Calcite

The teeth and bones of mammals, the shells of marine organisms, even the sharp spines of sea urchins, are all made of the same material, calcite. Calcite is a carbonate mineral and is the most stable form of calcium carbonate.

Marine organisms use the most readily available elements in the sea water, that is calcium, oxygen and carbon, to produce their teeth, bones or shells. In seawater solutions, organisms can use the available calcium and carbonate ions to precipitate calcium carbonate.

Calcite is also commonly found in sedimentary rocks, and especially in limestone which is formed from the shells of dead marine organisms. Calcite is the mineral found in cave formations such as stalactites and stalagmites. Overlying limestones and marbles are dissolved away by slightly acidic groundwater which then percolates into caverns below. As the water evaporates, calcite is precipitated.


Calcite has some unusual properties.
It becomes less soluble in water as the temperature increases, a property known as retrograde solubility.
Single crystals of calcite display an optical property known as birefringence which causes objects viewed through a piece of calcite to appear to be doubled.

The sea urchin tooth is a biomineral composed of calcite crystals in both plate and fiber forms, arranged crosswise and cemented together with super-hard calcite nanocement. Between the crystals are layers of organic materials which are weaker than the calcite crystals. These weaker organic materials allow pieces of the tooth to break off in predefined places which means that the sea urchin tooth is self-sharpening!

Reference
Christopher E. Killian, Rebecca A. Metzler, Yutao Gong, Tyler H. Churchill, Ian C. Olson, Vasily Trubetskoy, Matthew B. Christensen, John H. Fournelle, Francesco De Carlo, Sidney Cohen, Julia Mahamid, Andreas Scholl, Anthony Young, Andrew Doran, Fred H. Wilt, Susan N. Coppersmith and Pupa U. P. A. Gilbert. Self-Sharpening Mechanism of the Sea Urchin Tooth. Advanced Functional Materials, 2010; DOI: 10.1002/adfm.2010015

Further Reading
Naming Ionic Compounds
Writing Ionic Formulae
Molecular Mass
Percentage Composition
Shapes of Molecules
Lewis Structures
Solubility Product

Study Questions

1. Give the chemical formula for calcium carbonate.
2. List the names and formulae of other compounds that can be made out of carbon, oxygen and calcium.
3. Calculate the percentage composition of calcium carbonate as well as the compounds you listed in question 2.
   
4. Write a balanced chemical equation to show the precipitation of calcium carbonate from ions in sea-water.
5. What shape do you expect the carbonate ion to take? Explain your answer.
6. Draw a Lewis Structure, electron dot diagram, for a "molecule" of calcium carbonate.
7. Why is it inaccurate to describe calcium carbonate as a molecule?
   
8. Describe the process by which calcium carbonate can dissolve in water.
9. Would calcium carbonate more readily precipitate from fresh water or sea-water at the same temperature? Explain your answer.
   

Palmitoleic Acid

Scientists have discovered that trans-palmitoleic acid or trans-9-hexadecenoic acid, a fatty acid found in milk, cheese, yoghurt and butter, can reduce the risk of type 2 diabetes. Trans-palmitoleic acid is not produced in the body whereas cis-palmitoleic acid is produced in the body and is already known from animal experiments to protect against diabetes.

Cis-palmitoleic acid is made in the body using palmitic acid and the enzyme delta-9 desaturase.

In 2001, scientists suggested that fatty acids, such as palmitoleic acid found on the surface of skin, decompose to form 2-nonenal which has an unpleasant smell, a bit like old books, and could be the cause of what is commonly referred to as "old person smell".

Palmitoleic acid is used by the key enzymes in the body that control fat oxidation at very high rates. It has been suggested that palmitoleic acid could therefore be used to combat obesity.

Reference
Dariush Mozaffarian, Haiming Cao, Irena B. King, Rozenn N. Lemaitre, Xiaoling Song, David S. Siscovick, and Gökhan S. Hotamisligil. Trans-Palmitoleic Acid, Metabolic Risk Factors, and New-Onset Diabetes in U.S. Adults. Annals of Internal Medicine, December 21, 2010

Further Reading
Lipids
Carboxylic Acids
Functional Groups
Enzymes

Study Questions

1. Write the molecular formula for palmitoleic acid
2. On the structural formula for palmitoleic acid shown above, locate and name two different functional groups.
3. Draw a structural formula for palmitic acid, CH₃(CH₂)₁₄COOH.
4. Locate and name the functional group present in palmitic acid.
5. Draw a structural formula for oleic acid, CH₃(CH₂)₇CH=CH(CH₂)₇COOH.
6. Locate and name the functional groups present in oleic acid.
7. In what ways is palmitoleic acid similar to palmitic acid and oleic acid?
8. In what ways is palmitoleic acid different to palmitic acid and oleic acid?
9. Draw a structural formula for 2-nonenal.
10. Write the molecular formula for 2-nonenal.
11. Locate and name the functional groups present in 2-nonenal.
12. How would cis-palmitoleic acid differ structurally from trans-palmitoleic acid?
    

New Nitrogen Oxide Compound

Chemists already know about a number of compounds composed of nitrogen and oxygen:

• Nitric oxide is a colourless gas which is produced during the combustion of fossil fuels. It has a melting point of -163.6^oC, a boiling point of -150.8^oC, and rapidly oxidizes in air to form nitrogen dioxide. Its solubility in water is 7.4ml/100ml.
  
• Nitrogen dioxide is a reddish-brown toxic gas. Its melting point is -11.2^oC and its boiling point is 21.1^oC. It reacts with water to produce nitric acid.
• Nitrous oxide is a colourless gas commonly referred to as laughing gas. It is a greenhouse gas and also causes ozone depletion. Its melting point is -90.86^oC and its boiling point is -88.48^oC. Its solubility in water is 0.15g/100ml.
• Dinitrogen trioxide is a deep blue liquid at low temperatures. It has a melting point of -100.1^oC, a boiling point of 3^oC , and is very soluble in water.
• Dinitrogen tetroxide is a colourless liquid which is a powerful oxidizing agent and highly toxic. Its melting point is -11.2^oC, its boiling point is 21.1^oC, and it reacts with water to produce both nitrous aid and nitric acid.
• Dinitrogen pentoxide exists as colourless crystals. It is unstable and potentially dangerous oxidizer. It has a melting point of 30^oC and it sublimes at 47^oC. Dinitrogen pentoxide reacts with water to produce nitric acid.
  

Chemists at the Royal Institute of Technology in Sweden have discovered a new molecule in this nitrogen oxide group. The new molecule, composed only of nitrogen and oxygen, is called trinitramid. Trinitramid has the chemical formula N(NO₂)₃ and is shaped like a propeller.

Reference
Martin Rahm, Sergey V. Dvinskikh, István Furó, Tore Brinck. Experimental Detection of Trinitramide, N(NO₂)₃. Angewandte Chemie International Edition, 2011; (forthcoming)

Further Reading
Molecular Mass
Percentage Composition
Definitions of a Mole
Mass-Mole Calculations
Lewis Structures
Intermolecular Forces

Study Questions

1. Give the chemical formula for each of the following molecules:
   • nitric oxide
   • nitrogen dioxide
   • nitrous oxide
   • dinitrogen trioxide
   • dinitrogen pentoxide
2. Calculate the molecular mass (formula weight) of each of the molecules above.
3. Calculate the percentage composition of each of the molecules above.
4. Draw a Lewis Structure (electron dot diagram) for each of the molecules above.
5. Use the information in the article above, as well as your calculations, tabulate the melting points, boiling points and solubility of each molecule.
6. Graph melting points and boiling points against molecular mass.
   
7. Can you identify any trends in the melting points, boiling points, or solubilities of these molecules? Explain any trends you identify.
8. So far, scientists have only produced enough trinitramid to detect it. What do you predict its melting point, boiling point and solubility in water to be? Explain your answer.
   

Atomic Weights to Change

The atomic weights of 10 elements are to be changed in order to more accurately reflect how these elements are found in nature. These 10 elements are:

• hydrogen
• lithium
• boron
• carbon
• nitrogen
• oxygen
• silicon
• sulfur
• chlorine
• thallium

The atomic weights of these 10 elements will now be expressed as intervals, having upper and lower bounds.
For example, sulfur is commonly known to have a standard atomic weight of 32.065. However, its actual atomic weight can be anywhere between 32.059 and 32.076, depending on where the element is found. In sports doping investigations, performance-enhancing testosterone can be identified in the human body because the atomic weight of carbon in natural human testosterone is higher than that in pharmaceutical testosterone.

Elements with only one stable isotope do not exhibit variations in their atomic weights. For example, the standard atomic weights for fluorine, aluminum, sodium and gold are constant, and their values are known to better than six decimal places.

IUPAC will feature the change in the standard atomic weights table as part of associated International Year of Chemistry activities in 2011.

Reference
Michael E. Wieser, Tyler B. Coplen. Atomic weights of the elements 2009 (IUPAC Technical Report). Pure and Applied Chemistry, 2010; 1 DOI: 10.1351/PAC-REP-10-09-14

Further Reading
http://www.ausetute.com.au/isotopes.html
http://www.ausetute.com.au/atomicmass.html

Study Questions

1. What is meant by the term isotope?
2. How is atomic weight calculated?
3. If naturally occurring hydrogen contains 99.99% hydrogen-1 and 0.01% deuterium, what is the atomic weight of naturally occurring hydrogen?
4. If you took an air sample from a planet on which there was 100 times more deuterium than on earth, what would you expect the atomic weight of hydrogen to be then?
5. Why is tritium not included in the calculation of the atomic weight of hydrogen?
   
6. Why would the atomic weight of an element with only one stable isotope be more consistent than the atomic weight of an element with two or more stable isotopes?
7. Why are unstable isotope abundances not used when calculating the atomic mass of a naturally occurring element?
8. Why would the atomic weight of carbon in natural human testosterone be higher than that in pharmaceutical testosterone?

Calcium Carbide

Pure calcium carbide, CaC₂, is a colourless compound. It is a very important compound because it is used to produce ethyne (acetylene) which is itself an extremely important industrial compound. The combustion of ethyne (acetylene) in oxyacetylene welding and cutting produces a flame of over 3300^oC, making it the third hottest natural chemical flame, it and releases 11.8kJ/g of energy.

Calcium carbide is produced in an electric arc furnace in which a mixture of lime, CaO, and coke, C, is heated to about 2000^oC. The products of the reaction are calcium carbide and carbon monoxide gas. This reaction produces a calcium carbide yield of approximately 80%.

Calcium carbide reacts with water to produce ethyne (acetylene) and calcium hydroxide. The ethyne produced in this reaction can be used directly in combustion reactions such as in oxyacteylene welding and cutting, as well as in carbide lamps which are still in use in mines in some less wealthy countries.

Further Reading
http://www.ausetute.com.au/namsynes.html
http://www.ausetute.com.au/intrafor.html
http://www.ausetute.com.au/balcheme.html
http://www.ausetute.com.au/combusta.html
http://www.ausetute.com.au/tempconv.html
http://www.ausetute.com.au/enthchan.html
http://www.ausetute.com.au/manienth.html
http://www.ausetute.com.au/percentc.html
http://www.ausetute.com.au/yield.html

Study Questions

1. Write the molecular and structural formula for ethyne (acetylene).
2. What type of bonding is present in the calcium carbide compound? Explain your answer.
3. Write a balanced chemical equation for the reaction between lime and coke.
   
4. Write a balanced chemical equation for the production of ethyne (acetylene) from calcium carbide.
5. Convert these temperatures in ^oC to Kelvin:
   • 3300^oC
   • 2000^oC


6. Is the combustion of ethyne (acetylene) an endothermic or an exothermic reaction? Explain your answer.
7. Calculate the energy released during the combustion of :
   • 5kg of ethyne (acetylene)
   • 500g of ethyne (acetylene)
8. Calculate the energy released from the combustion of
   • 5 moles of ethyne (acetylene)
   • 0.1moles ethyne (acetylene)
9. Calculate the percentage composition of
   • calcium carbide
   • ethyne (acetylene)
10. Explain what is meant by the statement below:
    "This reaction produces a calcium carbide yield of approximately 80%".

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.
   

Graphene: AUS-e-NEWS December 2010

Excitement is growing in the scientific community about the possible uses for graphene.
This simple, naturally occurring allotrope of carbon could revolutionize our world.
The December 2010 issue of AUS-e-NEWS, AUS-e-TUTE's quarterly newsletter, takes a look at the chemistry of graphene, and at its possible future uses.

To subscribe to AUS-e-TUTE's free newsletter email:


and type subscribe as the subject.

Producing Organic Compounds from Bip-oils

Many chemical feedstocks such as ethene and propene, the building blocks of many plastics, as well as aromatic compounds such as benzene and toluene used in dyes and plastics, are currently produced from petroleum.
University of Massachusetts Amherst scientists have reported that they have developed a way to produce these feedstocks from pyrolytic bio-oils, the cheapest liquid fuels available today derived from biomass. These pyrolytic bio-oils can be made from non-food agricultural crops and woody biomass.
The two-step, integrated catalytic approach starts with a "tunable", variable-reaction hydrogenation stage followed by a second, zeolite catalytic step. The zeolite catalyst has the proper pore structure and active sites to convert biomass-based molecules into aromatic hydrocarbons and alkenes.

Journal Reference
Tushar P. Vispute, Huiyan Zhang, Aimaro Sanna, Rui Xiao, and George W. Huber. Renewable Chemical Commodity Feedstocks from Integrated Catalytic Processing of Pyrolysis Oils. Science, 26 November 2010: 1222-1227 DOI: 10.1126/science.1194218

Further Reading
Nomenclature of Carbon Compounds
Naming Simple Alkenes
Ethene: properties, production and uses
Polythene: properties, production and uses
Polymers and Polymerization

Study Questions

1. Give the molecular formula and structural formula for ethene.
2. Give the molecular formula and structural formula for propene.
3. Give the molecular formula and structural formula for benzene.
4. Give the molecular formula and structural formula for toluene.
5. What is meant when an organic chemist refers to hydrogenation?
6. What is meant by the term pyrolytic?
   
7. Write an equation for the hydrogenation of ethene.
8. Write an equation for the hydrogenation of propene.
9. Why is benzene classed as an aromatic compound and not as an alkene?
   

Tasty Chemistry

Taste refers to the ability to detect the flavour of substances. We receive tastes through sensory organs called taste buds which are concentrated on the upper surface of the tongue.
Among the 50 or so cells in each taste bud there are cells responding to each of the five tastes:

• sweetness
• bitterness
• sourness
• saltiness
• umami-ness or savoriness
  

Sweetness is often associated with foods rich in simple carbohydrates such as glucose and sucrose, but many compounds taste sweet. Examples include the amino acids alanine, glycine and serine as well as the glycosides glycyrrhizin (found in licorice root) and stevioside (from the Stevia rebaudiana shrub). Even some inorganic compounds, such as beryllium chloride and lead acetate, taste sweet.

Bitterness is perceived by many people to be unpleasant. It helps prevent us ingesting toxic substances. A bitterant is the chemical that makes a substance taste bitter. Examples of bitterants are sucrose octaacetate which is used as an inert ingredient in pesticides and herbicides, and, brucine which is a bitter alkaloid closely related to strychnine that is found naturally in a number of plant species.

Sourness is the sensation evoked by substances that are acidic such as lemons and pickles. The acids we ingest release protons which enter the cell and cause a direct, detectable, electronic response.

Saltiness is the taste produced by the presence of alkali metal cations such as Na⁺ and K⁺. The less sodium-like the ion is, the less salty the sensation will be, eg, Rb⁺ and Cs⁺ ions are larger than Na⁺ ions so they do not taste as salty.

The umami taste is due to the detection of the carboxylate anion of glutamic acid, a naturally occurring amino acid found in meat, cheese, and other protein-rich foods. Glutamates, the salts of glutamic acid, easily ionize resulting in the same carboxylate anions and therefore producing the same umami taste. As a consequence, glutamates are often used as flavour enhancers, the most common of which is monosodium glutamate (MSG).

Further Reading
Carbohydrates (sugars)
Amino Acids
Properties of Acids and Bases

Study Questions

1. Name the 3 elements common to all carbohydrates.
2. What is the structural difference between molecules classified as monosaccharides and those that are classed as disaccharides or polysaccharides?
   
3. Is glucose an example of a monosaccharide, a disaccharide or a polysaccharide?
4. Is sucrose an example of a monosaccharide, a disaccharide or a polysaccharide?
5. What elements are common to all amino acids?
6. What functional group or groups must a molecule contain in order for it be classified as an amino acid?
7. Draw the structures for glycine, alanine and serine. Identify the functional groups present in each molecule.
8. A number of amino acids are said to taste sweet, but acids generally are said to taste sour. Can you explain these apparently contradictory statements?
   

Cardanol

Chemists at The City College of New York have designed a molecule which has both water-adhering and water-repelling ends, from cardanol (the structure on the right), a naturally available material found in cashew nutshell liquid.

When mixed with water, the designer molecules formed a self-assembled structure called a micelle with a water-adhering exterior and water-repelling interior.

At 50^oC the micelles take on a 3-dimensional structure known as a vesicle that is about 200 times larger and more viscous. The molecules stick together enough to be draw out into a thin strand, just like glue.

Cooling the material allows the molecules to revert to their original micellar structure.

Heating causes the micelles to re-arrange themselves into an interlocking bi-layer which undergoes curvature. The structure is stabilized in part by the hydrogen bonding.

Reference
Vijai S. Balachandran, Swapnil R. Jadhav, Padmanava Pradhan, Sacha De Carlo, George John. Adhesive Vesicles through Adaptive Response of a Biobased Surfactant. Angewandte Chemie International Edition, 2010; DOI: 10.1002/anie.201005439

Further Reading
Detergents
Soaps and Saponification
Functional Groups
Percentage Composition
Intermolecular Forces
Intramolecular Forces

Study Questions

1. Identify the functional groups present in a molecule of cardanol.
2. Give the molecular formula for cardanol.
3. Calculate the percentage of carbon, hydrogen and oxygen present in a mole of cardanol.
4. On the molecular structure of cardanol, identify the water-adhering area and the water-repelling area.
5. What is the name given to a molecule that adheres to water?
6. What name is given to a molecule the repels water?
7. Draw a diagram to show how cardanol molecules could form a micelle.
8. Given the description of the behaviour of the designer molecule in the article above, in what ways do you think it differs from the structure of cardanol?
   

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.
   

Luminol - Detecting Blood

Luminol is a common reagent used to detect blood stains and other body fluids at crime scenes because it reacts with iron in blood to produce a blue glow.
Its IUPAC name is 5-amino-2,3-dihydro-1,4-phthalazinedione.

The luminol solution used by crime scene investigators is a solution of luminol and an activator, an oxidant such as hydrogen peroxide and a hydroxide salt in water. In the presence of a catalyst, such as the iron in haemoglobin, the hydrogen peroxide decomposes to form oxygen and water and the luminol reacts with the hydroxide salt to form a dianion. The oxygen produced during the decomposition reaction reacts with luminol dianion producing an organic peroxide which is very unstable and immediately decomposes to produce 3-aminophthalic acid with electrons in the excited state. As the excited state electrons relax to the ground state, energy is released as visible blue light.

Unfortunately, luminol reacts with other substances besides the iron in haemoglobin such as copper, bleaches and horseradish.

University of South Carolina Chemists are using a new thermal infrared technology to illuminate blood stained objects with pulses of invisible infrared waves, using filters to block out particular wavelengths, allowing certain chemicals to stand out from their surroundings. The technique can detect blood diluted to as little as one part blood in 100 parts water. It can also distinguish between blood, bleach, rust and coffee.

Journal References:

1. Heather Brooke, Megan R. Baranowski, Jessica N. McCutcheon, Stephen L. Morgan, Michael L. Myrick. Multimode Imaging in the Thermal Infrared for Chemical Contrast Enhancement. Part 3: Visualizing Blood on Fabrics. Analytical Chemistry, 2010; 82 (20): 8427 DOI: 10.1021/ac101107v
2. Heather Brooke, Megan R. Baranowski, Jessica N. McCutcheon, Stephen L. Morgan, Michael L. Myrick. Multimode Imaging in the Thermal Infrared for Chemical Contrast Enhancement. Part 2: Simulation Driven Design. Analytical Chemistry, 2010; 82 (20): 8421 DOI: 10.1021/ac101108z
3. Heather Brooke, Megan R. Baranowski, Jessica N. McCutcheon, Stephen L. Morgan, Michael L. Myrick. Multimode Imaging in the Thermal Infrared for Chemical Contrast Enhancement. Part 1: Methodology. Analytical Chemistry, 2010; 82 (20): 8412 DOI: 10.1021/ac101109w

Further Reading
Functional Groups
Molecular Mass (Formula Weight)
Percent Composition (percentage composition)
Oxidation and Reduction
Energy Profiles and Catalysts
Parts per million concentration

Study Questions

1. Write the molecular formula for luminol given the structural formula shown in the article above.
2. Calculate the molecular mass (formula weight) of luminol.
3. Calculate the percentage of each element present in luminol.
4. Write a balanced chemical equation for the decomposition of hydrogen peroxide as described in the article.
5. The new thermal infrared technique can detect 1 part blood in 100 parts of water. Express this as a concentration in parts per million.
6. On the structure of luminol locate the following functional groups:
   • amine groups
   • double bond
   • carbonyl group
7. Luminol reacts with the hydroxide salt to form a dianion. Explain what is meant by the term dianion.
   
8. Explain how luminol could produce a dianion.
9. Do you think that crime scene investigators should use luminol to detect blood in commercial laundry? Explain your answer.
   
   

Carbon Dioxide and Climate Change

Scientists at Utrecht University, working with colleagues at the NIOZ Royal Netherlands Institute for Sea Research and the University of Southampton have been studying one of the hottest episodes of Earth's climate history, the Middle Eocene Climatic Optimum (MECO), which occurred around 40 million years ago in order to understand the relationship between Earth's climate and atmospheric carbon dioxide.

Algae use photosynthesis to harvest the energy of the sun, converting carbon dioxide and water into the organic molecules required for growth. Different isotopes of carbon are incorporated into these molecules depending on the environmental conditions under which algae grow. Ancient climate can therefore be reconstructed by analysing the carbon isotope ratios of molecules preserved in fossilised algae.

Using fossilised algae preserved in sediment cores extracted from the seafloor near Tasmania, Australia, by the Ocean Drilling Program, the scientists refined their estimates of carbon dioxide levels using information on the past marine ecosystem derived from studying changes in the abundance of different groups of fossil plankton.

Their analyses indicate that MECO carbon dioxide levels must have at least doubled over a period of around 400,000 years. In conjunction with these findings, analyses using two independent molecular proxies for sea surface temperature show that the climate warmed by between 4 and 6^oC over the same period, suggesting that increased amounts of carbon dioxide in the atmosphere played a major role in global warming during the MECO.

The rapid increase in atmospheric carbon dioxide levels around 40 million years ago approximately coincides with the rise of the Himalayas and may be related to the disappearance of an ocean between India and Asia as a result of plate tectonics, the large scale movements of the Earth's rocky shell (lithosphere).

References:

1. P. K. Bijl, A. J. P. Houben, S. Schouten, S. M. Bohaty, A. Sluijs, G.-J. Reichart, J. S. Sinninghe Damste, H. Brinkhuis. Transient Middle Eocene Atmospheric CO2 and Temperature Variations. Science, 2010; 330 (6005): 819 DOI: 10.1126/science.1193654
2. P. N. Pearson. Increased Atmospheric CO2 During the Middle Eocene. Science, 2010; 330 (6005): 763 DOI: 10.1126/science.1197894

Further Reading
http://www.ausetute.com.au/greenhouse.html
http://www.ausetute.com.au/ccycle.html
http://www.ausetute.com.au/carbon14.html
http://www.ausetute.com.au/isotopes.html

Study Questions

1. Write a chemical equation showing the conversion of atmospheric carbon dioxide into glucose by photosynthesis.
2. Explain what is meant by the term isotope.
3. Give the names and symbols of the three naturally occurring isotopes of carbon.
4. Which isotope of carbon is the most abundant?
5. Which isotopes of carbon are stable?
6. Which isotopes of carbon are unstable (radioactive)?
7. Write a nuclear decay equation for the unstable carbon isotope(s).
8. Explain how ancient climate can be reconstructed by analysing the carbon isotope ratios of molecules preserved in fossilised algae.

Carbon Capture and Storage (CCS)

Combustion of fossil fuels, such as coal, fuel oil, or natural gas, liberates large quantities of carbon dioxide, a gas that significantly affects global climate. A key technology that would reduce emissions and lead to more environmentally friendly power plants is the capture and storage of carbon dioxide from flue gases of power plants (carbon capture and storage (CCS)). CCS might be able to reduce CO₂ emissions resulting from the employment of fossil fuels for power generation and other uses in industry to near zero and thereby contribute to reducing greenhouse-gas emissions.
The Technische Universität Darmstadt has dedicated a pilot plant for capturing carbon dioxide contained in flue gases of power plants using two new methods:

• carbonate looping
• chemical looping

Carbonate looping involves utilizing naturally occurring limestone to initially bind CO₂ from the stream of flue gases transiting power plants' stacks in a first-stage reactor. The resultant pure CO₂ is re-liberated in a second reactor and can then be stored. The advantage of the carbonate-looping method is that even existing power plants can be retrofitted with this new method.

Chemical looping allows CO₂ to be captured with hardly any loss of energy efficiency. Under this method, a dual-stage, flameless, combustion yields a stream of exhaust gases containing only CO₂ and water vapor. The CO₂ can then be captured and stored.

Reference
Technische Universität Darmstadt (2010, November 7). On the way to CO₂-free power plants. ScienceDaily. Retrieved November 8, 2010, from http://www.sciencedaily.com­ /releases/2010/11/101103082306.htm

Further Reading
http://www.ausetute.com.au/combusta.html
http://www.ausetute.com.au/idealgas.html
http://www.ausetute.com.au/heatcomb.html
http://www.ausetute.com.au/greenhouse.html
http://www.ausetute.com.au/ccycle.html

Study Questions

1. Explain what is meant by the term fossil fuel.
2. Write a balanced chemical equation to represent the complete combustion of coal.
3. Write a balanced chemical equation to represent the complete combustion of natural gas.
4. If you burnt 1kg of coal and 1kg of natural gas, which reaction would produce the greatest amount of carbon dioxide?
5. If you burnt 1000cm³ of solid coal, and 1000cm³ of gaseous methane, which reaction would produce the greatest amount of gaseous carbon dioxide?
6. The heat of combustion of methane is 890 kJ/mol. Is energy released or absorbed during this reaction?
7. When coal burns it releases energy, about 250 kJ/mol. At 25^oC and 1 atmosphere pressure, is methane or coal the better fuel?
8. What benefits are there in storing the carbon dioxide emitted during power generation?
9. What disadvantages are there in storing carbon dioxide emitted during power generation?
10. What impact could the storage of this carbon dioxide have on the natural carbon cycle?
    

Organic Aqua Regia

While noble metals such as platinum and palladium are becoming increasingly important, the world has limited supplies of these metals so that it is vitally important that industry can recycle these metals efficiently.

Many of the transition metals have negative standard reduction potentials, indicating that these metals will dissolve in dilute acid, eg, clean chromium will dissolve in dilute hydrochloric acid

2 x [Cr(s) ----> Cr³⁺ + 3e] E^o = 0.74V
3 x [2e + 2H⁺ ----> H₂(g)] E^o = 0.00
_____________________________________________
2Cr(s) + 6H⁺ -----> 2Cr³⁺ + 3H₂(g) E^o = 0.74V

Some transition metals have positive reduction potentials, so they are poorer reducing agents than hydrogen, and are difficult to dissolve in acid. These metals are referred to as the noble metals and include silver, gold and platinum as well as ruthenium, rhodium, palladium, osmium, and iridium. Dissolving the noble metals requires the use of an oxidizing agent and sometimes a complexing agent. The most common reagent used to dissolve noble metals is aqua regia.

Aqua regia is a highly corrosive, fuming yellow or red solution formed when 1 part of concentrated nitric acid is added to 3 parts of concentrated hydrochloric acid. The nitric acid part is a powerful oxidizer, it oxidizers the noble metal atoms to cations. The hydrochloric acid provides a supply of chloride anions which react with the noble metal cations. For example, gold can be dissolved in aqua regia:

• gold reacts with nitric acid to form gold (III) ions:

Au(s) + 3NO₃^-(aq) + 6H⁺(aq) -----> Au³⁺(aq) + 3NO₂(g) + 3H₂O(l)

• gold (III) ions react with chloride ions to form chloroaurate anions:

Au³⁺(aq) + 4Cl^-(aq) -----> AuCl₄^-(aq)

However, aqua regia will dissolve all the metals together which introduces impurities into the recycling process. Georgia Institute of Technology scientists have developed a new organic solvent process that may solve this problem since the concentration of each component of the solvent can be adjusted to preferentially dissolve gold or palladium, but will not dissolve platinum. This solvent has been dubbed organic aqua regia.

Reference
Wei Lin, Rong-Wei Zhang, Seung-Soon Jang, Ching-Ping Wong, Jung-Il Hong. 'Organic Aqua Regia'-Powerful Liquids for Dissolving Noble Metals. Angewandte Chemie, 2010; 122 (43): 8101 DOI: 10.1002/ange.201001244

Further Reading
http://www.ausetute.com.au/acidbase.html
http://www.ausetute.com.au/trmetals.html
http://www.ausetute.com.au/ligands.html
http://www.ausetute.com.au/redox.html
http://www.ausetute.com.au/calcelemf.html

Study Questions

1. What is meant by the term transition metal?
2. What are the typical properties of a transition metal?
3. Refer to the equation above for the reaction between chromium and hydrochloric acid. Is this an example of a redox reaction? Explain your answer.
4. Refer to the equation above for the reaction between gold and nitric acid. Has the gold been oxidised or reduced? Explain your answer.
5. Refer to the equation above for the reaction between gold and nitric acid. Has nitrogen been oxidised or reduced? Explain your answer.
6. Could the reaction between gold and nitric acid be described as a redox reaction? Explain your answer.
7. Refer to the equation for the reaction between gold (III) ions and chloride ions. Is this a redox reaction? Explain your answer.
8. Write suitable equations for dissolving the following metals in aqua regia:

• iron
• tin
• copper
  
• silver
• platinum
• palladium
  

Dioxins in Sydney Harbour

Data collected by the NSW Department of Environment, Climate Change and Water (Australia) in 2008 shows that large tracts of sediments in Sydney Harbour are more contaminated with dioxins than Tokyo Bay or New York Harbour, and are among the most contaminated in the world.
In the remediation area in Homebush Bay, the location of the 2000 Sydney Olympic Games, the dioxin levels were 610 picograms per gram of sediment compared with 2.3 for a "clean" environment. These high levels of dioxins in areas where fish feed means the warning not to eat fish caught west of the Sydney Harbour Bridge, and to eat only 150 grams a month of fish caught east of the bridge, will most likely have to remain in place for decades.

The source of the contamination is the former Union Carbide site where dioxins were used in the manufacture of the now-banned pesticide 2,4,5-T (2,4,5-trichlorophenoxyacetic acid) and the defoliant Agent Orange which was used during the Vietnam War.

Dibenzo-p-dioxin is made up of two benzene rings joined by two oxygen bridges, so it is an aromatic diether.
The name dioxin actually refers to the central dioxygenated ring. So, if other elements are substituted for the hydrogen atoms in the molecule, they too would be referred to as dioxins. This means there are many different compounds that can be referred to as dioxins!

In common use, the term dioxins usually refers to polychlorinated dibenzodioxins (PCCDs) which are a group of chlorinated dibenzo-p-dioxin molecules. In PCCDs the chlorine atoms can attach on 8 different places on the dibenzo-p-dioxin molecule (shown as 1,2,3,4 and 6,7,8,9 on the structure above). The toxicity of PCDDs depends on the number and positions of the chlorine atoms. The most toxic dioxin is 2,3,7,8-tetrachlorodibenzo-p-dioxin, and is well known as the contaminant of Agent Orange.


Dioxins are known to build up in the human body over time, mostly in fatty tissues.
Exposure to high levels of dioxins causes a severe form of persistent acne known as chloracne and leads to an increased risk of tumours.
Exposure to low levels of dioxins results in an elevated risk of sarcoma, a type of skin cancer.

Reference:
http://www.smh.com.au/environment/water-issues/the-poison-that-got-away-20101029-177i0.html?autostart=1

Further reading
http://www.ausetute.com.au/massconv.html
http://www.ausetute.com.au/partspm.html
http://www.ausetute.com.au/namctut1.html
http://www.ausetute.com.au/namhaloa.html
http://www.ausetute.com.au/mmcalcul.html
http://www.ausetute.com.au/percentc.html
http://www.ausetute.com.au/namisane.html

Study Questions

1. Convert 610 picograms per gram to
• micrograms per gram
• nanograms per gram
• micrograms per milligram
• milligrams per kilogram
• parts per million
• parts per billion
2. Write the molecular formula for each of the following:
   • dibenzo-p-dioxin
   • 2,3,7,8-tetrachlorodibenzo-p-dioxin
3. Calculate the percentage composition of dibenzo-p-dioxin.
4. Calculate the mass of chlorine present in 610 picograms of 2,3,7,8-tetrachlorodibenzo-p-dioxin.
5. Indicate the location of ether functional groups on a molecule of dibenzo-p-dioxin.
6. Give the structural formula of as many different structural isomers of 2,3,7,8-tetrachlorodibenzo-p-dioxin as possible.
7. Name each of the molecules you have drawn in question 6.
   

Fracking

Marcellus shale is a massive rock formation that is possibly the largest source of natural gas in the USA. It extends from New York through Pennsylvania, Ohio and West Virginia. Marcellus shale naturally traps metals such as uranium at levels higher than usually found naturally but lower than man-made contamination levels.
Hydraulic fracturing, or fracking, is a process that results in the creation of fractures in rocks in order to tap into oil and natural gas deposits such as those present in Marcellus shale. Millions of gallons of water and chemicals are pumped deep underground to blast through the rocks in order to release the natural gas. University of Buffalo scientists have shown that the metals and the hydrocarbons are chemically bonded, so, the process of drilling to extract the hydrocarbons could force the metals into the soluble phase, enabling them to move around. When the millions of gallons of water used in hydraulic fracturing, or fracking, come back to the surface, it is likely to contain toxic uranium contaminants, potentially polluting streams and other ecosystems and generating hazardous waste.

Reference:
University at Buffalo (2010, October 27). Uranium in groundwater? 'Fracking' mobilizes uranium in marcellus shale. ScienceDaily. Retrieved October 29, 2010, from http://www.sciencedaily.com­ /releases/2010/10/101025172926.htm

Further Reading:
http://www.ausetute.com.au/usehydrc.html
http://www.ausetute.com.au/combusta.html
http://www.ausetute.com.au/chemphys.html
http://www.ausetute.com.au/fuelsdef.html

Study Questions:

1. What is the name and chemical formula of the major constituent of natural gas?
2. What is meant by the term hydrocarbon?
3. Give the names, chemical formulae, and uses for 3 other hydrocarbons.
4. Explain what is meant by the phrase "force the metals into the soluble phase".
5. Is forcing the metals into the soluble phase an example of a chemical or a physical change? Explain your answer.
6. Explain what is meant by a Chemist when he/she refers to a substance as a fuel.
7. Is natural gas defined as a renewable or non-renewable fuel? Explain your answer.
   
8. Natural gas is combusted for use as a fuel. Is this an example of chemical or a physical change? Explain your answer.
9. Write a balanced chemical equation for the complete combustion of the main constituent of natural gas.
10. Of the 3 hydrocarbons you named in question 3, which one would be considered the "best" fuel? Explain your answer.
    

A New Look at Evaporation

As much as 71% of Earth is covered by oceans and seas which evaporate continuously. Since the heat of evaporation of water is very high, the evaporation determines Earth's climate. What is more, the content of water vapour, the main greenhouse gas, in the atmosphere changes as a result of evaporation. Its concentration in air may reach as much as 4%, more than hundred times higher than that of the infamous carbon dioxide. According to various estimates, if there was no water vapour in air, the temperature on Earth would fall by 20-30 degrees.
The first scientific publication concerning the mechanism of evaporation was written by the famous physicist James Clerk Maxwell, but Polish scientists investigating evaporation are questioning how well we understand the phenomenon.
The investigation studied a drop of liquid in a closed vessel in equilibrium with its vapour. During evaporation the most interesting events take place on the border of a liquid and a vapour. The thickness of this interface is more or less equal to the diameter of an atom.
"Maxwell assumed that evaporation took place at constant temperature. It is so, if we look at the initial state, that is a liquid, and the final state, that is a vapour. It is true that their temperatures are equal. But during the evaporation process itself, the nature acts in a completely different way," explains Ph.D. Marek Litniewski from IPC PAS.
The existing description assumed that the heat transfer in the system was stable and the rate of evaporation was limited by the efficiency of the process during which the particles break away from the surface of drops, i.e. diffusion. However, the simulation carried out in the IPC PAS showed that during the evaporation into vacuum or the liquid's own vapour the system gained mechanical equilibrium very quickly. Particles break away from the surface of a liquid and their mechanical recoil allows the equalisation of the pressure inside the drop. If the rate of evaporation on the surface achieved the maximum value and the system was still unable to equalise the pressures, spaces with new surfaces would open inside the drop and it would start to boil. However, it was observed that the mechanical equilibration of pressure can be insufficient and the temperature on the surface of the liquid decreases: the drop aims at maintaining the pressure equilibrium at the cost of its internal energy. This observation suggests that the factor that is crucial during evaporation is not the diffusion of particles into the environment but the heat transfer and the equality of pressures.

Reference:
Institute of Physical Chemistry of the Polish Academy of Sciences (2010, October 20). Everything evaporates, but how?. ScienceDaily. Retrieved October 21, 2010, from http://www.sciencedaily.com­ /releases/2010/10/101020084149.htm

Further Reading
http://www.ausetute.com.au/chemphys.html
http://www.ausetute.com.au/intermof.html
http://www.ausetute.com.au/equilibrium.html
http://www.ausetute.com.au/heatlatent.html
http://www.ausetute.com.au/greenhouse.html

Study Questions

1. Write a chemical equation to describe the evaporation of water.
2. Is the evaporation of water a chemical or a physical change? Explain your answer.
3. Give the names and formulae of 4 natural greenhouse gases.
4. Give the names and formulae of 4 human-induced greenhouse gases.
5. Briefly explain what is meant by the terms Greenhouse Effect and Enhanced Greenhouse Effect.
6. What would be the difference between studying the evaporation of a water droplet in a closed vessel compared to studying the evaporation of a water droplet in a vessel open to the air?
7. Imagine you were undertaking a study of the evaporation of a water droplet in a closed system. In the first experiment you maintain a constant temperature of 25^oC and in the second experiment you maintain a constant temperature of 65^oC. What differences would you expect in the results of your study?
   

Salivary Amylase

Wheat, potatoes, corn and rice contain starch and starch is a major component of the modern diet. Amylase enzymes secreted in saliva help break down starches into simple sugar molecules that can be absorbed into the bloodstream, influencing blood glucose levels.
Monell Center scientists have undertaken a study which revealed that changes of starch consistency in the mouth were directly related to salivary amylase activity. In this study:

• saliva was collected from 73 subjects
• saliva was mixed with a standardized starch solution, and a sensor measured the enzymatic break-down of the starch's consistency
• enzyme and protein assays directly measured the amount and activity of salivary amylase in the saliva samples
• subjects completed a survey to rate the perceived breakdown of a starch sample in the mouth over a minute

Foods with different starch levels were perceived differently by people depending on how much salivary amylase they produce. "What may seem like a thick and resistant pudding or starchy food to some may seem noticeably thin in the mouths of others", said Monell sensory geneticist Paul A. S. Breslin.
Individuals who have more salivary amylase may break down starchy foods more quickly, leading to more rapid increase of post-meal blood glucose levels. It is possible that high levels of salivary amylase contribute to the risk of insulin resistance and non-insulin dependent diabetes.

Reference:
Abigail L Mandel, Catherine Peyrot des Gachons, Kimberly L Plank, Suzanne Alarcon, Paul A S Breslin. Individual Differences in AMY1 Gene Copy Number, Salivary α-Amylase Levels, and the Perception of Oral Starch. PLoS ONE, 2010; DOI: 10.1371/journal.pone.0013352

Further Reading
http://www.ausetute.com.au/enzymes.html
http://www.ausetute.com.au/sugars.html

Study Questions

1. Give a general chemical formula for starch.
2. Starch is an example of a biological polymer. Of what monomers is this polymer made up of?
3. Another biological polymer is made up of the same monomers as that of starch, but, it is found in animals instead of plants. What is the name of this polymer?
4. Assuming you were given two sample bottles, one contained the plant polymer starch, and the other contained the animal polymer in question 3. What simple test or tests could you perform to identify which bottle contained the plant polymer and which contained the animal polymer?
5. What is meant by the term enzyme?
6. Draw a diagram to represent how amylase acts on starch to produce simple sugars.
7. Assume one of the subjects in the study had a fever and was found to have a temperature of 40^oC. What effect would this have on the results obtained during the survey phase of the study?
8. Imagine a well-wisher gave our sick subject above a "nice, hot lemon drink" to relieve the fever's symptons just before the saliva sample was collected. What impact would the lemon drink most likely have on the level of amylase activity?
   

Crystal Violet Lactone

Crystal violet lactone (CVL) is known as a leuco dye.
In a basic environment, the central carbon atom of crystal violet lactone (CVL) forms 4 covalent bonds and the molecule is colourless. In an acidic environment, the lactone ring is broken and the central carbon atom gains a positive charge through the loss of a valence electron, this is the coloured form of the molecule.
These reactions are shown below:

CVL was the first dye used in carbonless copy papers.
Carbonless paper consists of sheets of paper coated with a microencapsulated dye or a reactive clay.
The back of the first sheet is coated with the dye, the top of the lowest sheet is coated with a clay that quickly reacts with the dye to form a permanent mark. When you write on the sheets, the pressure of the pen tip breaks open the micor-capsules of dye, the dye reacts with the clay, and a permanent copy is made of the document.
Chemists in Poland have also discovered that CVL molecules emit white light with continuous spectrum covering almost the entire visible range. This is an important discovery because it is known that white light from artificial sources such as fluorescent lights is devoid of many colour components and that this is responsible for causing tired eyes. Making a better artificial white light could result in improved productivity in humans.

Reference:
Jerzy Karpiuk, Ewelina Karolak, Jacek Nowacki. Tuneable white fluorescence from intramolecular exciplexes. Physical Chemistry Chemical Physics, 2010; 12 (31): 8804 DOI: 10.1039/B927232A

Further Reading
http://www.ausetute.com.au/fungroup.html
http://www.ausetute.com.au/acidbase.html

Study Questions

1. Identify the various functional groups in each of the molecules shown above.
2. Name each of these functional groups.
3. Carefully read the introductory paragraph in the story above, and study the reaction diagram. Can you circle a lactone ring?
4. Imagine you could obtain pure samples of each of the two molecules shown. In what ways would the samples be similar? In what ways would they be different?
5. Describe two tests that you could used to distinguish between each of the pure samples above.
   

Your Phone: Your Spectrometer

Professor Alexander Scheeline of the University of Illinois has developed a method to turn a mobile (cell) phone into a portable spectrometer.

In a spectrometer, white light shines through a sample solution. The solution absorbs certain wavelengths of light. A diffraction grating then spreads the light into its colour spectrum like a prism. Chemists analyze the spectrum to tell them about the properties of the sample.

In Scheeline's device, a single light-emitting diode (LED) powered by a 3-volt battery (as used in key fobs to remotely lock a car) is used as the light source. Diffraction gratings are available from scientific supply companies, as are cuvettes, the small, clear containers to hold the sample solutions. The mobile (cell) phone is used to take a photo of the spectrum obtained. Then the JPEG photo is analyzed using a software program freely accessible online:
http://www.asdlib.org/onlineArticles/elabware/Scheeline_Kelly_Spectrophotometer/index.html

Further Reading
http://www.ausetute.com.au/spectros.html

Further Activities

1. Build a spectrometer as per the instructions given in here : http://www.asdlib.org/onlineArticles/elabware/Scheeline_Kelly_Spectrophotometer/HSFiles/3.html
   
2. Follow the instructions in the preparation of a solutions of different concentrations, including a blank.
3. Record each spectrum produced by taking a photo of it.
4. Upload the photos into the programme which you should download using the link above.
5. Data will be available as an exported csv file for excel.
6. Plot absorbance versus concentration.
7. Obtain a solution of unknown concentration.
8. Use the plot above to determine the concentration of this solution.
   

Nobel Prize for Work on Graphene

The 2010 Nobel Prize in Physics has been awarded to Andre Geim and Konstantin Novoselov for their "groundbreaking experiments regarding the two-dimensional material graphene".

Graphene is an allotrope of carbon, it is the thinnest and strongest material known. It conducts electricity as well as copper and outperforms all other materials as a conductor of heat. It is almost completely transparent, yet it is so dense that not even helium, the smallest known gas atom, can pass through it.

Geim and Novoselov extracted graphene from a piece of graphite such as is found in "lead" pencils. Using a piece of adhesive tape they obtained a flake of carbon that was just one atom thick, which is the allotrope known as graphene.

Reference:
http://static.nobelprize.org/nobel_prizes/physics/laureates/2010/info_publ_phy_10_en.pdf

Further Reading
Allotropes
Elements

Study Questions:

1. What is meant by the term allotrope?
2. Name two other naturally occurring allotropes of carbon.
3. Draw a table listing the physical properties of both of these allotropes and graphene.
4. Discuss the similarities and differences between these allotropes.
5. Draw a possible structure for graphene.
6. Describe the similarities and differences between the structure for graphene that you have drawn and the structures for the other two allotropes in your table.
7. Using your structure for graphene, explain the similarities and differences between the physical properties of graphene and the other two allotropes.
   

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.
   

Diacetylene in Space

Diacetylene, C₄H₂, has previously been discovered in the atmosphere of Titan and on the Moon. Polish scientists have recently observed it in translucent interstellar clouds.

The density of translucent interstellar clouds is extremely small, much less than the best vacuum we can produce in a laboratory, but because they are huge in size their gas molecules have a chance to interact with penetrating radiation, so scientists can use spectroscopy to study the composition of these translucent interstellar clouds.

Molecules absorb and emit photons of specific energies, and therefore wavelengths, corresponding to the differences between energy levels in their atomic structure. The light from stars that reaches the Earth is slightly changed as a result of interactions with gas particles in translucent clouds, it lacks the wavelengths absorbed by intervening interstellar atoms and molecules. Until now, compounds composed of no more than a few atoms have been found in these clouds, molecules such as C₃ andH₃⁺. It is possible that diacetylene is quite a common component of the interstellar medium, having now been located in two carbon-rich galaxy regions and in the averaged data coming from a dozen other lines of sight.

Reference
Institute of Physical Chemistry of the Polish Academy of Sciences (2010, September 17). Surprisingly complicated molecule found in outer space. ScienceDaily. Retrieved September 18, 2010, from http://www.sciencedaily.com­ /releases/2010/09/100915084456.htm

Further Reading
Spectroscopy : http://www.ausetute.com.au/spectros.html
Nomenclature : http://www.ausetute.com.au/namctut1.html
Alkynes : http://www.ausetute.com.au/namsynes.html

Study Questions:

1. Draw the structural formula for diacetylene, C₄H₂.
2. Give the systematic IUPAC name for diacetylene.
3. To which homologous series does the diacetylene molecule belong?
4. Give the empirical formula for the diacetylene molecule.
   
5. Is diacetylene an example of a saturated or unsaturated hydrocarbon? Explain your answer.
6. In Titan's atmosphere, diacetylene could be produced from the reaction between acetylene, C₂H₂, and the ethynyl radical C₂H. Write a possible chemical equation to represent this reaction.
7. Would you expect diacetylene to react with bromine water? Explain your answer.
8. Would you expect diacetylene to be easily oxidized? Explain your answer.
   

Looking Inside Lithium Ion Batteries

Lithium-ion batteries are used to power electronic devices such as mobile phones (cell phones) and are widely used because of their low weight, high energy density and recharging ability. If scientists could see the batteries working at the nanoscale, observing the functionality of the batteries at the level of a single grain or an extended defect, they could determine what makes one battery work and another one fail.
Department of Energy's Oak Ridge National Laboratory (ORNL) scientists have developed a new type of scanning probe microscopy called electrochemical strain microscopy (ESM) to examine the movement of lithium ions through a battery's cathode material. They showed that the lithium ion flow could concentrate along grain boundaries, leading to cracking and battery failure.

Reference:
N. Balke, S. Jesse, A. N. Morozovska, E. Eliseev, D. W. Chung, Y. Kim, L. Adamczyk, R. E. García, N. Dudney, S. V. Kalinin. Nanoscale mapping of ion diffusion in a lithium-ion battery cathode. Nature Nanotechnology, 2010; DOI: 10.1038/nnano.2010.174

Further Reading:
Batteries
Galvanic Cells
Oxidation and Reduction

Study Questions

1. What is the difference between a battery and an electrochemical (galvanic or voltaic) cell?
2. Is the lithium-ion battery described in the article an example of a primary or secondary cell? Explain your answer.
3. Draw a sketch of a galvanic (voltaic) cell. Label the anode, cathode, and electrolyte. Clearly show the direction of electron flow through the cell.
4. Explain how the galvanic (voltaic) cell above could be recharged.
5. In the lithium-ion battery in the article above, will lithium ions be produced at the anode or the cathode while the battery is being discharged?
6. Describe the movement of lithium ions in the lithium-ion battery described above during the process of recharging the battery.
   

Bilirubin

Bilirubin is the compound responsible for the yellow colour of bruises and urine. It is formed during the breakdown of red blood cells in animals.

Scientists at the Florida International University have now identified bilirubin in the Bird of Paradise plant. Using high-performance liquid chromatography (HPLC) and HPLC/electrospray ionization-tandem mass spectrometry, the scientists discovered bilirubin in the seeds and sepals of the plant.

Reference:
Pirone, Cary, Johnson, Jodie V., Quirke, J. Martin E., Priestap, Horacio A., Lee, David. The Animal Pigment Bilirubin Identified in Strelitzia reginae, the Bird of Paradise Flower. HortScience, 2010; 45: 1411-1415

Further Reading
Organic nomenclature
Functional groups
Chromatography

Study Questions

1. Give the molecular formula for the bilirubin molecule.
   
2. Identify the functional groups present in a molecule of bilirubin by circling them on the structure.
3. Name each of the functional groups above.
4. Is bilirubin an example of a saturated or an unsaturated organic molecule? Explain your answer.
5. Would you expect bilirubin to undergo a reaction with a mild oxidizing agent? Explain your answer.
6. Why do you think that bilirubin is a coloured compound?
7. Why do you think that scientists were initially surprised to find bilirubin in plants?
   

Magic Numbers

Scientists who study the nuclei of atoms apply the "magic" moniker to elements with a certain number of protons or combinations of protons and neutrons. At the magic numbers of 2, 8, 20, 28, 50, 82 and 126 the protons and neutrons are tightly bound together, giving many "magic" elements a high degree of nuclear stability.

Rutgers scientists have been studying an isotope of tin that is "doubly magic", it contains 50 protons and 82 neutrons. Unlike other magic nuclei that are stable, this isotope of tin is very unstable with a half-life of 40 seconds.

The scientists believe that this isotope of tin may be formed in supernova explosions or collisions of neutron stars, and could be part of the process that forms heavier elements.

Reference:
K. L. Jones, A. S. Adekola, D. W. Bardayan, J. C. Blackmon, K. Y. Chae, K. A. Chipps, J. A. Cizewski, L. Erikson, C. Harlin, R. Hatarik, R. Kapler, R. L. Kozub, J. F. Liang, R. Livesay, Z. Ma, B. H. Moazen, C. D. Nesaraja, F. M. Nunes, S. D. Pain, N. P. Patterson, D. Shapira, J. F. Shriner, M. S. Smith, T. P. Swan, J. S. Thomas. The magic nature of ¹³²Sn explored through the single-particle states of ¹³³Sn. Nature, 2010; 465 (7297): 454 DOI: 10.1038/nature09048

Further Reading
Isotopes
Nuclear Decay
Half-life

Study Questions

1. Explain what is meant by the term isotope.
2. What is the atomic number for the tin isotope described in the article above?
3. What is the mass number for the tin isotope described in the article above?
4. What are the names of the elements that have a nucleus containing the following "magic" numbers of protons:
   
• 2
• 8
• 20
• 28
• 50
• 82
5. Explain what is meant by the term half-life.
6. The half-life of the tin isotope described above is 40 seconds.
   
   • If the original sample had a mass of 0.1g, what mass of tin isotope would be present in the sample after 2 minutes?
   • What percentage of the mass of the original sample would be present after 80 seconds?
   
   

Phosphorus

Phosphorus deposits come from fossilized animals skeletons. Purifying these deposits produces white phosphorus, a tetrahedral P₄ molecule.

Organophosphorus compounds such as those found in pesticides are produced commercially in a two step process:

1. three of the atoms in P₄ are replaced with chlorine atoms to produce PCl₃
2. chlorine atoms are then displaced by organic molecules

This process is both wasteful and dangerous, chlorine is a toxic gas. It would be very beneficial if scientists could find a way of producing organophosphorus compounds without the need for chlorine.

It has been known since 1937 that P₄ can be broken into two molecules of P₂ using ultraviolet light and that the P₂ will polymerize into red phosphorus.

Massachusetts Institute of Technology (MIT) Chemists have just used UV light to break P4 molecules apart in the presence of unsaturated organic molecules in order to form tetra-organo diphosphane, a molecule made up of 2 atoms of phosphorus attached to 2 molecules of the organic compound.

Reference:
Daniel Tofan, Christopher C. Cummins. Photochemical Incorporation of Diphosphorus Units into Organic Molecules. Angewandte Chemie International Edition, 2010; DOI: 10.1002/anie.201004385

Further Reading
Allotropes

Study Questions

1. Name the allotropes of phosphorus
2. Explain the ways in which these allotropes of phosphorus are similar and the ways in which they are different to each other.
3. Write a sequence of chemical equations to represent the series of stages in the two step process to produce commercial organophosphorus compounds.
4. Write a chemical equation to represent the breaking up of P₄ molecules into P₂ molecules using UV light.
5. Explain what is meant by the term polymerize.
6. Explain the difference between saturated and unsaturated organic compounds.
   
7. Why do you think that MIT chemists used unsaturated rather than saturated organic compounds in their experiment with P₄?
   

Why Fish Don't Freeze

Ever wondered why fish don't freeze in polar oceans where the temperature of the water falls below 0^oC?
The September 2010 issue of AUS-e-NEWS takes a look at the chemistry behind this interesting question.
Contact AUS-e-TUTE to subscribe to AUS-e-NEWS.

Protonated Water Clusters

Water molecules are polar. This causes neighbouring water molecules to be attracted to each other, forming hydrogen-bonds that link them into chains or clusters. The evaporation of water requires relatively large amounts of energy in order to break the hydrogen-bond networks apart.

Protonated water clusters, which have protons bound to them, are important model systems for the study of proton hydration in aqueous solutions, the process that determines the acidity (pH) and electrical conductivity of water.

The smallest protonated water cluster is the hydronium cation consisting of a single water molecule with an associated proton.
The Zundel ion is another protonated water cluster and is formed when a single proton is shared by two water molecules.

Scientists have been using infrared spectroscopy to determine the bond strengths, geometrical structures and chemical properties of protonated water clusters. When molecules are irradiated with infrared light, they vibrate in ways that depend on the wavelength, the colour, of the light. The frequency of the resulting vibrations allows scientists to deduce the three-dimensional structure of the molecule and the strength of the bonds between its atoms.

Reference:

1. Marcel sBaer, Dominik Marx, Gerald Mathias. Theoretical Messenger Spectroscopy of Microsolvated Hydronium and Zundel Cations. Angewandte Chemie, 23 August 2010 DOI: 10.1002/anie.201001672
2. G. Mathias, D. Marx. Structures and spectral signatures of protonated water networks in bacteriorhodopsin. Proceedings of the National Academy of Sciences, 2007; 104 (17): 6980 DOI: 10.1073/pnas.0609229104

Study Questions

1. Draw the molecular structure of a water molecule.
2. Use the structure above to explain what is meant by water being a polar molecule.
3. Draw a diagram to show how a hydrogen-bond can be formed between two water molecules.
4. Write the molecular formula for the hydronium cation.
5. Give the structural formala for the hydronium ion.
6. Based on the description of the Zundel ion given above, write the molecular formula for the Zundel ion.
7. Give the structural formula for the Zundel ion.
8. Another protonated water cluster is the Eigen ion, H₉O₄⁺ . Give a possible structural formula for the Eigen ion.