Instant JChem question

Dear ChemAxon,





I am a beginner of JChem package and also I am not a chemist either (Environmental engineer). Therefore, I am having diffcult time to get the information I am trying to do. Here is my problem.





I have 160 organic micropollutants as SMILES notation and I also have these 160 compounds in CAS number as well. I have biodegradation probability data of selected 160 compounds from the model that shows the biodegradability of each known compound. My advisor asked me to compare the biodegradation data predicted from the model with following physical-chemical properties to find out which one of following perteries is more influence to biodegradation. First (i) C-C single bonds versus presence of a C=C bond, Second (ii) aliphatic chain versus presence of an aromatic ring and Third, (III) halogenated versus non-halogenated compounds.





Is it possible to these tasks with Instant JChem to calculate following task 1. the number of C-C single bond and double bond


2. the number of aliphat chain and aromatic ring





or do I have to use other tool?





I read calculator plugins (Topology Analysis Plugin) which calculate above information however I don't know how to start with selected compounds into this plugin to find out above information? I am sorry that my question is too novice. Thanks for your help!





Best Regards,





Andrew from TU-Delft, The Netherlands

Hi Andrew,





Yes, it seems that you have a long way to go. I will try to give you a few useful pointers here.





I agree that you should work with Instant JChem. This page shows you some animations where you can learn quickly how to use Instant JChem:


http://www.chemaxon.com/anim/ijc.html





First you need to import your smiles file into IJC, which I guess will not be a problem. Then I recommend to create calculated (Chemical Terms) columns for the properties you want to analyze:


http://www.chemaxon.com/anim/ijc/chemterms/chemterms.html


http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/help/htmlfiles/chemical_terms/adding_chem_terms_fields.html





For these columns, the property to calculate should be given in the Chemical Terms language: http://www.chemaxon.com/jchem/doc/user/ChemicalTerms.html





For the particular properties, you will need the matchCount() or match() Chemical Terms functions:


http://www.chemaxon.com/jchem/doc/user/EvaluatorTables.html#matchfunctions" target="_blank">http://www.chemaxon.com/jchem/doc/user/EvaluatorTables.html#matchfunctionshttp://www.chemaxon.com/jchem/doc/user/EvaluatorTables.html#matchfunctions





For the creation of the substructure queries for these functions, I recommend the SMARTS or ChemAxon extended SMARTS language.


The easiest to produce these is to draw the substructure in Marvin Sketch, and obtain the SMARTS using the Edit/Source menu and then View/SMARTS/SMARTS from the source window.


(For the query features that can be used in the queries, see the Query guide: http://www.chemaxon.com/jchem/doc/user/Query.html )





You can also find a detailed description of SMARTS on the Daylight page: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html





Finally, I recommend to export your structures and properties into your favourite statistics package (for example, through comma separated files or excel files), and try to find the correlation there.





I hope this helps,


Szabolcs