NMR help

[GradGrrl]

Does anyone here "get" NMR?

 

Can you explain J-coupling and NOE's? I get that j-coupling is through bond interactions, but what does that mean? And I get that NOE's are through space interactions, how are they different? And ok, if you can get me that far, can you break down the proton and carbon methods in "simple" language.

 

Any help is appreciated!

[timo]

I can´t really help you there but your chances of getting a usefull answer might be higher if you elaborated a bit on your question and what you are talking about.

Examples:

- What is NMR and NOE ? Perhaps someone who is not familiar with the apprevations still knows a bit about the subject.

- Same goes for the term J-coupling (what is "J"? Coupling between what?).

 

With all my non-knowledge about the topic I´ve shown above, let me at least try to give some direct help, even if it´s only a guess:

Assuming NMR is what I know as "magnetic resonance tomography" then I would further assume that proton and carbon methods are two different modes that are sensitive to the respective material: Protons (=water) or carbon (err... bones?). The two substances probably (I´m still guessing) have a different resonance frequency so by chosing an appropriate frequency for the outer magnetic field you can get sensitive to the material you want to investigate (make a picture of).

[GradGrrl]

Yeah ...all good guesses. As you can tell, I'm no expert either, just have qualifying exams tomorrow and would like to actually understand the stuff I memorized for this part of the exam. NMR deals with nuclear spin on a molecule, and you can deduce structural somponents using the technique, so the j-coupling and the nuclear overhauser effects, NOE's, are two ways to determine structural differences. i just hope I don't have to read a spectrum tomorrow, or I'm in deep shit.

[scicop]

whoops

[scicop]

Sad...NMR is one of those techniques where if you don't use it, you lose it. I did all that way back when my project involved isolation (Column chromatagraphy and HPLC isolation first..also TLC analysis of my fractions) and NMR structure determination of flavanoids in "phenax rogousus" plant (south american species). Back then, we had a NMR machine operating at 600 Mhz, that was considered state of the art. I did both H and C, NOE (there's another one I forgot) 2D and 3D spectra analysis. But that was like 10 years ago. I was in a natural pharmaceutical science department then.

 

You really need to find a good teacher in your department, find a post doc whose willing to sit down with you and over "real world" examples. Books can be useless. The only way to become proficient with deciphering the technique is to practice, practice, practice. I had a realatively decent teacher, and thus my abilities back then was "relatively decent"

 

I wish I stuck with it, but then I went more the molecular/classical pharmacology route (not very marketable these days). If you like it there are alot of pharma companies that would like to speak with you. That's is one part of the pre-clinicial drug discovery process that pharma are keeping active interest in, when they're not busy finding (and creating) new clinical indications for their already marketed drugs.

[GradGrrl]

If you like it there are alot of pharma companies that would like to speak with you. That's is one part of the pre-clinicial drug discovery process that pharma are keeping active interest in, when they're not busy finding (and creating) new clinical indications for their already marketed drugs.

 

So here is the really ironic part of this whole thing...we just started a big NMR project in lab, but we just send out our samples to the CORE facility and they send back the results! I read a little more on it and I think I'll be OK, there will be one question on the in-calss portion of my quals, one stinkin question and I have to know it all just in case...Thanks you guys for the help!

[Tartaglia]

GradGrrl- I know about it. I used to use 1H and 13C nmr a lot when I was a synthetic chemist. Its not particularly easy to explain though. What exactly don't you understand?

[ecoli]

I learned how to read NMR graphs in chem this year, and boy is it tough.

 

It was invented at my uni. by Paul Lauterbur (at uni of Illinois now) in the 70's, and we have the first machine on display in the chem building.

 

That's pretty much all I know about it.

[Tartaglia]

ecoli - nmr machines were used in the 1960's and Nobel prizes were awarded for work on nmr in the 1940's and 1950's

[GradGrrl]

GradGrrl- I know about it. I used to use 1H and 13C nmr a lot when I was a synthetic chemist. Its not particularly easy to explain though. What exactly don't you understand?

 

I think the main points were are suppossed to recognize are: How to determine structural differences in a biological sample using the spectrum. We will most likely have to interpret a small spectrum on the take home portion of the exam, but for the in-class portion, I would expect him to ask how J-coupling or NOE's would help determine structure...as well as relaxation, but I think I have releaxation down. Those are the 2 questions I missed last fall when I took the class exam. He was a really hard grader too, but they are suppossed to be very general main ideas on the in-class Qualifying Exam, and not specific.

[Tartaglia]

Possibly the best thing you could do is scan a few questions into a file and stick them up here. There are so many subtleties to nmr I could put up a load of stuff and still not really cover what you want.

[GradGrrl]

Possibly the best thing you could do is scan a few questions into a file and stick them up here. There are so many subtleties to nmr I could put up a load of stuff and still not really cover what you want.

 

I found every test but that one:-(

 

Thanks anyway though.

[Tartaglia]

The problem with general explanations on this theme is you need to draw a lot of diagrams and thats not easy in this format. Come up with something specific and I'll gladly help

[ecoli]

ecoli - nmr machines were used in the 1960's and Nobel prizes were awarded for work on nmr in the 1940's and 1950's

 

http://nobelprize.org/medicine/laureates/2003/

 

In the form of Magnetic resonance imaging.

[Tartaglia]

Yes Ecoli, Nuclear Magnetic Imaging is a much more recent application

 

I remember using an old continuous wave machine in 1983 that was almost 20 years old

[GradGrrl]

Yes Ecoli' date=' Nuclear Magnetic Imaging is a much more recent application

 

I remember using an old continuous wave machine in 1983 that was almost 20 years old[/quote']

 

LOL... don't worry about it Tartaglia, but I really appreciate the offer. It's only one question out of 30, in fact there is no guarantee it will be on there - only 30 questions and 45 lecturers- so he might not get an in-class question.

 

I can miss 7 and still pass anyway. (yeah we'll see how much winking I do tomorow at 5pm...lol...sorta...)

[Tartaglia]

Good luck anyway - I remember doing my PhD, loads of work no money, no responsibilities. Time of my life!

[timo]

Seeing that a surprisingly large number of people in here seem to know what "NMR" is, let me take the risk of souding stupid: What is "NMR" ?

[MattC]

NMR: Nuclear Magnetic Resonance

 

Some nucleo spin and some don't. Hydrogen and Carbon(13) both spin and thus have a magnetic moment. The spin of these nuclei will align themselves with an external magnetic field, and when subjected to certain frequences of radio, the spin is disrupted and then rights itself (releasing radio waves back out). The frequency (of light, typically radio waves I believe) at which this occurs differs for different nuclei, depending upon factors such as the electron cloud density and presence of other nuclei nearby. For instance, a carbon-13 that is methyl will require a very different frequency (lower, I believe) than a carbon-13 that is double-bonded to an oxygen, as in an aldehyde.

Carbon 12, by the way, doesn't rotate. Something to do with nuclear symmetry, I believe - iirc only nuclei with an even sum of neutrons and protons will rotate and have a magnetic field.

 

So, as for the graphs, I won't go into a great deal of data as there are plenty of sites with better guides than I could give (without supplying some NRM spectra and analyzing them, which I'm not so good at anyway). The very basics are simple, though:

H-NMR - clusters of readings refer to groups of hydrogens that are energetically equiv. The relative heights of the readings for the various hydrogen groups can be used to determine how many are in each group. The # of readings within a cluster itself refers not to the number of hydrogens that group represents, but rather the number of hydrogen neighbors it has. I.E. in ethane there are 6 hydrogens represented by one reading

in ethanol, there are five hydrogens (the OH hydrogen is not counted, it comes and goes too readily). Three are equivalent and will be represented by 3 lines (2+1 ... more on this in a second) that are 3/2 the height of the 4 (3+1) that represent the two hydrogens on the carbon with the -OH bonded to it.

Now, about the 2+1 and 3+1.

As I wrote before, a given cluster of lines represents a group of energetically equivalent nuclei (or even a single one) - but that cluster has a certain number of lines and these lines do NOT refer in any way to he # of nuclei in this energetically equivalent group. Instead, it refers to the number of neighboring hydrogen atoms (Nh) according to the equation:

Number of readings in cluster = Nh + 1

(where Nh= the number of hydrogens on adjacent atoms)

This is called J-coupling. Essentially these extra lines are the product of interactions that vary because the adjacent hydrogens. More detail than that is beyond my abilities.

 

NOE: Nuclear Overhauser Effect. More than that I do not know.

 

Carbon NRM is a bit different. <yawn> I'd suggest a google though ... others can give you a better explanation that I have.

[MattC]

Seeing as how I accidentally double-posted (some server bug, I swear.... I hit post once!), I will give another more useful definition (perhaps) that I just realized would have been useful:

NMR is a technique by which you can analyze some unknown chemical and determine the carbon skeleton and the placement of hydrogens and such. Other method can be useful for determining molecular weight and maybe determining the presence of functional groups, but it can be difficult to tell whether your carbon structure has a methyl branch, for instance, on the third or fifth carbon in a chain of 8 (3-methyl Octane vs 5-methyl octane)

[Tartaglia]

Atheist, Nuclear Magnetic Resonance spectroscopy is a technique used extensively in synthetic chemistry. It is usually used in identifying different chemical environments of spin 1/2 nuclei (mainly, 1H, 13C, 31P) when microwaves are aborbed when a magnetic field is applied to a dilute solution of the chemical. The precession of the magnetic moment of the spin is reversed on photon absorption. It is no exageration to say that when the technique was first introduced into chemistry (ca 1961) it completely revolutionised organic and inorganic synthetic chemistry

[GradGrrl]

So he did have an in class question. Good news, I got it right. Something about j-coupling and the difference in signal between alpha helices and beta sheets. Another part about T2 relaxation.

 

I totally missed the microscope question, how to measure conformational change inside a cell in real time. All I could remember was FRET, but I know that wasn't it. Then he asked for a design of the "necessary equipment" needed to get it to work???? WTF? I'm not microscope expert...that's why we PAY him to do the samples??? Right??

 

Missed the 5 things fibronectin and laminin have in common too. Jerk. Mr. immunology asked a dumb question about a protein he never even talked about. Ass. If you have to know one thing about basic immunology in a molecular context, you'd think he ask about Rag1 and Rag2. But NOooooooo. Ttd, or tdt, whatever it was. Missed it.

 

But NMR...no I got that right. I knew that helices were 4-5 mhz and beta sheets were 9-12...but ECM proteins - way over my head....

 

Just ranting...don't feel obligated to answer my pity party.

[timo]

Thanks to Tartaglia and expecially MattC for the answers. It was mostly the fact that I initially thought it might be magnetic resonance (tomography) but that no one commented on whether it is or not (all posters just wrote "NMR", too) - in fact, it was the "N" that confused me because I somehow thought of "N=nano" which didn´t make any sense.