User 8c3f17292e
09-10-2013 01:38:51
Hi, everybody!
I want to calculate the donor number in molecules that are used in solar cells.
However, when I run cxcalc donorcount $molecule,sometimes I found that the donor count is nincorrect.
Eg:
>cxcalc donorcount 'C(S1)=CC2=C1C(C(CC)CCCC)(C(CC)CCCC)C(S3)=C2C=C3C(=C1)C2=NSN=C2C=C1'
id donorcount
1 0
But, as we know, there are one acceptor and one donor in this molecule.
Why I get the wrong number? or the donor calculated in not the same with the 'donor' in solar cell?
I run cxcalc on a Mac OS machine.
Thank you!
ChemAxon 5fc3e8d7d0
09-10-2013 10:08:47
Hi,
Yes, the calculated donorcount is not the number of electron donors in solar cell.
You want to calculate electron donors in molecule, but the cxcalc donorcount command calculates hydrogen bond donor count.
BR,
Laszlo
User 8c3f17292e
09-10-2013 10:24:13
lantal wrote: |
Hi,
Yes, the calculated donorcount is not the number of electron donors in solar cell.
You want to calculate electron donors in molecule, but the cxcalc donorcount command calculates hydrogen bond donor count.
BR,
Laszlo
|
Hi, Laszlo,
I get it, Thank you very much!
User 8c3f17292e
04-11-2013 05:34:31
Hi Laszlo,
I am sorry to bother you again!
I am repeating a the work of one paper. I used cxcalc to calculate hydrogen bond donor count of some molecule and I get zero. But I have write a letter to the author, the author claim that of these molecules hydrogen bond donor count is not zero. I am confused now as the 'cxcalc' have not complicate input why we should give different result.
Could you please correct my command (see below) if there is any problem? Or could you please help me to calculate the below molecules and send me your results? Your help it very important to us, it is more than appreciated if you could help me!
Thank you very much!
Here is my command:
cxcalc donorcount 'C1=CC=C(C(N2C(CCCCCCCC)CCCCCCCC)=C1)C3=C2C=C(C=C3)C(S1)=CC=C1C(C=N1)=C2N=CC=NC2=C1C(S1)=CC=C1'
cxcalc donorcount "C1=CC=C(C(N2C(CCCCCCCC)CCCCCCCC)=C1)C3=C2C=C(C=C3)C(S1)=CC=C1C(=CC=1)C2=NSN=C2C=1C(S1)=CC=C1"
cxcalc donorcount "C1=CC=C(C(N2C(CCCCCCCC)CCCCCCCC)=C1)C3=C2C=C(C=C3)C(S1)=CC=C1C(=CN=1)C2=NSN=C2C=1C(S1)=CC=C1"
cxcalc donorcount "C1=CC=C(C(N2C(CCCCCCCC)CCCCCCCC)=C1)C3=C2C=C(C=C3)C(S1)=CC=C1C(=CC=1)C2=NON=C2C=1C(S1)=CC=C1"
cxcalc donorcount "C1=CC=C(C(N2C(CCCCCCCC)CCCCCCCC)=C1)C3=C2C=C(C=C3)C(S1)=CC=C1C(=CN=1)C2=NON=C2C=1C(S1)=CC=C1"
lantal wrote: |
Hi,
Yes, the calculated donorcount is not the number of electron donors in solar cell.
You want to calculate electron donors in molecule, but the cxcalc donorcount command calculates hydrogen bond donor count.
BR,
Laszlo
|
ChemAxon d76e6e95eb
04-11-2013 09:08:16
If I am not mistaken, none of these molecules contain any hydrogen atoms on their hetero atoms which could be donated, so it is unclear, where the author sees hydrogen bond donor sites. The pyridyl nitrogen can be in protonated form in extremely acidic conditions only. The hetero atoms here have lone pairs, however, but those can be acceptors only.