Bonding and structure
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Delivery guides are designed to represent a body of knowledge about teaching a particular topic and contain:
- Curriculum Content: A clear outline of the content covered by the delivery guide;
- Thinking Conceptually: Expert guidance and activities on the key concepts involved, common difficulties learners may have, approaches to teaching that can help learners understand these concepts and how this topic links conceptually to other areas of the subject;
- Thinking Contextually: A range of guidance and suggested teaching activities using a variety of themes so that different activities can be selected which best suit particular classes, learning styles or teaching approaches.
Learners should be able to demonstrate and apply their knowledge and understanding of:
EL(i) chemical bonding in terms of electrostatic forces; simple electron ‘dot-and-cross’ diagrams to describe the electron arrangements in ions and covalent and dative covalent bonds
EL(j) the bonding in giant lattice (metallic, ionic, covalent network) and simple molecular structure types; the typical physical properties (melting point, solubility in water, electrical conductivity) characteristic of these structure types
EL(k) use of the electron pair repulsion principle, based on ‘dot-and-cross’ diagrams, to predict, explain and name the shapes of simple molecules (such as BeCl2, BF3, CH4, NH3, H2O and SF6) and ions (such as NH4+) with up to six outer pairs of electrons (any combination of bonding pairs and lone pairs); assigning bond angles to these structures
EL(l) structures of compounds that have a sodium chloride type lattice
DF(b) the bonding in organic compounds in terms of s- and p-bonds
DF(c) the relation of molecular shape to structural formulae and the use of wedges and dotted lines to represent 3-D shape
OZ(a) the term electronegativity; qualitative electronegativity trends in the periodic table; use of relative electronegativity values to predict bond polarity in a covalent bond; relation of overall polarity of a molecule to its shape and the polarity of its individual bonds
OZ(b) intermolecular bonds: instantaneous dipole–induced dipole bonds (including dependence on branching and chain length of organic molecules and Mr ), permanent dipole–permanent dipole bonds
OZ(c) intermolecular bonds: the formation of hydrogen bonds and description of hydrogen bonding, including in water and ice
OZ(d) the relative boiling points of substances in terms of intermolecular bonds
OZ(k) the characteristic properties of haloalkanes, comparing fluoro-, chloro-, bromo- and iodo-compounds, considering the following aspects:
(i) boiling points (depend on intermolecular bonds)
CI(j) the following aspects of nitrogen chemistry:
(i) bonding in nitrogen gas, ammonia and the ammonium ion
PL(b) the primary, secondary and tertiary structure of proteins; the role of intermolecular bonds in determining the secondary and tertiary structures, and hence the properties of proteins
PL(d) the significance of hydrogen bonding in the pairing of bases in DNA and in relation to the replication of genetic information; how DNA encodes for RNA which codes for an amino acid sequence in a protein
PL(e) molecular recognition (the structure and action of a given pharmacologically active material) in terms of:
(i) the pharmacophore and groups that modify it
(ii) its interaction with receptor sites
(iii) the ways that species interact in three dimensions (size, shape, bond formation, orientation)
DM(b) the term coordination number, the shapes and bond angles of complexes with coordination numbers 4 (square planar and tetrahedral) and 6 (octahedral)
CD(a) how some dyes attach themselves to fibres in terms of intermolecular bonds, ionic bonds and covalent bonding
CD(b) the structure of a dye molecule in terms of the chromophore and:
(ii) functional groups that affect the solubility of the dye
(iii) functional groups that allow the dye to bond to fibres
Approaches to teaching the content
The chemical ideas in the Chemistry B (Salters) specification are developed through a ‘spiral curriculum’. This means that chemical ideas are introduced at one stage, then re-visited and deepened in later modules. This is particularly true for the concepts relating to chemical bonding and structure, which are progressively introduced across a number of modules in the first year of the A Level course (or AS course). This gives learners time to assimilate and reflect on new ideas. The concepts are then applied within a number of contexts in the second year of the course, which provides opportunities for learners to become accustomed to applying core concepts in familiar and unfamiliar contexts, as well as deepening understanding.
The key idea that is central to all aspects of chemical bonding is that all bonds are examples of electrostatic attractions. This idea should act as a connecting ‘thread’ throughout all modules.
The basic ideas of structure and bonding
In the first module (Elements of life, EL) the basic ideas and language of structure and bonding are established to be built upon in later sections:
- dot-and-cross diagrams are used as a shorthand way of describing bonding in ions, simple covalent bonds and dative covalent bonds
- structure types are described for simple molecules and for metallic, ionic, and covalent network giant lattices
- the link is made between structure type and the physical properties of melting point, solubility in water and electrical conductivity.
Learners will probably have seen dot-and-cross diagrams at an earlier stage in their studies of chemistry. Dot-and-cross diagrams can be used as a starting point to ask:
- what holds ions together in an ionic compound
- what holds atoms together in a covalent molecule
which is a useful approach that emphasises the key idea about electrostatic attractions. Explicitly link dot-and-cross diagrams of ionic compounds to the concept of the ionic lattice to avoid the misconception of treating ionic compounds as if they are made up of separate ion pairs. Showing a model of a sodium chloride lattice and asking learners to draw a small section of it helps to reinforce the importance of the ionic lattice and the electrostatic attractions that occur within it.
Bonding in metals can often appear to learners as quite different from covalent or ionic bonding, since there is no apparent electron transfer or pairing. Ask learners to identify the electrostatic interactions within a metallic lattice; this helps them to appreciate that bonding in metals has key similarities with other types of bonding, making the overall picture much more coherent and easier to understand.
It is important that learners achieve a sound understanding about basic ideas of structure and bonding by the end of EL. A number of probes are available that will identify learner misconceptions and these provide a very good way of checking on learners’ ideas. Some teachers will be used to using assessment for learning techniques as a powerful way of supporting learners. Several good assessment for learning worksheets are available to help learn the basic ideas in structure and bonding.
The link between structure, bonding and physical properties – including melting point – is established in EL. A simple card matching activity can be used initially to connect structure types to physical properties. At this stage learners will be able to explain the differences in electrical conductivity of different structures in terms of charged particles, as well as the general differences in melting points between simple molecular and giant lattice structures. The link between structure type and property can then be used later in EL to explain the periodic trends in the melting points of elements in Periods 2 and 3 of the periodic table which provides evidence for the way in which elements are arranged in the table (see the Delivery Guide on Atomic structure, periodicity and inorganic chemistry for more information on this topic).
The description of covalent bonding introduced in EL is deepened in Developing fuels (DF) to include s- and p-bonds. p-bonds are particularly important when explaining reactions of alkenes in DF and aromatic compounds in Colour by design (CD). The general ideas about ionic, covalent and dative bonds are applied to the specific examples of nitrogen, ammonia and the ammonium ion in The chemical industry (CI).
The idea of s- and p-bonds will be new to learners but there are many internet resources that include appropriate diagrams to illustrate these bonds. Care should be taken when using molecular models for molecules such as ethene since they do not usually include a sigma bond when representing a double bond. Asking learners about the limitations of the model can be an effective way of reinforcing the difference between s- and p-bonds.
Shapes of molecules
The shapes of molecules illustrate how one aspect of the covalent bond is developed in later modules. In EL the electron pair repulsion principle builds on the dot-and-cross diagrams to predict the shapes and bond angles of molecules. In DF, the principle is applied specifically to organic structures, and the relation between molecular shape and structural formula. The use of solid and dashed wedge bonds is formally introduced in the specification at this point, though it could be introduced in the classroom earlier in the context of simple molecules in EL. The topic of shape and bond angle is revisited and developed further in the context of complex ions in Developing Metals (DM).
Twisting sausage shaped balloons together is a really effective and fun way of introducing shapes of molecules. Molecular models are also a great help in enabling learners to see the connection between 2-D and 3-D representations of molecules. For more complex organic structures a free molecular structure drawing package such as ‘ChemSketch’ is very useful. The basic tools in the software are easy to master and the programme can be used whenever structures of organic molecules are drawn throughout the course.
N.B. In application of the electron pair repulsion principle, learners are expected to apply ideas of bond angles being affected by the greater repulsion of lone pairs relative to bonding pairs.
In The ozone story (OZ) the concept of electronegativity is introduced to build on the EL idea of a simple covalent bond and extend the concept to include polar molecules. This is an essential step before intermolecular bonds are introduced.
Intermolecular bonds (OZ) are further examples of the electrostatic attractions introduced in EL. In this specification they are referred to as intermolecular bonds (rather than forces) to reinforce this key similarity to the ionic, covalent and metallic bonds already met in EL. A good progression is to start with instantaneous dipole–induced dipole bonds, move on to permanent dipole–permanent dipole bonds and then introduce hydrogen bonds as a special kind of permanent dipole–permanent dipole bond.
An experiment in which streams of liquid are deflected by a charged rod is a good way of introducing electronegativity and provides a gateway into the study of intermolecular bonds. Simple demonstrations such as freezing of a plastic bottle of water and floating a needle on water can be used to introduce hydrogen bonds. This can be followed by plotting the boiling points of Group 16 hydrides to illustrate the anomalous value for water. This activity can be followed by a class experiment to make the polymer ’slime’ which is always very popular.
A note on the term ‘Van der Waals’. This specification does not use the term Van der Waals bonding/forces to describe any form of intermolecular bonding. The term is used widely in textbooks and other materials; however, while the IUPAC definition for this term covers all dipole–dipole bonds, many sources use the term to describe only instantaneous dipole–induced dipole bonds. (IUPAC recognises the terms London forces and dispersion forces to specifically describe instantaneous dipole–induced dipole bonds.) Learners should be made aware of the term Van der Waals as they are likely to encounter it, however due to the potential for confusion we recommend encouraging learners to use the descriptive terms given in the specification so that there is no doubt which form(s) of intermolecular bonding they are referring to.
Intermolecular bonds are important in many areas of chemistry, and may be applied in understanding and explanation of macroscopic properties as well as interactions between molecules in a variety of contexts. It is important to bring out the key ideas about electrostatic attractions when describing the following:
- the relative boiling points of haloalkanes (OZ)
- the secondary and tertiary structures, and hence the properties, of proteins (Polymers and life, PL)
- the significance of hydrogen bonding in base pairing in DNA (PL)
- the way a pharmacophore interacts with receptor sites (PL)
- the way that dyes stick to fabrics (CD) (this can also involve covalent and ionic bonds).
The role of intermolecular bonds in one context can be usefully used as a starting point when moving on to their role in a new context. Revisiting ideas learners have met before is an excellent way of reinforcing learning.
The structure of DNA is quite complex and it helps if learners make a model of a short length of the molecule themselves. Many sets of instructions are readily available on the internet using cheap materials. Colleagues who teach biology may also have models of DNA. It is important to stress that although the DNA molecule is very large, the important feature that allows replication is the hydrogen bonds between base pairs.
It is helpful to draw out similarities between the interactions that hold the secondary and tertiary structures of proteins together and the similar interactions that bind dyes to fabrics. Learners are usually not very good at making such connections and need to be prompted to look for them. An experiment in which different fabrics take on different colours when placed into a dye bath containing several dyes is an excellent way of promoting discussion about these interactions.
Common misconceptions or difficulties learners may have
The octet rule
Formation of ionic and covalent bonds is often taught in terms of the ‘octet rule’. Unfortunately this rule can get in the way of a proper explanation of why bonds form. The octet rule is a rule of thumb description of what often happens when atoms form bonds with other atoms. However, it can easily move from being a description to become an explanation using anthropomorphic ideas such as atoms ‘wanting to gain or share electrons in order to achieve a full electron shell’. This makes learning an appropriate explanation in terms of electrostatic attractions between electrons and positive nuclei or between oppositely charged ions more difficult.
Dot-and-cross diagrams are often used to support the octet rule approach to covalent bonding. This can lead to the misconception that the act of sharing electrons is in itself sufficient to hold atoms together. Learners need to move from this position to an appreciation that it is electrostatic attractions that explain why the atoms do not move apart. They will certainly need the electrostatic model to make sense of the more sophisticated treatment of s- and p-bonds and to understand organic reaction mechanisms.
A strong belief in the octet rule can also mean that intermolecular bonds are not considered to be ‘real’ bonds since they do not involve the achievement of a full electron shell. This view may be reinforced by many textbooks that use the phrase ‘intermolecular forces’ rather than intermolecular bonds, as if they were describing something fundamentally different from ionic and covalent bonds instead of something fundamentally the same. An emphasis on all bonds as descriptions of electrostatic attractions can go a long way to minimise the impact of these misconceptions.
Ionic bonding is often first introduced to learners in terms of electron transfer between individual metal and non-metal atoms. This does not fairly reflect what actually happens for example when sodium atoms in a metallic lattice react with covalent molecules of chlorine. The misconception that may arise is to think of ionic compounds in terms of separate ion pairs rather than in terms of a 3-D ionic lattice. The ion pair view of ionic bonding may be reinforced by the way we use similar formulae such as CH4 and NaCl to represent substances in which the bonding is very different. Understanding of ionic bonds in terms of ion-pair-like ‘molecules’ can cause considerable problems in understanding ideas such as precipitation reactions and electrolysis.
Learners meet relatively few examples of covalent network structures and sometimes think that their high melting point and insolubility in water is due to particularly strong intermolecular bonds. They are applying the ideas with which they are most familiar to situations they know little about. Suitably worded questions can usually identify if this is the case.
Covalent vs ionic bonding
Some learners believe that all bonds are one or other of the two types: covalent or ionic. Polar bonds are accommodated under this view of bonding as simply a modified form of covalent bonding rather than a form of bonding intermediate between covalent and ionic in terms of electrostatic attractions. It is much easier to understand heterolytic bond fission if the bond is seen as polar in terms of electrostatic interactions with the electron pair pulled closer to one of the atoms, rather than as simply covalent with electrons shared.
In a similar way, learners may see dative bonds as simply covalent bonds with the only difference being that one atom supplies both electrons to be ‘shared’. In some texts these bonds are called dative covalent, which tends to reinforce this view. This approach can obscure the fact that dative bonds are often quite polar and have considerable ‘ionic’ character.
Many learners find describing how instantaneous dipole–induced dipole bonds form difficult and this point requires a very careful exposition to include:
- the electrons are continually moving in a molecule
- at times, more electrons are at one end of a molecule than at the other, causing a separation of charge (instantaneous dipole)
- this dipole induces another dipole in an adjacent molecule; the two dipoles attract.
Learners sometimes think that any hydrogen atom will form a hydrogen bond. This may have been reinforced if they have met hydrogen bonding in biology without any detailed explanation. Teachers should reinforce the need for the hydrogen to be bonded to a strongly electron-withdrawing atom to form a hydrogen bond.
A related issue also arises in learning how a pharmacologically active material interacts with receptor sites. Some learners have met the ‘lock and key’ analogy to describe how a substrate binds to the active site of an enzyme and stick with this shape-based idea instead of thinking about the electrostatic interactions involved. Providing learners with an example of a pharmacologically active molecule and a receptor site and asking them to suggest the electrostatic interactions that might arise is a good way of overcoming this problem. A similar approach can be used to suggest how dyes with given structures can bind to particular kinds of fabrics.
Conceptual links to other areas of the specification – useful ways to approach this topic to set learners up for topics later in the course.
Basic ideas about dative bonds are introduced in EL and it is worth returning to them when polar bonds are met in OZ. This prepares the way for describing the bonding between ligands and a central metal ion in transition metal complexes in DM.
Use of molecular models in EL helps secure a sound understanding of shapes of organic molecules in DF. This provides an essential starting point for the study of isomerism in organic compounds including structural isomerism (DF), cis–trans and E/Z isomerism (DF) and optical isomerism (PL). The basic ideas about shapes of molecules also provide a useful starting point for the discussion of the shape of the benzene molecule (CD).
A good understanding of p-bonds is essential for learners to fully understand how stereoisomerism arises in alkenes, in terms of lack of rotation about the C=C bond (DF). The concept of p-bonding is also applied in understanding the bonding in benzene (CD).
An electrostatic treatment of covalent bonds in EL is an ideal platform on which to build when the energetics of bond breaking and making is introduced in DF. If covalent bonds are seen in this way then understanding why bond breaking is an endothermic process becomes a much more logical idea. In a similar vein, an electrostatic treatment of ionic bonding in EL involving the formation of an ionic lattice helps learners appreciate what is meant by lattice enthalpy and enthalpy change of hydration of ions when they reach Oceans (O). Understanding that ionic solids and compounds with polar molecules are often soluble in polar solvents because the newly formed bonds are stronger than the bonds broken helps prepare the way for understanding how and why ionic compounds dissolve.
A number of aspects of bonding need to be brought together to make sense of organic reaction mechanisms. These are covered in DF (electrophilic addition), OZ (nucleophilic substitution) and CD (electrophilic substitution and nucleophilic addition). Mechanisms make use of the ideas about s- and p-bonds (DF) and polarity of bonds and molecules (OZ). Nucleophilic substitution and addition reactions also involve the formation of dative bonds introduced initially in EL. Comparing the role of dative bonds in ligands in inorganic chemistry and nucleophiles in organic chemistry helps learners achieve a coherent view of chemistry across topics.
The physical properties of halogens are a consequence of the intermolecular bonds between covalent molecules. This topic is covered in ES before intermolecular bonds are met in OZ. The treatment of these physical properties may therefore be descriptive in ES but an explanation can be provided in OZ after the necessary new ideas have been understood.
Ideas of the tertiary structure of proteins and interaction between pharmacophores and receptors are applied in the treatment of enzyme catalysis (PL), where learners must be able to explain characteristics of catalysis in terms of the three-dimensional active site of the enzyme. Show learners that enzyme–substrate interactions are equivalent to pharmacophore–receptor interactions, and encourage them to think of specificity and inhibition in terms of electrostatic interactions. Learners should also be able to link temperature- and pH-sensitivity of catalysis to changes to the tertiary structure as a result of disruptions to electrostatic bonding within the enzyme.
Basic ideas about bonding and structure arise in EL during a study of the molecules of life and salts in the sea.
The introduction of organic chemistry in DF occurs in the context of contributions chemists have made to the development of better fuels and requires an understanding of s- and p-bonds and the shape of simple molecules.
Ideas about polarity of bonds and intermolecular bonds are used in OZ to help explain the role of CFCs in destroying ozone in the atmosphere and the anomalous properties of water. Ideas about polarity are specifically applied to explain the relative reactivities of haloalkanes.
The structure and bonding in proteins and DNA is a central feature of PL which has a focus on the chemistry of biomolecules.
The DM storyline ends with a review of biologically important complexes such as haemoglobin and cis-platin which are examples of transition metal complexes.
In CD the shape and bonding in benzene is explored in the context of dyes. Ionic, covalent and intermolecular bonds are used in the same storyline to explain the structure and functionality of dyes.
The simple teacher demonstration of a plastic bottle of water splitting when it is frozen can be used to initiate discussions about the properties of water in various states. Alternatively, a video could be shown in class to show how water expands when it freezes. Examples of available videos include:
A time-lapse video of water freezing in a beaker. It is possible to see the water slowly ‘grow’ as it freezes.
A video giving a dramatic demonstration of what happens when water freezes in a closed container.
In this OCR activity learners plot a graph of boiling point against Mr for alkanes, ketones and alcohols. This paves the way to an understanding of instantaneous dipole–induced dipole bonding and how this is present in all molecules, the strength increasing with the Mr. The relative strengths of the three types of intermolecular bond can be seen from the graph.
This activity could be offered after intermolecular bonding has been introduced in OZ, but can also be used in What’s in a medicine (WM) when ketones and alcohols are introduced. This would be a useful way of reinforcing the concepts of intermolecular bonding in a new context.
Studying the temperature changes on mixing liquids is an excellent activity to help learners think of mixing and related phenomena (e.g. dissolving) in terms of breaking and making intermolecular bonds. This activity can be conducted after introduction of ideas about intermolecular bonds in OZ, but should also be used to reinforce concepts about energetics that were introduced in DF.
Learners mix together equal volumes of cyclohexane and ethanol, and observe any resulting temperature change using a thermometer.
Learners should observe a drop in temperature and through prompted discussion should be able to work out that there are stronger intermolecular bonds in ethanol than in cyclohexane, so the cyclohexane is forcing apart the ethanol molecules and there is a net breaking of bonds. This requires energy from the surroundings (the liquid mixture), so the temperature falls (i.e. this mixing is an endothermic process).
This exercise also provides a good opportunity to explore learners’ conceptual models of ‘mixing’.
Following this short practical, learners should be able to predict what temperature changes would occur if the following mixtures were made. (This should not be done as a practical as many of these liquids are toxic, harmful to the environment and difficult to dispose of safely. Some of the mixtures are said to be explosive once formed.)
|Liquid 1||Liquid 2||Result||Bonds broken||Bonds made|
|hexane||heptane||little temp. change||id–id||id–id|
|propan-1-ol||propan-2-ol||little temp. change||hydrogen bonds||hydrogen bonds|
|trichloromethane||propanone||temp. rise||pd–pd||stronger pd–pd|
NB: The hydrogen in trichloromethane is usually regarded as sufficiently polarised (by CCl3) to form a hydrogen bond with the ketone group in propanone.
The final example introduces the idea of bond polarisations cancelling in certain molecules (such as CCl4), meaning there are no overall dipoles. Other common examples are CO2 and BF3.
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