Aqa - Blog Posts

Water: Making a Splash

You don’t have to be a genius to know that water is essential for life. After all, we’re made up of it, we sweat it, we drink it, some people even opt to give birth in it. But what is it about two hydrogens and an oxygen which make it so sensational?

The answer is to do with water’s structure. A H2O molecule is covalently bonded, which means each atom shares electrons. In this case, the covalent bonds are between two hydrogen atoms and one oxygen atom. Oxygen is cool because it is highly electronegative. Electronegativity is the ability for one atom to “pull” the electrons towards it in a covalent bond. Since oxygen is highly electronegative, it pulls the electrons in the bond towards it which gives the oxygen a slight negative charge because of the electron proximity. This is represented by  δ- (delta negative). The hydrogen is therefore δ+ (delta positive) and has a slight positive charge. Overall, the molecule is said to be polar, or to be dipolar in nature, because there is a difference in charge across the molecule.

Water being a dipole gives it different properties, which you need to know about if you are sitting the AS or A level biology exam. 

A quick note on hydrogen bonding…

Being a dipole, water has areas of different charge. When many molecules come together, hydrogen bonds can form between H+ on one molecule and O- on another, shown in the diagram with a dashed line. 

It is hydrogen bonds which give water a property called surface tension. Water has a high tendency to ‘stick together’, called cohesion. This is important in water transport through the xylem in later units. Surface tension is a bit like a “skin” because it can allow small organisms to walk along it. It occurs because water molecules on the surface bond to their neighbours much like throughout the whole liquid, but since one side is exposed to air and cannot form hydrogen bonds upwards, they will form stronger ones with the molecules beside them. The net attraction is downwards.

Water is good as a temperature buffer too. Heating a substance makes its particles gain more kinetic energy and therefore the overall temperature rises since particles are moving faster. With water, the temperature doesn’t rise as much as other liquids do. This is because it takes more heat energy to raise the temperature of water by 1 degree - it has a high specific heat capacity due to the many hydrogen bonds that have to be broken (even though they are weak on their own). It takes a lot of heat energy for water to raise its temperature significantly. 

This is useful in organisms because our cells are mostly water, which can absorb heat energy without raising our temperature very much. Therefore it “buffers” or reduces heat changes. Seas, lakes and oceans are all good environments to live in because they do not change temperature as quickly as air. Aquatic organisms have an environment with less temperature fluctuation than land organisms.

Having a high latent heat of vaporisation means water can cool down organisms by evaporating a small amount of water. Evaporation is when water becomes a gas due to the large amount of KE. Fast-moving molecules are removed when this occurs and take their energy with them, therefore decreasing the amount of energy left behind and cooling it. Sweat is a good example of high latent heat of vaporisation. A small quantity of water is removed with a large cooling effect, meaning temperature is stabilised without losing a lot of water.

Water is also a good solvent (a substance which can dissolve other substances) and this is due to more hydrogen bonding. Water’s charges of H+ and O- are attracted to the positive and negative charges on molecules and therefore solutes such as NaCl are split into Na+ and Cl-, then spread out. Solvent properties are important in transport (such as blood plasma dissolving glucose, vitamins, urea etc), metabolic reactions, urine production and mineral transportation through the xylem and phloem in plants.

Water molecules can also take place in metabolic reactions. Hydrolysis reactions involve breaking down the covalent bonds between hydrogen and oxygen and making new ones, for example, in digestion. Condensation reactions produce water as a byproduct e.g. the formation of phosphodiester bonds. Water is referred to as a metabolite.

Summary

Water is a dipole due to the slight opposite charges on oxygen and hydrogen atoms.

Hydrogen bonds form between hydrogens on one water molecule and oxygens on another. 

Because of this, water has the tendency to stick to itself - cohesion. Cohesion is the reason for surface tension.

Water is a good temperature buffer because of its high specific heat capacity. It takes a lot of energy to raise the temperature by a degree.

Water has a high latent heat of vaporisation so evaporating a little has a large cooling effect.

Water is a good solvent because of how the hydrogen bonds attract charged molecules and separate them. This is useful for transporting solutions.

Water is a metabolite important for hydrolysis reactions and produced in condensation reactions.

Happy studying!

Covalent and Dative Bonds

Covalent and dative (sometimes called co-ordinate) bonds occur between two or more non-metals,  e.g. carbon dioxide, water, methane and even diamond. But what actually are they?

A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms. They are found in molecular elements or compounds such as chlorine or sulfur, but also in macromolecular elements and compounds like SiO2 and graphite. Covalent bonds are also found in molecular ions such as NH4+ and HCO3-.

Single covalent bonds have just one shared pair of electrons. Regularly, each atom provides one unpaired electron (the amount of unpaired electrons is usually equal to the number of covalent bonds which can be made) in the bond. Double covalent bonds have two shared pairs of electrons, represented by a double line between atoms, for example, O=C=O (CO2). Triple covalent bonds can also occur such as those in N ≡ N.

Dot and cross diagrams represent the arrangement of electrons in covalently bonded molecules. A shared pair of electrons is represented by a dot and a cross to show that the electrons come from different atoms.

Unpaired electrons are used to form covalent bonds as previously mentioned. The unpaired electrons in orbitals of one atom can be shared with another unpaired electron in an orbital but sometimes atoms can promote electrons into  unoccupied orbitals in the same energy level to form more bonds. This does not always occur, however, meaning different compounds can be formed - PCl3 and PCl4 are examples of this.

An example where promotion is used is in sulfur hexafluoride (SF6). The regular configuration of sulfur atoms is 1s2 2s2 2p6 3s2 3p4. It promotes, as shown in the diagram (see excited state), two electrons: one from the 3s electrons to the 3d orbital and one from the 3p to the 3d. Therefore there are 6 unpaired electrons for fluorine atoms to join. It has an octahedral structure.

An atom which has a lone pair (a pair of electrons uninvolved in bonding) of electrons can form a coordinate bond with the empty orbital of another atom. It essentially donates an electron into this orbital which when formed, acts the same as a normal covalent bond. A coordinate bond therefore contains a shared pair of electrons that have come from one atom.

When ammonia reacts with a H+ ion, a coordinate bond is formed between the lone pair on the ammonia molecule and the empty 1s sub-shell in the H+ ion. An arrow represents the dative covalent bond (coordinate bond). Charges on the final ion must be showed.

Summary

A covalent bond is a chemical bond that involves the sharing of electron pairs between atoms. They are found in molecular elements or compounds as well as in macromolecular elements and compounds. Also found in molecular ions.

Single covalent bonds have just one shared pair of electrons.  Double covalent bonds have two shared pairs of electrons, represented by a double line between atoms. Triple covalent bonds can also occur.

Dot and cross diagrams represent the arrangement of electrons in covalently bonded molecules. A shared pair of electrons is represented by a dot and a cross to show that the electrons come from different atoms.

Unpaired electrons are used to form covalent bonds - they can be shared with another unpaired electron in an orbital but sometimes atoms can promote electrons into unoccupied orbitals in the same energy level to form more bonds. This does not always occur, however, meaning different compounds can be formed.

An example where promotion is used is in sulfur hexafluoride (SF6). 

An atom which has a lone pair (a pair of electrons uninvolved in bonding) of electrons can form a coordinate bond with the empty orbital of another atom.

 It donates an electron into this orbital which when formed, acts the same as a normal covalent bond. A coordinate bond therefore contains a shared pair of electrons that have come from one atom.

When ammonia reacts with a H+ ion, a coordinate bond is formed between the lone pair on the ammonia molecule and the empty 1s sub-shell in the H+ ion. An arrow represents the dative covalent bond (coordinate bond). Charges on the final ion must be showed.

Shapes of Molecules

his post is more information than trying to explain something - the truth is, you just need to learn shapes of molecules like you do with anything. I’ve got a physical chemistry mock tomorrow that I’m dreading since I’ve done zero revision. The fact that I run a study blog yet don’t revise myself is odd, but what else can I do? Oh, wait … revise. So here it is, my last minute revision for myself and you too - I present, shapes of molecules!

VSEPR stands for valence shell electron pair repulsion theory. If you’ve ever seen a moly-mod or a diagram of a molecule in 3D space, you may wonder how they decided it was that shape. Well, VSEPR answers all.

The theory essentially states that electron pairs are arranged to minimise repulsions between themselves - which makes sense, since electrons carry the same charge and therefore try to repel each other. Of course, there are different types of electron pairs, lone and bonding. The strongest repulsions happen between lone pair - lone pair followed by lone pair - bonding pair and finally, bonding pair - bonding pair have the least repulsion. 

Since the repulsion governs the shape of the molecule, to work out a molecule’s shape you must look at dot and cross diagrams or electron configurations to see how a molecule is bonded. There are many methods to do this, but the bottom line is that you must work out how many bonding pairs of electrons and how many lone pairs are involved.

The easiest shape to learn is linear. This has two bonding pairs and no lone pairs at an angle of 180 degrees, since that is the furthest the two can get away from each other. Examples of linear molecules include carbon dioxide and beryllium chloride.

Next up is trigonal planar. This has three bonding pairs and no lone pairs, each at the angle of 120 degrees. Trigonal means three and planar means on one plane, this should help you in identifying the molecules since after a fourth pair of electrons, the shape becomes 3D. Examples of trigonal planar molecules include boron trifluoride and sulfur trioxide.

What if you were to have two bonding pairs and two lone pairs? Well, then you’d have a bent molecule. Water is a good example of a bent molecule. Since it has two lone pairs that repel the other two bonding pairs more than they repel each other, the bond angle is 104.5. I’d be careful though, as in many textbooks it shows a bent molecule to have one lone pair and a different bond angle.

Another variation of the bent molecule I’ve seen is the one with two bonding pairs and one lone pair. It is deemed as bent with a bond angle of 109 or sometimes less than 120 degrees.

Tetrahedral molecules have four bonding pairs and no lone pairs. The bond angle is 109.5 degrees. Examples of this include the ammonium ion, methane and the phosphate ion. A good thing to note here is how these molecules are drawn. To demonstrate the 3D shape, where the molecule moves onto a plane, it is represented with a dashed line and triangular line along with a regular straight line. 

Trigonal pyramidal, sometimes just called pyramidal, is where there are three bonding pairs and a lone pair. Bond angles are roughly 107 degrees due to the repulsion from the lone pairs. An example of a trigonal pyramidal molecule is ammonia, which has a lone pair on the nitrogen.

Having five bonding pairs gives a trigonal bipyramidal structure. I guess the three bonding pairs on the trigonal plane accounts for that part of the name, where the rest comes from the position of the remaining two. These molecules have no lone pairs and have a bond angle of 90 degrees between the vertical elements and 120 degrees around the plane. Diagrams below are much clearer than my description! Examples of this include phosphorus pentachloride.

Six bonding pairs is an octahedral structure. I know this is confusing because octahedral should mean 8 but it’s one of those things we get over, like the fact sulfur isn’t spelt with a ph anymore. It’s actually to do with connecting the planes to form an octahedral shape.There are no lone pairs and each bond angle is a nice 90 degrees. Common examples include sulfur hexafluoride.

Square planar shapes occur when there are six bonding pairs and two lone pairs. All bond angles are 90 degrees! They take up this shape to minimise repulsions between electrons - examples include xenon tetrafluoride.

The final one to know is T-shape. This has three bonding pairs and two lone pairs. These molecules have bond angles of (less than) 90 degrees, usually a halogen trifluoride like chlorine trifluoride.

There are plenty more variations and things you could know about molecular geometry, but the truth is, there won’t be an extensive section on it. It’s a small part of a big topic!

I’m not going to do a summary today since I’d just be repeating the same information (I tried to keep it concise for you guys) so instead I’ll just leave you with, 

Happy studying!