The CAMISO fortan code can be downloaded
here by clicking your right mouse button:
code
Example CAMISO script
The
task now is to calculate the isotope effects using CAMISO. The input script of
CAMISO first provides the program with information on the type of isotope
effect to be calculated (RATE or EQUI) and the number of reactions to be investigated.
Each different isotopic substitution is regarded as a single reaction. To
evaluate four isotopic substitutions,
five reactions must be carried out (this includes the unsubstituted
reaction).
ISO
RATE 5
After
the title line, the absolute temperature is supplied (in this case 310.15K).
Below that, the barrier height is supplied for the process under study; it is
used to evaluate any tunnelling corrections needed for the system. The first
number on this line is a flag that can assume a value of zero or one; it
determines if the barrier height is included into the calculation. The next two
lines give the species studied and the relative stoichiometry. In this case,
one reactant molecule leads to one TS molecule.
ISOTOPIC RATE CONSTANTS FOR TS
1 310.15
0 6.50
1 REACT
1 TS
The
co-ordinates and force constants are now supplied for the reactant. The “1 1 0” line states the rotational
symmetry number and the electronic degeneracy (or multiplicity) of the reactant
molecule; the zero is a flag and is set to one if vibrational frequencies are
supplied as input data. The rotational symmetry number represents the number of
ways a molecule can be rotated into an identical orientation. For the ES
complexes, both the symmetry number and multiplicity is set to one. There are
no blank lines between the “1 1 0” or the previous line (i.e. the 1 TS line).
Similarly there is no newline character between the “1 1 0” and the reactant
input deck. The braces only indicate the start and end of the reactant input
deck and do not occur in the CAMISO script itself. The “0 2 1 2” line informs
CAMISO of respectively, the number of imaginary and the number of near-zero
frequencies in the system. In this case, there are no imaginary frequencies and
two near-zero frequencies in the reactant (these being the first and second
reported frequencies in the system).
1 1 0
{
Reactant
CAMISO input deck
}
0 2 1 2
Next
in the CAMISO script is the TS structure information; it immediately follows the
“0 2 1 2” line of the reactants. This time, however, there is one imaginary
frequency and two near-zero frequencies associated with the TS. The latter are
reported as the second and third frequency of the system.
1
1 0
{
TS
CAMISO input deck
}
1
2 2 3
After
reading in the TS information, the other reactions are defined with the
stoichiometry of the system given first. All the atomic masses of the atoms in
the system are then supplied with a maximum of 16 atoms declared on one line
before moving onto the next. The “.” in the following part of the script
represents a “space”; there should also be no white space characters inbetween
the reactions. Any deviation from this format will result in the script not
running successfully. The isotopically substituted species for each reaction is shown in bold.
Reaction
2:
1 REAC
1 TS
1 1 0 PRO-R EFFECT
.12C..12C..16O..12C..12C..12C..16O..12C..16O...1H...1H...1H...1H...1H...2H..16O
.12C..16O...1H...1H..12C..12C..16O..16O...1H...1H...1H...1H...1H..14N..12C..12C
..1H...1H...1H..16O...1H..16O..12C..12C..12C..12C..14N..12C..12C...1H...1H..16O
.16O...1H...1H..12C...1H...1H..12C..16O..16O...1H
0 2 1
2
1 1 0
.12C..12C..16O..12C..12C..12C..16O..12C..16O...1H...1H...1H...1H...1H...2H..16O
.12C..16O...1H...1H..12C..12C..16O..16O...1H...1H...1H...1H...1H..14N..12C..12C
..1H...1H...1H..16O...1H..16O..12C..12C..12C..12C..14N..12C..12C...1H...1H..16O
.16O...1H...1H..12C...1H...1H..12C..16O..16O...1H
1 2 2
3
Reaction 3:
1 REAC
1 TS
1 1 0 PRO-S EFFECT
.12C..12C..16O..12C..12C..12C..16O..12C..16O...1H...1H...1H...1H...2H...1H..16O
.12C..16O...1H...1H..12C..12C..16O..16O...1H...1H...1H...1H...1H..14N..12C..12C
..1H...1H...1H..16O...1H..16O..12C..12C..12C..12C..14N..12C..12C...1H...1H..16O
.16O...1H...1H..12C...1H...1H..12C..16O..16O...1H
0 2 1
2
1 1 0
.12C..12C..16O..12C..12C..12C..16O..12C..16O...1H...1H...1H...1H...2H...1H..16O
.12C..16O...1H...1H..12C..12C..16O..16O...1H...1H...1H...1H...1H..14N..12C..12C
..1H...1H...1H..16O...1H..16O..12C..12C..12C..12C..14N..12C..12C...1H...1H..16O
.16O...1H...1H..12C...1H...1H..12C..16O..16O...1H
1 2 2
3
Reaction 4:
1 REAC
1 TS
1 1 0 COMBINED PRO-R
and PRO-S EFFECT
.12C..12C..16O..12C..12C..12C..16O..12C..16O...1H...1H...1H...1H...2H...2H..16O
.12C..16O...1H...1H..12C..12C..16O..16O...1H...1H...1H...1H...1H..14N..12C..12C
..1H...1H...1H..16O...1H..16O..12C..12C..12C..12C..14N..12C..12C...1H...1H..16O
.16O...1H...1H..12C...1H.. 1H..12C..16O..16O...1H
0 2 1
2
1 1 0
.12C..12C..16O..12C..12C..12C..16O..12C..16O...1H...1H...1H...1H...2H...2H..16O
.12C..16O...1H...1H..12C..12C..16O..16O...1H...1H...1H...1H...1H..14N..12C..12C
..1H...1H...1H..16O...1H..16O..12C..12C..12C..12C..14N..12C..12C...1H...1H..16O
.16O...1H...1H..12C...1H.. 1H..12C..16O..16O...1H
1 2 2
3
Reaction 5:
1 REAC
1 TS
1 1 0 LEAVING GROUP
O
.12C..12C..16O..12C..12C..12C..16O..12C..16O...1H...1H...1H...1H...1H...1H..16O
.12C..16O...1H...1H..12C..12C..16O..16O...1H...1H...1H...1H...1H..14N..12C..12C
..1H...1H...1H..16O...1H..18O..12C..12C..12C..12C..14N..12C..12C...1H...1H..16O
.16O...1H...1H..12C...1H...1H..12C..16O..16O...1H
0 2 1
2
1 1 0
.12C..12C..16O..12C..12C..12C..16O..12C..16O...1H...1H...1H...1H...1H...1H..16O
.12C..16O...1H...1H..12C..12C..16O..16O...1H...1H...1H...1H...1H..14N..12C..12C
..1H...1H...1H..16O...1H..18O..12C..12C..12C..12C..14N..12C..12C...1H...1H..16O
.16O...1H...1H..12C...1H...1H..12C..16O..16O...1H
1 2 2
3
Finally,
the STOP command is issued to terminate the running of the script.
STOP