[Jmol-developers] [ jmol-Bugs-899782 ] add radical support

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Bugs item #899782, was opened at 2004-02-18 13:27
Message generated for change (Settings changed) made by migueljmol
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Category: None
Group: None
>Status: Closed
Resolution: None
Priority: 5
Submitted By: Miguel (michaelthoward)
Assigned to: Miguel (migueljmol)
Summary: add radical support

Initial Comment:
John said:
> A simple example:
> The allyl radical is formally   H2C=CH-CH2 and is
normally written with
> a  bullet
> superscript on the rightmost carbon atom C to
indicate the presence of
> an unpaired electron on that carbon.

Understood

> If the hydrogen atoms are not displayed then the
presence of the bullet
> is  essential
> as otherwise C=C-C could represent H2C=CH-CH3

That makes sense

> The following is my version of a mol file with the
'radical' information
> added but because it doesn't work I don't know if I
have followed the
> MOL format  specs.
> correctly.  The M RAD line is saying (?) there is one
atom, namely atom
> no. 2 which has an unpaired electron

[snip]
>   M  RAD  1  2  2

Q: What is that 'extra' 2 ?


OK.

The bad news is that these RAD records are not being
read by Jmol. Even
worse is that there is no support for anything like
this ... since this is
the first that I have heard of it :-)

The good news is that I don't think it would be too
difficult to add.

Q: Is it enough to say that it is a 'radical', or is
there some measure of
'radicalness'? :-) Basically, can I just use one bit as
a flag to tell
whether or not something is 'radical'?

Q: What is the relationship (if any) between 'radical'
and 'charge'?


You earlier asked about showing the atom 'name'. I
think this would be a
good case to give this atom a different 'name':
  if you say label "%e" you will get 'C'
  if you say label "%a" you will get 'C*' [bullet]

Q: does that sound right to you?


Separately, did
  label "%C" work for you?


Miguel


-------- Original Message --------
Subject: Re: [Jmol-users] JMol applet: label option
From: John Simmie <joh...@nu...>
Date: Wed, February 18, 2004 18:27
To: jmo...@li...

Miguel:
A simple example:
The allyl radical is formally   H2C=CH-CH2 and is
normally written with
a  bullet
superscript on the rightmost carbon atom C to indicate
the presence of
an unpaired electron on that carbon.

If the hydrogen atoms are not displayed then the
presence of the bullet
is  essential
as otherwise C=C-C could represent H2C=CH-CH3

The following is my version of a mol file with the
'radical' information
added but because it doesn't work I don't know if I
have followed the
MOL format  specs.
correctly.  The M RAD line is saying (?) there is one
atom, namely atom
no. 2 which has an unpaired electron
-----------------------------------------------------------------------------------
  HCOO_opt

   created with ArgusLab version 4.0.0 Beta Release #2
   4  3  0  0  0  0  0  0  0  0  0 V2000
    -0.4525    0.1224   -0.0000 C   0  0  0  0  0  0  0
 0  0  0  0  0
-1.0961    1.1697    0.0000 O   0  0  0  0  0  0  0  0
 0  0  0  0
-1.0725   -1.0434    0.0000 O   0  0  0  0  0  0  0  0
 0  0  0  0
     0.6576    0.0125    0.0000 H   0  0  0  0  0  0  0
 0  0  0  0  0
   1  3  2  0  0  0  0
   1  2  1  0  0  0  0
   1  4  1  0  0  0  0
  M  RAD  1  2  2
  M   END
-----------------------------------------------------------------------------------

All the best, John


----------------------------------------------------------------------

Comment By: Miguel (michaelthoward)
Date: 2004-02-19 04:43

Message:
Logged In: YES 
user_id=608250

At 17:52 18/02/2004, you wrote:
>John said:
> > correctly.  The M RAD line is saying (?) there is one
atom, namely atom
> > no. 2 which has an unpaired electron
>[snip]
> >   M  RAD  1  2  2
>Q: What is that 'extra' 2 ?

An atom can have no unpaired electrons, 1 unpaired e, or 2
unpaired es
but the coding used by the mol file is 1, 2 or 3 (singlet,
doublet or 
triplet electronic states)
So the second 2 means that carbon has one unpaired electron.

>Q: Is it enough to say that it is a 'radical', or is there
some measure of
>'radicalness'? :-) Basically, can I just use one bit as a
flag to tell
>whether or not something is 'radical'?
>
>Q: What is the relationship (if any) between 'radical' and
'charge'?

The short answer is none; note that the mol file treats them
separately
M CHG  2  4  1  6  -1
means that two atoms have charges with atom no. 4 having a
formal positive
charge whilst atom no. 6 has a formal -ve charge

>You earlier asked about showing the atom 'name'. I think
this would be a
>good case to give this atom a different 'name':
>   if you say label "%e" you will get 'C'
>   if you say label "%a" you will get 'C*' [bullet]
>
>Q: does that sound right to you?

Yes I think so; this is basically a labelling issue.

>Separately, did label "%C" work for you?
>Miguel

                Dr. John M. Simmie
Chemistry Department & Environmental Change Institute
    National University of Ireland, Galway::Ireland
      Phone: +353-91-750388::Fax: +353-91-525700





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