Practical Homonuclear NMR

CHE-555

Learning outcomes:  Students will acquire hands-on training in understanding, setting up, customizing, processing, analyzing and interpreting a set of very useful advanced one-dimensional and two-dimensional homonuclear (1H) NMR experiments.  Emphasis will be on actual performance of useful experiments.  Students will do this themselves, in small groups, under the instructor's guidance.  Each week we will set up more experiments and then process, analyze and interpret them.  Thus, students will acquire hands-on experience with some of the most useful current NMR methods applicable to small and large molecules.

Instructor:  Anne-Frances Miller  CP 113, 7-9349 or afm@uky.edu

Office hours:  Mon 4-5 pm (Please use this time.)

Expert assistance:  W. John Layton

Texts:

          High-Resolution NMR Techniques in Organic Chemistry, T. Claridge, 1999, Elsevier, ISBN 0080427987

          The Varian spectrometer manuals (excellent)

Lectures: Mon.  1-2 and Wed. 1-2 pm in CP 111.

Laboratory excercises:

Wednesdays from 2 pm - 5 pm in the NMR center or (hopefully CP137).

 

Prerequisites:

Introductory organic chemistry, a course on spectroscopy or quantum mechanics, familiarity with the solution of basic integrals and logarythms.

 

Evaluation:

 

Quizzes held at the beginning of class on a very regular but unannounced basis.  Read the reading assignments and solve problems before coming to class !!

25

 

Performance in lab

20

 

Practical exercises distributed weekly.  These must be turned in to Dr. Miller at the next week's lecture, stapled together with the student's name displayed.  Late submissions may be graded for a percentage of the full grade which will decrease as the lateness increases.  These exercices replace problem sets.  Students may seek help from colleagues in order to be able to perform the work, but the work turned in must have been performed alone by the named student only.  Departures from this standard will result in loss of grades and/or expulsion from the course.  For full marks the data sets collected should be saved in the studentís own subdirectory of the vnmrsys/data directory of the course account, with clear informative file names.

25

Written exam covering all course material, including assigned reading.

1d things to optimize

consequences of not doing so

choice of experiments for desired info

safety precautions

20

 

literature report / cross word puzzle

10

 

 

100

          Assignments will be practical in nature, students taking the course should be prepared to spend more than 5 hours each week practicing what they have learned and then performing the assignments.

          NMR samples will be provided, but students are encouraged to bring samples from their lab for any experiments.  Each student should use their own (different) one.  Please consult with the instructor and your advisor in advance.

                  

Literature or Crossword Puzzle:

          Due on or before March12. 

A cross-word puzzle of NMR terms.  Please avoid parameter and command names.  Alternately, submit a copy of an article describing a novel and elegant use of NMR, or new NMR methodology, along with a one page description of what was done, how it works and why it is significant.

Miscellany:

          The current course concentrates on taking students from being barely able to do what they have to, to knowing what their options are, being able to set up something brand new and having it produce publishable data the first or second time.

          We are very fortunate to have at our disposal the super facilities in the new NMR lab.  However we cannot restrict other people's research access to these machines for the sake of people not officially in the course.  Please be sure that you are registered before you attend.  Interested parties are of course most welcome to do all the reading and quizzes, and welcome to get their colleagues to demonstrate what they have learned each week.  This is very good for the students taking the class since repeating what was done promptly is the best way to come up with questions about the material and learn it.  I simply will not have space at the spectrometers for more than the registered students during the class time.  Only registered students will be checked out on the machines as part of the course (they may check out under their advisorís auspices as usual though).

          We also have the good fortune to have a staff spectroscopist W. John Layton who has troves of experience and can offer you expert guidance, instruction and advice.  You are encouraged to take full advantage of this resource but not John himself, personally.  Please respect the fact that he has numerous responsibilities and works hard to keep the facility in its current good condition.  Make appointments in advance when possible but ask questions liberally, certainly BEFORE trying something that could damage the hardware.  Similarly, Dr. Miller is always happy to help, but may be harder to find.

Since the instruments are truly cutting-edge and must serve the research needs of many people, we must consider ourselves a community of expert users who all share responsibility for maintenance of the machines in peak performing condition.  Please offer to help anyone you see doing something potentially damaging and immediately report any problems.  It is human to make mistakes, but anyone caught trying to cover up damage, or leave it behind for the next (innocent) user to confront, may loose the privilege of using the spectrometers.

IMPORTANT:

          You must be checked out for 1D 1H use of the 200s before the second laboratory meeting of the course on Jan 28, and before you do anything on the machines with your own hands.  Please see W. J. Layton to get checked out.  Do this well in advance, as even he cannot check out ten people in ten minutes on the morning of the 28nd.  You must also successfully advance to being checked out on the 400s before the lecture on February 11.


Outline: 

Week 1       Getting started: basics of every spectrum you will ever take: Sample insertion, locking, shimming collecting processing displaying and plotting a simple 1 dimensional spectrum.

Week 2       Optimizing the sensitivity of a 1d: choice of excitation pulse width, reduction of common artifacts, more detail on gradient shimming, simulation and deconvolution.

Week 3       Tailoring your protocol to the sample:  Measurement of T1 and T2.  Weighting functions to suit the sample T2s.  Linear prediction.  How to collect quantitative spectra.

Week 4       The relation between time and frequency, selective excitation with composite pulses and shaped pulses.  Advanced 1d methods:  Selective decoupling, difference nOe, controls needed in a well-designed difference experiment.

 

Week 5       Solvent suppression (time vs. frequency again): presaturation, counter-selective excitation with composite pulses and shaped pulses.  The 'wet' method.

 

Week 6       Principles of 2D spectroscopy: COSY, the uses of phase cycling.  Comparison of DQCOSY**eff of insufficient rel delay** with gDQCOSY: gradients are great.  Choosing the duration of the indirect evolution delay for appropriate resolution.

 

Week 7       TOCSY: choice of spinlock field strength so as to get good data without smoking a probe.  Processing 2D data intelligently.

 

Week 8       NOESY**zq**, and ROESY to assess through-space proximity.  The concept of frequency labelling / selection by a multi-pulse combination.

 

Week 9       13C 1d spectroscopy:  significant differences from 1H calibration and intelligent use of decoupling, DEPT for discrimination between CH, CH2 and CH3.

 

Week 10     Indirect detection of insensitive nuclei: many advantages, INEPT magnetization transfer, indirect pulse width calibration.

 

Week 11     HSQC : the enormous sensitivity advantages of exciting and observing sensitive nuclei.

 

Week 12     HMBC: extension of indirect detection to C not bound directly to H or F.  Comparison with HSQC, and use of isotope-filtering pre-senquences.

 

Week 13:    Putting it together:  use of the above NMR spectra to complete the assignment of a mid-sized molecule and evaluate its 3-dimensional conformation.

 

Week 14     Quantifying interactions between molecules: HOESY and transferred nOes, OR Solid-State NMR: basics including CP-MAS, OR other NMR topic based on popular demand.

 


First reading assignment:

          For 23 January, read chapter sections 2.0 - 2.2.3, 2.3 of Claridge's book.

Please turn in a list of things you would like to learn to do on the NMRs, on January 30.

 

 

Second reading assignment:

  For Sept. 6, Chapters 2 and 3 of Claridge's book.