Can anyone guide me on how to use the Gussain 09 program (Density Functional Theory (DFT) Method) to study the interaction between two molecules? #densityfunctionaltheory #dft
To study the interactions between two or several molecules, as shown in aploaded file, you must take into account the shape and size of these molecules. Best way is the SCAN caculation (relaxed or rigid).
This is done by following several methods, including:
- translation molecule to molecule (3, 4)
- rotation molecule around molecule (2)
- traversing molecule in other (1)
- translation/rotation combination
- molecular dynamic
- mont carlo
-.............
In addition to Belgacem Bezzina correct comments, some additional hint:
if you want to go along a certain trajectory, the straightforward way to do so would be to take the optimized isolated molecular structures and place them at the desired angles in the desired distances. Then pick a characteristic atom pair for which you freeze the distance and then run the optimization for all other molecular coordinates. The freezing is described here under "options":
https://gaussian.com/opt/
Jürgen Weippert and Belgacem Bezzina thank you for your response.
I have already optimized my monomer and analyte for which I have to observe the interaction study using DFT. I have optimized both the molecules independently using this basic set: DFT b3lyp/6-31g(d,p) geom=connectivity. I have obtained the optimized energy for both molecules separately.
But now I want to optimize both the molecules together.
I am using the Gaussian 09 program for optimization and Gauss View 6 for making the structures. How shall I proceed further?
I always drew my structures with Avogadro and don't know GaussView, does it not have the option to copy-paste one structure into the drawing of another one?
After the optimization step, you should calculate the vibrational frequencies to confirm that: imaginary frequency=0 (true minimum) not a transition state.
As I mentioned above, the appropriate method is determined according to the shape and size of your molecules.
I give you an example of our work with the inclusion complex formation:
1-opt+freq calculation (bothb molecules independently) of the host and the guest molecules.
2-aligning the host molecule with xy (the center of host being defined as the origin of the coordinate system).
3-the guest molecule was located on a Z-coordinate equal to X Å and was moved (manually or automaticly) ( translation or tranltion/rotation) into the host cavity along the Z axis to -X Å with 0.1 OR 0.5 OR 1 Å step into the cavity.
4-The generated structures at each step were optimized for the manually scan, while for the automaticly scan,the calculation is done automatically and you do not need to create new files (one input for all steps).
In general, this step is performed at low level of theory as semi-empirical method.
5- draw the energetic profile ( interacction or binding or complexation energy=f(Z-coordination) and localise the global minima. ........That's half the work...............The nature and strenght of interactions is caried out by NBO, AIM, NCL................
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