III 2014 Paper1

NATURAL SCIENCES TRIPOS Part III
Thursday 29th May 2014
9.00 to 12.10
CHEMISTRY: PAPER 1A
Candidates should attempt SIX questions.
Where a question is divided into sections, the approximate division of marks between
sections is indicated at the end of the question.
Linear graph paper is available if required.
A Periodic Table, the structures of the amino acids and nucleotide bases, the values of
physical constants, character tables and selected mathematical formulae will be found in
the data book provided.
Write on ONE side of the paper only.
The answers to each question should be returned separately.
A separate cover sheet for each question should be completed.
Calculator students are permitted to use an approved calculator.
STATIONERY REQUIREMENTS
Graph paper (2 sheets)
Lined paper
Rough work pad
SPECIAL REQUIREMENTS
Department of Chemistry Data Book
Question record card
You may not start to read the questions printed on

the subsequent pages of this question paper until
instructed that you may do so by the Invigilator.
During the first 10 minutes of the examination
you are permitted to read the paper, but you may
not start writing your answers until this time has
elapsed.
9.00 to 11.40
CHEMISTRY: PAPER 1B
Candidates should attempt FIVE questions.
Lined paper
Rough work pad

elapsed.
9.00 to 11.10
CHEMISTRY: PAPER 1C
Candidates should attempt FOUR questions.
Lined paper
Rough work pad

elapsed.
M2 Advanced Diffraction Methods

Answer all parts of the question.
1
(a) What are the two main advantages of powder diffraction methods, and why are they
so useful in neutron diffraction studies?
(b) A specimen of nanocrystalline CaZrO3 is studied by x-ray diffraction, using CuK
radiation ( = 1.5418 ). The positions of the first ten diffraction lines are:
line
2 (deg.) 21.68
10
30.84
38.01
44.18
49.72
54.85
64.26
68.68
72.97
77.16
Assuming that this is a cubic material, determine the lattice type and index the lines,
and hence determine the unit cell dimension. Which of the lines will give the most
accurate value, and why ?
(c) In a related experiment particles of composition Ba x Ca(1x) ZrO3 are prepared, and
give very similar powder x-ray diffraction patterns, as shown in the figure below.
intensity
BaZrO3
(Ca,Ba)ZrO3
CaZrO3
15
25
35
45
55
65
75
2 (degrees)
The line positions are unchanged from those in CaZrO3 , suggesting that the unit cell
is unaltered, but there are subtle changes in the line intensities. In particular, the
relative intensities of lines 5 and 9 are dramatically reduced as barium is substituted
for calcium, but this reduction is most marked at the intermediate composition shown
above, rather than in pure BaZrO3 .
[Qu. 1 continued on next page]
[Continuation of Qu. 1]
If it is assumed that all these phases have the perovskite structure, with atomic
positions:
Zr @ (0, 0, 0) : Ba or Ca @ ( 21 , 12 , 12 ) : O @ ( 12 , 0, 0), (0, 12 , 0) and (0, 0, 12 )
derive an expression for the structure factor, assuming that the site at ( 12 , 21 , 12 ) is
occupied by a fraction x of barium and (1 x) of calcium atoms. Bearing in mind
that the atomic scattering factor is proportional to atomic number, show how partial
substitution of calcium by barium could produce the observed intensity variations.
(d) X-ray emission analysis of individual CaZrO3 nanocrystals indicates an average
CaK/ZrK intensity ratio of 2.6, whereas in BaZrO3 the BaL/ZrK rato is 3.3.
The corresponding values in the Ba x Ca(1x) ZrO3 specimen above are 1.17 and 1.82.
Evaluate the composition of this phase and explain if it is in accordance with the
explanation for the intensity variations described above.
[Atomic numbers Ca 20 : Zr 40 : Ba 56]

Approximate division of marks: (a) 20%, (b) 20%, (c) 40%, (d) 20%.
[TURN OVER
M3 Magnetic Materials
2
(a) Briefly explain the reasons why nickel metal is a ferromagnet.
(b) Show how different MLM bridging angles may give rise to either ferromagnetic or
antiferromagnetic superexchange.
A new cluster containing octahedral Ni2+ , [Ni6 (LH)4 (MeO)4 (MeOH)6 ] has a NiO
core as shown below, where the numbers 16 represent the six different nickel ions.
O
O
O
O
OH
OH
O
OH
2
O
LH 3
Analysis of the susceptibility values gives the following values for the different
exchange interactions:
J1,6 = J6,2 = J2,5 = J5,3 = J3,4 = +1.7 K
J6,5 = J2,3 = +35.5 K
J1,2 = J5,4 = 2.5 K
Use these values to derive the most energetically favourable arrangement of spins for
the cluster, write down the spin Hamiltonian for this cluster and hence calculate its
degree of magnetic frustration.
Approximate division of marks: (a) 40%, (b) 60%.
M4 Energy Landscapes and Soft Materials

3
(a) Consider two identical, charged colloidal spheres with radius R in a monovalent
electrolyte solution. We assume that the interaction energy between the spheres can
be approximated as:
!
22 r
Uel (r) = R 2 e ,

where r is the surface-to-surface distance of the spheres, is the surface charge density, the dielectric permittivity of the fluid, and is the inverse of the DebyeHuckel
screening length DH .
(i) Sketch the interaction potential Uel (r).
0
On the same graph sketch Uel (r) for the case of a divalent electrolyte solution
of the same concentration in the same solvent. Clearly label both functions and
indicate the value of divalent /monovalent .
(ii) Now consider that the colloids are also subject to the dispersion interaction:
Udisp (r)
C
r
where C denotes a constant which depends on the material from which the
spheres are made, and the properties of the solvent. Is C positive or negative?
Explain your answer.
Sketch the dispersion interaction energy Udisp (r). On the same graph sketch
0
the dispersion interaction energy Udisp (r) if the absolute difference between the
refractive index of the solvent and the spheres is decreased. Clearly label both
functions.
(iii) Sketch the total interaction energy Utot = Uel (r)+Udisp (r) for the case where
the absolute value of the dispersion interaction is everywhere stronger than the
absolute value of the electrostatic repulsion, and for a case where that is not
true.
[TURN OVER
(b)
(i) Prove the uniqueness theorem for a steepest-descent pathway on the energy
landscape V(X), where X is a vector of 3N Cartesian coordinates for a molecule
with N atoms. Explain how this result enables basins of attraction to be defined
for local minima of V(X).
(ii) For the two-dimensional potential V(x, y) = y4 + 3x2 4y2 find and classify all
the stationary points. Derive analytical solutions for the steepest-descent paths
in the neighbourhood of the transition state and sketch contours for the function
together with the pathways.
Approximate division of marks: (a) (i) 15%, (ii) 15%, (iii) 20%, (b) (i) 20%, (ii) 30%.
M5 Stereocontrolled Organic Synthesis

4
(a) Account mechanistically for the following transformations and assign the configuration at the labelled stereocentres (*).
LDA, Me3SiCl,
THF, 78 to 60 oC;
HO
* *
O
aqueous HCl
O
OSiMe3
StBu
tBuS
H
O
BF3-OEt2,
CH2Cl2, 78 oC
OMe
*
O
OMe
OH
(b) Give a mechanistic account of this transformation, including a conformational drawing of the tricyclic product.
H
Cl
AIBN
Bu3SnH
tricyclic product
[TURN OVER
M6 Computer Simulation Methods in Chemistry and Physics

5
The one-dimensional Ising model in an external magnetic field is defined by
X
X
E = J
si sj B
si
hi ji
where E is the energy of a system of spins si , J is a coupling constant and B is an external

magnetic field, and for which si can take the values +1 and 1. In one dimension each
spin has two neighbours, one on the left and the other on the right. The symbol hi ji in the
first sum indicates that the sum is restricted to immediate neighbouring pairs of spins.
(a) Write a pseudo-code to simulate the one-dimensional Ising model with N spins and
with B = 0.
(b) Extend the pseudo-code to the case with non-zero B, and with periodic boundary
conditions (i.e. for which spin 1 is a neighbour of spin N). You may visualize this
situation by arranging the N spins in a circle.
(c) Define the radial distribution function g(r) for a two-dimensional Lennard-Jones fluid
and describe its limiting behaviour for small and for large values of r.
(d) Compare the behaviour of the radial distribution function g(r) for a two-dimensional
LennardJones fluid for two different volume fractions.
Approximate division of marks: equal for each part.
M7 Nano Science and Colloid Science Chemistry at small length scales

6
(a)
(i) Give an enthalpic and an entropic reason for the stability of vesicle structures
relative to lamella surfactant mesophases.
(ii) With reference to the concept of preferred interfacial curvature of a surfactant,
explain why di-chain lipids are usually to be found in cell membranes and in
vesicles.
(iii) Where in the bilayer structure would you expect to find (i) a small hydrophobic
solute and (ii) a hydrophilic solute?
(b) If an ionic lipid is used to make a vesicle, describe what you expect to happen if the
ionic strength of the interior of the vesicle is increased.
(c) Discuss the relative importance of the major interactions in self-assembly of
amphiphiles into micelles. Your answer should include hydrogen bonding, the
hydrophobic effect and electrostatic considerations.
Approximate division of marks: (a) 50%, (b) 20%, (c) 30%.
[TURN OVER
10
M8 Protein folding, misfolding and disease

7
It has been suggested that the mechanism of folding of any protein will fall on a spectrum
between two extremes: diffusion-collision and nucleation-condensation.
(a) Explain the differences between these two mechanisms, and explain how you might
expect the pattern of -values to differ.
(b) What properties of a protein are likely to determine the mechanism by which it folds?
Give examples.
(c) If a protein folds by nucleation-condensation what are the possible consequences of
making a destabilizing mutation of one of the residues in (i) the obligate nucleus or
(ii) the critical nucleus? Explain your reasoning.
11
M9 Supramolecular Chemistry and self-organisation

8
An equimolar mixture of the three molecules shown below (A, B and C) forms three
products (1, 2 and 3) upon self-assembly in dichloromethane.
N
N
N
Zn
N
N
A
N
N
B
N
N
Zn
N
N
N
N
[TURN OVER
12
(a) Show schematically the structures of products 1, 2 and 3, and predict in what ratio
you would expect them to be formed. Briefly explain your reasoning.
(b) Upon addition of two equivalents (per A) of copper(I) tetrafluoroborate to the mixture
noted above, a single product 4 is formed. Schematically show the structure of this
product, and briefly explain its formation.
(c) The 1 H NMR spectrum of 4 at 25 C is consistent with four-fold symmetry: only
one -pyrrolic proton resonance is observed, for example. Upon cooling to 75 C,
this symmetry appears to break, with two -pyrrolic proton resonances replacing the
single one observed at room temperature. Briefly explain these observations.
(d) Predict what happens to the 1 H NMR spectra of 4 at 25 C and 75 C following the
addition of two additional equivalents of copper(I) tetrafluoroborate.
Approximate division of marks: equal for each part.
13
M10 Medicinal Chemistry

9
(a) Erlotinib is a quinazoline treatment for advanced lung cancer. It can be made from a
trisubstituted benzene starting material as summarised below:
O
HO
OEt
HO
A
Br
O
(excess)
K2CO3, TBAI
O
O
O
OEt
O
O
Acetone, , 64 hours
(93%)
TBAI = tetrabutyl ammonium iodide
NHR
O
O
O
O
Erlotinib (C)
(i) Give reaction mechanisms for the formation of B, explaining the role of each
of the reagents and the solvent.
(ii) Erlotinib itself (C, abbreviated structure) is then synthesised from B. Propose
a synthetic pathway that would allow you to do this (mechanisms are not
required).
[TURN OVER
14
(b) One of the key steps in the synthesis of the pyrrole ring in Lipitor uses chemistry
shown in the scheme below. Suggest a mechanism for this reaction.
O
O
CONHPh
F
N
N
HO2C
Ac2O, reflux
O
Approximate division of marks: (a) (i) 30%, (ii) 30%, (b) 40%.
CONHPh
15
L1 Catalysis for chemical synthesis

10
(a) Propose a synthesis of C from A and B that uses asymmetric catalysis. Your synthesis
can involve multiple steps and you may use any common reagents. Provide a detailed
description of how the stereochemistry is controlled as part of your answer.
OH
HS
N
OH
Boc
A
(b) Propose a concise synthetic route to racemic F, starting from D and E. All of the
carbon atoms required are supplied by one equivalent of D and two equivalents of E;
you may use multiple synthetic steps in your answer. Provide detailed mechanisms
in support of your answer.
Br
H2N
Br
S
O2
S
O2
D
[TURN OVER
16
L2 Solid electrolytes
11
(a) Describe briefly the direct-exchange diffusion mechanism. Give an example of
diffusion by this mechanism.
(b) Consider an ion diffusing in a simple cubic lattice by the direct interstitial mechanism. The distance between nearest-neighbour interstitial sites in all directions is a.
Assume, for simplicity, that diffusional jumps occur instantaneously at discrete times,
with being the time interval between jumps.
(i) Derive expressions for the time dependence of the square root of the meansquared displacement, s(t), and of the length of the trajectory, `(t), covered by
a diffusing ion for t .
(ii) Sketch the graph of s(t)/`(t) for t .
(iii) Assuming = 108 s and a = 3 , estimate s(t) and `(t) for t = 1 s; comment
on their relative difference .
(c) The fluorite (CaF2 ) structure can be regarded as a face-centred-cubic array of Ca2+
ions, with the F ions located at the corners of a cube within the unit cell, each F ion
being at a distance of one quarter of the body-diagonal length of the unit cell from the
nearest corner Ca2+ ion.
Assuming that the ions are spherical, that the ionic radii of Ca2+ and F ions are
equal, and nearest neighbour Ca2+ and F ions touch, calculate the atomic packing
fraction (the proportion of volume in the unit cell actually occupied by the ions) for
this structure.
The atomic packing fraction for the rocksalt (NaCl) structure is 0.65. What does a
comparison of the values of packing fractions for the two structures indicate about
the likely mode of F ion diffusion in CaF2 ?
17
L3 Electronic structure of solid surfaces

12
Pyrrole-1-carboxylic acid (below) is deposited below room temperature on the {110}
surface of an fcc metal.
N
O
(a) Briefly explain the XPS (X-ray Photoemission Spectroscopy) and NEXAFS (NearEdge X-ray Absorption Fine Structure) techniques, highlighting their similarities and
differences, and discussing the type of information obtainable from each.
(b) XPS reveals a single N 1s peak, but the O 1s peak may be resolved into two
distinct components. Upon heating above room temperature, hydrogen is evolved
from the surface in a quantity consistent with one liberated H2 molecule per two
adsorbed molecules of pyrrole-1-carboxylic acid; the N 1s XPS peak retains its
original lineshape, but the O 1s peak can no longer be resolved into two components.
What can be deduced from this information about the structure of the adsorbed
molecules in the low temperature (i.e. below room temperature) and high temperature
(i.e. above room temperature) regimes?
(c) NEXAFS experiments are performed on the same system. Examining the O 1s edge
reveals a strong peak that may be interpreted as arising from excitation of electrons
into an unoccupied molecular orbital of symmetry; a similar peak is also observed
at the N 1s edge, which may likewise be interpreted as involving an unoccupied
state. In the low temperature regime, both peaks reach their maximum intensity when
polarised X-rays are employed with their electric field vector perpendicular to the
surface, and both disappear whenever the electric field vector lies within the surface
plane.
Based upon these observations, what may be deduced about the conformation and
orientation of the adsorbed molecules in the low temperature regime?
[TURN OVER
18

(d) Further NEXAFS data are obtained in the high temperature regime, in which case the
peak at the O 1s edge is found to vanish when the electric field vector of polarised
X-rays is either perpendicular to the surface or parallel to the close-packed rows, and
to reach its maximum intensity when the electric field vector lies within the surface
plane but perpendicular to the close-packed rows of the surface. The peak at the N
1s edge is similarly minimised when polarised X-Rays have their electric field vector
perpendicular to the surface, but it is maximised when the electric field vector lies
parallel to the close-packed rows and minimised when it lies perpendicular to them in
the surface plane.
What do these data imply about the orientation and/or conformation of the adsorbed
molecules in the high temperature regime?
(e) It is subsequently found that higher coverages of adsorbed molecules may be obtained
by depositing above room temperature (rather than depositing below room temperature and subsequently heating). At saturation, scanning tunnelling microscopy reveals
that the overlayer adopts a (21) periodicity with one molecule per such surface unit
cell.
How might we expect the NEXAFS data to vary with polarisation in this case?
Approximate division of marks: (a) 30%, (b) 20%, (c) 20%, (d) 20%, (e) 10%.
19
L4 Organic Solids
13
(a) Molecules X and Y form a cocrystal that is found to dissociate partially at high
humidity. Explain this observation and draw a ternary phase diagram for this system,
describing its main features and any assumptions or simplifications that you have
made. What phase(s) would you expect to exist at equilibrium at high humidity?
[The solubility of compound X in water at room temperature is 20 mg/ml and that of
compound Y is 50 mg/ml.]
(b) Outline the advantages and disadvantages of using the following techniques in the
preparation of cocrystals: (i) solution crystallisation, (ii) solid-state grinding (with
and without the addition of a few drops of liquid) and (iii) freeze-drying.
(c) Molecules I and II (shown below) form a cocrystal that is observed, by powder X-ray
diffraction, to dissociate upon heating. The dissociation is endothermic as determined
by DSC analysis.
Discuss these observations in terms of the free energies and likely crystal structures
of the relevant crystal forms, including a free energy against temperature diagram in
your answer.
O
N
N
O
H
N
N
O
II
Approximate division of marks: (a) 35% (b) 30%, (c) 35%.
[TURN OVER
20
L5 Chemical Dynamics
14
Answer both parts of the question.
(a)
(i) Explain why the scattering of particles takes place in a plane.

(ii) Derive the expression
= 2b
Z
a
dr

r2 1 b2 /r2 V(r)/E 1/2
relating the deflection angle to the impact parameter b and the total energy
E, where a is the distance of closest approach of the particles.
(b) Sodium atoms can be ionized in aqueous solution with the electron remaining in
solution
Naaq Na+aq + eaq
The solvated electron eaq can be treated as a large halide-like aqueous anion. Using the
Born approximation for the solvation free energy, estimate the change in the reaction
free energy compared to ionization in vacuum.
[The radius of the sodium cation is 1.6 and that of the solvated electron 4.8 . The
relative dielectric constant of water is 80. The solvation free energy of the neutral
atom can be ignored.]
21
L6 Main group organometallics

15
(a) Suggest the identities and aggregation states of the complexes formed when A and B
are monolithiated in the presence of one equivalent of Et2 O.
NH
t Bu
Ph
H
N
Ph
t Bu
(b) Compound C reacts in toluene with 100% 6 Li enriched n BuLi (1 eq.) to give
crystalline D and a gas.
O
P
Me
Ph
Ph
C
The 13 C{1 H} NMR spectrum of D reveals aromatic signals as well as a multiplet at

32 ppm. X-ray crystallography reveals an aggregate in which each Li interacts with
one C-centre and multiple O-centres.
(i) Propose a structure for D.
(ii) Explain the appearance of the 13 C{1 H} NMR spectrum of D and predict the
multiplicity of the 32 ppm resonance.
[6 Li, I = 1; 31 P, natural abundance 100%, I = 12 ]
[TURN OVER
22

(c) Semiconductor materials such as GaAs are prepared by Organometallic Chemical
Vapour Deposition (OMCVD). Precursors such as GaMe3 and AsH3 are fed into a
reactor where they form GaAs on a heated target.
GaMe3
target heated
film forms on
target surface
AsH3
reactor under
reduced pressure
What kinds of problems arise from the use of these types of precursors and how
can some of these difficulties be alleviated by using alternative precursors? What
particular problems are encountered when trying to make GaN and what solutions
have been developed?
Approximate division of marks: (a) 25 %, (b) 25%, (c) 50%.
23
L8 Total Synthesis
16
The following schemes contains key transformations from the total synthesis of a number
of natural products.
(a) Provide a detailed mechanism for the reaction between A and B to form C, giving an
explanation of how the stereochemistry of the reaction is controlled.
CH3
H
N(CH3)2
O
CH3
N(CH3)2
O
LDA, TMEDA
OPh
-78 C to 0 C
OBoc O
O
OTBS
OBn
OBoc O
OBn
OH O
OTBS
(b) Explain the mechanism of the following bromination reaction to form E. Account
for why there is no tetrahydrofuran formation involving the carbon atom that is
brominated and the proximal hydroxyl group.
[Hint: PhI(OAc)2 + Br2 = AcOBr]
OH
CH3
Br
CH3
PhI(OAc) 2, Br2, h
Br
OH
CH3
O
O
O
N
O
D
[TURN OVER
24

(c) Provide a detailed mechanism of the reaction shown below, giving an explanation of
how the stereochemistry of the reaction is controlled.
O
N
NHCO2Me
I
O
NH2
NH
H
Et3N
Br
Br
F
N
CO2Me
N
H
H
25
L9 Biosynthesis
17
Answer both parts of the question.
(a) Neoxanthin and capsanthin are among the many carotenoids produced by plants for
light-harvesting and protection from photochemical damage. Isopentenyl pyrophosphate (IPP) is a known precursor.
OP2O63IPP
OH
HO
C
O
OH
Neoxanthin
HO
O
Capsanthin
HO
(i) Give detailed mechanisms for the steps leading from IPP to the first common
precursor of the carotenoids that has the full number of carbons atoms.
(ii) Give mechanisms for the reactions that form the terminal ring-systems of
neoxanthin and capsanthin.
(b) Thromboxane A2 is derived from arachidonic acid and O2 . Propose a mechanism for
this transformation.
CO2H
CO2H
O
O
OH
Arachidonic acid
Thromboxane A2
END OF PAPER

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NATURAL SCIENCES TRIPOS Part III

Thursday 29th May 2014

You may not start to read the questions printed on

NATURAL SCIENCES TRIPOS Part III

Thursday 29th May 2014

You may not start to read the questions printed on

NATURAL SCIENCES TRIPOS Part III

Thursday 29th May 2014

You may not start to read the questions printed on

M2 Advanced Diffraction Methods

[Atomic numbers Ca 20 : Zr 40 : Ba 56]

Approximate division of marks: (a) 40%, (b) 60%.

M4 Energy Landscapes and Soft Materials

M5 Stereocontrolled Organic Synthesis

Approximate division of marks: (a) 50%, (b) 50%.

M6 Computer Simulation Methods in Chemistry and Physics

where E is the energy of a system of spins si , J is a coupling constant and B is an external

M7 Nano Science and Colloid Science Chemistry at small length scales

Approximate division of marks: (a) 50%, (b) 20%, (c) 30%.

M8 Protein folding, misfolding and disease

M9 Supramolecular Chemistry and self-organisation

[Qu. 8 continued on next page]

M10 Medicinal Chemistry

TBAI = tetrabutyl ammonium iodide

L1 Catalysis for chemical synthesis

Approximate division of marks: (a) 50%, (b) 50%.

L3 Electronic structure of solid surfaces

[Continuation of Qu. 12]

Approximate division of marks: (a) 35% (b) 30%, (c) 35%.

(i) Explain why the scattering of particles takes place in a plane.

L6 Main group organometallics

The 13 C{1 H} NMR spectrum of D reveals aromatic signals as well as a multiplet at

[Continuation of Qu. 15]

Approximate division of marks: (a) 25 %, (b) 25%, (c) 50%.

[Qu. 16 continued on next page]

[Continuation of Qu. 16]

Approximate division of marks: (a) 25%, (b) 50%, (c) 25%.

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