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<TITLE>Example: Building cyclohexane</TITLE>
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<H2><A NAME="SECTION00073000000000000000">
Example: Building cyclohexane</A>
</H2>
Cyclohexane in its chair configuration has a structure which seems quite
complicated to generate, but it can easily be built using V<SMALL>IEWMOL</SMALL>'s
molecule builder. First, start V<SMALL>IEWMOL</SMALL> without any parameter
on the command line and press <code>Cancel</code> in the file selection box
which pops up. You should now have an empty window on your screen. Press the right
mouse button within this window and select <code>Molecule/New molecule ...</code> from the
pop-up menu. The molecule editor will open up. We start building cyclohexane
by building one of the tetrahedra:
<UL>
<LI>Select <code>C</code> from the periodic table.
</LI>
<LI>Click with the left mouse button in V<SMALL>IEWMOL</SMALL>'s window. This will
place the first carbon atom at the origin.
</LI>
<LI>Click with the left mouse button on the first carbon atom. This will
attach the second carbon atom to the first.
</LI>
<LI>Click with the left mouse button on the second carbon atom. This will
attach the third carbon atom to the second.
</LI>
<LI>Select <code>H</code> from the periodic table and click twice on the central
carbon atom. The molecule should now look like the left one in
<A HREF="node15.html#cyclohexane">the Figure</A>.
</LI>
</UL>
To continue building cyclohexane we have to remember that the torsion
angles among the carbon atoms alternate between gauche and -gauche
which can be determined easily by looking at the Newman projection:
<DIV ALIGN="CENTER">
<IMG
WIDTH="157" HEIGHT="108" ALIGN="BOTTOM" BORDER="0"
SRC="newman.png"
ALT="Newman">
</DIV>
<UL>
<LI>Select <code>C</code> again and set the default torsion angle to gauche.
</LI>
<LI>Click on one of the end carbon atoms. Then select <code>H</code> and
click on the same carbon atom two more times.
</LI>
<LI>Change the default torsion angle to -gauche and repeat the last
two steps on the just added carbon atom. The molecule should now look
like the one in the middle of <A HREF="node15.html#cyclohexane">the Figure</A>.
</LI>
<LI>Change the default torsion angle to gauche again and add a carbon
atom and one hydrogen atom to the last carbon atom. The molecule will
now look like the right one in <A HREF="node15.html#cyclohexane">the Figure</A>.
</LI>
<LI>Change the default torsion angle to trans and add the second
hydrogen atom to the carbon atom added last.
</LI>
<LI>Now change the default torsion angle to -gauche and add one
hydrogen atom to the next carbon atom in the ring, then change the
default torsion angle to trans and add the second hydrogen atom.
</LI>
<LI>Finally, complete cyclohexane by adding first a hydrogen with
the default set to trans and than a hydrogen with the default set to
gauche to the next carbon atom in the ring.
</LI>
</UL>
<P>
<P></P>
<DIV ALIGN="CENTER">
<A NAME="cyclohexane">
<STRONG>Figure 13:</STRONG>
Building cyclohexane
<BR>
<IMG
WIDTH="482" HEIGHT="95" ALIGN="BOTTOM" BORDER="0"
SRC="cyclohexane.png"
ALT="Cyclohexane">
</DIV><P></P>
<P>
<BR><HR>
<ADDRESS>
<A HREF="mailto:joehill@users.sourceforge.net"><I>Jrg-Rdiger Hill</I></A><BR>Sun Dec 10 17:38:35 MET 2000
</ADDRESS>
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