W2L1: Non-Covalent Bonding and Resonance

Structure of an atom

• Protons are positively charged

• Neutrons have no charge

• Electrons are negatively charged

Atomic number = # of protons

Atomic number of carbon = 6

• Neutral carbon has six protons and six electrons

Isotope

Isotopes have the same atomic number but different mass numbers

What makes carbon so special

• Atoms to the left of carbon give up electrons

• Atoms to the right of carbon accept electrons

• Carbon shares electrons

Distribution of electrons in an atom

• The first shell is closest to the nucleus

• The closer the atomic orbital is to the nucleus, the lower its energy

• Within a shell, s < p

Aufbau principle

• An electron goes into the atomic orbital with the lowest energy

• Valence shell, lone pair

Pauli exclusion principle

No more than 2 electrons can be in an atomic orbital

Hund’s rule

An electron goes into an empty degenerate orbital rather than pairing up

Atoms on the left side of periodic table

Lose an electron

Atoms on the right side of the periodic table

Gain an electron

Hydrogen and electrons

Hydrogen can lose or gain an electron

Forming ionic bonds

An ionic bond is formed by the attraction between ions of opposite charge

Ionic bonds

• Ionic bonds normally form between atoms that have a big difference in their electronegativities

• No directionality - the attraction is purely electrostatic: any positive ion is attracted equally to any nearby negative ion, regardless of angle or orientation

Forming covalent bonds

Formed by sharing electrons

• Non polar covalent bond = bonded atoms are the same

• Polar covalent bond = bonded atoms are different

Electronegativity

The tendency of an atom in a molecule to attract electrons to it

Polar covalent bonds

A polar covalent bond is a covalent bond in which the electron pair is not shared equally between the 2 atoms

Neutral carbon forming bonds

Neutral carbon can form 4 bonds and it has a charge (or it is a radical)

Neutral nitrogen forming bonds

Neutral nitrogen forms 3 bonds

• If nitrogen does not form 3 bonds, it is charged

Neutral oxygen

Neutral oxygen forms 2 bonds

• Oxygen has 2 lone pairs

• If oxygen does not form 2 bonds it is charged

Non-covalent interactions

• Arises due to electrostatic interactions between molecules or atoms that are not bonded together (not sharing electrons via a covalent bond)

• Much weaker than a covalent bond but occurs very frequently

• Includes: Van der Waals interactions, hydrogen bonding, ionic interactions, hydrophobic effect

Van der Waals interactions

• A weak interaction due to fluctuating electrical charges between molecules

• Strength is strongly distance dependent - Van der Waals radius

Hydrogen bond

• A special type of dipole-dipole interaction between H and a non-bonding heteroatom (e.g. O or N)

• Stronger than van der Waals interactions, but weaker than covalent bonds

• Strongly dependent on geometry of atoms involves

Hydrogen bonds in proteins

• Backbone to backbone (pink): hydrogen bonds between atoms of two peptide bonds

• Backbone to side chain (yellow): hydrogen bonds between a peptide bond atom and an amino acid side chainSide chain to side chain (blue): hydrogen bonds between atoms of two amino acid side chains

• These bonds stabilize secondary and tertiary protein structures

Urea denaturation

• Purified protein isolated from cells → normally folded with correct hydrogen bonds

• Expose to high concentration of urea → protein becomes denatured (unfolded) because urea disrupts hydrogen bonds

• Remove urea → protein can refold into its original conformation (renaturation) because the sequence of amino acids (primary structure) contains all the information needed for correct folding

Urea can form hydrogen bonds with polar groups in the protein, competing with the protein’s internal hydrogen bonds and leading to unfolding.

• Urea denatures proteins by interfering with these hydrogen bonds, but removal of urea allows the protein to refold correctly

Electrostatic/Ionic interactions

• Occur between species that have full, permanent charges, e.g. cations and anions

• Stronger than other non-covalent interaction, but less common

• Some are pH dependent

• Particularly important in the binding between enzyme and substrate when the binding site has permanent charged side-chains

The ‘hydrophobic effect’

• Many organic/biological molecules are hydrophobic (water-hating) and tend to cluster together when place in water

• Try to minimise the number of hydrogen bonds lost in water molecule network

• Driving force for globular proteins and lipid bilayer formation

Comparison between non-covalent interactions

Resonance

• Resonance structures of a molecule or ion are two or more structures with identical arrangements of the atoms but different arrangements of the electrons

• The true structure of the molecule or ion is a resonance hybrid of the contributing resonance structures

Movement of electrons

• Curly arrows are used to represent electron movement in resonance structures and reactions

• Start at the initial position of electrons and end at their final destination

Conjugation

• 3 or more interacting p orbitals on adjacent atoms are known as conjugated

• If there is conjugation in a molecule, we can draw resonance structures

Benzene structure

Benzene is a very stable molecule (because of conjugation)

Aromaticity and aromatic compounds

• Cyclic groups or molecules

• All atoms on a planar ring and are sp2-hybridised

• The number of π electron in the ring equals to 4n+2 (n = 0, 1, 2...) - the Hückel rule

• Benzene and other aromatic compounds usually react in such a way as to preserve their aromatic structure

The resonance structures of amide

The amide is the functional group for peptides. The resonance ability of amide results in some key chemical and structural characters of peptides

• Neutral structure clearly favoured

• Delocalisation strengthens the C-N bond as it is partially a double bond

• Since the lone pair is being used, it can’t act as a base or nucleophile

• The O-C-N are all planar (sp2 hybridised)

• Peptide bond is rigid