HSP Application note #13
2010.2.13
HSPiP Team Senior Developer, Dr. Hiroshi Yamamoto
Smiles(Simplified Molecular Input Line Entry Syntax)
With HSPiP, you can enter molecular structure with smiles or MOL file.
Smiles(Simplified Molecular Input Line Entry Syntax) is very popular notation.
Please refer Daylight Home page what it is.
Smiles(Simplified Molecular Input Line Entry Syntax) SMILES is a string obtained by printing the symbol nodes encountered in a depth-first tree traversal of a chemical graph. Pirika JAVA Demo Applet getting Smiles. Draw2Smiles is available here. |
If you want to know how to draw molecules, please refer to Power Tools applications. The full version of this routine is implemented into Draw2Smiles Powert Tools in HSPiP ver. 4.
There are several free or not free software.
I recommend you "jchempaint". You can download this software by the net.
Please search of it.
I think latest version is ver. 3.0.1.
jchempaint is JAVA program and run on Mac, Linux and windows, if JRE is running.
If you run this program, and enter Smiles at TextField then push insert button, then you will get 2D chemical structure.
You can modify this structure as you like.
After you draw molecule, you can get Smiles Edit/Copy as Smiles.
And you can paste it to Excel or other text editor.
You can handle molecule with line ASCII string, so it is very easy to handle.
And run the HSPiP program and push sigma button, you will see the DIY panel.
Then choose Y-MB tab.
HSPiP(Hansen Solubility Parameters in Practice)The first edition of HSPiP that appeared in November, 2008, greatly enhanced the usefulness of the Hansen solubility parameters (HSP). The HSP values of over 1200++ chemicals and 500 polymers are provided in convenient electronic format and have been revised and updated using the latest data sources in the second edition (March, 2009). A third edition of the HSPiP appeared in March, 2010. There are now 10,000 compounds in the HSP file which also includes data on density, melting point, boiling point, critical parameters, Antoine constants and much more. The user is able to carry out many different sorts of optimisations of solubility, evaporation, diffusion, adhesion, create their own datasets (automatically if required) and explore the huge range of applications for HSP in coatings, paints, nanoparticles, cosmetics, pharma, organic photovoltaics and much more. The 3rd Edition v3.1 was released on 12 December 2010. Current users can upgrade free (now v3.1.09) by downloading the latest .msi installer from http://hansen-solubility.com The 4th Edition v4.0.x was released on 2 Jan. 2013. The Current users can upgrade with free charge. 2013.1.28 The Visual How to manual of HSPiP. You can understand what HSPiP can do. |
Y-MB Properties EstimationY-MB break Smiles into correspponding Functional Groups and Estimate various Properties. These estimation schemes are come from Pirika technologies.
Pirika JAVA Demo Applet calculate Properties. PirikaLight is available here. |
Paste the Smiles and push calculator button below X button on the right side.
Y-MB analyze Smiles and divid molecule into functional groups.
And Y-MB calculate several properties.
At this time, these calculation result is in the memory, so you can paste them into Excel directly.
So, it is very easy to handle molecule with spread sheet.
And Y-MB also search data base (10000) which has same functional groups same number.
And show the candidates.
Above case, HCode(Hansen Code) is 7 Acetone, and official HSP value is [15.5, 10.4, 7].
Sometime, there are several candidates so this information will not copy.
You need to copy manually.
You can do all the things in one spread sheet, so it is very easy to work with HSP.
(Notice: these picture is before release version. So it may differ slightly with final version)You can do with same thing for polymer.
I expand smiles a little bit for polymer.
You need to sandwich polymer repeat unit with dummy atom X.
For example,
polyethylene XCCX
polypropylene XCC(C)X
If you want to input ester polymer, you can not divid functional group with X.
O XCCC(=O)OX
X XOCCC(=O)X it become ether + ketone
JChemPaint does not support X atom, so you draw dummy atom by I(iode) and substitute on excel.
Once, you get polymer-smiles then it same with original smiles in HSPiP.
Y-MB divid polymer into functional groups for main chain and side chain.
With this merit of polymer-smiles, like HSP database search, Y-MB search polymer database(1200) and show the candidate from it functional groups information. There are several candidates, but if you search polymer by name, it is very hard to get right name. Pcode(Polymer code) search function is implemented into Draw2Smiles power tool in HSPiP ver.4.
So, I believe this polymer-smiles is very useful for polymer chemists.
(If you like polymer-smiles concept, please push it chemical depict software bender)
For the co-polymer, I put every component in polymer-smiles.
And put ratio information independently.
Then I can search certain co-polymer with polymer-smiles.
So, smiles notation is very important in HSPiP.
If you have the smiles for chemicals, medicines, fragrances, cosmetics, polymers, then HSPiP will work very immediately.
(Notice: polymer routine is on the developing, so result may differ from final version)
