Lecture 3

Question 1

What are electrostatic interactions?

Answer 1

transient electrostatic interactions between opposite charges
(sometimes called salt bridge)
e.g. side chains with charges (+ and -) may form electrostatic interactions

Question 2

How to increase electrostatic interaction?

Answer 2

Increase magnitude of charges, decrease distance between charges, decrease dielectric constant

Question 3

What are van der Waal forces?

Answer 3

include all intermolecular forces that act between electrically neutral molecules (so technically they include H-bonds)

exist because every atom has an electron cloud that fluctuates, yielding a transient electric dipole – the dipoles of one atom can influence the electron distribution in another, inducing a transient dipole in that atom

Question 4

Describe london dispersion forces

Answer 4

Nonpolar groups polarize electrons in neighbouring group; very weak & transient, fall off with distance

e.g. Ch3 - H3C

Question 5

Describe dipole-induced dipole interaction

Answer 5

a molecule w/permanent dipole inducing dipole in neighbouring group

e.g. C=O - H3C

Question 6

Describe permanent dipoles

Answer 6

polar molecules interacting with another polar molecule

C=O - C=O

Question 7

Describe hydrophobic interactions

Answer 7

Consequence of nrg needed to insert a non polar molecule into water (H-bonds in water must be broken to insert non polar molecule)

Question 8

What bonds do non polar molecules form in water and with what?

Answer 8

van der Waal interactions with other non polar molecules

Question 9

What are clathrates

Answer 9

cage-like structure water molecules form around non polar molecules

Question 10

are clathrates thermodynamically favourable?

Answer 10

no

Question 11

when non polar molecules spontaneously aggregate in aq sln, is that favourable?

Answer 11

yes reduces # of water molecules in ordered clatherate structures inc entropy of system

Question 12

Is folded protein thermodynamically favourable

Answer 12

yes, less ordered req for water molecules to solubilize protein

Question 13

Is Keq fixed at constant temperature or concentrations?

Answer 13

Keq fixed at constant temps

Question 14

What is the keq of water?

Answer 14

keq= [H+][OH-]/[H20]
[H+] = 10-7 M 
[OH-] = 10-7 M
[H2O] is 55.5 M
Keq = 1.8 x 10-16 M

Question 15

Kw of water?

Answer 15

10^-14 M^2

Question 16

When does Kw change?

Answer 16

NEVER

Question 17

What is the henderson-hasselbalch eqn?

Answer 17

pH = pka + log[A-]/[HA]

Question 18

What is the titration midpoint?

Answer 18

Buffer zone, where pH = pKa

Question 19

Characteristics of covalent bonds

Answer 19

• strong and short
• most stable
• formed by sharing of electrons between atoms
• holds atoms together in molecule (intramolecular)

Question 20

Characteristics of non-covalent bonds? Examples

Answer 20

• weaker, reversible bonds
• distances between atoms are greater than in covalent bonds
• intramolecular and intermolecular
• examples include hydrogen bonds, electrostatic interactions, van der Waal interaction (dipoles, dispersion forces), hydrophobic interaction

Question 21

How do hydrogen bonds form? Characteristics?

Answer 21

• between H atom covalently attached to an electronegative atom (donor) and lone pair of 2nd electronegative atom (acceptor)
• strongest of weak non-covalent bonds
• has directional property (won’t form if not properly oriented)
• “partially covalent bond:

Question 22

Why does water have a very high melting point, boiling point & heat of vaporization compared to other solvents?

Answer 22

Due to hydrogen bonding, which holds the molecules together & requires significant energy to break

Question 23

Why is water a good solvent

Answer 23

Water hydrates ions by electrostatic interactions

• its partial negatively charged oxygen interacts with positively charged ions, its partial positively charged hydrogens interact with negatively charged ions
• forms hydration spheres around ions, proteins, macromolecules

Question 24

Ability of water to surround ions in electrostatic interactions and diminish their attraction to one another is a measure of?

Answer 24

The dielectric constant

- the greater the dielectric constant of a solvent, the lower the force between 2 charges in that solvent

Question 25

Electrostatic interactions are sometimes called

Answer 25

Salt bridge

Question 26

How to calculate electrostatic interactions? Units?

Answer 26

Use Coulomb's law:
E= (k) q1 x q2 / D x r
E = energy of interaction
k = proportionality constant
q1 and q2 = charge on each species
D = Dielectric constant
R = distance between the charges 
- kcal/mol

Question 27

Why does van der Waal forces (dipole interactions exist)?

Answer 27

Every atom has an electron cloud that fluctuates fielding a transient electric dipole
- the dipole of one atom can influence the electron distribution in another, inducing a transient dipole in that atom

Question 28

What are the 3 dipole interactions (van der Waal interactions)

Answer 28

• Permanent dipole; polar molecules attracted to weakly w/negative or positive poles of another molecule e.g. H2O
• Dipole-induced dipole; permanent dipole can induce dipole in neighbouring group e.g. C=O and CH3
• London dispersion forces; non polar groups polarize electrons in neighbouring group due to rapid fluctuation of electrons e.g. CH3 and CH3

Question 29

What is the van der Waal contact distance

Answer 29

at this distance the attractive forces are highest - if the atoms get
closer than this optimal distance they will repel each other due to overlap btwn their electron clouds

Question 30

What are clathrates?

Answer 30

Cage-like structures that form from dissolving non-polar molecules in water requiring organization of water molecules which surround them

Question 31

Are clathrates favourable? Why or why not

Answer 31

• No this ordered arrangement of water molecules around each hydrophobic molecule is
  thermodynamically unfavorable - when the
  hydrophobic molecules associate with each other, this liberates part of the hydration shell, increasing the entropy (disorder) of the system, which is thermodynamically favorable

Question 32

What causes hydrophobic interactions

Answer 32

• Consequence of non-polar molecules in an aq environment

Question 33

Why do non polar molecules spontaneously aggregate in aq solution

Answer 33

• Reduces # of water molecules in clathrates thus inc entropy of system, is thermodynamically favourable

Question 34

How is protein folding driven by the hydrophobic effect?

Answer 34

In an unfolded protein nonpolar or “hydrophobic” regions are exposed to water, which must organize itself around these regions. In a folded protein hydrophobic regions often associate with each other and are thus shielded from the aqueous solvent.
This means that less order is required for the water molecules to solubilize the protein, which is more favorable energetically