I just downloaded MarvinSketch 5.12.2 to help me with my studies of organic chemistry. I am new to both organic chemistry and to MarvinSketch, so please bear with me.
I am trying to use MarvinSketch to generate resonance structures, but I do not get the expected result. Attached are two images to illustrate the problem. Why is MarvinSketch not generating the two relevant resonance structures for this molecule?
If someone could tell me what I am doing wrong it would be great.
This sturcture is symetric in delocalized state. This why only 1 resonance contributor generated.
Two major resonance contributors will be generated after substituting a carbon atom in the original structure with an isotop carbon. See the attached figure.
Thanks for the answer - that works.
Maybe something for a future release of the resonance plugin to be able to generate all relevant resonance structures (including symmetrical) without having to assign isotopes?
Only 1 major resonance contributor exist for this structure [CH2-]C=C. There is no 2 diferent major forms.
My intention with the counter-example of the "isotope atom" have been to explain the effect of the "symmetry" on the major contributor count which is apparently 2 for this structure [CH2-]C=[14CH2].
I thought that it may be not clear that the identical structures are filtered out automatically in the actual Marvin version. A "switcher" will be implemented for optional filtering of the identical structures in a near-future version.
On the other hand there is a chance to switch "on" or "off" the symmetry filter in your own Java appliacation via built in API function. In this way you can avoid the impact of the symmetry on the major contributor count.
Additional description given here: