Rhodium (Chief Bee)
10-09-02 09:23
No 366388
      State of the art  Bookmark   

What is it like out there - do you still need to interpret spectra manually from NMR or IR spectroscopy, or measure GC or HPLC printouts with a ruler to calculate the area under the graph (integrate) to be able to measure ratios between two compounds, or log retention time?

I mean, as you can learn how to interpret spectra as an undergraduate, you could sure make a computer to do it.
 
 
 
 
    Lilienthal
(Moderator)
10-09-02 10:11
No 366402
      Computers do everything for you  Bookmark   

No, usually you have sophisticated programs to do that for you. Companies don't have those ancient spectrometers without computer connection, but in some old-fashioned university labs you may still find them.
 
 
 
 
    Rhodium
(Chief Bee)
10-09-02 10:39
No 366407
      When did this computerization take place?  Bookmark   

When did this computerization take place?

I remember asking the TA's at my university the same thing in 1995, and they laughed at me and thought I was lazy for not wanting to do that menial repetitive task...
 
 
 
 
    GC_MS
(Hive Bee)
10-09-02 11:15
No 366415
      MS  Bookmark   

Don't know for NMR or IR, but for Quad MS systems (the standard version), computerization started beginning of the 80s. Memory was the main problem. MS identity confirmation occurs by database comparement.
NMR certainly is computerized. We have a lab somewhere equiped with a state of the art multiprocessor p4 running a unix based system calculating DNA and RNA conformations day and night.

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    Osmium
(Stoni's sexual toy)
10-09-02 12:32
No 366426
      A few years ago people needed to bring their own ...  Bookmark   

A few years ago people needed to bring their own salt plates and a pen when they wanted to record an IR in the undergraduate labs on the old Perkin Elmer, which used a big roll of paper to record the spectrum. Of course there were computerized IRs around, but the lowly students weren't given access to them. People wrote their reports by hand, and the IR was folded and glued into your lab journal. Or you had to struggle with this big photocopier machine and reduce the size of your spectrum until it was about the size of a regular page.
Today every spectrometer or chromatography machine is hooked up to a computer and you either use specialised software or regular spreadsheets to convert the data into a form suitable to be interpreted by humans.
A GC, IR or NMR is nothing but a huge stream of (X,Y) values which can easily be manipulated, resized, normalised etc. and transferred from one software to the next.

I'm not fat just horizontally disproportionate.
 
 
 
 
    GC_MS
(Hive Bee)
10-09-02 17:25
No 366510
      ms  Bookmark   

I remember asking the TA's at my university the same thing in 1995, and they laughed at me and thought I was lazy for not wanting to do that menial repetitive task...

It's not a bad thing though to demand from your students to do it 'the hard way', and change to computerized interpretation afterwards. It will help you a big deal in mastering the interpretation of such spectra. I don't know how important the personal interpretation of NMR or IR results is after the computer gives you a result, but for MS, personal interpretation is very important.
I've seen pretty stupid things during the last years when working with students. They come to you with a piece of paper that says that their calibration was perfect with a RC of 0.99998%. Off course, the computer printed it, but where does it come from? They don't know, and that is a shame because it is elementary knowledge, or at least should be elementary knowledge... Also, I've seen students injecting samples (typically 1 ÁL) in small openings of an old analogue recorder connected to an FID, mistaking that opening for the GC's inlet. Also, last week, a new student tried to install an HPLC column in a GC I reserve for working with the students. But what beats me most is that the students have to follow a course of Mass Spectrometry, and some of them know the theory of molecular decay in MS better than I do, but they just fail to understand how to make an interpretation of their GC/MS results...
So you might think it is an annoying task to do this repetitive task, but I can guarantee you that it will have its benefits. Students who start with ultra-modern equipment just know shit. Not to blame them, they can't help it... I had the luck to be educated by somebody who was grown into the world that is called GC. He made his own GC in the 50s when most labs couldn't afford such devices yet. He ordered one of the first books on the GC topic and with some collegues, they started constructing it. They even disassembled irons for the electrical components. Admitted, doing such things now for professional purposes would be extremely stupid, but for student education, extremely helpful.

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    Rhodium
(Chief Bee)
10-09-02 17:27
No 366512
      Even my PC would get bored by McLafferty fragments  Bookmark   

Long live progress! I hope they are still wasting their time looking up 13C-shifts in old tables, the TA's scorning me for saying that I would save an enormous amount of time during my organic chemistry career even by myself first learning a programming language and then teaching a PC to interpret the spectrums for me compared to the accumulated time spent my me doing the same thing myself on all the compounds I am to synthesize during my lifetime... I really thought that would be a waste of precious organic chemist's time to spend as much time on the spectra as synthezising it from the beginning (I really suck at doing it, as I am completely unable to concentrate on uninteresting things...).

Alcohol, an unconsciousness-expanding drug
 
 
 
 
    Osmium
(Stoni's sexual toy)
10-09-02 18:00
No 366517
      > I don't know how important the personal ...  Bookmark   

> I don't know how important the personal interpretation of
> NMR or IR results is after the computer gives you a
> result, but for MS, personal interpretation is very important.

Most people do not have a huge database with all the spectroscopic features of all kinds of compounds on their PC, so the computers only help you with handling the data and convert it into a presentable and readable format. You still have to figure out the results on your own. While there is software available, e.g. for NMR, to help you with the interpretation of the results you usually can do without. Even if there was software around which is able to figure everything out on its own you have to know at least the basics to check the results and figure out what exactly went wrong in the case of failure.

> They come to you with a piece of paper that says that
> their calibration was perfect with a RC of 0.99998%.

Oh yeah. The digital generation! They see a measuring device with I don't know how many digits and automatically take that result as 'true'. When you try to explain them that the last three digits are bullshit they don't believe you, and when they see an analog display device they break out in laughter even though that thing might give better results (and doesn't trick you into trusting its results).

I'm not fat just horizontally disproportionate.
 
 
 
 
    GC_MS
(Hive Bee)
10-09-02 18:50
No 366528
      digital generation  Bookmark   

Hehe, these digital generation kiddies can be a real pestilence... I always find it very funny when I have to guide our new students through the lab to explain them all our equipment. I show them our new GCs, GC/MS, LC/MS, and as a desert, I show them two old GCs and tell them: "well, and this is what we are going to use as a start". Then you see them looking for the computers (euhm... not there), for the laserjet printer (euhm... is that one of those recorders from the old text books?), and finally, you can read that expression "why do we have to use this old junk?" on their faces. After a while - depends how long it takes for them to understand the basics - we change to the new machines, but some of the students just ignore the fact they need to learn stuff on old crap first in order to understand what those new devices give as result. My experience says that especially women don't know what to do with all these analogue settings. They just need the newest software, where they only need to click buttons "yes" and "no".
I'm certainly not saying that old crap is better, on the contrary! These new GCs are a delight to work with; they require less maintainance and are more stable etc. Interpretation of the samples takes much less time as well. But there also is one major drawback... I have a GC/MS from the mid-80s. When it malfunctions, I can easily check what is wrong and can start fixing it. I also have a one-year old GC/MS. If there is something wrong, I'm almost fucked. Many parts of the new GC are electronic parts, which I cannot fix. That means: call the factory to send somebody who will tell you: "it's fucked, you have to send it to the factory". It will be sent back to you, running smoothly, and accompanied by a nice bill.

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    terbium
(Old P2P Cook)
10-10-02 08:27
No 366756
      NMR interpretation.  Bookmark   

Even in the early 80's I couldn't submit samples from my "private" research to the Supercon NMR at work but had to use a little desk type machine in part because the computer program on the Supercon would attempt to interpret the spectra. In addition to the computer printout of the spectrum you would also get the program's best guess of the structure. If the substance was in the database it was very accurate and did pretty good even on things that it didn't have a database entry for.

Baseline Does Not Exist.
 
 
 
 
    GC_MS
(Hive Bee)
10-10-02 21:32
No 366978
      the future...  Bookmark   

Let's also have a look at the nearby future. I've been to a presentation last week where company X gave some information about a new device they will launch at PittCon 2003: an LC/MS with sensitivity that can go as far as the amol range. That is euhm... sensitive smile. I can go into the fmol range now without to many problems, but amol, holy shit. In 2010, they can bust your ass because you have 3 MDMA molecules in your blood wink.

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    Rhodium
(Chief Bee)
10-10-02 21:36
No 366980
      Roughly how many molecules are there in an ...  Bookmark   

Roughly how many molecules are there in an attomole?

Alcohol, an unconsciousness-expanding drug
 
 
 
 
    Chicken
(Hive Bee)
10-10-02 21:58
No 366985
      Amol  Bookmark   

attomole: 10-18mole. One quintillionth of a mole.
Approx. 500,000 molocules
 
 
 
 
    GC_MS
(Hive Bee)
10-10-02 21:59
No 366987
      avogadro  Bookmark   

0.6e6

avogadro: 6.022e23 molecules/mol
attomole: 1e-18 mol = 0.6e6 molecules (6e23*1e-18)

EDiT: Chicken, stop editing your post tongue


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    Barium
(Hive Bee)
10-11-02 11:40
No 367252
      Ahem!!....As I said in a previous post, (HP)LC-MS ...  Bookmark   

Ahem!!....As I said in a previous post, (HP)LC-MS can be worth looking into. 

Catalytic hydrogenation freak
 
 
 
 
    GC_MS
(Hive Bee)
10-11-02 13:28
No 367278
      LC/MS  Bookmark   

The device I was refering to is not just LC/MS, but LC-FT/MS. The LC is coupled to an ion trap, which is connected to an FT. It shipped for the modest price of $625,000. But you'll have to wait for PittCon 2003, and need alot of space. The FT was as large as 2 ion traps, which on itself is a rather big apparatus.

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