomer rotates the plane of polarisation in an anticlockwise direction. This enantiomer is known as the (-) form.

When optically active substances are made in the lab, they often occur as a 50/50 mixture of the two enantiomers. This is known as a racemic mixture or racemate. It has no effect on plane polarised light. HOW OPTICAL ISOMERS ARISE These two models each have the same groups joined to the central carbon atom, but still manage to be different:

Obviously as they are drawn, the orange and blue groups aren't aligned the same way. Could you get them to align by rotating one of the molecules? The next diagram shows what happens if you rotate molecule B.

They still aren't the same - and there is no way that you can rotate them so that they look exactly the same. These are optical isomers of each other. They are described as being non-superimposable in the sense that (if you imagine molecule B being turned into a ghostly version of itself) you couldn't slide one molecule exactly over the other one. Something would always be pointing in the wrong direction. What happens if two of the groups attached to the central carbon atom are the same? The next diagram shows this possibility.

The two models are aligned exactly as before, but the orange group has been replaced by another pink one. Rotating molecule B this time shows that it is exactly the same as molecule A. You only get optical isomers if all four groups attached to the central carbon are different.

CHIRAL AND ACHIRAL MOLECULES The essential difference between the two examples we've looked at lies in the symmetry of the molecules. If there are two groups the same attached to the central carbon atom, the molecule has a plane of symmetry. If you imagine slicing through the molecule, the left-hand side is an exact reflection of the right-hand side. Where there are four groups attached, there is no symmetry anywhere in the molecule.

An object which has no plane of symmetry is described as chiral. Such an object cannot be superimposed to its mirror image. Think of your right hand. Its mirror image is your left hand and they cannot be superimposed although they both have the same fingers attached in the same position. Your hands are chiral objects. In fact chirality is a word derived from the Greek word for hand (cheir). Chiromancy, chiropractic have the same origin. The carbon atom with the four different groups attached which causes this lack of symmetry is described as a chiral centre or as an asymmetric carbon atom. The molecule on the left above (with a plane of symmetry) is described as achiral. Only chiral molecules have optical isomers. THE RELATIONSHIP BETWEEN THE ENANTIOMERS One of the enantiomers is simply a non-superimposable mirror image of the other one. That is to say that molecules with a chiral centre, and consequently non superimposable on their mirror images, will appear as two optically active enantiomers

In other words, if one isomer looked in a mirror, what it would see is the other one. The two isomers (the original one and its mirror image) have a different spatial arrangement, and so can't be superimposed on each other.

If an achiral molecule (one with a plane of symmetry) looked in a mirror, you would always find that by rotating the image in space, you could make the two look identical. It would be possible to superimpose the original molecule and its mirror image. Except for the optical activity, enantiomers have exactly the same physical and chemical properties as long as they do are not interacting or reacting with other chiral species. To visualise this fact think of fitting any of your feet in a left shoe or better any of your hands in a left glove. Results are really different!!! TO FIND AN ASSYMMETRIC CARBON To find an asymmetric centre is very simple: just inspect if there are any two equal groups bonded to a C atom and repeat for all the atoms in the molecule. In drawings, chiral carbons are often marked with a star. Some examples follow: Butan-2-ol It's extremely important to draw the isomers correctly. Draw one of them using standard bond notation to show the 3-dimensional arrangement around the asymmetric carbon atom.

Notice that you don't literally draw the mirror images of all the letters and numbers! It is, however, quite useful to reverse large groups - look, for example, at the ethyl group at the top of the diagram. It doesn't matter in the least in what order you draw the four groups around the central carbon. As long as your mirror image is drawn accurately, you will automatically have drawn the two isomers. So which of these two isomers is (+) butan-2-ol and which is (-) butan-2-ol? There is no simple way of telling that. The way to do this goes far beyond the scope of the course

2-hydroxypropanoic acid (lactic acid) Once again the chiral centre is shown by a star.

The two enantiomers are:

2-aminopropanoic acid (alanine) This is typical of naturally-occurring amino acids. Structurally, it is just like the last example, except that the -OH group is replaced by -NH2

The two enantiomers are:

Only one of these isomers occurs naturally: the (+) form. You can't tell just by looking at the structures which this is. It has, however, been possible to work out which of these structures is which. Naturally occurring alanine is the right-hand structure, and the way the groups are arranged around the central carbon atom is known as an L- configuration. Notice the use of the capital L. The other configuration is known as D-. So you may well find alanine described as L-(+) alanine. That means that it has this particular structure and rotates the plane of polarisation clockwise. Even if you know that a different compound has an arrangement of groups similar to alanine, you still can't say which way it will rotate the plane of polarisation. The other amino acids, for example, have the same arrangement of groups as alanine does (all that changes is the CH3 group), but some are (+) forms and others are (-) forms. It's quite common for natural systems to only work with one of the enantiomers of an optically active substance. It isn't too difficult to see why that might be. Because the molecules have different spatial arrangements of their various groups, only one of them is likely to fit properly into the active sites on the enzymes they work with.

DIASTEREOMERS Diastereoisomers also known as diastereomers are stereoisomers that are not related as mirror images. They have different chemical and physical properties. Molecules possessing more than one chiral centre also exhibit diastereoisomerism because inverting one or more but not all of the centres, leads to structures which do not have a mirror image relationship with the original. Inversion of a single chiral centre gives a diastereomer of the original structure. Inversion of all chiral centres gives the enantiomer. The figure below shows the four isomers for 2,3-dibromobutane: the enantiomers above are diastereomers to the second enantiomeric pair.

Molecular symmetry may reduce the number of enantiomeric pairs Cis-trans isomers are a case of enantiomeric pairs: two configurational isomers that are not mirror images to each other.

PROBLEMS 1The diagram shows a plant view (seen from above) of the six polycentric (delocalised) π molecular orbitals of benzene, their energies increasing from bottom to top. The two colours mean that the orbital functions change sign. Below the C – ring’s plane a symmetric figure would appear. aHow many p electrons are involved in the bond? bA nodal plane is a plane at which the functions change sign. Trace the nodal planes (other than the plane of the paper) for all six orbitals.

cAccording to your work is there any relationship between energy and nodal planes? dWhich orbitals are bonding and which are not bonding? eAccommodate the electrons in the orbitals f2Draw a diagram similar to the one that appears in page 2 (see right) showing the relative energies for the four molecular orbitals (bonding and antibonding) that form between the C atoms in ethane. 3Does the rotational profile of 2,3-dichloroethane resemble that of ethane or butane? Explain your choice. 4Draw the following structures and decide whether they show or not geometric isomerism: propene 1-chloropropene 2-chloropropene 1,2-dichlorocyclopentene 5The table shows the boiling point of the B. point (°C) cis and trans isomers of 1,2-dichloroethene. Explain isomer the figures considering the relative electronegativity cis 60 of chlorine and carbon

abcd-

trans

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6-

How can you tell if an unknown sample is optically active?

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Use wedges, dotted lines etc. to draw the configuration of both enantiomers of abc-

2-aminobutane propane-1,2-diol 2-chloropropanal

8The figure shows two molecules (geranial and neral). a- Suggest a reason for the ending of both names. b- A challenge: write their systematic names c- Write their molecular formula d- What class of isomers are they? e- Could they have other isomers of the same kind? f- Are thy optically active? g- In case they are active mark the chiral centre.

9This other two molecules belong to the same family of natural products: the terpenes. a- Do you think there are any possibilities for cis trans isomerism in them? b- Are they optically active? In case they are mark the chiral carbon