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.
   
   
   

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.