Lecture 4: Covalent and non-covalent bonding

How do atoms with nearly empty/nearly full shells interact together?

ionise easily to form salts

• energy gain is from the electrostatic interaction between charged species

• ionic bonding

what is ionic bonding

Strong electrostatic force of attraction between oppositely charged ions

structure of ionic lattices and why is it stable?

regular arrangements with each positively charged ion surrounded by a negatively charged ion

• stability comes from electrostatic forces of attraction

what is covalent bonding?

a shared pair of electrons between atoms to have a full outer shell(valency)

• the orbitals of 2 atoms overlap to form a sigma bond

• paired

what is bond dissociation energy?

• formation of the bond releases energy. Energy required to break the bond = bond dissociation energy (higher = stronger bond)

• The greater the orbital overlap, the stronger the bond

what are sigma bonds?

strongest type of covalent bond

• form when atomic orbitals overlap

• e- can be found anythwere in the orbital as electron density

what are pi bonds?

covalent bonds which form due to overlap of 2 orbitals laterally

• the node between the lobes has no electron density

• the plane has no electron density

why are pi bonds weaker than sigma bonds?

due to less overlap between orbitals due to parallel orientation

what does restricted rotation in pi bonds allow?

stereoisomerism

what are lone pairs on molcules seen as

they take up an orbital e.g.

• oxygen is a tetrahedral sp3 shape due to 2 lone pairs

• ammonia is a tetrahedral sp3 shape due to one lone pair

what does the lone pair do?

Lone pair generates more repulsion and reduces the bond angle by 2.5

what is electronegativity?

the ability of an atom to attract a pair of electrons towards itself in a covalent bond

what are the most electronegative elements?

F, O, N

what does delta plus delta minus acc mean?

in a bond, an electronegative atom pulls the bond more towards itself, its not shared evenly

what is hydrogen bonding?

electrostatic force of attaction between a hydrogen bound to an electronegative element (O,N,F) which is bound to an adjacent atom w lone pairs of electrons

lone pairs are Hydrogen bond __________

acceptors

what are VDWs?

large differences in electronegativity which result in permanent dipoles

• weaker than H bonding

• can induce dipoles in neighbouring molecules

what is pi stacking?

non-covalent interactions between aromatic rings in large molecules e.g proteins

what are the different types of pi stacking?

• sandwich(opposite rings)

• T-shaped( one perpendicular to another, 90 degrees)

• parallel displaced

what are amphiphiles?

molecules containing hydrophilic and hydrophobic regions

how do amphiphilic molecules work as micelles?

hydrophilic regions are facing the water and the hydrophobic regions are tucked away inside form the water. it allows transport of oils etc

what is the primary protein structure?

a sequence of AA joined together by peptide bonds

what is the secondary protein structure?

defined by hydrogen bonding patterns. Alpha helix and Beta sheets

what is the tertiary protein structure

the sheets further bond, the 3d globular structure

• involves hydrophobic interactions, salt bridges, hydrigen bonding, disulphide bridges

what is the quaternary structure

2 or more polypeptide chains combining into one functional protein

how do biomolecules fold(protein)

through various interactions, such as hydrophobic interactions and hydrogen bonding.