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Constructing computational model of a molecule
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1. Open Avogadro software by clicking on Avogadro icon from your desktop.

 

2. Select the “Pencil Draw Tool” which is displayed on the top of the window.

 

Figure 1 : Selecting Pencil Draw Tool

3. Here as a simple example, we are drawing Ethanol. Ethanol (ethyl alcohol or drinking alcohol) is a 2 carbon atom having a single bond between carbon atoms and an OH group attached to it.


             Molecular formula: CH3-CH2-OH


             Empirical formula: C2H6O

Figure 2: Structure of Ethyl Alcohol

 

 4. Select the element from the scroll bar “Element” which is displayed on the left side of the window.

Figure 3: Selecting the Element to draw molecule

 

5. After selecting element, draw the molecule by clicking on the main window, which will build the computational representation of the selected element on the work space panel.

 

6. Drag the mouse cursor by holding the left mouse button to draw the bond from one element to another.

 

7. User can select bond from the “Bond Order” which is displayed on the left side of the window or the user can simply click on the bond to make the bond. Each click on the bond will make it single/double/triple bonds.

 

 

 Figure 3: Selecting bond from Bond Order

8. Here the molecule is displayed in the “Ball and Stick” model which is the default representation. User can select different display options according to their preference by clicking on the “Display Types” which is on the bottom left side of the work space panel.

 

 

9. From the “Extension” tab, user can select “Optimize Geometry” which enables the user to optimize the geometry of the molecule which is drawn. Geometric Optimization is the process of managing the atomic arrangement to make the molecule more stable. Molecules with lowest energy are more stable.
 

 

 

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