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March 31, 2020

Bond angle selection by boxing the atoms Log Out | Topics | Search
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Marcus Bond
Unregistered guest
Posted on Monday, March 28, 2016 - 4:14 pm:   

In selecting bond lengths and angles, I have been giving students the instructions in the User Guide, i.e. click on the select tool, then select 2 or 3 atoms in a row. Some enterprising students have tried an alternate method in which they click on the select tool, then drag a box around the atoms. Dragged around 2 atoms it gives the correct bond length, but around 3 atoms it gives an incorrect bond angle. Water, optimized at the PM7 level in MOPAC 2016, gives an angle of 37.309 degrees, which corresponds to the O-H-H angle. Is this a hidden feature of the Results window? And, if so, is there a means of getting the correct bond angle out?
JR Schmidt
Username: Schmidt

Post Number: 500
Registered: 11-2006
Posted on Monday, March 28, 2016 - 4:22 pm:   

Both answers are "correct", but for different questions.

Note that the bond angle is always given for the atom 1-2-3 bond angle, where 1-2-3 is the order of selection. If you drag a box to select the first two atoms, it is somewhat indeterminate which is "1" vs "2". Hence in some cases students are getting (probably desired) H-O-H angle while other are getting the H-H-O angle.

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