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5. Press the Enter key.
TIP: The Text building tool will also accept structures in
SMILES notation, either typed in or cut and pasted from
other documents.
Another, simpler, way of building this model is to
type Pentane in the Name=Struct text box and then
modify the appropriate hydrogens.
Refine the model as follows.
1. Click the Select tool
2. Select the model by dragging diagonally across
it.
3. From the Structure menu, choose Clean Up.
If you want a more accurate representation of a low
energy conformation, optimize the geometry of the
model by clicking the MM2 tool on the
Calculation toolbar.
To specify text equivalent to the structure of
1,2-dimethyl cyclopentane shown below:
H 2 C
CH
H 2
C
CH
CH 2
H 3 C CH 3
1. From the File menu, choose New.
2. Click the Text Building tool .
3. Click in the empty space in the model window.
4. Type CH(CH3)CH(CH3)CH2CH2CH2.
5. Press the Enter key.
The trans-isomer appears.
6. Select the model and choose Clean Up from the
Structure menu.
TIP: You don’t have to click the Select tool every time
you want to select something. Just hold down the letter S
on your keyboard while working with any building tool,
and you temporarily activate the Select tool.
You cannot specify stereochemistry when you build
models with labels. The structure of 1,2-dimethyl
cyclopentane appears in the trans conformation.
To obtain the cis-isomer:
1. Click the Select tool .
2. Select C(1).
3. From the Structure menu, choose Invert.
The cis-isomer appears. You can rotate the
molecule to see the differences between the
isomers after you invert the molecule.
Using Substructures
Labels are useful to build simple structures.
However, if you make larger, more complex
structures, you will find it easier to use a
combination of labels and pre-defined
substructures.
Over 200 substructures are pre-defined in
Chem3D. These substructures include the most
commonly used organic structures.
TIP: Pre-defined substructures are listed in the
substructures.xml file. You can view the list by pointing to
Parameter Tables on the View menu and selecting
Substructures. Text typed in the text box is case sensitive.
You must type it exactly as it appears in the Substructures
table.
Build a model of nitrobenzene:
1. From the File menu, choose New.
2. Click the Text Building tool .
3. Click the empty space in the model window.
34 •Chem3D Tutorials CambridgeSoft
Tutorial 3: Building Models with the Text Building Tool