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Introducing Hydrogen atoms to a molecule
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Procedure

 

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

 

Figure 2: Selecting the Element to draw molecule


4. 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.

 

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

 

Figure 3: Drawing the molecule

 


6. Here as a simple example, we are drawing the structure of “Ethyl alcohol “.  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 4: Structure of Ethyl Alcohol


7. User can select bond type 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 respective bond.  Each click on the bond will make it single/double/triple bonds.

 Figure 5: Selecting bond from Bond Order


8. User can add Hydrogen by selecting “Element as Hydrogen” from the scroll bar options and thereby adding it to the builder molecule to satisfy atomic valency. This is done when the “Adjust Hydrogen” check box is unchecked.

Figure 6: Representation of Ethyl alcohol

 


9. User can also add hydrogen while building the molecule by selecting the “Adjust Hydrogen” which is displayed as check box on the left side of the work space panel.

Figure 7: Adjust hydrogen check box


10. 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.

Figure 8: Selecting Optimize Geometry

Figure 9: Optimized structure of Ethyl Alcohol

 

 

 


 

 

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