Saturday, January 14, 2012

Free the research #3

So this is the last part of the article I'm publishing as a serial. And I will talk about chemistry. In particular, I'm going to show you something about Avogadro, a very powerful program. By the way, did you know that this program takes its name from the italian chemist/physicist Amedeo Avogadro (, best known for the definition of the "mole" concept with his follower Stanislao Cannizzaro? Basically, the mole is a unit to describe the number of objects you have. For example, having a mole of molecules means you have 6,022*10^23 molecules. And having a mole of books means you have 6,022*10^23 books. This number is now called "the Avogadro number", in honour to the scientist.

Add a dimension to chemistry

Avogadro is one of the best programs to draw molecules in three dimensions. This program, anyway, can do a lot more: it has handy tools to build complex molecules, and gives you some informations about what you have drawn. There is another interesting program (that I will not describe since it's very easy to use): Kalzium. This one is very useful for its "calculators": these are some little tools allowing us to do some simple calculations (concentration of a soluzion, mass of  a compound, etc...). There is also a wonderful chemical equation solver, and a "reader" of risk and security phrases. If you are just starting to learn chemistry, there is also a good glossay, that will show you the main laboratory tools and explain some practices.

Okay, the following part is written in tutorial-style.
THE FIRST SKETCH – Pressing the F8 key we enter into the "draw" view: the Draw settings tab allows us to choose wich atom draw and with wich kind of bond link it to another one (the link can be built clicking on an atom and then arriving to the other keeping the left mouse button pressed).

IMPROVE IT – We can improve the drawing with the menù Extensions (the first one on the left) and choosing  Optimize geometry. Automatically, the program will move the atoms to reach the best geometry, based on the dimension of bonds and steric hindrance.

A BETTER VIEW – Pressing the F9 key we enter the navigation view: holding the left mouse button we can rotate the view, while using the right button it's possible to translate it. The central button controls the zoom. If you want to save the image, use File/Export menù.

Have a look to conformers, the energy, and some other things

CONFORMERS – In the second menù Extensions, is present the voice Molecular Mechanics/Find conformers: this way the program will give us a list of all the possible conformers (you can see the list using View/Properties/Conformation properties).

PROTEINS – It could also be useful to build a peptide: just click on Compile/Insert/Peptide and then choose the amino acids with wich we want to build the proteine. You can also choose the stereochemistry of the molecule and the initial/final terms.

ATOMS – The menù View/Properties/Atom allows us to see informations about every atom present in the molecule: for example, the valence value and the partial charge. Obiously, if the molecule is not an ion, the partial charge will always be zero.


  1. Is there a database of .cml molecules for students aged 13 to 16? Molecules like CO2, CO, H2O, ... that they study at this age (at least in France?) I could not find any so far...

  2. Hi annma, try using Kalzium: it contains a "molecular editor". In that window is possible to draw a molecule (like in Avogadro), load a file from the directory of kalzium, or download some molecules from internet. It's very easy to use, and rich of ready-to-use molecules. Anyway, it's difficult to find simple ones, since you can easily build with Avogadro water, carbon monoxide, etc...
    Kalzium has also a converter for chemical files, so you can turn some files in cml, if you already have molecules in a format you can't open.

  3. I use Kalzium and there's only complicated molecules available. In the purpose of Education I wanted easy molecules to show. I am not sure I can draw them, how would I know about the connections within atoms? I wanted to find CO2.cml and water.cml and such already done.

  4. Well, it's easy to draw bonds, just look at the first point of the tutorial up here.

  5. damn I was looking at already done stuff... Thanks anyway, it would be a nice addition to have some sets of molecules for pre-defined ages for schools.

  6. Thanks for the suggestion, I'm going to upload them on the Kalzium git repository

  7. Actually, it's possibile to find water, carbon monoxide and carbon dioxide in the official Kalzium repository:
    Have fun, and teach chemistry.