MarvinSketch: indistinguishable electron-flow arrows

I'm having a problem with electron-flow arrows. At least, with the way they are represented.

I have drawn two 2 EF arrows indicating that the double bond pi electrons are used to form a bond to the proton. Visually there's only a slight difference in length between them (I had to scale the image up to 200% for these images). If I mouse-over either one I get the exact same box drawn from the furthest C to the H+.

At the XML level the two arrow are distinguishable, but how would a student drawing the arrows be able to tell if they are different in the first place? Shouldn't these have different graphics on mouse-over?

The arrow that ends "lower" in the image moves the pi electron to a bond between the terminal C and the H+ (which is mechanistically correct). The arrow that ends "higher" seems to be spreading the electrons between both carbons in the double bond and the H+ (which is mechanistically incorrect, but visually practically indistinguishable).

Is it possible to adjust the graphics to denote the difference?

 

MarvinSketch 5.2.4 on XP SP3

 

Hi Michiel,

I am a bit mixed up by this "lower" and "higher... Do you mean that the electron flow arrow should be closer to the atom label when it is drawn by selecting the atom as end-point?

Best regards,

Akos

akospapp wrote:

Hi Michiel, I am a bit mixed up by this "lower" and "higher... Do you mean that the electron flow arrow should be closer to the atom label when it is drawn by selecting the atom as end-point? Best regards, Akos

No, I don't think so.

I'm trying to move an electron pair from the double bond to the gap next to the proton so I end up with a methyl at the end and a stable carbocation proximal. For some reason MarvinSketch thinks there are two ways of doing it and they result in slightly different arrows as can be seen in the images. They are disintuishable in the MRV in that the arrow that ends slightly higher lists 3 atoms: the upper C in the double bond, the lower C in the double bond, and the H as its connection list; the arrow that ends slightly lower lists only 2 atoms: the lower C in the double bond and the H as its connection list. From the graphics, however, I can't tell the difference.

I'm guessing that the "lower" arrow is the correct one. What does the "upper" arrow indicate? I don't know what such an electron movement would signify? How can an electron pair belong to three atoms at the same time?

How can a student (any viewer) distinguish between the arrows if there is no visual difference (the boxes indicating the arrow shape when you mouse over them) except the apparent length/termination position of the arrow? What if 50% of my students use one and the other 50% use the other arrow? How will I be able to score them all correctly? I'm using a reference MRV that I drew to parse their answers at the XML level, so only the ones with the C-H will be marked correct, and the ones with the C-C-H will be thrown out. (Try explain that to half a class.)

So, back to my original question: how does a user visually distinguish between these two arrows in order to decide which is the correct one?

In the upper case, C1=C2 H(+) -> H-C1-C2(+); in the lower case, C1=C2 H(+) -> C1(+)-C2-H.  In other words, in the upper case, the new bond forms between the distal C and the H; in the lower case, the new bond forms between the proximal C and the H.

The problem Michael raises is a general one whenever three atoms involved in bond-making are collinear.

A client-side solution is to train students to move the H(+) off of the C1-C2 line to make sure that the arrows are pointing between the desired atoms.

A better, applet-side solution would be to have Marvin use different colors for the boxes that highlight the origin and destination of the electron-flow arrow.  

Hi Bob and Michiel,

I agree with implementation of different coloring; I'll open a feature request task for that, and we will implement it soon. Until that please create examples according to Bob's suggestion (ie. where the H is not in the same line as the double bond; e.g. place a H already bonded in the same line, and H+ to one side). (Thanks Bob for the idea!)

If the new coloring is implemented I will inform you at this topic.

Best regards,

Akos