How Gen Chem Relates to Organic Chem, Pt. 1 – The Atom

by James

in General Chemistry, Understanding Electron Flow

(Part 1 of a series on how concepts in general chemistry relate to organic chemsitry)

If, in some cataclysm, all scientific knowledge were to be destroyed, and only one sentence passed on to the next generation of creatures, what statement would contain the most information in the fewest words? I believe it is the atomic hypothesis (or atomic fact, or whatever you wish to call it) that all things are made of atoms – little particles that move around in perpetual motion, attracting each other when they are a little distance apart, but repelling upon being squeezed into one another. In that one sentence you will see an enormous amount of information about the world, if just a little imagination and thinking are applied.

-Richard Feynman, The Feynman Lectures in Physics

More than Newton’s apple, or Einstein’s E=mc2, or even Watson and Crick’s double helix,  Dimitri Mendeleyev’s compilation of the periodic table has my vote as the most thrilling scientific insight of all time. As was wonderfully detailed in the BBC series “Chemistry – a Volatile History”, Mendeleyev was the first to make the connection between the masses of the elements and their properties in the periodic, tabular format we are familiar with today. It had its share of omissions – the noble gases, for one – but for the first time, all of the building blocks of the universe were laid out in a fashion that was not only logical but made predictions about the properties of unknown elements.


One of the amazing things about chemistry is how drastic the effect of changing the atomic number can be on the behavior of the elements. Consider:

  • Carbon – commonly encountered as soot, or  charcoal, which I had to deal with this weekend when I cleaned the barbeque we used for Thursday’s Canada Day party.
  • Nitrogen – the major component of our atmosphere, litres of which pass every minute through our bodies without leaving a trace.
  • Oxygen – the lifeblood of fires and human metabolism, without which our lives would be impossible.
  • Fluorine – the Tiger of chemistry, so incredibly dangerous it mauled a large number of 19th century chemists who first tried to isolate it (and as a gas, is on the shortlist of about six  chemicals you need special permission to work with at MIT).
  • Neon – the second-lightest of the noble gases. A (small) part of our atmosphere, we have been breathing neon for millenia but discovered it barely a century ago.

The properties of these elements are so different, it is hard to believe  that they each represent successive additions of a single proton to the nucleus of an atom. Yet they do.

The components of the atom

  • Protons – carry a positive charge.
  • Neutrons – the same mass as the proton, but neutral. Do not carry a charge.

Together, protons and neutrons are called nucleons, since they are present in the nucleus of atoms.

Then, on the periphery of the atom – for an atom is mostly empty space, are the electrons. Small particles – 1/1840 of the mass of the nucleons, they carry a negative charge.

Opposite charges attract, like charges repel. So under normal circumstances, an atom is neutral. When an atom carries a charge, it is called an ion. A positively charged ion (protons outnumber electrons) is called a cation, and a negatively charged ion (electrons outnumber protons) is called an anion. It’s got an extra “n” in there for negative – that’s how I always remembered it.

Everything you need to know about nuclei in organic chemistry

The defining property of an element is the number of protons, or the atomic number. Hydrogen has one proton and one electron. If you remove the electron, it’s still hydrogen, although this case we call it the hydrogen cation, hydrogen ion, or, more commonly just “proton”. Carbon has six protons. Nitrogen seven. The naturally occurirng elements go up to 92, but the elements up to 118 have been made and studied.

  • If you keep the number of protons and electrons the same, but change the number of neutrons, you have what we refer to as an isotope. Isotopes have the same atomic number but different atomic weight. Deuterium (D) is the isotope of hydrogen with a proton and one neutron, for an atomic mass of 2. Tritium (T) is the isotope of hydrogen with two neutrons, for an atomic mass of 3. Tritium is radioactive – the nucleus is unstable – it slowly decays, with a half-life of about 10 years. Isotopes have (practically) identical chemical properties and for the purposes of sophomore organic chemistry you can treat them as if they behave exactly the same.  If you go on in organic chemistry you learn that there are very subtle (and useful!) chemical differences between them, but I wouldn’t worry about that at this point. (FYI – this difference in behavior is what helped bust Floyd Landis, to give a prominent example).
  • We define a mole as the amount of substance that contains as many “elementary entities” (e.g. atoms, molecules, electrons, ions) as there are atoms in 12 grams of carbon-12. This is a big number: 6.02 x 10^23 to be exact.
  • The atomic weight is the weight of 1 mole of a naturally occuring sample of an element. For instance since the natural abundance of carbon-13 is about 1.1% relative to carbon-12, when we take 6.02 x 10 ^23 atoms of naturally occuring elemental carbon, we get a weight of 12.011 g.
  • Nuclei have a property called spin, which becomes important when they are put in a magnetic field. This is the basis for a useful spectroscopic technique called nuclear magnetic resonance which you will learn about later.  The explanation for this phenomena are more in the realm of nuclear physics, so we tend to gloss over them.

In organic chemistry, nuclei are not where the action is. We tend to take the nucleus for granted. It doesn’t really change very much. The real action is in the electrons.

As we shall see, in chemistry (especially organic chemistry), the study of chemistry is mostly about the study of how electrons flow between atoms. If economics is about following the flow of currencies, chemistry is largely about the flow of electrons.

Next Post: From Gen Chem to Organic Chem – Electrons and Orbitals

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{ 2 comments… read them below or add one }


Thanks! This makes me realize how wonder Chemistry is :)


Hamada Abulkhair

It’s an excellent introduction.


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