1 - Molecules & Jmol

Using Jmol to observe molecules in 3D

Objectives:
1. Access the online version of Jmol
2. Load a molecule into Jmol

Where to start?

You can start using Jmol in several ways. If you are using it on your computer or laptop, or even from a removable media (flash drive), you can access it by downloading, unzipping, and running the Jmol.jar file located in the main folder on the Jmol website.

Now, if you don’t want to install anything, you can also access it online from various sites. In this Course, we will use a very famous one, adapted from one of the program’s developers. Just click on this link in a new tab.

Alternatively, throughout this Course, you can copy the code from any example by clicking on the “folder” icon to the right of each shaded area. Done! The code is copied to the clipboard. Now just paste it somewhere (notepad or Jmol). In the case of Jmol, copy the link below and paste it into a new tab in your browser, then press Enter.

https://chemapps.stolaf.edu/jmol/jmol.php?model=water

Now, click on the molecule with the left button of your mouse or with the touchpad (for notebooks), and make random movements. Or rotate the middle mouse button, or perform pinch and zoom gestures with two fingers on the touchpad. The Figure 1 below illustrates the result.

Figure 1: Screen (clickable) showing the water molecule model rendered in a browser by the St. Olaff College website.

This is the main essence when we refer to the idea of flying molecules for this Course.

How to load a molecule online ?

To play around with another molecule, try changing the model on the internet page itself, at the end of the line. And now follow the MAP (Teaching support material).

Some representations of molecules. Source: MAP: high school - 1st semester, 3rd year, p.51. Natural sciences and their technologies.

Let’s illustrate this with the structure of vitamin C (ascorbic acid).

https://chemapps.stolaf.edu/jmol/jmol.php?model=ascorbic acid

You can try this with other molecules by typing their names in English, as this is a foreign website. However, the database for this search is not unlimited, and sometimes the system will not find the desired molecule.

But there are alternatives. One of them is to search for the name of the molecule on a website used as a database, PubChem. For example, for vitamin C (ascorbic acid):

Now it’s up to you:

Go to the PubChem website;
Search for tylenol;
If it exists, type that same term at the end of the JSmol online line, as follows, and see if it works:
https://chemapps.stolaf.edu/jmol/jmol.php?model=tylenol

How to upload a molecule online, but in 2D

Sometimes it can be interesting to view a molecular model statically and in two dimensions. To do this, simply add “image2d” to the line of code, as follows:

https://chemapps.stolaf.edu/jmol/jmol.php?model=tylenol&image2d

2 - Mouse clicks versus command text

Objectives:
1. Observe that there are two ways to perform actions in some programs: using the mouse or using text commands
2. Observe the characteristics of each method
3. Learn some principles for “Reproducible Teaching” and the advantages of using command lines instead of mouse movements