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General Questions and Answers / Passivation with elements other than Hydrogen
« on: August 12, 2017, 11:37 »
Hello all,
I am trying to passivate a spherical Carbon structure with elements other than Hydrogen (e.g. N, O, P).
Since such a function seems non existent in VirtualNanoLab (why?!), and I only have the "CustomPassivator" of the CoordinateTools at my disposal, I tried the following workaround: change the bond distance of CustomPassivator for Hydrogen to the desired values and after the passivation, replace H with the element I desire. By doing this I encountered a problem, namely that depending on the bond distance I select, the structure will be passivated by a different number of Hydrogen atoms, so that I have a varying number of passivation Atoms for N, O, P, when I would like to have the same number of passivations as I have when I use Hydrogen (with bond distance 1.09 Ang).
So my questions are:
Is there a passivation function, that I have somehow not found, with which I can passivate very easily using other elemens? If there is not, why is that not a tool somewhere in VNL (it seems to me that this might be something one commonly wants to do)?
Is there an option to change the bond distance (pairwise) by (for example) using the "Select by bond distance" tool?
Is there an option to adjust the bond distance to a desired value when changing Hydrogen elements (after I passivated my structure with it) to another element?
Currently, what I have to do, is to passivate my structure with hydrogen and then INDIVIDUALLY replacing Hydrogen with the desired element and then change the distance value to the corresponding bonded Atom by using the Z-Matrix to ensure it actually is the same number of passivations. That, I have to do around 800 times.
Please, if there is anything remotely related to solving or simplifying this problem, give me a hint.
I am trying to passivate a spherical Carbon structure with elements other than Hydrogen (e.g. N, O, P).
Since such a function seems non existent in VirtualNanoLab (why?!), and I only have the "CustomPassivator" of the CoordinateTools at my disposal, I tried the following workaround: change the bond distance of CustomPassivator for Hydrogen to the desired values and after the passivation, replace H with the element I desire. By doing this I encountered a problem, namely that depending on the bond distance I select, the structure will be passivated by a different number of Hydrogen atoms, so that I have a varying number of passivation Atoms for N, O, P, when I would like to have the same number of passivations as I have when I use Hydrogen (with bond distance 1.09 Ang).
So my questions are:
Is there a passivation function, that I have somehow not found, with which I can passivate very easily using other elemens? If there is not, why is that not a tool somewhere in VNL (it seems to me that this might be something one commonly wants to do)?
Is there an option to change the bond distance (pairwise) by (for example) using the "Select by bond distance" tool?
Is there an option to adjust the bond distance to a desired value when changing Hydrogen elements (after I passivated my structure with it) to another element?
Currently, what I have to do, is to passivate my structure with hydrogen and then INDIVIDUALLY replacing Hydrogen with the desired element and then change the distance value to the corresponding bonded Atom by using the Z-Matrix to ensure it actually is the same number of passivations. That, I have to do around 800 times.
Please, if there is anything remotely related to solving or simplifying this problem, give me a hint.