The 1 ns MD simulation in vacuo produced three types of aggregates after the MWCNT-FITC disintegration into the SWCNT and SWCNT-FITC components. The carbon nanotube aggregation ended up with a formation of the SWCNT dimer, SWCNT-FITC dimer, and SWCNT/SWCNT-FITC hybrid pentamer. Following the equation below, I calculated the VDW aggregation energies for my complexes using the VDW energetics for SWCNT (17.9 kcal/mol) and SWCNT-FITC (-0.177 kcal/mol):
Aggregation VDW energy for SWCNT dimer = -9.3 kcal/mol
Aggregation VDW energy for SWCNT-FITC dimer = -66.65 kcal/mol
Aggregation VDW energy for SWCNT/SWCNT-FITC hybrid pentamer = -187.27 kcal/mol
Is this approach correct? Please advise. Appreciate your critical comments.
Dear Sergey,
The approach you developed seems to be correct to me. However, in the numbers you've indicated, there should be the energy of the isolated FITC, do you use it?
For example, in the case of the SWCNT-FITC dimer, your energy should be of the form :
E^vdW_aggregation = E^vdW_dimer - E^vdW_SWCNT - E^vdW_FITC, is this the way you did it?
Dear Yannick,
In the case of SWCNT-FITC dimer, I used two SWCNT-FITC components where FITC was covalently bond to the nanotube. Therefore, there was no SWCNT and FITC separation in my MD simulations.
Oh, I didn't get initially that it was (SWCNT-FITC) dimer, I thought it was just the interaction between both, sorry. But then what are the SWCNT and SWCNT-FITC corresponding to? In particularm I don't understand why one is positive and the other is negative?
The possible explanation might be that the MWCNT-FITC structure experiences rapid disintegration into the SWCNT (inner nanotube) and SWCNT-FITC (outer nanotube) components after 5-10 ps caused by strong repulsion effect between both of them. Therefore, the VDW energy has to be positive (17.723 kcal/mol) due to overlapping between electron clouds of their atoms.
Actually, I think you should use the energy of each isolated compound .... I don't understand exactly what represents the vdW energy of the SWCNT alone, it should be the total energy of the isoalted SWCNT, and moreover, it should be negative. To my opinion, the present one is not the good reference, what do you think?
I understand your point. However, the entire mechanism of the MWCNT-FITC aggregation could be roughly depicted as MWCNT-FITC - disintegration -SWCNT+SWCNT-FITC - aggregation - SWCNT dimer + SWCNT-FITC dimer + hybrid pentamer. It is all approximation though. I took the vdW energies of SWCNT and SWCNT-FITC from MWCNT-FITC separately as the 'total' (initial state) energy of the isolated SWCNT and SWCNT-FITC. You could also take the energy for each component from the final (aggregate) or intermediate (disintegration) state, such as the SWCNT-FITC dimer aggregate or SWCNT alone. Although, as you can see, my calculation confirms the fact that the system aggregate through the total decrease of vdW energy and occupies a lower energetic level.
Well. that's true indeed, actually the energy you are looking for depends here on the path you follow to determine it. So yes using these references, I guess that can be decomposed this way.
Dear Yannick, could you be so kind to take a critical look at the manuscript regarding to the aggregation and molecular dynamics simulation of multi-walled carbon nanotube functionalized with fluorescein isothiocyanate? Appreciate your help and assistance.
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