International Chemistry Olympiad

IChO 2018

Bratislava and Prague, Slovakia and Czech Republic · 8 theory problems with complete solutions

  1. Problem 1: DNA

    Palindromic sequences are an interesting class of DNA. In a palindromic double-
    -stranded DNA (dsDNA) species, the sequence of one strand read in the \(5'\to3'\) direction matches the \(5'\to3'\) reading on the complementary strand. Hence, a palindromic dsDNA consists of two identical strands that are complementary to each other. An example is the so-called Drew–Dickerson dodecanucleotide (1):

    Figure 1

    1.1 How many different palindromic double-stranded DNA dodecanucleotides (i. e. dsDNA species with twelve base pairs) exist?

    1.2 How many different palindromic double-stranded DNA undecanucleotides (i.e., dsDNA species with eleven base pairs) exist?

    The melting temperature of dsDNA, \(T_m\) is defined as the temperature at which 50% of the original amount of DNA double strands are dissociated into separate strands.

    1.3 Consider the Drew–Dickerson dodecanucleotide (1). Assume that a G–C nucleobase pair contributes to the DNA duplex stability more than an A–T pair does.

    What is the probability that its \(T_m\) increases when a single randomly selected base pair is replaced by a G–C pair?

    Let us analyze the thermodynamics of formation of double-helical DNA from single strands, and its dependence on the length of the DNA and on the temperature. The equilibrium constant of association of single strands to form dsDNA differs for palindromic and non-palindromic dsDNA.

    A solution of dsDNA with the initial concentration of \(c_{\mathrm{init}}=1.00\times10^{-6}\ \mathrm{mol\,dm^{-3}}\) was heated to \(T_m\) and equilibrium was reached.

    1.4 Calculate the equilibrium constant of association of single strands at \(T_m\) for both non-palindromic and palindromic DNA.

    The mean contributions to the Gibbs energy of association of two single strands to form dsDNA were estimate over a certain range of experimental conditions, and they amount to \(-6.07\ \mathrm{kJ\,mol^{-1}}\) per one G–C pair, and \(-1.30\ \mathrm{kJ\,mol^{-1}}\) per one A–T pair present in a dsDNA.

    1.5 How many base pairs are there in the shortest dsDNA oligonucleotide that has \(T_m\) above \(330\ \mathrm K\)? At this \(T_m\), consider the following values of the equilibrium constant of association of single strands to form a dsDNA: \(K_{\mathrm{np}}=1.00\times10^6\) for a non-palindromic dsDNA, \(K_{\mathrm p}=1.00\times10^5\) for a palindromic dsDNA. Is the shortest oligonucleotide palindromic or non-palindromic?

    Finally, let us leave the simplified idea of base pairs contributing individually to the association of DNA strands. The Gibbs energy of this process may be considered explicitly dependent on temperature. The dependence of the inverse \(T_m\) of the Drew–Dickerson dodecanucleotide (1) on the logarithm of the initial duplex concentration \(c_{\mathrm{init}}\) is shown below. (Note: a standard concentration \(c_0=1\ \mathrm{mol\,dm^{-3}}\) is introduced.)

    \(c_{\mathrm{init}}/10^{-6}\ \mathrm{mol\,dm^{-3}}\) 0.25 0.50 1.00 2.0 4.0 8.0
    \(T_m/\mathrm K\) 319.0 320.4 321.8 323.3 324.7 326.2
    Figure 2

    1.6 Calculate the standard enthalpy \(\Delta H^\circ\) and the standard entropy \(\Delta S^\circ\) of the association of DNA single strands to form the palindromic double-stranded Drew–Dickerson dodecanucleotide (1). Assume that \(\Delta H^\circ\) and \(\Delta S^\circ\) do not vary with temperature.

    Official English text of the problem.

  2. Problem 2: Repatriation of remains in the middle ages

    At ambient temperatures, racemization is a slow reaction. As such, it can be used for dating biological objects and, moreover, for studying their thermal history. Let us take L-isoleucine (L-Ile) (\((2S,3S)\)-2-amino-3-methylpentanoic acid) as an example. It isomerizes on the \(\alpha\)-carbon and forms \((2R,3S)\)-2-amino-3-methylpentanoic acid, also known as D-allo-isoleucine. As the configuration changes on only one of the two stereogenic centres, this process is called epimerization rather than racemization.

    2.1 Choose all true statements.

    ☐ D-allo-isoleucine and L-isoleucine have the same values of specific optical rotation but they have different melting points.

    ☐ D-allo-isoleucine has an identical absolute value of specific optical rotation as L-isoleucine but the sign is opposite. The melting point is the same for both isomers.

    ☐ D-allo-isoleucine and L-isoleucine have different values of specific optical rotation but they have the same melting points.

    ☐ D-allo-isoleucine and L-isoleucine have different values of specific optical rotation and different melting points.

    ☐ D-allo-isoleucine is not optically active.

    2.2 Assign the absolute configurations for each stereoisomer of isoleucine.

    Figure 1

    ☐ \(2S,3R\) (L-allo-isoleucine)

    ☐ \(2R,3S\) (D-allo-isoleucine)

    ☐ \(2S,3S\) (L-isoleucine)

    ☐ \(2R,3R\) (D-isoleucine)

    2.3 The equilibrium constant \(K_{\mathrm{ep}}\) for L-isoleucine epimerization has the value of 1.38 (at 374 K). If we set molar Gibbs free energy of L-isoleucine \(G_{\mathrm m}^{\circ}=0\ \mathrm{kJ\,mol^{-1}}\) determine the Gibbs free energies for all structures A–D from question 2.2 at 374 K.

    2.4 If we take into account stereoisomerism at all stereocentres, what is the maximum possible number of the stereoisomers of the tripeptide Ile-Ile-Ile?

    At the start of the epimerization, we can neglect the reverse reaction. The epimerization then follows the first-order kinetics:

    Figure 2

    The value of the rate constant at 374 K is \(k_1(374\ \mathrm K)=9.02\times10^{-5}\ \mathrm{h^{-1}}\) and that at 421 K is \(k_1(421\ \mathrm K)=1.18\times10^{-2}\ \mathrm{h^{-1}}\).

    In the following calculation, shorten the concentration of L-isoleucine to \([\mathrm L]\) and of D-allo-isoleucine to \([\mathrm D]\).

    We can define a quantity \(de\) (diastereomeric excess):

    \[ de=\frac{[\mathrm L]-[\mathrm D]}{[\mathrm L]+[\mathrm D]}\times100(\%). \]

    2.5 Let us boil L-isoleucine for 1 943 hours at 374 K. What is the value of \(de\) (with three significant figures) for L-isoleucine a) before boiling and b) after boiling?

    2.6 How long does it take to convert 10% of L-isoleucine to D-allo-isoleucine at 298 K?

    In fact, the reverse reaction cannot be neglected. The correct kinetic scheme is expressed as

    Figure 3

    Let us define the deviation of concentration from its equilibrium value \([\mathrm L]_{\mathrm{eq}}\)

    \[ x=[\mathrm L]-[\mathrm L]_{\mathrm{eq}} \]

    It is possible to derive that \(x\) evolves with time according to the following equation:

    \[ x=x(0)\times e^{-(k_1+k_2)t}, \]

    where \(x(0)\) is the deviation from equilibrium at \(t=0\ \mathrm h\).

    2.7 Let us boil \(1.00\ \mathrm{mol\,dm^{-3}}\) L-isoleucine solution for 1 943 hours at 374 K. The rate constant for the forward reaction is \(k_1(374\ \mathrm K)=9.02\times10^{-5}\ \mathrm{h^{-1}}\), \(K_{\mathrm{ep}}\) for L-isoleucine epimerization has the value of 1.38 (at 374 K). In the following calculation, shorten the concentration of L-isoleucine to \([\mathrm L]\) and of D-allo-isoleucine to \([\mathrm D]\). Evaluate (with three significant figures)

    a) \([\mathrm L]_{\mathrm{eq}}\),

    b) diastereomeric excess (\(de\)) after boiling.

    Amino acids with a single chiral centre undergo racemization, e.g. L-arginine racemizes:

    Figure 4

    The time evolution of concentrations is governed by

    \[ \ln\frac{1+\dfrac{[\mathrm D]}{[\mathrm L]}} {1-\dfrac{[\mathrm D]}{[\mathrm L]}} =2k_1t+C \]

    Here \([\mathrm D]\) and \([\mathrm L]\) are concentrations of D- and L-arginine at time \(t\), \(k_1\) is the rate constant, and the term \(C\) is set according to the initial concentrations.

    Holy Roman Emperor Lothar III passed away during his journey to Sicily in 1137. To facilitate the repatriation of the remains, his body was, immediately after his death, boiled in water (373 K) for a certain time. Let us try to estimate the boiling time with the help of chemical kinetics. We know that the rate constant \(k_1\) of arginine racemization within the protein at 373 K and \(\mathrm{pH}=7\) has the value of \(5.10\times10^{-3}\ \mathrm{h^{-1}}\).

    In order to analyse the isomeric composition of arginine in Lothar’s bones, we need to start with transferring arginine into solution. Lothar’s bones were hydrolyzed in a highly acidic environment for 4 hours at 383 K. The ratio of the optical isomers was \(\dfrac{[\mathrm D]}{[\mathrm L]}=0.090\). Lothar’s wife Richenza was not boiled after her death. Her bones were hydrolyzed using the same procedure and in this case the ratio was \(\dfrac{[\mathrm D]}{[\mathrm L]}=0.059\). (Note that the racemization also takes place during the hydrolysis, with the rate constant \(k'_1\), different from \(k_1\)).

    2.8 How long was the Holy Roman Emperor Lothar III boiled in water in 1137?

    Note: The racemization of arginine is an extremely slow process at temperatures typically encountered in graves. As both bodies are only some 880 years old, we can neglect the natural racemization during this time.

    Official English text of the problem.

  3. Problem 3: Emerging electro-mobility

    Contemporary means of transportation rely on burning fossil fuels, although the efficiency of real combustion engines is inherently limited and typically ranges between 20 and 40%.

    3.1 Mark the factors that can make the efficiency of a heat engine higher:

    • ☐ Increasing the friction in the mechanical parts of the engine
    • ☐ Increasing the burning temperature of the fuel in the engine
    • ☐ Narrowing the working temperature interval of the engine
    • ☐ Increasing the working pressure of the gas

    Fuel cells represent a way to improve the engine efficiency for future vehicles. The engine efficiency can be improved by using hydrogen-based fuel cells.

    3.2 The standard enthalpy of formation of liquid water is \(\Delta_{\mathrm f}H^\circ(\ce{H2O},\mathrm l)=-285.84\ \mathrm{kJ\,mol^{-1}}\), and the standard combustion enthalpy of isooctane is \(\Delta_{\mathrm c}H^\circ(\ce{C8H18},\mathrm l)=-5\,065.08\ \mathrm{kJ\,mol^{-1}}\) (both at 323.15 K). Calculate the values of specific (per unit of mass) combustion enthalpy at 232.15 K of pure liquid isooctane and pure gaseous hydrogen.

    3.3 Calculate the standard electromotive force (EMF) of a fuel cell using gaseous oxygen and hydrogen, both ideal gases at 100 kPa and 323.15 K, to produce liquid water.

    Use the following entropy data for 323.15 K: \(S^\circ(\ce{H2O},\mathrm l)=70\ \mathrm{J\,K^{-1}\,mol^{-1}}\),

    \(S^\circ(\ce{H2},\mathrm g)=131\ \mathrm{J\,K^{-1}\,mol^{-1}}\),

    \(S^\circ(\ce{O2},\mathrm g)=205\ \mathrm{J\,K^{-1}\,mol^{-1}}\).

    3.4 Determine the ideal thermodynamic efficiency \((\eta)\) of a fuel cell producing liquid water at 353.15 K. At this temperature, the enthalpy of formation of water is \(\Delta_{\mathrm f}H^\circ(\ce{H2O},\mathrm l)=-281.64\ \mathrm{kJ\,mol^{-1}}\) and the corresponding reaction Gibbs energy change is \(\Delta_{\mathrm r}G^\circ=-225.85\ \mathrm{kJ\,mol^{-1}}\).

    3.5 A polymer membrane electrolyzer facility operates at the voltage of 2.00 V and is powered by a 10.0 MW wind turbine plant which was running at full power from 10 pm to 6 am. The electrolysis yielded 1 090 kg of pure hydrogen. Calculate the electrolysis yield defined as the mass of produced hydrogen divided by its theoretical produced mass.

    3.6 Calculate the mass of hydrogen required to drive the distance between Prague and Bratislava (330 km) at the average speed of \(100\ \mathrm{km\,h^{-1}}\) with a car fitted with a 310 kW electric engine running on average at a 15% rate of its maximum power. Assume that the efficiency of the hydrogen cell producing electrical energy is 75%, the efficiency of the electric engine is 95%, and the Gibbs energy change for combustion of hydrogen fuel is \(\Delta_{\mathrm r}G=-226\ \mathrm{kJ\,mol^{-1}}\).

    The low efficiency of hydrogen production and the safety issues connected with its storage impede spreading the hydrogen-based transportation technology. Hydrazine (\(\ce{N2H4}\)) fuel cells might be a suitable alternative.

    The following standard reduction potentials for aqueous hydrazine systems are available:

    Figure 1

    3.7 Fill in the following Latimer diagrams with the forms of hydrazine and ammonia prevailing at the given conditions and write the redox potential value for each arrow representing the electrochemical half-reaction. Record all the necessary calculations.

    a) Acidic environment (pH = 0)

    Figure 2

    b) Basic environment (pH = 14)

    Figure 3

    Due to the toxicity, odour and its environmental impact, it is extremely unfavourable to produce ammonia in fuel cells.

    3.8 Write down the net reaction for the decomposition of hydrazine under basic conditions to:

    (i) ammonia and nitrogen,

    (ii) nitrogen and hydrogen.

    Calculate the corresponding equilibrium constants at \(T=298.15\ \mathrm K\).

    Rechargeable lithium-based batteries are an alternative to fuel cells. Lithium-ion batteries commonly use graphite for one of the electrodes, in which lithium clusters intercalate in between the graphite sheets. The other electrode is made of lithium cobalt oxide, which can reversibly absorb lithium ions moving from one electrode to the other during the charge and discharge processes. The half-reactions relevant for the system can be formally written as:

    Figure 4

    3.9 Using the formalism given above, write down the overall chemical reaction occurring in the battery during the discharge process. Give the oxidation states of the cobalt atom.

    3.10 Tick the boxes to get the correct statements which are valid for the discharge of the lithium-based battery described in 3.9:

    \(\ce{Li(C)_n}\) electrode is ☐ cathode ☐ because lithium ions are reduced here.
    ☐ anode ☐ because lithium atoms are oxidized here.
    \(\ce{LiCoO2}\) electrode is ☐ cathode ☐ because cobalt ions are reduced here.
    ☐ anode ☐ because cobalt ions are oxidized here.

    3.11 Assume that a \(\ce{C6}\) unit, a \(\ce{CoO2}\) unit and \(\ce{Li}\) atom form the active battery mass required to transfer one electron between the electrodes. Using the corresponding standard EMF, calculate the theoretical specific reversible charge capacity (in \(\mathrm{mAh\,g^{-1}}\)) and the energy density (in \(\mathrm{kWh\,kg^{-1}}\)) of such a model lithium ion battery related to the whole active battery mass.

    Official English text of the problem.

  4. Problem 4: Column chromatography of radioactive copper

    \(\ce{^{64}Cu}\) for positron emission tomography is prepared by the bombardment of a zinc target with deuterium nuclei (further referred to as the activated target).

    4.1 Write down the balanced equation for the \(\ce{^{64}Zn}\) nucleus bombardment with deuterium nuclei, giving \(\ce{^{64}Cu}\). Specify the corresponding atomic and mass numbers of all species. Disregard the charges.

    The activated target is dissolved in concentrated hydrochloric acid (\(\ce{HCl (aq)}\)) to give a mixture containing \(\ce{Cu^2+}\) and \(\ce{Zn^2+}\) ions and their respective chlorido complexes.

    4.2 Calculate the mole fraction of negatively charged copper species with respect to the amount of copper prepared by zinc target activation. Assume \([\ce{Cl-}] = 4\ \mathrm{mol\,dm^{-3}}\). For the overall complexation constants, \(\beta\), see Table 1.

    Before you start the calculation, write down the charges in the upper right boxes:

    Figure 1

    Table 1. Overall complexation constants \(\beta\) of \(\ce{Cu}\) species (charges were omitted in the formula).

    \[ \beta_i=\frac{[\ce{CuCl_i}]}{[\ce{Cu}]\times[\ce{Cl}]^i} \]

    \(i\) in \(\ce{[CuCl_i]}\) 1 2 3 4
    \(\beta_i\) 2.36 1,49 0.690 0.055

    The mixture containing \(\ce{Cu^2+}\) and \(\ce{Zn^2+}\) ions and their respective chlorido complexes was separated with an anion exchange resin. Dry resin in \(\ce{OH-}\) form was dispersed in water and the suspension was transferred into a column. To occupy all sites with \(\ce{Cl-}\) ions (i.e. to obtain resin in a \(\ce{Cl-}\) form), the resin was washed with hydrochloric acid and then with deionized water to wash out all the unbound \(\ce{Cl-}\) ions.

    4.3 Everything was initially at laboratory temperature before washing with hydrochloric acid. Does the column temperature change during the washing with hydrochloric acid?

    ☐ No.

    ☐ Yes, the temperature decreases.

    ☐ Yes, the temperature increases.

    The mixture containing \(\ce{Cu^2+}\) and \(\ce{Zn^2+}\) ions and their respective chlorido complexes was transferred onto the resin-filled column. Hydrochloric acid solution was used as an eluent.

    Using the simple experimental formula below, you can calculate quantities that determine average elution properties of both copper species and zinc species on the column.

    The retention volume \(V_{\mathrm R}\) (the mobile phase volume at which 50% of the compound has been eluted from the column) can be calculated as follows:

    \[ V_{\mathrm R} =D_{\mathrm g}\times m_{\mathrm{resin,dry,OH\ form}}+V_0 \]

    4.4 Using the average mass distribution coefficients \(D_{\mathrm g}\) (\(D_{\mathrm g}(\ce{Cu}\text{ species})=17.4\ \mathrm{cm^3\,g^{-1}}\), \(D_{\mathrm g}(\ce{Zn}\text{ species})=78.5\ \mathrm{cm^3\,g^{-1}}\)), calculate the retention volumes \(V_{\mathrm R}\) in \(\mathrm{cm^3}\) of both copper species and zinc species. The mass of dry resin in \(\ce{OH-}\) form \(m_{\mathrm{resin,dry,OH\ form}}=3.72\ \mathrm g\) and the void volume of a column \(V_0=4.93\ \mathrm{cm^3}\).

    (If you cannot find the answer, use \(V_{\mathrm R}(\ce{Cu}\text{ species})=49.9\ \mathrm{cm^3}\) and \(V_{\mathrm R}(\ce{Zn}\text{ species})=324\ \mathrm{cm^3}\) for further calculations.)

    Using the simple experimental formula, separation of two sets of species, A and B, can be considered complete if

    \[ V_{0.001}(\mathbf A)-V_{0.999}(\mathbf B)>10V_{\mathrm c} \]

    where \(V_{0.001}\) is the mobile phase volume at which 0.1% of A has been eluted from the column, and \(V_{0.999}\) is the mobile phase volume at which 99.9% of B has been eluted from the column.

    \[ V_{0.001}(\mathbf A) =V_{\mathrm R}(\mathbf A)\times \left(1-6.91\sqrt{d_{\mathrm p}/L_{\mathrm c}}\right) \]

    \[ V_{0.001}(\mathbf B) =V_{\mathrm R}(\mathbf B)\times \left(1-6.91\sqrt{d_{\mathrm p}/L_{\mathrm c}}\right) \]

    \[ V_{0.999}(\mathbf B) =2V_{\mathrm R}(\mathbf B)-V_{0.001}(\mathbf B) \]

    4.5 Based on a calculation, decide whether copper species were separated completely from zinc species. The volume of the column filled with the swollen resin \(V_{\mathrm c}=10.21\ \mathrm{cm^3}\), the resin particle diameter \(d_{\mathrm p}=0.125\ \mathrm{mm}\), and the height of the wet resin in a swollen state in the column \(L_{\mathrm c}=13.0\ \mathrm{cm}\).

    4.6 Calculate the theoretical value of the total ion exchange mass capacity of the dry resin used in this problem, \(Q_{\mathrm{m,theor}}\), in \(\mathrm{mmol\,g^{-1}}\). Consider tetralkylammonium groups were the only ones responsible for ion exchange of the resin. No other nitrogen containing groups were present. The mass fraction of nitrogen in the dry resin was 4.83%.

    (If you cannot find the answer, use \(Q_{\mathrm{m,theor}}=4.83\ \mathrm{mmol\,g^{-1}}\) for further calculations.)

    In reality, not all tetraalkylammonium groups are involved in the ion exchange. To determine the total ion exchange volume capacity, \(Q_{\mathrm v}\), the column filled with 3.72 g dry resin converted to the \(\ce{Cl-}\) form was washed with the excess of sodium sulfate solution. The effluent was collected in a \(500\ \mathrm{cm^3}\) volumetric flask, which was then filled with water to the mark. An aliquot of \(100\ \mathrm{cm^3}\) was potentiometrically titrated with \(0.1027\ \mathrm{mol\,dm^{-3}}\) silver nitrate. The silver nitrate solution volume at the equivalence point was \(22.20\ \mathrm{cm^3}\). The volume of the column filled with the swollen resin, \(V_{\mathrm c}\), was \(10.21\ \mathrm{cm^3}\).

    4.7 Calculate the \(Q_{\mathrm v}\) of the swollen resin in mmol of active tetraalkylammonium groups per \(\mathrm{cm^3}\) of the swollen resin.

    (If you cannot find the answer, use \(Q_{\mathrm v}=1.00\ \mathrm{mmol\,cm^{-3}}\) for further calculations.)

    4.8 Calculate the mole fraction (\(x\)) of the tetraalkylammonium groups actively involved in the ion exchange.

    Official English text of the problem.

  5. Problem 5: Bohemian garnet

    The dodecahedral splitting diagram referred to in 5.4 and the formula defining \(x,y\) in 5.13 are not printed in this version of the problem.

    PROBLEM 5

    Bohemian garnet

    Bohemian garnet (pyrope) is a famous Czech blood coloured semi-precious stone. The chemical composition of natural garnets is expressed by the general stoichiometric formula of \(\ce{A3B2(SiO4)3}\), where \(\ce{A^{II}}\) is a divalent cation and \(\ce{B^{III}}\) is a trivalent cation. Garnets have a cubic unit cell that contains 8 formula units. The structure comprises 3 types of polyhedra: the \(\ce{A^{II}}\) cation occupies a dodecahedral position (it is surrounded with eight O atoms), the \(\ce{B^{III}}\) cation occupies an octahedral position (it is surrounded with six O atoms) and \(\ce{Si^{IV}}\) is surrounded with four O atoms arranged into a tetrahedron.

    The most common garnet mineral is almandine with the formula of \(\ce{Fe3Al2(SiO4)3}\). Its unit cell parameter is \(a = 11.50\ \text{Å}\).

    5.1 Calculate the theoretical density of almandine.

    The Bohemian garnet has the composition of \(\ce{Mg3Al2(SiO4)3}\). Pure compound is colourless and the colour of natural garnets comes from chromophores – transition metal cations that substitute the host material cations. The red colour of the Bohemian garnet comes from trace amounts of \(\ce{Cr^{III}}\) ions in the octahedral sites and \(\ce{Fe^{II}}\) ions in the dodecahedral sites.

    5.2 Draw the splitting diagram for the \(\ce{[Cr^{III}O6]}^{\mathrm{oct}}\) d-orbitals and fill it with electrons.

    5.3 Identify the 1st transition row element(s) whose trivalent cation(s) \(\ce{M^{III}}\) placed in an octahedral position is/are diamagnetic in the low-spin arrangement and paramagnetic in the high-spin arrangement.

    5.4 The figure below shows d-orbitals splitting in the dodecahedral crystal field. Fill in the electrons for the \(\ce{[Fe^{II}O8]}^{\mathrm{dod}}\) chromophore for both existing arrangements.

    5.5 Derive the inequalities (e.g. \(P < E_1 + E_2 + E_3\)) for the pairing energy (\(P\)) magnitude in relation to energies \(E_1\), \(E_2\) and \(E_3\) for both arrangements.

    5.6 Assuming that \(P > E_3\), identify the 1st transition row element(s) whose divalent cation \(\ce{M^{II}}\) placed in dodecahedral position is diamagnetic in the low-spin arrangement and paramagnetic in the high-spin arrangement.

    The figures below show simplified absorption spectra of four coloured minerals – blood-coloured Bohemian garnet, green uvarovite, blue sapphire and yellow-orange citrine.

    Figure 1

    5.7 Match the spectra with the minerals.

    5.8 If illuminated with monochromatic blue-green light, how will the Bohemian garnet look?

    ☐ Red  ☐ Blue  ☐ Yellow-orange  ☐ Black
    ☐ Yellow ☐ Blue-green ☐ Violet  ☐ White

    Andradite is another garnet mineral; its chemical composition is \(\ce{Ca3Fe2(SiO4)3}\). A double cation substitution – \(\ce{Ti^{IV}}\) for \(\ce{Fe^{III}}\) in the octahedral position and \(\ce{Fe^{III}}\) for \(\ce{Si^{IV}}\) in the tetrahedral position – gives rise to black schorlomite. Its chemical composition can be expressed as \(\ce{Ca3[Fe,Ti]2^{oct}([Si,Fe]^{tet}O4)3}\).

    5.9 Calculate the percentage of \(\ce{Si^{IV}}\) ions in a sample of schorlomite that must be substituted with \(\ce{Fe^{III}}\), if we know that 5% of \(\ce{Fe^{III}}\) ions in octahedral position are substituted with \(\ce{Ti^{IV}}\).

    The colour of the mineral is caused by two chromophores: \(\ce{[Fe^{III}O6]}^{\mathrm{oct}}\) and \(\ce{[Fe^{III}O4]}^{\mathrm{tet}}\). The central ions of both chromophores have equal number of unpaired electrons.

    5.10 Draw the d-orbitals splitting diagrams for both chromophores and fill in the electrons.

    Tetrahedral field causes a smaller splitting than the octahedral field \(\left(\Delta_{\mathrm{tet}} = \frac49\Delta_{\mathrm{oct}}\right)\). Surprisingly for the \(\ce{Fe^{III}}\) ion, the energy of the first d–d transition (although very weak) for the octahedral chromophore is smaller (\(11\,000\ \mathrm{cm^{-1}}\)) than for the tetrahedral one (\(22\,000\ \mathrm{cm^{-1}}\)).

    5.11 Calculate the size of pairing energy (\(P\)) and the sizes of \(\Delta_{\mathrm{oct}}\) and \(\Delta_{\mathrm{tet}}\) splitting. Assume that the pairing energy is equal in both chromophores.

    Synthetic garnet YAG (Yttrium Aluminium Garnet), used in optoelectronics, has the composition of \(\ce{Y3Al5O12}\). Its structure is derived from the general garnet structure \(\ce{A3B2(SiO4)3}\) by placing the ions \(\ce{Y^{III}}\) and \(\ce{Al^{III}}\) to the A, B and Si positions.

    5.12 Based on your knowledge of the relative ion radii, determine which cation occupies which position.

    5.13 For the use in LED technology, YAG is doped with \(\ce{Ce^{III}}\). Determine the values of \(x\) and \(y\) in the formula of YAG in which 5% of yttrium atoms are substituted with cerium. (If you don’t get result, use \(x = 2.25\) and \(y = 0.75\).)

    5.14 The \(\ce{Ce^{III}}\)-doped YAG is prepared by annealing the mixture of \(\ce{Y2O3}\), \(\ce{Al2O3}\) and \(\ce{CeO2}\) in \(\ce{H2}\) atmosphere. Use the formula from 5.13, write down a balanced equation for this reaction with the smallest whole-number stoichiometric coefficients.

    Doping the YAG structure with rare-earths ions enables the production of lasers with emission wavelengths ranging from the UV to the mid-IR region. In the scheme below, simplified f–f energy transitions of selected rare-earths ions are shown.

    Figure 2

    5.15 Which cation has a transition which corresponds to blue light emission.

    ☐ \(\ce{Er^{3+}}\)  ☐ \(\ce{Sm^{3+}}\)  ☐ \(\ce{Tm^{3+}}\)  ☐ \(\ce{Pr^{3+}}\)
    ☐ \(\ce{Yb^{3+}}\)  ☐ \(\ce{Nd^{3+}}\)  ☐ \(\ce{Tb^{3+}}\)

    5.16 Calculate the emission wavelength of this light.

    5.17 According to a legend, Noah used a stick with a garnet stone for illumination during his voyage. Assuming only the photoluminescence effect, determine the colour of the laser light emitted from his stick if the stone were the blood-coloured Bohemian garnet.

    ☐ Red  ☐ Blue  ☐ Yellow-orange  ☐ Black
    ☐ Yellow ☐ Blue-green ☐ Violet  ☐ White

    Official English text of the problem.

  6. Problem 6: Let’s go mushrooming

    Mushrooming belongs to Czech and Slovak traditional pastimes. While some of our mushroom species are edible, some are inedible or even poisonous.

    Inky cap (Coprinopsis atramentaria) is considered edible and delicious. It contains a natural compound called coprine (E), which can be easily synthesized from ethyl 3-chloropropanoate (1).

    Figure 1

    6.1 Draw the formulae of compounds A–E including stereochemistry when necessary.

    Hint: The first reaction affording compound A proceeds via an organometallic compound which then cyclizes.

    In the human body, coprine undergoes hydrolysis to L-glutamic acid (3) and compounds C and 4, which are responsible for the coprine adverse side-effects. They inhibit the enzyme acetaldehyde dehydrogenase, which is involved in the metabolism of alcohol. When the enzyme is inhibited, acetaldehyde formed by alcohol dehydrogenase accumulates in the body, causing strong symptoms of hangover (so called antabuse effect). The active site of the enzyme contains a cysteine \(\ce{SH}\) group, which is blocked either by compound C or 4.

    Figure 2

    Enzyme = acetaldehyde dehydrogenase

    6.2 Using the pictogram for acetaldehyde dehydrogenase above, draw the structure F of the enzyme inhibited by compound 4.

    The antabuse effect got its name after antabuse (5), the most known drug used in alcohol-addiction treatment. This drug can be synthesized according to the following scheme.

    Figure 3

    6.3 Draw the formulae of compounds G and H.

    Hint: Compound H contains five carbon atoms.

    6.4 Mark all possible reagents which could be used for I from the following list.

    ☐ m-chloroperbenzoic acid (mCPBA) ☐ diluted \(\ce{H2O2}\)
    ☐ \(\ce{Zn / CH3COOH}\) ☐ \(\ce{NaBH4}\)
    ☐ \(\ce{I2}\) ☐ hot concentrated \(\ce{H2SO4}\)
    ☐ \(\ce{K2CO3}, \ce{H2O}\) ☐ \(\ce{AlCl3}\)

    The way antabuse inhibits acetaldehyde dehydrogenase is similar to the effect of compounds C and 4.

    Figure 4

    Enzyme = acetaldehyde dehydrogenase

    6.5 Using the pictogram for acetaldehyde dehydrogenase above, draw the structure J of the enzyme inhibited by antabuse (5). Hint: Three sulfur atoms should be in the structure.

    False morel (Gyromitra esculenta) is another interesting mushroom. Although it was considered edible in the past (esculentus means edible in Latin), there is clear evidence that this mushroom is poisonous due to the content of gyromitrin (M). This natural compound can be prepared from N-methylhydrazine (6):

    Figure 5

    6.6 Draw the formulae of compounds K – M.

    In human body, gyromitrin (M) hydrolyzes and provides N-methylhydrazine (6), which is strongly hepatotoxic. Gyromitrin (M) hydrolysis occurs as soon as it enters the acidic environment in human stomach where both its amide and imine groups are hydrolyzed.

    Let us focus on the hydrolysis of the amide moiety within the gyromitrin molecule. The vibrational wavenumber of the stretching mode of the relevant \(\ce{C-N}\) bond amounts to \(1\,293.0\ \mathrm{cm^{-1}}\) and the potential energy surface does not significantly alter its shape with isotope substitution effect.

    6.7 Calculate the highest possible hypothetical kinetic isotope effect at the temperature of human body, \(37\,^\circ\mathrm{C}\), for the given hydrolysis reaction assuming that both relevant nitrogen and carbon atoms were simultaneously substituted, \(\ce{^{14}N}\) with the \(\ce{^{15}N}\) isotope and \(\ce{^{12}C}\) with the \(\ce{^{13}C}\) isotope. Consider that only the zero point vibrational energy affects the rate constants. Assume that the molar masses of all isotopes are integers. In all steps consider five significant digits.

    6.8 After making these isotopic changes, the rates of hydrolysis are not significantly different. Which of the following is the most likely the rate determining step?

    • ☐ Nucleophilic attack of water on a protonated amidic moiety
    • ☐ \(\ce{C-N}\) bond cleavage
    • ☐ Protonation of the gyromitrin molecule

    Official English text of the problem.

  7. Problem 7: Cidofovir

    Cidofovir (1), originally designed and prepared by the group of Professor Holy in former Czechoslovakia, is a nucleotide analogue with antiviral activity. It is used to treat viral infections, mostly in patients with AIDS.

    Figure 1

    Cidofovir (1)

    The key intermediate in the synthesis of cidofovir is optically pure diol 2, which can be prepared from L-mannitol (3).

    Figure 2

    7.1 Draw the structures of compounds A–D, including stereochemistry. One molecule of A produces two molecules of B.

    7.2 Draw the structural formulae of all alternative stereoisomers of compound 3 which could be used in the same reaction sequence to afford only the same product 2.

    Diol 2 is further modified to provide compound I. The synthesis of phosphonate 4 used to convert compound F to G will be discussed later.

    Figure 3

    7.3 Draw the structures of compounds E–I, including stereochemistry. Use the abbreviation MMT for the (4-methoxyphenyl)diphenylmethyl group.

    Official English text of the problem.

  8. Problem 8: Caryophyllene

    β-Caryophyllene (3) is a naturally occurring sesquiterpene present in clove tree and in some traditional Czech and Slovak plants, such as the hop plant or small-leaved linden.

    The synthesis of β-caryophyllene starts from a single enantiomer of dienone A. The reaction of A with silyl ketene acetal 1, followed by immediate reduction and aqueous work-up affords ketone 2. This intermediate then undergoes reaction with tosyl chloride, providing B. Basic cyclization of this compound affords C. Finally, the reaction of C with ylide D provides β-caryophyllene.

    Figure 1
    Figure 2

    8.1 Draw the structures of compounds A–D, including the appropriate stereochemistry.

    Hint: In transformation A → 2, the silyl ketene acetal acts as a nucleophile.

    Due to the large ring size, both compounds 2 and 3 are stable, even though they contain a double bond in the trans configuration. trans-Cyclooctene (4) is the smallest ring that can accommodate a trans double bond. It can be prepared according to the following scheme:

    Figure 3

    8.2 Draw the structures of reagent E and intermediates F and G, including the appropriate stereochemistry. For F and G, tick the box indicating the stereochemical outcome.

    Mark the correct answer:

    ☐ achiral, ☐ single enantiomer, ☐ racemic mixture, ☐ mixture of diastereoisomers

    8.3 Draw the structure of the enantiomer of cycloalkene 4.

    Figure 4

    The two double bonds in β-caryophyllene display different reactivity: the double bond in the ring (endocyclic) is more reactive than the other one (exocyclic) due to the ring strain.

    Figure 5

    8.4 Draw the structures of compounds Ha + Hb, I and Ja + Jb, including the appropriate stereochemistry. Hint: Ha + Hb and Ja + Jb are pairs of diastereomers.

    Interestingly, the reactivity of the double bonds is reversed when isocaryophyllene (5) is used instead of β-caryophyllene (3).

    Figure 6

    8.5 Draw the structures of compounds Ka and Kb.

    Hint: Ka + Kb are a pair of diastereomers.

    Isotope-labelled compounds are invaluable tools for reaction mechanism investigation, structure determination, and mass or NMR spectroscopy studies. Let us have a look at the synthesis of some labelled analogues of β-caryophyllene.

    Figure 7

    8.6 Draw the structures of compounds L and M, including the appropriate stereochemistry.

    β-Caryophyllene (3) undergoes acid-catalyzed cyclization, which leads to a complex mixture of products. Among them, the pair of diastereomers Na + Nb and the pair of diastereomers 7a + 7b are the most abundant. The reaction starts with protonation of the more reactive internal double bond affording cation O. This cyclizes without the cleavage of a carbon-carbon single bond to yield diastereomeric tricyclic cations Pa and Pb, which undergo hydration to give the target alcohols Na and Nb. Alternatively, the cations Pa and Pb rearrange with the cleavage of a carbon-carbon single bond to cations Qa and Qb, which deprotonate to compounds 7a and 7b.

    Figure 8

    8.7 Draw the structures, including the appropriate stereochemistry, of the three intermediates O, Pa, Qa leading to the diastereomer 7a, including the appropriate stereochemistry.

    8.8 Draw the structures of diastereomers Na + Nb.

    Official English text of the problem.