Mod:Hunt Research Group: Danharm

This page goes over how to produce spectra for deutrated system and how to compute anharmonic spectra

Set up: a normal frequency analysis

first optimise your molecule and perform a standard frequency analysis
you can then use a script to extract the vibrational modes and their intensity get_freq

to use the script copy it to your username/bin directory and make it executable: chmod o+x get_freq

then in the directory of your filename.log file type get_freq filename (ie drop the .log extension)

you will get two files filename.colfreq and filename.colint which contain the frequencies and intensities respectively

use a graphing package to view these

you can visualise the vibrations in gaussview via either the log or chk files

you can view the vibrations, displacement vectors and a vibrational spectrum

you can save the vibrational spectrum as a data file by clicking on the spectrum and choosing save data

if you save the spectrum, make sure that it starts at zero, and I normally reduce the step size to 1 wavenumber

Deuterated spectra

you have several options
you can run the freqchk utility, go here for instructions g16 freqchk utility

if you are running on cx1 you will need to load the gaussian module you are using explicitly first ie module load gaussian/g09-c01

you can then run this interactively by just typing freqchk

or you can pass several options directly via the command line

the options you want normally are

N to hyperchem files

0 for the default temperature 25 degrees C

0 for the default pressure 1atm

1.0 for no scaling of frequencies

N to use non-standard atomic masses (you want to deuterate one or more H's to D's)

at this point a list of atomic numbers will come up with their default masses, just step through accepting these until you get to the atomic masses you want to change, in the case of deuteration we change the atomic mass of hydrogen H which is 1 to the atomic mass of deuterium D which is 2

it will then list all your atoms, here is an example of the new atomic mass

 Atom     6 has atomic number   1 and mass   2.01410

N to not project out gradient direction

once this is done it will print all the information to your screen, which is good for a quick check but will be more useful in a file

so once you have worked out what you want use the command line option

freqchk filename.chk -o filename.vib N 0 0 1.0 N N

below is an example

freqchk emim_cl2_fesm_up_freq.chk -o emim_cl2_fesm_up_freq.vib N 0 0 1.0 N N

look inside your file filename.vib

one thing to be aware of is that the output of the frequencies will still have the old mass in AN column, but this is incorrect it will have computed the frequencies with your new specified masses.

you can then use a script to extract the vibrational modes and their intensity get_freq

to use the script copy it to your username/bin directory and make it executable: chmod o+x get_freq

then in the directory of your filename.log file type get_freq filename (ie drop the .log extension)

you will get two files filename.colfreq and filename.colint which contain the frequencies and intensities respectively

use a graphing package to view these

you can also use the script to extract info from your freqchk filename.vib job, just change its name to one with a logfile extension and run the script

you can run a separate job specifying the isotopic stubstitution

you want to copy the frequency job checkpoint file to a new name

create a new input file that will read the frequencies and also make the isotopic substitution

use the command (iso=2) next to the H you want to deuterate

below is an example from one of my molecules

%nprocshared=8
%mem=15000MB
%chk=Demim_cl2_fesm_up_freq.chk
# freq=readfc b3lyp/6-311g(d,p) geom=cartesian empiricaldispersion=gd3bj int=ultrafine scf=conver=9

Title Card Required

-1 1
 C                  1.40336200    0.72814600   -0.17805400
 H                  2.49007900    0.81492900   -0.12367700
 C                  0.38941900    1.61648200   -0.36622900
 H                  0.40607900    2.68164300   -0.51358000
 C                 -0.52323300   -0.39309500   -0.15231900
 H(iso=2)          -1.30269800   -1.15976500   -0.08219000
 N                  0.80623800   -0.51543600   -0.04638900
 N                 -0.79880900    0.90063300   -0.35344500
 C                 -2.15528100    1.46075100   -0.46391400
 H                 -2.79660000    0.66419800   -0.84651100
 H                 -2.09985400    2.27910500   -1.18541100
 C                 -2.68146000    1.92584900    0.88860600
 H                 -3.66390100    2.38573700    0.75717400
 H                 -2.80343200    1.06175800    1.54343300
 H                 -2.01282200    2.65448200    1.35586800
 C                  1.53629700   -1.77147100    0.16989600
 H                  2.60276500   -1.52842100    0.21578000
 H                  1.20521100   -2.22318300    1.10504900
 H                  1.33640900   -2.45185600   -0.65797300
 Cl                -3.48718700   -1.64872100   -0.02039300
 Cl                 4.59143000   -0.07333700    0.12880300

Anharmonic spectra

do some reading first so that you understand what the anharmonic correction is
run a job using the key word freq=anharmonic

read the gaussian manual intensity freq options

the options here are very confusing and not well explained and do not give the detail of the old manual

emim_cl2_fmse_up_anharm.com
[phunt@login-2]/work/phunt/shijia $ vi emim_cl2_fesm_up_anharm.com

%nprocshared=8
%mem=15000MB
%chk=emim_cl2_fesm_up_anharm.chk
# b3lyp/6-311g(d,p) geom=checkpoint guess=read empiricaldispersion=gd3bj int=ultrafine scf=conver=9
  freq=(anharmonic,readanharm)

Title

-1 1

Print=NMOrder=AscNoIrrep
DataSrc=NMOrder=Print