I mean how to know of this vibration is scissoring or wagging or twisting, ........ and what is meant by scaling and how to do it.
Hi,
In open output by Gauss view. Go to "Results" tab and select "Vibrations".
Select the desire frequency and then select "Start Animation". You can simply assign the type of frequency.
Note: Negative values are attributed to the imaginary frequencies.
Mr. Khattab,
The scaling usually carried out, comparing with the experimental data set for which you have unambiguous assignment.
You can use jmol (http://jmol.sourceforge.net/). Open your *.out file, right-click and scan through menu "Structures". After structures representing optimization steps there will be vibration modes. Select the one that interest you. Then navigate to menu "Animation" and start animation of the selected mode.
Dear Majid,You mean i assign it by my eye. There is no way to get it in a table form? my compound is 36 atoms.
Hi!
You should type on the top of your input file "%Chk=filename". Then if you open the file using the Gaussian View Software, you can see for example Occupied molecular orbital (OMO) and Unoccupied molecular orbital (UMO) for specific energy.
Also, you are able to see the curve of intensity via vibration frequency i.e., Raman and Infrared spectra using the Gaussian view software when you open the %Chk-file. On the curve you can choose the specific frequency and see its related intensity. Also you can change curve to separate points in 2D space of intensity-frequency.
Please note that following the file.out for finding the specific frequency is possible but it is very difficult work.
Best Regards
Dear Muhammad,
you can view the computed vibrations in this way:
- open the .log/.out/.chk/.fchk file of your calculation in GaussView and go to "Results" -> "Vibrations...".
- a new window will pop-up and you will find a table with the computed vibrational modes of the structure your studying. (along with Frequencies and Intensities)
- select one of these modes and click "Start Animation"
- the structure will begin to be displaced according to the computed vibrational mode.
- you can now assign the vibration type for each frequency.
...as for the scaling of the computed frequencies, one way I managed to do it is like this:
- while viewing the "Vibrations..." window click on "Spectrum".
- right-click on the spectrum in this new window and select "Save data..."
- when saving the data be sure to double-check the "Range" and "Stepsize" fields for the data you are about to export. (the lowest step-size available is 1, which corresponds with 1 cm-1).
- after saving the .txt file open it with Origin or Excell
- depending on the level of theory and basis set used for the calculation you have to chose the appropriate scaling factor (I use this article "Quadratic scaling functions for obtaining normal vibrational wavenumbers from B3LYP calculation" by Tomoe Osaki and Eiko Soejima)
- IT'S VERY IMPORTANT that if you didn't use DFT with B3LYP you will need to search for another paper that discusses the scaling factors suited for your calculation setup!!!
- apply the scaling factor/formula to your data...and...
vóila....
...now you can plot your scaled spectra....moreover, now you can add the experimental data on top of the computed data and efficiently assign vibrational modes to your experimental spectra!!!
P.S.: assigning vibrational modes requires a lot of attention so pay attention!!!
I hope this solves it for you! Take care and have a nice day! :)
Dear Khattab,
I got your question as I have also struggled with it. As per my knowledge, its impossible to tabulate the stretching frequencies in terms of their charecteristic mode (bending,scissoring,wagging etc). For this, you need to check the diplacement vectors or in particularly their orientations. If it crosses head to head over the atoms than it would be stretching (symmentric or asymmetric can be easily visualised by the nature of pointing arrows).
For further vibrations type, you can asign them in similar manner.
Remember, frequency assignment needs great care as most of the frequencies originates due to mixed molecular vibrarations.
InshaAllah, this wiill Helps you!!!!
I think the VEDA is suitable for your demand. You can download(http://smmg.pl/software/veda) and try it. This following is its introduction:
"The VEDA computer program is optimizing the set of internal coordinates for elucidation of IR and Raman experimental/theoretical spectra. As a result, the theoretical normal modes are represented by internal coordinates giving users a more intuitive view of the molecular movements. Each of the internal coordinates is expressed as a superposition of several local modes of two, three, or four atoms connected by bonds for stretching, bending, or torsional and out-of-plane local modes, respectively."
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