Tonight Is #BurnsNight2021, Which Is Always A Good Reason To Share This Graphic On The Chemistry Of Whisky!

It’s World Sleep Day

Log off.

Go back to bed.

Follow @productive-tips for more tips and content like this posted daily! Handpicked and curated with love :)

Around a year ago, scientists determined the structure of the SARS-CoV-2 spike protein. Here’s a look at how it was done and how it helped the fight against #COVID19 in the latest edition of #ChemVsCOVID with the Royal Society of Chemistry: https://ift.tt/3pZiZe9 https://ift.tt/3002NPh

The latest edition of #PeriodicGraphics in C&EN looks at some fruits and vegetables which we might not consider dangerous, but which can, in some cases, contain unwelcome natural toxins: https://ift.tt/3fNzwOE https://ift.tt/2K60CoM

Nomenclature - what in the organic chemistry is it?

Organic chemistry is so widely studied it requires a standard system for naming compounds, developed by IUPAC. Nomenclature is simply naming these organic compounds.

So, you want to be an organic chemist? Well, it starts here. Are you ready?

(psst… once you’ve learnt this theory, try a quiz here!)

1. Count your longest continuous chain of carbons.

Bear in mind that some chains may be bent. You’re looking for the longest chain of subsequent carbon atoms. This number correlates to root names that indicate the carbon chain length, listed below:

The second part of naming your base comes from the bonding in the chain. Is it purely single bonds or are there double bonds in there? If you are familiar with carbon chemistry, you’ll know that saturated hydrocarbons are called alkanes and unsaturated hydrocarbons are called alkenes. Therefore, the syllable -ane is used when it has only single bonds and the syllable -ene is used when it has some double bonds. For example:

Sometimes carbon chains exist in rings rather than chains. These have the prefix of -cyclo.

2. Identify your side chains attached to this main carbon and name them.

Side chains are added as prefixes to the root names. Sometimes called substituents, these are basically anything that comes off the carbon chain. Examples of the prefixes are listed below:

There are other prefixes such as fluoro (-F) and chloro (-Cl) which can describe what is coming off the chain.

3. Identify where each side chain is attached and indicate the position by adding a number to the name. 

We aim to have numbers as small as possible. For example, if bromine is on the second carbon of a 5-carbon saturated chain, we number it as 2-bromopentane instead of 4-bromopentane, since it would essentially be 2-bromopentane if it was flipped. Locant is the term used for the number which describes the position of the substitute group, e.g. the ‘2′ in 2-chlorobutane is the locant.

Sometimes there are two or more side chains e.g. a methyl group and a chlorine attached to a pentane. In these cases, these rules apply:

1. Names are written alphabetically.

2. A separate number is needed for each side chain or group.

3. Hyphens are used to separate numbers and letters.

This would be named 2-chloro-3-methyl-pentane. This is because the longest chain of carbons is 5 (pentane), the chlorine is on the second carbon (2-chloro) and the methyl group is on the third carbon (3-methyl). It is 2-chloro rather than 4-chloro as we aim to have as small as numbers as possible.

Another variation of this step to be aware of is how many of the same side chains or groups there are, for example, having two methyl groups would be dimethyl rather than solely methyl. Each group must also be given numbers separated by commas to show where each one is located. 

The list of these prefixes is found here:

Convention does not usually require mono- to go before a single group or side chain.

4. Number the positions of double bonds if applicable.

Alkenes and other compounds have double bonds. These must be indicated with numbers. For example, pent-2-ene shows that the double bond is between carbon 2 and carbon 3. The number goes in the middle of the original root name e.g. butene, pentene.

(!) Below is a list of functional groups that you may need to study for the AS and A Level chemistry exams. “R” represents misc. carbons. It is important to know that some groups are more prioritised than naming. From the most to least priority: carboxylic acid, ester, acyl chloride, nitrile, aldehyde, ketone, alcohol, amine, alkene, halogenalkane. It is worthwhile learning these.

bigger version here (I suggest downloading and printing it)

But wait, there’s more:

Here are some things to bear in mind when naming organic compounds:

1. The letter ‘e’ is removed when there are two vowels together e.g. propanone rather than propaneone. The ‘e’ isn’t removed when it is next to consonant, e.g. propanenitrile isn’t propannitrile.

2. When compounds contain two different, one is named as part of the unbranched chain and the other is named as a substituent. Which way round this goes depends on the priority. 

SUMMARY

Count your longest continuous chain of carbons.

Chains may be bent. You’re looking for the longest chain of subsequent carbon atoms. This number correlates to root names that indicate the carbon chain length, e.g. pentane.

The second part of naming your base comes from the bonding in the chain. Is it purely single bonds or are there double bonds in there? The syllable -ane is used when it has only single bonds and the syllable -ene is used when it has some double bonds.

Rings have the prefix of -cyclo.

Identify your side chains attached to this main carbon and name them.

Side chains are added as prefixes to the root names. Sometimes called substituents, these are basically anything that comes off the carbon chain. 

There are other prefixes such as fluoro (-F) and chloro (-Cl) which can describe what is coming off the chain.

Identify where each side chain is attached and indicate the position by adding a number to the name.

We aim to have numbers as small as possible. Locant is the term used for the number which describes the position of the substitute group, e.g. the ‘2′ in 2-chlorobutane is the locant.

Sometimes there are two or more side chains e.g. a methyl group and a chlorine attached to a pentane. In these cases, names are written alphabetically, a separate number is needed for each side chain or group and hyphens are used to separate numbers and letters.

When there are two or more of the same side chains or substituent groups, these must also be given numbers separated by commas to show where each one is located.

Number the positions of double bonds if applicable.

Alkenes and other compounds have double bonds. These must be indicated with numbers. The number goes in the middle of the original root name e.g. butene, pentene.

It is worthwhile learning the other functional groups that can be added on.They have varying priorities.

The letter ‘e’ is removed when there are two vowels together e.g. propanone rather than propaneone. The ‘e’ isn’t removed when it is next to consonant, e.g. propanenitrile isn’t propannitrile.

When compounds contain two different, one is named as part of the unbranched chain and the other is named as a substituent. Which way round this goes depends on the priority.

Happy studying guys!

Enthalpy - a thermodynamic property

When I first learned about enthalpy, I was shocked - it felt more like a physics lesson than a chemistry lesson. The thought of learning more about thermodynamics than my basic understanding from my many science lessons in lower school made me bored out of my mind. But enthalpy is actually pretty interesting, once you get your head around it…

Reactions which release heat to their surroundings are described to be exothermic. These are reactions like combustion reactions, oxidation reactions and neutralisation reactions. Endothermic reactions take in heat from their surroundings, such as in thermal decomposition. Reversible reactions are endothermic in one direction and exothermic in the other.

These facts are important when you start to look at enthalpy. Enthalpy is basically a thermodynamic property linked to internal energy, represented by a capital H. This is pretty much the energy released in bond breaking and made in bond making. We usually measure a change in enthalpy, represented by ∆H.  ∆H = enthalpy of the products (H1) - enthalpy of the reactants (H2). This is because we cannot measure enthalpy directly.

In exothermic reactions,  ∆H is negative whereas in endothermic reactions,  ∆H is positive.

∆H is always measured under standard conditions of 298K and 100kPa. 

In reversible reactions, the ∆H value is the same numerical value forwards and backwards but the sign is reversed. For example, in a forward exothermic reaction, the  ∆H value would be -ve but in the backwards reaction (endothermic) the  ∆H would be +ve. 

Reaction profiles are diagrams of enthalpy levels of reactants and products in a chemical reaction. X axis is enthalpy rather than ∆H and the Y axis is the progress of reaction, reaction coordinate or extent of reaction. Two horizontal lines show the enthalpy of reactants and products with the reactants on the left and the products on the right. These should be labelled with their names or formulae. 

In an endothermic reaction, product lines are higher enthalpy values than reactants. In an exothermic reaction, product lines are lower enthalpy values than reactants. The difference between product and reactant lines is labelled as  ∆H. Values are measured in kJ mol-1. 

Reaction pathways are shown with lines from the reactants to the products on enthalpy level diagrams. This shows the “journey” that the enthalpy takes during a reaction. They require an input of energy to break bonds before new bonds can form the products. The activation energy is the peak of the pathway above the enthalpy of reactants. It is the minimum amount of energy that reactants must have to react. 

Standard enthalpy values are the ∆H values for enthalpy changes of specific reactions measured under standard conditions, represented by ⊖. There are three of these:

1. Standard enthalpy of reaction ( ΔHr⊖ )

The enthalpy change when substances react under standard conditions in quantities given by the equation for the reaction.

2. Standard enthalpy of formation ( ΔfH⊖ )

The enthalpy change when 1 mole of a compound is formed from its constitutent elements with all reactants and products in standard states under standard conditions.

The enthalpy of formation for an element is zero is it is in it’s standard state for example, O2 enthalpy is zero.

3. Standard enthalpy of combustion ( ΔcH⊖ )

The enthalpy change when 1 mole of a substance is burned completely in excess oxygen with all reactants and products in their standard states under standard conditions.

Values for standard enthalpy of formation and combustion must be kept to per mole of what they refer.

Summary

Reactions which release heat to their surroundings are described to be exothermic. Endothermic reactions take in heat from their surroundings, such as in thermal decomposition. 

Reversible reactions are endothermic in one direction and exothermic in the other.

Enthalpy is a thermodynamic property linked to internal energy, represented by a capital H. We usually measure a change in enthalpy, represented by ∆H. 

 ∆H = enthalpy of the products (H1) - enthalpy of the reactants (H2). We cannot measure enthalpy directly.

In exothermic reactions,  ∆H is negative whereas in endothermic reactions,  ∆H is positive.

∆H is always measured under standard conditions of 298K and 100kPa. 

In reversible reactions, the ∆H value is the same numerical value forwards and backwards but the sign is reversed. 

Reaction profiles are diagrams of enthalpy levels of reactants and products in a chemical reaction. They 

In an endothermic reaction, product lines are higher enthalpy values than reactants. In an exothermic reaction, product lines are lower enthalpy values than reactants.

 The difference between product and reactant lines is labelled as  ∆H. 

Values are measured in kJ mol-1.

Reaction pathways are shown with lines from the reactants to the products on enthalpy level diagrams. They plot enthalpy against reaction progress.

Reactions require an input of energy to break bonds before new bonds can form the products. The activation energy is the peak of the pathway above the enthalpy of reactants. It is the minimum amount of energy that reactants must have to react.

Standard enthalpy values are the ∆H values for enthalpy changes of specific reactions measured under standard conditions, represented by ⊖. 

Standard enthalpy of reaction ( ΔHr⊖ ) is the enthalpy change when substances react under standard conditions in quantities given by the equation for the reaction.

Standard enthalpy of formation ( ΔfH⊖ ) is the enthalpy change when 1 mole of a compound is formed from its constitutent elements with all reactants and products in standard states under standard conditions.

The enthalpy of formation for an element is zero is it is in it’s standard state.

Standard enthalpy of combustion ( ΔcH⊖ ) is the enthalpy change when 1 mole of a substance is burned completely in excess oxygen with all reactants and products in their standard states under standard conditions.

Values for standard enthalpy of formation and combustion must be kept to per mole of what they refer.

Happy studying!

Happy #StPatricksDay2021! Ever wondered why the bubbles in Guinness appear to fall rather than rise, and what causes its dark colour? This graphic in C&EN has the answers! https://ift.tt/2WfNI8j https://ift.tt/3rY7DIW

Combusting Alkanes

If you follow this blog, by now you must be thinking, when will we be done with the alkane chemistry? Well, the answer is never. There is still one more topic to touch on - burning alkanes and the environmental effects. Study up chums!

Alkanes are used as fuels due to how they can combust easily to release large amounts of heat energy. Combustion is essentially burning something in the presence of oxygen. There are two types of combustion: complete and incomplete. 

Complete combustion occurs when there is a plentiful supply of air. When an alkane is burned in sufficient oxygen, it produces carbon dioxide and water. How much depends on what is being burnt. For example:

butane + oxygen -> carbon dioxide + water

2C4H10 (g) + 13O2 (g) -> 8CO2 (g) + 10H2O (g)

Remember state symbols in combustion reactions. In addition, this reaction can be halved to balance for 1 mole of butane by using fractions when dealing with the numbers.

C4H10 (g) + 6 ½ O2 (g) -> 4CO2 (g) + 5H2O (g)

Incomplete combustion on the other hand occurs when there is a limited supply of air. There are two kinds of incomplete combustion. The first type produces water and carbon monoxide. 

butane + limited oxygen -> carbon monoxide + water

C4H10 (g) + 4 ½ O2 (g) -> 4CO (g) + 5H2O (g)

Carbon monoxide is dangerous because it is toxic and undetectable due to being smell-free and colourless. It reacts with haemoglobin in your blood to reduce their oxygen-carrying ability and can cause drowsiness, nausea, respiratory failure or death. Applicances therefore must be maintained to prevent the formation of the monoxide.

The other kind of incomplete combustion occurs in even less oxygen. It produces water and soot (carbon).

butane + very limited oxygen -> carbon + water

C4H10 (g) + 2 ½ O2 (g) -> 4C (g) + 5H2O (g)

Internal combustion engines work by changing chemical energy to kinetic energy, fuelled by the combustion of alkane fuels in oxygen. When this reaction is undergone, so do other unwanted side reactions due to the high pressure and temperature, e.g. the production of nitrogen oxides.

Nitrogen is regularly unreactive but when combined with oxygen, it produces NO and NO2 molecules:

nitrogen + oxygen -> nitrogen (II) oxide

N2 (g) + O2 (g) -> 2NO (g)

and

nitrogen + oxygen -> nitrogen (II) oxide

N2 (g) + 2O2 (g) -> 2NO2 (g)

Sulfur dioxide (SO2) is sometimes present in the exhaust mixture as impurities from crude oil. It is produced when sulfur reacts with oxygen. Nitrogen oxides, carbon dioxide, carbon monoxide, carbon particles, unburnt hydrocarbons, water vapour and sulfur dioxide are all produced in exhaust fumes and are also pollutants that cause problems you need to be aware of for the exam as well as how to get rid of them.

Greenhouse gases contribute to global warming, an important process where infrared radiation from the sun is prevented from escaping back into space by atmospheric gases. On the one hand, some greenhouse gases need to continue this so that the earth can sustain life as it traps heat, however, we do not want the earth’s temperature to increase that much. Global warming is the term given to the increasing average temperature of the earth, which has seen an increase in the last few years due to human activity - burning fossil fuels like alkanes has produced more gases which trap more heat. Examples of greenhouse gases include carbon dioxide, methane and water vapour.

Another pollution problem the earth faces is acid rain. Rain water is already slightly acidic due to the CO2 present in the atmosphere but acid rain is more acidic than this. Nitrogen oxides contribute to acid rain although sulfur dioxide is the main cause. The equation for sulfur dioxide reacting with water in the air to produce oxidised sulfurous acid and therefore sulphuric acid is:

SO2 (g) + H2O (g) + ½ O2 (g) -> H2SO4 (aq)

Acid rain is a problem because it destroys lakes, buildings and vegetation. It is also a global problem because it can fall far from the original source of the pollution.

Photochemical smog is formed from nitrogen oxides, sulfur dioxide and unburnt hydrocarbons that react with sunlight. It mostly forms in industralised cities and causes health problems such as emphysema.

So what can we do about the pollutants?

A good method of stopping pollution is preventing it in the first place, therefore cars have catalytic converters which reduce the amount of carbon monoxide, nitrogen oxides and unburnt hydrocarbons come into the atmosphere by converting them into less toxic gases. Shaped like a honeycomb for increased SA and therefore rate of conversion, platinum and rhodium coat ceramic and act as catalysts for the reactions that take place in an internal combustion engine.

As they pass over the catalyst, they react with each other to form less pollution:

octane + nitrogen (II) oxide -> carbon dioxide + nitrogen + water

C8H18 (g) + 25NO -> 8CO2 (g) + 12 ½ N2 (g) + 9H2O (g)

nitrogen (II) oxide + carbon monoxide  -> carbon dioxide + nitrogen

2NO (g) + 2CO (g) -> 2CO2 (g) + N2 (g)

Finally, sulfur dioxide must be dealt with. The first way it is dealt with is by removing it from petrol before it can be burnt, however, this is often not economically favourable for fuels used in power stations. A process called flue gas desulfurisation is used instead.

In this, gases are passed through a wet semi-solid called a slurry that contains calcium oxide or calcium carbonate. These neutralise the acid, due to being bases, to form calcium sulfate which has little commercial value but can be oxidised to produce a more valuable construction material.

calcium oxide + sulfur dioxide -> calcium sulfite

CaO (s) + SO2 (g) -> CaSO3 (s)

calcium carbonate + sulfur dioxide -> calcium sulfite + carbon dioxide

CaCO3 (s) + SO2 (g) -> CaSO3 (s) + CO2 (g)

calcium sulfite + oxygen -> calcium sulfate

CaSO3 (s) + O -> CaSO4 (s)

SUMMARY

Alkanes are used as fuels due to how they can combust easily to release large amounts of heat energy. Combustion is essentially burning something in the presence of oxygen.

Complete combustion occurs when there is a plentiful supply of air. When an alkane is burned in sufficient oxygen, it produces carbon dioxide and water

Remember state symbols in combustion reactions. In addition, reactions can be halved to balance for 1 mole of compounds by using fractions when dealing with the numbers.

Incomplete combustion occurs when there is a limited supply of air. There are two kinds of incomplete combustion. 

The first type produces water and carbon monoxide.

Carbon monoxide is dangerous because it is toxic and undetectable due to being smell-free and colourless. It reacts with haemoglobin in your blood to reduce their oxygen-carrying ability and can cause drowsiness, nausea, respiratory failure or death. 

The other kind of incomplete combustion occurs in even less oxygen. It produces water and soot (carbon).

Internal combustion engines work by changing chemical energy to kinetic energy, fuelled by the combustion of alkane fuels in oxygen. When this reaction is undergone, so do other unwanted side reactions due to the high pressure and temperature, e.g. the production of nitrogen oxides.

Nitrogen is regularly unreactive but when combined with oxygen, it produces NO and NO2 molecules:

Sulfur dioxide (SO2) is sometimes present in the exhaust mixture as impurities from crude oil. It is produced when sulfur reacts with oxygen.

Nitrogen oxides, carbon dioxide, carbon monoxide, carbon particles, unburnt hydrocarbons, water vapour and sulfur dioxide are all produced in exhaust fumes and are also pollutants that cause problems you need to be aware of for the exam as well as how to get rid of them.

Greenhouse gases contribute to global warming, an important process where infrared radiation from the sun is prevented from escaping back into space by atmospheric gases. Some greenhouse gases need to continue this so that the earth can sustain life as it traps heat, however, we do not want the earth’s temperature to increase that much. Global warming is the term given to the increasing average temperature of the earth, which has seen an increase in the last few years due to human activity - burning fossil fuels like alkanes has produced more gases which trap more heat. 

Another pollution problem the earth faces is acid rain. Nitrogen oxides contribute to acid rain although sulfur dioxide is the main cause. 

Acid rain is a problem because it destroys lakes, buildings and vegetation. It is also a global problem because it can fall far from the original source of the pollution.

Photochemical smog is formed from nitrogen oxides, sulfur dioxide and unburnt hydrocarbons that react with sunlight. It mostly forms in industralised cities and causes health problems such as emphysema.

A good method of stopping pollution is preventing it in the first place, therefore cars have catalytic converters which reduce the amount of carbon monoxide, nitrogen oxides and unburnt hydrocarbons come into the atmosphere by converting them into less toxic gases. Shaped like a honeycomb for increased SA and therefore rate of conversion, platinum and rhodium coat ceramic and act as catalysts for the reactions that take place in an internal combustion engine.

As they pass over the catalyst, they react with each other to form less pollution.

octane + nitrogen (II) oxide -> carbon dioxide + nitrogen + water

C8H18 (g) + 25NO -> 8CO2 (g) + 12 ½ N2 (g) + 9H2O (g)

nitrogen (II) oxide + carbon monoxide  -> carbon dioxide + nitrogen

2NO (g) + 2CO (g) -> 2CO2 (g) + N2 (g)

Finally, sulfur dioxide must be dealt with. The first way it is dealt with is by removing it from petrol before it can be burnt, however, this is often not economically favourable for fuels used in power stations. A process called flue gas desulfurisation is used instead.

In this, gases are passed through a wet semi-solid called a slurry that contains calcium oxide or calcium carbonate. Since they are bases, these neutralise the acid to form calcium sulfate which has little commercial value but can be oxidised to produce a more valuable construction material.

Happy studying!

It’s #NationalCabbageDay! Cabbages aren’t just good for eating – you can make a colourful pH indicator from them, too 🧪 https://ift.tt/39JT2ro https://ift.tt/2LXZWTq