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Dihedral angle calculation of a molecule





Before starting this experiment's procedure, please kindly go through the general procedure described in experiments "To build a molecule using Avogadro software" and "To add Hydrogen to the molecule" for building and adding hydrogen to the molecule to satisfy the atomic valency.



In this exercise, we will be studying how to measure and how to change distance, angle or dihedral angle of the molecule.


1. Follow the preliminary steps as indicated above to build a computational model and add hydrogen using Avogadro's software.


2. The "Bond Centric Manipulation Tool" which is displayed on the top of the workspace panel enables to measure and change bond length and angle.



Figure 1: Selecting the "Bond Centric Manipulation Tool"



3. For measuring the distance between two bonded atoms, user can simply click on the two atoms.



4. From the screenshot below, bond angles can be observed around the selected atoms (pointed with arrows). Bond length is shown on the bottom left corner of work space panel as shown in screenshot.





Figure 2: Displaying the bond angle and bond length of the molecule.



5. To clear previous measurements as shown in above screenshot, right click on mouse or press "Ctrl" and click left mouse button to clear the list of selected atoms.



6. For changing bond length, click on the bond present between bonded atoms. A rectangle will be drawn connecting the bonded atoms and center. To rotate the plane about the bond, click on the bond and drag by holding the left mouse button.



7. Right click on the selected atoms and drag them to change bond length. It displays bond length at the bottom left corner.



8. To change bond angle, left click on the atom in the selected area and drag it. The atom which is rotating will move on a highlighted plane and the other atoms lie in the center. Angles of other atoms will update automatically.



Figure 3: Rotating the plane about the bond to change bond angle and length



9. The "Measure Tool" which is displayed on the top of the page, measures angles, dihedral angle or distance.



Figure 4: Selecting "Measure Tool" to measure dihedral angle



10. User can select upto 3 atoms by left clicking mouse button. Bond lengths are measured between atoms. Angles between them are measured consequently. Each click will display the number on the atoms. Appropriate angles and distance can be read as message on the left bottom corner of the work space panel. Right clicking will clear the selected atoms.



11. By clicking on the 4 atoms like shown in the below screenshot will display the dihedral angle between them. It can be seen on the bottom left corner of the page along with their bond angles and lengths.


Figure 5: Displaying the bond angle and bond length of the molecule with 3 atoms


 12. Click on an atom which is nearest to the bond and drag it to change the dihedral angle. Adjust the angle until it ranges in and around 90 degrees.


Figure 6: Displaying the dihedral angle of the molecule


13. The "Snap-to Bonds" (and Snap-to Threshold) option will allow the user to set angle to check whether the angle plane would "snap" when it comes close to the bond which is present adjacently.

Figure 7: Bond Centric Manipulation Settings


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