Article #9: Atoms into Molecules

Most of the articles I’ve posted, so far, have had something to do with basic chemistry, like what is an atom, an element, or a molecule?  Why is nitrogen such a big deal?  And so on.  We’ve started out this way because, if we’re working to develop a basic understanding of science, we have to start with fundamentals, such as what is everything made of.  Once we identify the pieces, we need to look a bit at how the pieces fit together.  WHY the pieces fit together is an even more fundamental question, and we’ll get to that soon.

We’ve established that everything is made of atoms and atoms are made of protons, neutrons and electrons.  How many protons there are in an atom determine what the atom is—if it has 1 proton, it’s Hydrogen, if it has 12 protons, it’s Carbon, if it has 92 protons, it’s Uranium, etc.  But most matter isn’t “pure”, like 100% iron or 100% Magnesium.  Most things are made up of building blocks that are composed of different atoms that are bound together—molecules.  Water, for instance, is a molecule that is composed of one atom of Oxygen bound to 2 atoms of Hydrogen.  That’s what H2O means—two Hydrogens and one Oxygen.  The main question we’re going to address in this article is why and how these atoms interact as they do.

The basic structure of an atom is that there is a nucleus, composed of protons and neutrons, in the center that is surrounded by electrons that orbit the nucleus like the Moon orbits the Earth.  Everyone has seen images that are meant to represent this structure.  They’ve been popular since the fifties as a symbol of mankind’s advanced science and technology.  If you’ve studied chemistry at all in high school or college, you’ve also seen other types of diagrams of atomic structure that are meant to help explain how atoms, particularly electrons, are put together.  All of these images are meant to help people visualize atoms in different ways, so they can understand different aspects of atomic structure and interactions.  It’s interesting to realize that none of those diagrams is remotely close to what an atom actually looks like.  The scale is always very wrong.  Protons and Neutrons are roughly the same size and mass.  An electron has about 2000 times less mass (2000 electrons would weigh about what a single proton or neutron weighs).  Electrons are also much smaller in diameter, but nobody really knows how much smaller, because no one has been able to measure an electron.

Source: Freepik

As I mentioned, the picture you may have in your mind of an atom is probably very wrong.  Your picture is like the image above, with a nucleus and a few electrons in close orbit.  The reality is that the electrons are really orbiting MUCH farther than that from the nucleus.  The real relationship is that, if you were to pretend that the nucleus of an atom was the size of a ping-pong ball and put that ball in the middle of the field in a football stadium, the electrons would be pinhole-sized particles orbiting out in the top tier of seats.  Atoms are 99.999999999% empty space.  Remember that for later.

The other important thing to know about atomic structure is that protons carry a positive electrical charge and electrons carry a negative charge.  Neutrons, as the name would suggest, are neutral and do not have a charge.  These positive and negative charges are key to a lot of the chemistry and physics that defines how the universe works.

The positively charged protons and the neutral neutrons are packed together in the nucleus at the center of the atom.  There is a VERY powerful force that binds the nucleus together, because, as you probably know, like charges repel each other while opposite charges attract, much like the poles of a magnet.  To keep all the positively charged protons together in the nucleus requires a lot of force.  This force is called the strong nuclear force, which is one of the four fundamental forces in the universe (gravity is also one of these forces).  We’ll talk about these forces a lot more in later articles.  With all the protons, the nucleus, then, is positively charged.  The electrons, being negatively charged, are attracted to the positively charged nucleus and repelled by other electrons.  This attraction is what keeps the electrons in orbit around the nucleus, very much like gravity keeps the Moon in orbit around the Earth.  Atoms (in general) always have the same number of electrons as protons, so the negative charges of the electrons balance out the positive charges of the protons.

The point to all of this, and why it’s important to understand it, is that it is the electrons in atoms that cause atoms to form bonds with other atoms to make molecules.  They do this two different ways, but for the same reason, which is to achieve a stable configuration.  This stability thing is something we’re going to talk about a lot, going forward, so we’ll just hit the points we need to today.  Don’t worry if you don’t really get all the details of this, at first.  It’s the basic concept that’s important for our literacy goal, not the details.

We described the basic structure of an atom, which is a nucleus, composed of protons and neutrons, surrounded by electrons in orbit about it.  The key is that some of those electrons are in stable orbits, and some of them are not.  This is a huge over-simplification, but I think it will serve our purpose of basic understanding. Electrons like to be paired up with other electrons, so the presence of a lone electron can be unstable.  The atom would like to either get rid of a lone electron or add another one, to make a pair.  Like I mentioned, there are two ways to do that.  The atom can either just give up the electron completely, or it can share it with another atom that also has a lone electron.  That way they both sort of end up with two electrons, that orbit one nucleus part of the time and the other nucleus part of the time, like a figure-8.

Only atoms of certain elements can completely give up an electron (or two).  Sodium is one of these, as is Calcium and quite a few other similar atoms.  This, however, causes a problem with the electric charge on the atom.  Remember, electrons are negatively charged.  If an atom gives up an electron, it’s giving up one negative charge.  Since all the positively charged protons are still there, the atom now has an unbalanced electrical charge, with one extra positive charge.  Atoms like this are called “ions”.  You’ve heard the term before.  Now you know what one is.  So a sodium ion has an extra positive charge, which is referred to as being “+1”, and is written as Na+.  To go along with this, there are some atoms that really want to attach an extra electron to get stable.  Elements like Chlorine are like this.  When they gain an extra electron, they now have an extra negative charge.  They are “negative ions”, “-1”, written like Cl.  Remember that opposites attract, right?  If there is a positive sodium ion that comes near to a negative Chloride ion, they will attract each other and form a type of chemical bond called an “ionic bond”.  The resulting molecule, NaCl, sodium chloride, is table salt.

Source: BruceBlaus, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons

Most of the time, however, atoms can’t completely give up or take on an extra electron.  What they do is share electrons so they can both have a stable pair, instead.  Think of hydrogen.  It is the simplest of all atoms with one proton and one electron.  One electron, as mentioned, isn’t stable, so it wants two.  Under certain circumstances, hydrogen can just shed its electron, like sodium, and become a positive ion.  Hydrogen ions, however, aren’t very stable and will tend to react with other atoms very quickly.  We’ll talk about that some more later when we talk about acids and biochemistry.  Most of the time, hydrogen will end up sharing a pair of electrons with another atom.  Take oxygen, for instance.  Oxygen has 8 electrons.  Six of them are orbiting as stable pairs, but two of them are by themselves.  For oxygen to get a stable configuration, it wants to pair those two single electrons with other single electrons, like maybe found in hydrogen atoms.  So one hydrogen atom shares its unpaired electron with one of the unpaired electrons in oxygen and another hydrogen atom shares with the other unpaired electron.  This creates two shared pairs between two hydrogens and an oxygen.  This makes the molecule H20 which, as we all know, is water.  This type of bond is called a covalent bond.

 Source: By DynaBlast – Created with Inkscape, CC BY-SA 2.5, https://commons.wikimedia.org/w/index.php?curid=995735

Everything in the universe is made like this.  Sometimes you just have collections of atoms, like in “pure” Neon (the gas in the lights).  Neon gas is just a bunch of neon atoms, not combined with anything else.  In fact, neon is one of a category of elements called the “noble gasses” or sometimes “inert gasses”.  Neon, Argon, Xenon and a few others.  These atoms are VERY stable, all by themselves and they almost NEVER form chemical bonds with anything.  That’s what “inert” means.  Inert is unreactive.  Most of the matter in the universe is hydrogen—about 75%.  Almost all the rest is helium.  All the other elements make up just a tiny fraction of one percent of all the matter in the universe, but that tiny fraction includes us, so we’ll talk more about that, too.

Now you should have some understanding of the structure of atoms and how atoms form bonds with other atoms to create more complex structures—molecules.  This basic understanding unlocks a whole slew of other questions.  That’s one of the really great things about science.  It’s all connected.  One thing builds on another.  That’s why, if we want to be scientifically literate, we need to know a little chemistry, a little physics, a little biology, a little of this, a little of that.  Once you start to get it, the universe you live in and are a part of will seem a whole lot more interesting.