1 intermolecular interactions

monomer of proteins?

amino acids

monomer of nucleic acids?

nucleotides

monomer of carbohydrates?

monosaccharides

equation linking enthalpy and entropy

ΔG = ΔH - TΔS

what do charge-charge interactions require

the presence of two ionisable groups

pH of living systems

approx 7.4

structure of amino acids in living systems at acidic, neutral and basic pH

show how phosphate-containing compounds are charged at neutral pH

show how the energy of an interaction varies with distance

what are the terms

how does ε vary with solvent

represent the dipole on this molecule both in terms of δ and arrow

show 2 examples of quadrupoles

what is a hydrogen bond

a hydrogen atom bridges the gap between two N or O atoms

bonding of the hydrogen atom in a hydrogen bond

formally bonded to the donor atom but much closer to the 2nd atom (acceptor atom) than normal

how close is the hydrogen atom to the acceptor atom

within the van der Waal radius

show an H bond between a secondary amine group and a carbonyl group

label donor/acceptor and show partial charges

show 4 possible H bonding interactions between -NH₂ and -OH

which is strongest/weakest?

what are the 2 factors contributing to van der Waals interactions? show a diagram for each

show on an energy vs distance graph

• the force response curve for van der Waals interactions

• the graphs for repulsive forces and attractive forces separately

what equation represents this graph (red) and each of the repulsive and attractive sections

how significant are vdW forces

effect of changes in packing?

individual interaction energies are very small but collectively they can make a substantial contribution to interaction

a small change in packing can have a substantial effect

ideal binding interaction

maximal shape complementarity between the two binding partners so that the attractive interactions are maximised

dominant intermolecular force?

h bonding

dominant intermolecular force?

vdW only

dominant intermolecular force?

charge-charge interaction

dominant intermolecular force?

dipole-dipole

rank the 4 intermolecular forces in order of least to most strong

favourable or unfavourable?

+ and +, not favoured

favourable or unfavourable?

name + type of interaction?

favourable (+ and -) - offset, face to face

π-stacking interaction - type of quadrupole interaction

favourable or unfavourable?

describe

- and -, not favoured

face to face interaction

favourable or unfavourable?

describe

favoured, + and +

T shaped, edge to face

favourable or unfavourable?

not favoured - + and +

effect of substituting with EDG on quadrupole interactions

increases the quadrupole moment/strength of the interaction

what is a cation-π interaction?

charge-quadrupole interaction

dependence of cation-π interactions on distance

1/r³ dependence

show the cation-π interaction between -N⁺H₃ and benzene

positive charge interacts with the concentration of negative charge above or below the plane of the ring

why might water as a solvent change the favourability of intermolecular interactions

hydrogen bonding with water can be as strong as hydrogen bonding between an acceptor and donor

?

enthalpy in this situation

no enthalpic penalty for lost interactions in these cases - same number of total H bonds as water is H bonding to itself anyway

explain the hydrophobic effect using cyclohexane (include diagram)

• cyclohexane cannot form H bonds with water - only vdW

• for all the water molecules to form H bonds high order is needed so they form constrained networks around each molecule of hydrophobic cyclohexane

• this is very entropically unfavourable

what does the hydrophobic effect refer to

how can this provide a driving force

refers to ‘hydrophobic’ portions of molecules packing together favourably - as water is immiscible with hydrophobic portions

release of water molecules into bulk solvent is a major entropic driving force for many interactions

what is ΔG for a biomolecular interaction

the sum of all the charges in binding interactions

what is ΔG_binding a sum of? (7)

group the components into 4 sections

what is ΔG_{rotation/translation}?

mostly an entropy penalty for bringing two molecules together to form a complex

what is ΔG_conformation?

mostly an entropy penalty for restricting conformational flexibility