valence error for H•

MarvinSketch incorrectly thinks that there is a valence error in H• (hydrogen atom).

Hi Bob, may I once more "chime in" in your important topic here ?

About 14 months ago we had a long discussion about radicals and there was no ending:

https://www.chemaxon.com/forum/ftopic5324.html

The inconsistent handling of radicals must be reorganized.

And now to the hydrogen problem. It took some time for me to find the way to produce a H radical, as can be seen in the attached image. And the red line below H now shows the incorrect assignment "valence error".

The inconsistent handling of hydrogen should be reorganized, too.

Regards, Hans-Ulrich

BTW: Hydrogen is the only element which is charged when you put it as single atom on the canvas. Why ? But this would start a new topic.

Hi,

We are refactoring valencecheck.

The new version will be available from 5.5.1. The new one will not give valence error for radical Hydrogen atom.

About the Hydrogen handling Akos will reply, but he is out for a few days.

Thank you for the report.

HUWagner wrote:

BTW: Hydrogen is the only element which is charged when you put it as single atom on the canvas. Why ? But this would start a new topic.

Oh, I can answer that one.  Because 99% of the time, when an organic chemist draws a lone H atom on the canvas, she intends to draw H⁺.  So I think the behavior is perfectly reasonable.  It may not be consistent with how other atoms are drawn, but H is in many ways unique among atoms.  

Hi,

I think all the questions have already answered here, but let me summarize:

1. The inconsistent handling of radicals (including hydrogen) will be solved by the new valence check algorithm coming in version 5.6

2. The behavior that when you place a H atom on the canvas, it automaticall gets a charge is intentional (as Bob correctly pointed out). Actually, there is a similar "feature" for the N atom (when you chage an atom having four bonds to N, then it gets a plus charge).

Best regards,

Akos

akospapp wrote:

The behavior that when you place a H atom on the canvas, it automatically gets a charge is intentional (as Bob correctly pointed out). Actually, there is a similar "feature" for the N atom (when you change an atom having four bonds to N, then it gets a plus charge).

As of at least Marvin 5.11.5, this behavior has changed.  When I place an H atom on the canvas, it is not given a +1 charge, and when I give a fourth bond to N or change a tetravalent C to N, it is not given a +1 charge.  Why?  I much preferred the old behavior.  

Hi, let me chime in here once more:

I think it's correct to show no charges automatically.

The first attached screenshot shows the result of inserting a nitrogen in a postion having four bonds: nitrogen is charged. Inserting an oxygen in a postion having three bonds produces no charge instead the valence error is correctly highlighted. These differences are inconsistent. So the new behaviour of the newer MarvinSketch versions is better, especially for education.

But I suggest to include in the preferences one more option, f.e. "Add charges to H, NR4..." or so, screenshot number 2.

Best regards, Hans-Ulrich

I'm OK with not adding a charge automatically to N.  But I still think that when an isolated H atom is placed on the canvas, it should automatically be given a + charge.  

OK, but it should be an option in the preferences.

While reimplementing it, it could be installed as good option, too.

Best regards, Hans-Ulrich