Discussion | DivCHED CCCE: Cheminformatics OLCC

Problem number 4 on Assignment 7

On assignment 7, I was able to complete the first three questions without any problems. I was able to download the spectra and view them through the JCAMP-DX. The two HNMR spectra on ChemSpider that I exported wouldn't show up on the JCAMP-DX. I downloaded the spectra from ChemSpider in every form that the website has and I still could not get the spectra to show up in JCAMP. Are there any other ways that I could get the HNMR spectra to show up?

NMR spectra

If you click on the green icon for spectra you should get the default attempt to load the JAVA programme which nowadays fails for JAVA security issues.
However there is another option which should give the JavaScript/HTML5 version.
Hopefully selecting this will display the spectrum

Once you see a display, right click in the spectral region which will bring up a menu.
Use File/ SaveAs/ and pick an option for flavour of JCAMP-DX type

Hope this helps
Robert

HNMR Spectra on chemspider

Hello, I went to the ChemSpider website and I only found the HNMR for two isomers. For some reason I don't see an option to download the NMR spectra in a JCAMP-DX format. Does anyone know how to do that? Thanks!

Spectra

I get 2 options for JSpecView and the 2nd option says (JAVA) and gives an error message but the first should be JavaScript/HTML5 which works for me on Win 8.1 with Firefox.
If you can see the text file on screen and can save it then you should be able to open it or drag it onto a page containing a copy of JSpecView and it will ask if you want to append or replace the existing spectrum... try this one. You may need to save it as a .JDX first
http://wwwchem.uwimona.edu.jm/spectra/JSVdisplay.html

Depends on whether you want to add emphasis on stereochemistry

Below is from “Graphical representation of stereochemical configuration” (IUPAC, Pure and Applied Chemistry 2006, 78, 1897–1970). <a href="http://www.iupac.org/publications/pac/2006/pdf/7810x1897.pdf">http://www.iupac.org/publications/pac/2006/pdf/7810x1897.pdf</a> === Beginning of the excerpt === If configuration is unknown, this can be indicated explicitly by a wavy line . The waves in such a line may be rounded or angular, but they should be of constant amplitude. The use of “wedged wavy” bonds is discouraged. In most cases, a wavy bond is conceptually identical to a plain bond, and a plain bond should be used instead. Wavy bonds are most often used in general usage when an author wants to place special emphasis on the unknown nature of the configuration at a specific position; the wavy bond would usually be accompanied by additional explanatory text in that case. === End of the excerpt === Simply put, a wavy bond is acceptable, but not necessary. Of course, both wavy bonds and plain bonds are okay. Which one to choose depends on whether you want to add emphasis on an undefined stereocenter or not, which is subjective. (I understand that some people think a wavy bond make a structure representation clearer.)

It's because of file/MIME type recognition

This problem is beyond the scope of this class, but I think you may encounter similar problems again in the future. So I suggest that you read this article about file extension and MIME (Multipurpose Internet Mail Extensions) type: <a href="http://www.howtogeek.com/192628/mime-types-explained-why-linux-and-mac-os-x-dont-need-file-extensions/">http://www.howtogeek.com/192628/mime-types-explained-why-linux-and-mac-os-x-dont-need-file-extensions/</a> Long story short, the problem you ran into is due to file type recognition. In windows, the file type is recognized by the file’s extension (e.g., .exe, .doc. .pdf, and .jpg). However, in Mac OS X, the file type is not recognized by the extension, but the file’s MIME type (embedded into the beginning of the file itself). (Of course, you can have a file with a three-three letter extension on your mac, but the extension itself is not used for file type recognition.) The reason why you ran into the issue when trying to save the .jdx file is that the file is essentially a text file. The spectral data are stored in a format specified in the “JCAMP-DX” format, but it is a text file with the “.txt” extension replaced with “.jdx”. Different web browsers are set to different things with the same file type. For example, when Safari encounters a text file (e.g., the .jdx file you tried to save), it is configured to open it in a browser by default. But FireFox seems to be configured differently, although I did not test it. These default behaviors of the web browsers can be changed by the user. More detailed information is available in the article who link is provided above.

In PubChem, why doesn't the

In PubChem, why doesn't the structure of Omeprazole contain a squiggly line showing that it can exist as either the (S) or (R) enantiomer?

I am viewing it in the Jspec

I am viewing it in the Jspec view option, the Jspec view Java application will not work it says it is blocked even though I added chemspider to the list of usable websites through my java security settings. I tried doing file save as to the data set through safari, and it just saves the actual data set in the file text format. It comes out just a bunch of letters and numbers, no spectra.

I ran into issues as well

I ran into issues as well when using safari on my mac. I could not even right click to save the spectra. When I used firefox it worked perfectly.

HNMR spectra

Should we be able to find HNMR spectra for all three isomers of xylene? I was only able to find two using chemspider.