65212: CHEMISTRY 2

Spring, Semester 2

Chemistry 2 Notes Contents

1 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 2 2.1 2.2 2.3 2.4 2.5 2.6 2.7 3 3.1 3.2 3.3 3.4 3.5 3.6 4 4.1 4.2

Introduction to criminal law Crime Structure of criminal law NSW criminal law Common law and code states Jurisdiction Legal definitions Burden of proof Standard of proof The golden thread General principles and introduction to elements of crime Elements of criminal liability Legal capacity Actus reus Mens rea Subjective and objective standard Strict and absolute liability Temporal coincidence Homicide Actus reus of homicide Concept of human being Requirement of voluntariness Voluntariness and the burden of proof Causation Responsibility for omissions Murder Actus reus of murder

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1.1

Acid-base chemistry
Bronsted-Lowry acids and bases

Proton transfer reactions An H+ ion is a proton with no surrounding valence electron Define acids and bases by ability to transfer protons: (a) Acid donates proton (b) Base - accepts proton E.g. HCl dissolves in water. HCl is Bronsted-Lowry acid and donates a proton to H2O, a Bronsted-Lowry base. HCl (g) + H2O (l) H3O+ (aq) + Cl- (aq)

Does not have to be in aqueous solution e.g. HCl and NH3. Ammonia is base because adding it to water increases concentration of OH-; accepts proton from H2O. NH3 (aq) + H2O (l) NH4+ (aq) + OH- (aq)

Conjugate acid-base pairs An acid and a base such as HX and X- that differ only in the presence or absence of a proton e.g. OH- is conjugate base of H2O Acid always has one more H

Strengths of acids and bases The more easily an acid gives up a proton, the less easily its conjugate base accepts a proton The stronger an acid, the weaker its conjugate base Types of acids: (a) Strong acid: Dissociate 100% (transfer all their protons to water); bases do not accept protons negligible base. [H+] is conc. of solution. (b) Weak acid: Partially dissociate; bases react partly with water to give small conc. of OH- weak base. [H+] < conc. of solution. (c) Negligible acid: Contain hydrogen but have no acidic behaviours; bases dissociate 100% to give OH- and a cation strong base.

Strong Acids HCl (hydrochloric) HBr (hydrobromic) HI (hyrdroiodic) HClO3 (chloric) HClO4 (perchloric) HNO3 (nitric) H2SO4 (sulfuric) Bases Group 1 alkali metal hydroxides: LiOH NaOH KOH RbOH CsOH Group 2 heavy alkaline earth hydroxides: Ca(OH)2 Sr(OH)2 Ba(OH)2

Weak Almost all other acids are weak e.g. HA = HF, HNO2, HClO, H2S, H2CO3, NH4+ Most cations are weak acids

Almost all other bases are weak e.g. NH3 Most anions are weak bases

Strengths of acids and position of equilibrium If the base in the forward reaction is a stronger base than the conjugate base of HX, equilibrium will lie to right (when HX is a strong acid). e.g. HCl (aq) + H2O (l) H3O+ (aq) + Cl- (aq)

If base in forward reaction is a weaker base than the conjugate base of HX, equilibrium will lie to left (when HX is a weak acid). e.g. CH3COOH (aq) + H2O (l) H3O+ (aq) + CH3OO- (aq)

Position of equilibrium favours transfer of proton to stronger base. Extent of dissociation (acid strength) measured by equilibrium constant Ka Ka = [H+] [A-] [HA]

Bigger Ka - stronger acid (Ka >1) Smaller Ka weaker acid (Ka < 1)

1.2

Autoionisation of water

Water as acid or base Water can act as Bronsted-Lowry acid or base In presence of acid, water acts as base (vice versa) Water molecule can donate proton to another water molecule: H2O (l) + H2O (l) Ion product of water The equilibrium constant for water is: Kw = [H3O+] [OH-] Can also be written H2O (l) H+ (aq) + OH- (aq) Kw = [H+] [OH-] = 1.0 x 10-14 (at 25C) Applicable to water and aqueous solutions (in water) Can use to calculate [H+] if [OH-] known (vice versa) If [H+] = [OH-] substance is neutral [H+] > [OH-] substance is acidic [H+] < [OH-] substance is basic H3O+ (aq) + OH- (aq)

1.3

pH and pOH [H+] in terms of pH pH = - log [H+] pOH = - log [OH-] pH + pOH = 14.00

For neutral solution, pH 7, [H+] = 1.0 x 10 -7 M Acidic when [H+] > 1.0 x 10 -7 M e.g. [H+] > 1.0 x 10 -3 M pH = - log (1.0 x 10 -3) =3

Basic when [OH-] > 1.0 x 10 -7 M

Calculating Ka from pH e.g. 0.10 M solution of formic acid (HCOOH) has pH 2.38 at 25C. (a) Calculate Ka for formic acid at this temperature. 1. Write equation for equilibrium reaction. Ionisation equilibrium for formic acid is: HCOOH (aq) Ka = [H+] [HCOO-] [HCOOH] 3. From the measured pH, can calculate [H+]: pH = -log [H+] log [H+] = -2.38 [H+] = 10-2.38 = 4.2 x 10-3 M 4. Can determine the concentrations of the species involved in equilibrium. HCOOH Initial Change 0.10 M - 4.2 x 10-3 M H+ 0 + 4.2 x 10-3 M HCOO0 + 4.2 x 10-3 M H+ (aq) + HCOO- (aq)

2. The equilibrium constant expression is:

Equilbrium

0.10 - 4.2 x 10-3 M

4.2 x 10-3 M

4.2 x 10-3 M

0.10 - 4.2 x 10-3 M is approximately 0.10 M

5. Insert equilibrium concentrations into Ka. Ka = (4.2 x 10-3 ) (4.2 x 10-3) = 1.8 x 10-4 0.10 6. Check: Answer reasonable as Ka for a weak acid is between 10 -3 and 10 -10 (b) What percentage of the acid is ionised in this 0.10 M solution? 1. % acid that ionises given by concentration of H+ or HCOO- at equilibrium / initial acid concentration, x 100% Percent ionisation = (4.2 x 10-3 ) x 100% = 4.2 % 0.10 6

Calculating pH from Ka For weak polyprotic acids (more than one proton to donate) both dissociations will be weak so no need to consider the contribution to pH of the second or third etc dissociation H2SO4 is an exception as first dissocation is strong

e.g. Determine the pH of a 0.0020 M Solution of carbonic acid (pKa1 = 6.35, pKa2 = 10.33) 1. Write the ionisation equilibrium H2CO3 (aq) H+ (aq) + HCO3- (aq)

2. Calculate what Ka equals First dissociation is weak, second is much weaker so can ignore. Ka1 = 10-6.35 = 4.5 x 10-7 3. Tabulate the concentrations of species involved in equilibrium reaction, where x equals [H+] H2CO3 Initial Change 0.002 -x H+ 0 +x HCO30 +x

Equilbrium

0.002 - x

4. Insert equilibrium concentrations into Ka. Ka = x2 0.002 x Neglect x as it is small compared to 0.002 5. Solve equation for x x = (0.002 x 4.5 x 10-7) = 3.0 x 10-5 [H+] = 3.0 x 10-5 pH = -log (3.0 x 10-5) = 4.5 = 4.5 x 10-7

1.4

Hydrolysis of ions Hydrolysis: when a cation or anion reacts with water to change its pH

Hydrolysis of cations Most cations act as acid in aqueous solution undergo acid hydrolysis Exceptions: group 1 and some group 2 metal ions pH neutral so no effect on pH Cations make solutions acidic Acid-dissociation constants for hydrolysis increase with increasing charge and decreasing radius of ion e.g. Cu2+ which has smaller charge and larger radius that Fe3+ forms less acidic solutions E.g. Fe(H2O)63+ (aq) Fe (H2O)5(OH)2+ (aq) Hydrolysis of anions The anion of a weak acid (HA) is a weak base hydrolyse to produce OHA- + H2O HA + OHExceptions: OH-, HSO4-, Cl-, Br -, I-, NO3-, ClO4- most neutral so dont affect pH, HSO4- is a weak acid not base e.g. CH3COO- + H2O CH3COOH + OHFe (H2O)5(OH)2+ (aq) + H+ (aq) Fe (H2O)4(OH)2+ (aq) + H+ (aq)

For anions that could be acidic or basic look at pKa and pKb and see which is smaller, or which K is bigger pKa < pKb then acidic pKb < pKa then basic e.g. H2PO4- and HPO42For phosphoric acid, H3PO4, pKa values are 2.12, 7.21, 12.38 pKa (H3PO4) = 2.12 pKb (H2PO4-) = 14 2.12 = 11.88 pKa (H2PO4-) = 7.21 (H2PO4-) is acidic pKa < pKb pKb (HPO42-) = 14 - 7.21 = 6.79 pKa (HPO42-) = 12.38 (HPO42-) is basic pKb < pKa

pH of salt solutions

Given the formula of salts able to see if acidic, basic or neutral in water E.g. NaF: Na+ is neutral (group 1 metal ion) F- is the anion of a weak acid basic So basic

E.g. KCN: K+ is neutral (group 1 metal ion) CN- is anion of a weak acid basic So basic

E.g. NH4Cl: NH4+ is an ammonium ion acidic Cl- is anion of strong acid neutral So acidic

E.g. NaNO3: Both ions are neutral so will be pH 7 If cation is acidic and anion is basic need to look at pKa and pKb smallest pK (biggest K) wins e.g. NH4F: pKa (NH4+) = 9.24 pKb (F-) = 10.83 pKa < pKb so salt is slightly acidic in water

1.5

Buffer solutions Buffer: solution that resists change in pH when small amounts of acid / base added to it Maintain pH at safe levels in body Mixture of weak acid (HA) and its conjugate weak base (A-) in similar conc. acid: consumes added H+ base: consumes added OH-

Best buffering occurs at pH values near pKa of conjugate acid Different pairs given buffering at different pH values can prepare buffers of any pH e.g. for buffering near pH 4-5 acetate buffer (CH3COOH / CH3COO-) as pKa of CH3OOH is 4.76 Reactions: CH3COO- + H+ CH3COOH or CH3COOH + OH- CH3COO- + H2O

Henderson-Hasselbalch equation Determine concentration of conjugate acid and base for desired buffering pH (vice versa)

Best buffer solutions have ration of [A-] / [HA] close to 1 pH = pKa + log10 [A-] [HA] pH = pKa + log10 [base] [acid]

CH3COOH e.g. If pH 9 buffer needed, choose NH4+/ NH3 because pKa (NH4+) is 9.25. What concentrations of the two species are needed? What approximation is being made in this type of calculation? concentrations in HH eqn are meant to be equilibrium concentrations but we usually put in initial concentrations. pH = pKa + log10 [NH3] [NH4+] log10 [NH3] = pH - pKa = 9 9.25 = 0.25 [NH4+] [NH3] = 10 -0.25 = 0.562 [NH4+] So any concentrations in the ratio 0.562 will work higher concentrations will be better (more buffer capacity)

e.g. Calculate the pH of a buffer which is 0.05M in acetic acid and 0.07M in sodium acetate. pKa (CH3COOH) = 4.76 pH = pKa + log10 [CH3COO-] [CH3COOH] pH = 4.76 + log10 (0.07 / 0.05) = 4.91

e.g. How much will the pH change if 10mL of 0.1 M NaOH is added to 20mL of water? Before: pH = 7 After: [OH-] = n/V = (0.01 L x 0.1 M)/0.03 L = 0.03333..M pOH = -log10 (0.0333) = 1.477 pH = 14 1.477 = 12.52

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e.g. How much will the pH change if 10mL of 0.1 M NaOH is added to 20mL of a solution containing 0.005 mol of NaH2PO4 and 0.006 mol of Na2HPO4? pKa (H2PO4-) = 7.21 Before: pH = pKa + log10 [Na2HPO4] [NaH2PO4] pH = 7.21 + log10 [0.006 / 0.02] = 7.29 [0.005/0.02] After: pH = 7.21 + log10 [0.007 / 0.02] = 7.45 [0.004/0.02]

Buffer capacity Amount of added acid or base a buffer can tolerate before pH changes significantly Determined by actual concentrations of conjugate acid and base that make up buffer I.e. can only add so much strong acid before base in buffer runs out (vice versa)

1.6

Titrations Titration: incremental addition of reactant of known concentration to another of unknown concentration, in order to determine unknown. Buffers made by titrating the conjugate acid with small volume of NaOH or the base with HCl until the desired pH is obtained. Plot pH vs volume of base added Equivalence point: equal number of moles of OH- and H+ - very steep rise in pH around the equivalence point Strong acid + strong base e.g. HCl and KOH Equivalence point = pH 7

Weak acid + strong base e.g. CH3COOH + NaOH Equivalence point = pH > 7 because solution contains conjugate base (CH3COO-) of weak acid and neutral Na+ ions (spectators)

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e.g. 20mL of 0.1 M CH3COOH + NaOH (0.1M) Moles of CH3COO- product = moles of CH3COOH reactant = c x v = 0.1 M x 0.02 L = 0.0002 mol

Final volume = original + added = 20 mL + 20 mL = 0.04L [CH3COO-] = n/v = 0.0002 / 0.04 = 0.005 M Equivalence pt. PH weak base calculation: e.g. What i pH of 0.005M solution of CH3COO-? Dissociation (hydrolysis) reaction: CH3COO- + H2O 0.005 x CH3COOH + OHx x

pKa (CH3COOH) = 4.76 (given), so pKb (CH3COO-) = 14 4.76 = 9.24 Kb = 10-9.24 = 5.75 x 10 10 Kb = [CH3COOH][OH-] = x2 = 5.75 x 10-10 [CH3COO ] 0.005 - x x2 = 0.005 x 5.75 x 10-10 x = 1.70 x 10-6 = [OH-] pOH = -log10 (1.70 x 10-6) = 5.77 pH = 14 5.77 = 8.23

Initial pH >1 NB: initial pH determined by the pKa of the weak acid Around the mid-point of the titration, half of the acid is gone, replaced by conjugate base solution in the flask is a buffer pH of solution = pKa of weak acid i.e. pKa can be read off graph

12

Strong acid + weak base E.g. HCl + NH3 Equivalence point = pH < 7 Initial pH < 13 NB: initial pH calculated by weak base calculation At midpoint pH = pKa of conjugate acid (NH4+)

1.7

Indicators in acid/base titrations Indicator is weak acid or base that undergoes dramatic colour change over narrow pH range Endpoint of titration corresponds to change of indicator colour Equivalence point it point at which an equivalent number of moles of one reactant has been added to the other not the same as endpoint! Choosing indicator Indicator endpoint should be close as possible to equivalence point Good indicator changes colour in steepest part of titration curve

pH of indicator Indicators have differently coloured base (Ind-) and acid (Hind) forms e.g. methyl red HInd (red, pKa = 5.1), Ind- (yellow) Can use equ. to work out pH range of colour change for indicator pH = pKa (Ind) + log10 [Ind-] [HInd] Colour change will occur between pH = pKa (Ind) 1 and pH = pKa (Ind) + 1 Choose indicator with pKa (Ind) close to pH of equiv point NB: dont confuse pKa of indicator with pKa of acid!!

Applying this Many diff indicators can be used for SASB titrations because steep section of curve is so long (6-7pH units) just because doesnt change colour at pH = 7 doesnt mean it is unsuitable Have to choose more carefully for SAWB and WASB

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1.8

Practice questions 1. Estimate the pH of the equivalence pt. when 25mL of 0.100 M ammonia (NH3) solution is titrated with 0.200 M HCl. Use pKb = 4.76. Hint: Vol HCl required: [NH4+] = NH4+ ... x Solve for x: H+ + NH3 x x

pH =

Ans: 5.20

2. Calculate the change in pH on addition of 0.040 mol of sodium hydroxide to one litre of an 0.05 M NH3/ 0.10 M NH4Cl buffer solution. Assume there is no volume change on addition of the sodium hydroxide. Ka for NH+ = 6.3 x 10-10 at this temp. Before: pH = pKa + log10 [NH3]/[NH4+] After: OH- reacts with NH4+ to form more NH3, so moles (and conc) of NH4+ drops to 0.06 and moles (and conc) of NH3 rises to 0.09 pH = Ans: 9.38

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2
2.1

Solubility equilibria
Insoluble salts All salts are soluble to some degree Equilibrium pt. is saturated solution no more solute can dissolve Some undissolved solid must be present for equilibrium

Salts which are sparingly soluble in water: Phosphates (PO43-) Carbonates (CO32-) Sulfides (S2-) Hydroxides (OH-) Some halides (Cl-, Br-, I-) Sulfates (SO42-)

Exceptions Na+, K+, NH4+ salts

2.2

The solubility of a salt Solubility of a salt (s), is the amount dissolved in a saturated solution / unit V Measured in g L-1 or mol L-1 Varies with temp When calcium hydroxide dissolves, dissociates according to: Ca(OH)2 (s) Ca2+ (aq) + 2OH- (aq) Because of 1:1 ratio, [Ca2+] same as s, molar solubility of Ca(OH)2 E.g. if 0.012 mol of Ca(OH)2 dissolves per litre of water, then s = 0.012 M Then [Ca2+] = 0.012 M, [OH-] = 2 x 0.012 = 0.024 M Solubility (s) of a salt not to be confused with solubility product Ksp E.g. for reaction AgCl (s) Ksp = [Ag+] [Cl-] = [Ag+] [Cl-] [AgCl] Solubility, s, of AgCl is 1.34 x 10-5 M So [Ag+] = [Cl-] = 1.34 x 10-5 M But Ksp = [Ag+] [Cl-] = s2 = 1.8 x 10-10 15 Ag+ (aq) + Cl- (aq)

Problem questions 1. The solubility product for calcium phosphate, Ca3(PO4)2 is 1.2 x 10-29 at 25 C. What concentration for calcium ions will exist in a saturated solution of this salt at this temperature? What is the molar solubility of this compound? Ca3(PO4)2 Equilib conc: 3Ca2+ + 2PO433x 2x (if had old table)

Ksp = [Ca2+]3 [PO43-]2 = [3x]3 [2x]2 = 108x5 = 1.2 x 10-29 x = 6.44 x 10-7M [Ca2+] = 3x = 1.93 x 10-6M So, solubility of compound is a third of [Ca2+] - molar ratio 1:3 i.e. it is x, so solubility of Ca3(PO4)2 is 6.44 x 10-7M

2.3

The ionic product Reaction quotient for ionic dissolution Determined by current concentrations (non-equilibrium) Qsp = [Ag+] [Cl-] If Q > K system is supersaturated... precipitation occurs until Q = K Q = K, system is at equilibrium Q < K, more solid can be dissolved until Q = K e.g. Will a precipitate form if 10mL of 1.0 x 10-2 M NaCl and 10mL of 1.0 x 10-4 M AgNO3 are mixed? Assume that the final volume of the solution is 20mL. For AgCl, Ksp = 1.7 x 10-10 at this temp. Finding out whether a precipitate of AgCl will form. NB: both ions are diluted upon mixing [Ag+] = 1.0 x 10-4 x (10mL/20mL) = 5.0 x 10-5 M [Cl-] = 1.0 x 10-2 x (10mL/20mL) = 5.0 x 10-3 M Qsp = [Ag+] [Cl-] = (5.0 x 10-5) x (5.0 x 10-3) = 2.5 x 10-7 Qsp > Ksp so precipitate will form ..... dilution!!

2.4

The common ion effect

16

Reaction has reached equilibrium and more ions already in solution are added For example adding AgNO3 to AgCl Ag+ is common ion The added Ag+ drives equilibrium to the left reduces solubility of AgCl (Le Chateliers Principle) AgCl (s) added Ag+ Ag+ (aq) + Cl- (aq)

Common ions reduce the solubility of ionic solutes i.e. decreases the solubility of the original substance 1. Determine the solubility of AgCl in pure water. Ksp = 1.8 x 10-10 AgCl (s) s = [Ag+] = [Cl-] Ksp = [Ag+] [Cl-] = s2 = 1.8 x 10-10 s = 1.34 x 10-5M 2. Determine the solubility of AgCl in 0.1 M NaCl (common ion Cl-). Compare this result with the answer to part 1. Let solubility, s = [Ag+] = x AgCl (s) Equilib. Conc: Ag+ (aq) + Cl- (aq) x x + 0.1 Ag+ (aq) + Cl- (aq)

Ksp = [Ag+] [Cl-] = x (x + 0.1) = 1.8 x 10-10 Neglect x in brackets, so: 0.1x = 1.8 x 10-10 x = 1.8 x 10-9 M Solubility decreased

2.5

Dependence of solubility on pH Most metal hydroxides e.g. Cu(OH)2 are insoluble sparingly soluble The solubility of many metal ions will depend on pH as it is related to [OH-] Can use Ksp to decide whether a metal cation will be soluble at given pH

17

Metals usually more soluble in acid e.g. Calculate the maximum pH required to prevent Cu(OH)2 precipitation from a 0.1M solution of Cu(NO3)2. Ksp of Cu(OH)2 = 2.2 x 10-20 Cu(OH)2 (s) Cu2+ + 2OH-

Ksp = [Cu2+] [OH-]2 = 2.2 x 10-20 For equilibrium, [OH-] = ( Ksp / [Cu2+]) = 6.49 x 10-10 M ??? pOH = 9.33, pH = 4.67: above this pH, [OH-] will be high enough for precipitation.

2.6

Salts with basic anions If sparingly soluble salt has anion which is weak base addition of H+ will increase its solubility E.g. adding H+ to CaF2 will move reaction to the right more CaF2 will dissolve CaF2 Ca2+ + 2F added H+

Chemical kinetics
The study of the rates of chemical reactions and the mechanisms by which they occur.

3.1

Reaction rate Rate: change in concentration per unit time mol L-1 s-1 Reaction rate positive: expressed in terms of products (concentrations increasing with time) Reaction rate negative: expressed in terms of reactants (concentrations decreasing with time) Example of data set for rate of decomposition reaction:

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Factors that determine reaction rate Concentration (surface area) Temperature Physical state Molecular structure / size Catalysts

3.2

Average rate Average rate = change in concentration time interval NB: positive if products, negative if reactants Can read values off graph to determine e.g. Using graph below: Average rate = - (6.66 x 10-3) (7.12 x 10-3) 600 -500 = 4.6 x 10 mol L-1 min -1
-6

3.3

Instantaneous rate Instantaneous rate = slope of tangent to curve at time t = - d [R] dt or d [P] dt

NB: positive if products, negative if reactants Instantaneous rate more useful than average rate Rate of reaction usually means instantaneous rate

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3.4

Reaction rates and stoichiometry For aA + bB cC + dD - 1 d [A] = - 1 d [B] = 1 d [C] = 1 d [D] a dt b dt c dt d dt Relates to molar ratio So for H2 (g) + I2 (g) 2HI (g): HI must be produces at twice the rate (in moles per second) that H2 or I2 is disappearing d [HI] = 2 x - d [H2] dt dt E.g. What are the relative rates of change in concentration of products and reactants in the following decomposition reaction? 2NOCl (g) 2NO (g) + Cl2 (g) - 1 d [NOCl] = 1 d [NO] = d [Cl2] 2 dt 2 dt dt

3.5

Rate laws - d [R] = k [R1]a [R2]b dt k is rate constant R1, R2... are reactants a, b... are orders of the reaction with respect to R1, R2... determined by experiment a + b + ... is overall order of the reaction

If the exponent is 1 rate first order, 2- second order etc. Exponents show how rate affected by concentrations of reactants In some cases change in concentration of reactant does not affect rate zero order concentration of component does not appear in rate law NB: Coefficients not relevant to rate law!! k large: reaction is fast (k > 10 sec-1) k small: reaction is slow (k < 10-3 sec-1)

Applying reaction order If reaction order for reactant is 1 rate proportional to conc. of that reactant E.g. for A + B products rate = k [A][B]2 Doubling the concentration of A will double rate of reaction

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If reaction order for reactant is 2 rate depends on concentration of that reactant squared E.g. rate = k [A][B]2 Doubling the concentration of B will quadruple rate of reaction Units of k change with overall order:

3.6

Determining rate laws experimentally There are two methods to find values for k, a, b, etc.: 1. 2. Initial rate method Integrated rate law method

3.7

Initial rate method Reaction repeated in series of experiments Initial concentration of one reactant at a time is altered between experiments Initial rate of reaction determined each time

Calculations arithmetic method 1. 2. 3. 4. 5. Pick a pair of experiments Find the reactant whose concentration does change between experiments Determine ratio (n) of reactants concs. in the two experiments If the order of this reactant is a the corresponding ratio of rates is n a Solve for a

Graphical method Can determine a using a graph. Since rate = d [I-] = k [I-]a[S2O82-]b and [S2O82-]b is fixed in the experiment can write: dt log10 d [I-] = a log10 [I-] + constant dt So plot log10 d [I-] vs. log10 [I-] dt Will be a straight line with slope = a

21

E.g. the reaction 2I- + S2O82- 2SO42- + I2 is assumed to have rate law of the form: - d [I-] = k [I-]a [S2O82-]b dt Determine the vales of k, a, and b using the data collected in the three experiments:

Determine the vales of k, a, and b using the data collected in the three experiments: So compare experiments 2 and 3 to obtain a (with respect to I-) [S2O82-] constant Rate 2 = k [I-]a [S2O82-]b = ([I-](2)/ [I-](3))a Rate 3 k [I-]a [S2O82-]b i.e. 1.5 x 10-4 = (6.0x 10-2 / 2.0 x 10-2)a 5.0 x 10-5 3 = 3a a=1

Having found a = 1, b = 1, rearrange rate law to find k. Rate = k [I-]a [S2O82-]b k = rate / ([I-]a [S2O82-]b) Substitute vales for rate, [I-] and [S2O82-] from any one experiment in the table to find k = 0.125 L mol-1 s-1 NB: second order reaction overall as a + b = 2

3.8

Integrated rate law method (rate and conc. vs. time) Aim to find a way of producing a straight line plot of the data - linear plot required depends on the order of the reaction. Integrated first order rate law If reaction A B + C is first order in A, rate law is: - d [A] = k [A] dt Rearranged as: [A]t = [A]0 e-kt A plot of reactant conc. vs. time shows exponential decrease Plot of ln[A] vs. time gives a straight line, slope = -k

22

Half-life (t1/2 ) of first order reactions Half life of first order reaction: time taken for concentration to decrease by half For first order reaction half-life is a constant and can be measured from any point in the reaction t1/2 = ln 2 k NB: if we know t, we know k (vice versa)

Integrated second order rate law If reaction 2A B + C is second order in A, rate law is: - d [A] = k [A]2 dt Rearranged as: 1 - 1 = kt [A]t [A]0 Plot of 1 vs. time gives a straight line, slope = k [A]

Distinguishing first and second order reactions Compare graphs to see which is linear E.g. 2 NOBr (g) 2 NO (g) + Br2 (g)

Reaction mechanisms
Rate laws are used to propose mechanisms for chemical reactions. Mechanisms: series of steps that describes the molecular events taking place in reaction.

4.1

Steps in mechanism

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Rate determining (or limiting) step (RDS) Slowest step in mechanism As reaction cannot go faster than slowest step RDS is also rate of overall reaction E.g. NO2 + CO NO + CO2 is found to have rate = k [NO2]2 [CO]0 Proposing a mechanism that is consistent with this rate law 2-step mechanism:

Here NO3 is an intermediate produced then consumed. As step 2 is must faster than step 1 (k2 >k1), step 1 is rate determining. Rate of overall reaction = rate of step 1. For step 1 rate = k [NO2]2 rate law predicted by this mechanism agrees with the one observed experimentally.

Elementary step One step reaction Rate law can be determined from stoichiometry (unlike for overall reaction!!) E.g. for elementary step 2A + B C rate = k [A]2 [B] Number of reactant molecules called molecularity Reactions usually unimolecular or bimolecular (1 or 2 reactant molecules in RDS) E.g. (CH3)3CCl + OH- (CH3)3COH + ClTwo different mechanisms proposed one unimolecular and one bimolecular Unimolecular mechanism: (CH3)3CCl (CH3)3C+ + Cl(CH3)3C + OH (CH3)3COH
+ -

slow, RDS fast

Rate law predicted: - d [(CH3)3CCl] = k [(CH3)3CCl] dt Bimolecular mechanism: (CH3)3CCl + OH- [(CH3)3CCl][(CH3)3CCl] (CH3)3COH + Cl
-

slow, RDS fast

Rate law predicted: - d [(CH3)3CCl] = k [(CH3)3CCl][OH-] dt 24

When kinetics experiments are performed, the rate law was found to be: rate = k [(CH3)3CCl] i.e. the unimolecular mechanism is supported

4.2

Dependence of reaction rates on temp Reaction rates increase by 2x with every 10 increase in temp (T) Rate and k increase exponentially with T E.g. T (C) 189.7 198.9 230.3 251.2 k (s-1) 2.52 x 10-5 5.25 x 10-5 6.30 x 10-4 3.16 x 10-3

4.3

Arrhenius equation rate and temp Explains exponential relationship between rate and temp by proposing: reactant molecules need a minimum energy (activation energy) to react. A pre-exponential factor (same units as k) Ea activation energy (J mol-1) T temperature (K) R ideal gas constant ( = 8.3145 J K-1 mol-1)

k = A e (Ea/RT) NB: reaction rates decrease as Ea increases Fraction of collisions As temp increases, a greater fraction of collisions occurs with sufficient energy (> Ea) to react. The fraction (f) of molecules that has energy equal to or greater than Ea i.e. with sufficient energy to react, is: f = e-Ea / RT

25

f increased by: - decreasing activation energy - increasing temp

Summary Collision between reactant molecules necessary for reaction Not all collisions lead to reaction, only the fraction f with energy greater than Ea A is the number of correctly-oriented collisions per second (molecules must make contact at right pts) Using the Arrhenius equation If the rate constant, k, is measured at different temps can determine Ea Plot ln k vs. 1/T. Taking logs of equ. ln k = ln A - Ea RT Plot is straight line with slope = -Ea RT

4.4

Reaction profiles The activation energy is a barrier that must be overcome for reaction to occur Energetic changes during reaction represented by reaction profile Plot of potential energy vs. extent of reaction

Exothermic reaction

26

Ea energy difference between reactants and top of barrier H amount of energy absorbed or released by the reaction (diff between reactants and products) Exothermic energy released by reaction (energy of reactants greater than energy of products i.e. H is negative) Endothermic energy absorbed by reaction (energy of reactants less than energy of products i.e. H is positive)

4.5

Catalysts A catalyst: (a) (b) (c) Increases rate of reaction w/out being consumed Is reactant and a product in reaction mechanism Reduces Ea by changing mechanism of reaction

Catalyst may be heterogeneous (different phase to reactants) or homogeneous (same phase). Phase refers to states (solid, liquid, gas) and different liquids such as water and oil. Heterogeneous e.g. solid catalyst with reactants as liquids or gases.

27

4.6

Enzymes Enzymes are biological catalysts that: (a) (b) (c) (d) Perform chemical reactions on substrate molecules Are very specific (lock and key model) Enable reactions that are normally impossible (too slow) Are proteins

4.7

Relationship between kinetics and equilibrium At equilibrium, rates of the forward and reverse reactions are equal. So for following reaction at equilibrium: aA + bB We may write: forward rate = reverse rate kf [A]a [B]b = kr [C]c [D]d [C]c [D]d / [A]a [B]b = kf / kr = Kc i.e. the equilibrium constant is the ratio of the forward and reverse rate constants cC + dD

5
5.1

Organic chemistry: part 1

Isomers Isomers (same parts): two or more compounds with the same molecular formula

28

5.2

Constitutional (structural) isomers Atoms connected in different order

Example: C8H8O3

5.3

Stereoisomers Atoms connected in same order but arranged differently in space. Non-superimposable.

5.4

Enantiomers (optical isomers) Non-superimposable mirror images of each other. Pairs of stereoisomers that are chiral mirror image actually a different molecule. Have identical physical and chemical properties. E.g. human hands.

29

Chirality Chiral molecules: non-superimposable mirror images have chiral centre or sterocentre lacks internal plane of symmetry! Achiral molecules: superimposable on mirror images (same molecule) possess plane of symmetry Chirality centre: an atom that has 4 different groups bonded to it

Cahn-Ingold-Prelog Rules (R, S sequence priority rules) Information about molecules absolute configuration

Method 1. 2. Locate the centre of chirality Assign priority to each substituent from 1 (highest) to 4 (lowest) based on atomic number

3.

Orient the molecule so that the group of lowest priority points away dont use priority group 4 for working out direction!

4.

Read the remaining groups from highest to lowest Clockwise = R Anticlockwise = S

30

e.g. Assign the absolute configuration as R or S to the following: 1. Locate the chirality centre.

2. Assign priorities, note for 2 and 3, if two atoms have same priority move along chain till there is difference here O has higher priority than H.

3. Read the remaining groups from highest to lowest.

Clockwise - R

e.g. Assign the absolute configuration as R or S to the following: 1. Locate the chirality centre.

2. Assign priorities and point lowest priority group away

3. Read the remaining groups from highest to lowest.

Clockwise - R

31

5.5

Diastereoisomers Stereoisomers that are not enantiomers Molecules with two or more stereocentres Stereocentre: molecule with at least 3 different attachments Cis/trans isomers Have different chemical and physical properties e.g. melting points

Cis/ trans isomers Cis = same side of bond Trans = different side of bond (diagonal)

Meso isomers An achiral (has internal plane of symmetry same molecules) molecule possessing two or more stereocentres

32

HOW TO DO R S PRIORITISING FOR LONGER MOLECULES!!

33

5.6

Unsaturated hydrocarbons Unsaturated hydrocarbons: contain one or more double or triple bonds Carbons arent attached to 4 separate molecules

Alkenes At least one C-C double bond.

Alkynes At least one C-C triple bond. Carbon in triple bond has linear geometry.

5.7

Aromatic hydrocarbons (arenes) Aromatic hydrocarbons: contain one or more benzene rings. Not alkenes Molecules have planar ring structure all atoms in common plane, symmetrical

34

Examples:

Benzene geometry The C atoms in benzene are sp2 hybridised with 120 bond angles (sp2 if three things attached to central atom, sp3 if four things attached etc. )

Unhybridised p orbitals are at 90 to the plane of the ring.

Benzene has delocalised bonds double bonds move in structure i.e. it is resonating e.g.

Can represent this by drawing two resonance structures or by a circle in middle of structure. (Hydrogens are assumed)

5.8

Aromaticy Aromatic: cyclic, conjugated molecule with stability (due to delocalisation) greater than that

35

of localized structure * Conjugated molecule: has double or triple bonds separated by single bond Huckels Rules for Aromaticity 1. 2. 3. Molecule must have a ring with at least one unhybridised p orbital on each atom Molecule must be planar The number of -electrons must equal [4n+2] where n is an integer (0, 1, 2) -electrons is number of electrons in double bonds (2 in each) E.g. Benzene We know every atom in ring is sp2 hybrid Molecule is planar Check if number of -electrons equals 4n+2 or 4n. (no. of -electrons = 6) 4n+2 = 6, n = 1 4n = 6, n =3/2

-electrons equals 4n+2 as n must be whole number. Therefore we know it is aromatic.

Anti-aromatic: number of -electrons = 4n Non-aromatic: sp3 hybrids 4 attachments to central atom E.g. Cyclopentadiene

Atom at top is sp3 hybrid (has 4 attachments) therefore non-aromatic.

E.g. Furan

If you can identify sp2 hybridised atom attached to another atom with lone pairs that atom is also sp2 hybridised Molecule is planar Check if number of -electrons equals 4n+2 or 4n. (no. of -electrons = 6) 4n+2 = 4, n = 1 4n = 6, n =3/2 Therefore aromatic. 36

Naming arenes Names of benzene-containing compounds derived from benzene common names retained in some instances Names end in benzene If benzene group has an OH attached, name ends in phenol Label as though the first group is 1

When benzene ring has two substituents has 3 constitutional isomers

5.9

Reactivity of benzene Benzene reacts differently to alkenes due to resonance

37

Aromatic compounds undergo substitution reactions electrophilic aromatic substitution Hydrogen replaced by a substituent (Lewis acid); often needs catalyst

Two step process: (1)

(2)

Examples:

5.10

Reactivity of alkenes

38

Naming alkenes 1. 2. 3. 4. Find and name longest carbon chain containing C=C bind No the chain from the end closest to C=C bond List position of double bond(s) using smaller number List each substituent and its position

e.g.

Reactions due to C=C double bound 1. 2. 3. 4. 5. 6. Hydrogenation Hydration Halogenation Polymerisation Hydroxylation Hydrohalogenation

Hydrogenation Alkenes react readily with H2 at room temp in presence of a metal catalyst (Ni, Pd, Pt) Reduction of alkene to corresponding alkane e.g. ethene ethane

Saturates compound Exothermic releases energy Carbon skeleton preserved

39

Hydration Addition reaction Adding water to double bond to produce alcohol Catalysed by strong acid Markovnikovs Rule when you add a molecule HX to carbon carbon double bond, hydrogen joins carbon atom that has more H atoms attached to it Ethene Ethanol

Halogenation Addition of Br2 and Cl2 One atom bonds to each side of the double bond (trans addition) Does not need light/ heat as catalyst Colour change indicates reaction brown/ orange clear colourless Reaction used for: testing presence of double bond distinguishing between alkanes and alkene/alyne

40

Hydroxylation Alkenes react with KMnO4 (potassium permanganate) Gives 1,2 diols diol: An alcohol containing two hydroxyl groups -OH Adds OH to each end of C=C bond Reaction used as test for double bond

Polymerisation C=C double bonds react with each other Form long chains of singly bonded carbons (more stable) Alkene molecules become polymer chain of repeating units

Polymer: large molecule composed of repeating structural units

41

Hydrohalogenation Addition of hydrohalic acids (composed of hydrogen and halogen group 17) to alkenes Yields corresponding haloalkanes (single bonds)

Example using symmetrical alkene

Example using asymmetrical alkene C(1) is bonded to 2 H atoms C(2) is bonded to 1 H atoms

Two structural isomers possible Markovnikovs Rule states H adds to C of double bond which is already bonded to more H atoms H adds to C(1) and Br adds to C(2)

Markovnikovs Rule In the addition of an acid to a double bond, the hydrogen attaches to the carbon already bonded to the greatest number of hydrogens.

42

5.11

Alcohols General formula R-OH where R is a carbon group

Naming alcohols Main chain must contain OH group (doesnt have to be at end of chain) 1. 2. Name the longest C chain which contains the OH group Number the chain from the end which gives OH the smallest number OH group gives suffix ol Two OH groups gives suffix diol 3. List any other substituents and their positions

Classification Determines reactions Primary (1) alcohol: Carbon atom bearing OH group also bonded to 2 hydrogen atoms

Secondary (2) alcohol: Carbon atom bearing OH group also bonded to 1 H

43

Tertiary (3) alcohol: Carbon atom bearing OH group not bonded to a H atom

Properties Difference in electronegativity between O and H allows alcohols to hydrogen bond Compared to alkanes: o o More soluble in water Higher boiling and melting pt

Soluble in both H-bond forming and non H-bond forming solvents

Phenols Phenols: class of alcohol with direct attachment of OH group to benzene ring Phenols more acidic than alcohols Negative charge can be delocalised!

Reactions Substitution (alcohol to haloalkanes) Glue in pic

44

 Elimination (haloalkane to alkene)

Nucleophiles (love +) have a pair of electrons which are used to form a bond to the electrophile (love -) Leaving group departs to make room for nucleophile Nucleophile converts lone pair to a bond and becomes positive by +1 Bond from C to leaving group collapses into a lone pair on the leaving group when becomes negative by -1 Nucleophile is lewis base, electrophile is lewis acid

Glue in pic

A base as catalyst can remove the leaving group and an adjacent H-creating a (double) bond.

Competition between elimination and nucleophilic substitution of alcohols

Glue in pic

Reactant is a strong base elimination Reactant is nucleophile but poor base substitution

Result is dependant on: 1. Accessibility of -carbon (first carbon that attaches to functional group) bearing the halide (group 17 metal + another element) o More accessible substitution favoured

2.

Size of the alkoxide (conjugate base of alcohol) o Bigger the alkoxide elimination favoured

45

3.

Accessibility of- hydrogen (hydrogen that attaches to second carbon) o More accessible elimination favoured

E.g. predict the major product from the following reaction:

Using rules:

Therefore the elimination reaction is favoured.

Nucleophilic substitution reactions of alkyl halides * alkyl halides: single bonded coumpound with C, H, and a halogen (Cl, Br, I, Fl) Alkyl halides react with nucleophiles and bases Nucleophiles replace the halide in C-X bonds of alkyl halides

5.12

Carboxylic acids Contain the functional group COOH

46

carboxylic acid

carboxylate ion

Naming carboxylic acids 1. 2. 3. 4. Name the longest C chain which contains the COOH group Number the chain so that the C of the COOH group is #1 Give suffix oic acid List any other substituents and their positions

Acidity and dissociation in water Weak acids Do not dissociate completely in water Any carboxylic acid that dissolves in water behaves in this way:

% dissociation depends on pH Knowing the pKa - calculate % dissociation using Hendersen-Hasselbalch equation: pH = pKa + log [conjugate base] conjugate acid e.g. In what form is acetic acid blood plasma (pH 7.4)? pH - pKa = log [CH3CO2-] CH3COOH 7.4 4.8 = 2.6 [CH3CO2-] = 102.6 = 400 CH3COOH 47 1/400 x 100 = 0.3% CH3COOH 100 0.3 = 99.7% CH3CO2-

Reaction with base Carboxylic acid + base carboxylate ion + water

When converted into salts they are more stable, soluble compounds

Resonance Carboxylic acids are more acidic than alcohols This is due to resonance in carboxylate ions The negative charge on the O atom is delocalised and spread between both Os weaker attraction for H+ - weaker bases This makes the carboxylic acid a stronger acid can donate H+ more easily

Trends in acid strength Electronegative groups (such as F or Cl) near the COOH group increases acidity This is because the negative charge is shared out amongst electronegatives in the ion weaker attraction for H+ - weaker base carboxylate is stronger acid NB: smaller pKa is more acidic!!

48

Separating acid from neutral compounds (experiment) Separating compounds 1. Place acid and neutral compound in separatory funnel with an organic solvent and water o Two compounds have similar polarities and both dissolve in organic layer (of moderate polarity) 2. Separate the compounds by converting the water insoluble acid into a water soluble salt by reaction with aqueous base (e.g NaOH) moves into aqueous layer o The other compound will not react with NaOH and remains dissolved in organic layer

3.

Use separatory funnel to separate aqueous and organic layer drain one out.

Recovering the compounds in pure form 4. 5. 6. 7. Dry organic layer and evaporate solvent Recrystallise the acid by adding strong acid to aqueous layer neutralises strong base Filter to isolate the solid then dry Measure the mass of each and melting points to test purity

5.13

Amines Weak organic bases related to ammonia One or more H atoms replaced by hydrocarbon groups

49

Amine

Ammonia

Naming amines 1. 2. 3. 4. Name the longest C chain Number the chain so that it gives the NH2 group smallest number Give suffix amine List any other substituents and their positions

Other rules If not the principal functional group give prefix amino Compound with multiple amino groups diamine, triamine, tetraamine

Reactions Lone pair on N accepts H+ Amine With Water Forms basic solution CH3NH2 + H2O CH3NH3+ + OHNH3 + H2O NH4+ + OHAmmonia

50

With Acid Forms salts of ammonium ion CH3NH2 + H3O CH3NH3+ + H2O NH3 + H3O NH4+ + H2O

Acidity and dissociation in water Weak bases Do not dissociate completely in water

% dissociation depends on pH Knowing the pKa - calculate % dissociation using Hendersen-Hasselbalch equation: pH = pKa + log [conjugate base] conjugate acid e.g. In what form is methyl amine (pKa 10.6) at pH 7.4? pH - pKa = log [CH3NH2] CH3NH3+ 7.4 10.6 = -3.2 [CH3NH2] = 10-3.2 = 0.00063 CH3NH3+ 0.00063/1 x 100 = 0.06% CH3NH2 100 0.06 = 99.94% CH3NH3+

Classification How many carbons bonded to N Primary (1): 1 carbon bonded to N

Secondary (2): 2 carbons bonded to N

Tertiary (3): 3 carbons bonded to N

Quaternary (4): 4 carbons bonded to N

51

1, 2, 3 ammonia ions react with OH- to form amine (donate H+ to form water) 4 ammonia ions not able to donate H+ as there is no H on the N atom

Physical properties of amines 1. Boiling points: alcohol > amine > alkane o 2. o 3. 4. Increases with number of lone Hs available for H bonding Amines with fewer than 6Cs / N are 100% soluble

More soluble than alcohols

Less soluble than ammonium salts (ionic) in water Have fishy odour

Separating base from neutral compounds (experiment) Separating compounds 1. Place base and neutral compound in separatory funnel with an organic solvent and water o Two compounds have similar polarities and both dissolve in organic layer (of moderate polarity) 2. Separate the compounds by converting the water insoluble base into a water soluble salt by reaction with dilute acid (e.g HCl) moves into aqueous layer o The other compound will not react with HCl and remains dissolved in organic layer

3.

Use separatory funnel to separate aqueous and organic layer drain one out.

Recovering the compounds in pure form 4. 5. 6. Dry organic layer and evaporate solvent Recrystallise the base by adding base to aqueous layer neutralises acid Filter to isolate the solid then dry

52

7.

Measure the mass of each and melting points to test purity

Reactions Reaction with a haloalkane (alkyl halide) Ammonia and 1, 2, 3 amines

+ OH-

+ H2O

Reaction with a ketone or aldehyde imine Ammonia and 1 amines

Reaction with a carboxylic acid amide

Synthesis of amines Reduction of imines

53

5.14

Esters Close relatives of carboxylic acid (just no H)

Identifying esters

Naming esters Useful to think of ester containing an acid part and an alcohol part

First component of name alkyl 1. 2.

(alcohol)

Root name based on longest chain containing OH group Chain numbered so as to give OH lowest possible number

Second component of name oate 1. 2. 3.

(carboxylic acid)

Root name based on longest chain including COOH group Since COOH group is at the end of the chain it must be C1 Suffice -anoate

Complete name: alkyl alkanoate

54

Example:

Solubility Methyl acetate 24% soluble Water solubility decreases with increasing chain length Longer chains dissolve well in organic solvents e.g. dimethyl ethyl

Synthesis of esters 1. Condensation reaction of carboxylic acid and alcohol Condensation: 2 molecules form one 1 molecule with water as byproduct

2.

Reaction of acid chlorides and alcohol Cl and H from alcohol bond No water formed

3.

Reaction of acid anhydrides and alcohol First half of anhydride (without centre O) and OH from alcohol bond No water formed

55

Reactions

Hydrolysis Forms carboxylic acid and alcohol (reverse of synthesis) o Ester formation in equilibrium with ester hydrolysis (double arrows)

Ester splits at O-C, H added to first half, OH added to second half

Hydrolysis promoted by a base soap production!

5.15

Amides Carboxylic acids, esters and amides are interconverted by condensation and hydrolysis reactions.

Naming amides Useful to think of amide containing an acid part and an amine part

56

1. Name the longest C chain with amide group 2. Number so amide group is smallest 3. Give suffix amide 4. List any other substituents and their positions 5. N precedes nitrogen substituent(s)

Synthesis of amides 1. Condensation reaction of carboxylic acid and amine

2.

Reaction of acid chlorides and amine

57

Physical properties Due to strong hydrogen bonds!!

1.

Amides have higher mp and bp than corresponding carboxylic acids

2.

Amides more water soluble than corresponding carboxylic acids

Reactions Hydrolysis Amides hydrolyse to acid and amine o o Does not occur at room temp Promoted by boiling with strong acid or base

58

Hydrolysis with base

Hydrolysis with acid

Difference between amides and amines

1. 2.

Amides have C=O double bond Amides are not basic o Lone pair of electrons on N is delocalised

5.16

Amino acids Building blocks of peptides and proteins 20 amino acids amine + carboxylic acid group on SAME CARBON o o Differ in side chain Classified by polar, non-polar, acidic and basic sidechains

59

Polar

Non-polar

Acidic and Basic

Properties Apart from glycine, they are chiral! (glycine has two Hs) S configuration (clockwise)

Reactions 1. Acid-base equilibria

60

Have acidic COOH and a basic NH2 group so equilibrium possible Amino acids are ionic at any pH Position of equilibrium depends on pH of solution Isoelectric point: pH at which amino acid has no net electrical charge pI = (pka1 + pka2) pH < pI, charge positive pH > pI, charge negative

2.

Side chain reactions Similar calculations to above Work out isoelectric point

61

3.

Peptide bond formation Peptides are amino acids joined together Amino acids bonded by condensation reaction (water byproduct) OH comes off end of first one H comes off start of next one ect.

5.17

Peptides and proteins Peptide: has two or more amino acids joined by peptide bonds

62

Sequence of amino acids determines biological activity

Proteins Protein: typically has 50+ amino acids held in 3D shape Held by intermolecular forces including H bonds Sequence of amino acids determines 3D shape and function Some proteins have extra components bound to polypeptide chain e.g. metal ions, sugars Structure (in water-soluble protein) Non-polar side chains point inwards Polar and ionic side chains point outwards in contact with water

Levels of protein structure

Primary (1) structure: amino acid sequence

Secondary (2) structure: folding of chain due to H bonds between amide groups in polypeptide chain

Tertiary (3) structure: final folded shape of polypeptide chain

Quaternary (4) structure: more than one polypeptide chain makes protein

63

Active sites Enzymes and receptors rely on one or more active sites specific 3D orientation of amino acid side chains May provide polar or non-polar space (lock and key model)

Protein folding 3D structures of proteins are limited Small proteins can fold spontaneously into 3D structure Many large proteins need chaperone to fold chaperone: enzyme that guides folding Can fold incorrectly called prions pass on conformations causing disease

Protein denaturation Changes in enviro may cause protein to unfold o o o H-bonding substances e.g. alcohols, phenols H bonding Detergents - hydrophobic interactions pH change salt bridges b/ween side chains

64

o o

Reducing agents salt bridges Heavy metal ions - -SH groups e.g. cysteine residue bound to Hg2+

Inactivates protein

Separation and detection Separated by electrophoresis Detected by UV absorption

5.18

Carbohydrates Often formula: Cx(H2O)y

Family tree

Monosaccharides Classified and named by whether it is aldose or ketose, hexose or pentose Do not dissolve in organic solvents High mps Do dissolve in water H bonding

65

Aldose or ketose Depends whether ketone or aldehyde group is present e.g. triose (3 C sugar)

Pentose or hexose Most monosaccharides have 5 or 6 carbons 5 Cs pentose 6 Cs hexose e.g. glucose and fructose are 6 C sugars

D or L configuration Whether OH group shown is drawn on right or left (bottom OH group) When C=O is on top Right D

66

Left L Enantiomers non-superimposable mirror images

Family tree of D-aldoses

Diastereoisomers Differ in: o o o o Shape Polarity Mp, bp, density Solubility

67

Hemiacetal groups Sugars are predominately cyclic hemiacetals The hemiacetal functional group is: (where O-R is not OH) e.g. identifying hemiacetal groups:

Closed ring or open chain structure

68

Anomeric carbon in cyclic sugars C bonded to 2 Os in a cyclic sugar

Anomers of cyclic monosaccharides -anomer: OH on bottom of ring (opposite side to CH2OH) -anomer: OH on top of ring (same side as CH2OH)

Anomers are stereoisomers and enantiomers differ in physical properties Anomers come to equilibrium in water

69

Chemical reactions of monosaccharides 1. Easily oxidised

o o

Oxidising agents used to test for presence of reducing sugar Reducing sugar has free hemiacetal group aldoses not ketoses

2.

Undergo condensation to form disaccharides catalysed by enzymes! o Glycoside/acetal formation

3.

Substitution reaction with alcohol

70

Disaccharides Linkage of two monosaccharides Undergoes oxidation (i.e. is reducing) if there is free hemiacetal group Undergo hydrolysis to form monosaccharides o Glycosidic bond is cleaved

5.19

Nucleic acids Nucleotides Composed of sugar, phosphoric acid, and a nitrogen base Two types of bases: - purine base (2 rings) - pyrimidine base (1 ring)

71

Formation of sugar and base Produces nucleoside

Nucleoside is missing no. 1 carbon in below picture

DNA and RNA RNA less stable than DNA Differ in their sugar DNA: deoxyribose RNA: ribose

72

Differ in their bases DNA: A-T, C-G RNA: A-U, G-C

DNA forms double helix Two strands wound around each other like spiral staircase Pairs of bases supported by two sugar-phosphate backbones One strand is the compliment of the other There are 2 H bonds between A-T and 3 between G-C

DNA replication Double helix unwound and chains separated Nucleotides are added to build two new complementary strands Results in two identical copies of original molecule

Transcription From DNA to m-RNA Ribonucleotides are added to the strands

Translation From m-RNA to peptide sequence

73

Dideoxynucleotides and DNA sequencing In DNA replication, deoxyribonucleotides are added only to the 3 ends of DNA strands Dideoxyribose has no OH group in the 3 position, so once a dideoxynucleotide is incorporated chain cannot grow! 2 and 3 position OHs missing!

74

When dd-TTP is added, the chain stops growing Produces mixture of all possible fragments ending in T

When dd-CTP is added, the chain stops growing Produces mixture of all possible fragments ending in C

Thermochemistry
Thermodynamics: study of transformations of energy (e.g. heat into work) Thermochemistry: branch of thermodynamics examines heat released/absorbed by chemical reactions Applied to fuels, combustion, nutrition, biological metabolism etc.

6.1

Enthalpy of reactions Enthalpy (H): total heat content of a system Enthalpy change (H) = heat transferred to a system at constant pressure (approximation of total energy change of system different being work done) H = nHproducts mHreactants n and m are coefficients of the products and reactants in balanced equ. State function - H depends only on initial and final enthalpies, and not on intermediate values Use balanced chemical equations to show enthalpy change, called thermochemical equations Endothermic (H > 0) Heat is transferred from surroundings to system Heat absorbed H2O (l) H2O (g) H = +44.0 kJ

75

Exothermic (H < 0) Heat is transferred from system to surroundings Heat released H2O (g) H2O (l) H = - 44.0 kJ

NB: when process is reversed, H has same magnitude but opposite sign

H and quantity of material undergoing change H is proportional to quantity of material undergoing change 2H2O (l) 2H2O (g) H = +88.0 kJ

e.g. Given the following thermochemical equation: H2 (g) + Cl2 (g) 2HCl (g) Calculate H when: a) 1 mole of HCl is formed H = -185 kJ /2 = -92.5 kJ b) 1.00g of Cl2 reacts n = m/M n = 1.00g/70.9 g mol-1 n = 0.0141 mol H = 0.0131 mol x -185 kJ mol-1 = -2.61 kJ H = -185 kJ

76

e.g. The major source of aluminium in the world is bauxite (mostly aluminium oxide). Its thermal decomposition is represented by: Al2O3 (s) 2Al (s) + 3/2 O2 (g) H = 1676 kJ

If Al is produced in this way, how many grams of Al can from when 1000 kJ of heat is transferred? 2 mole of Al forms when 1676 kJ of heat is absorbed. Heat transferred for 1 mole: 1676 kJ / 2 mol = 838 kJ mol-1 Number of moles when 1000 kJ transferred: 1000 kJ / 838 kJ mol-1 = 1.193 mol m=nxM m = 1.193 mol x 26.98 g mol-1 m = 32.19 g Al

6.2

Standard enthalpy of reaction Set standard to compare enthalpies of different reactions Standard enthalpy (H) : enthalpy change when all reactants and products are in standard states Standard states: Liquids and solids (l) (s) pure form at 1atm Solutes in solution (aq) 1M concentration Gases (g) partial pressure of 1atm

Most enthalpy values for temp of 25C (298 K) e.g. for the themochemical equation: 2H+ (aq) + Zn (s) H2 (g) + Zn2+ (aq) This means: (a) (b) (c) Start with 2 moles of H+ (aq) in a 1M solution and 1M of zinc Finish with one mole of H2 (g) at 1 atm pressure and one mole of Zn2+ (aq) in 1 a 1M solution Enthalpy change -154 kJ H = -154 kJ

77

6.3

Calorimetry Calorimetry: measurement of heat flow to determine H using a calorimeter. Determining H experimentally Measure the heat flow accompanying a reaction at constant pressure When heat flows in or out of substance, temp changes

6.4

Heat capacity (C) Amount of heat required to raise the temperature of object/substance by 1C (1 K) Measured in JK-1 or JC-1 Usually recorded on a per mole or per gram basis

Specific/ molar heat capacity Specific heat capacity (Cs): amount of E needed to increase temp of kilogram by one Kelvin measured in JK-1 g-1 or JC-1 g-1 Molar heat capacity same as specific heat capacity but units differ Molar heat capacity (Cm): amount of E needed to increase temp of one mole by one Kelvin measured in JK-1 mol-1 or JC-1 mol-1 Cm = Cs x mmole mmole is atomic weight (mass per mole) Calculating heat transfer with temp change Heat (q) is measured in joules; temp change (T) Use relationships: q = nCmT ..... for n moles of substance q = mCsT ..... for m grams of substance q = CT ......... for an object such as a calorimeter NB: T = Tfinal - Tinitial

78

Problem questions e.g. a 466 g sample of water is heated from 8.5C to 74.6C. Calculate the amount of heat absorbed by the water. The specific heat capacity of water is 4.184 JC-1g-1. q = mCsT = mCs (Tfinal Tinitial ) = 4.66 g x 4.184 JC-1g-1 x (74.60 8.50)C = 1.29 x 105 J = 129 kJ

e.g. a 0.295 kg aluminium component at an initial temperature of 276 K absorbs 85.0 kJ of heat. What is the final temperature of the part? The specific heat capacity of aluminium is 0.900 JK-1g-1. q = mCsT T = q/ mCs Tfinal = q/ mCs + Tinitial = 85.0 x 10-3 J / 0.900 J K-1g-1 + 276 K = 596 K NB: check units!!

6.5

Constant-pressure calorimetry (coffee cup) Simple apparatus known as coffee cup calorimeter Measures heat transfers at lab atm pressure Consists of known mass of solution in insulated container equipped with a thermometer and stirrer Tinitial of solution measured stirred as reaction takes place and Tfinal is measured Heat gained by calorimeter = heat lost by reaction (opposite sign) qsoln = -qrxn qsoln = (specific heat capacity of solution) x (grams of solution) x T = -qrxn qsoln: heat gained by solution qrxn: heat produced by reaction

79

e.g. when 50.0mL of 0.100 M AgNO3 and 50.0mL of 0.100 M HCl are mixed in a constant-pressure calorimeter, the temperature of the mixture increases from 22.30C to 23.11C. The temperature increase is caused by the following reaction: AgNO3 (aq) + HCl (aq) AgCl (s) + HNO3 (aq) Calculate H for this reaction expressed in kJ mol-1 of HCl, assuming that the combined solution has a mass of 100.0 g and a specific heat capacity of 4.18 JC-1 g-1. q = mCsT = 100 g x 4.18 J C-1 g-1 x (23.11C 22.30C) = 338 J Heat gained by solution is equal to heat released in reaction: q = -338 J Number of moles of HCl n=cxV = 0.100 M x 50.0 x 10-3 L = 5.00 x 10-3 mol H = -388 J / 5.00 x 10-3 mol = -6.76 x 104 J mol-1 = -67.6 k J mol-1 e.g. a 25.0 mL sample of 0.500 M HCl at 25.0C is added to 25.0 mL of a 0.500 M NaOH, also at 25.0C, in a coffee-cup calorimeter. After mixing, the temperature of the solution is found to have increased to 28.3C. Calculate H for the reaction expressed in kJ mol-1 of HCl. The specific heat capacity of the solution is 4.1 JC-1g-1. Heat transferred during the reaction: q = mCsT = (25.0 g +25.0 g) x 4.18 J C-1 g-1 x (28.3C 25.0C) = 690 J Heat gained by solution is equal to heat released in reaction: q = - 690 J Number of moles of HCl n=cxV = 0.500 M x 25.0 x 10-3 L = 0.125 mol H = -690 J / 0.0125 mol = -55.2 kJ mol-1 = -6.76 x 104 J mol-1 80

6.6

Constant-volume calorimetry (bomb) Apparatus known as bomb calorimeter Measure heat released in combustion reaction Electrically heated coil ignites a substance within a steel bomb containing O2 Heat released from the combustion reaction is transferred to rest of calorimeter and temp is measured qrxn = -Ccal x T Ccal: heat capacity of calorimeter

e.g. A 0.5865 g sample of lactic acid (C3H6O3) is burned in a bomb calorimeter, the heat capacity of which is 4.812 kJC-1. The temperature increases from 23.10C to 24.95C. Calculate the enthalpy of combustion of lactic acid per gram and per mole. qrxn = -Ccal x T T = 24.95C 23.10C = 1.85C Ccal = 4.812 kJC-1 qrxn = -Ccal x T = - (4.812 kJC-1) (1.85C) = -8.902 kJ qrxn (per gram) = -8.902 kJ / 0.5865 g = -15.18 k J g-1 qrxn (per mole) = -8.902 kJ / 6.511 x 10-3 mol = -1.367 x 103 k J mol-1 81

e.g. In a bomb calorimeter, a 0.332 g sample of benzoic acid (C7H6O2) is burned and causes a temperature rise from 23.13C to 24.61C. The heat of combustion of benzoic acid is -3227 kJ mol-1. Determine the heat capacity of the calorimeter. qrxn = -Ccal x T T = 24.61C 23.13C = 1.48C qrxn (per mole) = -3227 kJ mol-1 qrxn = -3227 kJ mol-1 x (2.72 x 10-3 mol) = -8.78 kJ -Ccal = qrxn / T = -- 8.78 kJ / 1.48C Ccal = 5.93 kJC-1

6.7

Foods and fuels Fuel value: energy released when 1g of a substance is combusted Most energy in our bodies comes from carbs (av. fuel value: 17 kJg-1) and fats (av. fuel value: 38 kJg-1)

6.8

Hesss law If a reaction is carried out in steps, H (enthalpy change) for overall reaction = sum of enthalpy changes for individual steps

Hoverall = H1 + H2 + H3

82

H for a reaction may be calculated from other known enthalpies do not need to determine experimentally. Therefore, in following illustration any one of three enthalpy changes can be calculated if other two are known.

Method for calculating unknown H 1. 2. Identify target reaction with unknown H Rearrange equations of known H so that target reactants and products are on correct sides with correct number of moles 3. Change sign of H if equation is reversed Adjust moles and H by same factor

Add altered equations, cancelling substances not in target reaction (should be present on both sides of reaction!).

E.g. Given the following combustion reactions: (1) (2) C (s) + O2 (g) CO2 (g) ............H = -393.5 kJ CO (g) + O2 (g) CO2 (g) .......H = -283.0 kJ

Determine the enthalpy of combustion of C to CO: C (s) + O2 (g) CO (g) Reaction (1) has correct number of moles and reactants and products Reaction (2) needs to be reversed to have CO (g) as a product C (s) + O2 (g) CO2 (g) ............H = -393.5 kJ CO2 (g) CO (g) + O2 (g) .......H = 283.0 kJ Add equations together and cancel out. C (s) + O2 (g) + CO2 (g) CO2 (g) + CO (g) + O2 (g) C (s) + O2 (g) CO (g) H = -110.5 kJ

83

E.g. Calculate H for the reaction: 2C (s) + H2 (g) C2H2 (g) (acetylene) Given the following thermochemical reactions: (1) (2) (3) C2H2 (g) + 5/2 O2 (g) 2CO2 (g) + H2O (l)........H = -1299.6 kJ C (s) + O2 (g) CO2 (g) .....................................H = -393.5 kJ H2 (g) + O2 (g) H2O (l)................................H = -285.8 kJ

Reaction (1) needs to be reversed to make C2H2 a product. Reaction (2) needs to be multiplied by 2 to get the right number of moles. Reaction (3) left unchanged. (1) (2) (3) 2CO2 (g) + H2O (l) C2H2 (g) + 5/2 O2 (g) ........H = 1299.6 kJ 2C (s) + 2O2 (g) 2CO2 (g) .....................................H = -787.0 kJ H2 (g) + O2 (g) H2O (l)................................H = -285.8 kJ

Add equations together and cancel out. 2CO2 (g) + H2O (l) + 2C (s) + 2O2 (g) + H2 (g) + O2 (g) C2H2 (g) + 5/2 O2 (g) + 2CO2 (g) + H2O (l) 2C (s) + 2O2 (g) + H2 (g) C2H2 (g) + 2O2 (g) 2C (s) + H2 (g) C2H2 (g) H = 226.8 kJ

6.9

Enthalpy of formation Enthalpy of formation f H: enthalpy change associated with formation of compound from constituent elements Depends on temp, pressure and states of products and reactants Standard enthalpy of formation: enthalpy change when one mole of the compound is formed from its elements with all substances in their standard states. - most stable form of element is used in reaction e.g. for glucose at 25C: 6C (graphite) + 6H2 (g) + 3O2 (g) C6H12O6 (s) H = -1268 kJ mol-1

NB: elemental source of carbon is graphite not diamond, O2 rather than O or O3 because it is stable form and standard pressure, H2 is most stable form of hydrogen under standard conditions. Unit: kJ mol-1

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Standard enthalpy of formation of most stable form of any element is zero no formation reaction needed when element in standard state. E.g. O2 (g) f H = 0 kJ mol-1.

Standard enthalpies of formation tabulated and can be used to calculate enthalpy change for any chemical reaction rxn H = nfH (products) - mfH (reactants) Standard enthalpy change of reaction = sum of standard enthalpies of formation of products standard enthalpies of formation of reactants.

E.g. calculate the standard enthalpy of reaction for the following process: 2C2H6 (g) (ethane) + 7O2 (g) 4CO2 (g) + 6H2O (g) Use f H (kJ mol-1) for: C2H6 (g) CO2 (g) H2O (g) -84.7 -393.5 -241.8

rxn H = nf H (products) - mf H (reactants) = [4f H (CO2) + 6f H (H2O)] [2f H (C2H6) + 7f H (O2)] = [4 (-393.5) + 6 (-241.8)] [2 (-84.7) + 7 (0)] = -2855.4 kJ

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E.g. calculate the enthalpy of reaction for the following process: SiO2 (s) + 4HF (g) SiF4 (g) + 2H2O (g) Use f H (kJ mol-1) for: SiF4 (g) H2O (g) SiO2 (s) HF (g) -1614.9 -241.8 -910.9 -273

rxn H = nf H (products) - mf H (reactants) = [f H (SiF4) + 2f H (H2O)] [f H (SiO2) + 4f H (HF)] = [(-1614.9) + 2 (-241.8)] [ (-910.9) + 4 (-273)] = -95.6 kJ

Enthalpy of formation of H+ ions in solution = zero E.g. determine enthalpy of reaction - rxn H for the following reaction: 2H+ (aq) + CO32- (aq) CO2 (g) + H2O (l) Use f H (kJ mol-1) for: CO32- (aq) CO2 (g) H2O (l) -677.1 -393.5 -285.8

Recall that f H (kJ mol-1) for H+ = 0. rxn H = nf H (products) - mf H (reactants) = [f H (CO2) + f H (H2O)] [2 f H (H+) + f H (CO32-)] = [(-393.5) + (-285.8)] [ 2(0) + (-677.1)] = -2.2 kJ

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E.g. determine the heat of formation - f H of lead sulfate from the following reaction: PbO2 (s) + SO42- (aq) + 4H+ (aq) + 2I- (aq) PbSO4 (s) + 2H2O (l) + I2 (s) H= -194.4 kJ Use f H (kJ mol-1) for: PbO2 (s) SO42- (aq) I- (aq) H2O (l) -277.4 -909.3 -55.2 -285.8

Recall that f H (kJ mol-1) for H+ = 0. rxn H = nf H (products) - mf H (reactants) = [f H (PbSO4) + 2f H (H2O) + f H (I2)] [f H (PbO2) + f H (SO42-) + 4 f H (H+) ] = [f H (PbSO4) + 2(-285.8) + (-110.4)] [ (-277.4) + (-909.3) + 4(0)] f H (PbSO4) = -649.1 kJ mol-1 ?? -918.9 ?? Test: question at bottom of pg 149 of text.

6.10

Spontaneous processes Spontaneous process: occurs of its own accord, without any ongoing outside intervention Occurs in a definite direction cannot be reversed. e.g. brick falling or brick rising into a waiting hand Processes that are spontaneous in one direction are non spontaneous in opposite direction. Temp and pressure determine whether process is spontaneous. e.g. T > 0 ice melts spontaneously into liquid, T < 0 water freezes spontaneously to ice. At T=0 the states are in equilibrium and neither conversion occurs spontaneously. Speed not relevant.

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6.11

Entropy Entropy: thermodynamic function associated with number of different energy states or spatial arrangements in which system may be found randomness. Helps us understand why processes are spontaneous or not. State function depends only on initial and final states of the system. S = Sfinal Sinitial Absolute entropies: 0 for perfectly crystalline solids at 0 K

Determining whether entropy is positive or negative Entropy is measure of disorder. Order = low entropy Disorder = high entropy

Positive when creates disorder, negative when creates order. E.g. positive ice melting (solid to liquid), liquid vaporising (liquid to gas), sugar dissolving in water (solid to liquid)

Scale of disorder (randomness) Gases Liquids Solids Entropy S increases in processes in which: a) b) c) Gases are formed from either solids or liquids Liquids or solutions are formed from solids The number of gas molecules increases

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E.g. predict whether S is positive or negative for the following process: H2O (l) H2O (g) Liquid to gas randomness increases - S is positive.

E.g. predict whether S is positive or negative for the following process: C2H2 (g) + 2H2 (g) C2H6 (g) Number of gas molecules decrease randomness decreases - S is negative.

E.g. predict whether S is positive or negative for the following process: (a) 4Fe (s) + 3O2 (g) 2Fe2O3 (s) Solid and gas to solid randomness decrease - S is negative. (b) Ag+ (aq) + Cl- (aq) AgCl (s) Liquid to solid randomness decrease - S is negative.

6.12

Entropy changes in chemical reactions Standard molar entropy (S): entropy values of a substance in its standard state Observations about S values: S of elements at 298 K are not zero (unlike H) S values of gases are greater than those of liquids and solids S values increase with molar mass (M) S values increase with number of atoms in substance

Formula for entropy change S = nS (products) - mS(reactants) NB: n and m are coefficients in chemical equation

89

E.g. determine the standard entropy change S for the following reaction at 298K: Al2O3 (s) + 3H2 (g) 2Al (s) + 3H2O (g) Use S (JK-1 mol-1) for: Al (s) H2O (g) Al2O3 (s) H2 (g) 28.22 188.83 51.00 130.58

S = nS (products) - mS(reactants) = [2(28.22) + 3(188.83)] [51.00 + 3(130.58)] = 180.39 JK-1 E.g. determine the standard entropy change S for the synthesis of ammonia (the Habor process) from N2 (g) and H2 (g) at 25C. Is the value of S in agreement with your qualitative prediction? So equation is: N2 (g) + 3H2 (g) 2NH3 (g) Use S (JK-1 mol-1) for: N2 (g) H2 (g) NH3 (g) 191.5 130.6 192.5

S = nS (products) - mS(reactants) = [2 S(NH3)] [S(N2) + 3S(H2)] = [2(192.5)] [(191.5) + 3(130.6)] = -198.3 JK-1 This agrees with our prediction that S will be negative. We came to this conclusion as the number of gas molecules decreased, thus reducing randomness.

6.13

Gibbs free energy Gibbs free energy: the energy associated with a chemical reaction that can be used to do work.

90

Way to use H enthalpy and S entropy to predict whether a reaction at constant temp and pressure will be spontaneous. Gibbs free energy (G) of a system is defined as: G=HTS T is absolute temperature (in degrees Kelvin).

For a reaction at constant temp, determine the change in free energy of the system by: G = H T S G is the fraction of total energy change that is free to do work. T is absolute temperature (in degrees Kelvin).

Using sign of G to determine spontaneity G < 0: forward reaction is spontaneous G = 0: system is at equilibrium (no tendency for reaction to occur in either direction) G > 0: reverse reaction is spontaneous

Standard free energy changes (G) Free energy is a state function - only use final and initial values. Tabulate standard free energies of formation for substances usually at 25C Standard conditions to note: Gases Solids Liquids Substances in solution 1 bar pressure Pure solid Pure liquid 1M concentration

As with standard heats of formation f H - free energies of elements in most stable form = 0. Use standard free energies of formation to calculate the standard free energy change: G = nf G (products) - mf G (reactants) m and n are coefficients in chemical equation.

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E.g. determine the standard free energy change G for the reaction: CH4 (g) + 2O2 (g) CO2 (g) + 2H2O (g) What does the sign of your answer tell you about the reaction? Use G (kJ mol-1) for: CO2 (g) H2O (g) CH4 (g) -394.4 -228.6 -50.8

G = nf G (products) - mf G (reactants) = [f G (CO2) + 2 f G(H2O)] [f G (CH4) + 2f G (O2)] = [-394.4 + 2(-228.6)] [-50.8 + 2(0)] = -800.8 kJ As G is negative, we know the forward reaction will be spontaneous.

6.14

Free energy and temperature To estimate G at temps other than 25C, use Gibbs-Helmholtz equation: G = H T S Spontaneity depends on the sign and magnitude of H and TS Often H and S have the same sign and spontaneity depends on temp. E.g. the production of ammonia via the Haber process involves the equilibrium: N2 (g) + 2H2 (g) 2NH3 (g)

Assuming that H and S for this reaction do not change with temperature, determine the standard free energy change at 500C. If G is -33.3 kJ for the Haber process at 25C, comment on the effect of temperature on the equilibrium. Use fH (kJ mol-1) for: NH3 (g) -46.2

Use S (JK-1 mol-1) for: N2 (g) H2 (g) NH3 (g) 191.5 130.7 192.5 92

nf G (products) - mf G (reactants)

rxn H = nf H (products) - mf H (reactants) = [2f H (NH3)] [f H (N2) + 3f H(H2)] = [2(-46.2)] [0 + 3(0)] = -92.4 kJ S = nS (products) - mS(reactants) = [2S(NH3)] [S(N2) + 3S(H2)] = [2(192.5)] [191.5 3(130.7)] = -198.6 JK-1 = 198.5 kJ K-1 500C = 500 + 273 K = 773K G = H T S G = -92.4 kJ 773K(-198.6 x 10-3 kJ K-1) = 61.1 kJ As the temp increases from 25C to 500C the G changes from a negative value (33.3 kJ) to a positive value (61.1 kJ). The spontaneous reaction will change from being a forward reaction to being the reverse reaction. E.g. estimate the standard free energy change for the following reaction at 400K: 2SO2 (g) + O2 (g) 2SO3 (g) Use fH (kJ mol-1) for: SO3 (g) SO2 (g) -395.2 -296.9

Note fH for O2 as standard state is 0 kJ mol-1. Use S (JK-1 mol-1) for: SO3 (g) SO2 (g) O2 (g) 256.2 248.5 205.0

rxn H = nf H (products) - mf H (reactants) = [2f H (SO3)] [2f H (SO2) + f H(O2)] = -196.6 kJ S = nS (products) - mS(reactants) = -189.6 x 10-3 kJ K-1 G = H T S = -196.6 kJ (400K x -189.6 x 10-3 kJ K-1) = -120.8 kJ 93

6.15

Free energy and the equilibrium constant Calculating G under non-standard conditions Most chemical reactions occur under non-standard conditions Free energy change for any conditions: Not at equilibrium: G = G + RT ln Q At equilibrium: 0 = G + RT ln K G = - RT ln K R ideal gas constant: 8.314 J mol-1 K-1 T temperature in Kelvin Q / K reaction quotient / equilibrium constant (same formula) Larger K = more negative G Smaller K = more positive G E.g. calculate the equilibrium constant at 25C for the Haber process: N2 (g) + 3H2 (g) 2NH3 (g)

For this process G = -33.3 kJ mol-1 NB: per mole means per mole of the reaction as written So G = -33.3 kJ mol-1 means per 1 mole N2, per 3 mole H2, per 2 mole NH3). G = - RT ln K -33.3 kJ mol-1 = -8.314 J mol-1 K-1 x 298K ln K K = 6.9 x 105 This is a large K which indicates that NH3 is favoured in the equilibrium mixture at 25C (forward reaction).

Electroochemistry
Electrochemistry: study of chemical reactions involving transfer of electrons (e-)

7.1

Redox reactions Oxidation-reduction reactions

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Involve the transfer of electrons between two chemicals

Definitions Oxidation: loss of electrons by a substance Oxidant/oxidising agent: causes something to be oxidised it is reduced Reduction: gain of electrons by substance Reductant/ reducing agent: causes something to be reduced it is oxidised

Oxidation numbers Use to keep track of electron transfer Do not always correspond to real charges on atom Increase in oxidation number oxidation Decrease in oxidation number reduction Rules for assigning oxidation numbers: 1. 2. Atom in elemental form 0 Monatomic ion (one atom) charge on ion e.g. K+ has oxidation number +1 3. Non-metals have negative oxidation numbers, can be positive Oxygen: -2 except peroxides H2O2: -1 Hydrogen: +1 when bonded to non-metals, -1 when bonded to metals Fluorine: -1 4. Sum of oxidation numbers of all atoms in neutral compound is 0 e.g. H2O2 Oxidation number of each hydrogen is +1 Oxidation number of each oxygen is -1 2(+1) + 2(-1) = 0

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5.

The sum of oxidation numbers of all atoms in polyatomic ion equals charge of ion e.g. H3O+ Oxidation number of each hydrogen is +1 Oxidation number of oxygen is -2 3(+1) + 1(-2) = +1 equals net charge of ion

Balancing redox equations half equation method Electrons lost in oxidation must equal electrons gained in reduction The overall balanced equation can be written down by adding the half-equations to eliminate electrons (simultaneous equations) Multiply half-reactions by integers if necessary

Balancing rules: 1. 2. 3. 4. Balance for main element first Balance for O by adding H2O to O deficient side Balance for H by adding H+ to H deficient side Balance for charge by adding e to more +ve side

E.g. Zn(s) + 2 H+ (aq) Zn 2+(aq) + H2 (g) Oxidation half-equation: Zn(s) Zn 2+(aq) + 2eReduction half-equation: 2 H+(aq) + 2e- H2 Overall with cancelling: Zn(s) + 2 H+ (aq) + 2e Zn 2+(aq) + H2 (g) + 2e Zn(s) + 2 H+ (aq) Zn 2+(aq) + H2 (g)

7.2

Galvanic cells/voltaic cells Use spontaneous reaction to generate electrical energy Difference in chemical potential energy between reactants and products converted to electrical energy

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How it works Two half reactions are separated so that e- can be diverted through a wire Two electrodes, anode (negative) and cathode (positive) conduct electricity Oxidation occurs at anode Reduction occurs at cathode Electrodes inserted into electrolyte: ions involved in reaction Circuit completed with salt bridge: - cations migrate towards cathode - anions migrate towards anode

Cell notation Anode (oxidation half cell) written first Single vertical lines represent phase boundaries Double vertical lines represent salt bridge Reactant then product on each side

e.g. for above cell Zn| Zn2+ || Cu2+ | Cu

7.3

Standard reduction potentials

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Standard reduction potential (Ecell) is potential difference between metal electrodes, measured in volts (V) when all substances present in standard states i.e. solutions: 1M gases: 1 atm

Measuring reduction potential of single electrode Impossible to measure potential of half-cell single electrode Measure half-cells relative to standard hydrogen electrode (SHE) o o o Potential is 0 Hydrogen gas bubbled over a Pt electrode in a 1M acid solution H+ (1M) | H2 (1 atm) | Pt

In cell constructed with half-cell of interest and SHE SHE is anode Other half cell has standard reduction potential of +Ecell SHE is cathode Other half cell has standard reduction potential of -Ecell

Ag+ (aq) + e- Ag (s)

E = +0.80V

Zn2+ (aq) + 2e- Zn (s)

E = -0.76V

Tables of standard reduction potentials Values tabulated with relevant half equations Species at top left most easily reduced Species bottom right most easily oxidised

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E.g. arrange the following species in order of decreasing strength as oxidising agents: Fe3+, Br2, Cu2+ Fe3+ (aq) + e- Fe2+ (aq) Br2 (l) + 2e- 2br- (aq) Cu2+ (aq) + 2e- Cu (aq) E = +0.77V

E = +1.06V

E = +0.34V

Strongest oxidising agent is species on left with high highest potential so: Br2 > Fe3+ > Cu2+

Predict cathode and anode in galvanic cells Cathode half-cell that site highest in table Cathode (reduction) half-reaction will occur in direction appearing in table Anode (oxidation) will occur in opposite direction appearing in table

Predict cell potential Once cathode and anode identified, standard potential of galvanic cell given by:

99

Ecell = Ecathode - Eanode

Predict spontaneity of redox reaction Ecell > 0 spontaneous reaction Ecell > 0 non-spontaneous reaction

7.4

Free energy and redox reactions Relationship between cell potential and free energy G = - nFE G: free energy n: electrons transferred F: Faradays constant (9.65 x 104 JV-1mol-1) E: reduction potential When reactants and products in standard states: G = - nFE

E > 0, G < 0 spontaneous reaction

7.5

Nernst equation Predict changing cell potential as concentrations of reactants and products change Potential of cell drops as reactants converted to products

E = E - RT ln Q nF E: E: R: T: F: Q: reduction potential for reaction standard reduction potential universal gas constant (8.314 JK-1mol-1) temperature (usually 298K) Faradays constant (9.65 x 104 Cmol-1) reaction quotient (pure solids not included)

7.6

Corrosion Oxidation of metals by substances in environment (mostly H2O and O2)

100

Electrochemical process

Corrosion of iron Iron is oxidised by O2 because standard reduction potential for Fe2+ is less than O2

Anode is iron at the centre of the drop, cathode is iron at outer edge of the drop

Overall reaction: 2Fe + O2 + 2H2O 2Fe2+ + 4OH- Fe(OH)2 (s) This compound will oxidise further to product Fe2O3.3H2O (rust) Salt accelerates corrosion

Prevention of corrosion 1. 2. Protecting the surface from O2 and H2O (e.g. paint) Cathodic protection o o o Metal to be protected is made the cathode, and another metal is oxidised sacrificial anode Galvanised iron: iron coated with thin layer of zinc Standard reduction potential for Zn2+ is more negative than for Fe2+ so Zn easier to oxidise than Fe

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