BCM 223

CHEMICAL KINETICS, BIOENERGETICS AND THERMODYNAMICS

Kinetics
Kinetics studies the rate at which a chemical process occurs. Besides information about the speed
at which reactions occur, kinetics also sheds light on the reaction mechanism (exactly how the
reaction occurs).

REACTION RATES
Rates of reactions can be determined by monitoring the change in concentration of either
reactants or products as a function of time t.
Notation for Stoichiometry:
[A] = concentration of reactant A
[B] = concentration of reactant B

For the reaction A  B there are two ways of measuring rate:

(1) the speed at which the reactants disappear
(2) the speed at which the products appear
Reversible reactions: as products accumulates, they can begin to turn back into reactants.
Early on, the rate will depend on only the amount of reactants present. We want to measure the
reactants as soon as they are mixed.
A general way of measuring the rate of the reaction is in terms of change in concentration per
unit time.
Instantaneous rate: Δ[A]/dt limits to d[A]/dt
Most Common Units…Rate = M/s
Where Molarity (M) = moles/Liter

CHEMICAL KINETICS
Reaction rate is the change in the concentration of a reactant or a product with time (M/s).
A B
rate = Δ[A]/dt Δ[A] = change in concentration of A over time period Δt.
rate = Δ[B]/dt Δ[B] = change in concentration of B over time period Δt.
Because [A] decreases with time, Δ[A] is negative.

REACTION RATES AND STOICHIOMETRY

To generalize, for the reaction
aA + bB  cC + Dd

Reactants (decrease) Products (increase)

FACTORS AFFECTING REACTION RATE CONSTANTS

1. Temperature: At higher temperatures, reactant molecules have more kinetic energy, move
faster, and collide more often and with greater energy
Collision Theory: When two chemicals react, their molecules have to collide with each other (in
a particular orientation) with sufficient energy for the reaction to take place.
Kinetic Theory: Increasing temperature means the molecules move faster.
2. Concentrations of reactants: As the concentration of reactants increases, so does the
likelihood that reactant molecules will collide.
3. Catalysts: Speed up reactions by lowering activation energy
4. Surface area of a solid reactant: More area for reactants to be in contact
5. Pressure of gaseous reactants or products: Increased number of collisions
REACTION RATE EXAMPLES

C4H9Cl(aq) + H2O(l) à C4H9OH(aq) + HCl(aq)

A plot of concentration vs. time for this reaction yields a curve like this. The slope of a line

tangent to the curve at any point is the instantaneous rate at that time.
The reaction slows down with time because the concentration of the reactants decreases.

In this reaction, the ratio of C4H9Cl to C4H9OH is 1:1.

Thus, the rate of disappearance of C4H9Cl is the same as the rate of appearance of C4H9OH.

Rate = -D[C4H9Cl] = D[C4H9OH]

Dt Dt

REACTION RATE LAWS

Concentration and Rate Each reaction has its own equation that expresses its rate as a function of
the concentrations of the involved species (e.g., reactants, products, catalysts). This is called its
rate law.
Rate Law
In general, rates of reactions increase as concentrations increase since there are more collisions
occurring between reactants.
The overall concentration dependence of reaction rate is given in a rate law or rate expression.
Reactions follow simple rate laws:

v = k [A]m [B]n…

- [A], [B]: reactant concentrations

- The exponents m and n are the reaction orders (w.r.t. specific reactant)
- The constant k: rate constant
- The overall reaction order is the sum of the reaction orders: m + n

Determination of Rate Laws

Rate laws, rate constants, and orders are determined experimentally.

The order of a reactant is NOT generally related to its stoichiometric coefficient in a balanced
chemical equation.

EXPRESSION OF RATE LAWS

Reactions with simple rate laws:

ELEMENTARY REACTIONS

Always follow simple rate laws

Reactant order reflects molecularity

SIMPLE EXAMPLE REACTIONS

Example of chemical reaction that models degradation of molecule A

Example of chemical reaction that models generation (from D) and degradation of molecule
A
Example of chemical reaction that models generation (from A and B) of molecule C

ORDER OF REACTIONS

A reaction is zero order in a reactant if the change in concentration of that reactant produces no
effect.
A reaction is 1st order if doubling the concentration causes the rate to double.
A reaction is 2nd order if doubling the concentration causes a quadruple increase in rate.
-3rd order…doubling concentration leads to 23 (or 8 times) the rate.
- extremely rare.
Zero-Order Processes

This equation has the general form for a straight line, y=mx+b, so a plot of [A]t vs. t is a straight
line with slope (-k) and intercept [A]0.

First-Order Processes

For 1st order reactions: ln[A]t = −kt + ln[A]0

where [A]t = concentration of [A] after some time, t
k= reaction rate constant in units of s-1
t= time in seconds
[A]o = initial concentration of A

This equation has the general form for a straight line, y=mx+b, so a plot of ln[A]t vs t is a straight
line with slope (-k) and intercept ln[A]0.
Second order processes

For 2nd order reactions: 1/[A]t = kt + 1/[A]0

where [A]t = concentration of [A] after some time, t
k= reaction rate constant in units of M-1s-1
t= time in seconds
[A]o = initial concentration of A
This equation has the general form for a straight line, y=mx+b, so a plot of l/[A]t vs t is a straight
line with slope (k) and intercept of 1/[A]0.

Half-Life

Half-life is the time taken for the concentration of a reactant to drop to half its original value.

Substitute into integrated rate laws: t½ is the time taken for [A] to reach ½[A]0

** NOTE: For a first-order process, the half-life does not depend on [A]0.
Half-Life - 1st order

For a first-order process, set [A]t = 0.5[A]0 in integrated rate equation:

What is the half-life of N2O5 if it decomposes with a rate constant of 5.7 x 10-4 s-1?

How do you know decomposition is first order?

hint: units of k (S-1)
Half-Life - 2nd order

For a second-order process, set [A]t = 0.5 [A]0 in 2nd order equation:
EQUATIONS OF REACTIONS OF VARIOUS ORDERS

Summary of the Kinetics of Zero-Order, First-Order and Second-Order Reactions

SUMMARY OF KINETICS
REACTION MECHANISMS

The sequence of events that describes the actual process by which reactants become products is
called the reaction mechanism.
Reactions may occur all at once or through several discrete steps.
Each of these processes is known as an elementary reaction or elementary process.
The overall progress of a chemical reaction can be represented at the molecular level by a series
of simple elementary steps or elementary reactions.
The sequence of elementary steps that leads to product formation is the reaction mechanism.

Rate laws and rate determining steps

Writing plausible reaction mechanisms:

The sum of the elementary steps must give the overall balanced equation for the reaction.
The rate-determining step should predict the same rate law that is determined experimentally.
**The rate-determining step is the slowest step in the sequence ofsteps leading to product
formation.**

Up until now, we have only been concerned with the reactants and products. Now we will
examine what path the reactants took in order to become the products.
The reaction mechanism gives the path of the reaction.
Mechanisms provide a very detailed picture of which bonds are broken and formed during the
course of a reaction.

Elementary Steps and Molecularity

Elementary step: any process that occurs in a single step.

Molecularity: number of molecules present in an elementary step.
Unimolecular: one molecule in the elementary step,
Bimolecular: two molecules in the elementary step, and
Termolecular: three molecules in the elementary step.
(It is uncommon to see termolecular processes…statistically improbable for an effective collision
to occur.)

Rate Laws of Elementary Steps

Since this process occurs in one single step, the stoichiometry can be used to determine the rate
law!
Law of Mass Action: The rate of a simple (one step) reaction is directly proportional to the
concentration of the reacting substances.

ELEMENTARY STEPS AND THEIR RATE LAWS

** Notice that the coefficients become the exponents.

The molecularity of a process tells how many molecules are involved in the process.
The rate law for an elementary step is written directly from that step.

REACTION INTERMEDIATES

Intermediates are species that appear in a reaction mechanism but not in the overall balanced
equation.
An intermediate is always formed in an early elementary step and consumed in a later
elementary step.
MULTISTEP MECHANISMS

In a multistep process, one of the steps will be slower than all others.
The overall reaction cannot occur faster than this slowest, rate-determining step.

ACTIVATION ENERGY

There is a minimum amount of energy required for a reaction: the activation energy, Ea.
Just as a ball cannot get over a hill if it does not roll up the hill with enough energy, a reaction
cannot occur unless the molecules possess sufficient energy to get over the activation energy
barrier.

Activation Energy
Molecules must possess a minimum amount of energy to react. Why?
In order to form products, bonds must be broken in the reactants. Bond breakage requires energy.
Molecules moving too slowly, with too little kinetic energy, don’t react when they collide.
Activation energy, Ea, is the minimum energy required to initiate a chemical reaction.
Ea will vary with the reaction.

Catalysts
A catalyst is a substance that increases the rate of a chemical reaction without itself being
consumed.
Catalysts increase the rate of a reaction by decreasing the activation energy of the reaction.
Catalysts change the mechanism by which the process occurs.
BIOENERGETICS AND THERMODYNAMICS
INTRODUCTION

Cells need energy to do following:

all their work
generate and maintain its highly ordered structure (biosynthesis of macromolecules).
generate all kinds of movement.
generate concentration and electrical gradients across cell membranes.
maintain body temperature.
generate light in some animals.
The “energy industry”(production, storage and use) is central to the economy of the cell society.

Bioenergetics : The field of biochemistry concerned with the transformation and use of energy
by living cells and the chemical nature underlying these processes.

CELLS HAVE TO USE CHEMICAL ENERGY TO DO ALL THEIR WORK

Antoine Lavoisier`s insight on animal respiration in the 18th century: it is nothing but a slow
combustion of carbon and hydrogen (the same nature as a lighting candle).
Living cells are generally held at constant temperature and pressure: chemical energy (free
energy) has to be used by living organisms, no thermal energy, neither mechanical energy is
available to do work in cells.
THERMODYNAMIC PRINCIPLES

Biological energy transformation obeys the two basic laws of thermodynamics revealed by
physicists and chemists in the 19th century:
These laws help us to understand
(a) the direction of a reaction, whether from left to right or vice versa,
(b) the accomplishment of work, whether useful or not and
(c)whether the energy for driving a reaction must be delivered from an external source.

The first law of thermodynamics:

For any physical or chemical change, the total amount of energy in the universe remains constant;
energy may changed from or it may be transported from one region to another, but it can not be
created or destroyed.

The second law of thermodynamics

The universe always tends toward increasing disorder: in all natural processes the entropy of the
universe increases.

SYSTEM AND ITS SURROUNDINGS

The reacting system may be an organism, a cell or two reacting compounds. The reacting system
and its surroundings together constitute the universe.
In the laboratory, some chemical or physical processes can be carried out in closed systems and
no material or energy is exchanged with the surroundings.
However living organisms are open systems. They exchange both material and energy with their
surroundings.
Living systems are never at equilibrium with their surroundings.

THERMODYNAMIC QUANTITIES

Gibbs free energy (G): expresses the amount of energy capable of doing work during a reaction at
constant temperature and pressure
When a reaction proceeds with the release of free energy (that is, when the system changes so as
to posses less free energy) ΔG has a negative value and the reaction is said to be exergonic.
In endergonic reactions, the system gains free energy and ΔG is positive.
The unit of ΔG is joules/mole or calories/mole.
Enthalpy (H): H is the heat content of the reacting system. H reflects the number and kinds of
chemical bounds in the reactants and products.
When a chemical reaction releases heat, it is said to be exothermic, the heat content of the
products is less than that of the reactants and ΔH has a negative value
Reacting systems that take up heat from their surroundings are endothermic and have positive
values of ΔH.
The unit of ΔH is joules/mole or calories/mole

Entropy (S): S is a quantitative expression for the randomness or a disorder in a system

The unit of ΔS is joules/mole. Kelvin
Under the constant temperature and pressure changes in free energy, enthalpy and entropy in
biological systems are related to each other by the equation
ΔG = ΔH -TΔS
ΔG = Change in Gibbs free energy of the reacting system (Gproducts–G reactants)
ΔH =Change in enthalpy of the reacting system (H products -Hreactants)
T = Absolute temperature
ΔS = Change in entropy of the reacting system (Sproducts-Sreactants)

Living organisms preserve their internal order by taking free energy from their surroundings in
the form of nutrients or sunlight and returning to their surroundings an equal amount of energy as
heat and entropy.

CONCEPT OF FREE ENERGY

Free energy is the portion of a system’s energy that is able to perform work when temperature
and pressure is uniform throughout the system, as in a living cell.
Free energy also refers to the amount of energy actually available to break and subsequently form
other chemical bonds.
Gibbs’ free energy (G) in a cell is the amount of energy contained in a molecule’s chemical
bonds (Temperature and Pressure constant).
Change in free energy -ΔG.
Endergonic -any reaction that requires an input of energy.
Exergonic -any reaction that releases free energy.