Chemistry: Learning a New Language

 

Many of us are intimidated by chemistry. For those of us who don’t look at chemistry journals everyday, or examine molecular structures very often,  it can be daunting trying to understand chemical structures. 

Nature recently published a quick guide to establishing consistent rules for drawing molecules and understanding what they mean. If you have a basic understanding for how chemist’s draw structures, you can see Nature’s recommendations for particular structures here.

For the rest of us, we have provided a guide to quickly and efficiently see a structure and understand what it is telling us.

 

Chemical Bonds:

I am sure that many of us are familiar with drawing basic bond structures. For example, when you need to draw a small molecule, you can connect two elements with a line, signifying a bond. For example; Carbon (C) bonding with Hydrogen (H) would look like C-H

If we want to draw a full molecule, we can show the bonding between the elements that would represent a molecule.

Methane, a very simple molecule, has one Carbon atom bound with four Hydrogen atoms, as shown below.  In the simplest of terms, a molecule can be described by a chemical equation. This simply lists what elements are in the molecule, and how many of them there are.  The chemical structure of methane is written as CH4 (meaning one Carbon atom, and four Hydrogen atoms). 

003-methane_formula
Source

The image above is a two-dimensional representation of what methane looks like. The drawing does give us more information that the chemical equation. We now know that that the four Hydrogen atoms each bind to Carbon, but what does the molecule look like in reality?

Chemist’s have spent a long time analyzing how molecules look in a 3-D space, and a more accurate representation of methane is below.

Methane-3d
Source

This representation of methane shows that two hydrogen atoms and the carbon atom are in the same plane as the article you are reading. However, two of the hydrogen atoms are out of plane. The black bar indicates that the hydrogen is sticking out of the page (or computer screen), and the dotted lines indicate that the hydrogen is sticking into the page. This is how chemists commonly draw a 3-D structure of molecules.

With modern advancements, software programs can now show molecules in a slightly different way.

molecule_methane_275

Very similar to the previous figure, we see a three dimensional structure of methane. These computer representations however, are not drawn by chemists, and can become extremely complicated for larger molecules that involve several atoms.

 

Basic Drawing:

Now that we understand how bond are normally represented, we can expand our knowledge of drawing molecules.

For simple molecules with a small amount of atoms, it is easy to draw representations the way we have already explored. However, when you need to draw a structure with several atoms, it can take a significant amount of time.

Take for example, octane. The chemical name for octane is C8H18.

octane
Source

While this structure is still relatively simple, it can take a little bit longer to draw.

Chemists have come up with a way to draw long chains of carbon and hydrogen atoms, by simply drawing zig-zag lines (officially dubbed bond-line structures).

octane kink

Each “kink” and “end” in the molecule, represents a Carbon atom. The lines just as before, still represent bonding. In this case we directly see the bonding between the eight Carbons of the molecule (in chemistry, long strings of Carbon are called the ‘Carbon backbone’)

As already mentioned, Carbon is able to make four bonds with other molecules. When drawing a zig-zag representation, the Hydrogen atoms are omitted from the drawing, even though they are present. For example, looking at the far left of the molecule, we see an end that represents carbon. We also see that this Carbon is bonding with another Carbon, that is represented by the first kink.

The Carbon at the end therefore has 3 more bonds to form. Therefore we can assume that 3 Hydrogen bonds are bound to the terminal Carbon molecule.

The Carbon atom located at the first kink has 2 bonds already formed; one with the terminal Carbon, and one with the Carbon in the next kink. There are still two more bonds for Carbon to form, and we can assume that hydrogen will be binding.

The zig-zag method is extremely common in chemistry journals and texts. While drawing octane by showing each atom may not take an abundant amount of time, with larger complex structures however, this can be a real lifesaver.

 

Complex Structures:

Chlorophyl20B
Source

The figure above (depicting chlorophyll, a molecule that gives leaves their green color) shows all of the rules we discussed above, with a few additives. Looking at the molecule, we see that there are 5 carbon ring structures (again each kink represents a Carbon atom unless replaced by another symbol) and some double bonds (representing two bonds between molecules). We also see a few more elements, such as Oxygen (O), Nitrogen (N), and Magnesium (Mg).

Understanding how chemist’s draw is crucial to understanding their research. Now that you have had a crash course in drawing chemical structures, you should be able to apply this knowledge in chemistry classes, and in reading chemistry papers.

If you have any questions on this topics, or other scientific topics, please feel free to comment below or email us directly at copernicuscalledblog@gmail.com. You can also reach us via social media on Facebook, Twitter, or Tumblr.

Note: The information above primarily came from my own experience in my undergraduate and graduate education. Listed below are links that can provide additional information and videos I find helpful. 

And as usual, remember to always be curious and be mindful!

Written by: Cody Wolf

Additional Sources:

  1. https://www.nature.com/articles/d41586-017-05898-6
  2. https://www.khanacademy.org/science/organic-chemistry/gen-chem-review/bond-line-structures/v/bond-line-structures-new
  3. https://socratic.org/organic-chemistry-1/ways-to-draw-and-represent-molecules/bond-line-notation
  4. https://www.wikihow.com/Draw-Organic-Molecules-in-Bond%E2%80%90Line-Notation
  5. https://www.youtube.com/watch?v=ohA3dMqDOqY
  6. Featured Image source: http://aschoonerofscience.com/drugs/mac-for-3d-molecular-visualisation-apple-makes-drug-design-sexy/attachment/scientist-drawing-molecule-structure/
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