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In addition to static calculations, MOPAC can simulate a variety of animations. The main types are:
Time dependent: This is the Dynamic Reaction Coordinate (DRC)
and models the time-evolution of a system. Energy is normally conserved,
that is, as time passes there is an exchange of potential and kinetic energy,
but the sum of the two is a constant. Such simulations never reach a
stationary point, so some mechanism must be used for limiting the run.
Usually keywords CYCLES=n or T=n are used here.
Normally, the step size in a DRC would be 0.1 or 0.2
femtoseconds, 10-15s, specified by T-PRIORITY=0.1 or T-PRIORITY=0.2,
but an alternative is a step-size in change in geometry. This can be
specified by X-PRIORITY=n.nn where n.nn is the step in mass-weighted Angstroms,
a typical value would be 0.2 A.
Heating or cooling can be simulated by use of CRD=n.nn, where
n.nn is the half-life in fs for the loss of kinetic energy - a negative
value of n.nn simulates heating, that is, the gain in kinetic energy.
Time independent: This is the Intrinsic Reaction Coordinate (IRC), and models the change in geometry of the system in response to the forces acting on the atoms. All kinetic energy is annihilated at every step, so the concept of time is missing in this visualization. The IRC is best used in generating paths from reactants through the transition state to a product.
All the examples given here assume the user has
Active-X and Java installed.
|
Sodium plus Chlorine => NaCl |
In this gas-phase DRC reaction, a sodium ion interacts with a chloride ion, but because energy is conserved, no stable diatomic is formed. |
|
Cesium plus Fluorine => CsF |
This DRC reaction illustrates the effect of a large difference in atomic masses. |
|
Ring-opening of Cyclobutene to form Butadiene |
In this reaction, cyclobutene thermally rearranges to 1,3-butadiene. (DRC) (IRC) |
| Sn2 Walden inversion | A fluoride ion collides with a chloromethane in this DRC and IRC reaction to give rise to fluoromethane and a chloride ion. The reaction can be simulated by giving the fluoride ion a velocity in the direction of the chloromethane. |
| Ammonium plus Chloride => Ammonia plus hydrogen chloride | In this DRC, an ammonium cation and a chloride anion react to form ammonia and hydrogen chloride. |
| Vibrations of Formaldehyde | A comparison of the vibrational frequencies predicted using the Hessian matrix and by explicit calculation of the normal modes is presented. |
| The following are still being written | |
| Polymerization of Ethylene | The addition of an ethylene molecule to an ethyl radical is catalyzed by the presence of a titanium complex. (DRC) (IRC) |