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Title: Molecular science and Physical Chemistry
Description: A brief overview of molecular sciences, physical chemistry and pharmacutical science. Biomed
Description: A brief overview of molecular sciences, physical chemistry and pharmacutical science. Biomed
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Physical Chemistry
Dr S Pickering
Lecture 1
Topics
Spectroscopy
•
Electromagne1c radia1on
•
Interac1on with atoms and molecules
•
Spectrophotoreceptors
Electrochemistry
•
Ionic solu1ons
•
Conductance
•
Poten1al
Kine1cs
•
Rate equa1ons
•
Order of reac1on
•
Reac1on mechanism
•
Ac1va1on energy
•
Analysis methods
Prac1cals
•
H3 Spectroscopy
•
E4/E5 conductance
•
K1 Kine1cs
•
K5 Kine1cs
Spectroscopy
Spectroscopy is the analysis of the electromagne1c radia1on that is emiGed, absorbed or scaGered
by atoms and molecules
...
Several different types of analy1cal instruments are available but each works in a similar way
...
The resultant
radia1on is then passed through a prism or diffrac1on gra1ng, to split the radia1on into its individual
components
...
Source
Prism or
diffreaction
grating
Sample
Detector
Recorder
The Electromagne
radia1on
...
Block diagram of a typical spectrometer
Waves are characterised by their wavelength, amplitude and frequency
...
A cycle represents a por1on of the wave between
two consecu1ve iden1cal posi1ons of the wave
...
The amplitude of the wave is half the distance between the top of the crest
and the boGom of the trough
...
SI units – Hertz, Hz
1Hz = 1 cycle per second
Lecture 2
Waves
SI units are Hertz
so 1 Hz = = s-‐1
Where 1Hz = 1 cycle per second
1Hz = 1/s = s-‐1
Velocity of a wave depends on the wavelength of the radia1on and the chemical structure of
substance though which the wave is passing
...
This
constant speed is referred to as the speed of light through a vacuum c = 2
...
Waves can
have the same frequency but different amplitudes (height of the wave)
...
Varia
intensity
...
e
...
So…
or
Calculate the frequency GHz of an x-‐ray radia1on of wavelength 0
...
0x108m s-‐1
=1
...
Energy is inversely propor1onal to
wavelength
...
Radio waves have long wave lengths
and a low energy
...
The energy of a wave, ε, is propor1onal to its
frequency
...
62 x 10-‐34 Js
...
Spectra for plural
...
g
...
Emission spectra are produced when radia1on emiGed from a source is
analysed
...
These missing wavelengths give important
informa1on in chemical structure determina1on, as the energy of the radia1on is directly linked to
the energy level differences of atoms and molecules
...
The visible spectrum forms a small narrow band between infra red and UV regions of the
electromagne1c spectrum
...
In a traffic signal the frequency changes from 5
...
2 x 1014 Hz and then to 4
...
Light waves can interfere with each other
Construc1ve interference is when two crests meet
Double the amplitude, but the same wavelength,
giving the result of a higher intensity and a brighter
light
...
Waves cancel each other out with each other
producing darkness and shadows
...
g
...
This behaviour is
explained by thinking of light as being mass less par1cle which have discrete amounts of energy such
par1cles are referred to as photons and energy of a photon , t = hv J per photon
...
Increasing intensity of radia1on at specific wavelengths does increase the number of electrons
released, this is observed at specific wavelengths depends on mel1ng point of metal
...
Io , intensity of
incident radia1on
I , intensity of
emergent radia1on
In a spectrophotometer the ra1o I/IO is measured and is called the transmiGance of the
sample, symbol T
So T = I/Io
Or T% = I/Io x 100
Infra red spectrum every sample has the same fingerprint
...
Where A = -‐log10 I/Io
A = -‐log10 T
which = log10 Io/I
which = A = log10 1/T
A has no units, as it is dimensionless
The absorbance of the solu1on depends on:
•
The iden1ty of the absorbing species
•
The concentra1on of the absorbing species, c
...
This equa1on is known as the beer Lambert law
1
...
The absorbance of unknown samples is measured and the concentra1on is determined from
the graph
...
If the
concentra1on of the solu1on is increased a plot of A v C plateaus
...
Transi1on to
higher states requires the absorp1on of specific amounts of energy
...
With atoms absorp1on of radia1on leads to the promo1on of electrons from their
ground state orbit to higher level orbits
...
This is electronic transi1on
...
In
addi1on molecules also possess vibra1onal and rota1onal energy so transi1ons between different
rota1onal and vibra1onal levels are possible
...
Lecture 6
Proper
present in much greater quan1ty than any other
...
When the solvent is water the solu1on is
referred to as an aqueous solu1on
...
Some substances are completely soluble in water, some sparingly (slightly) soluble and others almost
totally insoluble
...
The structure of NaCl – A crystalline solid where the ions are stacked together in an orderly array, in
which each Na+ ion is surrounded by 6 Cl-‐ ions and each Cl – ion is surrounded by 6 Na+ ions in an
octahedral arrangement
...
The Na+ ions being much smaller than the
Cl-‐ ions, occupy the spaces in between the Cl-‐ ions
...
Water molecule structure
!
Polar bond one end is a bit more posi1ve and one end a bit more nega1ve
...
This results in a par1al nega1ve charge
where the electron density is concentrated and a posi1ve charge the opposite end
...
When very electronega1ve atoms such as F, O, and N are aGached to a hydrogen atom a special type
of dipole to dipole bond called a hydrogen bond is formed
...
Hydrogen bonds are represented by doGed lines in water; each molecule can aGract 4 other
water molecules
...
When an ionic solid is placed in a polar solvent, aGrac1on occurs between the ions and the par1ally
charged polar molecules
...
He overall
forces of aGrac1on between the ion and several water molecules are greater than the ion – ion
forces
...
This opens up other ions to solvent aGrac1on and these in turn are pulled from the solid into the
solu1on
...
MaGer is
categorised as a solid, liquid or gas
...
The par1cles can vibrate back
and forth about their posi1on but they will not move past their immediate neighbours
...
In liquids and gasses par1cles have fewer restric1ons and can move around reluctantly
...
In a gas the par1cles are remote from each other most of the 1me as they fly around the container
...
Increasing temperature results in more rapid vibra1onal energy
...
In liquids and solids intermolecular forces such as ion – dipole interac1ons and van der waals forces
operate between the par1cles, thus keeping maGer together
...
Immiscible liquids do not mix together and will exist as separate
layers, in contact with one another with the denser material forming the boGom layer
...
In the body some co2 from the lungs
dissolves in h2o to form carbonic acid H2CO3
...
Under pressure gases will become more soluble this can result in – nitrogen levels in deep sea divers,
produc1on of fizzy drink
...
For the compounds the larce energy is so large that
the solute to solvent interac1ons are not sufficient to pull the ions from the larce
...
In any solvent the interac1ons between solute and the solvent molecules determine whether a
solute will dissolve in a par1cular solvent and how much of it will dissolve
...
Lecture 8
Scien
Which means substances with similar intermolecular forces are likely to be soluble with each other
...
6g/100g H2O at 20oC
Ethanol
CH3-‐CH2-‐O -‐ H
Three hydrogen bonds can be formed so each ethanol molecule is surrounded by water molecules;
there is a lot of hydrogen bonding so it is soluble
1 – hexanol
CH3-‐CH2-‐CH2-‐CH2-‐CH2-‐CH2-‐O-‐H
Hydrogen bonds cannot form for most of the structure
...
The longer the hydrocarbon chain the stronger
the non polar interac1on
...
Examples of solu1ons can be found as either gases liquids or solids
...
g air, sugar – water, brass
The extent at which a solute dissolves in a given solvent and at a given temperature is measured in
terms of its solubility
...
In a
saturated solu1on the dynamic equilibrium is set up between dissolved and undissolved solid:
Solute and solvent →← solvated solute
The equilibrium constant Kc = the solute concentra1on is equal to the solubility
In a supersaturated solu1on the solute conc
...
A super saturated solu1on
is made at a higher temperature and then the solu1on is slowly cooled
...
Solubility is oken
quoted in units of g solute per 100g water for aqueous solu1ons
...
The solubility product is the equilibrium constant for the chemical equilibrium that is set up between
an ionic solute and its ions in a saturated solu1on
...
Electrical conduc1on refers to the ability of a solu1on to allow electric current to pass through it
...
In a metal a current is carried
by electrons, in a solu1on current is carried by the movement of ions
...
Substances that remain in molecule form when dissolved are called non electrolytes
...
Lecture 9
These are proper1es of a solu1on that are affected by the number of solute par1cles
present, (but not their iden1ty)
...
The effects
of a solute in a solvent are that they cause
1
...
Decrease the freezing point
3
...
Since the concentra1on of
the solute is in compartment a than in compartment b there is a concentra1on gradient
between the two solu1ons, that drives the solvent molecules in compartment B across the
membrane into A
...
To rehydrate pa1ents a saline solu1on is used (isotonic) instead of pure water as this would
cause water to enter the cells which would swell and burst
...
Acids and Bases
An acid is a substrate that increases the concentra1on of hydrogen ions in a solu1on
...
H+ does not exist instead it combines with a water molecule to form the
hydronium ion, H30+
...
Some acids dissociate completely
in a solu1on – strong acid
...
H2O + CH3COOH CH3CO-‐ + H3O+
At any one 1me only about 5% of these molecules are ionised
...
Example – Sulphuric acid
H2S04-‐ + H2O à H3O+ + HSO4-‐ Hydrogen sulphate ion
Strong acid
HSO4-‐ (aq) + H2O H3O+ + SO4+ Sulphate ion
The strength of an acid can be determined in terms of the acid dissocia1on constant Ka
...
8x 10-‐5
The values are oken represented in logarithmic form as pKa value = log Ka
So pKa of CH3COOH = 4
...
Bases can also be classified as strong or weak depending on the degree of
dissocia1on
...
g
...
g WEAK BASE
NH3 reacts with water to form NH4OH (ammonium hydroxide)
NH4 OH(aq) ↔ NH4+(aq) + OH-‐(aq)
Less than 5% of NH4OH molecules are ionised at any one 1me
...
E
...
1HCl(aq) + Mg(OH)2(aq) à MgCl2(aq) + 2H2O(l)
Similarly with organic acids:
CH3CH2
Propanoic acid
Some acids are also strong electrolytes
...
Note: salts of weak acids tend to be fully ionised, so are stronger electrolytes than their acid
form
...
R1 –COOH + H2N – R2
Carboxylic group + Amino grou
➔ H2 O is eliminated:
R1 – CONH – R2
2
...
i
...
H2O(l) + H2O(l) ↔H3O+(aq) + OH(aq)
Congugate Congugate Congugate Congugate
Acid Base Acid Base
The equilibrium constant is determined as:
Kw = [H3O+] [OH-‐]
K = equilibrium constant, where Kw is called ‘the ion product constant for water’
...
0X10-‐14
In pure water at 25oC
√Kw = [H3O+] [OH-‐] = 1
...
0X10-‐14
If [H3O+] = 1X10-‐3 mol dm-‐3
Then [OH-‐] = 1X10-‐11
If [OH-‐] = 1
...
0X10-‐14
1
...
0X10-‐14) = -‐14
Or -‐log (1
...
0X10-‐3
-‐log (1
...
00
In taking logs, quote the same number of decimal places as the number of significant digits
in the original number
...
Molar conduc
...
The conductance of an ion in solu1on is related to the size, change and viscocity of the
solvent
...
Mobility of an ion tends to increase with decreasing size and lower viscocity of the solvent
...
For strong electrolytes, a plot of Λ ư √C is
linear
...
Λ/SM2 Mol-‐1
0
...
04
HCl
0
...
02
0
...
00
√C/Mol L-‐1
NaOH
NaCl
CH3COOH
The equa1on of the straight line takes the term:
Λy = Λco -‐ K√C MX (M = gradient of the line)
For strong electrolytes, K can be found from the gradient of the line and Λo, the molar
conduc1vity at infinite dilu1on, (the limi1ng molar conduc1vity) can be found by
extrapola1ng the line to the intercept
...
Generally, the limi1ng molar conduc1vity is the
sum of the contribu1ons from the anions and ca1ons
...
E
...
04267 SM2 Mol-‐1
Λo NaCl = 0
...
00931 SM2 Mol-‐1
Calculate Λo CH3 COOH
Solu1on:
1
...
04267 SM2 Mol-‐1
2
...
01265 SM2 Mol-‐1
3
...
000931 SM2 Mol-‐1
4
...
03933
Λo CH3COOH = λHCl + Λo CH3COONa -‐ Λo NaCl
Lecture 10
Finding the concentra
Finding from pH
If pH = -‐log
Then – pH = log
10-‐pH =
Type inverse log (– pH value)
Buffer Solu1ons
Adding a small amount of acid and base can significantly alter the pH of a solu1on
...
For humans this is:
pH 7
...
4
A buffer system is a chemical system that works to resist small changes in a pH
...
Example
CH3COOH (aq) + CH3COO-‐ Na+(aq)
Ethanoic acid + sodium ethanoate
This buffer is controlled by the ethanoic dissocia1on
CH3COOH (aq)
CH3COO-‐ + H+
Dynamic equilibrium
If more H+ is added this will counteract the right hand side forming more ethanoic acid on
the lek
...
Addi1on of OH-‐ ions or
removal of H+ ions drives the dissocia1on to the right
...
Resistance is found to vary with the length, L, and cross sec1onal area, A, of the resistor as
follows,
R α L
Larger the diameter the easier to flow
R α (1/a)
R = P x
P = resis1vity
Units of resis1vity = Ωm
Current is the flow of charge
•
In metals, charge is carried by electrons
•
In solu1ons charge is carried by the ions present
In solu1ons we measure the conductance rather than the resistance of the solu1ons
Conductance, G, is the inverse of resistance
So G α à G α
G = K
Where K is the conduc1vity
The units of K are Sm-‐1 -‐ siemen
A conductance call consists of two pla1num foil electrodes which dip into the solu1on and
which are connected by wire to an external circuit
...
So K =G x cell constant
L is the distance between the electrodes, A is the cross sec1onal area of pla1num
...
The data is ploGed in the
form of a concentra1on vs 1me graph
...
Generally the stronger the gradient, the faster the reac1on, is occurring
...
e rate α
Rearranging gives
Integra1ng between the limits
T = 0 to t = t gives
Ln = ln
Where is the ini1al concentra1on of
A plot of ln v t gives a linear graph with intercept ln and gradient equal to –k
Gradient = -‐k
ln
K = -‐ gradient
!
Lecture 12
Second order reac1ons
Units of second order rate constant k
K =
Units of K =
conc units-‐1 1me-‐1 i
...
A plot of ln(r) v ln is linear, with gradient x – order and intercept ln(k) -‐ rate constant
...
The method of ini1al rates is used to determine the rates of
reac1on
...
Determina1on of rate of different concentra1ons by using the method of ini1al rate
A1
A2
With reac1ons involving 2 or more reactants the order with respect to each species is found
by having all of tA3 other concentra1ons effec1vely constant (in excess)
...
The
A4
rate constant under these condi1ons is called the apparent rate constant
...
Molar conduc1vity
Solu1ons which can carry current are referred to as electrolyte or electroly1c solu1ons
...
The conductance of an individual ion is related to its size, its charge and the viscosity of the
solvent
...
Mobility of an ion lends to increase with decreasing size and
lower viscosity of the solvent
...
Ω has units of S m2 mol-‐1
Studies have shown that the rela1onship between molar conductance and concentra1on
follows 2 dis1nc1ve types of behaviour
...
For a weak electrolyte Ω is small in dilute
solu1on but in very low concentra1ons it goes up steeply
...
For weak acid Ω0 is found by calcula1on, generally the limi1ng molar conduc1vity is the sum
of the contribu1ons from anions and ca1ons
...
Example for
HCl Ω0=ʎH+ + ʎH-‐
CuCl2 Ω0=ʎCu2+ + 2ʎCl-‐
Given Ω0 HCl = 0
...
01265 S m2 mol-‐1
Ω0 CH3COONa = 0
...
Ω0 HCl = ʎH+ + ʎCl-‐ =0
...
Ω0 NaCl = ʎNa+ + ʎCl-‐ = 0
...
Ω0 CH3COONa = ʎNa+ + ʎCH3COO-‐ =0
...
Ω0 CH3COOH = ʎH+ + ʎCH3COO-‐ =0
...
Rela1onship between K, t½ and 0
If t = tv2 then
Subs1tu1ng info
Rearranging gives
Ktv2 = ln 0 -‐
t½ = or K =
Units of rate
Rate =
so units of rate =
example, if has units mol L-‐1 then rate = mol L-‐1 s-‐1
Units of first order reac1on rate constant k if rate = k for example
K has units 1me-‐1 , e
...
s-‐1 , min-‐1
For the reac1on
A à products
When rate = x
If x = 2 the reac1on is second order
So 2
Rearranging gives
Which integrates between the limits t =0 to t=t to become the linear equa1on
Y = c – mx
Where a plot of is linear woth gradient – l and intercept =
t
Rela1onship between k and t½ for a second order reac1on
If
If t = t½ and
Then = kt½
=
If α
Or
Lecture 15
Ac1va1on energy
For many reac1ons the rate of reac1on and the value of the rate constant vary with
temperature
...
Current theory of reac1on rates suggests that the pathway of a reac1on involves the
forma1on of a transi1on state
...
This then reacts
further to form the final product
...
Diagram for the reac1on A + BC AB + C
!
Ac1va1on energy of the forward reac1on is E1
Ac1va1on energy of the backward reac1on E2
If is posi1ve the reac1on is said to be endothermic and if the is nega1ve the reac1on is
exothermic
...
Generally as temperature increases then more reactant molecules gain sufficient
energy to react, so the rate of reac1on increases
...
!
Catalysts may be homogeneous (same state) acid or base in either aqueous or organic
solu1ons
...
Solids in gas phase reac1ons
The Arrhenius equa1on describes the rela1onship between rate constant and temperature
for many reac1ons
...
314 J mol-‐1 K-‐1)
The logarithmic form is linear
ln K = ln A -‐
y = c – mx
Plot ln K versus 1/T à linear graph, gives intercept ln A and gradient
Gradient = =
!
Ea = -‐ gradient x R
Title: Molecular science and Physical Chemistry
Description: A brief overview of molecular sciences, physical chemistry and pharmacutical science. Biomed
Description: A brief overview of molecular sciences, physical chemistry and pharmacutical science. Biomed