chapter-1-NMR-theory

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NMR . BY PRADEEP PHR.PRADEEP@YAHOO.COM

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SPECIAL TOPICS IN ANALYTICAL CHEMISTRY Introduction to NMR CHEM 921, Fall 2005 MWF 11:30-12:20pm, Rm 548 Hamilton Hall COURSE OUTLINE Instructor: Dr. Robert Powers Office Labs Address: 722 HaH 720 HaH Phone: 472-3039 472-5316 Office Hours: 10:30-11:30 am MWF or by Special Appointment. web page: http://bionmr-c1.unl.edu  Text: “NMR and Chemistry: An Introduction to Modern NMR Spectroscopy”, by J. W. Akitt & B. E. Mann; Stanley Thornes, 2000 Course Work: Written Report: 50 pts (Fri., Sept. 9th) Exam 1: 100 pts (Fri., Sept 23rd) Exam 2: 100 pts (Wed., Nov. 2nd) Structure Problems (5) 150 pts (as assigned) Total: 400 pts

PAPER ON NMR METHOD : 

PAPER ON NMR METHOD Paper General >2-3 pages single space text Additional pages for figures, references 12 pitch font, 1” margins Double spacing between paragraphs and headings Paper Topic Review a Manuscript that Describes an NMR Technique useful for the Structural Analysis of a Chemical Structure The paper should not cover a method discussed in class or in the text book The paper can describe a new modification or an improvement of a method discussed in class or in the text book

PAPER ON NMR METHOD : 

PAPER ON NMR METHOD When Writing your Review Consider the Following: Principals/theory behind technique Issue or problem the technique is addressing How does the new technique compare to existing approaches? How the technique is used What results were achieved? Advantages/disadvantages Recommended Journals: Journal of Magnetic Resonance, Journal of Biomolecular NMR, Magnetic Resonance in Chemistry, Magnetic Resonance Quarterly, and Progress in NMR Spectroscopy Grading (50 points total) Due Date: 11:30 am, Friday Sept. 9th

STRUCTURE PROBLEMS : 

STRUCTURE PROBLEMS Using NMR Data to Determine the Structure of Unknown Organic Compound Total of 5 unknown structures to solve Structures will be randomly assigned one week before due date NMR data sets for unknowns will be available in the NMR computer lab (832 HaH) Each unknown will include the following data: Chemical formula 1D 1H & 13C spectra 2D 1H COSY, 2D 1H NOESY, 2D 1H-13C HMQC, 2D 1H-13C HMBC Software Training You will need to know how to use Bruker’s TopSpin/XWinNMR software to analyze the NMR data. Schedule a Training time Dr. Dumais (834 HaH,472-6255) and Ms. Basiaga (832B,472-3797) will oversee training and scheduling of the NMR computer lab. A sample data set will be available for practice. Please use this opportunity to familiarize yourself with the software ASAP.

STRUCTURE PROBLEMS : 

STRUCTURE PROBLEMS Completed Reports for the Unknown Structure Determination will contain: Unknown Number Chemical Structure of the Unknown 1H and 13C chemical shift Assignments Summary of Key Experimental Information that Support the Structure

STRUCTURE PROBLEMS : 

STRUCTURE PROBLEMS The Goal of these Problem Sets is to Develop Your Skills in Analyzing NMR Data These are individual projects Do Not Work Together on the Assignments Do Not Share Your Results with Other Students Graded Problem Sets will be Returned After all Five Problem Sets have been Completed The Due Dates for the Structure Problem Sets are: Structure Problem #1 Fri. Sept. 30th Structure Problem #2 Fri. Oct. 7th Structure Problem #3 Fri. Oct. 14th Structure Problem #4 Fri. Oct. 21st Structure Problem #5 Fri. Oct. 28th Grading (30 points/structure; 150 total points)

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Lecture Topics Topic Chapters in NMR & Chemistry BASIC NMR Theory Introduction to NMR Theory 1 Quantum and classical description Obtaining an NMR Spectra 5 Data acquisition and processing Instrumentation Chemical Shifts () 2 Select examples of chemical shift trends Predicting chemical shifts Coupling Constants (J) 3 Simulation of second-order spin systems One and Two Dimensional NMR NMR Pulses 6 1D NMR 8 NOE, J modulation, INEPT, DEPT, INADEQUATE 2D NMR 9 Theory COSY,TOCSY,NOESY,HMQC,HMBC Examples of Spectral Interpretation 8 NMR Dynamics Relaxation 4 T1,T2,Dipole-Dipole,CSA,Quadrupolar Exchange 7 NMR time scale Solid State NMR (as time permits) 11

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>>> “Spin Dynamics – Basics of Nuclear Magnetic Resonance” M. H. Levitt <<< >>> “Structure Determination of Organic Compounds: Tables of Spectral Data” <<< Pretsch, E., Bühlmann, P., and Affolter, C. “Spectrometric Identification of Organic Compounds” Silverstein, Bassler and Morrill “Basic One- and Two-Dimensional NMR Spectroscopy” Horst Friebolin “Modern NMR Techniques for Chemistry Research” Andrew E. Derome “Nuclear Magnetic Resonance Spectroscopy” R. K Harris “Protein NMR Spectroscopy: Principals and Practice” John Cavanagh, Arthur Palmer, Nicholas J. Skelton, Wayne Fairbrother “Biomolecular NMR Spectroscopy” J. N. S. Evans “NMR of Proteins and Nucleic Acids” Kurt Wuthrich Some Suggested NMR References

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Some NMR Web Sites The Basics of NMR by J.P. Hornak Hypertext based NMR course http://www.cis.rit.edu/htbooks/nmr/nmr-main.htm Integrated Spectral Data Base System for Organic Compounds http://www.aist.go.jp/RIODB/SDBS/menu-e.html Educational NMR Software All kinds of NMR software http://www.york.ac.uk/depts/chem/services/nmr/edusoft.html NMR Knowledge Base A lot of useful NMR links http://www.spectroscopynow.com/ NMR Information Server News, Links, Conferences, Jobs http://www.spincore.com/nmrinfo/ Technical Tidbits Useful source for the art of shimming http://www.acornnmr.com/nmr_topics.htm BMRB (BioMagResBank) Database of NMR resonance assignments http://www.bmrb.wisc.edu/

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1937 Rabi predicts and observes nuclear magnetic resonance1946 Bloch, Purcell first nuclear magnetic resonance of bulk sample 1953 Overhauser NOE (nuclear Overhauser effect) 1966 Ernst, Anderson Fourier transform NMR 1975 Jeener, Ernst 2D NMR 1985 Wüthrich first solution structure of a small protein (BPTI) from NOE derived distance restraints 1987 3D NMR + 13C, 15N isotope labeling of recombinant proteins (resolution) 1990 pulsed field gradients (artifact suppression) 1996/7 new long range structural parameters: - residual dipolar couplings from partial alignment in liquid crystalline media - projection angle restraints from cross-correlated relaxation TROSY (molecular weight > 100 kDa) Nobel prizes 1944 Physics Rabi (Columbia) 1952 Physics Bloch (Stanford), Purcell (Harvard) 1991 Chemistry Ernst (ETH) 2002 Chemistry Wüthrich (ETH) 2003 Medicine Lauterbur (University of Illinois in Urbana ), Mansfield (University of Nottingham) NMR History

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NMR History First NMR Spectra on Water Bloch, F.; Hansen, W. W.; Packard, M. The nuclear induction experiment. Physical Review (1946), 70 474-85. 1H NMR spectra of water

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NMR History First Observation of the Chemical Shift 1H NMR spectra ethanol Modern ethanol spectra Arnold, J.T., S.S. Dharmatti, and M.E. Packard, J. Chem. Phys., 1951. 19: p. 507.

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Nuclear Magnetic Resonance Introduction: Nuclear Magnetic Resonance (NMR) measures the absorption of electromagnetic radiation in the radio-frequency region (~4-900 MHz) - nuclei (instead of outer electrons) are involved in absorption process - sample needs to be placed in magnetic field to cause different energy states NMR was first experimentally observed by Bloch and Purcell in 1946 (received Nobel Prize in 1952) and quickly became commercially available and widely used. Probe the Composition, Structure, Dynamics and Function of the Complete Range of Chemical Entities: from small organic molecules to large molecular weight polymers and proteins. NMR is routinely and widely used as the preferred technique to rapidly elucidate the chemical structure of most organic compounds. One of the MOST Routinely used Analytical Techniques

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Typical Applications of NMR: 1.) Structural (chemical) elucidation ‚ Natural product chemistry ‚ Synthetic organic chemistry - analytical tool of choice of synthetic chemists - used in conjunction with MS and IR 2.) Study of dynamic processes ‚ reaction kinetics ‚ study of equilibrium (chemical or structural) 3.) Structural (three-dimensional) studies ‚ Proteins, Protein-ligand complexes ‚ DNA, RNA, Protein/DNA complexes ‚ Polysaccharides 4.) Drug Design ‚ Structure Activity Relationships by NMR 5) Medicine -MRI MRI images of the Human Brain NMR Structure of MMP-13 complexed to a ligand Taxol (natural product)

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2-phenyl-1,3-dioxep-5-ene 13C NMR spectra 1H NMR spectra Each NMR Observable Nuclei Yields a Peak in the Spectra “fingerprint” of the structure

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Information in a NMR Spectra 1) Energy E = h h is Planck constant  is NMR resonance frequency Observable Name Quantitative Information Peak position Chemical shifts () (ppm) = obs –ref/ref (Hz) chemical (electronic) environment of nucleus Peak Splitting Coupling Constant (J) Hz peak separation neighboring nuclei (intensity ratios) (torsion angles) Peak Intensity Integral unitless (ratio) nuclear count (ratio) relative height of integral curve T1 dependent Peak Shape Line width  = 1/T2 molecular motion peak half-height chemical exchange uncertainty principal uncertainty in energy

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A Basic Concept in ElectroMagnetic Theory A Direct Application to NMR A moving perpendicular external magnetic field will induce an electric current in a closed loop An electric current in a closed loop will create a perpendicular magnetic field

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For a single loop of  wire, the magnetic field, B through the center of the loop is: o – permeability of free space (4 x 10-7 T · m / A) R – radius of the wire loop I – current A Basic Concept in ElectroMagnetic Theory

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Faraday’s Law of Induction If the magnetic flux (B) through an area bounded by a closed conducting loop changes with time, a current and an emf are produced in the loop. This process is called induction. The induced emf is: A Basic Concept in ElectroMagnetic Theory Simple AC generator

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Lenz’s Law An induced current has a direction such that the magnetic field of the current opposes the change in the magnetic flux that produces the current. The induced emf has the same direction as the induced current A Basic Concept in ElectroMagnetic Theory Direction of current follows motion of magnet

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Quantum Description Nuclear Spin (think electron spin) Nucleus rotates about its axis (spin) Nuclei with spin have angular momentum (p) or spin 1) total magnitude 1) quantized, spin quantum number I 2) 2I + 1 states: I, I-1, I-2, …, -I I=1/2: -1/2, 1/2 3) identical energies in absence of external magnetic field Theory of NMR

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NMR Periodic Table NMR “active” Nuclear Spin (I) = ½: 1H, 13C, 15N, 19F, 31P biological and chemical relevance Odd atomic mass I = +½ & -½ NMR “inactive” Nuclear Spin (I) = 0: 12C, 16O Even atomic mass & number Quadrupole Nuclei Nuclear Spin (I) > ½: 14N, 2H, 10B Even atomic mass & odd number I = +1, 0 & -1

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Magnetic Moment () spinning charged nucleus creates a magnetic field Similar to magnetic field created by electric current flowing in a coil Magnetic moment “Right Hand Rule” determines the direction of the magnetic field around a current-carrying wire and vice-versa

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Gyromagnetic ratio () related to the relative sensitive of the NMR signal magnetic moment () is created along axis of the nuclear spin where: p – angular momentum  – gyromagnetic ratio (different value for each type of nucleus) magnetic moment is quantized (m) m = I, I-1, I-2, …, -I for common nuclei of interest: m = +½ & -½

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=  h / 4 Magnetic alignment In the absence of external field, each nuclei is energetically degenerate Add a strong external field (Bo) and the nuclear magnetic moment: aligns with (low energy) against (high-energy)

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Spins Orientation in a Magnetic Field (Energy Levels) Magnetic moment are no longer equivelent Magnetic moments are oriented in 2I + 1 directions in magnetic field Vector length is: Angle () given by: Energy given by: where, Bo – magnetic Field  – magnetic moment h – Planck’s constant For I = 1/2

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Spins Orientation in a Magnetic Field (Energy Levels) Magnetic moments are oriented in one of two directions in magnetic field (for I =1/2) Difference in energy between the two states is given by: E =  h Bo / 2  where: Bo – external magnetic field h – Planck’s constant  – gyromagnetic ratio

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Frequency of absorption:  =  Bo / 2 Spins Orientation in a Magnetic Field (Energy Levels) Transition from the low energy to high energy spin state occurs through an absorption of a photon of radio-frequency (RF) energy RF

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NMR Signal (sensitivity) The applied magnetic field causes an energy difference between the aligned () and unaligned () nuclei NMR signal results from the transition of spins from the  to  state Strength of the signal depends on the population difference between the  and  spin states The population (N) difference can be determined from the Boltzmman distribution and the energy separation between the  and  spin states: N / N = e E / kT

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NMR Signal (sensitivity) Since: E = h and  =  Bo / 2 then: The E for 1H at 400 MHz (Bo = 9.39 T) is 6 x 10-5 Kcal / mol  Very Small ! ~60 excess spins per million in lower state N/N = e(hBo/2kT) N / N = e E / kT

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NMR Sensitivity EhBo /2 NMR signal (s) depends on: Number of Nuclei (N) (limited to field homogeneity and filling factor) Gyromagnetic ratio (in practice 3) Inversely to temperature (T) External magnetic field (Bo2/3, in practice, homogeneity) B12 exciting field strength (RF pulse) N / N = e E / kT Increase energy gap -> Increase population difference -> Increase NMR signal E ≡ Bo ≡  s  4Bo2NB1g()/T

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NMR Sensitivity Increase in Magnet Strength is a Major Means to Increase Sensitivity

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NMR Sensitivity But at a significant cost! ~$800,000 ~$2,00,000 ~$4,500,000

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 - Intrinsic property of nucleus can not be changed. C)3 for 13C is 64x N)3 for 15N is 1000x 1H is ~ 64x as sensitive as 13C and 1000x as sensitive as 15N ! Consider that the natural abundance of 13C is 1.1% and 15N is 0.37% relative sensitivity increases to ~6,400x and ~2.7x105x !! NMR Sensitivity Relative sensitivity of 1H, 13C, 15N and other nuclei NMR spectra depend on Gyromagnetic ratio () Natural abundance of the isotope 1H NMR spectra of caffeine 8 scans ~12 secs 13C NMR spectra of caffeine 8 scans ~12 secs 13C NMR spectra of caffeine 10,000 scans ~4.2 hours

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Classical Description Theory of NMR Spinning particle precesses around an applied magnetic field

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Classical Description Angular velocity of this motion is given by: o = Bo where the frequency of precession or Larmor frequency is:  = Bo/2 Same as quantum mechanical description

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Classical Description Net Magnetization Nuclei either align with or against external magnetic field along the z-axis. Since more nuclei align with field, net magnetization (Mo, MZ) exists parallel to external magnetic field. Net Magnetization along +Z, since higher population aligned with Bo. Magnetization in X,Y plane (MX,MY) averages to zero.

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RF pulse B1 field perpendicular to B0 Mxy Mz Classical Description Observe NMR Signal Need to perturb system from equilibrium. B1 field (radio frequency pulse) with Bo/2frequency Net magnetization (Mo) now precesses about Bo and B1 MX and MY are non-zero Mx and MY rotate at Larmor frequency System absorbs energy with transitions between aligned and unaligned states Precession about B1stops when B1 is turned off

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 = Bo/2 RF pulse along Y Detect signal along X X y Classical Description Observe NMR Signal Remember: a moving magnetic field perpendicular to a coil will induce a current in the coil. The induced current monitors the nuclear precession in the X,Y plane

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Classical Description Rotating Frame To simplify the vector description, the X,Y axis rotates about the Z axis at the Larmor frequency (X’,Y’) B1 is stationary in the rotating frame +

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Classical Description NMR Pulse Applying the B1 field for a specified duration (Pulse length or width) Net Magnetization precesses about B1 a defined angle (90o, 180o, etc)

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Net Magnetization Classic View: - Nuclei either align with or against external magnetic field along the z-axis. - Since more nuclei align with field, net magnetization (Mo) exists parallel to external magnetic field Quantum Description: Nuclei either populate low energy (, aligned with field) or high energy (, aligned against field) - Net population in  energy level. - Absorption of radio- frequency promotes nuclear spins from   .

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Absorption of RF Energy or NMR RF Pulse Classic View: - Apply a radio-frequency (RF) pulse a long the y-axis - RF pulse viewed as a second field (B1), that the net magnetization (Mo) will precess about with an angular velocity of 1 -- precession stops when B1 turned off Quantum Description: - enough RF energy has been absorbed, such that the population in / are now equal - No net magnetization along the z-axis 1 = B1 90o pulse Bo > 0 Please Note: A whole variety of pulse widths are possible, not quantized dealing with bulk magnetization