Coordinate driving

Both of die above methods can be considered as approximations to the Fukui reaction path, discussed later in this article. The maxinmm of the Fukui reaction path also yields the transition state, although usually at significantly more expense than coordinate driving or the synclironous transit method. A more modem development of these ideas has been given by Ionova and Carter [68]. 

Some of the other features of this program are the ability to compute transition states, coordinate driving, conformation searches, combinatorial tools, and built-in visualization. The builder includes atoms and fragments for organics, inorganics, peptides, nucleotides, chelates, high-coordination geometries, and... 

As explained above, the QM/MM-FE method requires the calculation of the MEP. The MEP for a potential energy surface is the steepest descent path that connects a first order saddle point (transition state) with two minima (reactant and product). Several methods have been recently adapted by our lab to calculate MEPs in enzymes. These methods include coordinate driving (CD) [13,19], nudged elastic band (NEB) [20-25], a second order parallel path optimizer method [25, 26], a procedure that combines these last two methods in order to improve computational efficiency [27],... 

Initially, we have applied the modified NEB method to the calculation of both steps of the 40T catalyzed reaction. The free energy profiles and relative free energies obtained with this method were compared to our previously determined profiles [33], As we had previously shown, the calculated MEPs for Ref. [33] determined with the reaction coordinate driving method, and the MEPs for Ref. [25] calculated with the parallel path optimizer method, agree in the overall shape and relative potential energies. This provides a good starting point for our comparison. 

We have compared the potential and free energies from four different calculated paths for the first step of the isomerization of 2o4hex catalyzed by 40T. Two of these paths were determined with a combined chain-of-states method. The remaining two paths were obtained with the coordinate driving method. 

The energies E [Pn] in Eq. [35] depend on the nuclear solvent polarization that serves as a three-dimensional (3D) nuclear reaction coordinate driving electronic transitions. The two-state model actually sets up two directions the vector of the differential field AS b and the off-diagonal field Sab-Therefore, only two projections of Vn need to be considered the longitudinal field parallel to ASab and the transverse field perpendicular to ASab- In the case when the directions of the differential and off-diagonal fields coincide, one needs to consider only the longitudinal field, and the theory can be formulated in terms of the scalar reaction coordinate... 

Density functional methods are competitive with the above traditional wave function methods for numerous applications such as the computation of ground-state PES. A few applications of transition metal photochemistry have been proposed on the basis of the A-SCF approach implying several approximations on the excited-state reaction-path definition by symmetry constraints not always appropriate in a coordinate driving scheme. Excited-state gradients have been recently implemented in DFT for various functionals, the feasibility of the approach having been tested for small molecules... 

A basic means of modelling approximate reaction paths is the adiabatic mapping or coordinate driving approach [123,149]. The energy of the system is calculated by minimizing the energy at a series of fixed (or restrained, e.g. by harmonic forces) values of a reaction coordinate, which may be the distance between two atoms, for example. More extensive and complex combinations of geometrical variables can be chosen. This approach is only valid if one... 

Calculations (AMI) were carried out using the coordinate drive feature of the Spartan molecular modelling program (Wavefunction, Inc., Irvine, CA), Version 4.0, on a Silicon Graphics workstation... 

At each point in the RGF point, the gradient, g, has a constant direction given by the unit vector r. Typically, this direction is chosen in a similar manner to the coordinate driving algorithms. As we will see in Section 10.5, the second term in Eq. (39) comes from the steepest descent path definition used in reaction path following [162]. 

With the QM/MM model of the system constructed, a straightforward means of modeling approximate reaction paths is the adiabatic mapping or coordinate driving approach. The energy of the system is calculated by minimizing the... 

---