ChemAxon Forum Archive » Drawing & visualization: Marvin/Sketch /View /Space

Volume of a molecule

User bf27213fcf

02-12-2009 18:18:48

Hello,


Is there a way with ChemAxon to calculate the Van Der Waals volume of a molecule?  If there is no direct way can you point me in a direction to utilize the atomic radius & bond lengths displayed in the space filling mode to estimate a rough molecular volume?


Thank you,


Ben Chittick

ChemAxon 990acf0dec

03-12-2009 22:09:30

Hi,


Sorry, but presently it is not possible to calculate the Van der Waals volume. Furthermore, even though you can display the bond length, there is no calculation for atomic radius yet.


Best regards,


Akos

ChemAxon efa1591b5a

04-12-2009 08:59:52

Hello Ben,


We are working on volume calculation, an experimental solution is already in the development pipeline. The release of the production code is expected in version 5.3.1 probably in Q1 2010. I hope this isn't too late and you will give it a try.


Are you perhaps interested in evaluation/early adoption of our molecular volume calculation?


 


BR 


Miklos

User bf27213fcf

04-12-2009 16:47:01

Hi Miklos,


I'm glad to hear that there will be a molecular volume calculator soon.  I'd be very interested in an early adoption of your molecular volume calculator. Unfortunately I don't have any of my own experimental volumes to check for accuracy.  If you're at a stage where you're just looking for "beta testers" I would be more than happy to help out.


Ben

ChemAxon efa1591b5a

16-12-2009 15:22:00

Hi Ben,


Thank you very much for volunteering to take part in beta-testing. We plan to create a dedicated web page that focuses on such 3D calculations were you can upload or sketch your molecules and carry out the calculations. Do you think this can work? Or you'd prefer to download the software and install and run it locally on your computer?


Does anyone posses experimental volume data at all? Is it possible to measure molecular volume? Apologies for the naive question but I'm not a chemist. Do you know about databases (public or commercial) that provide trusted molecular volume data?


Regards,


Miklos

User bf27213fcf

16-12-2009 18:38:46

Hello Miklos,


I would prefer a program that I could download.  I want to find the volume of approximately 200 molecules.  Using a web page sounds like it might be slower, although if I could load all the molecules at once, that would work.


Your question about experimental volume data is actually a very good one.  I didnt really think through what I said earlier.  There is a molar volume that can be calculated from density but that of course takes into account space between molecules.


 


Ben

ChemAxon efa1591b5a

05-02-2010 12:45:17

Hi Ben,


I'm glad to inform you that the molecular volume calculation is available for online try-out.  


I know that your preference would be a standalone program that you can download and run locally in batch mode. This will be released in version Marvin 5.3.1 around the end of Q1 2010. Till then, the online version can be used for beta testing, validation and for discussion. 



There are two similar web based implementations provided, one of them using the AJAX technology and the other uses plain HTML. The AJAX is more trendy, though right now the HTML is somewhat more stable. These two are "inter-switchable".



Originally, these pages have been built to demonstrate Generate3D, our 2D->3D structure converter, but it appeared to be straightforward to add the molecular volume calculation to this try-out page. This was the fastest and simplest way to deliver the new functionality to your customer. 

However, there is one limitation at present, which we will resolve within the next few days: the input is always a 2D structure and the tool generates one low energy conformer and calculates the volume of that particular conformer. Apparently, the user may want to upload a particular 3D structure and calculate the volume specific to that conformation without altering the geometry at all. We will implement this option shortly.


The usage is quite simple: either type a SMILES string or a chemical name (traditional or IUPAC) in the edit field (like CCCCC or benzene etc.) and hit the "Generate" button (only in case if you see a green tick mark in front of the edit slot). Then a new window pops up showing the 3D structure and under the structure, at the bottom of this window the calculated volume is displayed.

If you hit OK in this window then you get back to the initial screen where a new molecule can be entered.

If smiles or chemical name input is not convenient, MarvinSketch can be launched by pressing the 'Edit' button.


I believe that this simple web based interface enables a quick test drive without the hassle of downloading and deployment etc. It is suitable to assess the accuracy of the volume calculation, though not directly applicable to test its performance (due to network lag).



Your feedback is warmly welcome.


regards,

Miklos



ChemAxon 990acf0dec

25-02-2010 14:05:07

Hi Ben,


I would like to inform you that we had to make an urgent patch release that was named 5.3.1, therefore the standalon program promised in this topic will be included only in the patch release coming at the end of March (probably named 5.3.2).


Best regards,


Akos

User 31ecf54205

21-01-2011 12:14:00










mvargyas wrote:

Hi Ben,


I'm glad to inform you that the molecular volume calculation is available for online try-out.  


I know that your preference would be a standalone program that you can download and run locally in batch mode. This will be released in version Marvin 5.3.1 around the end of Q1 2010. Till then, the online version can be used for beta testing, validation and for discussion. 


 


There are two similar web based implementations provided, one of them using the AJAX technology and the other uses plain HTML. The AJAX is more trendy, though right now the HTML is somewhat more stable. These two are "inter-switchable".



Originally, these pages have been built to demonstrate Generate3D, our 2D->3D structure converter, but it appeared to be straightforward to add the molecular volume calculation to this try-out page. This was the fastest and simplest way to deliver the new functionality to your customer. 

However, there is one limitation at present, which we will resolve within the next few days: the input is always a 2D structure and the tool generates one low energy conformer and calculates the volume of that particular conformer. Apparently, the user may want to upload a particular 3D structure and calculate the volume specific to that conformation without altering the geometry at all. We will implement this option shortly.


The usage is quite simple: either type a SMILES string or a chemical name (traditional or IUPAC) in the edit field (like CCCCC or benzene etc.) and hit the "Generate" button (only in case if you see a green tick mark in front of the edit slot). Then a new window pops up showing the 3D structure and under the structure, at the bottom of this window the calculated volume is displayed.

If you hit OK in this window then you get back to the initial screen where a new molecule can be entered.

If smiles or chemical name input is not convenient, MarvinSketch can be launched by pressing the 'Edit' button.


I believe that this simple web based interface enables a quick test drive without the hassle of downloading and deployment etc. It is suitable to assess the accuracy of the volume calculation, though not directly applicable to test its performance (due to network lag).



Your feedback is warmly welcome.


regards,

Miklos



 

I will try this and I think it will work