Create Molecule

We are going to start tutorial in computational chemistry with a simple example, in which the beginner should know about computational chemistry. When computational chemist want to study the electronics structure or chemical properties of molecule, they have to model and optimize the geometry of molecule first. Then they continue to compute the electronics properties using theoretical technique. In reality, we cannot calculate all computational parameter by hand because the mathematical equation is very complicate and very difficult. Instead, we use the program or software to help us to perform the calculation and solve the problem as not wasting of time.

This lesson begins with how to draw or create structure of molecule in both 2D and 3D by a Chemdraw program. Howiver, there is another efficient open-source program becuase Chemdraw is not free even for education, unless your university havve bought the its license. Therefore, in this lession, you are encouraged to learn drawing a 2D structure first, and then 3D structure. You have to watch a video of introduction to drawing molecule by Chemdraw program and then do some exercise. by yourself.

After you have finished with 2D structure, we will continue to create 3D structure by another program. There is many Graphical User Interface (GUI) molecular editor for modelling 3D structures. We will use Avogadro program , a popular open-source software and easy for novice, for this purpose. You can download Avogadro from here and install Avogadro yourself by following instruction below (in Thai).

Introduction to Chemdraw program and How to simply draw a molecule structure in 2D [video is in Thai]

Introduction to Gaussview and Avogadro programs to simulate the 3D molecular structure.

Supplement

1. ChemDraw http://www.cambridgesoft.com/software/overview.aspx
2. Gaussview http://gaussian.com/gv6features/
3. Avogadro https://avogadro.cc/