trivalent radical N

User 870ab5b546

25-09-2009 18:21:16

A N atom with a trivalent radical that is making two bonds should have a valence error.  The trivalent radical means that three unshared electrons occupy three different valence orbitals, so the N can only have one valence orbital left to make a bond.  


A lot of my students were using trivalent radical for a N atom with a lone pair and a radical -- it looks exactly the same as monovalent radical N with lone pairs turned on -- and ACE was grading it incorrect.  I've had to go through the exam and regrade all those questions.

ChemAxon 990acf0dec

29-09-2009 18:17:01

Hi Bob,


I apologize for the late answer. We will fix this issue: If there is a charge on an atom of the template, this will be fixed, so valence check will not be able to modify it.


We will notify you when it is ready.


Best regards,


Akos

User 870ab5b546

01-10-2009 16:17:33

I don't understand your statement.  There's nothing here to do with charge or a template.  Simply, a trivalent radical N can have no more than 2 bonds, and a trivalent radical quartet N can have no more than one bond.  If it does, there should be a valence error.  

User 25d107bd42

02-10-2009 08:09:59

Hi Bob,


could you please post an image of this "trivalent radical N-atom", and how it is drawn.


I find this topic very important.


Best regards, Hans-Ulrich


 

User 870ab5b546

02-10-2009 13:25:38

I can't give you a screenshot in Marvin 5.2.5, because when I use Safari and then try to get the image, Safari hangs; and in Firefox, there is about a 3-second delay between my actions and Marvin's reaction.  Grrr.  


Safari also hangs if I try to get the SMILES source from Marvin 5.2.5.


However, just draw H2C=C=NH, right-click on the N, and choose Radical -> Trivalent or Trivalent doublet. 


I'm not even sure what is meant by "trivalent radical doublet".  Can anyone give me an example of a "trivalent radical doublet" that is not better described as a "monovalent radical"?  It seems to me that if an atom is a trivalent radical, it must be a quartet, and if an atom with three unshared electrons is a doublet, it is best described as a monovalent radical that happens to have a lone pair as well.  

User 25d107bd42

02-10-2009 15:40:08

In the attached image there are all Marvin-possibilties given by the options right-click on the N, and choose Radical and View Misc Lone Pairs is on. On the right side there is a crude description of the orbital occupation for the four valence orbitals of nitrogen. The colors show the origin of the electrons and the spin is shown as arrows.


Radical Off  -  Monovalent  are OK for the neutral species.


Radical Divalent - Divalent Triplet are also OK for the cation, which is produced automatically.


For Radical Divalent Singlet Marvin shows a lone pair, which is not correct.


But for the Trivalent options it seems to me you must have more than four valence orbitals for N. This does not correspond to the octett rule for elements of the second row Li Be B C N O F Ne. (Nitro-groups are normally drawn as resonance formulas to obey the octett rule).


Regards, Hans-Ulrich


2nd image version.The attached image has been changed and the red descriptions have been added, Sat Oct 03, 2009,  HUWagner.


3rd image version. After reading the IUPAC rekommendations for radical-nomenclature I have changed my statement to the red question, Thu Oct 08, 2009,  HUWagner.

User 870ab5b546

02-10-2009 15:56:14

Re trivalent radicals, that's what I was saying.  "Trivalent doublet" shouldn't be an option because it's the same as a monovalent radical, and "trivalent quartet" for N should generate a valence error if the N is making more than one bond already.


However, I don't agree with you on "divalent singlet."  In Marvin, this term refers to an atom that has one lone pair and one empty orbital, like a carbene or nitrene.  As a result, showing the lone pair is perfectly acceptable.  Granted, the term "divalent singlet radical" is a misnomer, as it should in principle refer to an atom with two half-filled orbitals whose electrons have opposite spins, as in your drawing; and besides, atoms with one filled and one empty orbital are not radicals, so they shouldn't even be found in the Radical menu.  But given that there is no generally accepted term that encompasses carbenes, nitrenes, and related species ("free ylidenes"?), "radical -> divalent singlet" will have to do.

User 25d107bd42

05-10-2009 07:49:24

Hi Bob,


being a "systematist" I have evaluated the tool "Atom - Radical - Valencies" for the elements C N O S F Cl Br I and I have found more failures than the failure of this topic here. Is it OK when I open a new topic with the new title "Failures in the tool Atom - Radical - Valencies" ?


Regards, Hans-Ulrich


 

ChemAxon 990acf0dec

05-10-2009 09:57:37

Hi Bob and Hans-Ulrich,


Thank you for the comments on radicals. My first reply was really no connection to this topicit was posted here accidentally (there is another topic regarding templates and charges on N atoms).


Your comments are fair enough; I think we have to enhance the valence check to properly take all radical types into account, plus probably review the names of the options, and maybe reorganize the menus to better follow the reality. Your suggestions are wellcome here, and I am looking forward to read the new topic from Hans-Ulrich.


Best regards,


Akos


 

User 25d107bd42

07-10-2009 07:10:15

Hi Akos,


before posting my suggestions for handling radicals I have a question:


What is in Marvin-nomenclature the difference between "Radical Divalent" and "Radical Divalent Triplet" ?


It seems to me, "Divalent" means "Diradical" and for these the Triplet is normally the most stable multiplicity.


The same question comes for "Radical Trivalent" , "... Doublet", "... Quartet".


I'm now studying the IUPAC nomenclature. For me there are some inconsistencies.


I will discuss it also with my colleagues.


Regards, Hans-Ulrich

ChemAxon 990acf0dec

07-10-2009 13:49:23

Hi Hans-Ulrich,

Divalent alone means that the user doesn't know if it is Singlet or Triplet. And yes, its display is the same as of the Divalent Triplet, because that is more stable.

I also feel inconsistencies here, so I will also discuss this subject with the developer who implemented these states in the past. But your help is highly appreciated, thank you!

Best regards,

Akos

User 870ab5b546

07-10-2009 20:33:26

It seems to me that here is what is meant by the radical menu:


monovalent radical = at least 1 unshared electron + 1 hole


divalent radical = at least 2 unshared electrons + 2 holes



trivalent radical = at least 3 unshared electrons + 3 holes



*(although it is possible to have a singlet with two electrons occupying different orbitals, this situation is not common)


These definitions exclude compounds such as carbocations (two holes but no lone pairs) but capture compounds such as nitrenes (a lone pair and an empty orbital).


Now, how to capture these definitions succinctly in a menu is another matter entirely.  I think the best idea is to have a "Radical" menu with options doublet, triplet, and quartet, and then a separate "Carbenes and analogs" menu with options unknown spin state, singlet, and triplet.  Radical -> triplet and Carbenes and analogs -> triplet would give the same result.  There would no longer be a trivalent doublet radical or a trivalent radical of unknown state.  

User 25d107bd42

08-10-2009 18:48:24

Hi,


this discussion gets more and more complicated. I will discuss the topic with colleagues once more on Monday.


Regards, Hans-Ulrich


 

User 870ab5b546

09-10-2009 00:15:54

Regarding valence errors for radicals: for row 2 elements, radical valency + sum of bond orders > 4 should trigger a valence error, because each order of valency "uses up" one orbital.  

User 25d107bd42

09-10-2009 07:45:39

Hi Bob, yes: " > 4 should trigger a valence error".


And the red "mark" should be much much larger.


Many user will not recognize this tiny red line and the meaning is not clear. Normally a underline is a positive sign.



The attached image shows one more wrong "radical".


Regards, Hans-Ulrich