L2 - Non covalent interactions

How strong are covalent bonds?

Strong

200 - 800 kJ/mol

What is a covalent bond?

Shared pair of electrons in the valence shell

How strong are non covalent bonds?

Weaker

Under 30 kJ/mol

What are non covalent bonds?

Based on unequal sharing of electrons between nuclei (polarised bonds and polar molecules)

Interaction between biomolecules and domains of biomolecules

What are intermolecular bonds?

Between biomolecules

What are intramolecular bonds?

Interactions between domains of biomolecules

What do noncovalent bonds determine?

Solubility in water

What is bond polarity to do with?

Different electronegativities of the elements

Put the most common elements in order of electronegativity

1. Flourine

2. Oxygen

3. Nitrogen

4. Sulfur and carbon

5. Hydrogen

What is an example of a non-polar covalent bond?

C - H

What is an example of a moderately polar bond?

S - H

What are some examples of polar bonds?

What do polar bonds have?

Partial ionic character

The electrons tend to be more on the side of the atom with a higher electronegativity

How are carbonyl groups polar?

How are amino groups polar?

How are hydroxyl groups polar?

What does the uneven distribution of charge turn the molecule into?

An electrical dipole

What makes a molecule a dipole?

If it has a net dipole movement which depends on the geometry of the molecule

Why do polar molecules have a high BP than apolar?

Partial positive and negative attract each other so more polar molecules have a higher boiling point than apolar molecules of the same size

What are the different type of noncovalent interactions?

• Dipole - dipole interactions and hydrogen bonds

• Charge - charge interactions (ion pairs)

• Van der Waals forces

• Hydrophobic interactions

What are the criteria for Hydrogen bonds to form?

• If H and H acceptor are 0.18 nm apart

• If all 3 atoms are aligned

Strength of the bond will decrease the further away from the ideal

How do hydrogen bonds form between water molecules?

How many other water molecules can 1 water molecule form hydrogen bonds with?

4

2 as donors

2 as acceptors

When are all 4 bonds in water realised?

When ice forms

Forming a hexagonal lattice

Why do all 4 bonds not form in water?

In liquid water, the molecules are too restless to align in the right way with 4 other molecules so they move about so hydrogen bonds are formed and broken all the time

How long do hydrogen bonds last in water?

Not longer than 10ps

How much energy is required to break a H bond?

20 kJ/mol

Why does ice have a lower density than water?

The hydrogen bonds wake the molecules space themselves further apart

What are the 2 main types of hydrogen donor in biomolecules?

• Amino group

• Hydroxyl group

What are the 3 main hydrogen acceptors?

What type of interaction is a hydrogen bond?

Dipole - dipole

(the most common one in biology)

Describe a hydrogen bond

H atom bonded to electronegative atom can hydrogen bond to another electronegative atom with lone pair electrons

How strong are hydrogen bonds?

30 kJ/mol

What are charge - charge interactions also known as?

Electrostatic interactions

What do electrostatic interactions occur between?

Opposite charges

Are electrostatic interactions stronger than H bonds?

Yes

How are electrostatic interactions different to other noncovalent interactions?

• Can extend over greater distances than other noncovalent

• Doesn’t depend on molecular geometry like H bonds

• Potentially strongest non-covalent interaction

What is a salt bridge / ion pair?

Charge- charge interaction between acidic and basic amino acids in proteins

What happens if salt bridges/ ion pairs are on the surface of proteins?

If they are on the surface of proteins the interaction is sometimes weakened by shielding or screening effect by water molecules that arrange themselves around the ionized groups

Ions in solution can also screen charged groups

Why are ion pairs stronger if they are buried in the hydrophobic interior of a protein?

There is no screening so bridge is much stronger than between solvent exposed ion pairs on the surface

More stable

What are Van der Waals forces?

Act between stable dipoles in polar molecules or inducible dipoles

eg permanent dipoles or inducible dipoles

How do VDW forces induce dipoles?

• Even completely non-polar bonds (eg C-H) are sometimes temporarily polarised because of random asymmetries in the distribution of electrons around the nuclei in a chemical bon

• If there is asymmetry in one place, it has a knock-on polarising effect on its neighbour - flickering back and forth quickly

If 2 carbonyl groups are stacked head to tail in the right orientation and right distance, what will there be?

attractive Van der Waal forces of about 10kJ/mol

Why do results in attractive forces between 2 atoms depend strongly on the distance between them?

When theyre too close, there is a repulsive force because negatively charged electron clouds repel each other - results in the curve

Trough = where Van der Waals attraction is greatest

What is the distance between the 2 atoms at the trough?

The sum of their Van der Waal radiis

How big are Van der Waals radiis?

0.12 - 0.19 nm

In large clusters of atoms tightly packed in biomolecules, what stabilises them?

A large number of Van der Waals interations stabilises the molecule

eg In DNA, the stacked base pairs are also held together by VDW forces

Why are VDW forces important?

These interactions add up to a quite significant contributing factor to macromolecular structures

What distances do VDW forces work?

At very short, optimal distance

Are VDW strong?

No much weaker than other dipole interactions but add up

Why can hydrophobic molecules not engage in hydrogen bond with water molecules?

Few or no polar bonds

What do hydrophobic molecules do when they dissolve?

They force the water molecules around them into a specific arrangement so the bulk water is free to form H bonds in all directions

By clustering the hydrophobic molecules, fewer water molecules are forced into a more ordered arrangement

Why is the right more favoured?

Increase in entropy

For every CH2 group of a hydrocarbon that is moved out of the water, __kJ/mol are gained in entropy

3

What is this gain in entropy enough to do?

It is enough to screen the hydrophobic group from interactions with water (huddling together with other hydrophobic molecules)

What are hydrophobic interactions?

Association of non-polar groups with most energy attributed to the exclusion of water

How strong are VDW?

0.4 - 4 kJ/mol

How strong are hydrophobic interactions?

3 - 10 kJ/mol

How strong are H bonds?

2 - 30 kJ/mol

How strong are electrostatic interactions?

40 - 200 kJ/mol