Covalent And Dative Bonds

Halogenoalkanes

Halogenoalkanes are a homologous series of saturated carbon compounds that contain one or more halogen atoms. They are used as refrigerants, solvents, flame retardants, anaesthetics and pharmaceuticals but their use has been restricted in recent years due to their link to pollution and the destruction of the ozone layer.  

They contain the functional group C-X where X represents a halogen atom, F,Cl, Br or I. The general formula of the series is CnH2n+1X.

The C-X bond is polar because the halogen atom is more electronegative than the C atom. The electronegativity decreases as you go down group 7 therefore the bond becomes less polar. Flourine has a 4.0 EN whereas iodine has a 2.5 EN meaning it is almost non-polar.

The two types of intermolecular forces between halogenoalkane molecules are Van Der Waals and permanent dipole-dipole interactions. As the carbon chain length increases, the intermolecular forces (due to VDWs) increase as the relative atomic mass increases due to more electrons creating induced dipoles. Therefore the boiling point of the halogenoalkanes increases since more forces must be broken.  

Branched chains have lower boiling points than chains of the same length and halogen because the VDWs are working across a greater distance and are therefore weaker.

When the carbon chain length is kept the same, but the halogen atom is changed, despite the effect of the changing polar bond on the permanent dipole-dipole interactions, the changing VDWs have a greater effect on the boiling point. Therefore as RAM increases, the boiling point increases meaning an iodoalkane has a greater boiling point than a bromoalkane if they have the same carbon chain length.  

Halogenoalkanes are insoluble or only slightly soluable in water despite their polar nature. They are soluble in organic solvents such as ethanol and can be used as dry cleaning agents because they can mix with other hydrocarbons.

Summary

Halogenoalkanes are saturated carbon compounds with one or more halogen atoms. Their general formula is CnH2n+1X, where X is a halogen. Their functional group is therefore C-X.

They are used as refrigerants, solvents, pharmaceuticals and anaesthetics but have been restricted due to their link to the depletion of the ozone layer.

C-X bonds are polar due to the halogen being more electronegative than the carbon. The polarity of the bond decreases down group 7.

Van der Waals and permanent dipole-dipole interactions are the intermolecular forces in halogenoalkanes.

When carbon chain length increases, boiling points increase due to RAM increasing and the number of Van Der Waals increasing too.

In branched halogenoalkanes, Van Der Waals are working across a greater distance therefore attraction is weaker and boiling points are lower than an identical unbranched chain.

When the halogen is changed, the boiling point increases down the group due to the effect of a greater RAM  - more VDWs mean more intermolecular forces to break.  

Halogenoalkanes are insoluble in water but soluble in organic solvents like ethanol.

Bonus: free radical substitution reactions in the ozone layer

Ozone, O3, is an allotrope of oxygen that is usually found in the stratosphere above the surface of the Earth. The ozone layer prevents harmful rays of ultraviolet light from reaching the Earth by enhancing the absorption of UV light by nitrogen and oxygen. UV light causes sunburn, cataracts and skin cancer but is also essential in vitamin D production. Scientists have observed a depletion in the ozone layer protecting us and have linked it to photochemical chain reactions by halogen free radicals, sourced from halogenoalkanes which were used a solvents, propellants and refrigerants at the time.  

CFCs cause the greatest destruction due to their chlorine free radicals. CFCs – chloroflouroalkanes – were once valued for their lack of toxicity and their non-flammability. This stability means that they do not degrade and instead diffuse into the stratosphere where UV light breaks down the C-Cl bond and produces chlorine free radicals.

RCF2Cl UV light —> RCF2● + Cl●

Chlorine free radicals then react with ozone, decomposing it to form oxygen.

Cl● + O3 —> ClO● + O2

Chlorine radical is then reformed by reacting with more ozone molecules.

ClO● + O3 —-> 2O2 + Cl●

It is estimated that one chlorine free radical can decompose 100 000 molecules of ozone. The overall equation is:

2O3 —-> 3O2

200 countries pledged to phase of the production of ozone depleting agents in Montreal, leading to a search for alternatives. Chemists have developed and synthesised alternative chlorine-free compounds that do not deplete the ozone layer such as hydroflurocarbons (HFCs) like trifluromethane, CHF3.

SUMMARY

Ozone, found in the stratosphere, protects us from harmful UV light which can cause cataracts, skin cancer and sunburn.  

Ozone depletion has been linked to the use of halogenoalkanes due to their halogen free radicals.  

CFCs were good chemicals to use because they have low toxicity and were non-flammable. The fact they don’t degrade means they diffuse into the stratosphere. 

Chlorine free radicals are made when CFCs are broken down by UV light.

These go on to react with ozone to produce oxygen.

Chlorine free radicals are then reformed by reacting with more ozone.

It is a chain reaction that can deplete over 100 000 molecules of ozone.

There is a 200 country ban on their use and scientists have developed alternatives like hydrofluorocarbons to replace them

Happy studying!

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i just learned from animal crossing that pondskaters stay on top of the water by secreting an oil from their feet

that seems kinda obvious in hindsight. i always figured they were just, like, light enough to not break surface tension

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!

Metallic Bonding

A short one to finish off my first ever mini-series on bonding – ionic, covalent and finally metallic. There are metallic and metallic compounds and elements but for the A Level exam, we must look at the bonding within metals themselves. Don’t worry – I saved the easiest to last!

Metals are most usually solid so have particles packed close together. These are in layers which mean that the outer electrons can move between them rather than being bound to particular atoms. These are referred to as delocalised electrons because of this.

It’s pretty common knowledge that metals are good conductors of heat and electricity and it’s these delocalised electrons that give them this property.

Metals are therefore without their electrons so become positive ions. The metallic bond is actually the attraction between delocalised electrons and positive metal ions in the lattice. And that’s pretty much metallic bonding, you just need to know the properties of metals which are touched upon at lower levels of education.

These are the properties of metals:

1.       High melting points

Metals have large regular structures with strong forces between the oppositely charged positive ions and negative electrons, meaning these must be overcome to melt the metal – this requires a large amount of heat energy. Transition metals tend to have higher melting points than the main group metals because they have large numbers of d-shell electrons which can become delocalised creating a stronger metallic bond. Melting points across a period increase because they can have progressively more delocalised electrons: Na+, Mg 2+ and Al 3+ for example.

2.       Heat conductivity

Heat is conducted if particles can move and knock against each other to pass it on. Delocalised electrons allow this to happen.  Silver is a particularly good conductor of heat.

3.       Electrical conductivity

Delocalised electrons can carry charge and move, the two requirements of electrical conductivity. Current can flow because of these delocalised electrons.

4.       Ductile and malleable

Metals can be stretched and hammered into shape, making them ideal for things such as wires. Layered lattices mean that layers can slide over each other without disrupting the bonding – it is all still held together by the delocalised electrons and their strong attraction to the positive metal ions.

5.       High densities

Being a solid, metal ions are packed closely together so they have a high density, which makes them ideal for musical instrument strings. These can withstand the frequency of vibration whilst also being thinner.

 SUMMARY

Metals are  solid so have particles packed close together. These are in layers which mean that the outer electrons can move between them rather than being bound to particular atoms. These are referred to as delocalised electrons because of this.

Metals are therefore without their electrons so become positive ions. The metallic bond is actually the attraction between delocalised electrons and positive metal ions in the lattice. 

Metals have high melting points.

Metals have large regular structures with strong forces between the oppositely charged positive ions and negative electrons, meaning these must be overcome to melt the metal – this requires a large amount of heat energy. Transition metals tend to have higher melting points than the main group metals because they have large numbers of d-shell electrons which can become delocalised creating a stronger metallic bond. 

Metals conduct heat.

Heat is conducted if particles can move and knock against each other to pass it on. Delocalised electrons allow this to happen.

Metals have good electrical conductivity

Delocalised electrons can carry charge and move, the two requirements of electrical conductivity. Current can flow because of these delocalised electrons.

Metals are ductile and malleable.

Metals can be stretched and hammered into shape, making them ideal for things such as wires. Layered lattices mean that layers can slide over each other without disrupting the bonding – it is all still held together by the delocalised electrons and their strong attraction to the positive metal ions.

Being a solid, metal ions are packed closely together so they have a high density. 

 Happy studying!

It’s World Sleep Day

Log off.

Go back to bed.

Plenty of opportunities to wear sunglasses this week! 😎 Here’s the science behind how the protect your eyes from the sun’s UV radiation in C&EN: https://ift.tt/2XW7h8L https://ift.tt/3gT8PI6

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!

Biochemistry

Update: Pictures are working!

Atoms

There are a few basic chemistry concepts that are essential to understand. For starters, understanding what an atom is and its basic properties.

Atoms are the building block of all matter. They have a positive nucleus, with positive protons, and neutral neutrons. In a large area surrounding the nucleus, is the electron cloud, made of negatively charged electrons.

An atom in its elemental state is always neutral.

When an element has a charge, it is because it has an unequal number of protons an electrons, making it an ion. Sometimes an element’s nucleus has an unequal number of neutrons and protons, making it an isotope. Carbon-14, for example, has 8 neutrons, instead of the 6 that Carbon-12 has. Carbon-14 is also a radioisotope, meaning it emits particles and decays at a rate called a half-life, making it useful for fossil dating. Along with that, radioactive carbon can be used as a tracer. This means it is incorporated in CO2 molecules and used to track metabolic pathways.

The location of the electron affects how the atom will react with other elements. When electrons are in the lowest available energy level, they are in the ground state. When they absorb energy, they move to a higher energy level, entering the excited state. For instance, when chlorophyll absorbs light energy, electrons within it are boosted to higher energy levels. This provides the energy necessary to produce sugar when they return to their ground state level as they release the energy they absorbed.

Bonding

Elements bond when two nuclei are attracted to each other. Energy is released when a bond is formed. All atoms want to either get rid of all their electrons on their outer shell or fill their outer shell with 8 (or in hydrogen’s case, 2) electrons, which makes them stable. There are 3 kinds of bonds, but for biochemistry, Ionic and covalent bonds are what is relevant.

Ionic bonds form ions (hence the name.) They occur when electrons are transferred. The atom that gains electrons becomes a negatively charged anion. The atom that loses electrons becomes a positively charged cation.

Covalent bonds are made when electrons are shared. This occurs when the two atoms have electronegativities that are closer together than in an ionic bond. Electronegativity is the tendency of an atom to pull electrons towards it. These bonds can be polar if the electronegativity is high enough. A polar molecule is a molecule with a partial charge. For example, water is a polar molecule, as oxygen is extremely electronegative, and water is partially electronegative.

Hydrogen Bonding

Hydrogen bonding is a specific kind of intermolecular force that is essential to life. It is what keeps the 2 strands of DNA bonded together, and gives water its unique characteristics. Since oxygen has a partial negative charge, and hydrogen has a partial positive charge, they are naturally drawn to each other.

Hydrophobic vs Hydrophilic

Polar molecules are hydrophilic. This is because they are attracted to the partially charged ends of water. Hydrophilic means they are attracted to water. (Not in that way… sick) NaCl or table salt is hydrophilic. This is why salt dissolves in water.

Non-polar molecules are hydrophobic. This means they are repelled by water. (They’re filthy water haters.) Lipids are hydrophobic, which is why fats and oils do not dissolve in water.

The cell membrane is a phospholipid bilayer, only allowing nonpolar substances to dissolve through it. Large polar molecules have to use specific hydrophilic channels.

Characteristics of Water

Water is a unique molecule, and without its unique properties, life on earth would not exist as it does, or even at all.

Water has a high specific heat: Because hydrogen bonds are so strong, it requires a lot of heat energy to break them. This is why large bodies of water remain the same temperature, and why coastal cities have a consistent temperature because the water absorbs all the heat energy before it can warm up.

Water has a high heat of vaporisation: A large amount of energy is needed for water to vaporise, which is why sweating is such an effective cooling method.

Water has high adhesion properties: Adhesion is when one substance clings to another. Adhesion causes capillary action, which occurs in the xylem of plants, and is used to bring water up from the roots without expending energy.

Water is a universal solvent: Due to its high polarity, water makes an excellent solvent.

Water is extremely cohesive: Molecules of water tend to stick to each other. This is observed in surface tension and allows for small insects to run across the surface of the water. Cohesion is also necessary to bring water up from the roots, by transpirational-pull cohesion tension.

Ice is less dense than water: Instead of freezing all the way through, ice crystallises, leaving large amounts of space, causing ice to float. This is essential for the survival of marine life during the winter, as they can live beneath the ice.

pH

pH is calculated by taking the -log of the chance of finding hydronium (H30+) ions within a certain amount of water. Hydronium is made in rare circumstances, where a hydrogen ion breaks off from a water molecule. Normally, there is a 1 in 10 million chance of there being a hydronium ion. This is the equivalent of 1x10^-7. The -log of this number is 7, the neutral pH.

Any pH below 7 is acidic. Any pH above 7 is basic. Stomach acid has a pH of 2, while bleach has a pH of 11. Human blood has a pH of around 7.4

Most living cells need to have an internal environment with a pH of around 7. Buffers exist to regulate pH by either absorbing excess hydrogen ions or donating missing hydrogen ions. In human blood, the bicarbonate ion (HCO3) is essential.

Macromolecules

There are 4 types of macromolecules: carbohydrates, lipids, proteins, and nucleic acids.

Carbohydrates

Carbohydrates are made of carbon, hydrogen, and oxygen. They supply quick and easy energy. 1 gram of all carbohydrates will release 4 calories of energy. In our diet, they can be found almost everywhere in foods such as rice, pasta, bread, cookies, etc.

There are 3 kinds of carbohydrates: monosaccharides, disaccharides, and polysaccharides.

Monosaccharides

All monosaccharides have a chemical formula of C6H12O6. It is the placement of the carbon, oxygen, and hydrogen that determines its properties. Glucose, fructose, and galactose are all examples. They are isomers, meaning they have the same chemical formula, but a different structure.

Disaccharides

When 2 monosaccharides join together, they create disaccharides. They all have the chemical formula C12H22O11. Dehydration synthesis is the process that creates them. This process releases 1 molecule of water, hence the name. Lactose, maltose, and sucrose are all examples.

Hydrolysis is the exact opposite of dehydration synthesis. It is used during digestion. One molecule of water is used to breakdown polymers into monomers.

Polysaccharides Polysaccharides are long polymers of carbohydrates. Cellulose (plant cell wall), chitin (exoskeleton, fungi cell wall), glycogen (how animals store carbohydrates) and starch (how plants store carbohydrates) are all examples.

Lipids

Lipids include fats, oils, and waxes. Most contain 1 glycerol and 3 fatty acids. Glycerol is alcohol.

Fatty acids are the building blocks of lipids and are hydrocarbon chains with carboxyl groups at the end. There are 2 varieties; saturated and unsaturated. (3 if you count trans-fats when extra hydrogen is added to the fat to make the lipid solid)

Saturated fats are solid at room temperature, and are famously unhealthy as they are linked to heart disease.

Unsaturated fats are liquid at room temperature and are good dietary fats.

Lipids store much more energy than carbohydrates. 1 gram of any lipid will release 9 calories of heat per gram. They can be structural, as in the phospholipids of the cell membrane, or they can be hormones.

Proteins

Proteins are polymers of amino acids linked together by peptide bonds.

Amino acids are identifiable by their carboxyl group, amine group, and variable R, attached to a central carbon atom.

Proteins are complex and perform a vast array of duties, such as growth and repair, being enzymes, membrane channels, and hormones.

1 gram of protein releases 4 calories of heat.

Proteins contain the elements C H O N P S

There are only 20 amino acids coding for the thousands of proteins in the human body.

Protein Structure

There are 4 levels to the structure of a protein.

The primary structure results from the sequence of amino acids making up the polypeptide

The secondary structure results from hydrogen bonding within the molecule. This causes a helical structure

The tertiary structure is an intricate 3-dimensional shape or conformation of a protein and most directly decides the function of the protein. Enzymes denature in high temperatures or in the wrong pH because the tertiary structure is compromised.

The quaternary structure is only found in proteins that have more than 1 polypeptide chain, such as in haemoglobin.

Enzymes

Enzymes are large proteins

Enzymes lower the energy of activation, speeding up the reaction, as it lowers the amount of energy needed to start the reaction.

The chemical an enzyme works on is known as a substrate

Enzymes are specifically designed for specific substrates. For example, lactase only works on lactose. Notice the naming pattern for enzymes and their substrates.

The induced fit model is an explanation for how they work. When the substrate enters the active site, it induces the enzyme to change its shape to fit the substrate.

Enzymes can be reused as they do not degrade during a reaction

Enzymes are assisted by cofactors (minerals) or coenzymes (vitamins)

Prions

Prions are proteins that cause diseases. Mad cow disease is an example. It is a misformed protein able to influence other proteins to fold in the same way.

Nucleic Acids

There are 2 kinds of nucleic acids: RNA and DNA. They are necessary for carrying genetic information.

Nucleic acids are polymers of nucleotides

The nucleotides are the two purines: Adenine and Guanine, and the 3 pyrimidines, Thymine, Uracil, and Cytosine. Uracil is only found in RNA, and thymine is only found in DNA. Adenine connects with thymine/uracil, and guanine connects with cytosine.

Haloalkanes and Their Angelic Reactions: Part One

Haloalkanes are more commonly referred to as halogenoalkanes. Obviously you’ve already read my post on halogenoalkanes and their properties so there’s no surprise that you’re itching to read what I’ve got to say about these beauties and their reactions! Should we delve in?

There are a few different kinds of reactions you must learn for the A Level exam that involve halogenoalkanes. 

The first is the synthesis of chloroalkanes via the photochemical chlorination of the alkanes. I know it looks scary, but don’t worry, it is simpler than it sounds. It essentially means “forming chloroalkanes through chlorinating an alkane in the presence of sunlight”.

Chlorine will react with methane when UV light is present and will form several kinds of chloroalkanes and fumes of hydrogen chloride gas. Chloromethane was once commonly used as a refridgerant. Depending on how many chlorine molecules there are, there will be different compounds formed:

methane + chlorine -> chloromethane + hydrogen chloride

CH4 + Cl2 -> CH3Cl + HCl

or

methane + chlorine -> trichloromethane + hydrogen chloride

CH4 + 3Cl2 -> CHCl3 + 3HCl

When undergone in real life, mixtures of halogenoalkanes are produced with some long chain alkanes which can be separated out with fractional distillation. 

To understand what happens in an overall chemical reaction, chemists use mechanisms. These basically show the step-by-step process that is usually shown by a simple symbol equation that summarises everything.

The chlorination of methane is something you must learn the mechanism for. It’s pretty easy but involves a lot of steps and must be revised periodically to remember them.

The actual reaction is a substitution reaction because one atom or group is replaced by another. Since the chlorine involved is a free radical, it can also be called a free-radical substitution reaction.

1. Initiation

UV light is essential for the first step in the mechanism. This breaks the Cl-Cl covalent bond so that each chlorine leaves with one electron from the shared pair. Chlorine free radicals, with one unpaired electron in the outer shell, are formed. Free radicals are only formed if a bond splits evenly - each atom getting one of the two electrons. The name given to this is homolytic fission.

2. Propagation

This has two sub-steps

(a) Chlorine free radicals (highly reactive) react with methane to form hydrogen chloride and leave a methyl free radical.

Cl• + CH4 -> HCl + •CH3

(b) This free radical then reacts with another chlorine to form chloromethane and another chlorine free radical. Producing free radicals is a chain reaction which is why it is such a problem in ozone depletion - a little amount can cause a lot of destruction.

•CH3 + Cl2 -> CH3Cl +  •Cl

3. Termination

This step stops the chain reaction. It only happens when two free radicals collide to form a molecule in several ways:

Cl• + Cl• -> Cl2

UV light would just break down the chlorine molecule again, so although this is technically a termination reaction it is not the most efficient.

Cl• +  •CH3 -> CH3Cl

Forming one molecule of methane uses one chlorine and one methyl free radical.

•CH3 +  •CH3 -> C2H6

Ethane can be formed from two methyl free radicals - this is why there are longer chain alkanes in the mixture. 

This whole process is how organic halogenoalkanes are the product of photochemical reactions of halogens with alkanes in UV light - made via free radical substitution mechanisms in chain reaction.

Another reaction you need to know is a nucleophilic substitution reactions. A nucleophile is an electron pair donor or proton acceptor - the name comes from Greek origins (”loves nucleus”) - such as hydroxide ions, cyanide ions or ammonia molecules. Hydroxide and cyanide ions are negative but ammonia is neutral.

Halogenoalkanes have a polar bond because of the difference between the highly electronegative halogen and the carbon atom. The 𝛿+ carbon can go under nucleophilic attack. The mechanism for negatively charged nucleophiles these in general is:

Nu represents the nucleophile. This example is with a bromoalkane. Make sure to include curly arrows that begin at a lone pair or the centre of a bond and end at an atom or centre of bond, and delta (slight) charges.

Lets look at a more specific example:

One nucleophile that can be used is a hydroxide ion, found in either water or sodium hydroxide. In this case, you need to know about aqueous sodium hydroxide or potassium hydroxide and a halogenoalkane. This takes place at room temperature but is slow so is often refluxed (continuously boiled and condensed back into the reaction flask). Reflux apparatus is shown below:

The halogenoalkane is dissolved into ethanol since it is insoluable in water and this solution along with the aqueous hydroxide can mix. The product produced is an alcohol, which is organic.

The general reaction is:

R-CH2X + NaOH -> CH3CH2OH + NaX

Where X represents a halogen.

You must learn the mechanism for this reaction. The lone pair on the hydroxide attacks the carbon atom attached to the halogen and this causes both carbon electrons to move to the halogen which becomes a halide ion.

The reaction of a hydroxide ion can also be classed as a hydrolysis reaction as it breaks down chemical bonds with water or hydroxide ions. The speed of reaction depends on the strength of the bond - a stronger carbon-halogen bond, a slower reaction.

C-I is the most reactive (reactivity increases down group 7) and C-F is therefore the least reactive and strongest.

Part two of this post will cover nucleophilic substitution of cyanide ions and ammonia molecules, as well as elimination reactions.

SUMMARY

You need to know about the synthesis of chloroalkanes via the photochemical chlorination of the alkanes. - “forming chloroalkanes through chlorinating an alkane in the presence of sunlight”.

Chlorine will react with methane when UV light is present and will form several kinds of chloroalkanes and fumes of hydrogen chloride gas. Depending on how many chlorine molecules there are, there will be different compounds formed.

When undergone in real life, mixtures of halogenoalkanes are produced with some long chain alkanes which can be separated out with fractional distillation. 

To understand what happens in an overall chemical reaction, chemists use mechanisms. These basically show the step-by-step process.

The chlorination of methane is something you must learn the mechanism for. The actual reaction is a substitution reaction because one atom or group is replaced by another. 

The first step is initiation - UV light is essential for the first step in the mechanism. This breaks the Cl-Cl covalent bond so that each chlorine leaves with one electron from the shared pair. Chlorine free radicals, with one unpaired electron in the outer shell, are formed. Free radicals are only formed if a bond splits evenly - each atom getting one of the two electrons.

Step two is propagation: (a) Chlorine free radicals (highly reactive) react with methane to form hydrogen chloride and leave a methyl free radical (b) this free radical then reacts with another chlorine to form chloromethane and another chlorine free radical. Producing free radicals is a chain reaction which is why it is such a problem in ozone depletion - a little amount can cause a lot of destruction.

To stop the chain reaction, the final step is termination. It only happens when two free radicals collide to form a molecule in several ways: two chlorine free radicals forming a chlorine molecule, two methyl FRs forming ethane or a chlorine FR and a methyl FR forming chloromethane.

Ethane contributes to the longer chain alkanes in the mixture. 

Another reaction you need to know is a nucleophilic substitution reactions. A nucleophile is an electron pair donor or proton acceptor, such as hydroxide ions, cyanide ions or ammonia molecules. Hydroxide and cyanide ions are negative but ammonia is neutral.

Halogenoalkanes have a polar bond because of the difference between the highly electronegative halogen and the carbon atom. The 𝛿+ carbon can go under nucleophilic attack. 

Nu represents the nucleophile. Make sure to include curly arrows that begin at a lone pair or the centre of a bond and end at an atom or centre of bond, and delta (slight) charges.

One nucleophile that can be used is a hydroxide ion, found in either water or sodium hydroxide. In this case, you need to know about aqueous sodium hydroxide or potassium hydroxide and a halogenoalkane. This takes place at room temperature but is slow so is often refluxed (continuously boiled and condensed back into the reaction flask). The halogenoalkane is dissolved into ethanol since it is insoluable in water and this solution along with the aqueous hydroxide can mix. The product produced is an alcohol, which is organic.

The general reaction is :R-CH2X + NaOH -> CH3CH2OH + NaX where X represents a halogen

The lone pair on the hydroxide attacks the carbon atom attached to the halogen and this causes both carbon electrons to move to the halogen which becomes a halide ion.

The reaction of a hydroxide ion can also be classed as a hydrolysis reaction as it breaks down chemical bonds with water or hydroxide ions. 

The speed of reaction depends on the strength of the bond - a stronger carbon-halogen bond, a slower reaction. C-I is the most reactive (reactivity increases down group 7) and C-F is therefore the least reactive and strongest.