Location of transition states is still perceived as a very difficult problem
in practical applications of quantum chemical methods. Certainly this task is
not yet as routine as that of finding minimum-energy (equilibrium) structures.
One reason for the difficulty is the numerical problem involved in finding a
stationary point on a multidimensional potential energy surface which is a minimum in
all dimensions, except for one direction (the "reaction coordinate"), which is
a maximum. Even more serious, is an overall lack of knowledge of what
transition states "look like". Whereas chemists can easily construct accurate
representations of stable molecules, and thereby provide very good starting points for
structure optimizations, they lack the experience to do the same for transition states.
The situation will change with time, as more and more reactions are
investigated theoretically. No doubt, systematics in transition state structures will
be uncovered. A third problem is that the same quantum mechanical methods
which have proven to be suitable in descriptions of stable species may not be
adequate for transition states, i.e., species in which bonds are partially formed or broken.
The procedure built into Spartan for guessing a transition state is based on
the Linear Synchronous Transit method, and provides a geometry
intermediate between those of reactant and product molecules. There is a single
parameter, indicating the relative weighting of reactant and product structures to be used
in the construction (recall the Hammond postulate). This ranges from 0.0
(reactant structure) to 1.0 (product structure), the default value being chosen as 0.5.
Such a procedure is directly applicable to intramolecular reactions, and as
discussed in Section 7.3.3, may easily be extended to intermolecular processes.
Prior to selecting Transition Search under the
Build menu, structures corresponding both to the reactant and to the product must be open on
screen, and one of these structures (corresponding to the reactant) must be selected.
In the case of a degenerate rearrangement, i.e., reactant and product are the
same, only a single copy needs to be open. (Structures other than reactant and
product open on screen have no effect on the guessing procedure.)
Selecting Transition Search results in the selected molecule being
designated as the "reactant" and leads to a message in the menu bar.
Transition Search: Select a molecule to specify the product.
Clicking on a second molecule (or on the original molecule in the case
of degenerate reaction) designates it as the product, and results in a
split-screen display, with the reactant at the right and the product at the left.
Note that reactant and product must be isomers, i.e., contain the same number
of each element. Attempts to enter the dialog with molecules which are not
isomers will lead to an error message. Structural representations used in the
transition search dialog are the same as those employed in builder and conformer
search dialogs, atoms being designated by small balls and bonds by thin lines.
A button bar, immediately below the menu bar, accesses functions
(Add Pair, Remove Pair, Show
Pair, Generate and Clear) to assist in the generation of
a guess transition state. These may also be accessed from the
Edit menu (see Section 7.3.2.3). The bar also provides a message.
0 of X Atoms Paired
X is the number of atoms (which need to be paired) in the reactant and
product molecules. The first number will be incremented by 1 each time an atom on
one molecule is successfully paired with an atom on the other, until the number
of atoms paired equals the total number of atoms.
Atom pairing is accomplished by first
clicking on the ball designating an atom on one molecule, followed by
clicking on the ball designating the atom on the
second molecule to which the first atom is to be associated. Upon selection of the
first atom of a pair, the associated ball will be colored gold;
clicking on this atom a second time (without
clicking on an atom in the second molecule) deselects
it, returning the ball to its original color. Another atom (in either molecule) may
then be selected. Upon selection of the remaining atom both balls will disappear.
In addition, the counter at the bottom of the screen will be incremented by 1.
Attempts to click in succession on two atoms on the same molecule, or to
click on an atom on the second molecule of different type (atomic number) will result in a
bell, signaling that pairing is not allowed. Try again. This procedure needs to be
repeated until all atoms are associated. Following this, a transition-state guess
is automatically generated and the original split-screen (showing reactant and
product) is replaced by a single screen displaying the guess at the transition structure.
In addition, a dialog appears which allows the guess to be altered.
Weighing Factor is a measure of the extent to which the transition state
guess resembles reactant or product.
"0.0" is fully reactant-like and
"1.0" is fully product-like. The default
value (0.5) may be changed and a new transition
state guess generated by clicking on
Apply.
When the guess is satisfactory, the Transition
Search dialog may be exited by selecting
Quit from the File menu (see discussion below).
