Sunday, February 18, 2018

Short Chain Fatty Acids?

I came across this story in the Sydney Morning Herald this morning, "A make-or-break moment for what may be a new molecule". Sounds exciting doesn't it. A hint of uncertainty, is it or isn't it a new molecule? What will it "make or break"?

It appears that Charles Mackay, a Professor of Microbiology at Monash Biomedicine Discovery Institute has, "demonstrated that dietary fibre and its breakdown fermented products, the short chain fatty acids (SCFAs) influence gut homeostasis, the composition of the gut microbiota, immune tolerance, and inflammatory responses."  I must apologize, I've never been particularly interested in biology, so I actually have no idea what any of that means, but from the story in the newspaper it appears that Professor Mackay thinks we should be eating more "short chain fatty acids" as are present in fermented foods such as vinegars and hence vegetables pickled in vinegars, and this will help regulate our blood pressure and immune system, keeping us healthy. Good news for me, I love pickled onions and gherkins, and have been known to indulge in sauerkraut and kimchi.

But what on earth is a "short chain fatty acid"?

Now, a fatty acid is a long chain carboxylic acid.
A carboxylic acid is a molecule with a carboxylic acid functional group (COOH) at the end of a hydrocarbon chain.
For example, formic acid is the carboxylic acid which is present in an ant's sting. It has only one carbon atom in the chain, its formula is HCOOH (CH2O2)
Acetic acid is the carboxylic acid that gives vinegar it's tang. It has 2 carbon atoms in its chain,

But fatty acids have lots of carbon atoms in the chain, common fatty acids have 12 or 14 or 16, or 18 carbon atoms in the chain. These fatty acids (long chain carboxylic acids) are found naturally in the oils and fats of plants and animals. If the long hydrocarbon chain is saturated (contains only single bonds between the carbon atoms in the chain) it is called a saturated fatty acid. If there is one, or more, double bonds between carbon atoms in the long chain then it is referred to as an unsaturated fatty acid.

So a "short chain fatty acid" would be what? A short long chain carboxylic acid? Sounds like nonsense doesn't it? Maybe it's a medium length chain carboxylic acid?

According to wikipedia (which may or may not be a reliable source of information),  a "short chain fatty acid" is a fatty acid with 2 to 6 carbon atoms. Included in wikipedia's list of "short chain fatty acids" are the two carboxylic acids we used as examples above, formic acid (which has only 1 carbon atom in its chain and hence does not actually fit within wikipedia's own definition and hence my concern about the reliability of the information it provides), and, acetic acid. So, a "short chain fatty acid" is in fact NOT a short chain "fatty acid", it is simply a short chain carboxylic acid!

Is the "molecule" new, as claimed by the headline? Most unlikely because:
  • "short chain fatty acids" is just a poor description of a group of molecules sharing a carboxylic acid functional group, not just 1 molecule
  • we've known about these short chain carboxylic acids for a very, very long time


Suggested Study Questions:
  1.  Draw the 2-dimensional structure formula for each of the following carboxylic acids:
    • formic acid
    • acetic acid
    • propanoic acid
    • butanoic acid
    • pentanoic acid
    • hexanoic acid
  2. Draw a condensed structural formula for each of the carboxylic acids in question 1.
  3. Draw a skeletal structural formula for each of the carboxylic acids in question 1.
  4. Give the molecular formula for each of the carboxylic acids in question 1.
  5. Give the empirical formula for each of the carboxylic acids in question 1
  6. Are the carboxylic acids in question best described as saturated or unsaturated? Explain your answer.
  7. On each 2-dimensional structural formula, identify, circle and name the functional group common to all the molecules.
  8. Draw at least 2 structural isomers with the molecular formula C5H10O2
  9. Circle the functional groups in the molecules you draw in question 8. Name these functional groups.
  10. Choose 2 of the structural isomers drawn in question 8. Would you expect these 2 molecules to have very similar, or very different, physical and chemical properties. Explain your answer.

Sunday, January 28, 2018

Omega-3 Acids Fight Cancer

Scientists at the University of Guelph have found that omega-3s from fish are better at preventing cancer than omega-3s from plants.

"Omega-3s" refer to omega-3 fatty acids which are a type of long-chain, polyunsaturated carboxylic  acid. Long-chain carboxylic acids are referred to as "fatty acids".
The three omega-3 fatty acids studied were: 
  • α-linolenic acid (ALA) which is found in plant seeds and oils
  • eicosapentaenoic acid (EPA) which is found in fish, algae and phytoplankton
  • docosahexaenoic acid (DHA) which is found in fish, algae and phytoplankton
 The skeletal structural formula for α-linolenic acid is shown below:
 The IUPAC name of α-linolenic acid is (9Z,12Z,15Z)-9,12,15-octadecatrienoic acid. 
The carbon atom of the carboxyl functional group (COOH) is labelled as 1, the next carbon atom in the chain is 2, then 3, etc, up until we reach the last carbon in the chain, carbon 18. The parent hydrocarbon for this molecule is therefore octadecane, with a suffix added for the carboxyl functional group, so we have octadecanoic acid. 
Along the way we find 3 (tri) double bonds (en) at carbons numbered 9, 12 and 15, so we modify the name of the carboxylic acid in one of two ways:
  • 9,12,15-octadecatrienoic acid
  • octadeca-9,12,15-trienoic acid
The "Z" indicates the 3-dimensional geometry,  in this case the "Z" geometry equates to a "cis" geometry.
So why would  (9Z,12Z,15Z)-9,12,15-octadecatrienoic acid be called an omega-3 acid?
There is an alternative naming "system" (not IUPAC)  in which the first carbon atom is not labelled 1, but instead it is called "alpha" (α), and, the carbon atom at the end of the long hydrocarbon chain is called "omega" (ω). Then, the last carbon atom in the chain (omega) is labelled 1, and you start counting back towards the carboxyl functional group. If you do this, you will find that carbon 3 has a double on it, hence, (9Z,12Z,15Z)-9,12,15-octadecatrienoic acid is called an omega-3 fatty acid. The 3 indicates the position of the first double bond from the omega carbon atom.

The skeletal structural formula of eicosapentaenoic acid is shown below:
The IUPAC name for this molecule is (5Z,8Z,11Z,14Z,17Z)-5,8,11,14,17-Icosapentaenoic acid. 
There are 20 carbon atoms in the chain so the parent hydrocarbon chain is icosane, which is modified with a suffix because there is a carboxyl functional group, icosanoic acid.
There are 5 (pent) double bonds (en) located on carbons 5, 8, 11, 14 and 17, so the name of this molecule is either:
  • 5,8,11,14,17-icosapentenoic acid
  • icosa-5,8,11,14,17-pentenoic acid
Once again, the Zs in the name refer to the geometry (same as a "cis" geometry in this case).
Notice that, in the alternative naming "system" in which the last carbon atom in the chain is labelled "omega" and then you count backwards from this, we see that the first double bond encountered is on carbon 3, so this molecule is also referred to as an omega-3 fatty acid.

The skeletal structural formula below is that of docosahexaenoic acid:
This molecule has the IUPAC name (4Z,7Z,10Z,13Z,16Z,19Z)-4,7,10,13,16,19-Docosahexaenoic acid. 22 carbon atoms in the chain (docosa), 6 (hexa) double bonds on carbons 4, 7, 10, 13, 16, 19 and a carboxyl functional group: 4,7,10,13,16,19-docosahexaenoic acid or docosa-4,7,10,13,16,19-hexenoic acid. Zs indicate geometry (same as "cis" in this case).
Using the alternative numbering system, the first double bond occurs of the third carbon atom from the omega carbon atom (last carbon in the chain) so it is also classified as an omega-3 fatty acid.

While all three of these omega-3 fatty acids were shown to be effective in reducing the size of tumours in mice, however, higher doses of the plant-based α-linolenic acid was required to deliver the same impact as the omega-3 fatty acids found in fish (icosapentaenoic acid and docosahexaenoic acid)


Jiajie Liu, Salma A. Abdelmagid, Christopher J. Pinelli, Jennifer M. Monk, Danyelle M. Liddle, Lyn M. Hillyer, Barbora Hucik, Anjali Silva, Sanjeena Subedi, Geoffrey A. Wood, Lindsay E. Robinson, William J. Muller, David W.L. Ma. Marine fish oil is more potent than plant based n-3 polyunsaturated fatty acids in the prevention of mammary tumours. The Journal of Nutritional Biochemistry, 2017; DOI: 10.1016/j.jnutbio.2017.12.011

Further Reading:
Introduction to naming organic molecules:
Introduction to functional groups:
Fatty acids: 
Structure and properties of carboxylic acids:
Molecular formula:
2-Dimensional structural formula:
Condensed structural formula:
Skeletal structural formula:
Cis-trans isomers: 

Suggested Study Questions:
  1. What functional group is common to all fatty acids? 
  2. Define the following terms as they are used in chemistry:
    • saturated
    • unsaturated
    • monounsaturated
    • polyunsaturated
  3.  Give the molecular formula for each of the three omega-3 acids in the article
  4. The structural formula given in the article are referred to as "skeletal". What does this mean in chemistry?
  5. Draw a 2-dimensional (full display) structural formula for each of the omega-3 acids in the article.
  6. On the structural formula of each of the three omega-3 acids circle the:
    • carboxyl functional group in red
    • double bonds in blue
  7. What features are common to three omega-3 acids in the article?
  8.  In what ways do the the three omega-3 acids in the article differ?
  9. You have probable heard about omega-6 acids. How do you think an omega-6 acid will be similar to an omega-3 acid?
  10. How will an omega-6 acid be different from an omega-3 acid?
  11. What is meant by a cis isomer and a trans isomer?
  12. All the omega-3 fatty acids in the article are the cis isomers. Build a model, and draw, a trans isomer of one of the fatty acids.

Friday, January 26, 2018

Spontaneous Chemical Reactions

What makes a chemical reaction spontaneous?
If I add hydrochloric acid (HCl(aq)) to metallic magnesium (Mg(s)), bubbles of hydrogen gas (H2(g)) are given off and the remaining solution contains chloride ions and magnesium ions (MgCl2(aq)):
Mg(s) + 2HCl(aq) → H2(g) + MgCl2(aq)
But if I try to bubble hydrogen gas through an aqueous solution of magnesium chloride, nothing happens. No solid magnesium forms! Why?
AUS-e-TUTE has just added a new tutorial, game, test and exam to help you understand what makes a reaction spontaneous, nonspontaneous, reversible or irreversible.
AUS-e-TUTE Members should log-in to use these new resources (listed under Thermodynamics in the Physical Chemistry section).

Not an AUS-e-TUTE Member?
A "free-to-view" spontaneous reactions tutorial is currently available for evaluation purposes at:

Friday, January 19, 2018


Triclosan is an organic compound used as an antibacterial and antifungal agent in some products. The structure of triclosan is given below
Triclosan has the systematic IUPAC name of 5-chloro-2-(2,4-dichlorophenoxy)phenol.
Since its development in the 1960s, it has been used as a hospital scrub. Its use spread beyond our hospitals and into our homes where it can be found as an additive in toothpaste, soaps and detergents.
In 2007, University of Michigan School of Public Health undertook a study which found that consumer-grade antibacterial soaps containing Triclosan are just as effective as plain soap for removing bacteria from your hands.
University of Cambridge researchers may have found a new use for Triclosan; as an anti-malarial agent.
Malaria kills more than 500,000 people every year. Unfortunately, malaria parasites are becoming more resistant to the drugs we have been using to treat malaria.. It appears that Triclosan inhibits an enzyme in the malaria parasite and works even in drug-resistant parasites! It is hoped a new anti-malarial drug based on Triclosan can be developed in the future.

Elizabeth Bilsland, Liisa van Vliet, Kevin Williams, Jack Feltham, Marta P. Carrasco, Wesley L. Fotoran, Eliana F. G. Cubillos, Gerhard Wunderlich, Morten Grøtli, Florian Hollfelder, Victoria Jackson, Ross D. King, Stephen G. Oliver. Plasmodium dihydrofolate reductase is a second enzyme target for the antimalarial action of triclosan. Scientific Reports, 2018; 8 (1) DOI: 10.1038/s41598-018-19549-x

Further Reading:
IUPAC Nomenclature (organic):
Introduction to functional groups:
Molecular Formula:
2-dimensional structural formula:
Condensed structural formula:
Skeletal structural formula: 
Pure substances and mixtures:
Solutions concepts:
Percentage composition:
Mass-mole calculations:
Concentration (molarity):
Parts per million (ppm):
weight/weight (mass/mass) concentration:

Suggested Study Questions:
  1.  Use the skeletal structural formula for Triclosan to draw a 2-dimensional structural formula.
  2. On your structural formula, identify each halogen.
  3. On your structural formula, identify a hydroxyl functional group
  4.  On your structural formula, identify an ether link
  5. On your structural formula, identify a benzene ring
  6. Give the molecular formula for Triclosan
  7.  An antibacterial handwash contains 0.5% by mass Triclosan. For 250 g of this handwash, calculate:
    • mass in grams of Triclosan present
    • moles of Triclosan present
  8. Calculate the concentration of Triclosan in the same 250 g of handwash in units of:
    • mol L-1
    • g/100g
    • parts per million (ppm)
  9. Is toothpaste a pure substance or a mixture? Explain your answer.
  10. Is Triclosan a pure substance or a mixture? Explain your answer.


Sunday, January 14, 2018

Bee Killing Chemicals?

This morning I read a story in the Sydney Morning Herald, "Bunnings to pull pesticide allegedly linked to bee deaths".  According to the story, cans of Yates "Confidor" which have been stocked by the homewares and hardware giant Bunnings, contains neonicotinoid, a class of compounds used as an insecticide that some studies have suggested affects bee's navigation and immune systems and ultimately leads to the death of the bee colony. Indeed, a story on this appeared in New Scientist in July 2017 in which Dave Goulson at the University of Sussex, UK, is quoted as saying, "Although the field trial results varied between countries, the overall evidence points to harmful effects for bees. I think you’d have to be pretty unreasonable at this point not to accept that, at least some of the time, these chemicals harm bees when used in normal farming practice.”  The same story quoted Richard Schmuck of Bayer, one of the makers of this class of insecticides, as saying, "We remain confident that neonicotinoids are safe when used and applied responsibly."

As the name neonicotinoids suggests, these are "new" molecules based on the molecular structure of nicotine shown below:
 Nicotine has been used as a pesticide for over 200 years. It is found lots of plants.  Up to 3% of the mass of the tobacco plant is nicotine, and trace amounts of nicotine are found in vegetables like eggplants, potatoes and tomatoes. When used as a pesticide,  it degrades rapidly in the environment and is not very selective so it is not really a good pesticide. For instance, a dose of 1mg per kg of body mas can kill a human.
Development of neonicotinoids began in the 1980s by Shell and1990s by Bayer. Neonicotinoids are generally less toxic to birds and mammals than they are to insects, and, some of the breakdown products are also toxic to insects, this is why they can be used as insecticides.
Consider the structural formula of imidacloprid, an example of a neonicotinoid and one of the most widely used insecticides:
 Imidacloprid was patented by Bayer in 1985 as the first commercial neonicotinoid. Traditionally insecticides were coated onto plants, "crop dusting", but neonicotinoids like  imidacloprid are water soluble and break down slowly in the environment so they are absorbed by plants. Bees are exposed to these compounds in the plant's pollen.
The early 2000s saw the introduction of two other neonicotinoid compounds;  clothianidin and thiamethoxam. 

clothianidin thiamethoxam

Clothianidin can be used as a spray, dust or injectable liquid, depending on which plants it is being to protect.
In 2013 the European Union restricted the use of imidacloprid, clothianidin and thiamethoxam on crops that attract bees.


Suggested Further Reading
IUPAC Nomenclature:
Introduction to Functional Groups:
Molecular Formula:
2-Dimensional Structural Formula:
Skeletal Structural Formula:
 Introduction to Polarity of Molecules:
Intermolecular Forces and Solubility:
Aqueous Solutions (water as a solvent):

Suggested Study Questions:
  1. Use molecular model kits to build models of  the following molecules:
    • nicotine
    • imidacloprid
    • clothianidin
    • thiamethoxam
  2. Draw a 2-dimensional (full display) structural formula for each of the following molecules:
    • nicotine
    • imidacloprid
    • clothianidin
    • thiamethoxam
  3. Write the molecular formula for each of the following molecules:
    • nicotine
    • imidacloprid
    • clothianidin
    • thiamethoxam
  4. Consider the nicotine molecule. Do you expect it to be soluble in water? Explain your answer.
  5. Consider a molecule of imidacloprid. Do you expect it to be soluble in water? Explain your answer.
  6. What property of clothianidin enables it to be used as a spray? Explain this property in chemical terms.
  7.  What alteration to the structure of a nicotine molecule could you make so that it would become more soluble in water?
  8. Carefully compare the structure of clothianidin and thiamethoxam (the molecular models you built could be useful here). In what ways are the molecules:
    • similar
    • different
  9. Considering only the structure of nicotine and the neonicotinoids in this article, explain why nicotine might be more toxic to humans than the neonicotinoids.
  10. Compare the quotes from Dave Goulson and Richard Schmuck in the article. In what ways are the two quotes:
    • similar
    • different
  11. Imagine you have been asked by your government to decide whether or not to ban the use of neonicotinoids in agriculture. What would you advise? Explain why.

Wednesday, January 10, 2018

Gutful of Gas

People can eat interesting things.
In the 1960s in Australia, Leon Samson was eating razor blades to amuse audiences, he even started to eat, slowly, in bits, a car for a bet. A little later, France produced Michel Lotito who was also eating odd things to entertain us, including an airplane between 1978 and 1980.

A razor blade is made out of steel, a particular kind of steel known as razor blade steel. A 2.61 gram razor blade contains between about 13% chromium, 0.6% carbon, and  the rest is iron. Samson would chew up a razor blade and swallow it.

After leaving the mouth, the chewed-up bits of razor blade travel to the stomach. An empty stomach has a volume of about 75 mL but when we eat the volume of the stomach can expand out to about 1 L. Protein-digesting enzymes known as proteases are released into the stomach to help begin the break up of the proteins like you find in meat, fish, eggs and cheese. The optimum pH for these proteases is at about pH 2, so hydrochloric acid is also released into the stomach.

So the small bits of razor blade now find themselves surrounded by hydrochloric acid. Hydrochloric reacts with metals, like the iron in steel, to produce hydrogen gas. Now gases have an interesting property, they expand out to fill the available space. This suggests that eating razor blades might result in a feeling of being bloated. Thankfully, it appears that it takes about 24 hours for the complete reaction between a razor blade and hydrochloric acid in the stomach, plenty of time to remove the gas build-up via burping or, um, farting.

Hydrogen gas is commonly found in our intestines, along with other gases like carbon dioxide, oxygen and nitrogen. Some of these gases get there when we swallow air along with our food and drink, but they also come from chemical reactions inside our bodies. If our bodies are healthy and working well, all the usual gases will be present in the usual concentration, but if there is something wrong, if we are sick, the nature and composition of the gases will change.

Researchers at RMIT University in Melbourne, Australia, have developed and trialed an "ingestible electronic capsule" which is capable of sensing and measuring the gases in the gut like hydrogen, carbon dioxide and oxygen. These capsules offer a new, non-invasive way to monitor the health of our gut. The capsules can be collected after they have been excreted (apparently painlessly).

Kourosh Kalantar-Zadeh, Kyle J. Berean, Nam Ha, Adam F. Chrimes, Kai Xu, Danilla Grando, Jian Zhen Ou, Naresh Pillai, Jos L. Campbell, Robert Brkljača, Kirstin M. Taylor, Rebecca E. Burgell, Chu K. Yao, Stephanie A. Ward, Chris S. McSweeney, Jane G. Muir, Peter R. Gibson. A human pilot trial of ingestible electronic capsules capable of sensing different gases in the gut. Nature Electronics, 2018; 1 (1): 79 DOI: 10.1038/s41928-017-0004-x

Suggested Further Reading 
Experimental Design:
Name and Formula of Binary Covalent Compounds:
Percentage Composition:
Mass-moles Calculations:
Molar Gas Volume Calculations:
Ideal Gas Law Calculations:
Metal + Non-Oxidising Acid Reaction:
Hydrogen Ion Concentration of Strong Acids: 
Reaction Calculations: Mass and Moles 

Suggested Study Questions
  1.   Design an experiment to determine how long it would take for a razor blade to react completely with the hydrochloric acid in the stomach. Investigate ways to speed up, or, to slow down, this reaction.
  2. Give the formula for each of the following:
    • hydrogen gas
    • nitrogen gas
    • oxygen gas
    • carbon dioxide gas
    • hydrochloric acid
  3.   Determine the percentage composition of each of the following compounds
    • hydrogen chloride gas
    • carbon dioxide gas
  4. From the information in the article, calculate the mass of each of the following elements found in a razor blade:
    • iron
    • chromium
    • carbon
  5. Using the information above, calculate the moles of each of the following elements found in a razor blade:
    • iron
    • chromium
    • carbon
  6. Calculate the moles of hydrogen gas that occupy the entire volume of a "full" stomach under the following conditions:
    • 0oC and 100 kPa
    • 25oC and 100 kPa
    • 37oC and 100 kPa
  7. Write a balanced chemical equation for the reaction between the hydrochloric acid in the stomach and the iron in a razor blade.
  8. Calculate the concentration of acid released into the stomach using the information in the article. 
  9. Use the balanced chemical equation to determine the volume of hydrogen gas produced when all the iron in a razor blade has reacted with hydrochloric acid.
  10. Consider all the information in the article, and the calculations you have performed so far. Explain why it takes 24 hours for a razor blade to be completely digested in the stomach.

Sunday, December 31, 2017

Introduction to Entropy

What is entropy?
What is meant by a chemical system having low entropy or high entropy?
What is the relationship between disorder, energy and entropy?

If you are asking these questions, then you will find AUS-e-TUTE's new entropy introductory tutorial, game and test very helpful! AUS-e-TUTE Members should log in to use these new resources (under the topic heading Thermodynamics in the Test Centre).

Not an AUS-e-TUTE Member?
A "free-to-view" tutorial is currently available at