lecture 2 - noncovalent interactions with water

order of polarity from least to most

H < C=S << N < O < (F)

moderately polar bond

S-Hmos

most polar bonds and groups

• O-H

• C-O

• carbonyl, amino, hydroxyl

what does the dipole depend on

• net dipole moment of partial charges

• geometry of molecule

most common non covalent bond

hydrogen bond

hydrogen donor

O or N directly bonded to the hydrogen forming hydrogen bond

hydrogen acceptor

non-covalently bonded N or O

length of hydrogen bond

double that of the covalent bond

arrangement in ice

• hexagonal

• 4 alignments of hydrogen bonds

• lower density

• larger spatial arrangement

hydrogen donor example groups

• amino

• hydroxyl

hydrogen acceptor example groups

amide

carbonyl

ion salt bridge characteristics

• stronger than H

• extend over greater distance

salt bridges when on surface

weakened by water molecules

salt bridges when deep in protein

• stronger

• more stable

example of permanent dipole van der waals

two carbonyls head to rail

relationship between distance and strength of the van der waals

• closer the stronger

• too close creates repulsion

macromolecular illustration of van der waals

• many van der waals in DNA

• provides strength

hydrophobic interactions

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

entropy and hydrophobic interactions

• increased entropy

• makes interactions more favourable