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Resonance Arrows and Reaction Arrows are different things.
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Hans-Ulrich

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Link to postPosted: Tue Nov 04, 2008 10:19 pmPost subject: Resonance Arrows and Reaction Arrows are different things. Reply with quote

Hi,
evaluating the reaction options of MarvinSketch I found a severe failure in the tool "Reaction Arrows".

The Two-headed Single arrow is restricted to resonance hybrids (mesomeric).
And this is not a reaction. It is only "shifting" of electrons
.

I cite http://en.wikipedia.org/wiki/Resonance_(chemistry):
"Therefore one calls the two Lewis structures canonical, contributing or resonating structures and the real molecule is considered to be their average, called a resonance hybrid. Resonance structures of the same molecule are connected with a double-headed arrow." In the screenshot there is the enolat example.

Regards, Hans-Ulrich



 Filename: bf0188.png    Filesize: 31.94 KB    Viewed: 122240 Time(s)
 Description:  Resonating structures for the enolat ion.
bf0188.png


Last edited by Hans-Ulrich on Tue Nov 11, 2008 6:56 pm; edited 1 time in total
Akos
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Link to postPosted: Wed Nov 05, 2008 5:50 pmPost subject: Two headed reaction arrow Reply with quote

Hi Hans-Ulrich,

You are right, it is not correct to interpret sketches with two headed arrows as reactions (although it is useful to store them in reaction form, because it is easier to refer to the structures on the two sides).

We also have a graphical two-headed arrow, please use that one instead. (You can find it in the Insert > Graphics group.)

In the meantime, we will rename the "Two-headed single reaction arrow" to "Two-headed single arrow".

Thanks for the notification.

Best regards,

Akos
Hans-Ulrich

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Link to postPosted: Thu Nov 06, 2008 10:40 amPost subject: Reply with quote

Hi Akos,
I will add another example, the pentamethincyanine-cation, an important chromophore, formulated in the usual VB resonance structures, see screenshot bf0189 (I used the graphical arrows). This cation is normally formulated in one of the formulas in the upper line. But the formulas in the lower line are also important according to quantum chemical results (including HMO) or to NMR chemical shifts for the CH-groups. The old problem is in the deficensies of the Valence Bond formulas.

But to say it once more:The two-headed single arrow must be totally eliminated from the "Reaction" buttons. Resonance (or "Mesomerie") is not a reaction.
In the actual form it is inoperative to use the program for teaching.
Quote:
(although it is useful to store them in reaction form, because it is easier to refer to the structures on the two sides).
What do you mean by this? How to do with the 5 structures in the example ? Can you please post an example.

Regards, Hans-Ulrich



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 Description:  Pentamethincyanin-cation
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Akos
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Link to postPosted: Thu Nov 06, 2008 12:17 pmPost subject: Reply with quote

Quote:
>(although it is useful to store them in reaction form, because it is easier to refer to the structures on the two sides).
What do you mean by this? How to do with the 5 structures in the example ? Can you please post an example.
Presently it is useful only in case of two mesomeric structures, but as soon as we support multistep reactions, your example will also be possible to be saved e.g. in RXN format.
Hans-Ulrich

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Link to postPosted: Thu Nov 06, 2008 12:49 pmPost subject: Reply with quote

Hi Akos,

this is an argument more not to handle and not to store mesomeric structures in a reaction format.
What's the purpose to have these structures in a reaction format ?
The formulas above are stored in the mrv-format and that's OK.

Regards, Hans-Ulrich
Hans-Ulrich

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Link to postPosted: Thu Nov 06, 2008 1:29 pmPost subject: Reply with quote

Hi Akos,

And one example more, see screenshot bf0190. This is one compound. To do now "Aromatize" doesn't help. The cation above is also one cation, and there is no "Aromatize". Sometimes there are in the literature those cations with dotted lines for the pi-system.

And the two-headed arrow does not represent a reaction.

With the "Aromatize"-tools of Marvin there are also problems. One discussion is in the context "Double Bonds in MarvinSpace", but this will be discussed in that topic.

Regards, Hans-Ulrich



 Filename: bf0190.png    Filesize: 2.49 KB    Viewed: 122204 Time(s)
 Description:  2 mesomeric formulas for benzene
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Akos
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Link to postPosted: Thu Nov 06, 2008 2:17 pmPost subject: Reply with quote

My first question is why is it such a serious problem if we are able to save the double headed arrows in reaction format as well? If you need only the sketch, it is also there. Where does the reaction representation (in file format) cause problem for you?

The other question is related to your comment in the first paragraph:
Quote:
The cation above is also one cation, and there is no "Aromatize". Sometimes there are in the literature those cations with dotted lines for the pi-system.
This is not related to "aromatization", it would require a delocalize action, and the capability of displaying delocalized structures. This is on our feature request list, but not with high priority.
Hans-Ulrich

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Link to postPosted: Thu Nov 06, 2008 10:39 pmPost subject: Reply with quote

Hi Akos,
I think the following result concerns the first question.

I have saved the enolat-mesomers shown in the first post of this topic in a file enolat-mesomer.mrv. Later I opened it in MarvinSketch and there were the resonance formulas back shown in the upper part of the screenshot. OK.

Then I simply selected the "Two-Headed Single Reaction Arrow" and deleted it. I got the result shown in the lower part of the screenshot. How to explain ?

This effect is only present when saving and reopening the formulas. It is not present when editing the example and deleting the arrow immediately without saving the formulas.

Regards, Hans-Ulrich



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 Description:  Deleting a "Two Headed Single Reaction Arrow"
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Akos
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Link to postPosted: Fri Nov 07, 2008 8:53 amPost subject: Reply with quote

Hi Hans-Ulrich,

What you've found is rather a bug I think. We will investigate it; thanks for the report.

Best regards,

Akos
Hans-Ulrich

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Link to postPosted: Fri Nov 07, 2008 8:56 pmPost subject: Reply with quote

Hi Akos,

it is very difficult to teach the concept of electronic resonance structures (In German called "Mesomerie Grenzstrukturen"). Very often chemists think a resonance structure is a real molecule and they don't realize the "Two-Headed Single Arrow (THSA)" as a special symbol which has nothing to do with reaction arrows. So it is counterproductive to have the "THSA" even near the reaction arrows and to store it in a "RXN reaction" format.

The "Two-Headed Single Arrow" in the reaction arrow menu should be immediately deleted. To have the Graphics-version is enough. I must repeat: In the actual form it is inoperative to use the program for teaching. And the description in the help files must be changed also.

And the program is in this form in the internet !

Using the Marvin-applet one can do the Hueckel calculation for the two resonance formulas of an amide and the result is (now) the same for both resonance structures. OK.
But the arrow changes to a reaction arrow. How to explain if students show you this experience ?

Regards, Hans-Ulrich



 Filename: bf0203.png    Filesize: 33.87 KB    Viewed: 122156 Time(s)
 Description:  HMO calculation for the two resonance structures methylamino-acetaldehyde
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Akos
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Link to postPosted: Fri Nov 07, 2008 9:58 pmPost subject: Reply with quote

Hi Hans-Ulrich,

I understand your point, and as I mentioned, theoretically you're right. The question here is that how many people may have already used two-headed arrows in their reactions, because if we simply deprecate this feature, they might be hurt. See for example the following topic:

http://www.chemaxon.com/forum/viewtopic.php?p=19278

So I have to investigate this issue carefully. We probably should remove the two-headed (reaction) arrow from the reaction group (so your students cannot find it there), and place it somewhere else (so others can still use their sketches on the same way, and save their structures in RXN), or even rename the reaction arrow group to whatever... I don't know yet.

Best regards,

Akos
Hans-Ulrich

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Link to postPosted: Fri Nov 07, 2008 11:16 pmPost subject: Reply with quote

Hi Akos,

so I have the question: Since the "Two-headed Single Arrow" is reserved to resonance formulas, why not to use the "Two-headed Double Reaction Arrow for "to and fro" reactions, i.e. chemical equvilibriums.
What is the use of this Double Arrows ? What is the difference ? I didn't find it in the documentation.

And what is the difference between the "Regular Single Reaction Arrow" and the "Regular Double Reaction Arrow" ?

In the topic you have cited, it seems to me this type of arrow definition is free.

Regards, Hans-Ulrich
Akos
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Link to postPosted: Mon Nov 10, 2008 12:24 pmPost subject: Reply with quote

Hi Hans-Ulrich,
Quote:
why not to use the "Two-headed Double Reaction Arrow for "to and fro" reactions, i.e. chemical equvilibriums
Exactly because it is used for chemical equilibrium. (BTW, ISIS/Draw doesn't accept this type of arrow as reaction arrow either.)
Quote:
And what is the difference between the "Regular Single Reaction Arrow" and the "Regular Double Reaction Arrow" ?
AFAIK nothing except the design, but some users prefer to use the "Double" type in some sketches. (And there should be even more arrow types I think, and probably will really be in the future if we have time to implement.)

So in summary, we have to continue to support the possibility to save resonant forms in reaction format, where each form is a separate molecule object, because several users need it. On the other hand, we should delete the "reaction" term from the name of the resonant arrow type and the corresponding menu items.

Best regards,

Akos
Hans-Ulrich

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Link to postPosted: Tue Nov 11, 2008 9:13 pmPost subject: Reply with quote

Hi Akos,

it's not a tiny problem. I have discussed it with my colleagues and they also argue:
To use the double-headed single arrow for reactions is simply wrong.
And to store resonance structures in a RXN-file is also wrong.

And for use of Marvin in teaching, those wrong options should not be present. For teaching one must be highly accurate and one cannot use "workarounds".

To emphasize the point I attach a IUPAC paper I found in the web. And I have also found the definitions of Linus Pauling, who has developed the resonance formalism (afaik).

Concerning Hueckel calculations Marvin is now handling all resonance structures as equal, see the topic http://www.chemaxon.com/forum/ftopic3612.
But to other calculations, f.e. pKa, logP, there a bugs in the handling of resonance. I will post these in new topics.

Regards, Hans-Ulrich



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 Description:  Definition of resonance structures
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Akos
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Link to postPosted: Tue Nov 11, 2008 11:02 pmPost subject: Reply with quote

Hi Hans-Ulrich,

I didn't say it is a tiny problem. And again, theoretically you are right: the two-headed arrow should not be used in reactions. But since the feature was in Marvin for long, some users get used to it, and this is why it is really not a tiny problem.

I ask again: if we rename the two-headed arrow, and move it to a separate menu group as well, why is it so important for you to avoid saving resonance forms to reaction file format?

Just one more addition: in the meantime, we are working on the development of a Structure Checker, which will be implemented in Marvin soon. This module will be able to notify the user that the file format selected is not proper for storing the info reflected by the sketch. This can further help the student in understanding that resonance forms are not real reactions.

Best regards,

Akos
Hans-Ulrich

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Link to postPosted: Wed Nov 12, 2008 8:31 amPost subject: Reply with quote

Hi Akos,
now there is a solution:

rename the two-headed single arrow, and move it to a separate menu group as well

It must be clearly seperated and the word "resonance" must be in the menu.
(I would prefer a word like "Mesomerie" because it means "in between", but this is not used in the English speaking chemical literature).

Storing those resonating structures in a clear defined file format is not the problem.

And the bugs in handling of those resonating structures must be fixed (See the bugs mentioned above). If I find more I will post it here or in a new topic. This one is a little long now.

Regards, Hans-Ulrich
Akos
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Link to postPosted: Fri Nov 14, 2008 5:22 pmPost subject: Reply with quote

Hi Hans-Ulrich,

OK, we will do the following modifications in 5.2:

- Rename the "Reaction Arrow" group to "Arrow" group (in the insert menu)
- Rename the "Two-headed Single Reaction Arrow" to "Resonance Arrow"
- Rename the "Two-headed Double Reaction Arrow" to "Equilibrium Arrow"

We will also rearrange the group (in the insert menu and also on the toolbar) to move the resonance arrow and the equilibrium arrow to the bottom, and separate them from the reaction arrows with a separator. In addition (but only in the insert menu), we will include the "Single Graphical Arrow" on the bottom of the list (also after a separator).

I hope it will be satisfactory for you.

Best regards,

Akos
Hans-Ulrich

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Link to postPosted: Fri Nov 21, 2008 10:24 pmPost subject: Reply with quote

Hi Akos,

after discussing other problems with Marvin I analysed this topic here further, see the attached picture.

Type 1 arrow is stored in mrv-format as "DEFAULT". OK
Type 2 arrow is stored in mrv-format as "RESONANCE". OK
Type 3 arrow is stored in mrv-format as "RETROSYNTHETIC". ???
Type 4 arrow is stored in mrv-format as "EQVILIBRIUM" OK

Here I have only problems with type 3. For "RETROSYNTHETIC" descriptions there is often used a backward arrow (blue in the picture). "Retro" means "backward". In the present Marvin menu I cannot see an essential difference between type 1 and type 3, only the design is different.

In SMILES format all four types are stored with ">>", which is wrong for type 2 (resonance).
Is there a definition in the SMILES format for ideas as "<>" for equivilibrium and "<<" for retrosynthetic ? (BTW: Where is an exact definition of the SMILES format ?)

Having this analysis and your modifications above I will suggest to extend these in the following way and order:
- Rename the "Reaction Arrow" group to "Arrows" group (in the insert menu)
===
Reaction Types
F) - Then "Regular Single Reaction Arrow"
B) - Rename the "Regular Double Reaction Arrow" to "Retrosynthetic Arrow" and change its direction to backwards
E) - Rename the "Two-headed Double Reaction Arrow" to "Equilibrium Arrow"
--- separator
Mesomeric resonance structures
M) - Rename the "Two-headed Single Reaction Arrow" to "Resonance Arrow". But the storage to formats as smi (and other) must be controlled.
===

To your sentence to move the resonance arrow and the equilibrium arrow to the bottom I must say NO. The equivilibrium arrow belongs to the three types of reaction arrows and the resonance arrow must be separated alone and with a special separator.

And the same arrangement should be in the "Insert - Graphics" menu. Here should be added the backward "retrosynthetic arrow" and the "equivilibrium arrow", too.

Best regards, Hans-Ulrich



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 Description:  Four types of arrows
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Hans-Ulrich

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Link to postPosted: Thu Dec 11, 2008 9:55 pmPost subject: Separate reaction arrows and the resonance arrow Reply with quote

Hi Akos,
having now MarvinSketch 5.1.4pre1 I found better labelling for the different arrow types.
But the resonance arrow is still mixed in between the reaction arrows.

I suggest a clear separation.

What is the purpose of the fifth "Single Arrow" ? This arrow is already in the Insert Graphics menu.

A GUI must be as intuitive as possible.

Regards, Hans-Ulrich


Last edited by Hans-Ulrich on Fri Dec 12, 2008 2:52 am; edited 1 time in total
Akos
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Link to postPosted: Fri Dec 12, 2008 12:48 amPost subject: Reply with quote

Hi Hans-Ulrich,

Until we do not support the multistep reactions with "real" reaction arrows, and those can be sketched only with this type of arrow, we feel it important to have this arrow in the same group to find it easily.

Best regards,

Akos
Hans-Ulrich

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Link to postPosted: Fri Dec 12, 2008 2:51 amPost subject: Reply with quote

Hi Akos,

OK. Then I would suggest the following arrangement, see screenshot.

Best regards, Hans-Ulrich



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 Description:  Separation of resonance arrow.
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Bob

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Link to postPosted: Sat Dec 27, 2008 9:16 pmPost subject: Reply with quote

I'd like to put my two cents in. I agree with most of Hans's suggestions below, except I think the type 3 arrow should be retained as a retrosynthetic arrow. I do *not* agree that it should be changed to a backwards-pointing arrow, whether single- or double-bodied. The double-bodied forward arrow is very widely used in drawing retrosynthetic analyses. It does not represent a single reaction, but a thought process. It is read as, "is prepared from". It should be retained as it is with the "retrosynthetic" name. If a user wants to draw a single arrow pointing right to left, he can just draw it pointing from right to left.

On equilibrium arrows: you should provide a way to make the top and bottom arrows of the equilibrium arrow different lengths. This convention is sometimes used to show which side of an equilibrium is favored. Alternatively, you can provide the user the option of drawing two single-bodied, half-headed reaction arrows pointing in opposite directions. This last option would require a fifth kind of arrow, the half-headed reaction arrow.

So, to sum up, all arrows should be drawn from tail to head, and you should have EITHER a reaction arrow, an equilibrium arrow where the two lines can be made different lengths, a retrosynthetic arrow (double-bodied, forward-pointing), and a resonance arrow (single-bodied, two-headed), OR a reaction arrow, a half-headed reaction arrow, an equilibrium arrow, a retrosynthetic arrow, and a resonance arrow.

Finally, I agree that it is important to distinguish graphical arrows from reaction arrows. We do not ever use the reaction arrows in ACE (because, as you say, you do not support multiple reaction arrows); in fact, we turn off the ability to draw them.

-- Bob
HUWagner wrote:
Type 1 arrow is stored in mrv-format as "DEFAULT". OK
Type 2 arrow is stored in mrv-format as "RESONANCE". OK
Type 3 arrow is stored in mrv-format as "RETROSYNTHETIC". ???
Type 4 arrow is stored in mrv-format as "EQVILIBRIUM" OK

Here I have only problems with type 3. For "RETROSYNTHETIC" descriptions there is often used a backward arrow (blue in the picture). "Retro" means "backward". In the present Marvin menu I cannot see an essential difference between type 1 and type 3, only the design is different.

Having this analysis and your modifications above I will suggest to extend these in the following way and order:
- Rename the "Reaction Arrow" group to "Arrows" group (in the insert menu)
===
Reaction Types
F) - Then "Regular Single Reaction Arrow"
B) - Rename the "Regular Double Reaction Arrow" to "Retrosynthetic Arrow" and change its direction to backwards
E) - Rename the "Two-headed Double Reaction Arrow" to "Equilibrium Arrow"
--- separator
Mesomeric resonance structures
M) - Rename the "Two-headed Single Reaction Arrow" to "Resonance Arrow". But the storage to formats as smi (and other) must be controlled.
===

To your sentence to move the resonance arrow and the equilibrium arrow to the bottom I must say NO. The equilibrium arrow belongs to the three types of reaction arrows and the resonance arrow must be separated alone and with a special separator.

And the same arrangement should be in the "Insert - Graphics" menu. Here should be added the backward "retrosynthetic arrow" and the "equivilibrium arrow", too.
Hans-Ulrich

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Link to postPosted: Sun Dec 28, 2008 12:29 pmPost subject: Reply with quote

Hi,
to get accordance and to develop a new management of the chemical arrows, I first analyzed the situation given in MarvinSketch 5.1.4.

In the arrow menu there are now 5 options.
The handling of the resonance arrow (3) is still wrong, especially the saving in the mrv- and the smi-formats.

Number (5) and (6) are exactly the same, one given in the arrow menu, the other in the graphics menu.
That's confusing for new users of Marvin, especially for users of the web applet.

Number (7) is the resonance arrow, but only with the design description.

In the next post there is my suggestion for a new management.

Regards, Hans-Ulrich



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Hans-Ulrich

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Link to postPosted: Sun Dec 28, 2008 1:17 pmPost subject: Reply with quote

Hi,
here comes my suggestion for a revised management of the arrow tools., see the attached picture Arrows2.png.

Two menus, either only in the menus at top of the canvas or in the toolbar icons on the left side:
"Arrows" with the 3 options "Reaction Arrow", "Retrosynthetic Arrow" and "Equilibrium Arrows"
"Graphical Arrows" with the 4 options "Graphical Reaction Arrow", "Graphical Retrosynthetic Arrow", "Graphical Equilibrium Arrows" and "Graphical Resonance Arrow".
Please repeat each time the word "Graphical", so that the user sees exactly what the program is doing. Redundance is important in teaching.

The options of the menu "Graphical Arrows" correspond to the usage of Bob only to use the graphical arrows and to avoid the menu "Arrows".

And the "Equilibrium Arrows" could be further optimized by giving the possibilty to draw these with different lengths, as suggested by Bob.

Option "Arrows-Equilibrium Arrow" is saved in SMILES as a simple reaction. I am not an expert in SMILES, so I have the question: Has SMILES the possibility to distinguish reactions and equilibriums?

Options "Graphical Arrows" (2) and (3) must get new MPolyline ids and definitions.

To have the option "Graphical Resonance Arrow" only in the Graphical form would be the solution to all the problems discussed in this topic.

Regards, Hans-Ulrich



 Filename: Arrows2.png    Filesize: 123.54 KB    Viewed: 120814 Time(s)
 Description:  New management for the arrow menus.
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Akos
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Link to postPosted: Sat Jan 03, 2009 4:10 pmPost subject: Reply with quote

Hi Hans-Ulrich and Bob,

I agree with several of your suggestions, so I agree that:
- We should rename the Double Reaction Arrow to Retrosynthetic arrow both in the menu and on the toolbar.
- We need more reaction arrow types, first of all for the representation of the favored direction of equilibrium arrows.

On the other hand, I do not agree that the Resonance arrow should be removed from the reaction arrow group, and I still think that we should provide the capability to save it into reaction form (since as I mentioned, several user may use this functionality).

And I am also not sure we should start the name of the graphical arrows with "Graphical". The graphical objects should rather have names that directly describe the lookout of the object (usually as they used in graphics programs); e.g. the resonance arrow in its graphical object form should rather be named as "Left Right Arrow" (if we change its name at all). (For reference, please see page 201 in the attached document of UNICODE characters.)

Best regards,

Akos



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Hans-Ulrich

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Link to postPosted: Sun Jan 04, 2009 12:16 pmPost subject: Resonance Arrows and Reaction Arrows are different things Reply with quote

Hi Akos,
first I will repeat here the title of this topic: Resonance Arrows and Reaction Arrows are different things.
And then my answer to your sentence:
"I do not agree that the Resonance arrow should be removed from the reaction arrow group ..."
It must be very clear that Resonance does not belong to the reaction arrow group.

There are many chemists thinking resonance formulas as real molecule structures.
The Marvin software has still tools giving wrong results for different resonance formulas.
The Hueckel tool is now free from this misunderstanding, at least for the formulas I have tested.

And:
" ... and I still think that we should provide the capability to save it into reaction form (since as I mentioned, several user may use this functionality)"
Saved as a resonance arrow: OK. But not as a reaction arrow.
smi makes no difference, see my earlier evaluation in this topic.

In which file-formats is this "reaction form" saved: mrv, smi and other ?
Have the several file formats different "reaction forms" ? In an earlier post you mentioned, ISIS/Draw has not.
Is it necessary to use here the resonance arrow, why are the equilibrium arrows not enough to have this functionality ?

And a comment: The JAVA language has many "deprecated" classes and as a programmer I must often change my programs.

I agree with your sentences about "Graphical arrows".

Regards, Hans-Ulrich
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Link to postPosted: Sun Jan 04, 2009 2:41 pmPost subject: Re: Resonance Arrows and Reaction Arrows are different thing Reply with quote

Hi Hans-Ulrich,

If we keep the possibility to save sketches having resonance arrow to reaction file format (which you disagree here; see my comments below), we should keep the Resonance Arrow itself somewhere near the reaction arrows. There is already placed a separator between the two reaction arrows and the Resonance Arrow, and the group itself does not include the word "Reaction". I think we should move the Resonance Arrow further down, and to insert an additional separator after the Equilibrium Arrow (since we will have two more Equilibrium Arrow types soon). In addition, I think we should add the graphical pair of the resonance arrow (probably renamed as Left Right Arrow) to the last section of the group.

I think the most important question here is whether the sketches having resonance arrow can be saved to reaction format or not. My point of view is that since in molecule file formats separate structures handled as different fragments of the same compound, and not as separate compounds as in reaction format; and to have the resonance forms stored as separate compounds makes the reference to them easier.

Now my answers to your questions:

-Presently the SMILES/SMARTS notation has only one symbol for reactions: ">>" (http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html). I agree that it would be helpful to have different symbols for the three other types, (e.g. "><" for the equilibrium, and "<>" for the resonance, but no idea for the Retrosynthetic Arrow yet), but it belongs to Daylight, not us (I'll check what we can do here).

- Presently each reaction sketch (including those having Resonant Arrow) can be saved into any file format that supports the storage of reactions, but now only Mrv can make difference between the different reaction arrows (although soon we will support the export to cdx, and the import/export of skc is under development as well), so in the other file formats (e.g in SMARTS or in RXN) the reaction arrow is changed to Single Reaction arrow.

-Regarding ISIS/Draw: it does not allow to export sketches having either resonant arrow or equilibrium arrow into RXN (or other reaction file) format, but for example ChemDraw does.

Best regards,

Akos
Hans-Ulrich

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Link to postPosted: Sun Jan 04, 2009 3:40 pmPost subject: Reply with quote

Hi Akos, you have been very fast with your answer ! And thank you for the answers at the end.
I was just writing this post as your Topic Reply Notification came in.

So I will change the text, I think there is a way to solve the problem of this topic without annoying the users having used the resonance arrow for reactions.

First my evaluation for a real (biochemical important) reaction, see the attached image.
The image shows 5 times four molecules, connected without an arrow and with 4 different arrows.
And the saving in SMILES format is also shown.
In SMILES the 4 molecules in the first line are saved as "dot-disconnected" formulas, that's OK. The four lower lines are stored in the same notation as reactions ">>", which is wrong for the resonance arrow.
In the Marvin mrv format the first line is stored as one molecule, the four "arrow connections" are stored with the notations "DEFAULT", "RETROSYNTHETIC","RESONANCE" and "EQUIVILIBRIUM".

The way to solve could be:
1) As you have already planned the resonance arrow is placed below all other arrows and seperated.
2) Using the resonance arrow <-> does not produce automatically the +signs, as the other three arrows do. So the user who is accustomed to use the <-> arrow for reactions would recognise something has changed, and the user can find the explanation in the User's Guide.
3) The saving of molecules connected with the resonance arrow produces in SMILES dot-disconnected molecules and in Marvin something new, f.e. "MESOMER". And the opening of these mrv files produces the resonance arrow back, without +signs.
Of course, for correct <-> connections there is only one molecule on each side of the arrow.
4) Reading old mrv files with the notation "RESONANCE" produces the same arrow and +signs as "EQUIVILIBRIUM". The user would notice only the other double headed arrow, but the information in the file is not lost !
The user would get the exact formulation of an equilibrium and all is OK.

And opening SMILES files (old or new) produces already the same: single reactions.

What do you mean by this?

Regards, Hans-Ulrich



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Akos
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Link to postPosted: Sun Jan 04, 2009 4:44 pmPost subject: Reply with quote

Hi Hans-Ulrich,

Thank you for your answer; you are very fast as well ;-). Thank you for all of your comments.
HUWagner wrote:
The four lower lines are stored in the same notation as reactions ">>", which is wrong for the resonance arrow.
As well as it is wrong for the "Retrosynthetic" and the Equilibrium Arrow". This comes from the fact that SMILES does not support the differentiation between reaction arrow types. ON the other hand, I understand your point that a sketch having Resonant Arrow should not be saved into reaction format; see my answers to that below.
HUWagner wrote:
2) Using the resonance arrow <-> does not produce automatically the +signs, as the other three arrows do. So the user who is accustomed to use the <-> arrow for reactions would recognise something has changed, and the user can find the explanation in the User's Guide.
It is a good idea, I'll see whether we can solve it. (Presently if a reaction arrow is placed to the canvas, the molecules are converted to reaction components, and plus signs are automatically generated. But components can be merged, and in then the plus signs disappears between them, so if a resonant arrow is placed we may merge the components on one side. I have to discuss it with the developers.)
HUWagner wrote:
3) The saving of molecules connected with the resonance arrow produces in SMILES dot-disconnected molecules

I am not sure; it would be much better I think if the SMARTS notation used different symbols for different reaction arrows (as I mentioned, I will check what could we do here), but if that is not possible, we could really solve it this way. (This could be solved inside the SMILES/SMARTS export, although not easy, since reactions are presently handled commonly.) And if you use the dot to separate between the resonance structures, than you cannot draw e.g salts, because than the counter ion would be handled as a separate resonance structure, too.
HUWagner wrote:
and in Marvin something new, f.e. "MESOMER". And the opening of these mrv files produces the resonance arrow back, without +signs.
I don't understand this. We already have the Resonance Arrow type stored in Mrv, why would we need another storage format?
HUWagner wrote:
Of course, for correct <-> connections there is only one molecule on each side of the arrow.
Just a question: do you ever need to draw salts when sketching resonance structures?
HUWagner wrote:
4) Reading old mrv files with the notation "RESONANCE" produces the same arrow and +signs as "EQUIVILIBRIUM". The user would notice only the other double headed arrow, but the information in the file is not lost !
The user would get the exact formulation of an equilibrium and all is OK.
I strongly disagree with this. We should be able to read out the information from old Mrv files in the way it was meant when it was saved.
HUWagner wrote:
And opening SMILES files (old or new) produces already the same: single reactions.
Yes, but only because the file format itself does not support the storage of the reaction arrow type. We cannot do the same with Mrv.

Best regards,

Akos
Bob

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Link to postPosted: Sun Jan 04, 2009 5:40 pmPost subject: Reply with quote

akospapp wrote:
And I am also not sure we should start the name of the graphical arrows with "Graphical". The graphical objects should rather have names that directly describe the lookout of the object (usually as they used in graphics programs); e.g. the resonance arrow in its graphical object form should rather be named as "Left Right Arrow" (if we change its name at all). (For reference, please see page 201 in the attached document of UNICODE characters.)
"Left right arrow" is confusing to me, and it removes the chemical meaning of the arrow from its name. I don't think it's a good idea.

Perhaps the real problem here is that Marvin has two different classes of arrows: Graphical arrows, which are not imported into SMARTS, and the other kind of arrows -- let's call them "SMARTS arrows" -- which are. As I understand the history, ChemAxon introduced the graphical arrows so that users could draw multiple arrows in a single document, which was not possible with SMARTS arrows. SMARTS arrows also cause those + signs to appear in the document.

Either we need to differentiate clearly the SMARTS arrows from the graphical arrows, or we need to merge the two types. I don't think a merge is likely to happen in the near future, especially because some users might be taking advantage of the differentiation between the two types. So we need to differentiate them clearly. If you group them into two different menus, one called "Graphical" and the other called "SMARTS", you will have accomplished the differentiation. Using the term "SMARTS" will avoid the problem that Hans keeps pointing out, that you should not call a resonance arrow a reaction arrow.
Akos
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Link to postPosted: Sun Jan 04, 2009 9:41 pmPost subject: Reply with quote

Hi Bob,
bobgr wrote:
"Left right arrow" is confusing to me, and it removes the chemical meaning of the arrow from its name. I don't think it's a good idea.

This is how this graphical arrow is called in the UNICODE character set, but of course we can call it on any other name that describes its lookout better. (The present name, two-headed arrow is actually an arrow with two heads on one side according to the same document; but we can keep this name if it is understandable. The small icon is next to the name, anyway.)
bobgr wrote:
Perhaps the real problem here is that Marvin has two different classes of arrows: Graphical arrows, which are not imported into SMARTS, and the other kind of arrows -- let's call them "SMARTS arrows" -- which are.
Interesting idea, but unfortunately the term "SMARTS" is already occupied by the SMARTS notation (of Daylight), so if we do it this way, we have to find another attribute I think.
bobgr wrote:
Either we need to differentiate clearly the SMARTS arrows from the graphical arrows, or we need to merge the two types. I don't think a merge is likely to happen in the near future
Actually, we just started to do this, as you could realize it already in version 5.1.4, where the single arrow is placed into the same menu and toolbar group as the reaction arrows (although it still can be found in the Graphics menu, as well). And if we follow this way, we should place the graphical pair of the resonance arrow (called as "Left Right Arrow" or "Two-headed Arrow" or in whatever name) here as well. It helps the users to find out that graphical arrows can be used instead of reaction arrows (which is, as you also pointed out, presently important in case someone wants to use multiple arrows, until we support multistep reactions).

On the other hand, we can make two submenus, one called something equivalent with your "SMARTS Arrows" idea (but with another attribute), and the other called Graphical Arrows.

Best regards,

Akos
Bob

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Link to postPosted: Mon Jan 05, 2009 3:29 amPost subject: Reply with quote

akospapp wrote:
Interesting idea, but unfortunately the term "SMARTS" is already occupied by the SMARTS notation (of Daylight), so if we do it this way, we have to find another attribute I think.
Of course the term SMARTS already has a meaning, that's why I chose it. Isn't SMARTS used to describe reactions?

I was just trying to distinguish the graphical arrows, which are not imported into SMILES or SMARTS format, with the "reaction" arrows, which are.

If you don't like "SMARTS arrows" or "SMILES arrows", maybe you can call them "Daylight arrows".
Akos
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Link to postPosted: Mon Jan 05, 2009 11:43 amPost subject: Reply with quote

Hi Bob,
bobgr wrote:
Of course the term SMARTS already has a meaning, that's why I chose it. Isn't SMARTS used to describe reactions?
Not just reactions; AFAIK it was originally introduced to define queries.
bobgr wrote:
I was just trying to distinguish the graphical arrows, which are not imported into SMILES or SMARTS format, with the "reaction" arrows, which are.
Only the Single Reaction Arrow is exported into SMILES/SMARTS correctly, so it is not a proper reference either.
bobgr wrote:
If you don't like "SMARTS arrows" or "SMILES arrows", maybe you can call them "Daylight arrows".
I think the reaction arrows have no relation to Daylight; we should find an attribute that refers to their chemical meaning... but I have no idea yet. Maybe "Chemical Arrows"?

Best regards,

Akos
Hans-Ulrich

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Link to postPosted: Fri Jan 23, 2009 2:47 pmPost subject: Resonance Arrows and Reaction Arrows are different things. Reply with quote

Hi, I must come back to the title of this topic as an answer to:
Quote:
On the other hand, I do not agree that the Resonance arrow should be removed from the reaction arrow group, and I still think that we should provide the capability to save it into reaction form (since as I mentioned, several user may use this functionality).
            

 Resonance Arrows and Reaction Arrows are different things.

And users which have used these arrows in a wrong way must accept that saving resonances as reactions is deprecated.

I suggest now the toolbar menu shown in the attached image.

Saving resonance Lewis formulas combined with the graphical double sided resonance arrow produces in MRV-format still the attribute "RESONANCE". Opening old and new MRV-files with the attribute "RESONANCE" produces the graphical resonance arrow and all is OK.

Saving resonance Lewis formulas combined with the graphical double sided resonance arrow produces in SMILES-format dot.disconnected formulas. (This is done in the topic resonance smiles www.chemaxon.com/forum/ftopic4459.html  by avoiding arrows at all). Opening old SMILES-format with the >> symbol produces already always reaction arrows. These had to be changed already to the right arrows.

Regards, Hans-Ulrich



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Akos
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Link to postPosted: Wed Aug 19, 2009 4:12 pmPost subject: resonance arrows to be only graphical objects Reply with quote

Hi Hans-Ulrich,

Now I'm seriously considering your suggestion. Since this topic opened there was no any objection here, so this might mean that not too many users use resonance arrows in reactions... on the other hand, I need more feedback to be sure, so I will ask some users who frequently use reactions about their opinion.

Thank you for your continuous feedback.

Best regards,

Akos

 

 

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