Author Topic: uv/vis spectrum of dye when interact with other molecule  (Read 4756 times)

biyonur

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Hi,
I'm trying to perform TD-DFT calculations for uv/vis spectrum of dye molecule. I wonder if it is possible to add/dock a new molecule into a system and compare the uv/vis spectrum of dye whether interacting with an surface molecule. So I would see the effect of the surface molecule on the visualization of the dye molecule. Is it possible with turbomole modules?
Thank you for your help.
Best Regards.


antti_karttunen

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Re: uv/vis spectrum of dye when interact with other molecule
« Reply #1 on: May 15, 2013, 12:00:16 pm »
Hi,

Turbomole does not limit the molecular systems you want to study in any way (other than atom/basis function limits, but these are in the order of 10^3/10^4). So, just build up the dye + surface molecule system with any molecule builder and calculate the spectra you want to study.

Antti

biyonur

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Re: uv/vis spectrum of dye when interact with other molecule
« Reply #2 on: May 15, 2013, 12:43:58 pm »
If I calculate the UV/vis spectrum of the system, turbomole will give spectrum of both dye and surface.  How can I separate the spectrum of system into individual dye and surface molecules? I think the spectrum of the system would make sense if surface and the dye molecule is found in a solution. I real life, the light is mostly reflected by the dye molecule, not by the surface. That's why, I think I need to found UV/vis spectrum of dye while it is interacting with the surface.

Thank you for your help.

Hauke

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Re: uv/vis spectrum of dye when interact with other molecule
« Reply #3 on: May 15, 2013, 01:41:46 pm »

Did you try to two three different calculations:
- surface+dye
- just surface
- just dye

antti_karttunen

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Re: uv/vis spectrum of dye when interact with other molecule
« Reply #4 on: May 15, 2013, 01:55:05 pm »
Hauke's approach is the straightforward way. In addition, you could just to visualize the excitations in the dye+surface system and see if the important excitations are actually so localized that you can assign them on the dye or surface. But as far as I know there isn't any approach to simply neglect the effect of some atoms. Possibly you could look into some other programs and their fragment-based methods (e.g. GAMESS-US), but I'm not sure if this would be any more helpful.

Antti

biyonur

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Re: uv/vis spectrum of dye when interact with other molecule
« Reply #5 on: May 16, 2013, 01:53:23 pm »
Is there any way to look for each wavelength (exited states that gives a peak) and calculate the atomic contributions for the given oscillator strength? Eventually, it can be possible to separate the spectrum of the dye molecule?

Hauke

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Re: uv/vis spectrum of dye when interact with other molecule
« Reply #6 on: May 16, 2013, 02:56:33 pm »
In the output of escf you will find something like
Quote
                        1 singlet a excitation
 Total energy:                           -1517.375862532501
 Excitation energy:                      0.1209489824994023
[...]
 Dominant contributions:
    occ. orbital  energy / eV   virt. orbital  energy / eV   |coeff.|^2*100
      91 a          -6.05          92 a          -2.14           99.2

As  Antti Karttunen pointed out you can then try to see (by visualization) if orbitals 91 and 92 are mainly located at the dye or the surface. But don't expect that you can assign all the molecular-orbital to certain individual atoms. And in most cases also several orbitals have some contribution to one single excitation which makes it even more difficult.

If you "survived" the calculation of surface+dye, why not to do the two smaller once of the separated parts.