Is anyone aware of reliable resources (ideally public) which allow the user to download the raw spectroscopic data such as infrared spectrum of small organic molecules, or rotational spectrum of HCl/DCl mixtures or NMR spectra of molecules? I was looking at the NIST database but apparently there is no option for downloading the spectrum as an Excel, csv or txt file. Thanks.
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1$\begingroup$ Excellent question! The last time I needed an IR spectrum, for ethyl acrylate, I had to settles for a JCAMP format file and hack it to get data into a simple .txt file I could use. I hope a good answer appears! $\endgroup$– Ed VApr 2, 2020 at 15:54
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1$\begingroup$ @EdV If working with a Windows computer, try JDXview (cf. my answer). $\endgroup$– ButtonwoodApr 2, 2020 at 16:48
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1$\begingroup$ @EdV: JCAMP-DX is actually pretty self-explanatory and easy (unless it's in one of the weird compressed subformats) - says the maintainer of a number of spectroscopic file format import filters for R... ;-) ... who is usually very wary of .txt or Excel files since the converters usually throw away lots of meta-information that may have been available. $\endgroup$– cbeleites unhappy with SXMay 8, 2020 at 15:56
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1$\begingroup$ @cbeleitesunhappywithSX Very good point! But the ultimate reason I need ASCII text files is that they are used with my free LightStone simulation software that instantiates both the Jones optical calculus and the Mueller optical calculus. If you are interested at all, please send me an e-mail at [email protected] and I will send along a link to my website and a couple of published papers that explain what I have developed over 30 years. $\endgroup$– Ed VMay 8, 2020 at 17:35
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2 Answers
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As a quick fix: To access the IR spectral data of $\ce{HCl}$, I opted for a seach by (Hill) formula on NIST's web page, which yielded three entries here. For $\ce{HCl}$ in particular (here) I opted for the first one here, indeed offering the spectrum as image file or as JCAMP-DX.
As in the comment by @EdV, this JCAMP-DX an ASCII file indeed. Note JDXview by Norbert Haider (Department of Drug Synthesis, University of Vienna, Austria) is a very handy program (only 560 kb, installation free executable) for a quick display of this file by NIST. Via File -> Save, the export of the data in a two-column, tabulator separated .txt file is just a click away. The program works perfectly well in Windows, and with wine libraries equally in Linux, too. (The author equally distributes the underlying Delphi / Pascal code.)
Note 1: Because of the tags physical chemistry, and spectroscopy, you may be interested in a python module like jcamp to access either IR, or NMR spectra in the JCAMP-DX formats (there are multiple).
Note 2: Sometimes, all you have indeed is an image (a scanned) spectrum. If you pay attention and proceed in sections (e.g., $4000 - 2000$, then $2000 - 800\,\pu{cm^{-1}}$) to account for the break on the abscissa in IR spectroscopy, a digitizer like WebPlotDigtizer may be worth to use. If you want, the program works via a web browser, installation free, with «normal image files» like .png, and since some time with images embedded in a .pdf (think about publications), too.
answered Apr 2, 2020 at 16:46
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$\begingroup$ (+1) Even better than the good answer I hoped for! Many thanks: I just got a new windows laptop yesterday, dumped the “S” kiddie mode and I will download the JDXview program ASAP. $\endgroup$– Ed VApr 2, 2020 at 17:57
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$\begingroup$ Thanks for a very useful response. Can we use the spectra for publication purposes i.e., NIST data open to re-use? I wanted to try out a new deconvolution algorithm to enhance resolution on rotational spectra or vibrational spectra. $\endgroup$– AChemApr 2, 2020 at 19:26
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$\begingroup$ @M.Farooq Re use of NIST data for a publication: I do think it is possible because there is a note how to cite parts / all of it (webbook.nist.gov/cgi/cbook.cgi?Contrib=). Wider use probably is a case for Customer support ([email protected], Expiration Date: 06/30/2021, nist.gov/srd/standard-reference-data-contact-form). An other source might be the SDBS spectra collection (sdbs.db.aist.go.jp): «If more [than 50] spectra are required for some specific purpose or commercial use, you should consult us and describe the intended usage or purpose of our SDBS.» $\endgroup$ Apr 2, 2020 at 19:42
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$\begingroup$ @M.Farooq: (still SDBS spectra collection): sdbs.db.aist.go.jp/sdbs/LINKS/contact_eng.html. Re IR-data, I speculate sources like Aldrich, Hummel, Sadtler, Biorad/KnowItAll, Specinfo (Wiley, application.wiley-vch.de/stmdata/specinfo.php) equally probably require contact prior engaging such a work because they invested time / man power / infra structure into their databases and obtaining (c) clearance from the publishers of primary publication. $\endgroup$ Apr 2, 2020 at 19:46
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1$\begingroup$ @M.Farooq Maybe IR: ncbi.nlm.nih.gov/pubmed/27795739 / osdb.info which seems to be dormant a little in comparison to the Raman sibling COD/ROD (ncbi.nlm.nih.gov/pmc/articles/PMC6557180, solsa.crystallography.net/rod) which by intent is open domain. $\endgroup$ Apr 2, 2020 at 19:50
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This is "such as":
- For Raman spectra of minerals, there's the RRUFF database
They use a JCAMP-DX-like ASCII format - Raman spectra of a number of small molecules important in biochemistry (amino acids, sugars, some fatty acids):
De Gelder, J.; De Gussem, K.; Vandenabeele, P. & Moens, L.: Reference database of Raman spectra of biological molecules J Raman Spectrosc, 2007, 38, 1133-1147. They send the spectra upon asking, IIRC as Matlab file.
answered May 8, 2020 at 15:52
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1$\begingroup$ Thank you. I sent a request to the author. This article is from 2007, let us if the email is still valid or if they are willing to respond. $\endgroup$– AChemMay 8, 2020 at 16:31
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