Module 7: Assignment

Assignment 1. Go to the NIST WebBook and download the following spectra in JCAMP-DX format Mass spectra for each of the three isomers of nitrobenzoic acid Gas phase IR spectra for each of the three isomers of nitroaniline 2. Go to ChemSpider and download the HNMR spectra of the three isomers of xylene in JCAMP-DX (can you find them?) 3. Go to the first JSpecView page above or download the JCAMP Viewer software for your OS. Import each of the spectra into the viewer you choose and export them to X,Y format. 4.Finally, import each of the X,Y data files into Excel with one sheet for the MS data, one sheet for the IR data, and another sheet for the NMR data. Plot the three IR spectra on one graph (so they are overlaid) and do the same for the MS and NMR data (so you end up with three graphs). Save the file. 5. Write a short paragraph comparing/contrasting for each of the thr

ee plots of overlaid IR, MS, and NMR spectra.

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Number 2

Hello, I am using a mac with safari as a browser. Every time I attempt to save the spectra data for one of the xylene isomers on chemspider it does not send it to my downloads or my documents, it just spits out a new web tab with a list of data. I don't know how to get it to actually save the spectra data in its original format to my computer.

JCAMP-DX files

Sarah,
If you are seeing the file data on screen are you able to then do a file save through Safari?
When I go to ChemSpider and click on a spectrum logo I get the option to display as the JSpecView Java application or the option above that which is for the JavaScript version which should run OK on the MAC.
The file should look something like...
##TITLE= a description
##JCAMP-DX= 5.0

...

##END=

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.

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

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.

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.

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.

Confirmed

I believe that is the case, I also was only able to find 2 HNMR for Xylene.

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!

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

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

Kourtnei,
need more details. You say you downloaded the spectra in JCAMP-DX format and could view them. What did you use to view them?
When you exported them what filename extension did you give? It probably needs to be .JDX and if you are using Windows with the default setting whereby the extension is hidden then you may have a file called xylene.jdx.txt or some variation of this and the JSpecView viewer is ignoring it.
If you are using Linux or Windows there is a JAVA standalone application that you can download to run and display files. It is available from Sourceforge
http://sourceforge.net/p/jspecview/svn/HEAD/tree/dev2/JSpecView/build/JS...

I tried p-xylene and downloaded the file and then dropped it onto a page with JSV running and it opened without issue

Robert

Graphing questions

When plotting the HNMR data, excel seems to be multiplying the data by a thousand once put into the graph. So instead of integrating for 5 hydrogens, its reads 5000. So is the case for the chemical shift. What type of graph within excell 2013 should I use for plotting the mass spectra data? The clustered collum graph fails when adding additional data sets.

Mass Spec Data

Why is JSpecView unable to export the data from a Mass Spec into XY formats? I would have thought that the data would have just been arranged in a X:Mass/Charge Y:Intensity format.

JCAMP-DX files

Alex,
the JCAMP-DX standard was originally intended for X,Y data where the x values were all the same distance apart and so the compression into the various "flavours" SQZ, DIF, DIFDUP then came about to end up with text files that were about the same size as a ZIP but were not binary and so could move across early data networks without loss of integrity.
Many Mass Spec files were in the form of Tables where only a relatively small number of intensities were reported often less than 20 peaks. These can not be readily converted to equally spaced XY pairs so compression was not used.
I'm not sure what type of Mass Spec file you are opening but you should be able to check if it is a PEAK TABLE type file or an XYDATA type file with a simple text editor like Notepad etc.
The Peak Table type will be just a set of X,Y pairs but with a number across a line separated by tab or space.
Pretty easy to move to a spreadsheet for plotting etc.
If the file does contain XYDATA and you are unable to convert to XY then that would seem to be a bug.

Robert

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