6
$\begingroup$

A question about the IR absorption modi of diiron nonacarbonyl on chemistry.se found two answers. One of them provided an illustration with animated vibrations.

In the 1990s, the Gasteiger group offered with TeleSpek the interested the possibility to submit organic structures, e.g., as a SMILES string for a simulation/prediction of likely IR spectra. At present, this service appears as no longer active:

enter image description here

(a couple of screen photos taken from the project's page, tab «how to use»).

The question to the readers of mattermodelling.se: Do you know about a similar, yet ongoing service which is able to provide such a (I guess, by today's standards much more affordable) quick, installation free prediction of IR modi (incl. animation), which would be instructive, e.g. for teaching/self study? With this purpose in mind, the implementation searched needn't be at high level of theory.

A first idea I had was MolCalc by Jensen and Kromann. Likely to preserve resources, the submission of the SMILES string O=C1[Fe]2(=C=O)(=C=O)(=C=O)C(=O)[Fe]1(=C=O)(=C=O)(=C=O)C2=O Wikipedia uses to describe the complex is deflected with «Stop Casper. Max ten heavy atoms.» when aiming to enter the calculation of properties. (As far as I recall, the service by Gasteiger et al sent an e-mail about a successful computation, even if this meant multiple hours of work.)

Improve this question
$\endgroup$
1
  • 1
    $\begingroup$ +1. I know PGOPHER is free and is used to simulate IR and other types of spectra, but I'm not sure if I've seen it do something like this. You may also consider tweeting this question to Jan Jensen here: twitter.com/janhjensen?lang=en. $\endgroup$
    – Nike Dattani
    Jan 11, 2022 at 23:50

2 Answers 2

Reset to default
5
$\begingroup$

There's now a web server that uses GFN2 and GFN-FF to calculate vibrations and visualize them, thanks to Berend Smit:

https://ir.cheminfo.org

You can draw a structure or insert a SMILES, and the server will run the vibrational calculation (up to 60 atoms for GFN2 or 100 atoms for GFN-FF), and offer several visualizations:

ir.cheminfo.org screenshot

  • standard transmittance vs. wavenumber plot
  • JSMol animation of the vibration
  • table of modes, calculated intensity, and wavenumber
  • bond depiction to connect between bonds and vibrations (e.g., the C=O bond is highly localized)

There's also a nice description of the resource and some educational discussion:

"Making Molecules Vibrate: Interactive Web Environment for the Teaching of Infrared Spectroscopy" J. Chem. Ed. 2022

The authors also provide the service as a Docker image to run yourself: https://github.com/cheminfo-py/xtbservice

Improve this answer
$\endgroup$
1
  • $\begingroup$ This is wonderful. In the spectrum, you zoom into the region of interest, pick an absorption band and voilà, the animation changes for the corresponding vibration. You may define a second (different) molecule, and eventually the simulated spectra for both, simultaneously, are in one plot in common. $\endgroup$
    – Buttonwood
    Jan 28, 2022 at 9:19
7
$\begingroup$

For most organic molecules, you can use xtb as a low level of theory to generate an optimized structure with a full frequency analysis. While xtb is semi-emperical, you might find that for a qualitative or even semi-quantitative analysis it can be quite good. You will also find calculations can be performed in at most a couple minutes for even fairly large molecules on a standard desktop or laptop.

Improve this answer
$\endgroup$

You must log in to answer this question.

Not the answer you're looking for? Browse other questions tagged .