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Nicer coordination bonds?
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Guntram

Joined: 04 Feb 2009
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Link to postPosted: Thu Feb 05, 2009 12:01 pmPost subject: Nicer coordination bonds? Reply with quote

Hello together,

I start using MarvinSketch because it looks very promising in way of cross-system performance.


Unfortunately, MarvinSketch (like many other Drawing Software) is not really helpful in drawing inorganic structures, e.g. complexes.

Yes, there is this "coordination bond". But this one is very uncommonly used by inorganic chemists and it is getting worse, when you have a ligand, who has neutral and charged coordination sites, e.g. salicylaldehyde or the example in the online documentation (http://www.chemaxon.com/marvin/help/sketch/sketch-basic.html).



From the experienced chemical point of view, there is NO DIFFERENCE between a bond, which arises from a neutral ligand (e.g. the aldehyde function) or a bond from a charged ligand (e.g. chloride and phenolate anions). But MarvinSketch forces me the make two different kinds of bonds!

There may be two solutions of this problem:

1.) Switch off all this "chemical intuition", which makes an oxoanion-donor a hydroxylgroup, when applying a bond to it, two have the freedom to draw structures beyond the imagination of the MarvinSketch-Development team.

2.) Offer a "line"-tool, which behaves "drawingly" like a bond, but not "chemically".




I also tried the "any bond" tool, but this one just gave invisible things on my Ubuntu Intrepid Ibex (8.10). But this one also would be not accepted by real inorganic chemists.





I would of course prefer solution number 1, as the best automatic is always the one, which you also can switch off!




:),

pheidrias
Guntram

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Link to postPosted: Mon Feb 09, 2009 11:04 pmPost subject: Reply with quote

For those who have similar problems: I now found the option to change the bond-style of "any bond" to solid and this is now a possible workaround. Edit-->Preferences-->Bonds


I really start to like this software - although I still do have crashes when trying to save a structure (unfortunately a somewhat crucial step...)!
Akos
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Link to postPosted: Wed Feb 11, 2009 12:01 pmPost subject: Reply with quote

Hi Guntram,



Thank you for your useful comments here. Just a quick note that might help for the first solution in your original comment:

If the target is just to draw the structure, you can switch off the display of the implicit hydrogens (View > Implicit Hydrogens > Off) as well as the valence error highlighting (Edit > Preferences -> Structure tab -> Highlight Valence Errors).


Best regards,

Akos
Jack

Joined: 19 May 2010
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Link to postPosted: Wed May 19, 2010 12:38 pmPost subject: Reply with quote

Sorry to revive a dead thread, but its pretty sad to see that these kinds of issues still haven't been resolved (3 years after the comments here?).  It's a nightmare trying to specify the stereochemistry of say, an octahedral complex... you need to use wedges, but can't since it disrupts the number of implicit hydrogens on lone-pair donors like amines.  Changing the valency of the coordinating atom fixes that, but then I end up stuck with 5, 10 or even 15 (vX) labels everywhere which makes the image look, well... awful.  Would've been a pretty good idea to take the 2 minutes to include an option not to display those I think.

Same goes for drawing the Hs explicitly -- the image becomes so crowded you can't even make out what the complex actually is.

The only solution I've found is to treat NH2, OH2, etc, as a "group", which is frustrating since I have to constantly change the name (ie OH2 vs H2O) after rotating in 3D, and even then its impossible to avoid some situations where the bond appears to link non-coordinating atoms.

Is there any way to fix this, and if not, how long until the next version (I note an earlier thread where it was mentioned that it might include an option to remove valence tags)?

Jack

Joined: 19 May 2010
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Link to postPosted: Wed May 19, 2010 2:20 pmPost subject: Reply with quote

At the risk of sounding like an idiot...

I just drew [Cu(en)2(H2O)2], using explicit hydrogens because of the problem I explained above... but when I erased them all, the coordinating atoms (4 x N, 2 x O) instantly appeared with the right number of implicit hydrogens (even though this makes the N's tetravalent and O's trivalent) -- and with none of those stupid (vX) labels or charges...

What's going on!?  I'm very pleased but confused...

Edit: appears to be a glitch whereby explicit H's are automatically converted to (the same number of) implicit hydrogens when deleted, even if this doesn't accord with the valency of the atom they're bound to.  When saved and reopened, the implicit hydrogens go back to "normal."

Akos
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Link to postPosted: Mon May 31, 2010 1:49 pmPost subject: Reply with quote

Dear Jack,

If you want to handle the valences corectly, coordinate compounds have to be drawn with coordinate bonds in Marvin; the stereochemistry of the coordinate compounds presently are not handled, even if you use wedge bonds instead.

On the other hand, we decided to implement the option to be able to switch off the valence display (but of course it is much more than 2 minutes, especially taking its consequenses in queries into account; if you think so, you'd better start developing your own software to understand).

Best regards,

Akos

Guntram

Joined: 04 Feb 2009
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Link to postPosted: Sun Oct 31, 2010 5:07 pmPost subject: Reply with quote

Hello again!

 

After some time, I need to draw some structures again and I'm stuck again ;-).


With the above posted workaroumd, it is possible to draw non-H-substituted ligands.

But is there another solution to draw H-substituted ones, like water or ammonia?

When they are attached via an "any"-bond, they either loose one hydrogen or they loose all of them, if automatic hydrogens are switched off.

Is there still no option, to make the "coordination bonds" look like usual bonds (as from an inorganic chemists point of view, there is no difference between them ;-) ) ?

 

Please help the suffering community of inorganic illustrators!

Akos
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Link to postPosted: Tue Nov 02, 2010 3:59 pmPost subject: Reply with quote

Hi,

 

Both related feature requests are on the list: The valence display option already has a high priority (probably coming in 5.4.x in a few months), while the display of the coordinate bonds as single bonds is in medium priority right now (probably coming in 5.5 next spring).

 

Best regards,

 

Akos

Guntram

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Link to postPosted: Tue Nov 02, 2010 8:07 pmPost subject: Reply with quote

Will there be some "sneak preview"-possibility in the next few weeks (alpha/beta-versions)? I need to finish my PhD-thesis and would really like to use MarvinSketch for it, which I nowadays recommend every student at my university!

 

Thanks,

Guntram

Akos
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Link to postPosted: Tue Nov 02, 2010 10:38 pmPost subject: Reply with quote

Hi Guntram,

Yes, the 5.4.0 beta is ready, so if you need it, I can send you the link where you can download it from, but the features I mentioned are not included yet. So, unfortunately, you cannot have these features in a couple of weeks.

Best regards,

Akos

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