Shapes and hybridization

Background

Two related topics that students seem to find difficult are ‘Shapes of simple molecules and ions” and’ Hybridization’. Shapes of simple molecules and ions is covered using VSEPR theory for 2, 3 and 4 pairs of electrons under sub-topic 4.3 - Covalent structures for Standard Level and extended to include 5 and 6 pairs in 14.1 at Higher Level. In addition shapes for sp, sp2 and sp3 hybridization are covered at Higher Level in 14.2. Because of the difficulty that students have with shapes of molecules and simple ions in exams I have addressed this on a separate page on VSEPR which analyses the causes of this problem with suggestions as to how to overcome them.

Typical questions for the core (SL and HL) include multiple choice questions such as: 

What is the shape of PCl3?

A. Trigonal planar
B. Trigonal pyramid
C. Tetrahedral
D. V-shaped (bent)

or questions involving bond angles such as:

Which of the molecules below have a bond angle of 109.5o or less?

I. NH3

II. CO2

III. CHCl3

A. I and II
B. I and III
C. II and III
D. I, II and III

Typical HL questions on hybridization include recognising the type of hybridization exhibited by different carbon atoms within the same molecule. For example:

Which types of hybridization are shown by the carbon atoms in CH2=CH-CH3?

I. sp

II. sp2

III. sp3

A. I and II
B. I and III
C. II and III
D. I, II and III

The problem with all of these questions and the many other similar ones each year is that they are rather dry and abstract. It can help students to understand shapes, bond angles and hybridization if they can see the importance of them in a concrete example they can relate to.

Example 1. How does penicillin kill bacteria?

In Section 37 of the data booklet the general structure of penicillins is given. You can either just use the general structure given or encourage students to search on the Internet to find the structures of specific penicillins. The first penicillin used was Penicillin G. The structure of Dicloxacillin, a penicillin used now, is:

Dicloxacillin

Both Penicillin G and Dicloxacillin contain a phenyl group (benzene ring). By using either the shapes of alkenes (three bonding pairs) for Standard Level (or the sp2 hybridization of the C atoms in benzene at Higher Level) students should be able to see that the expected bond angle of 120o accounts for the regular hexagonal ring of the phenyl group. The phenyl group is quite stable and is part of the R- group – i.e. it is not an integral part of what makes penicillin a good antibiotic. What is much more interesting is the four-membered ring containing the N atom. This is known as the beta-lactam ring and is present in all penicillins. Ask students to predict the bond angles for the three C atoms and the N atom in the ring. The C atom with the double bond to the O atom should be 120o and the other two carbon atoms and the N atom should all be 109.5o. Higher Level students should be asked to identify the types of hybridization on each of the atoms – three of them will be sp3 and the remaining C atom will be sp2 which will lead to the same bond angle predictions of 109.5o and 120o. However because there are only four atoms making up the ring the actual bond angles must all be close to 90o. This means that the ring is ‘strained’ so that the bonds are weaker and will break easily. This is the clue as to how penicillin works. The beta-lactam ring breaks and the resulting two parts (which resemble the structures of the amino acids cysteine and valine) can become covalently bonded to the enzyme that synthesizes the cell walls of a bacterium. This blocks its action so that the bacterium eventually dies. It might be worth mentioning that some bacteria have developed resistance by producing an enzyme called penicillinase which breaks down penicillin. Changing the R- group but retaining the beta-lactam group results in new structures of penicillin which are resistant to penicillinase and hence are effective antibiotics. However some bacteria (‘super bugs’) such as MRSA are now virtually resistant to all forms of penicillin.

Example 2. Relating 2-D data book structures to 3-D models

Get students to discuss the bond angles (and hybridization if they are Higher Level) for some of the relatively simple molecules and then get them to see if their answers match up with the 3-D models. A good example is paracetamol (acetaminophen).


2-D structure of paracetamol

Students should be able to deduce that the phenyl group is flat, the bond angle between the phenyl group and the hydrogen atom of the phenol oxygen atom should be about 105o, the H to N to C bond angle should be about 107o and the carbonyl bond angle 120o. All the carbon atoms are sp2 hybridized except the methyl carbon atom on the -CH3 group which is sp3 hybridized. The nitrogen and oxygen atoms will also both be sp3 hybridized.

In many ways these deductions appear easier to make when the 3-D model is used:


3-D model of paracetamol

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