Physical Chemistry

Organic & Biochemistry

Nuclear Chemistry

Lecturer: Nelson Garcia

 Physical Chemistry
Chemical Thermodynamics
Chemical Equilibrium & Chemical Kinetics
THERMODYNAMICS

Thermodynamics – the study of energy, work,

and heat
 applied to chemical change
 applied to physical change

The laws of thermodynamics help us to understand why

some chemical reactions occur and others do not
 Change in Energy and Surroundings
System – contains the process under study
Surroundings – the rest of the universe

 Absolute value for energy stored in a chemical

system cannot be measured
 Can measure the change in energy during these
chemical changes
Changes in the System
Energy can be lost from the system to the
surroundings
Energy may be gained by the system at the
expense of the surroundings
This energy change is usually in the form of heat
This change can be measured
First Law of Thermodynamics – energy of
the universe is constant
 Changes in Chemical Energy

For reactants, each chemical bond is stored

chemical energy
 If a reaction will occur
Bonds must break
Breaking bonds requires energy
 Exothermic Reactions

If the energy required to break the bonds

is less than the energy released when the
bonds are formed, there is a net release
of energy
This is called an Exothermic reaction
 Endothermic Reactions

If the energy required to break the

bonds is larger than the energy
released when the bonds are formed,
there will need to be an external
supply of energy
This is called an Endothermic reaction
Enthalpy
Change in Enthalpy (DHo) – energy difference
between the products and reactants of a
chemical reaction
 Energy released, exothermic reaction,
enthalpy change is negative
 Energy absorbed, endothermic, enthalpy
change is positive.
 Exothermic & Endothermic Reactions
C2H5OH(l) + 3O2(g)  2CO2(g) + 3H2O(l) + 1367 kJ
C2H5OH(l) + 3O2(g)  2CO2(g) + 3H2O(l) DH0 = -1367 kJ

CaCO3(S) + 178.1 kJ  CaO(s) + 2CO2(g)

CaCO3(S)  CaO(s) + 2CO2(g) DH0 = 178.1 kJ
Combustion of Fuels

Higher Heating Value (HHV)

CH4(g) + 2O2(g)  CO2(g) + 2H2O(l) DH0 = - 890 kJ
Lower Heating Value (LHV)
CH4(g) + 2O2(g)  CO2(g) + 2H2O(g) DH0 = - 802 kJ
 Activation Energy and the
Activated Complex
 Reaction proceeds from
reactants to products
via the activated
complex
 Activated complex –
can’t be isolated from
the reaction mixture
 Activation energy (Ea) is
the difference between
the energy of the
reactants and that of
the activated complex

•To be an Exothermic reaction requires a net release of energy (DHo)

 Activation Energy in the
Endothermic Reaction
 Reaction takes place
slowly due to the large
activation energy
required
 The energy of the
products is greater than
that of the reactants
Second Law of Thermodynamics –
entropy of the universe is increasing
Spontaneous and Nonspontaneous
Reactions
Spontaneous reaction - occurs without any
external energy input
Most, but not all, exothermic reactions are
spontaneous
Thermodynamics is used to help predict if a
reaction will occur
Another factor is needed, Entropy
Spontaneous and Nonspontaneous
Reactions

o
DS is positive

o
DS is negative
Chemical Kinetics

Reaction Rate – how fast the chemical

reaction is taking place (rate)

Reaction mechanism - step-by-step

description of how reactants become
products
Activation Energy and the Activated
Complex
Activation energy – the minimum amount of
energy required to initiate a chemical reaction

o Chemical reaction in terms of changes in potential

energy occurring during the reaction
o Activated complex – an extremely unstable, short-
lived intermediate complex
o Formation of this activated complex requires energy
(Ea) to overcome the energy barrier to start the
reaction
Activation Energy and the Activated
Complex

 Reaction proceeds from

reactants to products via the
activated complex
 Activated complex – can’t be
isolated from the reaction
mixture
 Activation energy (Ea) is the
difference between the
energy of the reactants and
that of the activated complex
Activation Energy in the Endothermic
Reaction

Reaction takes place

slowly due to the large
activation energy
required
The energy of the
products is greater
than that of the
reactants
Factors That Affect Reaction Rate
 Structure of the reacting species
 Concentration of reactants
 Temperature of reactants
 Physical state of reactants
 Presence of a catalyst
 Structure of Reacting Species
Oppositely charged species react more rapidly
• Dissociated ions in solution whose bonds are
already broken have a very low activation energy
Ions with the same charge do not react
Bond strength plays a role
• Covalent molecules bonds must be broken with the
activation energy before new bonds can be formed
• Magnitude of the activation energy is related to
bond strength
Size and shape influence the rate
• Large molecules may obstruct the reactive part of
the molecule
• Only molecular collisions with correct orientation
lead to product formation
The Concentration of Reactants

Rate is related to the concentration of one or

more of the reacting substances
Rate will generally increase as concentration
increases
Higher concentration means more reactant
molecules per unit volume
More reactant molecules means more collisions
per unit time
The Temperature of Reactants
Rate increases as the temperature
increases
Increased temperature relates directly to
increased average kinetic energy
Greater kinetic energy increases the speed of
particles
Faster particles increases likelihood of collision
Higher Kinetic Energy means a higher
percentage of these collisions will result in
product formation
 The Physical State of Reactants
Reactions occur when reactants can collide
frequently with sufficient energy to react
Solid state: atoms, ions, compounds are close
together but restricted in motion
Gaseous state: particles are free to move but often
are far apart causing collisions to be relatively infrequent
Liquid state: particles are free to move and are in
close proximity
Therefore: Liquid > Gas> Solid
 The Presence of a Catalyst
 Catalyst – a substance that increases the reaction
rate
Undergoes no net change
Does not alter the final product of the reaction
Interacts with the reactants to create an alternative
pathway for product production
The Presence of a Catalyst
Rate Expression

D
2 N 2O5 ( g ) 
 4 NO2 ( g )  O 2 ( g )

1 ∆[𝑁2 𝑂5 ] 1 ∆[𝑁𝑂2 ] ∆[𝑂2 ]

𝑟 =− = =
2 ∆𝑡 4 ∆𝑡 ∆𝑡
Mathematical Representation of Reaction Rate
D
2 N 2O5 ( g ) 
 4 NO2 ( g )  O 2 ( g )
Reaction rate is proportional to reactant
concentration –
Concentration of N2O5 is denoted as [N2O5]
Replace proportionality symbol with = and
proportionality constant k
k is called the rate constant
Mathematical Representation of Reaction Rate

D
2 N 2O5 ( g ) 
 4 NO2 ( g )  O 2 ( g )
𝑟 𝛼 [𝑁2 𝑂5 ] 𝑚

𝑟 = −𝑘 [𝑁2 𝑂5 ]𝑚
 Rate Equation (Rate Law)
For a reaction Aproducts we write the
equation: rate = k[A]n
This is called the rate equation (or rate law)
The exponent n is the order of the
reaction
If n=1, first order
If n=2, second order
n must be determined experimentally
This exponent is not the same as the coefficient
of the reactant in the balanced equation
Rate Equation
A + B  products
rate = k[A]n[B]m

CH4+2O2CO2+2H2O
Rate = k[CH4]n[O2]m
 Equilibrium
Rate and Reversibility of Reactions
 Equilibrium reactions – chemical reactions that do not
go to completion
Completion – all reactants have been converted to
products
Equilibrium reactions are also called Incomplete
reactions
Seen with both physical and chemical processes
 After no further observable change, measurable
quantities of reactants and products remain the same
Chemical Equilibrium Expression: Ammonia Synthesis

kf [NH3 ]p
K eq   n m
kr [N 2 ] [H 2 ]
• The exponents in the rate expression are numerically
equal to the coefficients

[NH3 ]2
K eq 
[N 2 ][ H 2 ]3
• Keq is a constant at constant temperature
Writing Equilibrium-Constant Expressions
Equilibrium constant expressions can only be
written after a correct, balanced chemical
equation
Each chemical reaction has a unique
equilibrium constant value at a specified
temperature
Writing Equilibrium-Constant Expressions

The brackets represent molar concentration

All equilibrium constants are shown as
unitless
Only the concentration of gases and
substances in solution are shown
• Concentration for pure liquids and solids are NOT
INCLUDED IN THE EXPRESSION
Equilibrium Expression
Equilibrium Expression
Interpreting Equilibrium Constants

 Reversible arrow in chemical

equation indicates equilibrium exists
 The numerical value of the
equilibrium constant tells us the
extent to which reactants have
converted to products
Le Chatelier’s Principle

1. Changes in concentration
2. Changes in pressure/volume
3. Changes in temperature
4. Presence of catalyst
Le Chatelier’s Principle

State of equilibrium

Stress is applied

System adjust to
relieve the stress

Attain state of
equilibrium
 Effect of Concentration
Adding or removing either reactants or
products at a fixed volume is saying that the
concentration is changed
Removing material decreases concentration
System will react to this stress to return
concentrations to the appropriate ratio

A: Reaction at equilibrium
B: Shift to reactant with
more red color
C: Shift to product with loss
of red color

A B C
Effect of Concentration

Legend:
Orange solution (equilibrium)
Red solution (reactant)
Yellow solution (product)
Effect of Heat: Addition of heat is treated
as increasing the amount of product

Heat favors the blue species

while cold favors the pink
Effect of Pressure

Pressure affects the equilibrium only if one or

more substances in the reaction are gases
Increasing the pressure favors the side with a
fewer number of moles of gas
Effect of Pressure
N2(g) + 3H2(g) 2NH3(g)
 If increase pressure, which way will the
equilibrium shift?

2HI(g) H2(g) + I2(g)

 If increase the pressure in this reaction, which
way will the equilibrium shift?
Effect of a Catalyst
A catalyst has NO EFFECT on the equilibrium
composition
It increases the rate of both the forward and
reverse reaction to the same extent
While equilibrium composition and concentration
do not change, equilibrium is reached in a
shorter time
Organic Chemistry
and
Biochemistry
Aliphatic Hydrocarbon
Alkenes having more than one double bond:
2 double bonds = alkadiene
3 triple bonds = alkatriene
Same rules for alkynes
Haloalkenes (alkyl halides)
 Aromatic Hydrocarbons
Benzene’s structure was first proposed 150 years
ago
A cyclic structure for benzene, C6H6
Something special about benzene
 Although his structures showed double bonds, the
molecule did not react as if it had any unsaturation
Originally named aromatic compounds for the
pleasant smell of resins from tropical trees (early
source)
Now aromatic hydrocarbons are characterized by a
much higher degree of chemical stability than
predicted by their chemical composition
 Most common group of aromatic compounds is based
on the 6-member aromatic ring, benzene
 Benzene Structure
 The benzene ring consists of:
 Six carbon atoms
 Joined in a planar hexagonal arrangement
 Each carbon is bonded to one hydrogen atom
 Two equivalent structures proposed by Kekulé are
recognized today as resonance structures
 The real benzene molecule is a hybrid with each
resonance structure contributing to the true structure

H H
C C
HC CH HC CH
HC CH HC CH
C C
H H
 Benzene Structure – Modern

Modern concept of benzene structure is

based on overlapping orbitals
Each carbon is bonded to two others by sharing a
pair of electrons
These same carbon atoms also each share a pair of
electrons with a hydrogen atom
Remaining 6 electrons are located in p orbitals that
are perpendicular to the plane of the carbon ring
These p orbitals overlap laterally
Form a cloud of electrons above and below the ring
Pi Cloud Formation in Benzene
Benzene derivatives

Cl

NO2
CH2 CH3
chlorobenzene

nitrobenzene
ethylbenzene
Substituted Benzenes: o,p,m

CH2 CH3
Br CH3

1-bromo-2-ethylbenzene
o-bromoethylbenzene NO2
3-nitrotoluene
m-nitrotoluene
Cl Cl
1,4-dichlorobenzene
p-dichlorobenzene
Historical Nomenclature of Substituted
Benzene

CH3
OH
NH2
COOH
Toluene
Phenol
Aniline
Benzoic
acid
Benzene As a Substituent
When the benzene ring is a substituent
on a chain (C6H5), it is called a phenyl
group

CH2 CH CH2
CH CH3
4-phenyl-1-pentene
Polynuclear Aromatic Hydrocarbons (PAH)
Alcohols (ROH)
 CH3
CH3 C CH3 CH3CH CH3
OH OH
t-butyl alcohol isopropyl alcohol
Phenol (Ar-OH)
Ethers (ROR)
CH3 CH2O CH2 CH3
Diethyl ether -
First successful
general anesthetic

F Cl
CH3O C C H Penthrane
F Cl
12.9 Thiols
THIOLS (R-SH)

CH3
CH3 CH CH2 CH2
SH
3-methy-1-butanethiol
Disulfide Formation: disulfide bridge
Carbohydrates
Carbohydrate : CnH2nOn, where n varies from 3 to 8
a polyhydroxyaldehyde or polyhydroxyketone, or a
substance that gives these compounds on hydrolysis

Monosaccharide
a carbohydrate that cannot be hydrolyzed to a simpler carbohydrate

Aldose: a monosaccharide containing an aldehyde group

Ketose: a monosaccharide containing a ketone group

Structures of Sugars
taken from: [Link]
Biological Functions of Lipids
 As an energy source, lipids provide 9 kcal of energy
per gram
 Triglycerides provide energy storage in adipocytes
 Phosphoglycerides, sphingolipids, and steroids are
structural components of cell membranes
 Steroid hormones are critical intercellular messengers
 Lipid-soluble vitamins (A, E, D, K)
 Dietary fat acts as a carrier of lipid-soluble vitamins
into cells of small intestine
 Provide shock absorption and insulation
Classification of Lipids
Four Main Groups
Fatty Acids
Saturated
Unsaturated
Glycerides glycerol-containing lipids
Nonglyceride lipids
Sphingolipids
Steroids
Waxes
Complex lipids lipoproteins
A Scheme to Classify Lipids
 Fatty Acids
 Long straight-chain carboxylic acids
no branching
 Most common chains range from 10–20 carbons in
length
 Usually, an even number of carbons in the chain,
including the carboxyl carbon
 Can be saturated or unsaturated, but usually no
other functional groups present
 Any fatty acid that cannot be synthesized by the
body is called an essential fatty acid
 Structure
 Stearic acid: a typical saturated fatty acid
with 18 carbons in the chain

 Oleic acid: a typical unsaturated fatty acid

with 18 carbons in the chain
Saturated and Unsaturated Fatty Acids

 Saturated fatty acids have no double bonds

 Unsaturated fatty acids do contain double bonds
 The double bond is normally in a cis
configuration
 Double bonds lower the melting temperature
• The cis configuration doesn’t allow fatty
acids to pack as close together
Fatty Acid Properties
 Melting point increases with increasing carbon
number
 Melting point of a saturated fatty acid is higher than
an unsaturated fatty acid with the same number of
carbons
 Typical saturated fatty acids are tightly packed
together
 cis double bonds prevent good alignment of
molecules in unsaturated fatty acids leading to poor
packing
 Double bonds lower melting point relative to
saturated acid
Chemical Reactions of Fatty Acids
Esterification reacts fatty acids with
alcohols to form esters and water
Fatty Acid Hydrolysis
Acid Hydrolysis reverses esterification
o Fatty acids are produced from esters
Saponification
Saponification is the base-catalyzed
hydrolysis of an ester
Products of the reaction are
o An alcohol
o An ionized salt which is a soap
 Soaps have a long uncharged hydrocarbon tail
 Also have a negatively charged carboxylate group at end
 Form micelles that dissolve oil and dirt particles
Triglycerides
Glycerides are lipid esters
A triglyceride places fatty acid chains at
each alcohol group of the glycerol

O
Glycerol
CH2O C R1
part O Fatty acid
CH O C R2 chains

O
CH2O C R3
 Fats and Oils

Triglycerides or triacylglycerols
Fats are a combination of glycerol and the
fatty acids
Fats mainly come from animals, unless
from fish, and are solid at room
temperature
Oils mainly come from plants, and are
liquid at room temperature
Phosphoglycerides

 Phospholipid is a more
general term
 Any lipid containing G
phosphorus l Fatty Acid

 Phosphoglycerides contain: y
c
Fatty Acid
 Glycerol e
r
 Fatty acid o
Phosphoric Acid
l
 Phosphoric acid with an
amino alcohol
Alcohol
 Replace an end fatty acid of
a triglyceride with a
phosphoric acid linked to an
amino alcohol
 Nonglyceride Lipids
Sphingolipids
These lipids are based on sphingosine
o Long-chain
o Nitrogen-containing
o Alcohol
Amphipathic, like phospholipids
o Polar head group
o Two nonpolar fatty acid tail
Structural component of cellular membranes
Major categories
o Sphingomyelins
o Glycosphingolipids
Major categories
o Sphingomyelins
o Glycosphingolipids
Types of Sphingolipids
Sphingomyelins
Glycosphingolipids
Types of Sphingolipids

Sphingomyelins
Structural lipid of nerve cell membranes
Myelin sheath feature
Glycosphingolipids: Built on a ceramide
Types of Sphingolipids
Glycosphingolipids
Cerebrosides have a single monosaccharide
head group
 Glucocerebroside
 Galactocerebroside
Structure Taken from:
[Link]
Structure of a nucleotide
Nitrogenous Bases
Taken from: [Link]
Numbering Nitrogenous Bases
Uracil

Thymine

Cystosine

Pyrimidine
b-D-ribofuranose found in RNA

b-D-ribofuranose found in DNA

Guanine-Cytosine

Adenine-Thymine
 The Central Dogma of Molecular Biology
figure taken from : [Link]
Nuclear Chemistry
Nuclear Chemistry

Fission – splitting of heavy nucleus to a

lighter nuclei

Fussion – combination of lighter nuclei to

form a heavy nucleus
Natural Radioactivity
Radioactivity – process by which atoms
emit energetic particles or rays
Radiation – the particles or rays emitted
comes from the nucleus
Nuclear symbols – what we use to
designate the nucleus
Atomic symbol
Atomic number
Mass number
Nuclear Symbols

mass number
11
(number of protons
and neutrons)
5 B
atomic number
(number of protons)
ISOTOPES, ISOBARS, ISOTONES

11 12 13
5 B 5 B 5 B
31 31 31
14 X 15 X 16 X
26 27 28
12 M 13 M 14 M
Properties of Alpha, Beta, and
Gamma Radiation
Ionizing radiation – produces a trail of ions
throughout the material that it penetrates
The penetrating power of the radiation
determines the ionizing damage that
can be caused
• Alpha particle < beta particle < gamma rays
Types of Radioactive Decay: Balancing Nuclear Equations

Total A Reactants = Total ATotal Z Products

Total Z

Alpha decay - A decreases by 4 and Z decreases by 2. Every element

heavier than Pb undergoes a decay.

Beta decay - ejection of a b particle from the nucleus from the conversion
of a neutron into a proton and the expulsion of 0-1b. The product nuclide
will have the same Z but will be one atomic number higher.

Positron decay - a positron (01b) is the antiparticle of an electron. A

proton in the nucleus is converted into a neutron with the expulsion of the
positron. Z remains the same but the atomic number decreases.
Electron capture - a nuclear proton is converted into a neutron by the
capture of an electron. Z remains the same but the atomic number
decreases.

Gamma emission - energy release; no change in Z or A.

Particles emitted by radioactive materials:

1. Alpha (a) particles – positive (+) charge,

highly ionizing, least penetrating.

2. Beta (b) particles – negative (-) charge,

less ionizing, more penetrating.

3. Gamma () particles – neutral charge, least

ionizing, most penetrating
 Alpha Particles

Alpha particle (a) – 2 protons, 2 neutrons

• Same as He nucleus (He2+)
• Slow moving, and stopped by small
barriers
• Symbolized in the following ways:

2
4
2 He 4
2 He α 4
2 α
 Beta Particles and Positrons
Beta particles (b) – fast-moving electron
• Emitted from the nucleus as a
neutron is converted to a proton
• Higher speed particles, more
penetrating than alpha particles
• The symbol is…
0
1 e 0
-1 β β
Beta Decay
Upon decomposition, nitrogen-16 produces
oxygen-16 and a beta particle

In beta decay, one neutron in nitrogen-16 is

converted to a proton and the electron,
the beta particle is released

16
7 N O  e 16
8
0
-1
 Positron Emission
A positron has same mass as an electron, or beta
particle, BUT opposite charge (+)
the product nuclide has the same mass number as the
parent BUT the atomic number has decreased by one

11
6 C 11
5 B 0
1 e

11
6 C 11
5 B b 0
1
Gamma Rays
Gamma Rays () – pure energy
(electromagnetic radiation)
Highly energetic
The most penetrating form of radiation
Symbol is simply…

Gamma Production
Gamma radiation occurs to increase the
stability of an isotope
The atomic mass and number do not change
Usually gamma rays are emitted along with
alpha or beta particles

99m
43 Tc  Tc   99
43
Writing a Balanced Nuclear Equation

Nuclear equation – used to represent

nuclear change
Balancing nuclear equation
the total mass on each side of the reaction
arrow must be identical
the sum of the atomic numbers on each side of
the reaction arrow must be identical
238
92 U 234
90 Th  He 4
2

238 = 234 + 4

mass number

92 = 90 + 2

atomic number
 Balancing Equations for Nuclear Reactions

PROBLEM: Write balanced equations for the following nuclear reactions:

(a) Naturally occurring thorium-232 undergoes a decay.
(b) Chlorine-36 undergoes electron capture.
PLAN: Write a skeleton equation; balance the number of neutrons
and charges; solve for the unknown nuclide.

SOLUTION: (a) 232 228 4

90Th 88Ra + 2He

A = 228 and Z = 88 232 228 4

90Th 88Ra + 2He

(b) 3617Cl + 0-1e A

ZX

A = 36 and Z = 16 36 + 0-1e 36
17Cl 16S
Nuclear Stability and Mode of Decay
•Very few stable nuclides exist with N/Z < 1.

•The N/Z ratio of stable nuclides gradually increases a Z increases.

•All nuclides with Z > 83 are unstable.

•Elements with an even Z usually have a larger number of stable

nuclides than elements with an odd Z.

•Well over half the stable nuclides have both even N and even Z.

Predicting the Mode of Decay

•Neutron-rich nuclides undergo b decay.

•Neutron-poor nuclides undergo positron decay or electron capture.

•Heavy nuclides undergo a decay.

Figure 24.2 A plot of neutrons vs. protons for the stable nuclides.
 Half-Life

Half-life (t1/2) – the time required for one-half

of a given quantity of a substance to
undergo change
Ranges from a fraction of a second to a billion years
The shorter the half-life, the more unstable the isotope
 Nuclear Fusion
Fusion (to join together) – combination of two small
nuclei to form a larger nucleus
Large amounts of energy is released
Best example is the sun

2
1 H  H  He 
3
1
4
2
1
0 n  energy
 Radiation Exposure and Safety

Time of Exposure
Effects are cumulative

Types of Radiation Emitted

Alpha and beta emitters are generally less hazardous then
gamma emitters

Waste Disposal
disposal sites are considered temporary
 Decay rate (A) = DN/Dt

SI unit of decay is the becquerel (Bq) = 1d/s.

curie (Ci) =
number of nuclei disintegrating each second in 1g of radium-226 =
3.70x1010d/s

Nuclear decay is a first-order rate process.

Large k means a short half-life and vice versa.

Units of Radiation Measurement
The Curie
The amount of radioactive material that
produces 3.7 x 1010 atomic disintegrations
per second
Independent of the nature of the radiation
Units of Radiation Measurement

The Roentgen
 The amount of radiation needed to produce 2 x 109 ion
pairs when passing through one cm3 of air at 0oC
 Used for very high energy ionizing radiation only
 Units of Radiation Measurement

Rad – Radiation absorbed dosage

The dosage of radiation able to transfer 2.4 x 10-3
cal of energy to one kg of matter
This takes into account the nature of the absorbing
material
 Units of Radiation Measurement
The Rem
Roentgen Equivalent for Man
Obtained by multiplication of the rad by a factor
called the relative biological effect (RBE)
• RBE = 10 for alpha particles
• RBE = 1 for beta particles
Lethal dose (LD50) - the acute dosage of radiation
that would be fatal for 50% of the exposed
population
LD50 = 500 rems