Mass Spectroscopy and Organic Molecules

What happens when an organic chemist makes a new molecule?
How do they know what the structure of the new molecule is?
They use lots of different techniques to determine the molecular mass and structure of the new molecule, one of which is mass spectroscopy.
Mass spectroscopy tells you the molecular mass of the molecule, and, it gives a good indication of how the atoms making up the molecule are put together. And it does this by breaking the molecule up!
Find out more about how mass spectroscopy can be used to determine the structure of organic molecules in our tutorial
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pH of Weak Acid After Dilution

What happens to the pH of a solution of weak acid, such as acetic acid, if you dilute it by adding water to it?
How much water would you have to add to 100 mL of 0.20 mol L^-1 acetic acid in order to make a solution with a pH of 3.0 ?
What is the pH of 1 × 10^-11 mol L^-1 acetic acid?
AUS-e-TUTE can help you answer these questions with our new resources.
AUS-TUTE Members should log-in to access the new "pH of Weak Acid After Dilution" tutorial, game and test (with worked solutions).
A "free-to-view" tutorial is currently available for non-members at:
https://www.ausetute.com.au/phdilwa.html

pH after mixing acid and base

If you add enough strong base to a strong acid you can neutralise the solution and its pH will be 7.
But what if you don't add enough base to the acid.
Will the solution be neutral?
Will the pH of the solution be 7?
These are all very good questions which is why AUS-e-TUTE has just added a new tutorial, game, test and exam on this topic.
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Effect of Dilution on pH of Strong Acid Solution

Need to know what the pH of your hydrochloric acid is after you dilute it?
Need to know how much water to add to your hydrochloric acid to make a solution with a particular pH?
AUS-e-TUTE has just added a new tutorial, game, test and exam to help you with this.
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If you're not an AUS-e-TUTE Member, there is a "free-to-view" tutorial currently available at https://www.ausetute.com.au/phdilsa.html

Water-Soluble Plastic

I buy boxes of dishwasher detergent containing plastic bags filled with the detergent. I place these bags straight into the dishwasher. When the dishes are clean and I remove them from the machine there is no trace of either detergent or the plastic bag that held it.

What happened to the plastic bag?

Can plastic dissolve in water?

Find out in the December 2018 edition of AUS-e-NEWS, AUS-e-TUTE's free, quarterly, newsletter for chemistry students and teachers. 

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Gibbs Free Energy of Formation

You can use standard enthalpy change (ΔH°) and standard absolute entropy (S°) data to calculate the change in Gibbs free energy (ΔG°) for a chemical reaction or physical change using the equation:

 ΔG° = ΔH° - TΔS°

... OR ....
you can use tables of values for the standard Gibbs free energy of formation of compounds (ΔG_ƒ°).
For a chemical reaction or physical change:

reactants → products 

ΔG° = ΣΔG_ƒ°(products) - ΣΔG_ƒ°(reactants)

If you would like to understand where this comes from and how it can be applied solve problems in chemistry, visit our new tutorial Standard Gibbs Free Energy of Formation Calculations

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Effect of Temperature on GIbbs Free Energy

Imagine a reaction in which you decompose liquid water to produce oxygen gas and hydrogen gas:

H₂O_(l) → H_2(g) + ½O_2(g)

The reaction is endothermic, ΔH > 0, and the change in entropy is also positive, ΔS > 0
At room temperature and pressure this reaction is not spontaneous ( ΔG > 0).
But could I heat, or cool, the reaction sufficiently to make the reaction spontaneous?
Can I turn a nonspontaneous reaction into a spontaneous reaction by changing the temperature?
Want to know?
Go to https://www.ausetute.com.au/gibbstemp.html

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Gibbs Free Energy Calculations

For a chemical system, either a chemical reaction or a physical change, at a constant temperature and pressure we define a function called the Gibbs Free Energy (G) so that we can determine whether the system will be spontaneous or non-spontaneous:

• spontaneous if ΔG < 0 (ΔG is negative)
• non-spontaneous if ΔG > 0 (ΔG is positive)

In this new tutorial we will calculate the change in Gibbs free energy of a reaction at constant temperature and pressure (ΔG) using:

• standard absolute entropy of each reactant and product (S°)
• standard enthalpy of formation of each reactant and product (ΔH_ƒ°)

For a chemical system under standard conditions, we can calculate the change in standard Gibbs free energy using the equation shown below:

ΔG° = ΔH° - TΔS°

AUS-e-TUTE members can access the new Gibbs free energy calculations tutorial, game, test and exam when they log-in (Go to Physical Chemistry Heading, then "Thermodynamics").

If you are not an AUS-e-TUTE member, there is a "free-to-view" Gibbs free energy calculations tutorial currently available for evaluation purposes at https://www.ausetute.com.au/gibbscalc.html

Calculating Entropy Changes

If you stick some clean reactive metal, like magnesium, into an aqueous solution of hydrochloric acid... Hey presto! Bubbles of hydrogen gas! This gas production is a dead giveaway that the entropy of the system has increased.
But what if all the reactants and products are soluble in water and the entire chemical process occurs in aqueous solution. Has the entropy of the system increased or decreased?
Thankfully, chemists have a tool they can use to make quantitative predictions about the changes in entropy of a chemical system (ΔS). This tool is called the Standard Absolute Entropy (S°), and we have just added a new tutorial, game, test and exam to help you understand what this is and how it can be used.
AUS-e-TUTE Members should log-in to access the new resources under the heading "Thermodynamics".
If you are not already an AUS-e-TUTE there is a "free-to-view" tutorial currently available at https://www.ausetute.com.au/entropychange.html

Bleach

Lurking in my laundry cupboard is an opaque, plastic bottle containing bleach. I use it to whiten white clothes when they start to look a bit grey, but I also use it to clean blood stains, to remove mildew from walls and ceilings, and to remove the mould from bathroom tiles. The active ingredient in laundry bleach is sodium hypochlorite, NaOCl, and you will find a similar substance present in the "liquid chlorine" you add to swimming pools as a disinfectant.

Sodium hypochlorite is a very useful chemical, but it can also be dangerous if used incorrectly. 

The September 2018 issue of AUS-e-NEWS, AUS-e-TUTE's free quarterly newsletter for chemistry students and teachers, looks at the chemistry of bleach.

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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).

Name and Formula of Inorganic Molecules

Non-metallic elements combine to produce covalent compounds, that is, molecules in which the atoms are held together by covalent bonds.
But do you know how to name these molecules using IUPAC recommendations?
Can you write the formula for these molecules using IUPAC recommendations?

AUS-e-TUTE has just added new resources on these topics.
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If you are not an AUS-e-TUTE member, there are two "free-to-view" tutorials currently available:

Naming Binary Inorganic Non-metallic Compounds

Molecular Formula of Binary Inorganic Non-metallic Compounds

Explosive Medicine

You’ve probably heard of Alfred Nobel, the inventor of dynamite and gelignite. The commercialisation of these explosives enabled him to accumulate great wealth during his lifetime which, by the terms of his will signed in 1895, was used to establish the Nobel Prize. In later life he was prescribed Trinitrin, a medication used to relieve a heart condition known as angina.

What do dynamite, gelignite and Trinitrin all have in common?

They all contain nitroglycerin!

This is not a story about the life of Alfred Nobel.

It is a story about the fascinating chemistry of nitroglycerin…

Read more in the June 2018 issue of AUS-e-NEWS, AUS-e-TUTE's free quarterly newsletter for chemistry students and teachers.

Subscribe to AUS-e-NEWS at https://www.ausetute.com.au/ausenews.html

Writing the Formula of an Inorganic Salt

Organic chemistry deals with compounds of carbon.
Inorganic chemistry deals with compounds of any other element.
One of the earliest known classes of inorganic compounds were salts.
Salts are binary, ionic compounds, that is, salts are made up of two ions:

• a positively charged ion called a cation
• a negatively charged ion called an anion 

The International Union of Pure and Applied Chemistry (IUPAC) is establishing rules to help us name, and write the formula, for compounds.
In an earlier tutorial we looked at how we name inorganic salts, in this tutorial we look at how to write the formula of an inorganic salt.

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 Anions

How do you write the formula of an anion?
How do you use IUPAC nomenclature to name an anion?
AUS-e-TUTE has new resources to help you understand this and to help you apply these rules to writing formula and names of anions.
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If you are not a member then you can access a "free-to-view" tutorial at
https://www.ausetute.com.au/anions.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

Gibbs Free Energy and Spontaneity of Reactions

Whether or not a chemical reaction proceeds in a particular direction depends on a balance between the enthalpy of the system and its entropy.
Gibbs Free Energy allows us to quantify this relationship, and determine whether a particular reaction will be spontaneous.
AUS-e-TUTE members can now access a new tutorial, game, test and exam on this topic.
Not a member?
There is a "free-to-view" tutorial currently available at http://www.ausetute.com.au/freeenergy.html

Sodium Bicarbonate

One of the single most useful and versatile chemicals I have in my kitchen pantry is a box of sodium bicarbonate, also known as baking soda or bicarbonate of soda.
Read the March 2018 issue of AUS-e-NEWS to find out what makes this compound so special.

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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.

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)



Reference:

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: http://www.ausetute.com.au/namctut1.html
Introduction to functional groups: http://www.ausetute.com.au/fungroup.html
Fatty acids: http://www.ausetute.com.au/fattyacid.html 
Structure and properties of carboxylic acids: http://www.ausetute.com.au/carboxyl.html
Molecular formula: http://www.ausetute.com.au/molecularformula.html
2-Dimensional structural formula: http://www.ausetute.com.au/structural2D.html
Condensed structural formula: http://www.ausetute.com.au/condensedsf.html
Skeletal structural formula: http://www.ausetute.com.au/skeletal.html
Cis-trans isomers: http://www.ausetute.com.au/cistranso.html 


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.