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Atoms and Ions

Duncan Griffiths Copyright © april, 2003, D, GRIFFITHS, ALL RIGHTS RESERVED

This page will be a very brief overview of how atoms and Ions in water chemistry work, to be honest it is said the we are not keepers of koi, but of water, (in other words take care of the water and the koi will take care of themselves) you cannot maintain water unless a little effort is made to understand chemical reactions and their inter-relationships and it's also a nice subect to know, it can be very intimidating when hobbyists and professionals start chemical reaction jargon

ah I remember it well

So for those who are not interested? I promise, now would be a good time to hit the back button, for those who would wish they had paid more attention at school ( I include myself in this category) and would like to learn just a little more, stay with it and i will attempt to make things a little clearer, and at the end there will be a periodic table, ( a list of Atomic Elements and their symbols), this will include Atomic numbers and Atomic mass, most of them you will not need to know but I have included them because it gives the table a meaning and purpose and to do otherwise would only be doing half a Job

What is an Atom

All things are made of Elements, examples of which are helium, oxygen, gold, iron, hydrogen, nitrogen, to name just a few.

All elements are made up of Atoms, an Atom is the smallest part of an element that can exist and still keep its chemical properties.

Atoms are the building blocks of an element, all things are made of something,( an obvious statement) just as a car is made of different parts, if we take the engine for example, this must be made of something and it is! Namely metal elements and these elements must be made from something, and they are, Atoms. An Atom is about as far down the line as it goes till you analyse the structure of the Atom, and that's where this article is heading.

Elements are the purist form of matter that cannot be spilt by chemical reactions. Elements are made just from atoms.

if we differ the composition of an atom we get differing types of Element. You could say, An Atom is an Atom. just as a car is a car ,but just like cars; atoms differ slightly, it's these different atomic structures that makes one

element different from another. Just as the characteristics of one car to another is determined by the arrangements of a cars components making it different.

E.G. think of it like a brick wall in a building, the brick wall represents an element. Think of the bricks as the Elementary Atoms, typical bricks used can be engineering bricks, common bricks, concrete bricks, breeze blocks etc, some or all can be used on a building construction, if we decided to build the wall out of common bricks ourwall or element takes the characteristic of that brick, and so our element is formed, but if we make the wall out of breeze blocks the wall or element becomes different, so according to which is the main choice of brick or Atom this will shape the characteristics of the wall or the element, and thus the functionality of that element.

Take the wall example yet again. Take one brick out of the wall at a time and ask a question, is what I have left still a wall? Yes! Continue taking the bricks out one at a time and asking the question, do I still have a wall. If the answer is yes,continue to take bricks away from the wall. At last we get to the point, where we have one brick left, do we still have a wall? No! we have a brick and that's all, so we have got to the last indivisible part of our wall. that is our ATOM!


A molecule is the smallest unit of a compound that still retains the chemical properties of the compound. A molecule's properties are determined by the various atoms it contains and their arrangement within the structure

The structure of a molecule can also be determined by the amount of atoms that make up that particular molecule, in other words different molecules can have differing amounts and types of Atoms,

e.g. the element oxygen or the oxygen at is O or O 1 = 1 oxygen atom, the oxygen molecule = O2 = two oxygen Atoms. if we now add a third oxygen atom to the two in the example above we no longer have breathable oxygen but now we have O3 = Ozone molecule = three oxygen atoms

If we relate this to our example building wall once again, we can see that if one wall has more bricks than the next, it can be seen that even though the two walls are made of bricks, clearly the characteristics of each wall will be different, the same is true of the amount of atoms of any given element that form different molecules.

We can also put different atoms together to form other molecules water being the obvious one The water molecule consists of two hydrogen atoms and one oxygen atom = H2+O

Can you work out what this is? ( answer at the bottom)

some more common molcules


What happens if we put several different elements together? In this event we form a compound. A compound is several elements that CAN be split by chemical reaction back to their original base elements

Back to our example brick wall, imagine we have our wall of common bricks giving the characteristics of a wall made from that type of brick, but now we want to provide insulation to that wall and make it stronger, so, along side the original wall we build another wall out of breeze blocks close to the original. Now we have a wall with totally different characteristics, it has become stronger and has the new combination has given our wall insulation properties,

This in essence is a "compound", but we can still take the newly formed wall away leaving the original wall or element.

what can we do with these reactions

In the koi hobby this is where we can really relate to what we have learned from the above structures.

If we combine two or more elements we form a compound and that’s what makes and shapes our water quality right through to our treatments.

For instance if we take:

1 Nitrogen atom and add 2 oxygen atoms we get   nitrite, NO2

1 nitrogen atom and three oxygen atoms we form nitrate, NO3

1 nitrogen atom and three hydrogen atoms we get ammonia, NH3

1 nitrogen atom and four hydrogen atoms we get NH4, ammonium

Lets take a common pond treatment "Potassium permanganate" or KMnO4 this equals 1 part Potassium + 1 part manganese + 4 parts oxygen three elements combined together in different quantities to make a one new compoun

What is an atom made from?

An atom consists of a central nucleus surrounded by several energy layers, the nucleus and the energy layers are commonly made up of three components namely

1, Protons

The protons and the neutrons are packed into the central nucleus with the electrons occupying the outer shell energy levels. All except one element, which consists of just 1 protons and 1 electrons and NO neutrons, its name is hydrogen this is the most abundant element in the universe. Incidentally the most common gaseous element on earth is Oxygen although oxygen only makes up 21% of the air we breath, it does however make up 47% of rocks and 89% of the oceans.

This is a diagram of what the water molecule would look like if you could see into each Atom

If we think back to our example brick wall think of these three particles protons neutrons and electrons as the components that make up the brick. (cement, sand & fine gravel)

Or, if you want to think of it another way, compare an atom to colours, there are just three primary colours, red, green and blue, these would represent protons, neutrons, and electrons,   from these three primary colours a whole array of different colours are made and it’s the same with the three components that make up an atom, by arranging the numbers and the mixing of protons, neutrons and electrons we end up with a whole array of different atoms, which in turn make a whole array of elements, however pending discovery of new elements, which is unlikely there elements unlike colours are not endless, there being just over 100 of them in total.

Atomic numbers and masses

All atoms have an atomic number and an atomic mass this is determined by the arrangement and relationship of the amount of protons contained in an atom to the amount of neutrons

The atomic number represents the number of protons contained in an atom and the atomic mass is the total number of both protons and neutrons contained in that atom

So hydrogen has an atomic number of 1 and an atomic mass 1 so if we know that the atomic number is 1 and that represents the number of protons and the atomic mass is also 1 that means the Hydrogen atom must contain NO neutrons

Take the metal sodium

Atomic number = 11 that’s the number of protons it contains and the mass number for sodium is 23, (23 minus 11 = 12) so 12 is the number of neutrons sodium contains, however it is possible to get more than one type of atom for a given element

and these are called Isotopes.

Oxygen is prime example of an isotope

Oxygen – 16

Oxygen – 17

Oxygen – 18

The number of protons are the same for all but the number of neutrons change

Oxygen – 16 = 8 protons this would be indicated by the atomic number   8 from 16 leaves 8 so the number of neutrons for    Oxygen-16 = 8

Oxygen – 17 = 8 protons this would be indicated by the atomic number   8 from 17 leaves 9 so the number of neutrons for    Oxygen-17 = 9

Oxygen – 18 = 8 protons this would be indicated by the atomic number   8 from 18 leaves 10 so the number of neutrons for Oxygen-18 = 10.

There are two isotopes of the gas Chlorine, Chlorine-35 and Chlorine-37 the atomic number for Chlorine gas is 17 so from what you now know, work out the neutron numbers for each isotope (answers at the bottom of page)


Electrons spin around the nucleus of an atom in several energy levels giving an atom its energy, these levels follow set patterns, if we look again at the picture of the atomic structure of an atom we can see these electron levels.

The innermost energy level is called the K shell, this level can host either one or two electrons but a maximum or two electrons, then any electrons in excess of this number spill over into the next outer level called the L shell.

The second level or L shell can hold a maximum of eight electrons any electrons in excess of this will spill to the next level called the M shell.

The M shell can hold a maximum of 18 electrons, however when we get to the third M shell level, when 8 electrons occupy this level a great degree of atomic stability is achieved then electrons 9 and 10 will spill into the fourth energy level after this the third level will continue to fill to a maximum of 18 electrons

There are further energy levels containing even more numbers of electrons

The above is referred to as the electron configuration

Ions and their formation.

Another constant characteristic of an atom is. Atoms have the same amount of Protons to electrons thus Atoms have no overall charge they are neither positive   + or negative -. However it is possible to find atoms with differing amount of electrons to protons and these are called Ions. Ions are formed when an atom either gains an electron or loses an electron thus altering an atoms neutral state of charge.

Its works like this, Protons are positively charged, Neutrons are neutral, and Electrons are negatively charged

So if you have the same number of protons to electrons we have in effect a stalemate with no overall charge as one cancels the other out, the neutrons, being neutral add nothing to the overall charge of the atom, but if we lose an electron or gain one this will upset the overall charge of the atom we then refer to an atom in this state as an   Ion's or Cation's or more specifically anions and cations

Electrons can only be lost or gained because they are on the outside of the atoms nuclei. The nucleus remains in the same composition.

When Metals lose electrons they form a positive Ion's   (or cations) now the atom has become an ion and is positively charged

  Non-metals, gain electrons to become negative Ions/ or anions, but in these newly formed states we refer to these as ions and not atoms although they clearly are still atoms.

The gain of electrons are of particular interest to us a koi hobbyist,when the hydrogen atom loses an electrons it become positively charged free hydrogen H+ and this is the basis for pH the "power of hydrogen" when we measure pH (acidity or alkalinity) we are actually measuring one thing? Positively charged hydrogen H+ ions/atoms the acidity and not the alkalinity. Negative anions are termed hydroxyl anions.

By measuring the amount of Positive ions (cations) in a measured volume of water we can work out the amount of negative hydrogen H-ions ( anions)that sample must contain, Positively charged hydrogen cations being acid base, and the negative hydrogen anions being the alkaline base. Remember all pH test kits measure one thing and one thing only H+ ions( positively charged hydrogen cations)

Water is being broken down all the time in our ponds by fish respiration and bacterial consumption of oxygen in the bio filter, Lets take a look at a fish by-product ammonia that will be broken down in our filters to form nitrite these two molecules are the most important toxins that reside in our ponds.

Ammonia = Nh3= 1 nitrogen atom + 3 hydrogen atoms bacteria in the filter oxidise the ammonia and in the process add oxygen O2 = 1N +O2 = No2= nitrite, but what happened to the Hydrogen? Here they are! >>>> H+ H+ H+ >>>> all freed up and floating around the pond, all these H+'s are adding to your acid base and lowering your pH this is why without adding something to your water your pH will always be on a downward slide and never on an upward slope.

So how does this occur?

If we look at the above example of the electron patterns in an atom, we said that because the number of protons to electrons was equal the protons being positive and the electrons negative that the overall charge was neither + or - we also stated that, all the energy levels around the nucleus that host the electrons must have a set number and pattern, two electrons in the first shell/level eight in the next, etc:

If we take the Hydrogen gas atom it has one proton and just one electron and no neutrons, so it has no overall charge. But because it has one outer shell containing just one electron and should really have two electrons in that shell the hydrogen atom is unstable and will try and find a more stable state.

The oxygen atom has 8 protons + 8 neutrons + 8 electrons giving still no overall charge but! The first shell of the atom contains two of the eight electrons leaving 6 in the next shell, which just like the hydrogen atom is less than it should have to complete the its outer energy level (8 being the figure needed ) so the oxygen atom is unstable as well.

When two hydrogen atoms meet an oxygen atom they combine to share electrons and use each others outer shell to complete there own, the hydrogen atom utilizes one of the oxygen atoms electrons so it now has two and a complete outer shell compliment of electrons, the other hydrogen atom does the same thing and also now has a complete outer shell, the oxygen atom has to do the same thing but, one Hydrogen atom will not supply it with enough electrons so it borrows the one electron from each hydrogen atom and utilizing the one electron each hydrogen atom has available, the oxygen atom completes its own outer level/shell and becomes stable but they are now all bonded together and rely on each other for atomic stability. So the water molecule is born..

BUT, how do two gasses become a liquid?

Well the bonding of these atoms generates huge amounts of energy and heat, and till finally there is a small atomic explosion and they make a huge transformation from a gas to a liquid.

Some folks refer to the formula for salt as NaCl but this formula equals = (Na) sodium + (Cl) chlorine, but salt is Sodium chloride not sodium chlorine? Never the less Cl is in fact chlorine, but there is no element in the periodic table for chloride, however the formula has one subtle difference from a sodium+ chlorine NaCl,   Chloride is in fact a negatively charged chlorine atom so now its know as a chloride ion"anion". thus when we show the negativity in the formula it makes more sense the actual formula is NaCl -

Chlorine has 17 protons +18 neutrons + 17 electrons giving a neutral charge, but as chloride is an ion of the chlorine atom containing 17 protons,18 neutrons and 18 electrons, the chlorine atom has gained one electron and because the negatives outweigh the positives, the chlorine atom has change to become negatively charged chloride anion, hence the minus symbol after the Cl-


1, Elements are the purist form of matter that cannot be spilt by chemical reactions, containing one or several atoms

2, the smallest particle of an element that can exist is an atom

3, an atom is made up of a nucleus and outer energy levels or shells

4, protons and neutrons pack into the nucleus and electrons spin around the outer levels

5, an atom has equal number of protons to electrons, the protons are positively charged and the electrons are negatively charged thus cancelling each others   charge out, the neutrons are as the name implies neutral( no charge at all)so add nothing to the overall charge of the atom.

6,when an atom loses or gains an electron the atom becomes charged.

7, an atom with a state of charge is known as an "ion", a negative charge atom is called an "anion", a positive charge atom is called a "cation".

I do hope this has helped clear things for those of you who maybe struggled a bit, if this is the case we must do this again sometime, when my brain has had the reset button pressed

Below is the a table of common elements with there electron arrangments followed by the periodic table and of course the all important answers.

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