Hydrogenation of Alkenes

How can you convert an unsaturated hydrocarbon such as an alkene, into a saturated hydrocarbon (an alkane)?
With the magic of chemistry (a catalyst), you can add hydrogen across the double bond in an alkene!
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Vanadium Phosphate Catalyst

Methane, CH₄, in natural gas can be used as a raw material to produce bromomethane, CH₃Br. Bromomethane (methyl bromide) can then be used in the chemical industry to produce fuels, chemicals, polymers and pharmaceuticals. When  bromomethane is converted into fuels and other chemicals, bromine is released in the form of hydrogen bromide, HBr. Using oxygen and a suitable catalyst, bromine from the hydrogen bromide by-product is embedded back into bromomethane so that no bromine is lost from the system.
Researchers at ETH, Zurich, have identified vanadium phosphate as an ideal catalyst for this reaction.
Vanadium(III) phosphate (vanadium(3+) phosphate), has the structure shown below:

It is a relatively mild oxidising catalyst.
It is a strong enough oxidising catalyst to allow hydrogen bromide to react with oxygen at the surface of the catalyst, but, it is not strong enough to oxidise the methane and brominated reaction products.
It is therefore possible to brominate methane in a single step at atmospheric pressure and at a temperature below 500°C.  The catalyst is also stable, able to resist the corrosive reaction environment.
This makes it an attractive catalyst for this important, industrial, chemical reaction.

Reference:
Vladimir Paunović, Guido Zichittella, Maximilian Moser, Amol P. Amrute, Javier Pérez-Ramírez. Catalyst design for natural-gas upgrading through oxybromination chemistry. Nature Chemistry, 2016; DOI:10.1038/nchem.2522

Further Reading:
Lewis Structures (electron dot diagrams): http://www.ausetute.com.au/lewisstr.html
2-Dimensional Structural Formula: http://www.ausetute.com.au/structural2D.html
Molecular Formula: http://www.ausetute.com.au/molecularformula.html
Halogenation of Hydrocarbons: http://www.ausetute.com.au/halogalk.html
Energy Profiles: http://www.ausetute.com.au/enerprof.html
Reaction Rates: http://www.ausetute.com.au/reactrate.html
Redox Reaction Concepts: http://www.ausetute.com.au/redoxreactions.html

Suggested Study Questions:

1. Draw the Lewis Structures (electron dot diagrams) for each of the following molecules:
   • methane
   • bromomethane
   • hydrogen bromide
2. Draw the 2-dimensional structural formula for each of the following molecules:
   • methane
   • bromomethane
   • hydrogen bromide
3. Give the molecular formula for each of the following molecules:
   • methane
   • bromomethane
   • hydrogen bromide
4. Write a chemical equation to represent the reaction between methane and bromine to produce bromomethane
5. Name the type of reaction given in question 4.
6. Give the reaction conditions necessary for this reaction in question 5 to occur at room temperature and pressure in your laboratory.
7. Why do you think a catalyst is required for this reaction above in order to produce commercial quantities of bromomethane?
8. Which organic compound, methane or bromomethane, do you expect to be the most chemically reactive? Explain your answer.
9. What is meant by the term "oxidising agent"?
10. Is the bromination of methane using bromine a redox reaction? Explain your answer.
11. Refer to the structure of vanadium(III) phosphate given in the article. Give the oxidation state (oxidation number) for each of the following:
    • vanadium
    • oxygen
    • phosphorus
12. Why do you think vanadium phosphate is talked about as being an "oxidising catalyst" rather than as an "oxidising agent"? Explain your answer.

Turning Polyethylene Waste into Fuel

Low density polyethylene, LDPE, is used to make many things we use everyday such as plastic milk containers, cling wrap, and plastic bags. LDPE can be recycled quite easily, but a lot of LDPE ends up as rubbish in land fills.
Chemists in India have developed a commercially viable way to turn LDPE into a liquid fuel by heating the LDPE waste to between 400 and 500^oC over a kaolin catalyst which causes the long chain polymer chains to break apart. This process is known as thermo-catalytic degradation: thermo means heat, the catalyst is kaolin, and degradation means breaking apart. This thermo-catalytic degradation of LDPE produces much smaller carbon-based molecules. Gas Chromatography was used to characterise these smaller molecules, and it was found that they were mainly alkanes and alkenes between 10 and 16 carbon atoms long. This makes the mixture very similar to that found in petrochemical fuels. For example, the hydrocarbons in gasoline (petrol) typically have a chain length of between 4 and 12 carbon atoms while diesel fuel typically contains hydrocarbons with a chain length between 8 and 21 carbon atoms.

The catalyst, kaolin, is a layered, aluminosilicate clay mineral with the formula Al₂Si₂O₅(OH)₄. It acts as a catalyst by providing a large surface on which the polymer molecules can sit in an orientation favourable to the degradation under heat.

Using the kaolin catalyst at 450^oC, the thermo-catalytic degradation of 1 kg of LDPE produced 700 g of liquid fuel.

Reference:
Achyut Kumar Panda, Raghubansh Kumar Singh. Thermo-catalytic degradation of low density polyethylene to liquid fuel over kaolin catalyst. International Journal of Environment and Waste Management, 2014; 13 (1): 104 DOI: 10.1504/IJEWM.2014.058803

Further Reading:
Polythene (polyethylene): Properties, Production and Uses 
Gas Chromatography 
Alkanes: properties and uses
Alkenes: properties and uses
Ethene (ethylene): properties and uses
Silicates: structure and formula

Suggested Study Questions:

1. Give the molecular structure for ethene (ethylene).
2. Write an equation showing how ethene (ethylene) molecules can be polymerized to form polythene (polyethylene).
3. Name the type of polymerization reaction being described by the equation in question 2.
4. Explain, using a diagram of the partial structure of polythene (polyethylene), what happens when polyethylene undergoes thermo-catalytic degradation.
5. Describe the differences in the structures of alkanes and alkenes.
6. Draw a straight chain alkane with 10 carbon atoms.
7. Draw a structural isomer of the molecule in question 6.
8. Draw a straight chain alkene with 10 carbon atoms.
9. How many structural isomers of the molecule in question 8 do you think there would be? Support your answer with the structural formula for each of these structural isomers.
10. Why do you not find short carbon chain alkanes, between 1 and 4 carbon atoms long, in the liquid petrochemical fuels like gasoline (petrol) and diesel?

Nobel Prize countdown

As students head back to the class room for a new term of exciting learning, the scientific community is gearing up for a major annual event, the announcement of the Noble Prizes.
With just days to go before the Nobel Prize in Chemistry is to be announced, there is much discussion (and possibly even a bit of betting) about who is likely to be this year's laureate.

Among the contenders this year are:

• Louis E. Brus (Columbia University) for the discovery of colloidal semiconductor nanocrystals (quantum dots)
• Akira Fujishima (University of Tokyo) for the discovery of photocatalytic properties of titanium dioxide (the Honda-Fujishima Effect)
• Masatake Haruta (Tokyo Metropolitan University) and Graham J. Hutchings (Cardiff University) for their discoveries of catalysis by gold

Quantum dots are semiconductors, but their electronic properties are related to the size and shape of the individual crystals. In general, the smaller a crystal is, the more energy is needed to excite the dot, which means that more energy is released when the crystal returns to its ground state. It is hoped that quantum dots will lead to practical quantum computing and increase the efficiency of photovoltaic cells. Quantum dots are being used in preference to some dyes in biological analyses because quantum dots are brighter and more stable.

While working on his Ph.D in 1967, Akira Fujishima exposed a titanium dioxide electrode to strong light and discovered that this catalyzed the decomposition of water into hydrogen and oxygen. This became known as the Honda-Fujishima Effect (Professor Kenichi Honda was Akira Fujishima's supervisor). Finding cheap, effective methods for providing hydrogen would enable the development of hydrogen as fuel.

In the 1980's Masatake Haruta showed that colloidal gold, gold clusters with diameters of 5 nanometers or less, could catalyze reactions involving oxygen gas.
Graham J Hutchings has extended the number of reactions  we now know of that can be catalyzed by gold. Hutchings has shown that primary alcohols can be oxidized to aldehydes using a gold-palladium/titanium dioxide combination without the need for a solvent. He has also developed the rapid synthesis of hydrogen peroxide, H₂O₂, from hydrogen and oxygen  without the formation of water as a by-product.

Hydronium Ions in Fermentation

Ethanol or ethyl alcohol (C₂H₅OH) can be produced from glucose (C₆H₁₂O₆) by fermentation using an enzyme as a catalyst:

C6H12O6

enzyme -------->

2 C2H5OH + 2 CO2

Chemists are very interested in studying this reaction because it has the potential to convert the sugars in woody biomass into alcohols which can be used as a fuel in place of non-renewable fuels obtained from petroleum. It is known that the enzyme in yeast which is commonly used in the production of ethanol loses its effectiveness when the pH of the reaction mixture is lowered.

In aqueous solutions, as soon as protons (H⁺) are released by an acidic species they bond with water molecules (H₂O) to form hydronium ions (H₃O⁺) :

H⁺ + H₂O → H₃O⁺

and pH is a measure of the hydronium ion concentration:
pH = -log[H₃O⁺]although we often think of this as being the same as a measure of the proton concentration:
pH = -log[H⁺]since we reasonably expect all the protons to have reacted with water molecules to form hydronium ions.

Los Alamos National Laboratory scientists substituted hydrogen in their enzyme samples with deuterium, an isotope of hydrogen (hydrogen-2). Unlike hydrogen-1 atoms, deuterium atoms provide a clear signal when bombarded with neutrons so they are visible to X-rays, this fact can be used to study the enzyme catalyzed process of fermentation.

The scientists found that as the pH fell below 6, hydronium ions (H₃O⁺) that are vitally important in the conversion of the sugar molecule into its fermentable form suddenly became dehydrated.
H₃O⁺ → H₂O + H⁺
The space in the enzyme occupied by the relatively large hydronium ion collapsed into a tiny volume occupied by the remaining proton (H⁺). This spatial change in the molecular structure prevented the sugar from being attacked by the enzyme.

The observed phenomenon provided an answer about why pH plays such an important role in the process and renders the enzyme inactive under acidic conditions. More important, it definitively illustrated that the hydronium ion plays a key role in the transport of protons in these types of biochemical systems.

Reference
Andrey Y. Kovalevsky, B. L. Hanson, S. A. Mason, T. Yoshida, S. Z. Fisher, M. Mustyakimov, V. T. Forsyth, M. P. Blakeley, D. A. Keen, Paul Langan. Identification of the Elusive Hydronium Ion Exchanging Roles with a Proton in an Enzyme at Lower pH Values. Angewandte Chemie International Edition, 2011; 50 (33): 7520 DOI: 10.1002/anie.201101753

Further Reading:
Mass-Mole Calculations
Gas Volume Calculations
Molarity Calculations
Yield Calculations
pH Calculations
Enzymes

Study Questions:

1. A Chemist undertook a fermentation experiment using 10g of glucose dissolved in 1L of water.
   • How many moles of glucose were present in the solution?
   • What was the concentration of the initial glucose solution?
   • What is the maximum yield of ethanol that could be produced from this reaction mixture?
   • If the actual yield of ethanol was 4% by mass, how many moles of ethanol was produced?
   • If the actual yield of ethanol was 4% by mass at 25^oC, what volume of carbon dioxide gas was be produced?
2. Assuming the fermentation of glucose reaction occurs at a constant temperature of 25^oC
   • Calculate the concentration of hydronium ions present in a reaction mixture with a pH of 6.
   • Calculate the concentration of hydroxide ions present in a solution with pH of 6
   • Calculate the pOH of a solution with a pH of 6.
3. What is meant by the term catalyst?
4. What is meant by the term enzyme?
5. Explain why the hydronium ion is larger than the hydrogen ion.
6. Would the hydronium ion be larger or smaller than a water molecule? Explain your answer.
7. How would you define the term isotope?
8. Explain why deuterium is considered to be an isotope of hydrogen.
   
   
   

Isobutene

Isobutene and isobutylene are other names used for the organic compound with the IUPAC name 2-methylpropene. 2-methylpropene is one of the four structural isomers of butene and it exists as a highly flammable, colourless gas at standard temperature and pressure. Isobutene can be converted into fuel additives that increase the octane rating and prevent engine knocking.
Addition polymerization of isobutene results in polyisobutene (PIB) a rubbery substance which is used in the manufacture of tires, adhesives, ball bladders, caulks and sealants, cling film, rubber modification, fuel additives, and chewing gum.

Researchers at the Department of Energy's Pacific Northwest National Laboratory and at Washington State University have developed a new catalyst material composed of zinc oxide and zirconium oxide that will convert bio-ethanol into isobutene in one production step.
If the catalyst was composed only of zinc oxide, the ethanol was mostly converted into acetone (the chemical used in nail polish remover).
If the catalyst was composed only of zirconium oxide, the ethanol was mostly converted into ethylene (the chemical made by plants that ripens fruit).
When the catalyst is composed of a 1:10 ratio of zinc oxide to zirconium oxide, 83% of the ethanol was converted into isobutene.

Reference
Junming Sun, Kake Zhu, Feng Gao, Chongmin Wang, Jun Liu, Charles H. F. Peden, Yong Wang. Direct Conversion of Bio-ethanol to Isobutene on Nanosized ZnxZryOzMixed Oxides with Balanced Acid–Base Sites. Journal of the American Chemical Society, 2011; 133 (29): 11096 DOI: 10.1021/ja204235v

Further Reading
Naming Carbon Compounds
Structural Isomers of Alkenes
Ideal Gas Law
Polymers and Polymerization
Fuel Definitions
Energy Profiles

Study Questions

1. Give the molecular formula and structural formula for 2-methylpropene.
2. Draw the structural formula for all four structural isomers of butene.
3. Write an equation to represent the polymerization of 2-methylpropene to polyisobutene.
4. Use diagrams to show why the polymerization reaction above is considered to be an addition polymerization reaction.
5. On the diagram produced in response to question 4, clearly label the monomer and polymer compounds.
   
6. Give likely formulae for both zinc oxide and zirconium oxide.
7. Give the IUPAC name, the molecular formula and the structural formula, for each of the following:
   • isobutene
     
   • acetone
   • ethylene
8. Write equations for each of the following catalyzed reactions:
   • the conversion of ethanol into acetone
     
   • the conversion of ethanol into ethylene
9. Which of the following compounds could undergo addition polymerization? Justify your answer.
   
   • acetone
   • ethylene
10. Name the products of any successful addition polymerization in question 8.
    
    
    

Rhodium

Rhodium, symbol Rh, is the rarest of all non-radioactive metals on Earth, and therefore an expensive metal. On the 22nd July 2011, 1 gram of rhodium cost $(AUD)38 compared to 1 gram of gold which cost $(AUD)31 or 1g of silver for only 78 cents !
Rhodium is a transition metal with a density of 12.41 gcm^-3 and is found in nature as the free metal, or alloyed with similar metals such as platinum or nickel, but not as a chemical compound.
Naturally occurring rhodium is composed of only one isotope, rhodium-103.
Only about 3 tonnes of rhodium are produced in the world each year, and most of this is used for catalyzing chemical reactions.
Approximately 80% of the rhodium produced is used as a reduction catalyst in the three-way catalytic converters of cars.
In a three-way catalytic converter three processes occur simultaneously:

1. Reduction of nitrogen oxides to nitrogen and oxygen: 2NO_x → xO₂ + N₂
2. Oxidation of carbon monoxide to carbon dioxide: 2CO + O₂ → 2CO₂
3. Oxidation of unburnt hydrocarbons (HC) to carbon dioxide and water

Other uses of rhodium include :

• plating white gold to make it appear more silvery (white gold is actually an alloy of gold with atleast one other metal such as nickel, manganese, palladium)
• plating sterling silver to make it appear more silvery (sterling silver is an alloy of silver containing 92.5% by mass silver and 7.5% by mass of other metals such as copper)

Queen's University chemists have just discovered that rhodium that is modified using carbon, nitrogen or hydrogen-based complexes changes colour to yellow in the presence of nitrogen, deep blue in the presence of oxygen, and brown in the presence of carbon monoxide. Modified metals, such as modified rhodium, that change colour in the presence of particular gases could warn consumers if packaged food has been exposed to air or if there's a carbon monoxide leak at home. This finding could potentially influence the production of both industrial and commercial air quality sensors.

Reference
Queen's University (2011, July 21). Modified metals change color in the presence of particular gases. ScienceDaily. Retrieved July 23, 2011, from http://www.sciencedaily.com­ /releases/2011/07/110721131159.htm

Further Reading
Periodic Table
Definitions of a Mole
Mass-Mole Calculations
Density
Isotopes
Relative Atomic Mass
Metals & Non-metals
Percentage Composition

Study Questions

1. Locate rhodium in the Periodic Table and give its
   • atomic number
   • relative atomic mass
2. Using the prices per gram of metal given in the story above, calculate
   • the price of the 3 tonnes of rhodium produced in the world each year
     
   • the price of 1 mole of rhodium
   • the price of 10 cubic centimeters of rhodium
   • the mass of $57,000 worth of rhodium
   • the volume of $57,000 worth of rhodium
3. Naturally occurring rhodium has only 1 isotope, rhodium-103. For this isotope give:
   • the number of protons in the nucleus of a rhodium atom
   • the number of neutrons in the nucleus of a rhodium atom
   • the mass number of this isotope of rhodium
   • the atomic number for this isotope of rhodium
4. If naturally occurring rhodium only has 1 isotope why is its relative atomic mass 102.9?
5. List the physical properties you would expect rhodium to have based on its position within the Periodic Table.
6. Why would coating white gold in rhodium make it appear more silvery?
7. A 25 kg sample of sterling silver contains only silver and copper.
   • What mass of silver is present in the sample?
   • What mass of copper is present in the sample?
8. A sample of white gold is found to contain only 1.39 g gold and 0.09g of nickel. Calculate the percent by mass of each element present in the sample.
   
   
   
   
   

Hydrogen from Water Splitting

The production of hydrogen as an alternative fuel to current fossil fuels relies on the creation of a suitably cheap and efficient way to split water using the power of sunlight. Monash University scientists in Australia, working with UC Davis scientists in the USA, have found that a manganese mineral known as birnessite can be used as a catalyst to speed up the splitting of water into hydrogen and oxygen gases.

Birnessite, a soft, black mineral formed from precipitation reactions in lakes, oceans and groundwater, is predominantly an oxide of manganese, but calcium, potassium and sodium are also present in smaller amounts.
The formula for birnessite is (Na_0.3Ca_0.1K_0.1)(Mn⁴⁺,Mn³⁺)₂O₄ · 1.5 H₂O
As a catalyst for the water splitting reaction, the manganese in the birnessite cycles between oxidation states. First, when a voltage is applied manganese (II) is oxidized to manganese (IV). Then in sunlight, birnessite goes back to the manganese (II) state.

The water splitting reaction has two steps:

1. Two molecules of water are oxidized to form one molecule of oxygen gas, four protons and four electrons.
   
2. The protons and electrons combine to form two molecules of hydrogen gas

Reference:
Rosalie K. Hocking, Robin Brimblecombe, Lan-Yun Chang, Archana Singh, Mun Hon Cheah, Chris Glover, William H. Casey, Leone Spiccia. Water-oxidation catalysis by manganese in a geochemical-like cycle. Nature Chemistry, 2011; DOI: 10.1038/nchem.1049

Further Reading
Oxidation States (Numbers)
Oxidation and Reduction
Balancing Half Equations
Electrolysis - Electrolytic Cells
Percentage Composition

Study Questions:

1. What is meant by the term oxidation state (or oxidation number)?
2. What is the oxidation state (or oxidation number) for each of the following:
   
   • Mn³⁺
   • Mn⁴⁺
   • manganese (II)
   • manganese (IV)
     
3. Write equations to represent each of the following:
   
   • The oxidation of manganese (II) to manganese (IV)
   • The reduction of manganese (IV) to manganese (II)
4. For each reaction in question 3 above, identify:
   • the oxidant
   • the reductant
     
5. Write an equation to represent the first step in the water splitting reaction.
6. Write an equation to represent the second step in the water splitting reaction.
7. Use the equations in question 5 and 6 above to write an overall reaction for the water splitting reaction.
8. For each equation in questions 5 and 6,
   • label the reaction as an oxidation or reduction reaction
   • identify the oxidizing agent(s)
   • identify the reducing agent(s)
9. In the formula of birnessite, (Na_0.3Ca_0.1K_0.1)(Mn⁴⁺,Mn³⁺)₂O₄ · 1.5 H₂O, what does the 1.5 H₂O mean?
   
10. Calculate the percentage composition of birnessite.
    
    

Methane Reactions

By using gold dimer cations as catalysts, Georgia Institute of Technology and the University of Ulm scientists have converted methane into ethene at room temperature, and into methanal at temperatures below 250K (-9^o F). In both the room temperature reaction-producing ethene, and the methanal generation colder reaction, the gold dimer catalyst is freed at the end of the reaction, thus enabling the catalytic cycle to repeat again and again.

The temperature-tuned catalyzed methane partial combustion process involves activating the methane carbon-to-hydrogen bond to react with molecular oxygen.
In the first step of the reaction process, methane and oxygen molecules coadsorb on the gold dimer cation at low temperature.
Subsequently, water is released and the remaining oxygen atom binds with the methane molecule to form methanal.
If done at higher temperatures, the oxygen molecule comes off the gold catalyst, and the adsorbed methane molecules combine to form ethene through the elimination of hydrogen molecules.

Reference
Sandra M. Lang, Thorsten M. Bernhardt, Robert N. Barnett, Uzi Landman. Temperature-Tunable Selective Methane Catalysis on Au2 : From Cryogenic Partial Oxidation Yielding Formaldehyde to Cold Ethylene Production. The Journal of Physical Chemistry C, 2011; 115 (14): 6788 DOI: 10.1021/jp200160r

Further Reading
Balancing Chemical Equations
Nomenclature
Combustion of Hydrocarbons
Oxidation and Reduction
Oxidation States (Numbers)

Study Questions

1. Write the molecular formula for each of the following:
   
   • methane
   • methanal
   • ethene
2. Draw the structural formula for each of the following:
   
   • methane
   • methanal
   • ethene
3. On the structural formula above, identify the functional groups present in methanal and ethene.
   
4. The following molecules are known by other names. Give atleast one other name used for each of the following:
   
   • methane
   • methanal
   • ethene
5. Write a balanced chemical equation for each of the following reactions involving the gold dimer cation catalyst:
   
   • methane and oxygen react to form methanal and water
     
   • methane and oxygen react to form ethene and water
6. Classify each reaction above as an oxidation or a reduction reaction. Justify your answer.
   
7. Write balanced chemical equations to represent the combustion of methane at high temperature, without the aid of a catalyst, under each of the following conditions:
   
   • excess oxygen
   • excess methane
8. Compare the chemical equations in question 7 to those in question 5. In what ways are the reactions similar? In what ways are the reactions different?
   

PCL : polycaprolactone

Polycaprolactone (PCL) is a biodegradable polyester used in medical devices and disposable tableware. It is produced using the caprolactone monomer and a suitable catalyst as shown below:


The catalyst used to help bring about this polymerization reaction is usually an organic tin-based catalyst such as tin (II) ethylhexanoate:
The tin (II) ethylhexanoate catalyst is highly toxic and has to be disposed of appropriately.

Biochemists found a more environmentally friendly catalyst in the form of an enzyme produced by a yeast strain known as Candida antartica. In a standard batch process, the raw materials such as caprolactone monomers and a solvent such as toluene, are dumped into a vat, along with tiny beads that carry the enzyme, and stirred. This process is too inefficient to be used commercially, and the enzyme residue is a contaminant in the final polymer product.

Researchers at the National Institute of Standards and Technology (NIST) and the Polytechnic Institute of New York University are now studying the use of a new catalyst, a small block of aluminium with a tiny groove carved into it containing the enzyme coated beads.

In this continuous flow process, the feedstock chemical flows through the narrow channel, around the enzyme-coated beads, and is polymerized out the other end. This arrangement accelerates the rate of reaction and improves the ability to recover the enzyme and reduce contamination of the product.

Reference
Santanu Kundu, Atul S. Bhangale, William E. Wallace, Kathleen M. Flynn, Charles M. Guttman, Richard A. Gross, Kathryn L. Beers. Continuous Flow Enzyme-Catalyzed Polymerization in a Microreactor. Journal of the American Chemical Society, 2011; : 110325123921095 DOI: 10.1021/ja111346c

Further Reading
Polymers and Polymerization
Enzymes
Functional Groups
Esters
Ligands and Complex Ions
Reaction Rate
Intermolecular Forces

Study Questions

1. What is the molecular formula for each of the following:
   
   • caprolactone
   • ethylhexanoate
2. When caprolactone monomers react to form polycaprolactone, the ring structure must open up. Draw a diagram of this open-ring structure.
3. On the diagram of the open-ring caprolactone structure, identify and name the functional groups present.
4. Draw a diagram of showing how 3 caprolactone monomers join together to form part of the polycaprolactone polymer.
5. On the diagram of the polycaprolactone polymer you have drawn, identify and name the functional groups present.
6. Why do you think it is common for industrial chemists to look to naturally occurring enzymes to replace more environmentally hazardous metal-based catalysts?
   
7. Why do you think the caprolactone polymerization reaction is carried out in an organic solvent like toluene rather than in water?
   

Atom Transfer Radical Polymerization

Atom transfer radical polymerization (ATRP) is a way of forming carbon-carbon bonds in a controlled piece-by-piece fashion using a transition metal catalyst. ATRP is used to make polystyrene, poly(methyl methacrylate) and polyacrylamide.

The ATRP process relies on paired reduction-oxidation (redox) reactions between two species of copper:

• the activator, Cu⁺
  
• the deactivator, Cu²⁺
  

where the two catalysts exchange electrons back and forth.
Occasionally, one of the exchanges will spontaneously stop, called a radical termination, resulting in the accumulation of Cu²⁺. To keep the polymerization going, chemists must re-balance the system by compensating for the excess Cu²⁺. Simply adding more Cu⁺ to the system produces materials with high, sometimes toxic, levels of copper, up to 5,000 ppm. Such levels of copper are hard to remove using current industrial equipment. It has been found that reducing agents like sugars or vitamin C are highly effective in reducing the amount of copper catalyst used in ATRP reactions.

In a new study, Carnegie Mellon University chemists have found that they can use electricity from a battery to drive these ATRP reactions. Adding electricity capitalized on the redox reaction by moderating the transfer of electrons. This allowed them to compensate for the radical terminations and reduce the amount of copper needed to run ATRP. As a result the amount of copper in the system was reduced to 50 ppm, a 100-fold decrease.

Reference
Andrew J. D. Magenau, . Nicholas C. Strandwitz, . Armando Gennaro and Krzysztof Matyjaszewski. Electrochemically Mediated Atom Transfer Radical Polymerization. Science, 1 April 2011: Vol. 332 no. 6025 pp. 81-84 DOI: 10.1126/science.1202357

Further Reading:
Parts per Million (ppm)
Polymers and Polymerization
Oxidation and Reduction
Le Chatelier's Principle

Study Questions:

1. If 1kg of polystyrene contained 5000 ppm copper, what mass of copper would be present?
2. If 1kg of polyacrylamide contained 50 ppm copper, what mass of copper would be present?
   
3. Name the monomer that is used to produce each of the following polymers:
   
   • polystyrene
   • poly(methyl methacrylate)
   • polyacrylamide
4. Provide the structural formula for each of the monomers in question 1.
5. Draw the structure for each of the polymers listed in question 1.
6. In the reaction:
   Cu⁺ Cu²⁺ + e
   which species is
   • being oxidized?
   • being reduced?
   • the oxidant?
   • the reductant?
7. What is meant by each of the following terms:
   • oxidation
   • reduction
   • redox
     
   
   
8. Explain the statement "Adding electricity capitalized on the redox reaction by moderating the transfer of electrons. "
9. In the article, it is suggested that adding Cu⁺ or using electricity can moderate the transfer of electrons. Suggest another way that this might be accomplished.
   
   

Catalysis by Gold Nanoclusters

Since the early 1980s, experiments have indicated that gold nanoparticles exhibit unexpected catalytic activity towards many industrially important chemical reactions that involve activation of atomic bonds inside oxygen or hydrocarbon molecules. Room-temperature formation of carbon dioxide, CO₂, from carbon monoxide, CO, and oxygen molecule, O₂, is one of the most extensively studied processes. A number of different factors have been suggested to contribute to the ability of gold particles to activate the O-O bond, which is considered to be the key reaction step.

Finnish scientists recently exposed monolayer-thick gold clusters to a variable number of oxygen molecules. It was found that even one gold cluster can effectively adsorb multiple oxygen molecules at the boundaries of the cluster, simultaneously weakening, stretching, the O-O bond by transferring electrons to the oxygen molecules. Taking into account the effects of temperature and ambient pressure, the calculations predicted that the oxygen molecules will completely dissociate and the oxygen and gold atoms will form one-dimensional alternating chains at the cluster boundary. The oxygen atoms in these chains are negatively charged and the gold atoms positively charged, creating a system that is reminiscent of a one-dimensional gold-oxide chain. These chains are expected to be the highly catalytically active part towards conversion of carbon monoxide to carbon dioxide at room temperature.

At room temperature and pressure, it appears that gold can catalyse an oxidation reaction by first oxidizing itself to gold oxide, which seems to contradict the known properties of gold in the macroscopic level.

References

1. Pentti Frondelius, Hannu Häkkinen and Karoliina Honkala. Formation of Gold(I) Edge Oxide at Flat Gold Nanoclusters on an Ultrathin MgO Film under Ambient Conditions. Angewandte Chemie International Edition, 2010; DOI: 10.1002/anie.201003851
2. X. Lin, N. Nilius, H.-J. Freund, M. Walter, P. Frondelius, K. Honkala, H. Häkkinen. Quantum Well States in Two-Dimensional Gold Clusters on MgO Thin Films. Physical Review Letters, 2009; 102 (20) DOI: 10.1103/PhysRevLett.102.206801

Further Reading
Naming Compounds
Writing Formula
Balancing Chemical Equations
Oxidation States
Transition Metals
Energy Profiles
Reaction Rate

Study Questions:

1. Write a balanced chemical equation for the formation of carbon dioxide from carbon monoxide and oxygen.
2. For the reaction above, what other possible steps in the reaction mechanism could be rate determining steps?
3. Why do you think that scientists believe that the activation of the O-O bond is the key reaction step in the reaction mechanism for this reaction?
4. What is meant by the term catalysis?
5. Why is gold described as a catalyst for the reaction described in the article?
   
6. What is meant by the term dissociate?
7. Describe how oxygen molecules can dissociate.
8. What is meant by the term oxidize?
9. Given the position of gold in the Periodic Table, what oxidation states are possible?
10. Give the formula for two possible oxides of gold.
11. Name each of the oxides above.
    

Reaction Rates and Evolution

University of North Carolina scientists have been studying the effect of temperature on extremely slow chemical reactions in order to determine whether life on Earth originated in a hot or cold environment and whether enough time has passed in order for life to have evolved to its current complexity. Their investigations suggest that the time required for evolution on a warmth earth is shorter than critics might expect.

They found that the influence of temperature on reaction rates varies dramatically. In one slow reaction, raising the temperature from 25 to 100^oC increased the rate 10 million fold!
High temperatures were probably a crucial influence on reaction rates when life began forming in hot springs and submarine vents. Later, the cooling of the earth provided elective pressure for primitive enzymes to evolve and become more sophisticated.

Using two different reaction catalysts which are not protein enzymes but that resemble the precursors to enzymes, they found that the catalyzed reactions were indeed less sensitive to temperature.

Reference
R. B. Stockbridge, C. A. Lewis, Y. Yuan, R. Wolfenden. Impact of temperature on the time required for the establishment of primordial biochemistry, and for the evolution of enzymes. Proceedings of the National Academy of Sciences, 2010; DOI: 10.1073/pnas.1013647107

Further Reading
http://www.ausetute.com.au/reactrate.html
http://www.ausetute.com.au/enerprof.html
http://www.ausetute.com.au/enzymes.html
http://www.ausetute.com.au/proteins.html

Study Questions

1. Explain why an increase in temperature generally speeds up the rate of a chemical reaction.
2. Define both the following terms :
   • catalyst
   • protein
   • enzyme
3. Draw an energy profile diagram to show the effect of a catalyst on a reaction.
   
4. Why would the researchers choose to use a non-protein based catalyst to study reactions that possibly occurred early on in the Earth's history?
5. Why is the study of catalyzed reactions, especially enzyme catalyzed reactions, important when studying the origins of life on Earth?
6. There is an enzyme, catalase, present in liver that speeds up the rate of decomposition of hydrogen peroxide. Design an experiment to demonstrate the effect of temperature change on this reaction.
   

Ammonia Production

Ammonia (NH₃) is one of the most important chemicals in the modern world, mostly due to its use in the manufacture of artificial fertilisers. The Haber, or Haber-Bosch process, is used to produce ammonia and is vital to the production of 100 million tons of fertiliser per year, responsible for sustaining one-third of the Earth's population.

Ammonia is generated naturally by plants and certain bacteria, which extract nitrogen from the atmosphere in a process known as nitrogen fixation. Natural nitrogen fixation occurs at ambient temperatures and pressures, but artificial nitrogen fixation via the Haber-Bosch process requires high pressures (150-250 atmospheres) and high temperatures (300-550 degrees Celsius) to produce the vast quantities of ammonia necessary to satisfy global demand.

The key to the Haber-Bosch process is an iron catalyst which encourages the dissociation of N₂ molecules, and provides a platform on which the resulting N atoms can be successively hydrogenated to yield NH, NH₂ and finally NH₃.

Scientists at the University of Cambridge exposed their iron sample to nitrogen ions, in order to readily build up a coverage of nitrogen atoms on the surface (to a density of just over one nitrogen atom per two top-layer iron atoms at the surface). Under uhv conditions, they can utilise Auger Electron Spectroscopy (AES) to quantify the amount of nitrogen on the surface. Then, they expose the sample to 0.6 mbar H₂ gas for a period of several minutes. This pressure is still very low compared with industrial conditions, but it allows the reaction to proceed sufficiently rapidly for them to take meaningful measurements over a timescale of minutes. If they used only uhv pressures of H₂, the reaction would be so slow that it would take hours, during which time contamination would build up on the surface and ruin the experiment.
After an exposure of several minutes, they rapidly evacuate the experimental chamber to return to uhv conditions and use AES to evaluate how much nitrogen is left on the surface, then expose to H₂ again and repeat. By doing this several times, they can measure the drop in surface nitrogen (corresponding to production of ammonia) as a function of time and temperature.

Their results suggest that, under certain conditions, namely when the ammonia pressure is kept low, the hydrogenation steps (from N to NH to NH₂ to NH₃) may actually be the most important.

Journal Reference:

1. Poobalasuntharam Iyngaran, David C. Madden, Stephen J. Jenkins, David A. King. Hydrogenation of N over Fe{111}. Proceedings of the National Academy of Sciences, 2010; DOI: 10.1073/pnas.1006634107

Further Reading
Haber Process
Nitrogen Cycle

Study Questions

1. Write a balanced chemical equation for the production of ammonia from hydrogen and nitrogen gas.
2. Predict the effect of high pressure in the reaction vessel on the yield of ammonia.
3. The Haber Process is an exothermic reaction. Explain what is meant by the term exothermic.
4. Explain what would happen to the yield of ammonia if the reaction vessel were cooled.
5. It is estimated that between 3 and 5% of the world's natural gas production is used in the production of ammonia. What would the natural gas be used for in the is process?
6. The Haber process typically produces an ammonia yield of between 10 and 20%. Describe 4 ways that this yield could be improved.
7. In the article above it is said that measuring the drop in surface nitrogen corresponds to measuring production of ammonia. Explain why this is true.
8. Describe another way you could measure the production of ammonia.
   

Hydrogen Production for Fuel Cells

Only small amounts of hydrogen occur naturally on Earth, yet the US Department of Energy estimates that the USA uses about 9 million tons per year, and, that this is set to grow if the "hydrogen economy" ever eventuates.

About 95% of the hydrogen in use is produced through steam reforming of natural gas, a catalytic process in which steam reacts with methane to yield carbon monoxide and hydrogen. This mixture is known as synthesis gas, or syngas, and is an intermediate in production processes for synthetic fuels, ammonia, methanol and other compounds.

Hydrogen is a high energy density fuel that is being considered as a cleaner source of future energy, particularly for low-temperature fuel-cell powered devices including vehicles. Fuel cells use electrochemical process to convert hydrogen and oxygen into water, producing current that powers a motor. Fuel cell vehicles require highly purified hydrogen such as is produced in the water-gas-shift reaction. This reaction strips residual carbon monoxide from the hydrogen generated through steam reforming of fossil fuels. Water-gas-shift catalysts decrease the amount of carbon monoxide in hydrogen and increase the hydrogen content by harvesting hydrogen from water molecules.

Currently, copper-based catalysts supported on zinc oxide and alumina are in use. Copper is pyrophoric, it can spontaneously ignite when exposed to air, so researchers have been looking for other more stable catalysts.

Platinum supported on cerium oxide is known to work, but platinum is expensive and cerium occurs in only a few places around the world. Scientists have discovered that sodium improves the platinum activity in the water-gas-shift reaction, which can now take place at low temperatures, even on inert materials such as silica. Less platinum is required, so the cost of hydrogen production should decrease.

Reference:
Yanping Zhai, Danny Pierre, Rui Si, Weiling Deng, Peter Ferrin, Anand U. Nilekar, Guowen Peng, Jeffrey A. Herron, David C. Bell, Howard Saltsburg, Manos Mavrikakis, and Maria Flytzani-Stephanopoulos. Alkali-Stabilized Pt-OHx Species Catalyze Low-Temperature Water-Gas Shift Reactions. Science, 24 September 2010: Vol. 329. no. 5999, pp. 1633 - 1636 DOI: 10.1126/science.1192449

Further Reading
Reaction Rates
Batteries and Fuel Cells

Study Questions

1. What are the 6 most abundant elements on Earth?
2. Natural Gas is the name given to a hydrocarbon. Give the IUPAC name and formula for this compound.
3. Write a balanced chemical reaction for the reaction between steam and natural gas to yield carbon monoxide and hydrogen.
4. Write equations to represent the electrochemical process to convert hydrogen and oxygen into water in a hydrogen fuel cell.
5. Cerium oxide is also known as ceria. Write a possible chemical formula for ceria.
6. Give the systematic name for alumina, and write its formula.
7. Give the systematic name for silica, and write its formula.
   

Pentane from Oil

Crude oil is refined by "cracking", the process in which large molecules are broken up into smaller molecules. The products of the cracking process include gasoline (petrol), kerosene, heating oil and lubricants. Catalysts can be used to further refine these hydrocarbons.

Rice University scientists have discovered that sub-nanometer clusters of active tungsten oxide lying on top of inert zirconium oxide (zirconia) are a highly efficient catalyst that turns straight-chain molecules of pentane, one of the many hydrocarbons present in gasoline (petrol), into better burning branched-chain hydrocarbons. This process of rearranging the carbon and hydrogen atoms in a molecule is referred to as isomerization.

Reference:
Nikolaos Soultanidis, Wu Zhou, Antonis C. Psarras, Alejandro J. Gonzalez, Eleni F. Iliopoulou, Christopher J. Kiely, Israel E. Wachs, Michael S. Wong. Relatingn-Pentane Isomerization Activity to the Tungsten Surface Density of WOx/ZrO2. Journal of the American Chemical Society, 2010; : 100903140709054 DOI: 10.1021/ja105519y

Further Reading
Organic Nomenclature
Naming Straight Chain Alkanes
Naming Branched-Chain Alkanes
Isomers of Alkanes
Uses of Hydrocarbons
Ethene

Study Questions

1. What is meant by the term hydrocarbon?
2. Give the names of 4 hydrocarbons.
3. Give the molecular formula for each of the hydrocarbons named above.
4. Give the molecular formula and the condensed molecular formula for pentane.
5. Draw the structural formula for pentane.
6. Draw the structural formula for all the possible isomers of pentane.
7. Name each of the isomers drawn above.
8. Why do you think that the branched-chain isomers of pentane are referred to as "better burning" hydrocarbons? Explain your answer.
   

Growing Egg Shells

For a long time scientists have believed that a chicken egg shell protein called ovocledidin-17 (OC-17) played a part in the formation of egg shells. This protein is only found in the mineral region of the egg which is the hard part of the shell, and, it appears to influence the transformation of amorphous calcium carbonate into calcite crystals by acting as a catalyst for crystal growth.

Scientists have now created simulations to show how the protein binds to the amorphous calcium carbonate surface using two clusters of arginine residues located on two loops of the OC-17 protein and creating a chemical clamp to nano sized particles of calcium carbonate. While clamped in this way, the OC-17 protein encourages the nanoparticles of calcium carbonate to transform into calcite crystallites that form the tiny nucleus of crystals that can continue to grow on their own. When the crystal nucleus is sufficiently large to grow on its own, the OC-17 protein desorbs, or, falls off. This frees up the OC-17 protein to promote yet more crystallization.

Reference:
Colin L. Freeman, John H. Harding, David Quigley, P. Mark Rodger. Structural Control of Crystal Nuclei by an Eggshell Protein. Angewandte Chemie International Edition, 2010; 49 (30): 5135 DOI: 10.1002/anie.201000679

Study Questions

1. What are the elements common to all proteins?
2. Proteins are actually polymers. What is the name given to the monomers that make up a protein?
3. What kind of bond binds these monomers together within the protein?
4. What is the formula for arginine?
5. Would the "loops" referred to in reference to the structure of OC-17 be part of its primary, secondary or tertiary structure? Explain your answer.
6. What does the term amorphous mean?
7. How does amorphous calcium carbonate differ from calcite crystals?
8. What is the definition of a catalyst?
9. Do you think OC-17 could be accurately described as a catalyst? Explain your answer.
   

Trifluoromethyl Groups in Pharmaceuticals

The trifluoromethyl group is a component of several commonly used drugs including the antidepressant Prozac, arthritis medication Celebrex, and Januvia which is used to treat the symptoms of diabetes. Trifluoromethyl groups are also a common component of agricultural chemicals such as pesticides.

Chemists often use hydrogen fluoride to attach a trifluoromethyl group to an organic compound, but under the conditions of the reaction this might produce unwanted reaction products. MIT chemists have designed a new way to attach a trifluoromethyl group to certain compounds using a palladium catalyst. The key to the success of this catalyst has been the use of a ligand called BrettPhos. During the reaction, a trifluoromethyl group is transferred from a silicon carrier to the palladium, displacing a chlorine atom. The trifluoromethyl containing molecule is then released and the catalytic cycle begins again. The chemists have tried the synthesis with a variety of aryl compounds and have achieved yields between 70% and 94%.

Reference:
Eun Jin Cho, Todd D. Senecal, Tom Kinzel, Yong Zhang, Donald A. Watson, Stephen L. Buchwald. The Palladium-Catalyzed Trifluoromethylation of Aryl Chlorides. Science, 2010; 328 (5986): 1679-1681 DOI: 10.1126/science.1190524

Study Questions

1. Write the chemical formula for the trifluoromethyl group and for hydrogen fluoride.
2. Write a chemical equation to show the possible reaction between hydrogen fluoride and cyclohexane.
3. Write a chemical reaction to show the possible reaction between hydrogen fluoride and cyclohexene.
4. For each reaction above, assuming you start with 100g of each reactant, what mass of fluorinated product would be produced if the yield was 70%?
5. For each reaction above, assuming you begin with 25 moles of each reactant, what mass of fluorinated product would be produced if the yield were 94%?
6. For the catalytic reaction discussed in the above article, why do you think the reaction does not produce a 100% yield?
   

Life on Mars?

Was there life on Mars?
Scientists continue to look for organic compounds such as proteins in Martian soil, but to date none have been found, even though organic molecules are found in many other places in the Solar System.

Astrobiologists are beginning to wonder if the iron oxides that make up the soil on Mars, giving the planet its distinctive red colour, are photocatalysts which use energy from ultraviolet light to oxidize carbon-containing molecules trapped in soil particles converting them to carbon dioxide and gases such as methane. This suggests that the absence of proteins or other organic molecules on Mars does not necessarily mean it has never supported life forms.

Reference:
Ilya A. Shkrob, Sergey D. Chemerisov, Timothy W. Marin. Photocatalytic Decomposition of Carboxylated Molecules on Light-Exposed Martian Regolith and Its Relation to Methane Production on Mars. Astrobiology, 2010; 10 (4): 425 DOI:
10.1089/ast.2009.0433

Study Questions:

1. Define an organic compound.
2. What elements are proteins made up of?
3. Proteins are produced when what smaller compounds react?
4. What is the name given to the bond between these smaller compounds making up a protein?
5. Why do you think Astrobiologists look for proteins in order to determine if life existed on Mars in the past?

Further Reading:

1. http://www.ausetute.com.au/proteins.html
2. http://www.ausetute.com.au/aminoacid.html