(Modeling proteins)

Verifying Transition States


The final result of a LOCATE-TS calculation should be a transition state.  Sometimes the result is a stable intermediate, i.e., a ground state and not a transition state structure.  To check whether the final geometry is in fact a transition state for the reaction being studied, two steps are necessary.  In the first step, the vibrational frequencies of the atoms in the region of the reaction site are calculated.  If one of these frequencies is large and imaginary (printed as a negative number), and all the rest are positive or small and imaginary, then the system is confirmed to be a transition state.  In the second step, the geometry is displaced by a small amount in the direction of the imaginary vibrational normal mode, and the Intrinsic Reaction Coordinate, using IRC, is generated.  This is repeated after reversing the displacement.  The two IRC curves are then joined together.  If the ends of the resulting curve corresponds to the reactant and product, then the imaginary mode is confirmed to be correct.

Verifying that the system is a transition state

The starting point for validating a transition state is the final ARC file from a  LOCATE-TS run.  Edit this file to remove everything except the data set, i.e. everything except the keyword, title, and comment line, and the geometry.  Edit the keywords to replace the LOCATE-TS keyword with FORCETS ISOTOPE MOZYME EPS=78.4.  Having ISOTOPE is very useful here because it allows a restart to be done in a later calculation, either for for modeling a Kinetic Isotope Effect or to start an IRC calculation. Save the file as a MOPAC data set using a suitable name, e.g., Step_1_2_FORCE.mop, then run it using MOPAC.

Only atoms with optimization flags set to "+1" or "1" will be included in the FORCETS calculation. 

When LOCATE-TS  is used, the option exists to select only the atoms involved in bond making and breaking (Set:1) or these atoms plus those attached to them (Set:2).  The ARC file from a LOCATE-TS run can easily be edited to convert from Set:1 to Set:2 or vice versa.  To go from Set:1 to Set:2, look in the LOCATE-TS output file for the two sets. Set:2 includes Set:1, so identify the new atoms in Set:2 that are not in Set:1.  Edit the FORCETS data set to change the optimization flags of these new atoms from "+0" to "+1" then save the resulting data set with a new name, e.g., Step_1_2_FORCE_Set2.mop.

After running the data set, examine the output to verify that there is exactly one negative vibrational frequency. (Genuine transition states have exactly one imaginary vibrational frequency, but for convenience in computational chemistry programs, this is normally displaced as a frequency preceded by a minus sign, so such vibrational frequencies are often called negative vibrations.  This convention will be used here.) If there are no negative frequencies, the system is a ground state, possibly a stable intermediate.  If there is more than one negative frequency more negative than ~-100cm^(-1), then something is wrong.

If everything is okay, run the Intrinsic Reaction Coordinate.