Chemtube3d

A GUIDE TO MAKING ANIMATED
REACTIONS
Contained within these pages is a simple guide on how to make your own
interactive reactions. There are several techniques that can be used to
construct these animations; it all really depends on the molecules involved
in the chosen reaction.
The steps involved in producing these animations will be explained using a
simple diels-alder reaction as anexample, that of ethylene and 1,3butadiene.
NOTE: This guide is specific for a Mac computer and some of the options may vary
from that of a PC.

• Finding the transition state:
Open up ‘SPARTAN’ and on a blank page construct the two molecules
relatively close together as shown below: (Make sure you are comfortable
with the use of Spartan)

From here select the ‘transition state’ arrow optionand move the relative
electrons into the positions that you require. Once this is done press the
R⇒P button to give something similar to below:

Under the setup menu select calculations. Tick the frequencies option, and
if any of the molecules possess a charge, adjust that setting as required.
Select the transition-state geometry option and the level of calculation
you wish to perform. Agood starting block is always the Hartree-Fock, 321G option. However, if this produces undesirable results, a higher level of
calculation may work better, but takes much longer. Semi-Empirical
methods are also good for some examples, either AM1 or PM3. To
increase the number of steps to perform, type OPTCYCLES=X into the
options box. (X indicates the number of iterations). Submit thecalculation.

Once the calculation is complete, click on spectra from under the display
menu. Check that there is only one imaginary frequency and select it. (The
imaginary frequency is at the top of the list indicated with an (i), and for
this example should be about 818.85). If the vibration resembles that which
you would expect for the reaction then proceed as described below, if not, adifferent level of calculation is required, try Hartree-Fock, 6-31G*.
Finding the transition state geometry is performed in this way for all
examples.

• Producing the IRC: (Intrinsic reaction coordinate)
For very simply molecules it is possible to find the IRC using Spartan
directly. To do this simply tick the IRC box on the calculations screen, and
perform the calculation again. That said, formost examples this just
produces static models, making its use very limited.
A much more successful way to produce an IRC involves using ‘GAMESS’
and ‘MacMolPlt’. Through Spartan, export the transition state geometry
structure as a .xyz file. From here, open up the .xyz file in MacMolPlt and
under edit select copy coordinates.
Now using a text program, such as Text Wrangler, open up a new pageand
copy the contents of the table below onto the page:
$CONTRL SCFTYP=RHF RUNTYP=hessian COORD=UNIQUE
MAXIT=200 ICHARG=0 MULT=1 exetyp=run $END
$STATPT OPTTOL=1.0E-5 purify=.t. hssend=.t. $END
$BASIS GBASIS=N21 NGAUSS=3 NDFUNC=1 $END
$FORCE purify=.t. $END
$irc saddle=.t. npoint=50 FORWRD=.f. $end
$GUESS GUESS=HUCKEL $END
$SYSTEM MWORDS=2 $END
$DATA
C1
$END

Be sure to copy thisexactly, including all the spaces that are present. If the
reaction has a charged component, be sure to change the ‘ICHARG=0’
command accordingly, and for larger molecules, alter the number in the

‘$SYSTEM MWORDS=2’ command to about 5, which should be
adequate for most examples.
Now insert the coordinates of the transition state in between the C1 and
$END command, which will give thefollowing:
$CONTRL SCFTYP=RHF RUNTYP=hessian COORD=UNIQUE
MAXIT=200 ICHARG=0 MULT=1 exetyp=run $END
$STATPT OPTTOL=1.0E-5 purify=.t. hssend=.t. $END
$BASIS GBASIS=N21 NGAUSS=3 NDFUNC=1 $END
$FORCE purify=.t. $END
$irc saddle=.t. npoint=50 FORWRD=.f. $end
$GUESS GUESS=HUCKEL $END
$SYSTEM MWORDS=2 $END
$DATA
C1
C 6.0 1.41299999
C 6.0 1.41299999
C 6.0 0.54759997
H 1 .0 1.94729996
H 1 .0...