Identifying vib modes that contribute to entropy

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kra268
Posts: 11
Joined: Fri Sep 25, 2020 3:41 pm

Identifying vib modes that contribute to entropy

Post by kra268 »

Hello everyone!

I am new to the entropy calculation from vib frequencies. I have attached a completed vib freq calculation with some surface atoms(17) included and I am trying to identify the modes responsible for entropy contribution in the adsorbed state. I see a lot of literature where people consider all modes above 200 cm-1. However, a diatomic molecule like CO can only have 3N modes on the surface of which two could be due to hindered translation. The hindered modes would be the first two that are near zero? So for the total entropic contribution, how should I consider the modes from the freq.dat file?
It would be great if you could help me understand this! Thank you!
Regards,
Keerthan.
Attachments
dym_calc_CO.tar.gz
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kra268
Posts: 11
Joined: Fri Sep 25, 2020 3:41 pm

Re: Identifying vib modes that contribute to entropy

Post by kra268 »

For convenience, here's the freq.dat file:

77.734380 cm^{-1} ... 0
89.764817 cm^{-1} ... 0
99.958151 cm^{-1} ... 0
103.766658 cm^{-1} ... 0
104.791463 cm^{-1} ... 0
124.317975 cm^{-1} ... 0
132.243987 cm^{-1} ... 0
134.403241 cm^{-1} ... 0
135.684423 cm^{-1} ... 0
138.396969 cm^{-1} ... 0
140.342585 cm^{-1} ... 0
141.282883 cm^{-1} ... 0
145.625875 cm^{-1} ... 0
148.170613 cm^{-1} ... 0
148.756847 cm^{-1} ... 0
150.317013 cm^{-1} ... 0
152.071825 cm^{-1} ... 0
156.406394 cm^{-1} ... 0
158.128923 cm^{-1} ... 0
158.527172 cm^{-1} ... 0
162.171647 cm^{-1} ... 0
163.147356 cm^{-1} ... 0
165.220130 cm^{-1} ... 0
169.585108 cm^{-1} ... 0
171.179709 cm^{-1} ... 0
172.813760 cm^{-1} ... 0
179.929085 cm^{-1} ... 0
181.664112 cm^{-1} ... 0
183.127998 cm^{-1} ... 0
188.539094 cm^{-1} ... 0
190.241408 cm^{-1} ... 0
190.900865 cm^{-1} ... 0
193.659113 cm^{-1} ... 0
194.570629 cm^{-1} ... 0
196.211914 cm^{-1} ... 0
197.333358 cm^{-1} ... 0
202.115891 cm^{-1} ... 0
203.485895 cm^{-1} ... 0
209.601383 cm^{-1} ... 0
210.522917 cm^{-1} ... 0
211.435731 cm^{-1} ... 0
215.223056 cm^{-1} ... 0
216.645609 cm^{-1} ... 0
219.800162 cm^{-1} ... 0
223.113443 cm^{-1} ... 0
224.326131 cm^{-1} ... 0
231.704347 cm^{-1} ... 0
235.840906 cm^{-1} ... 0
237.864555 cm^{-1} ... 0
238.659165 cm^{-1} ... 0
242.039940 cm^{-1} ... 0
247.077950 cm^{-1} ... 0
247.520727 cm^{-1} ... 0
253.052137 cm^{-1} ... 0
257.736541 cm^{-1} ... 0
257.893459 cm^{-1} ... 0
306.397337 cm^{-1} ... 0
307.697731 cm^{-1} ... 0
404.685490 cm^{-1} ... 0
1752.726289 cm^{-1} ... 0
graeme
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Re: Identifying vib modes that contribute to entropy

Post by graeme »

Hi Keerthan,
You will have to be a little careful about how to convert these frequencies to the entropy of the system. First though, if you are at a temperature where you can consider all of these modes as harmonic, then you can calculate the harmonic vibrational entropy using all of the modes. Note that you will almost certainly be calculating a difference in entropy or a free energy difference and so the most important issue is to consider a consistent set of modes in the two states that you care about. If you want to focus on the CO molecule, that could be fine, but you can't just guess at which modes are associated with CO. For that, you can look at the modes.dat file. A quick look shows that the highest frequency modes is the C-O stretch (as you would expect) but the 4-6th highest modes are also associated with CO. We have a simple script: dymmodes2xyz.pl , which can help make movies of the modes so that you can visualize them. Then, if you want to go beyond the harmonic approximation, for example, hindered translation, then I think you would want a diffusion barrier for translation, rather than just a vibrational frequency in the binding site.
Graeme
kra268
Posts: 11
Joined: Fri Sep 25, 2020 3:41 pm

Re: Identifying vib modes that contribute to entropy

Post by kra268 »

Hello Graeme,

Thank you so much for helping me understand this! I was able to visualize the modes with dymmodes2xyz.pl script! Have a nice day!

Regards,
Keerthan.
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