DEAR READER


85. “DEAR READER”

To our delight you folks are beginning to send ‘letters’ and where at all possible we will reproduce them. Please keep up the good work!

Last time I raised a question or two with Bob Lancashire and remarked how lucky he is to be at the University of the West Indies – you know – lectures on the beach beneath those swaying palm trees! He replies as follows:

86. “Life in Jamaica is never dull. The sun shines every day (well almost) and the temp never drops below about 15C, even on the top of Blue Mountain Peak. On the other hand I have only been getting water for a few hours per day recently, since we have been in the worst drought for 70 years. We have just started the hurricane season and the experts are predicting about 11 hurricanes to watch for this year!! It rained a lot last week so the drought is officially over. For the chemistry of “Things Jamaican” including bauxite, coffee, exotic fruits and vegetables, see

http://wwwchem.uwimona.edu.jm:1104/lectures/index.html

Anyway, re spectra. Over the last year we have produced a plugin for Netscape that can display a JCAMP-DX file using a simple embed statement. This means that instead of a static bitmap, you get the real data that can be manipulated and zoomed etc. at will. The JCAMP-DX specifications have been taken up by all IR manufacturers (more so than by UV/Vis, NMR or MS). Our plugin will display all spectral types in JCAMP-DX format not just IR.

We are about to merge our code with MDL CHIME and then it should be possible to display both 3D molecular graphics and spectrum on the one page and have links between them such that clicking on a peak in an IR will highlight the bond etc.

Our plugin is available at

http://wwwchem.uwimona.edu.jm:1104/software/jcampdx.html

and test data and FTIR spectra are at

http://wwwchem.uwimona.edu.jm:1104/spectra/testdata/index.html

http://wwwchem.uwimona.edu.jm:1104/spectra/IRIndex.html

and examples with CHIME scripts at

http://wwwchem.uwimona.edu.jm:1104/spectra/chime/index.html

87. Anybody using a PE machine will nowadays be running some form of GRAMS, either Analyst or the latest GRAMS/32. These can convert .SPC files to JCAMP-DX format easily. Hence there should be no shortage of spectra to work with.

The NIST have a database of about 5000 IR spectra in JCAMP-DX format as well as their new site called webbook

http://webbook.nist.gov/chemistry

that has a database of about 5000 IR and 8000 MS and when you search for info it displays both spectra in JCAMP-DX format using a JAVA applet. Well worth a link from IJVS.

Regards, Robert.”

Thanks, Bob.

Really valuable stuff. Glad to hear you are able to make tea with water now, rather than having to use the local beverage! We will certainly look up your prompts ourselves. If anyone would like to contact Bob directly, his addresses are

Dr. Robert Lancashire

Department of Chemistry
University of the West Indies
Mona Campus
Kingston 7, JAMAICA

http://wwwchem.uwimona.edu.jm:1104/uwichem.html

Tel: (876) 927-1910
Fax: (876) 977-1835
e-mail to:rjlanc@uwimona.edu.jm

Please look up the article Bob has co-authored with Antony Davies at para 57

EDITOR


Kristine Moore here in the UK wrote me an amusing letter commenting on IJVS so far and reproduced below:

88. “Scientists in general (I’m not criticising spectroscopists in particular here!) can come over as a pretty humourless bunch of buggers. The occasionally “light hearted” tone improves peoples willingness to read on and probe further. I’m sure such levity is considered a “bad thing” in scientific writing but I, personally, find it stimulates rather than depresses!

The fokeloric elements (e.g. origin of Nujol) and practical asides (e.g. fixing windscreen stone chips) are well worth including. Have I said enough – I think it is excellent.”

Kristine is interested in Pharmaceuticals. Her address is:
Pharmacy Department
King’s College London
Manresa Road
London SW3 6LX
Tel: 0171 333 4940
email: kristine.moore@kcl.ac.uk


Alexander Shchegolikhin from the Russian Academy of Science in Moscow has written an extremely interesting letter, full of great suggestions.

89. “Dear Editor,

Please, take my congratulations for your starting the IJVS project! Though I am relatively a novice in WWW, for several last months I have managed to visit most of the sites which are directly concerned with vibrational spectroscopy. Being a practising spectroscopist (FTIR + NIR-FT Raman, in particular) eventually coming into the field from organic synthesis and polymer chemistry, I rank the IJVS simply as The Best of Show. So, once more, congratulations and thanks! Nonetheless, dare I make a couple of suggestions.

  1. Why not build up IJVS’s own vibrational spectra collection or library? It seems that the idea is in line with the aims of IJVS Hot Sources: How often has someone asked you to recommend a reference which explains the infrared spectrum of this or the vibrational behaviour of that? Well, Hot Sources will be the answer as the database builds up and it will be simply and reliably machine searchable. Moreover, I think that:
    1. author signed spectra submitted to IJVS by different groups or individuals would help people to make friends through spectra;
    2. to differ from already existing and useful sites with their own FTIR spectra collections (FBI FTIR Fibers Library, or the David Sullivan FT-IR Library), IJVS could specialise, e.g. on complete (FTIR + Raman) vibrational spectra;
    3. I guess another and probably more important specific for the future of an IJVS spectral library – its diversity – could it eventually crystalize that readers of IJVS (and hence potential contributors of the spectra) are dealing with highly diversified classes of materials and molecules;
    4. possibly IJVS could concentrate on vibrational spectra of new molecules and new materials (i.e. those which have been synthesized recently or are currently under investigation).

    This would attract to IJVS synthetic chemists, physico-chemists and material science people. Again this would facilitate making friends between spectroscopists and molecule makers;

    1. sometimes spectra of the same compounds recorded by different techniques, on instruments of different manufacturers, under different conditions etc. can bring useful information. So, perhaps (as a first principle) multiple submission of already existing in IJVS library spectra from different sources should not be prohibited, and
    2. I suspect that in some cases absence of IR or Raman spectrum from a complete VS set for a material or molecule would stimulate some people to fill the blank – again to everyone’s mutual satisfaction.

    There are some other points on my mind – all concerning the hypothetical IJVS spectral collection arrangement. But, suddenly, this letter becomes a bit too lengthy.

  2. My second suggestion-question is: could IJVS be a place for discussion of not-so- good laboratory practice? As a matter of fact, the answer seems to be obvious: Yes, it could. Indeed, about 50% of space in the IJVS issues that have appeared seems to be spent just for that.

90. Several years ago I devised a simple spectroscopic technique. I wrote a kind of paper on the method – just for fun. I put it into a drawer and never published. Maybe the funniest thing is that over all these years I use the technique extensively. I know that it gives distorted spectra, but it is rather general and very often brings me the information I need. Moreover, I suspect that the exercise of interpretation of the distorted spectra helped me to obtain some extra knowledge in the IR field in general. The manuscript follows.

Perhaps it will lead to some sort of public discussion. If so, I could replay an impressive trick by throwing candies into the audience, which I have seen once at the ESOPS-10 in St.Petersburg (Russia). But this time I could throw a candy (DRAFT technique) and after a while you would highlight its poison.

On a serious note, in this report I would like to illustrate the considerable freedom in sampling which is permitted now due to availability of different accessories, possibly to warn a novice against careless sample preparation and, in general, to provoke a discussion about the “human rights” which should be enjoyed by distorted spectra (ATR, DRIFT, RR, etc.) in the current literature.

Please, excuse my poor and lengthy English. Looking forward to your reply. My e-mail address is shchegol@deom.chph.ras.ru

Sincerely, Alexander Shchegolikhin

P.S. I’ve almost forgotten to say that, to seed an avalanche of vibrational spectra to IJVS library from all over the world, I am ready to download to IJVS a hundred or two of my own FTIR and FT Raman spectra.

91. A wonderful letter – full of ideas. The publication of an ever expanding spectral library is a fine idea. With the appropriate search algorithm, this could become really valuable. One of the few snags is that spectra submitted might not be reliable.

Library publishers like Sadtler go to great lengths to check their source compounds and crosscheck the spectra recorded to make sure that rogue information does not contaminate the library. There is no way IJVS could do this. To reduce the problem and to enable people to check with the source if they have doubts, we could put the contributors’ name and address on the spectra. Now – READERS – what do YOU think about this idea?

Alexander’s paper was an early draft and it needed considerable attention. I duly behaved like a cow – chewed it up and then regurgitated it (with Alexander’s approval) and the paper appears – for the first time “after all these years” in the Contributed Section.

I was amused that Alexander remembered the candy throwing incident at ESOPS-10 in St. Petersburg. I was the thrower! At the end of a talk on FT-Raman of polymers, (and FT was very new at the time) to stress how versatile FTR had become, I showed an overhead of the Raman spectrum of the three layers in a MARS BAR – the chocolate, the toffee, and the gooey stuff underneath. Mindful that at that time the Russians had been spared the delights of this incredibly sticky and sweet confection, my lady wife bought a huge bag of Mars mini-bars and put them in my case. So, as I showed the overhead, I threw the “candies” to the crowd. No-one remembers the overhead – such is science!

EDITOR


In Edition I, Geoff Dent presented an article describing how KBr discs should be made, emphasising good and bad practice. Don Clark at Pfizer has sent an e-mail commenting on Geoff’s effort:

92. Preparation of Potassium Bromide for Infrared Spectroscopy

This communication is prompted by a previous article on KBr disc preparation (G.Dent IJVS Vol.1/Section 1) and amendments in the IR sections of the latest United States and European Pharmacopoeias (USP and EP respectively). Potassium bromide is an important sample matrix for IR spectroscopists. Its spectroscopic and hydroscopic properties are well documented. However until recently little has been written about the preparation of this material prior to its use in the production of KBr discs.

For many years I have used commercially available spectroscopic grade KBr powder for all my disc preparations. To avoid/minimise water uptake, the KBr is stored in a sealed bottle which is placed in a drying cabinet heated to 40°C. I believe that this is a common practice amongst IR spectroscopists. The latest publications of the EP (3rd Edition) and USP (5th Supplement 15/11/96) have caused me to reconsider my disc preparation procedures. The methods are as follows:

U.S. Pharmacopeia 23 – National Formulary 18, 5th Supplement

…..preparation of the test specimen include…..incorporating it in a transparent disk or pellet obtained by mixing it intimately with previously dried alkali halide salt (usually potassium bromide) and pressing the mixture in a die. Typical drying conditions for potassium bromide are 105°C in vacuum for 12 hours, although grades are commercially available that require no drying.

European Pharmacopoeia 3rd Edition

Potassium bromide. A disc 2 mm thick prepared from the substance previously dried at 250°C for 1h, has a substantially flat baseline over the range 4000cm-1 to 620cm-1. It exhibits no maxima with absorbance greater than 0.02 above the baseline, except maxima for water at 3440cm-1 and 1630cm-1.

93. These methods attempt to set a quality standard for potassium bromide to be used in the preparation of samples for IR spectroscopy. However, there is a degree of ambiguity and/or insufficient information detailed such that KBr prepared in these ways may have a significant impact on the sample under test and ultimately in the spectrum produced. Both the EP and USP give clear directions on how the sample should be dried. The temperature, length of drying time and oven pressure are different in the two methods. Both provide dry KBr, but this will provide operational difficulties for laboratories who wish to be both USP and EP compliant. Subsequent storage of the dried KBr is also an issue. The Pharmacopoeias are particularly vague; How long is previously dried? Similarly, allowing the KBr to cool before use in anything other than a dessicator will allow the KBr to take up water, yet this fact is overlooked in these methods. Neither method adresses particle size. Grinding dried KBr in the lab will promote water uptake, and may negate the previous drying process. (This is an important factor for diffuse reflectance measurements where KBr is used as the sample diluent).

Only the EP offers a numerical standard for KBr, which indicates its suitability of use for IR spectroscopy. The specification enables KBr contaminated with organic or inorganic material to be identified, as these will show absorbance bands of greater than 0.2 a.u. Most surprising is no absolute specification for water content, particularly as this has the potential of being the major contaminant in the KBr powder.

I would appreciate any comments you may have on these views. These can be sent directly to me, or via the IJVS to stimulate debate on this issue. The ultimate goal is to recommend a method, with specifications, for the preparation and storage of KBr for use in IR spectroscopy that meet the criteria detailed in both pharmacopoeias.

The views expressed here are personal, and are not those of Pfizer Central Research.

DON CLARK

Don’s e-mail address is: Don_Clark@sandwich.pfizer.com. Obviously, anyone can contact Don directly, but it would be much more valuable to have any discussion through IJVS, for obvious reasons.

94. Don has been in conversation with David Soderstrom at Pharmacia & Upjohn of Uppsala in Sweden. His e-mail to Geoff Dent is reproduced with permission, as it raises several questions:

“Hello Mr. Dent.

My name is David Soderstrom and I work with FTIR and Raman at Pharmacia & Upjohn in Uppsala, Sweden. I happened to find the announcement of the Internet Journal in the March/April 1997 edition of Spectroscopy Europe (page 6), so I thought that I would check out the Journal. I think that it is a wonderful idea and have added it as a bookmark. I started reading through Volume 1 and of course started with your article.

I have several questions about your procedure, as I have been recently reviewing the European Pharmacopoeia general IR method (2.2.24) and have made comments to the method specifically about the preparation of KBr disks. Above all I was wondering about your procedure about grinding the sample and KBr together. In some samples I believe that this can cause problems in the spectrum. If you look at “Laboratory methods in Vibrational Spectroscopy”, 3rd Edition, by H.A.Willis, on page 212 he gives a similar procedure but mentions that the sample should be “preground” before mixing with the KBr. This is a small point, but we believe that it is important.

Additionally, is it correct to say “absorption spectrum” as you have used it, or is the correct usage absorbance spectrum? It is of course correct to talk of absorption spectrophotometry etc. but when we are referring to spectra in the absorbance mode, shouldn’t we talk of absorbance spectra too and not absorption spectra? Again just a small point, but I am interested in your comments.

Sincerely,

David Soderstrom
david.soderstrom@eu.com.pnu

PLEASE NOTE

The comments of David Soderstrom are personal and do not represent in any way the policy or opinions of his company.