I have a bit strange but sweet tradition, to buy people the chocolate if they teach me something, usually some lab trick or the secret ingredient in the protocol.

What I will show you today, in this Part II about the prediction of the properties of molecules cost me about 1 kg of chocolate and the equal amount of cookies – but it was worth.

We will start with the something that you can use as the wallpaper for your desktop, continue with the more scientific and less attractive examples of the application and we will finish with the advice what crypto to buy with the caution.

When the Science Meets the Art

This part was easy and no “chocolate bribe” was needed. I will start with the Chem3D Pro, you can install the free trial version if you follow the link below.

Let’s start with the beautiful infographic from one of my favorite websites - CompoundInterest

And because I like milk chocolate, let's draw the vanillin.

There are some positive sides of living in Flandres: cycling on legendary roads, a lot of historical sites and Belgian Chocolate.

This looks cool, but wait, it will be even better:





What we need to do next is to optimize the conformation (3D arrangement) of our molecule.

This step is very important because it can help us to predict:

how molecules can bond together

how strong the chemical bonds are

can we expect the reactivity or stability

we can even simulate the spectra (vibrational, EPR...)

And all that in a computer!

After the short dance and tweaking, our lovely smelling molecule looks like this:

It probably looks the same and you are right, but even the slightest changes can completely ruin the calculations.

Do you want to see how the solvent can access to this molecule? Check this out:





Here I combined the charges (mesh) and the molecular orbitals and painted it into the colors of the national flags of maybe 10 countries or more: "Vive la France"

The real job starts Now...

After this funny and easy part, rest is usually done in Gaussian and that cost me a lot of chocolates.

I desperately needed it on two occasions, once to see if some free radical really reacts with my molecule or it just interacts with the ingredients of the reaction that generates the radicals.

The second time was really important. I was trying to find what radicals are involved in the decay of some petrochemical products, but... I couldn't find any reference because all the studies were done in water and what I had was all but the water.

If you want to play with the Gaussian and simulate the spectra, it would be the best to start with the YouTube lectures, like this one. Not me, not my voice...