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2398 Words Sep 4th, 2014 10 Pages
What is the Scale of Chemistry?

Chemistry is the study of matter and its transformations. Everything that you can taste, touch, see or smell is composed of chemicals. All the chemicals around you are made from various combinations of the elements on the periodic table. These elements can range considerably in size; specifically, atoms at the top of the periodic table are smaller than those near the bottom. The study of atoms and the reasons for the trend in their sizes will be covered in class later this semester.

Many of the chemicals we encounter everyday are molecular in structure. Molecules are specific combinations of atoms. The oxygen we breathe in and the carbon dioxide we breathe out are both molecular in their structure.
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NMR is the scientific technique that is familiar to the public as magnetic resonance imaging (MRI), used in medical centers today. We will learn a lot more about NMR in organic chemistry next year.

Opening JMOL software & Selecting a Chemical Structure:

1. On the desktop, double click on the icon labeled ‘Jmol-Shortcut’.

2. From the top menu, click ‘File’, then click ‘Open’. In the new window next to ‘Look in’, there is a dropdown window; click on the dropdown arrow and scroll up to ‘Desktop’. Then double-click on ‘Scale of Chemistry Lab Files’. A list of chemical structure should be available with the extension “.pdb”.

3. Find the DNA chemical structure and open the file.

4. Notice that there is a color code to identify the atoms in the DNA structure. Right click to ‘Style’ ‘Labels’  ‘With Element Symbol’ to see how each color corresponds to each atom. (Right click the chemical structure using the lower right side of the mouse pad)

5. Change the display to “Ball and Stick”. To do this, right mouse click anywhere on the DNA structure. Choose ‘Style’ → ‘Scheme’ → ‘Ball and Stick’.

You should now see an image similar to the one shown in the figure on the right.

6. To measure the distance between two atoms:

Right mouse click anywhere on the DNA structure

Choose

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