Hi,
I want to do DFT calculations for the interaction of dye with the Ag nanocluster using GAUSSIAN 09 software. I want to create an input file using GaussView 5.0.8. But unable to build an Ag nanocluster in GaussView 5.0.8.
Could anyone please help me out with this?
Thanks in advance!
Hi Shreyas,
Structure of Ag nanoclusters are available in the literature, you can take those (with proper citation) and reoptimize in Gaussian. For example:
1.Article Elucidation of the molecular and electronic structures of so...
2.Article Density Functional Study of Neutral and Charged Silver Clust...
You can find more papers in the literature just by doing a quick Google scholar search (or in RG). Sometimes the authors report the coordinate within the supporting information, which will make your job easier. Alternatively, you can make the structure in Gaussview just by looking in the figures and then optimize.
If you are searching for any specific cluster whose structure is not known, then you have to predict those first before doing any calculation.
Dr. Turbasu Sengupta Sir,
Thank you so much for answering the question. I found research articles shared useful. But simulation and optimization of silver nanocluster is a bit of a hassle. Can you guide me about doing the optimization of silver nanocluster along with one additional organic molecule?
Dr. Bojidarka B. Ivanova Ma'am,
Can you please share the comprehensive manual as I am unable to find it online.
Hi Shreyas,
If you tell me exactly what problems you are facing, I may be able to help. Let me know. In short, your optimization scheme should follow the following steps.
1. Find out the global minima (Including ground state spin multiplicity) of the desired cluster from literature. If not available then you have to find it on your own. There are softwares available for this kind of search (e.g., Calypso: http://www.calypso.cn/ or ABCluster: http://www.zhjun-sci.com/software-abcluster-download.php, etc). However, predicting the ground state for a reasonably sized cluster is a very time-consuming job and also requires reasonable CPU facilities. So make sure you have that, otherwise, my suggestion is to take a suitable one from the literature (with proper citations).
2. Prepare the geometry in Gaussview. If coordinates are available you can directly use that in Gview. Alternatively, you have to build (draw) the structure in Gview by hand. In this case, try to make a structure as close as possible as given in the paper. You can use various utilities provided with Gview (e.g., 'clean') to create a good initial structure.
(If you are using some cluster structure prediction software (as I have mentioned in 1) then at the end of the calculation you will get coordinates to use with Gview, so no issue there)
3. After you build your structure (Global minima) in Gview, optimize with a good level of theory. If you are using DFT choose a good functional and basis set for Ag. At the same time optimize the organic molecule separately).
4. After that, you just have to attach the optimized molecule at all possible potion to the Ag cluster and reoptimize all of them. Then check which one is lowest in energy. That one will be your ground state for the molecule attached cluster.
Turbasu Sengupta Thank you so much for your guidance. The answer is helpful.
Nice to share the outstanding guide about "How to use GaussView" as follows:
1) https://www.mtholyoke.edu/courses/jwijngaa/PS/Gaussview2.pdf
2) https://www.tau.ac.il/~ephraim/intro2gaussview.pdf
3) https://gaussian.com/gv6main/
Have a good day!!!
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