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ChemOffice.Com - CambridgeSoft

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To perform an inversion:<br />

1. Select the atom.<br />

2. From the Structure menu, choose Invert.<br />

The Invert command only repositions side<br />

chains extending from an atom.<br />

For example, if you choose Invert for the structure<br />

below when C(1) is selected:<br />

The following structure appears.<br />

Plane, all of the X coordinates are negated. You can<br />

choose Reflect Through X-Z Plane to negate all of the<br />

Y coordinates. Likewise, you can choose Reflect<br />

Through X-Y Plane to negate all of the Z coordinates.<br />

You can choose Invert through Origin to negate all of<br />

the Cartesian coordinates of the model.<br />

If the model contains any chiral centers, each of<br />

these commands change the model into its<br />

enantiomer. If this is done, all of the Pro-R<br />

positioned atoms become Pro-S and all of the Pro-S<br />

positioned atoms become Pro-R. All dihedral<br />

angles used to position atoms are negated.<br />

NOTE: Pro-R and Pro-S within Chem3D are not<br />

equivalent to the specifications R and S used in standard<br />

chemistry terminology.<br />

For example, for the structure below, when any<br />

atom is selected:<br />

• From the Structure menu, point to Reflect Model<br />

and choose Through X-Z Plane.<br />

To invert several dihedral angles (such as all of the<br />

dihedral angles in a ring) simultaneously:<br />

1. Select the dihedral angles to invert.<br />

2. From the Structure menu, choose Invert<br />

stereochemistry.<br />

All of the dihedral angles that make up the ring<br />

are negated. Atoms positioned axial to the ring<br />

are repositioned equatorial. Atoms positioned<br />

equatorial to the ring are repositioned axial.<br />

Chem3D produces the following structure (an<br />

enantiomer):<br />

Reflection<br />

use the Reflect command to perform reflections on<br />

your model through any of the specified planes.<br />

When you choose the Reflect commands certain<br />

Cartesian coordinates of each of the atoms are<br />

negated. When you choose Reflect Through Y-Z<br />

<strong>ChemOffice</strong> 2005/Chem3D Building and Editing Models • 67<br />

Changing Stereochemistry

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