Mode Refinement
***************

DFTB UFF Spectroscopy Mode Refinement IR spectrum Normal modes AMS
Driver

In this tutorial we use the Mode Refinement method to calculate the
high energy end of the IR spectrum of the dydrogesterone molecule. In
order to reduce the computational time of this tutorial we are using
DFTB as the target method and UFF as the approximate method providing
the basis in which to express the DFTB modes. In reality one would
rather use DFTB as the approximate method and refine the modes at the
DFT level.

More information on these features can be found in the AMS user
manual:

* Vibrational spectroscopy section of the AMS manual

* Mode Refinement section of the AMS manual

Let us first calculate the entire IR spectrum of dydrogesterone at the
DFTB level. This is our reference spectrum which we will later try to
reproduce using the Mode Refinement method. Since DFTB is a fast
engine, calculating the entire spectrum does not take a long time.

   **1.** Start AMSjobs.
   **2.** Click on **SCM → New Input**. This will open AMSinput.
   **3.** In AMSinput, insert the dydrogesterone molecule by clicking the search icon [image: Search][image] and typing "dydrogesterone" into the box. Select the "C21H28O2: Prodel" entry from the molecules section.
   **4.** Select the DFTB panel: [image: ADFPanel][image] **→** [image: DFTBPanel][image]
   **5.** In order to calculate the full IR spectrum, make sure **Task** is set to **Geometry Optimization** and tick the **Frequencies** checkbox.
   **6.** Select **Model → DFTB3**, and **Parameter directory → DFTB.org/3ob-freq-1-2**.

Your AMSinput window should look like this:

[image]

We are now ready to run the calculation:

   **1.** Click on **File → Save As...** and give it the name "DFTB_GOFREQ".
   **2.** Click on **File → Run** . This will bring the **AMSjobs** window to the front.
   **3.** Wait for the calculation to finish ...
   **4.** Click the 'Update molecule' button that pops up in the AMSinput window to update the geometry

We now have optimized the geometry of dydrogesterone at the DFTB3
level of theory, and calculated its IR absorption spectrum. Let us
look at the spectrum we obtained.

   **1.** Click on **SCM → Spectra**. This will show the IR spectrum of dydrogesterone in AMSspectra.

You should see the following IR spectrum (to obtain the same graph,
make sure to set the peak **width** to **11**):

[image]

A useful tool for understanding the IR spectrum is the Partial
Vibrational Spectra (PVDOS) analysis.

   **1.** In AMSspectra click on  **Spectra → Partial Vibrational Spectra (PVDOS)**
   **2.** Select, for example, all atoms with a double bond

You will see that the normal modes involving C=C and C=O bonds atoms
are mostly located at around 1600cm^-1.

[image]

By clicking the individual peaks in the spectrum you can see the
corresponding mode in the viewpoint on the left. Looking at the
spectrum and the contained modes one can see that:

1. The spectral region around 3000cm^-1 contains all modes with C-H
   stretch character. There are 28 modes in this window, since there
   are 28 C-H bonds in the system.

2. Around 1600cm^-1 we have 4 IR intense modes involving the
   stretching of the C=C and C=O bonds.

3. The other 115 modes below 1500cm^-1 feature all kinds of collective
   bending modes involving large parts of the entire molecule.

We will now attempt to reproduce the first two bands mentioned above,
that is the C-H stretch and C=C/C=O stretch bands, using Mode
Refinement, i.e. without calculating the *entire* spectrum at the DFTB
level.

In order to use Mode Refinement, we first need a basis of approximate
normal modes. These are typically normal modes obtained at a lower
(and therefore faster) level of theory. Here we will use UFF to
calculate these approximate modes.

   **1.** Return to the AMSinput window that has the optimized geometry of dydrogesterone.
   **2.** Select the ForceField panel: [image: DFTBPanel][image] **→** [image: ForceFieldPanel][image]
   **3.** Select **Task → Single Point** and make sure that **Frequencies** is still enabled on the **Properties → Frequencies, ...** panel.

Note:

  We have to switch the **Task** to a **Single Point** calculation
  here. For Mode Refinement the calculation of the approximate normal
  modes should always be done at the equilibrium geometry of the
  target level of theory, in our case DFTB.

Your AMSinput window should now look like this:

[image]

   **1.** Click on **File → Save As...** and give it the name "UFF_FREQ".
   **2.** Click on **File → Run** . This will bring the **AMSjobs** window to the front.
   **3.** Wait for the calculation to finish. It should be almost instantaneous.
   **4.** Click on **SCM → Spectra**.

AMSspectra will give a warning that the spectrum is a flat line. This
can be explained because by default UFF does not use charges, and
hence the dipole is always exactly zero, and consequently also the
intensities. For that reason AMSspectra shows the normal mode count.
Make the width a bit broader, say 20.

We should now have our approximate modes from UFF in AMSspectra.

[image]

While the C-H stretch band is also separately visible in the UFF
spectrum, we can not really see the C=C/C=O stretches and the
collective bending modes as distinct bands, as we could in the DFTB
spectrum. Note that UFF does not give us IR intensities, and we just
have the number of normal modes on the y-axis here.

We will now use Mode Refinement with DFTB on the approximate UFF modes
to obtain only the high energy end of the DFTB spectrum.

   **1.** Return to the AMSinput window that has the optimized geometry of dydrogesterone.
   **2.** Switch back to the DFTB panel: [image: ForceFieldPanel][image] **→** [image: DFTBPanel][image]
   **3.** Select **Task → Vibrational Analysis** and disable the **Frequencies** checkbox.
   **4.** Go to the panel **Model → Vibrational Analysis**.
   **5.** Select **Type → Mode Refinement**.
   **6.** Select the approximate UFF modes by selecting the **UFF_FREQ.results/forcefield.rkf** file in the **Mode file** field.

Let us as a first step just target the C-H stretch region, and see if
we can reproduce the DFTB spectrum in this region. For this we select
all modes with frequencies >2500cm^-1 from the UFF spectrum. This
covers the entire C-H stretch region in the UFF spectrum, and we
should therefore have a good basis of normal modes in which to express
the DFTB normal modes we are looking for.

   **1.** Select **Frequency range → 2500 ... 10000 cm^-1**.
 [image]

We are now ready to run the Mode Refinement job and inspect the
results.

   **1.** Click on **File → Save As...** and give it the name "MR2500+".
   **2.** Click on **File → Run** . This will bring the **AMSjobs** window to the front.
   **3.** Wait for the calculation to finish. It should be almost instantaneous.
   **4.** Click on **SCM → Spectra**.
   **5.** Click on **File → Add...** and select **DFTB_GOFREQ.results/dftb.rkf**.

We now have the reference DFTB spectrum (in blue) as well as the
result of the Mode Refinement (red) in the same plot. Zooming into the
C-H band, we can compare the results.

[image]

The overall shape, position and intensity of the band is well
reproduced by the Mode Refinement, though there is a small extra peak
around 2860cm^-1, which does not match the full DFTB spectrum.

Let us increase the size of the basis for the Mode Refinement in order
to also get the C=C/C=O stretch band seen in the full DFTB spectrum.
In the UFF spectrum we calculated earlier, it is not clear where the
C=C/C=O modes are. As such we don't know precisely what modes from the
UFF spectrum to include in our basis. Nevertheless, we can just select
a large enough part of the spectrum and hope that the resulting basis
is suitable to express the C=C/C=O stretch modes we are looking for.
For this tutorial we will use all UFF modes with frequencies
>1200cm^-1 as our basis, but we encourage users to play with this
value and observe the effect on the resulting spectra.

   **1.** In the AMSinput window of the Mode Refinement job, change the **Frequency range** to **1200 ... 10000 cm^-1**.
   **2.** Click on **File → Save As...** and give it the name "MR1200+".
   **3.** Click on **File → Run** . This will bring the **AMSjobs** window to the front.
   **4.** Wait for the calculation to finish.
   **5.** Click on **SCM → Spectra**.
   **6.** Click on **File → Add...** and select **DFTB_GOFREQ.results/dftb.rkf**.
 [image]

The C-H stretch band is now basically perfect, indicating that UFF
modes from <2500cm^-1 region still have some contribution to the C-H
stretch band at the DFTB level. The four peaks of the separate C=C/C=O
stretch band are also reproduced, though there still some small
deviations in peak position. The beginning of the band of collective
bending modes is also reproduced very accurately.

It should be noted that this tutorial actually shows a rather
difficult case for the Mode Refinement: The UFF modes are quite
different from the DFTB mode we wanted to calculate. Therefore a
relative large part of the UFF basis is needed to perfectly reproduce
the DFTB spectrum. Much better results can be obtained if the
approximate and target methods are more closely related (e.g. DFT/DFTB
or DFT/DFT with different basis sets). We encourage users to repeat
this tutorial using DFT/TZP/BP86 and DFTB3 as target and approximate
method. Both methods have a distinct C=C/C=O stretch band in
dydrogesterone, which can be picked out in the DFTB spectrum to
predict just this band at the DFT level, without calculating the
higher energy C-H stretch band. This calculation is demonstrated in
this example from the AMS manual, and was also performed in the
original article on Mode Refinement.

This concludes the tutorial on Mode Refinement in AMS.
