Energy. Entropy.

Molecular interactions

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

• Free energy. Equilibrium constant
• Noncovalent interactions • Water and hydrophobic interactions

in + ergon. a system is a part of the universe (e. the rest of the universe is called surroundings . 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. work) • Thermodynamics (Greek: therme.g.Energy • The normal activities of living organisms demand a constant input of energy (Greek: en. although the form of the energy may change • In thermodynamics. heat + dynamis. a cell).

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

Spontaneous Process • A spontaneous process occurs without the input of energy (heat exchange. half in each bulb Fig. 1-10 . gas expansion) When the stopcock is opened. the gas molecules diffuse between the bulbs and eventually become distributed evenly.

Entropy • Entropy (S) indicates the degree of randomness of a system S = kB ln W • The Boltzmann constant kB= R/N (Gas  constant  /  Avogardo’s  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 Δ  S Δ  H / T .

Δ  G = 0 G G 0 [C ] [ D] RT ln [ A] [ B] K eq [C ] [ D] [ A] [ B] e G o / RT Δ  G0 refers to a standard state (all components are at 1 M ) .and .TΔ  S Δ  G < 0 Spontaneous Δ  G > 0 Nonspontaneous (at constant T and P) C + D is at equilibrium.= Spontaneous only at low temp or whe + and + Spontaenous at high temp or when T is + and .= non spontaenous at all temp • Neither Δ  S nor Δ  H alone can be used to determine the spontaneity of a process • The true criterion for spontaneity: Δ  H .annd + = Spontaneous at all Temp .TΔ  S < 0 Δ  G =  Δ  H .Free Energy • Free energy: G = H .TS Exergonic process: Endergonic process: • When reaction A + B Enthalpy vs Entropy vs Spontaneity .

Cyclohexane Conformations .

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

the gas constant = 1.probability to find the system in state 1 p2 .temperature Kalvin* R .7185 148 E1 .The Boltzmann Equation Relates probabilities of two states with their energies p1 p2 = exp (-E1/RT) exp (-E2/RT) = exp [(E2-E1)/RT] p1 .001987·300) e5 =2.the energy of state 2 T . T= 300 K p1/p2 = e3/(0.probability to find the system in state 2 E1 .the energy of state 1 E2 .987 cal K-1 mol-1 E2 !"#$%&'()) E2-E1=3 kcal/mol.

9 4.9 •  1010 1. kcal/mol 3 9 12 17 25 k. s-1 3.8 •  106 1.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.2 •  104 2.6 • 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 .

+ . N . O< >N-H . O=C -O-H . . .Interaction of water with solutes >N-H .Recognition of small molecules by biopolymers . O=C< >N-H . . . N -O-H . .Properties of water and ice . . .Protein folding .+ • H-bonds can occur within a molecule and between molecules • H-bonds determine: . . . O< -O-H . .DNA base pairing • H-bonds influence: .Hydrogen Bonds Donor Acceptor . . .

nonbonded atoms synchronize their electron fluctuations yielding a weak attractive force – London dispersion force energy is negative at 2.Dipole-Dipole Interactions Energy kJ/mol R e p u l s i o n At a short distance.4 6. 2-5 2.0 Distance.0. because there is attraction -dipole/dipole interaction is the cause of the attraction for the hydrogen molecules - Fig. Å .4(x).15 CH3 H H CH3 H H Attraction CH3 H CH3 CH3 H CH3 .

· · · +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 .Strong and Weak Bonds Type of Bond Covalent Noncovalent Ionic Hydrogen bond Dipole-dipole London dispersion forces Example O-H C-C -COO.

water acts as an acid or base (donates or accepts a proton) 68+*/0&/9%+2$722/% 7#$2)%4*.21:.4 neighbors and reorients every 10-12 s • Almost all biochemical reactions occur in water • In many biochemical reactions. 2.6 .2'% Fig.Water • Water accounts for about 70% of the body weight • Each water molecule is H-bonded to 3.

2-8 .9 Fig.2 .TΔ  S -22.7 9.9 -15.6 -25.1 Δ  G -10.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 Δ  H 11.

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 .

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

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