Covalent and Non-covalent Bonding

Do atoms want a have complete outer valence shell?

Yes

Atoms with nearly empty or nearly complete shells tend to ionise easily to form salts. Is there energy gain in salt formation?

Yes, the energy gain from the electrostatic interaction of the charged species.

This is an example of salt formation - ionic bonding

What is salt formation also known as?

Ionic bonding

Example of Ionic Bonding

NaCl

What is a covalent bond?

A chemical bond that involves the sharing of pairs of electrons between atoms

Example of Covalent Bonding

H₂

• The 1s orbitals of both atoms merge into a single bond orbital that contains both electrons

What is the bond dissociation energy?

• When two atoms bond, their electrons and nuclei arrange into a lower-energy state, releasing energy.

• The bond dissociation energy is the energy required to break this bond and separate the atoms.

• It is a measure of bond strength:

  • Higher bond dissociation energy = stronger bond.

• For a pair of atoms, greater orbital overlap → stronger bond → higher bond dissociation energy.

Name 2 types of chemical covalent bonds:

• Sigma (σ) bonds

• Pi (π) bonds

Are sigma (σ) bonds strong?

• Strongest type of covalent chemical bond

How do sigma (σ) bonds form?

• Forms when atomic orbitals overlap in head on arrangement

Sigma (σ) bond in H₂

The 1s atomic orbitals overlapping to form the new sigma (σ) bonds, also known as a single bond

How do pi (π) bonds form?

Formed from overlap of two orbital lobes on one atom with two orbital lobes on another – in a lateral sense (side to side).

What do pi (π) bonds form with?

An existing sigma bond - thus they are double or triple bonds

Why does NH₃ have bond angles of 107° instead of 109.5° (tetrahedral)

The lone pair exerts a slightly greater repulsion than the sigma bonds, compressing the bond angle from 109.5° to 107°

Why is the bond angle for H₂O 104.5°?

There are 2 lone pairs on the O

What is a hydrogen bond?

A partially electrostatic attraction between a H which is bound to a more electronegative atom such as N, O, or F, and another adjacent atom bearing lone pair of electrons

Most electronegative atoms

N, O, F

Example of Hydrogen Bonding

How are hydrogen bonds described?

• Typically described as an electrostatic dipole-dipole interaction.

• The partial positive charge of the proton is attracted to the lone pair of electrons

Hydrogen bonds are generally regarded as primarily electrostatic, however they have some covalent nature. When we say hydrogen bonds have some covalent nature, it means what?

• A hydrogen bond is not purely electrostatic (attraction between charges).

• There is partial sharing of electrons between the hydrogen atom and the electronegative atom it is hydrogen-bonded to (e.g. O, N, or F).

How do hydrogen bonds have covalent nature?

• It has direction (not like ionic bonding)

• Produces bond distances that are shorter than would be expected from the sum of Van der Waals radii

In hydrogen bonds, the more electronegative the donor…

….the more covalent character is observed

Strength of Hydrogen Bonds

What does hydrogen bonding do in small molecules?

• Increases the melting point

• Increases the boiling point

• Increases the solubility

• Increases the viscosity

What are Van der Waal forces?

• Weak intermolecular attractions that act between all atoms and molecules.

• aka London forces

• Weakest type of intermolecular force

• Present in all molecules

• Strength increases with:

  • More electrons / larger atoms

  • Greater surface area

Where do Van der Waal forces arise from?

• Electrically neutral molecules may exhibit permanent electric dipoles

• A permanent dipole molecule and a non permanent dipole molecule

• Molecules with no permanent dipoles

1) Van der Waals forces

• Some electrically neutral molecules may exhibit permanent electric dipoles.

• For instance consider water – a bent molecule with a bond angle of around 105°.

• The oxygen atom is always somewhat negatively charged and the hydrogen atoms (side) somewhat positive

• These dipoles  have a tendency to align, and this results in a net attractive force.

• Note – this is a lot smaller than any H-bonding interaction present (e.g. in water).

2) Van der Waals forces

• Molecules with a permanent dipole may temporarily distort the electric charge in a nearby molecule (polar or non-polar).

• The extra attraction is between the permanent dipole and the ‘induced’ dipole on the nearby molecule.

3) Van der Waals forces

• Thirdly in molecules with no permanent dipole, temporarily, dipoles result from the random electron motion within the atoms.

• At any given time the centre of positive charge arising from the nucleus and the centre of negative charge arising from the electrons are unlikely to coincide.

• This leads to instantaneous, but short lived dipoles, even though over time the average polarisation is zero.

• The resulting instantaneous dipoles are too short lived to align with other molecules to give an attractive force, however they can induce polarization in adjacent molecules.

• These specific interactions (forces) are known as London forces, or dispersion forces.

What is pi stacking (π- π interactions)?

Pi stacking refers to attractive, noncovalent interactions between aromatic rings (which contain pi (π) bonds).

What are the 3 recognised arrangements of pi stacking (π- π interactions)?

Hydrophobic interactions

• Water features a relatively strong network of hydrogen bonds.

• In solution this network is dynamic (constantly changing).

• Non-polar molecules, such as hydrocarbon chains, cannot form hydrogen bonds, and thus attempts to mix result in breaking up of the h-bond network.

What is an amphiphile?

Molecules with both hydrophobic and hydrophilic domains

What will amphiphilic molecules form in water?

Micelles

• Hydrophilic heads outside

• Hydrophobic tails inside

Why are micelles biologically important?

• Proteins obviously contain residues (amino acids)

• Amino acids can have strongly hydrophobic elements, like glycine, alanine, valine, etc

• When the protein folds into its 3D shape, it is common to have the hydrophobic core compose of these residues

• Charged and polar residues can interact with the surrounding water molecules

• Minimizing the number of hydrophobic solvation sphere is the principle driving force behind the folding process

Primary structure of Protein

Refers to the sequence of amino acids in the polypeptide chain. The chain is held together by peptide bonds (formed from the acid group of one and the amine group of the other).

Secondary structure of Protein

Refers to highly regular sub-structures on the polypeptide backbone chain. Two main types are the α-helix and the β-sheet, and they are defined by patterns of hydrogen bonds between the main-chain peptide groups.

Tertiary structure of Protein

Refers to the overall three dimensional shape of the protein molecule. The α-helices and the β-sheets are folded into a compact globular structure. This is primarily driven by the non-specific hydrophobic interactions (the burial of the hydrophobic residues in the core, away from water). However further stability is also introduced by some specific tertiary interactions such as salt bridges, hydrogen bonds, the tight packing of side chains (van der Waals) and disulphide bonds.

Quaternary structure of Protein

Refers to assemblies of two or more individual polypeptide chains into one single functional unit (stabilized in a similar way to the tertiary structure).

The primary structure of a protein is reported starting at which end?

Amino terminal (N) end

Protein secondary structure - β-sheets

Protein secondary structure – α-helix

The carbonyl of residue n interacts with the amide proton of residue n+4.

Tertiary and Quaternary structure

• The hydrophobic effect is the primary driving force in protein folding – the hydrophobic residues are forced into core of the forming globular structure, while the hydrophilic residues remain at the surface.

• The gain in energy resulting from van der Waals forces in the hydrophobic regions is a big contributor to the stability of the folded protein.

• Additional factors are π-stacking, salt bridges and disulphide bonds.