Chem3D Users Manual - CambridgeSoft

To position Atom D in Pro-S Orientation (left) and
Pro-R Orientation (right):
1. Orient the Distance-Defining atom, C, the
First Angle-Defining atom, B, and the Second
Angle-Defining atom, A, such that the plane
which they define is parallel to the X-Y plane.
2. Orient the First Angle-Defining atom, B, to be
directly above the Distance-Defining atom, C,
such that the bond joining B and C is parallel to
the Y-axis, and the Second Angle-Defining
atom, A, is somewhere to the left of C.
Because H(14) is positioned by two bond angles,
there are two possible positions in space about C(5)
for H(14) to occupy; the Pro-R designation
determines which of the two positions is used.
If an atom is positioned by a dihedral angle, the
three atoms listed in the information about an atom
would all be connected by dashes, such as
C(6)-C(3)-C(1), and there would be no Pro-R or
Pro-S designation.
In this orientation, D is somewhere in front of the
plane defined by A, B and C if positioned Pro-R,
and somewhere behind the plane defined by A, B
and C if positioned Pro-S.
When you point to or click an atom, the
information box which appears can contain
information about how the atom is positioned.
Positioning Example
If H(14) is positioned by C(5)-C(1), C(13) Pro-R,
then the position of H(14) is a specified distance
from C(5) as described by the H(14)-C(5) bond
length. Two bond angles, H(14)-C(5)-C(1), and
H(14)-C(5)-C(13), are also used to position the
atom.
The commands in the Set Z-Matrix submenu allow
you to change the Z-matrix for your model using
the concepts described previously.
Because current measurements are retained when
you choose any of the commands in the Set Z-
Matrix submenu, no visible changes in the model
window occur.
Positioning by Bond Angles
To position an atom relative to three previously
positioned atoms using a bond distance and two
bond angles:
1. With the Select tool, click the second
angle-defining atom.
2. Shift-click the first angle-defining atom.
3. Shift-click the distance-defining atom.
4. Shift-click the atom to position.
You should now have four atoms selected,
with the atom to be positioned selected last.
5. From the Structure menu, point to Set Z-Matrix,
and then choose Position by Bond Angles.
ChemOffice 2005/Chem3D Manipulating Models • 103
Changing the Z-matrix