Energy. Entropy.

Molecular interactions

Learning Objectives
Energy, heat, work, enthalpy Spontaneous processes. Entropy

Free energy. Equilibrium constant

Noncovalent interactions Water and hydrophobic interactions

Energy
The normal activities of living organisms demand a constant
input of energy (Greek: en, in + ergon, work)

Thermodynamics (Greek: therme, heat + dynamis, power) studies

relationships between heat and other forms of energy

The First law of thermodynamics: the total amount of energy

in the universe is constant, although the form of the energy may change

In thermodynamics, a system is a part of the universe

(e.g. a cell), the rest of the universe is called surroundings

Enthalpy
The energy change of a system (U) is the difference between heat (Q) exchanged with the surroundings and the work (W) done by the system on the surroundings: U = Q - W Q = U + W Under constant pressure (P), the work is defined by the volume change (W = PV). Therefore, Q= U + PV Enthalpy (Greek: enthalpien, to warm in) H = Q = U + PV In most biochemical reactions, V is small and H = U

Spontaneous Process
A spontaneous process occurs without the input of energy (heat exchange, gas expansion) When the stopcock is opened, the gas molecules diffuse between the bulbs and eventually become distributed evenly, half in each bulb

Fig. 1-10

Entropy
Entropy (S) indicates the degree of randomness of a system S = kB ln W The Boltzmann constant kB= R/N (Gas constant / Avogardos number) W is the number of energetically equivalent ways of arranging the components of a system The second law of thermodynamics: spontaneous processes are characterized by an increase of the entropy in the universe For a spontaneous process under constant T S H / T

Free Energy
Free energy: G = H - TS Exergonic process: Endergonic process: When reaction A + B

Enthalpy vs Entropy vs Spontaneity - annd + = Spontaneous at all Temp - and - = Spontaneous only at low temp or whe + and + Spontaenous at high temp or when T is + and - = non spontaenous at all temp

Neither S nor H alone can be used to determine the spontaneity of a process The true criterion for spontaneity: H - T S < 0 G = H - T S G < 0 Spontaneous G > 0 Nonspontaneous
(at constant T and P)

C + D is at equilibrium, G = 0

[C ] [ D] RT ln [ A] [ B]

K eq

[C ] [ D] [ A] [ B]

G o / RT

G0 refers to a standard state (all components are at 1 M )

Cyclohexane Conformations

Cyclohexane Conformations

!"#$%&'%#%()*+#+&,&$-%$*%.&/0%1-1,*"23#/2%&/%#%1"#&)%1*/.*)4#$&*/5% !"#$%&'%#%()*+#+&,&$-%$*%.&/0%1-1,*"23#/2%&/%#%+*#$%1*/.*)4#$&*/5% 6*7%*.$2/%1-1,*"23#/2%$)#/'&$'%+2$722/%1"#)%1*/.*)4#$&*/'5%

The Boltzmann Equation

Relates probabilities of two states with their energies

p1 p2

exp (-E1/RT) exp (-E2/RT)

= exp [(E2-E1)/RT]

p1 - probability to find the system in state 1 p2 - probability to find the system in state 2 E1 - the energy of state 1 E2 - the energy of state 2 T - temperature Kalvin* R - the gas constant = 1.987 cal K-1 mol-1

E2

!"#$%&'()) E2-E1=3 kcal/mol; T= 300 K p1/p2 = e3/(0.001987300) e5 =2.7185 148

E1

The Arrhenius Equation

Relates a reaction rate with the energy barrier

k = A exp (-Ea/RT)
k A Ea R T the reaction rate coefficient (s-1) atomic vibration frequency ( 5.8 1012 s-1) the activation energy the gas constant temperature

Transition State

!"#$%&'*()

Ea

Ea, kcal/mol 3 9 12 17 25

k, s-1 3.9 1010 1.8 106 1.2 104 2.9 4.6 10-6

Event rotation around Csp3-Csp3 bond ion current via Ca2+ channel ion channel gating protein folding double bond isomerization

E2

E1
Reaction coordinate

Hydrogen Bonds
Donor Acceptor - + - + H-bonds can occur within a molecule and between molecules H-bonds determine: - Properties of water and ice - Interaction of water with solutes

>N-H . . . O=C< >N-H . . . O< >N-H . . . N -O-H . . . O=C -O-H . . . O< -O-H . . . N

- DNA base pairing

H-bonds influence: - Protein folding - Recognition of small molecules by biopolymers

Dipole-Dipole Interactions
Energy kJ/mol

R e p u l s i o n

At a short distance, nonbonded atoms synchronize their electron fluctuations yielding a weak attractive force London dispersion force

energy is negative at 2.4(x); because there is attraction -dipole/dipole interaction is the cause of the attraction for the hydrogen molecules -

Fig. 2-5
2.4 6.0
Distance,

- 0.15

CH3
H H

CH3
H H

Attraction CH3
H

CH3

CH3

CH3

Strong and Weak Bonds

Type of Bond Covalent Noncovalent Ionic Hydrogen bond Dipole-dipole London dispersion forces Example O-H C-C -COO- +H3N-OH O< >C=O >C=O Any two atoms Strength,kJ/mol 460 348 80 20 9 <1

Noncovalent bonds:
Stabilize 3-D structure of proteins and other biopolymers Enable molecules to recognize each other to accomplish integrated functions Are easily formed and broken providing flexibility to the biological interactions

Water
Water accounts for about 70% of the body weight Each water molecule is H-bonded to 3.4 neighbors and reorients every 10-12 s Almost all biochemical reactions occur in water In many biochemical reactions, water acts as an acid or base (donates or accepts a proton)
68+*/0&/9%+2$722/% 7#$2)%4*,21:,2'%

Fig. 2.6

Hydrophobic Interactions
Hydrophobic effect is the tendency of water to minimize its contacts with nonpolar molecules Thermodynamic changes (kJ/mol) for transferring hydrocarbons from water to benzene
Substance CH4 C2H6 H 11.7 9.2 - T S -22.6 -25.1 G -10.9 -15.9

Fig. 2-8

Water Molecules in Cages are Unhappy

Ordering of water molecules around a nonpolar solute is entropically unfavorable

Text

Released Water Molecules Are Happy

Text

Aggregation of nonpolar molecules (groups) in water minimizes the entropy loss of the system

pH
In pure water, one water molecule in 500 million is ionized H2 O H+ + OHKw = [H+][OH-] = 10-14 M2 pH = - log [H+]