Vibrational circular dichroism (VCD)
************************************

ADF Spectroscopy Vibrational circular dichroism GCO Analysis VCDtools

This tutorial will teach you how to calculate and analyze the
vibrational circular dichroism (VCD) spectrum of a small molecule
using ADF and VCDtools.


Create your oxirane molecule
============================

These are the coordinates of the oxirane molecule:

   C      -1.44589917      -0.26968372      -0.00000000
   C       0.02774960      -0.35459913      -0.00000000
   O      -0.64012001       0.88449058      -0.00000000
   H      -1.94641916      -0.41741698       0.97962259
   H      -1.94641916      -0.41741698      -0.97962259
   H       0.50817848      -0.55867470      -0.97957478
   H       0.50817848      -0.55867469       0.97957478

Copy-paste these into AMSinput:

   **1.** Start **AMSinput**
   **2.** Select the oxirane coordinates above, and **copy** and **paste** in the molecule drawing area of AMSinput

Now you should have the oxirane molecule.

   [image]

To ensure chirality, two hydrogen atoms should be changed to deuterium
atoms:

   **1.** Select two hydrogen atoms diagonally across from each other (holding shift)
   **2.** In the menu bar: **Atoms → Details (Color, Radius, Mass)** command

The panel area changes to display the atom details menu.

   Set the **Mass** of the two selected Hydrogens to 2
 [image]

Note that if the two other hydrogen atoms are changed to deuterium
atoms then one has the mirror image of this molecule, and one would
get an inverse VCD spectrum.


Set up and run the calculation
==============================

We will perform a geometry optimization followed by frequency + VCD

   **1.** Click on the **Main** tab in the **panel bar**.
   **2.** Select **Task → Geometry Optimization**
   **3.** Check the **Frequencies** check-box
   **4.** Select **GGA:BP86** as **XC functional**
   **5.** Select **Frozen Core → None**

   [image]

To request the calculation of VCD intensities:

   **1.** In the **panel bar**, select **Properties → IR (Frequencies), VCD**
   **2.** Check the **VCD** check-box

   [image]

Now run ADF:

   **1.** Select the **File → Run** command
   **2.** In the file select box, choose a name for your file ("Oxirane") and click 'Save'

Now ADF will start automatically, and you can follow the calculation
in the logfile.

   **1.** Wait until the calculation is finished (should take a minute or so)
   **2.** Click the [image: UpdateMolecule][image] button that pops up in the right-hand panel to update the geometry
   (or before AMS2026, click 'Yes' when asked if you want to update the coordinates)


Analyze the VCD Spectra
=======================

Next start analyzing the VCD spectrum with AMSspectra. To open the
spectra:

   **SCM → Spectra**

Basically, two types of analysis methods are offered by the analysis
program VCDtools. First, it can visualize the properties relevant for
the VCD intensity, *i.e.*, the **Electric and Magnetic Dipole
Transition Moments (EDTM and MDTM)** and the normal mode motion.
Second, a **General Coupled Oscillator (GCO)** analysis can be
performed.

Normal modes can be selected either by clicking in the spectrum or by
clicking in the *'Vibrations Window'*. After a normal mode is selected
the vibration will be shown in the molecule and some details will be
given in the right side of the *'Vibrations Window'*. In the next
picture '1/cm' is chosen as horizontal unit, with a 'Lorentzian
Height' line shape and a width of '8.0'.

[image]

   Select normal mode 15, a large positive peak at 3100 wavenumbers
   In the '*Vibration Window*'' click the header **EDTM** to sort the atoms accordingly.
   Click on the row with the highest electric dipole transition moment.

Now one of the hydrogens should be selected. In general, atoms with a
high contribution to the EDTM are important for the VCD intensity. To
show this a GCO analysis will be performed in the following section.

   Select the **VCDtools →  Default Visualization for GCO Analysis**
 [image]

The atom sizes are now scaled by their EDTM and the nuclear
displacement vectors are shown as arrows. To scale the size of these
arrows, use the "*up*" and "*down*" keys. Using these visualization
settings, we immediately see that two of the C-H groups are important
for the VCD signal in this normal mode. You can change which vectors
are visualized, the phase of these vectors and the scaling of the
atoms by clicking the buttons underneath the molecule. The buttons
that are active will have a glow effect.

The next step in a GCO analysis is to select VCD active fragments:

   Select one of the important C-H groups by pressing the 'shift button' while clicking on the atoms
   Select the **Regions → Set Selection As → New Region** command
   Select the other important C-H group
   Select the **Regions → Set Selection As → New Region** command again
 [image]

The two important regions will be highlighted by transparent red and
green spheres. Additional tools for setting up the regions can be
found under the “*Regions*” menu.

   Select the **Regions → Save Regions** command
   Enter a Name (for example *'NM15'*)
   Press the *'Return'* -key or press OK

The current regions will have been saved in the
*'.results/adf.results'* folder in the file 'Regions.txt' and can be
loaded by the command: **Regions → Load Regions → 'Name'**.

To determine whether the coupling between two important C-H groups is
important to the rotational strength it can be decomposed using the
GCO formalism.

   Click the **GCO analysis** button with the text *'GCO'*
 [image]

An *'AMStail'* window will now have opened showing the
*'vcdtools.txt'* file. In this file all output from VCDtools is
stored. Each output entry begins by defining the settings such as the
selected regions and normal modes. For normal mode 15 we see that
indeed the major part of the VCD signal is caused by the GCO
interaction between the two selected regions. The rest of the molecule
barely contributes and also the VCD signal from the individual
fragments is insignificant. We have thus successfully determined the
source of the VCD intensity for normal mode 15.

If needed arrows can be shown inside the molecule to indicate the EDTM
and the MDTM. This can be done per atom or per regions. For example:

   Select the **VCDtools → EDTM Vectors (regional)** command

Two arrows will have appeared at the geometric centers of the regions
displaying the relative size and direction of the EDTMs.

Under the "**VCDtools**" menu there are many other commands. For
example, VCDtools can guess the best fragments for GCO fragments and
can compute the normal mode localization on the selected regions
within the molecule. Feel free to test them out.
