Three features:
• Configuration (atom organization).
• Conformation (atom spatial arrangement).
• Shape (Surface landscape, steric packing)

I. Configuration:

 

• The organization of atoms and chemical bonds.
 
• Change of configuration requires breaking bonds.

 
Example:

         NH₂
          |
   H--C--OH
          |
         CH₃

 
Switch between H and NH2 requires bond breaking.
 
 
 
 


The image on the right is an mirro image of the one at left.
 
 

 
 
 
II. Conformation:
 
• Determined by the spatial positions of its constituent atom.
 
 
• Interconvertible without breaking and making bonds.



 
 
• Conformation change is the key in many chemical reactions in living system. Click here to view ilustration movies.
 
 
 

III. Shape
 

• Steric packing (what part of space is covered by the compound).
 

 
 
 
 
• Surface features (cavities, grooves where other molecules can bind to).
 
 
 
• Molecular shape determines the binding of two molecules.

 
 

 
 
 

 
 
 
 
 
 
 
• Introduction to 3D molecular graphics software: Rasmol.

• Rasmol converts xyz coordinate of a molecule into 3D graphics in several display modes.

• Molecule can be moved and rotated to view it in different angle.

• Individual bond can be measured and rotated.

• Input file can be in different format (the most popular are MDL Mol format: file.mol, and Brookhaven databank format: file.pdb).

• Output graphics in several standard format (such as bmp and gif).
 

 Basic operations:

• Open a xyz coordinate file:

File=>Open=>List Files of Type=>MDL Mol File Format=>(Select File)

• Move and rotate the molecule:

Use the mouse.

• Change the display mode:

Display=>(Make selection).

• Export image:

Export=>(Select the desired format such as GIF)

• Measure and rotate chemical bond:

Step 1: Select item on the side window.
Step 2: Click on the relevant atoms.
Step 3: To rotate a bond, hold down the left button of the mouse and move.