Syntactic and Syndiotactic are NOT Synonymous

 

Question 20 from paper 1 of the QCAA chemistry exam 2022 is shown below. Can you answer it?

 

 You can if you make a couple of assumptions first:

1/ The 3D structure isn't given, so you have to assume (given the possible answers) that methyl groups above the chain are in fact coming out of the plane, while methyl groups below the chain are behind the plane.

2/ You have to assume that "syntactic" is a misprint of "syndiotactic" since there was no mention of this being a composite material.

Then you can choose (A) as the answer, and according to the answer sheet you would be correct.

 

However, here is an excerpt from the draft new Queensland Chemistry syllabus (for implementation in 2025 I believe),

      "Describe the structure features of

           -polyethene (LDPE and HDPE), polypropene (syntactic, isotactic and atactic) and                                             polytetrafluorethene."

(Cross my heart, this is what is says, the syllabus writers seem to have difficulties with adjectives as well as chemical nomenclature, where are the round brackets around tetrafluoroethene?)

 

So, it appears that students will study tacticity of polymers but only isotactic and atactic not syndiotactic, then they will look at composite materials in the form of syntactic foams.

Really?

 

Dear Queensland Chemistry syllabus and exam writers, the 3D structure of a polymer results in an isotactic, syndiotactic or atactic polymer.

A syntactic foam refers to a composite material in which hollow spheres are bound together by a polymer.

Homologous Series

What is a homologous series in organic chemistry?
Homologous series refers to a group of compounds that have:

1. the same functional group
2. constant successive differences in composition

The individual molecules making up a homologous series  are referred to as homologues (or homologs).

Find out more about homologous series and homologues at https://www.ausetute.com.au/homologous.html

AUS-e-TUTE Members should log-in to use the new Members Only tutorial, game, test and exam (with worked solutions ofcourse).

Naming Nitriles

How do you name a molecule like H-C≡N?
If you are an inorganic chemist you might call it:

• hydrogen cyanide (hydrogen name)
• hydridonitridocarbon (additive name)
• methylidyneazane (substitutive name)

If you are an organic chemist you might call it:

• hydrogen cyanide (functional class name)
• formonitrile (preferred IUPAC name)
• methanenitrile (substitutive name) 

The CN functional group at the end of a hydrocarbon chain results in a molecule that belongs to a class of organic compounds called nitriles. All nitriles contain a terminal CN group known as the cyano functional group.
AUS-e-TUTE has a new tutorial, game and test to help our members understand and apply IUPAC naming rules to nitriles. Members should log-in to use these new resources.

If you are not a member of AUS-e-TUTE you can access a "free-to-view" tutorial on naming nitriles at https://www.ausetute.com.au/namnitrile.html

Omega Fatty Acids

"Health Food" companies are always trying to sell us something new.
Instead of eating tasty fish they recommend we consume fish oil wrapped in plastic as a pill. Apparently this is because we are suddenly deficient in "omega-3 fatty acids".
So what are omega-3 fatty acids?
Where do they come from?
Do we really need them?

AUS-e-TUTE Members should log-in to access the new omega fatty acid resources (tutorial, game, test, exam).

If you are not an AUS-e-TUTE Member you can access a free-to-view tutorial at
https://www.ausetute.com.au/omegafat.html

Hydroxyacid or Carboxyalkanol?

So, you've learnt how to name organic molecules containing the OH (hydroxy) functional group, and, you can name molecules that have the COOH (carboxyl) functional group, the carbonyl functional group (C=O), and the NH₂ (amine) functional group.
Excellent!
But what happens when there are 2 or more different functional groups on the same molecule?
Can you still name it?
We can help!
AUS-e-TUTE has just added a new tutorial, game, test and exam to help you learn the IUPAC rules and confidently apply them to these sorts of molecules.
AUS-e-TUTE Members should log-in to use the new resources (under Organic Nomenclature).
If you are not an AUS-e-TUTE Member you can view the tutorial for free at
https://www.ausetute.com.au/nam2fung.html

Name and Formula of Inorganic Acids

There are systematic ways to name inorganic acids, however, for many acids no-one uses these systematic names because the "acid name" for these particular acids has been in use for a very long time. So, IUPAC recognises the "acid name" for a number of acids.
AUS-e-TUTE has just added a new tutorial, game, test, quiz and worksheet wizard, as well as a card game, to help you give the name and molecular formula of these acids. AUS-e-TUTE members should log-in to use these new resources.

If you are not an AUS-e-TUTE member, there is a "free-to-view" tutorial currently available at
https://www.ausetute.com.au/acidnames.html

Don't forgot to download our free "Inorganic Acid Names Card Games" when you visit!
(includes instructions for 3 games and a set of game cards).

Naming Salts

How do you name a salt?
There are several different ways to name salts (binary inorganic ionic compounds).
The most common method used in school as an introduction to naming inorganic compounds is based on compositional nomenclature.
AUS-e-TUTE has a step-by-step guide to how to name a salt if you know the formula of the salt:
https://www.ausetute.com.au/namiform.html

IUPAC Name and Formula of Cations

Naming chemical compounds can be a bit tricky. One of the biggest problems is that people started naming compounds before they understood what they were! And, the problem just gets bigger as we discover new classes of compounds.
Even naming simple binary inorganic ionic compounds (well ... salts!) can produce enormous headaches.
Well, we've started sorting through some of the mess, starting with a whole let new set of resources for writing the formula of cations and naming cations using the current IUPAC recommendations.
Members should log-in to AUS-e-TUTE to use the new resources, but if you are not a member you can go to the "free-to-view tutorial" at https://www.ausetute.com.au/cations.html

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,

CH₃-COOH (C₂H₄O₂)

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

References:
http://www.smh.com.au/national/a-make-or-break-moment-for-what-may-be-a-new-miracle-molecule-20180216-p4z0ky.html
https://research.monash.edu/en/persons/charles-mackay 
https://en.wikipedia.org/wiki/Short-chain_fatty_acid 

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.

Betaines

Betaines are found in plants, animals and microorganisms. Rich sources of betaines in the human diet are seafood, spinach and wheat germ or bran. Research is beginning to indicate that betaines are important nutrients for the prevention of chronic disease. Researchers are also interested in incorporating betaines into polymer brushes used for antifouling and lubrication.

Betaines are compounds with a positively charged functional group linked to a negatively charged functional group with an alkyl chain in between. The alkyl chain is often referred to as an alkyl chain spacer.  The general structure of an N-alkyl betaine is shown below:

The first betaine discovered was found in sugar beets in the nineteenth century. This betaine is (trimethylammonio)acetate, also known as trimethylglycine, and its skeletal structure is shown below:

Another example of a betaine is 2-(trimethylammonio)octadecanoate (also known as hexadecylbetaine) with the skeletal structure shown below:

2-(Trimethylammonio)tetradecanoate, or dodecylbutaine or laurylbutaine, is also a butaine and its skeletal structure is shown below:

Betaines are strongly attracted to water molecules because of these two charged functional groups.
The solubility of betaines in water is dependent on the length of the carbon chain, as well as on temperature and pH. 
In acidic solution, betaines acquire a net positive charge and act like a cationic surfactant. In anionic solutions, betaines acquire a net negative charge and act like an anionic surfactant.

Betaines can also be used in polymer brushes which are polymers bound to a surface. Polymer brushes can be used for antifouling and lubrication because the hydration of the ionic groups reduces the ability of other materials to adhere to the surface. 

Researchers at Kyushu University recently investigated a series of alkly chain spacers of different lengths bound to a silicon surface. They found that the polymer brushes swelled in humid air and water. It is believed that this is due to electrostatic repulsion between charged groups, and not dependent on the length of the alkyl chain.
In deionised water, net positive cations and net negative anions are repelled because of the  electrostatic force which causes the chain dimension to expand, whereas they shrink under high ionic strength by a charge screening effect of the bound ions.

Reference:
https://www.sciencedaily.com/releases/2017/08/170821094302.htm

Further Reading
Introduction to Functional Groups
2-Dimensional Structural Formula
Condensed Structural Formula
Molecular Formula
Amino Acids
Surfactants ( as found in synthetic detergents)
Intermolecular Forces and Solubility

Suggested Study Questions

1. Locate and identify each functional group on the skeletal structural formula of
• general formula N-alkyl betaine 
• (trimethylammonio)acetate
• 2-(trimethylammonio)octadecanoate
• 2-(trimethylammonio)tetradecanoate
2. Draw a 2-dimensional structural formula for each of the following molecules:
• (trimethylammonio)acetate
• 2-(trimethylammonio)octadecanoate
• 2-(trimethylammonio)tetradecanoate
3. Write the condensed structural formula for each of the following molecules:
• (trimethylammonio)acetate
• 2-(trimethylammonio)octadecanoate
• 2-(trimethylammonio)tetradecanoate
4. Write the molecular formula for each of the following molecules:
• (trimethylammonio)acetate
• 2-(trimethylammonio)octadecanoate
• 2-(trimethylammonio)tetradecanoate
5. Compare the structure of betaines to that of 2-amino acids. Can N-alkyl betaines be classified as alpha amino acids (2-amino acids) ? Justify your answer.
6. Write chemical equations to describe what happens to an N-alkyl betaine in:
• acidic aqueous solution
• basic aqueous solution
7. Compare the structure of N-alkyl betaines to the surfactants found in synthetic detergents. In what ways are surfactant molecules 
• similar to N-alkyl betaines
• different from N-alkyl betaines
8. Explain how N-alkyl betaines act like 
• a cationic surfactant in acidic aqueous solution
• an anionic surfactant in basic aqueous solution
9. Consider the structure of (trimethylammonio)acetate and 2-(trimethylammonio)octadecanoate. Which molecule do you expect to be more soluble in water? Justify your answer.
10. Consider the structure of (trimethylammonio)acetate and 2-(trimethylammonio)octadecanoate. Which molecule do you expect to be more soluble in paraffin oil? Justify your answer.

Naming Esters the IUPAC Way

IUPAC naming of esters is not a bit hard, it's just a bit different to the way you name other organic molecules.

Follow AUS-e-TUTE's step-by-step guide to :

• naming esters
• drawing the structure of ester molecules
• writing the molecular formula for ester molecules

and you'll be amazed at how easily you can name, and draw the structure of, esters.

Then, when you think you've got the hang of that, why not try our ester naming game?
Or, test your skill with our ester test.
Preparing for an exam? We've got you covered! You can use our ester exam to practice your exam technique before you sit your exam.
And remember, AUS-e-TUTE's test and exam questions come with immediate feedback to help you understand where you go wrong and help you get the next question right.

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Not an AUS-e-TUTE Member?
There is currently a "free-to-view" tutorial available at http://www.ausetute.com.au/namester.html

Find out more about AUS-e-TUTE membership at : http://www.ausetute.com.au/membership.html
and you can join AUS-e-TUTE at http://www.ausetute.com.au/register.html

Amides

You spell amine with an "n" and amide with a "d", but what other differences are there?

AUS-e-TUTE has just added new resources for naming primary amides (primary alkanamides).
AUS-e-TUTE Members should log-in to use the new tutorial, game and test.

If you are not an AUS-e-TUTE Members then there is a "free-to-view" tutorial currently available for evaluation purposes at http://www.ausetute.com.au/nampamide.html

You can find out about how AUS-e-TUTE can help you improve your chemistry results at http://www.ausetute.com.au/membership.html

and when you're ready to start improving your chemistry results you can join AUS-e-TUTE at http://www.ausetute.com.au/register.html

Naming Amines

Need help to name amines?

AUS-e-TUTE has just added new resources for naming primary alkanamines (simple amines) using the preferred IUPAC system of nomenclature.
Members should log-in to use the new tutorial, game, test and exam.

Non-members can access a "free-to-view" tutorial at http://www.ausetute.com.au/nampamine.html

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Aldehydes and Ketones

Help with naming aldehydes and ketones is now available.
AUS-e-TUTE has just uploaded new resources (games, tests, tutorials) to introduce students to the preferred IUPAC system for naming alkanals (simple aldehydes) and alkanones (simple ketones).

AUS-e-TUTE members should log-in to use these new resources: http://www.ausetute.com.au

"Free-to-view" tutorials are currently available for non-members:
Naming Alkanals: http://www.ausetute.com.au/namalkanal.html
Naming Alkanones: http://www.ausetute.com.au/namalkanone.html

Information about membership is available at: http://www.ausetute.com.au/membership.html
and you can join AUS-e-TUTE at http://www.ausetute.com.au/register.html

IUPAC Nomenclature and Organic Compounds

Imagine you are sitting a Chemistry exam.
The first question on the exam paper reads,

"Name the molecule shown below:"

How would you answer this question?

My first response is to name it Molly, short for molecule ofcourse. Not a very useful name, especially if I'm asked to name another molecule later on. It might get a bit confusing if I name every molecule Molly, even when the molecules are very different from each other.

So, the International Union of Pure and Applied Chemistry (IUPAC) has developed systems for naming compounds.
For this reason, you probably won't be asked to "name" the molecule, but you might be asked to "systematically name" the molecule, or to give the "systematic IUPAC name" for the molecule.

Even for the relatively simple molecule shown above, there is more than one way to systematically name the molecule using IUPAC nomenclature rules!

You could give a systematic IUPAC name based on the functional class of the compound. This molecule belongs to the functional class known as ketones (non-terminal C=O), two methyl (CH₃) groups are attached to the carbonyl carbon atom, so, according to the IUPAC rules for functional class nomenclature, I could systematically name it as dimethyl ketone.

I could give the same molecule a different systematic IUPAC name by applying the rules of substitutive nomenclature. In this case I name the parent hydride, propane, drop the final "e" and add a suffix denoting the non-terminal C=O functional group so that I get propanone, then I add in an infix which locates the functional group along the carbon chain, with the final name propan-2-one.

Because this is a simple molecule with just one functional group, I could use the infix as a prefix, so that the systematic IUPAC name would become 2-propanone. Or, because there is only one position for the C=O functional group to be in if this molecule is to be a ketone, I could drop the infix altogether and just systematically name the molecule as propanone.

So, some of the possible systematic IUPAC names for this molecule are:

• dimethyl ketone
• propan-2-one
• 2-propanone
• propanone

Because molecules can be named systematically in more than one way, there is a recommendation to adopt "preferred IUPAC names", or PINs. Usually the Preferred IUPAC Name is arrived at by using one of the recognized IUPAC systems for nomenclature, but not always.

If you were asked to give the Preferred IUPAC Name for the molecule shown above, the correct answer would be acetone ("Preferred names in the nomenclature of organic compounds" (Draft 7 October 2004) page 9), or, possibly propan-2-one ("Preferred names in the nomenclature of organic compounds" (Draft 7 October 2004) page 374). Acetone is the traditional name for this compound, literally meaning 'derived from acetic acid', and has been in use for more than 200 years, which is probably why the IUPAC would consider retaining the name "acetone" as the Preferred IUPAC Name for this compound.

Further Reading:
Introduction to Naming Organic Compounds

PBDEs

Polybrominated diphenyl ethers, PBDEs, have been used as flame retardants in many common household products such as blankets, couches, food wrappers, as well as in motor vehicles and airplanes.
A diphenyl ether molecule has the following structure:

One of the polybrominated diphenyl ether compounds is 2,2',4,4',5-pentabromodiphenyl ether and it has following structure
There are 209 possible substances which are included in the family of polybrominated diphenyl ethers (PBDEs) and these are called congeners. Congeners include dibromodiphenyl ethers, tribromodiphenyl ethers, tetrabromodiphenyl ethers, pentabromodiphenyl ethers, hexabromodiphenyl ethers, heptabromodiphenyl ethers, octabromodiphenyl ethers, nonabromodiphenyl ethers and decabromodiphenyl ethers.

PBDEs with 1-5 bromine atoms per molecule are considered to be more dangerous than PBDEs with more bromine atoms per molecules because they are more efficient at accumulating in living things. In humans they effect hormone levels in the thyroid which can lead to alterations in behaviour. Studies have shown that children in developed countries have higher levels of blood PBDEs than adults, ranging from 24 to 114 parts per billion.

Most PBDEs have either been banned or are in the process of being phased out, eg,:

• Penta and octa PBDEs are no longer manufactured in the USA because of the health risks while the European Union banned their use in 2004.
• Deca PBDE has commonly been used in the electronics industry but has now been banned in Europe.

There is, however, growing concern that PBDEs may have a long environmental life.

Reference
Crystal Y. Usenko, Eleanor M. Robinson, Sascha Usenko, Bryan W. Brooks, Erica D. Bruce. PBDE developmental effects on embryonic zebrafish. Environmental Toxicology and Chemistry, 2011; DOI: 10.1002/etc.570

Further Reading
Nomenclature
Haloalkanes
Structural Isomers
Functional Groups
Percentage Composition
Parts per Million Concentration

Study Questions

1. For the diphenyl ether molecule:
   • identify the ether functional group
   • give the molecular formula
   • calculate the molecular mass (formula weight)
   • calculate the percentage composition
2. For the 2,2',4,4',5-pentabromodiphenyl ether molecule:
   • identify the ether functional group
   • give the molecular formula
   • calculate the molecular mass (formula weight)
   • calculate the percentage composition
3. How many bromine atoms would be found in a molecule of each of the following:
   
   • dibromodiphenyl ether
   • tribromodiphenyl ether
   • tetrabromodiphenyl ether
   • pentabromodiphenyl ether
   • hexabromodiphenyl ether
   • heptabromodiphenyl ether
   • octabromodiphenyl ether
   • nonabromodiphenyl ether
   • decabromodiphenyl ether
4. Draw one structural isomer of each of the molecules above.
5. Name each of the molecules you have drawn in question 4 above.
6. Give the molecular formula for the molecules you have drawn that have been considered to be the least dangerous.
7. The blood of a child is found to have 70ppb PBDE. Convert this to:
   • ppm
   • mg/g
   • g/L
8. Assuming the child above has 4.7L of blood in his/her body, calculate the mass of PBDE present.
9. In the USA, the EPA set a "safe" limit of 7 micrograms per kilogram of body weight for PBDE. If the child above has a mass of 18kg, is the amount of PBDE in his/her blood considered safe? 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?