Molecular dimensions

Friends:





I use MarvinSketch (5.0.6) to draw structures. In the tool bar option, a good number of propeties such pKa, logP, logD etc. are available. I am interested to know/calculate molecular dimensions (or molecular diameter/radius) of some dyes such as methylene blue, crystal violet etc. Are these available in the Chemaxon Academic Package? If no, will some one please suggest me suitable (free) sites for the same?





Thanks a lot





Dilip Amritphale

I moved this topic from 'Structure search and chemical database' forum.

Hi,





The calculator plugin you would really need to measure molecular dimensions is not yet downloadable, but we are planning to launch it after the 5.2 release.





Best regards,


Norci

Hi:





Many-many thanks. When to expect the release of 5.2? And will the calculator plug-in for molecular dimensions be available within the academic package?





Dilip Amritphale

Dear Dilip Amritphale,





We are expecting the release of 5.2 by the end of this year. The discussed calculator plugin will be available in the academic package.





Btw, as a workaround it is possible to manually "measure" interatomic distances in msketch by selecting Wiew - misc - bond lengths and drawing a bond between atom pairs.





Regards,


Gabor

Dear Gabor:





Thanks. I shall try and return.





Dilip

Dear friends:





Please accept my best wishes for a happy Christmas and a prosperous New Year!








In the mid-July 2008, I posted the following query:





I use MarvinSketch (5.0.6) to draw structures. In the tool bar option, a good number of propeties such pKa, logP, logD etc. are available. I am interested to know/calculate molecular dimensions (or molecular diameter/radius) of some dyes such as methylene blue, crystal violet etc. Are these available in the Chemaxon Academic Package? If no, will some one please suggest me suitable (free) sites for the same?





In response, I came to know that it would be available by the end of 2008.


I hope it is already on the web site. Should I need a fresh key to download this plug-in for molecular dimensions?





Best wishes





Dilip

My colleagues who deal with calculation plugin questions are on holiday. They can give you exact answer after 5th of January.


We plan to release Marvin 5.2 the end of February.

Dear Dilip,





The geometry plugin now can calculate maximal molecular projection radius. (See http://www.chemaxon.com/marvin/help/applications/cxcalc-calculations.html#maximalprojectionradius ) Is it suitable for Your application?





Regards,


Gabor

Thanks a lot for kindly introducing me to the Geometry plug-in. I am sorry to reply so late but some personal engagements kept me away from the work bench for a considerable time period. My sincere apologies.





 





I shall check in with the Geometry plug-in for molecular dimensions and return to the forum in the due course of time. Please bear with me till then.





 





Thanking you once again,





 





Dilip

Hi,

I could calculate the minimal projection radius and maximal projection radius of methylene blue using the geometric plug-in. I am interested to know how the minimal (or maximal) projection radius of methylene blue (or, of any other dye for that matter) corresponds with its Stokes radius. Are they same? Please help.

 

Dilip Amritphale

amritphaledrd wrote:

Hi, I could calculate the minimal projection radius and maximal projection radius of methylene blue using the geometric plug-in. I am interested to know how the minimal (or maximal) projection radius of methylene blue (or, of any other dye for that matter) corresponds with its Stokes radius. Are they same? Please help.   Dilip Amritphale

Hi,
The radius (minimal or maxinal projection) has no connection to the Stokes radius, as our radii are purely computed from the molecular geometry of the lower energy conformer. The radii are computed in 2D for the projections which show maximal or minimal projection area.

Hi

Thanks a lot for the prompt clarification of my doubts. Can any one help me finding the Stokes radii for the anions of a few synthetic dyes viz.,  (i) methyl orange, (ii) Eosin Y, (iii) Evans blue, (iv) 2,6 dichlorophenolindophenol, and the cations of some synthetic dyes viz., (i) methylene blue, (ii) Janus green B, (iii) Crystal violet, (iv) 2,3,5-triphenyltetrazoliun chloride? I am in much need of these values.

Dilip Amritphale

 

Hi,

I'm afraid that your enquiry is not related to our products and services thus we cannot help you. 

Regards

Miklos

 

So sad! But thanks anyway for reply.

Dilip

 

Hi Friends:

Is there a calculator plugin for Molar volume in MarvinSketch 5.1.5 or other version?

Dilip

Hi,

There is no calculator plugin for molecular volume calculation (yet).

Zsolt

Hi

Hope ChemAxon would come up with one soon.

Dilip

Hi Dilip,

Indeed, we have something under development. It would be a great opportunity to start some collaboration: do you have test data that we could use for validation? Can you participate in the development as a beta tester?

Best regards

Miklos