Atoms, and molecules, and bonds, OH my!

Introduction

Everything in the world is chemistry … wait, come back, don’t be scared! It’s fun, I promise. Knowing a little something about the fundamentals of chemistry and matter will help you navigate the contents of your food and health products. At the most basic level, the things that are good for you and things that are bad are made of all the same stuff: chemicals.

The atom and the periodic table

The atom is the smallest basic building block of chemistry. Pretty much the chemical Lego brick of matter. It has three basic internal components (subatomic particles): the proton (electrically positive) and neutron (electrically neutral) are in its core (nucleus) and are orbited by electrons (electrically negative) in a number of layers (shells). This if often called the solar system model of the atom.

atom

Figure 1: Solar system model of the atom.[1]

There are 92 naturally occurring types of atom (the elements) determined by the number of protons it its nucleus, e.g. one proton is hydrogen (H), 16 is oxygen (O), etc (see Periodic Table below). Neutrons are kinda just along for the ride, chemically speaking, but the number of electrons, that’s where it gets interesting (and chemistry-y). The number of electrons is the same as the number of protons for an electrically neutral atom. A few more or a few fewer gives the atom an electric charge and it’s this sharing or transfer of electrons that are the basis for chemical reaction and bonding.

PeriodicTable

Figure 2: Periodic Table of Elements.[2]

Our friendly neighbourhood Periodic Table orders the elements by number of protons (atomic number) left to right, and then in columns based on the number of electrons in the outer most layer (shell) of the atom which determines its chemical properties and chemical reactions. The table hides a treasure-trove of patterns: most of them are metals, those lovely yellow bordered ones (transition metals) make a rainbow of colours when you start stealing their electrons, and those higher blue bordered ones make the chemistry of life possible.

Ions

One big pitfall people often fall into is the difference between an atom and an ion. Very rarely does an element like to be found as a pure element with all its electrons present. It’s usually gained or lost some or it’s sharing with other atoms. This gives atoms and ions completely different chemistries: e.g. chlorine (element) is a gas which is super toxic and chloride (+1 electron) is often found as a part of a solid and is harmless. Different elements have a preference to gain or lose electrons but in general your metals will lose while the other atoms prefer to gain.

ion

Figure 3: Electron transfer (ionisation) of a neutral sodium & chlorine atom to sodium and chloride ions.[3]

Above we can see an example of sodium (explosive solid) giving an outer shell electron to a chlorine (green, burny gas) resulting in a sodium ion (Na+) and chloride ion (Cl) which together exist as table salt (white solid, pretty harmless, NaCl). Naming-wise positive ions don’t always change their name but negative ions (chlorine to chloride) get an -ide on the end to tell them apart, and it’s this little change that results in comment wars online when people don’t realise they’re actually having two conversations talking about different chemicals. Such fun.

Bonding and molecular structure

So a lot of the most important elements (carbon, nitrogen, oxygen, etc) that are involved in organic chemistry, health, food, and well being don’t just gain/lose electrons and leave it at that, they prefer to share with other atoms and form covalent bonds. When they do they become molecules.

water-covalent-bond

Figure 4: Covalent bonding in a molecule of water.[4]

Above, an oxygen atom shares one electron each with two hydrogen atoms forming a water molecule. The oxygen has a couple of extra electrons that are paired up in its outer shell (lone pairs) which don’t need to share with another atom; electrons like to come in twos. These drawings become messy pretty quick so for bigger molecules we just draw the bonds with lines and ignore electrons that aren’t shared – we know how many are there based on the atom type.

Light (electromagnetic radiation) and matter

And finally, a quick note on light (electromagnetic radiation). It may seem a little out of place here but the way light interacts with molecules is often overlooked and yet it pops up in odd contexts. So, radio, microwaves, visible light, UV, and X-Rays are all the same thing, they just differ in how much energy the light has and this changes how it interacts with molecules.

EMSpec

Figure 5: Light: the electromagnetic spectrum.[5]

Pretty much everything less energetic (higher wavelength) than the pretty rainbow visible light we can all see is generally harmless and may just cause heating in molecules if the conditions are right. This is why heating your food using a microwave is completely fine – it’s all the same molecules when it comes out as it goes in; perfectly safe just a little warmer – or a lot warmer in the case of jam tarts. Remember to blow on the pie!

Higher energy light like UV and X-Rays can be dangerous and break bonds in molecules, chemically changing the molecules – sometimes in things you’d rather they didn’t like food …or your body. This is a type of ionizing radiation. It can be used for good too where we can use UV radiation to kill bacteria and in small amounts X-Rays are obviously useful in medical imaging. Remember: dose makes the poison – it always matter how much of anything you use.

Final Thoughts

Hopefully this has been a useful (and brief) overview of the essential ideas needed to talk about chemistry and molecules in the context of this blog (I know…chemistry scary, biology fun). There’s heaps more detail available online (Wikipedia is actually pretty good for all this) if you wanted to dig deeper, but the aim here was more to fill in those gaps that I’ve heard pop up in conversation about food and health and that’s what I hope to continue with the Matter Matters section of this blog. Just remember, it’s all one big picture: chemistry, physics, biology – they all just describe the world around us.

References and Sources

[1] What is meant by atom?: Atom. http://www.physics-and-radio-electronics.com/electronic-devices-and-circuits/introduction/atom.html (accessed September 12, 2017).
[2] Science Notes and Projects: Printable Periodic Tables. https://sciencenotes.org/printable-periodic-table/ (accessed September 12, 2017).
[3] Ions. http://web.sbu.edu/chemistry/wier/atoms/ions.html (accessed September 12, 2017).
[4] Covalent Bonding & Example, What is Covalent Bonding? | Chemistry@TutorVista.com. http://chemistry.tutorvista.com/physical-chemistry/covalent-bonding.html (accessed September 12, 2017).
[5] Electromagnetic Spectrum.  http://www2.lbl.gov/MicroWorlds/ALSTool/EMSpec/EMSpec2.html (accessed 13th September 2017).

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