Lecture 4 - Covalent and non-covalent bonding

Question 1

Atoms want complete….

Answer 1

outer valence shells

Question 2

Hydrogen has one electron in it’s outer valence shell. It will either…

Answer 2

• lose it and become a proton
• share the electron to form a covalent bond

Question 3

Atoms with nearly empty or complete shells tend to…

Answer 3

ionise easily to form salts.

Question 4

Give an example of a salt and why/how it forms.

Answer 4

NaCl
- Chlorine has seven outer valence electrons. It will gain one electron to get a full shell.
- Sodium has one electron in its outer valence shell. It wants to lose the electron.
- Sodium and chlorine form a salt in this way.

Question 5

Basic definition of covalent bond

Answer 5

the electrostatic attraction between positively charged nuclei of the bonding atoms and the shared pair of negatively charged electrons.

Question 6

Explain covalent bonding in hydrogen.

Answer 6

Both hydrogen atoms have an unpaired electron in the 1s orbital. When the two atoms get close together the two 1s orbitals overlap and merge into a single bond orbital that contains both electrons.

Question 7

Two important points about covalent bonding

Answer 7

Electrons must have opposite spins and each electron is able to exist in any part of the bond orbital and so belongs to both atomic nuclei.

Question 8

Explain why the formation of a bond is accompanied by excess energy release and therefore what bond dissociation energy is

Answer 8

The molecule formed is at a lower energy than two atoms on their own. Therefore, the formation of a bond is accompanied by excess energy being released. To break the bond, the energy must be put back in- this is the bond dissociation energy (a measure of how strong the bond is)

Question 9

How does orbital overlap effect strength of bond?

Answer 9

greater overlap of orbitals= stronger bond

Question 10

What is a sigma bond?

Answer 10

• single bond
• strongest type of covalent bond
• orbitals overlap head on.

Question 11

Give an example of S-S sigma bonds and the shape you would get.

Answer 11

• The simplest example is in dihydrogen. Two 1s atomic orbitals- one from each hydrogen atom will overlap to form a sigma bond. A single bond.
• The new molecular orbital in H2 (sigma s-s) has a shape that you would get from merging two s orbitals- sausage shaped

see notes

Question 12

Sigma bonds can also form with an s and a p orbital. Draw this. Explain the shape of the sigma s-p orbital formed. What is the smaller lobe involved in?

Answer 12

The new molecular orbital formed has two lobes- one is much larger than the other. The smaller lobe is involved in substitution reactions.

Question 13

Sigma bonds can also form with an s and an sp orbital. Draw this and describe the shape of the new sigma s-sp hybrid molecular orbital formed. What is the smaller lobe used for?

Answer 13

The new molecular orbital- sigma s-sp hybrid has two lobes. One lobe is bigger than the other. The smaller lobe is involved in substitution reactions.

Question 14

What is a Pi bond?

Answer 14

• Covalent bonds formed from the sideways overlap of two p orbital lobes on one atom with two p orbital lobes on another

Question 15

The node between the lobes in a p orbital have no electron density. What is the effect of this?

Answer 15

In a pi bond when the two p orbitals overlap there is a plane between the molecular orbitals with no electron density.

Question 16

Pi bonds form with an existing sigma bond. What is the result of this?

Answer 16

double/triple bond is formed

Question 17

Why is a Pi bond weaker than a sigma bond?

Answer 17

There is less of an overlap between p orbitals in a pi bond because of their parallel orientation, in contrast to sigma bonds where the bond is formed by the head on overlap of orbitals.

Question 18

Lone pairs of electrons affect the shape of molecules. Explain this concept using ammonia an example (refer to hybridization)

Answer 18

• For nitrogen to form ammonia it is hybridized. Creates four sp3 hybrid orbitals. Three of the orbitals are filled with paired electrons. The fourth is home to two unpaired electrons- a lone pair of electrons. The lone pair behaves like a bond. The ammonia molecule adopts a tetrahedral shape- one arm is occupied by the lone pair. The result of this is a molecule shaped like a pyramid. The lone pair has a stronger repulsion than the sigma bonds which compresses the bond angle to 107. Reduces the bond angle by 2.5

Question 19

What is a hydrogen bond?

Answer 19

A hydrogen bond is a partially electrostatic attraction between a hydrogen which is bonded to a more electronegative atom (hydrogen bond donor) and another atom with a lone pair of electrons (hydrogen bond acceptor)

Question 20

What does the strength of the hydrogen bond depend upon?

Answer 20

the environments and geometries of the donor and acceptor atoms.

Question 21

Hydrogen bonds do have some covalent nature. Explain

Answer 21

• they have direction
• bond distances are shorter than would be expected of van der waals.

Question 22

In hydrogen bonds, the more electronegative the donor….

Answer 22

the more covalent the nature of the bond.

Question 23

Hydrogen bonds increase…

Answer 23

• melting points
• boiling points
• solubility
• viscosity

Question 24

What is the hydrogen bond donator?

Answer 24

The atom covalently bonded to hydrogen

Question 25

What is the hydrogen bond acceptor?

Answer 25

Electronegative atom with lone pair of electrons not covalently bonded to hydrogen

Question 26

• where are the hydrogen bond donors in this molecule?
• where are the hydrogen bond acceptors?
• Why are some of the nitrogen NOT hydrogen bond acceptors?

Answer 26

• N-H bond - bond donors
• oxygen, fluorine are hydrogen bond acceptors.
• The nitrogen are not H bond acceptors because the their lone pair is not available due to the mesomeric effect.

Question 27

Why is solid ice less dense than liquid water?

Answer 27

The network of hydrogen bonds in ice keep the water molecules apart. Makes it less dense.

Question 28

What are Van der Waals forces?

Answer 28

Really weak forces found between gaseous molecules and almost all liquids and solids. The forces attract neutral molecules together.

Question 29

Three ways Van der Waals forces arise….

Answer 29

1. permanent dipole-dipole interactions
2. molecules with a permanent dipole can distort the electric charge/induce a dipole in a nearby molecule. These will then attract.
3. London forces/dispersion forces- electrons move around atoms randomly. At any given time there may be more electrons on one side of the atom than the other. This leads to an instantaneous dipole. The instantaneous dipole can induce polarization in adjacent molecules.

Question 30

Hydrophobic interactions refers to…

Answer 30

segregation of water and non-polar substances.

Question 31

What is an amphiphile?

Answer 31

both hydrophobic and hydrophilic domains. E.g. detergents.

Question 32

How does a micelle form?

Answer 32

• Amphiphilic molecules form micelles in water.
• They arrange in such a way that the hydrophilic head unit is found on the outside and the hydrophobic tails face inside.

Question 33

Proteins will contain amino acids with hydrophobic elements. What is the effect of this?

Answer 33

• Proteins will contain amino aids with hydrophobic elements. As a result when proteins fold into 3D shapes it is common to have a hydrophobic core composed of these amino acids.
• Charged and polar amino acids that can interact with water molecules are found on the outside. Hydrophobic side chains will face inside. This effects folding.

Question 34

Primary structure of a protein

Answer 34

Polypeptide chain made up of amino acids held together by covalent peptide bonds.

Question 35

Secondary structure of protein

Answer 35

Alpha helix and beta pleated sheet. Formed as a result of patterns of hydrogen bonds between polypeptide chain.

Question 36

Tertiary structure of protein

Answer 36

3D shape of the molecule. Alpha helix and beta sheet are folded. Mainly due to hydrophobic interactions but also as a result of ionic, hydrogen bonding and disulphide bridges

Question 37

Quaternary structure of protein

Answer 37

two or more polypeptide chains assembled to form one unit.

Question 38

Beta pleated sheet

Answer 38

• Hydrogen bonds form between partially negatively charged oxygen atoms in the carboxyl group (hydrogen bond acceptor) and partially positively charged hydrogen in the amine group (hydrogen bond donors)
• The result= beta pleated sheet.

Question 39

Alpha helix

Answer 39

The partially negatively charged oxygen atom in the carboxyl group forms a hydrogen bond with the hydrogen atom bonded to the nitrogen in the amine group four residue along the polypeptide chain. The result is an alpha helix