Biomedical Engineering Reference
In-Depth Information
from which we note that a (triangular) stationary point has indeed been found. But is it a
transition state? I included the freq control word to check, and sure enough
****** 1 imaginary frequencies (negative Signs) ******
Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scatter-
ing
activities (A**4/AMU), depolarization ratios for plane and unpolarized
incident light, reduced masses (AMU), force constants (mDyne/A),
and normal coordinates:
1
2
3
A
A
A
Frequencies -- -1004.9940
2058.3451
2151.5200
Red. masses --
1.1934
1.0539
11.8266
Frc consts --
0.7102
2.6307
32.2554
IR Inten --
79.7952
218.6471
5.1097
Atom AN
X
Y
Z
X
Y
Z
X
Y
Z
1
6
0.08
0.06 0.00
-0.06
0.00 0.00
-0.01
0.72 0.00
2
1
0.16 -0.98 0.00
0.99
0.13 0.00
-0.18
0.24 0.00
3
7
-0.08
0.02 0.00
-0.02 -0.01 0.00
0.02 -0.63 0.00
22.2 The Reaction Path
A transition structure is a maximum on the reaction pathway, but for some reactions the
potential energy surface can be complicated. It may not be obvious whether the transition
state connects the desired reactants and products and in such cases it is advisable to follow
the reaction path from the transition state to the reactants and to the products. A reaction
path can be defined for any coordinate system as the minimum energy path from the
transition state down to the reactants and to the products; if the coordinates are mass-
weighted Cartesians this path is the
intrinsic reaction coordinate (IRC)
. The key reference
for IRC calculation is the paper by Gonzalez and Schlegel (1989), and this algorithm is
implemented in Gaussian 03. The following is part of the abstract.
Anew algorithm is presented for obtaining points on a steepest descent path from the transition
state of the reactants and products. In mass-weighted coordinates, this path corresponds to the
intrinsic reaction coordinate. Points on the reaction path are found by constrained optimizations
involving all internal degrees of freedom of the molecule. The points are optimized so that the
segment of the reaction path between any two adjacent points is given by an arc of a circle, and
so that the gradient at each point is tangent to the path. Only the transition vector and the energy
gradients are needed to construct this path. The resulting path is continuous, differentiable and
piecewise quadratic...
We now take the HCN
→
HNC example.
- -Link1- -
%chk=c:/hcn.chk
# mp2/6-311g(2d,1p) irc=rcfc geom=check
