how to make cyclic molecule in molecular builder

[shank]

Dear all
Please help to draw cyclic molecule by molecular builder.When I tried to join two end, error message comes stating atoms are connected.
thanks
with reagrds

[Anders Blom]

Right, it is not really possible to join atoms to make a ring structure, you should instead import the relevant cyclic sidegroup from the Molecular Cupboard. There are ready 4,5,6 rings to use.

[shank]

Thanks alot.One more query is it possible to get I-V using iv curve module for voltage range -2 to2V.

with regards

[zh]

Of course, you can.

[shank]

thanks.

[shank]

I have experimental I-V. I found while cycling the bias  , there is high conduction state in forward direction of cycle and low condution state at reverse direction.If I want to find out transmission spectra of such syatem.How should i go.One more query is it possible to get .nc file for each voltage while using iv curve module.So that once I-v generated i may restore .nc file at particular volatge and measure transmission spectra.

with reagrds

[Anders Blom]

I assume you refer to http://quantumwise.com/forum/index.php?topic=19.0.

First of all, make sure to always sweep the voltage from 0 V bias. Thus, from 0 V to 2 V and then from 0 V to -2 V. That's just a recommendation, if it works any other way that might be fine too, but this is often the best (and only...) way to ensure convergence.

Second, yes, the module produces a unique NC file for each bias. If you check the script, you will see that the files are named according to the specified checkpoint filename (as passed in the runtime_parameters variable) with the voltage appended. So, you will get for instance "myfile-0.nc" at zero bias, "myfile-0.1.nc" at 0.1 V bias, etc.

Actually it might have been a bad idea to use the dash "-" here; it should have been an underscore, so that for -0.1 V bias you get "myfile_-0.1.nc", instead of, as now "myfile--0.1.nc". I suggest you change this yourself (line 58, change '-%s' to '_%s').

Later on you can indeed restore each checkpoint file to compute the transmission at each bias.

[shank]

thank you very much. The  experimental data what I have  is when I scan bias from 0 to -2 around -1.3V   high conduction observed and when bias is reversed from -2 to 0V  current is low.So two  conduction states  are around -1.3v.So i have doubt when i will calculate tranmission spectra at -1.3V it will be only states for -1.3V irrespective of bias direction.If I proceed in one direction 0V as initial SCF and i calculate transmission spectra at -1.3V and again -2V SCF for initial value and calculate transmission at -1.3V.Will it work.i want to explain the reason for this type of I-V.this I-V was repaeted many times.waiting for suggestion.

with bets reagrds

 

[Anders Blom]

What you are describing seems to be a very interesting effect, which I'm sure ATK can be helpful in explaining. It might not be a trivial task, and will probably involve a lot of thinking and clever application of your general knowledge of chemistry.

The approach I described, sweeping the voltage from 0 V to, say, -2 V, is not the same thing as what happens in the experiment, however. In ATK, each bias is a static calculation, the only thing related to the "sweep" is that we use the already converged state of a lower (absolute) bias to provide a good starting guess at a higher bias.

Most likely the effects you are seeing in the experiment have something to do with conformational changes in the molecule, driven by the changing bias. What ATK could help you verify, is if you have an understanding of the different geometries that might be involved (and for that you have to use your chemistry knowledge, or some direct or indirect measurements), you can compute the current and see if they are very different. That could then be used to corroborate your assumption about the conformational changes.

Of course, I'm just providing ideas here; without detailed knowledge of your system, that's all we can do.

[shank]

Thanks for reply and ideas.I like to  know if geometry is optimized at -2V by applying constraints to electrode.Then change of conformation may be known.
with best regards.

[Anders Blom]

No, unfortunately ATK cannot be used to simulate the mechanism of the conformational change, only the transport characteristics once you know the geometry.

[shank]

thanks.