Modifying Angles

Bond angles and dihedral angles are modified with Angle and Dihedral SmartSlides.


The Angle and Dihedral SmartSlides

Once you have modified a parameter using the SmartSlide, the OK button must be pressed before any of the changes made on any SmartSlide are actually applied to the molecule. Clicking the close box will discard any changes; it is equivalent to selecting the Cancel button.

The figure following illustrates some of the combinations of various Displacement settings for bond angles (they work in the same way for dihedral angles). The possible choices for each popup menu are:

original
Original Molecule
angle_f_f_ra.tif
1,2=Fixed, 3=Rotate Atom
angle_f_f_rg.tif
1,2=Fixed, 3=Rotate Group
angle_f_f_tg.tif
1,2=Fixed,
3=Translate Group
 
angle_ra_f_ra.tif
1,3=Rotate Atom, 2=Fixed
angle_rg_f_rg.tif
1,3=Rotate Group, 2=Fixed
angle_tg_f_tg.tif
1,3=Translate Group,
2=Fixed

Bond Angle Modification Options

All six of these structures result from increasing the 1-2-3 bond angle. In the top row, atoms 1 and 2 are both held fixed. Compare the results of increasing the bond angle to the same value in the three cases (keeping in mind the “normal” position for the ring atoms and the methyl groups). The movement of the methyl group attached to atom 3 ranges from substantial in the first frame to a little in frame 2 to almost none in frame 3. In the second row, atom 2 is held fixed while other choices are used for atoms 1 and 3. Comparison of these illustrations as well as experimentation will make the differences between the choices clear and familiar.

Modifying Dihedral Angles via Newman Projections

The View Along popup menu in the lower left corner of the Dihedral SmartSlide dialog allows you to reposition the molecule using a Newman projection along the 2,3 internuclear axis or the 3,2 internuclear axis.


Viewing a Dihedral along the 2,3 Internuclear Axis
You may choose to reposition the molecule so that the 1,2 or 3,4 axis is vertical.