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.
    
    
    

Sweet Chemistry

Table sugar, or sucrose, C₁₂H₂₂O₁₁, is a disaccharide of glucose and fructose.
When a pure substance melts, it melts at a consistent, repeatable temperature, and retains its chemical identity when moving from the solid state to the liquid state.
The melting point of sucrose is usually given as a range, such as 160^oC to 180^oC, not as a well-defined melting point. This is because sucrose decomposes as it is heated. University of Illinois scientists have shown that glucose and fructose also decompose on heating.

If no oxygen were present, then sucrose would decompose into carbon and water. Caramelized sugar is due to the process of sucrose decomposing, and the brown colour is due to the presence of carbon in the mixture.

Carbon and water are also the products of the exothermic reaction between sucrose and sulfuric acid. This is an example of a dehydration reaction in which water is eliminated from the organic molecule during the reaction. The sulfuric acid then oxidizes the carbon produced as a result of the dehydration reaction, producing both carbon dioxide and toxic sulfur dioxide gases.

If potassium nitrate is used to oxidize sucrose, the products are potassium carbonate, water, nitrogen gas and carbon dioxide gas.

48 KNO₃ + 5 C₁₂H₂₂O₁₁ → 24 K₂CO₃ + 24 N₂ + 55 H₂O + 36 CO₂

This reaction can be used as the basis for a propellant for model rockets, such as in the Sugar Shot to Space program.

Reference
Joo Won Lee, Leonard C. Thomas, Shelly J. Schmidt. Can the Thermodynamic Melting Temperature of Sucrose, Glucose, and Fructose Be Measured Using Rapid-Scanning Differential Scanning Calorimetry (DSC)? Journal of Agricultural and Food Chemistry, 2011; 59 (7): 3306 DOI: 10.1021/jf104852u

Further Reading
Carbohydrates
Pure Substances and Mixtures

Study Questions

1. Draw a structural formula for both glucose and fructose.
2. Give the molecular formula for both glucose and fructose.
   
3. Explain why glucose and fructose are considered to be monosaccharides.
4. Explain what is meant by the term disaccharide.
5. Draw the structural formula for a disaccharide composed of:
   • glucose
   • fructose
   • glucose and fructose
6. Draw a sketch of the temperature vs time graph you expect to see if a sample of sucrose was:
   • a pure sample
   • a mixture of different sugar
7. Write a balanced chemical equation to represent the decomposition of sucrose into carbon and water in the absence of oxygen.
   
8. Write a balanced chemical equation for the dehydration of sucrose using sulfuric acid.
9. What is the difference between the decomposition of sucrose reaction and the dehydration of sucrose sucrose? Why is the reaction with sulfuric acid not considered to be a decomposition reaction?
   
   
   

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.
   
   
   
   
   

Sepiolite

Sepiolite has been known since Roman times when it was used to filter and purify wine. No other mineral is known to absorb more water or other liquids as efficiently as sepiolite, which is why sepiolite is commonly used in cat litter. Sepiolite is also used to absorb liquid spillages, such as in oil spills, and odours and stabilise aqueous products like paints, resins and inks.
Sepiolite is an aluminosilicate clay mineral with a typical formula of Mg₄Si₆O₁₅(OH)₂·6H₂O.

Sepiolites absorb moisture by using tiny tunnels in the crystals. The elongated, needle-shaped sepiolite crystals pack very loosely into a lightweight porous material. The surface area ranges between 75 and 400 m²/g, meaning that 20g of mineral have an internal surface equivalent to that of a football court. This is why sepiolite can absorb 2.5 times its weight in water. The tunnels in the crystal structure along with the empty space between the needles form a capillary network through which liquids can easily flow deep inside the bulk where the molecules attach to the surface of the crystals.

A team of scientists from Spain and France has obtained, for the first time, single-crystal X-ray diffraction images of sepiolite, opening the path to industrial synthesis and further improvement of its properties. In synthetic form, sepiolite could bind food products and stabilise drugs, extending their shelf life and making sepiolite an edible product.

Reference
Manuel Sanchez del Rio, Emilia Garcia-Romero, Mercedes Suarez, Ivan da Silva, Luis Fuentes Montero, and Gema Martinez-Criado. Variability in sepiolite: Diffraction studies. American Mineralogist, 2011 DOI: 10.2138/am.2011.3761

Further Reading
Percentage Composition
Balancing Chemical Equations


Study Questions

1. Calculate the percentage composition of sepiolite, Mg₄Si₆O₁₅(OH)₂·6H₂O
2. Explain what the ·6H₂O part of the formula refers to.
3. Write a balanced chemical equation for the dehydration of hydrated sepiolite to form anhydrous sepiolite.
4. Calculate the maximum mass of water you could obtain from 1kg of hydrated sepiolite.
5. If the sepiolite in question 2 has a surface area of 200m²/g, what is the total surface area of the sample in question 4?
   
6. Use the equation in question 3 to explain why sepiolite is used in cat litter.
7. Sepiolite is an aluminosilicate mineral. Explain what is meant by the term aluminosilicate.
8. Sepiolite is sometimes referred to as a zeolite-like mineral. In what ways is sepiolite similar to a zeolite mineral?
   

Hydrogen Peroxide in Space

Molecules of hydrogen peroxide, H₂O₂, have been found for the first time in interstellar space by astronomers using the European Southern Observatory-operated APEX telescope in Chile.
The hydrogen peroxide has been detected in a region of our galaxy about 400 light-years away where it is very cold (around -250^oC) and contains dense clouds of cosmic gas and dust in which new stars are being born. The clouds are mostly made of hydrogen, but contain traces of other chemicals, and are prime targets for astronomers hunting for molecules in space. The amount of hydrogen peroxide in the cloud is just one molecule for every ten billion hydrogen molecules.

Hydrogen peroxide is a key molecule for both astronomers and chemists. Its formation is closely linked to two other familiar molecules, oxygen and water, which are critical for life. Because much of the water on our planet is thought to have originally formed in space, scientists are keen to understand how it is created. Hydrogen peroxide is thought to form in space on the surfaces of cosmic dust grains, very fine particles similar to sand and soot, when hydrogen (H) is added to oxygen molecules (O₂). A further reaction of the hydrogen peroxide with more hydrogen is one way to produce water (H₂O).

Reference
P. Bergman, B. Parise, R. Liseau, B. Larsson, H. Olofsson, K. M. Menten, R. Güsten. Detection of interstellar hydrogen peroxide. Astronomy & Astrophysics, 2011; 531: L8 DOI: 10.1051/0004-6361/201117170

Further Reading
Lewis Structures (electron dot diagrams)
Intramolecular Forces
Intermolecular Forces
Temperature Conversions
Ideal Gas Calculations


Study Questions

1. Draw a Lewis Structure (electron dot diagram) for hydrogen peroxide.
2. Describe the nature of bonding that occurs within the hydrogen peroxide molecule.
3. The melting point of pure hydrogen peroxide is -0.43^oC . Explain why the melting point of pure hydrogen peroxide is slightly less than the melting point of pure water.
4. The boiling point of pure hydrogen disulfide, H₂S₂, is 70.7^oC while the boiling point of hydrogen peroxide is 150.2^oC. Explain why the boiling point of hydrogen peroxide is more than twice the boiling point of hydrogen disulfide.
5. Convert the following temperatures in ^oC to temperatures in Kelvin:
   • -250 ^oC
   • -0.43 ^oC
   • 70.1 ^oC
   • 100 ^oC
   • 150.2 ^oC
6. The amount of hydrogen peroxide in the cloud is just one molecule for every ten billion hydrogen molecules. Convert this to:
   • a concentration of hydrogen peroxide in parts per million.
   • a concentration of hydrogen peroxide in grams of hydrogen peroxide per kilogram of hydrogen
7. In outer space, 'atmospheric' pressure is about 100μPa Convert this to a pressure in:
   • kPa
   • atm
   • mmHg
   • Torr
8. Calculate the temperature of outer space if the atmospheric pressure of 100μPa is caused by the presence of 10 hydrogen molecules per cubic metre of space.
   
   
   
   

Smell of Danger

Harvard Medical School scientists have discovered a single compound, found in high concentrations in the urine of carnivores, that lets rodents like rats and mice sense carnivores in general from a safe distance.
Mice have about 1200 kinds of odour receptors and 14 kinds of TAARs (Trace Amine-Associated Receptors), in comparison, humans have about 350 odour receptors and 5 TAARs because humans rely much more on sight than on smell.
Working with commercially available predator and prey urine, used by gardeners to keep pests out of their crops and by hunters to mask their own scent or as lures for prey, the scientists discovered that one of the 14 mice TAARs, TAAR4, detected the odour of several carnivores.
The compound that activates TAAR4 is 2-phenylethylamine, a product of protein metabolism.
Elevated levels of 2-phenylethylamine are found in many species of carnivores, but not found in non-carnivores (including rabbits and deer). In a series of behavior tests, rats and mice showed a clear, innate avoidance to the smell of 2-phenylethylamine.
The structural formula of 2-phenylethylamine is shown here.
2-phenylethylamine is an amine, consisting of a benzene ring and an aminoethyl group. It is a colourless liquid at room temperature, is strongly basic, and has a fishy odour to
humans, but has the smell of danger to mice and rats..


Reference
D. M. Ferrero, J. K. Lemon, D. Fluegge, S. L. Pashkovski, W. J. Korzan, S. R. Datta, M. Spehr, M. Fendt, S. D. Liberles. Detection and avoidance of a carnivore odor by prey. Proceedings of the National Academy of Sciences, 2011; DOI: 10.1073/pnas.1103317108

Further Reading
Amines
Functional Groups
Structural Isomers
Percentage Composition

Study Questions

1. Write the molecular formula for 2-phenylethylamine.
2. Draw a structural formula for a possible structural isomer of 2-phenylethylamine.
3. Calculate the percentage composition of 2-phenylethylamine.
4. Circle the functional group in the structural formula of 2-phenylethylamine.
5. Circle the benzene ring in the structural formula of 2-phenylethylamine.
6. Is 2-phenylethylamine a primary, secondary, or tertiary amine? Explain your answer.
7. 2-phenylethylamine is soluble in water and ethanol (ethyl alcohol). Explain why 2-phenylethylamine dissolves in water and ethanol.
8. Ethylamine, CH₃CH₂NH₂, has a boiling point of 17^oC and K_b=4.7 x 10^-4. Predict the boiling point and base dissociation constant for 2-phenylethylamine giving reasons for your answer.
   
9. Write a balanced chemical equation for the reaction between 2-phenylethylamine and hydrochloric acid.
10. Trimethylamine, a compound related to 2-phenylethylamine, activates TAAR5 receptors in humans.
    • Draw the structural formula for trimethylamine.
    • Give the molecular formula for trimethylamine.
    • Discuss the similarities between trimethylamine and 2-phenylethylamine.