University of Ottawa NMR Facility Web Site

Please feel free to make suggestions for future posts by emailing Glenn Facey.

Thursday, June 30, 2016

NMR and Food Chemistry - Maple Syrup

Maple syrup is arguably one of the tastiest traditional Canadian condiments.  In honor of Canada Day (July 1), it is appropriate to take a look at this delicious golden treat.  The bottom trace of the figure below shows the 600 MHz 1H NMR spectrum of pure Quebec maple syrup dissolved in D2O.
The spectrum is overwhelmingly dominated by sucrose.  Clearly, nature gives us the maple flavor with very low concentration components.  The top trace is a similar spectrum of "table" syrup which has a taste somewhat similar to maple syrup.  The spectrum is much more complicated than that of pure maple syrup.  In order to mimic the flavor of pure maple syrup, the food chemists resort to a complex mixture of sugars and artificial flavors.  Canada keeps it simple and of course better!  Happy Canada Day.

Wednesday, May 11, 2016

Non-uniform Sampling (NUS)

Collecting 2D or 3D NMR data can be very time consuming. The indirect dimension of a 2D experiment is sampled linearly via the t1 increments in the pulse sequence.  An FID must be collected for every single linearly spaced t1 increment. In the interest in collecting 2D or 3D NMR data in a more time efficient manner, a great deal of effort is made towards faster data collection techniques.  While some of these methods are based on spatial selectivity, others are based on sparse sampling techniques in the indirect dimensions of nD NMR sequences.  One such sparse sampling method, given the name non-uniform sampling (NUS), samples a sub-set of the indirect dimension in a random (or weighted random) manner and then predicts the uncollected data based on the data sampled, in much the same way data are predicted in the forward and backward linear prediction methods.  The reconstructed data is then used for the indirect Fourier transforms.  A comparison of the conventional and non-uniform data sampling methods is illustrated in the figure below.
Collecting only a fraction of FID's reduces the experiment time by the same fraction.  The figure below shows a superposition of partial 600MHz 1H-13C HSQC spectra of a D2O solution of sucrose.
All of the spectra were collected with 2 scans per increment using a 1.5 second recycle time.  The lower spectrum in black was collected conventionally with 256 increments in 15 minutes. The middle spectrum in blue was collected conventionally with 64 increments in 3.75 minutes. The top spectrum in purple was collected using NUS with 25% of 256 increments (i.e. 64 increments) collected in 3.75 minutes.  A comparison of the two conventionally collected data sets shows the expected loss in F1 resolution with the 4-fold reduction in experiment time by reducing the number of increments by a factor of 4. The bottom (black) conventional spectrum and the top (purple) NUS spectrum are however virtually indistinguishable despite the 4-fold reduction in experiment time for the NUS spectrum.  NUS is a very valuable technique for reducing experiment times without sacrificing resolution.

Friday, April 22, 2016

CEST - Chemical Exchange Saturation Transfer

Chemical Exchange Saturation Transfer (CEST) is a technique where one resonance, in slow exchange with a second resonance, is saturated with a selective low power pulse followed by a hard non-selective 90° pulse.  The intensity of the second resonance is then diminished due to the transfer of saturation from the first resonance as the result of  chemical exchange.  The figure below demonstrates this for a 25 mM solution of salicylic acid in H2O/D2O buffered at pH 7.
The left-hand panel of the figure is a stacked plot of extracted spectra collected in a pseudo 2D acquisition as a function of saturation frequency.  The saturation frequency was varied from an initial value of 20 ppm to a final value of -20 ppm in steps of 0.2 ppm.  The spectra are plotted such that only the water resonance is on scale.  One can see that the intensity of the water resonance dips when a saturation frequency of ~14 ppm is applied, corresponding to the resonance frequency of the –COOH and –OH protons of the salicylic acid (which appear to be in fast or intermediate exchange with one another).  The water resonance of course also dips to zero when a saturation frequency of ~4.7 ppm is used, corresponding to a simple presaturation of the water.  The right-hand panel of the figure is a plot of the integral of the water resonance as a function of saturation frequency, showing again a dip at ~14 ppm.

CEST is used in MRI to provide image contrast where a chemical exchange agent is introduced and images are collected with and without saturation of the exchange agent.  The difference provides an image enhanced by the presence of the chemical exchange agent.

Thank you to Dr. Mojmir Suchy of Prof. Adam Shuhendler’s group at the University of Ottawa for arousing my interest in the use of CEST for MRI and preparing the sample used in this post. 

Monday, April 11, 2016


The sensitivity of a low γ, spin I = ½ nucleus is determined by the difference in populations between the low energy and high energy states, governed by the Boltzmann distribution. If the low γ, spin I = ½ nucleus is coupled to a proton the energy level diagram is more complicated than simply two levels and is shown in the figure below where a 13C-1H spin pair is used as an example.
The populations of the states involved in the 13C transitions and hence the sensitivity of the 13C signal can be altered by inverting the H1 or H2 1H transitions with 180° pulses. This is illustrated in the figure below.
In the left panel, the H1 transition of a 13C-1H spin pair is inverted (i.e. the populations of the two energy levels of the H1 transition are swapped). This also affects the populations of the energy levels involved in the C1 and C2 13C transitions. After inversion of the H1 1H transition, the intensities of the C1 and C2 13C transitions have changed from their equilibrium value of 1:1 to an enhanced value of 5:-3. If the H2 transition is inverted (right-hand panel), the C1:C2 intensity ratio is -3:5. In both cases the sensitivity of the 13C doublet has been enhanced compared to its equilibrium value. This enhancement is called INEPT (Insensitive Nuclei Enhanced by Polarization Transfer) and is one of the most common sensitivity enhancement techniques used in NMR pulse sequences. The simplest implementation of INEPT is shown in the figure below along with the vector diagrams.
Phase cycling can be employed to obtain a -4:4 anti-symmetric doublet, rather than doublets with components of unequal magnitude. This is represented in the figure below.
A refocusing element can be added to the end of the sequence to refocus the anti-symmetric doublets and data can be collected with proton decoupling.
The result is a singlet with 4 times  (i.e. γHC) the intensity of the singlet one would expect under equilibrium conditions without an NOE.  For 15N, one obtains a sensitivity gain of ~10. The results of these implementations of INEPT are compared to the equilibrium situation in the figure below.
INEPT has the additional advantage that its repetition rate is determined by the 1H T1 rather than the 13C T1.  This is a tremendous additional sensitivity improvement when multiple scans are collected because the 1H T1 is often shorter than the 13C T1 by an order of magnitude.  One can collect approximately ten times as many scans per unit time.  This advantage is even more significant for 15N.  Reverse INEPT is used in the collection of 1H data for  carbon-proton pairs to suppress the protons bound to 12C. 

Wednesday, March 30, 2016

Solid-State 13C NMR of Chicken Eggshells

13C CP/MAS and direct single pulse 13C MAS NMR with high power decoupling can give very different results for a wide variety of materials.  13C CP/MAS NMR relies on the transfer of magnetization from protons to 13C via the dipolar coupling mechanism whereas the direct single pulse method does not.  An interesting material to demonstrate this principle is the shell of a chicken egg.  Chicken eggshell is a complex bio-mineral consisting largely (~ 95%) of the calcite polymorph of calcium carbonate as well as proteins and lipids.  The 13C CP/MAS and 13C single pulse MAS NMR spectra of a sample of dry ground eggshell, from which the membranes had been removed, are shown in the lower and upper traces in the figure below, respectively.

The 13C CP/MAS spectrum in the lower trace has very broad resonances in the aliphatic region of the spectrum due to the proteins and lipids.  The carbonyl region of the spectrum  consists of two resonances; one at ~173 ppm due to the carbonyl carbons of the amino acid residues of the proteins and a resonance at  ~169 ppm which has been shown1,2 to originate from bicarbonate ions (HCO3)-.  Although ~95% the eggshell consists of CaCO3, the carbonate resonance is not present in the 13C CP/MAS spectrum as there are no proximate protons for cross polarization.  In contrast, the single pulse 13C MAS spectrum in the top trace shows only the 13C resonance from the carbonate ions which has a coincident chemical shift with that of the bicarbonate ions.  All of the other 13C resonances are buried in the noise as they are in much lower concentration. These spectra are an excellent example of how one can obtain different information from 13C CP/MAS and single pulse 13C MAS spectra.

1. D.M. Pisklak, L. Szcleszczuk, I. Wawer, Journal of Agricultural and Food Chemistry, 60, 12254 (2012).
2. J. Feng, Y.J. Lee, R.J. Reeder, B.L. Phillips, American Mineralogist, 91, 957 (2006).

Wednesday, February 24, 2016

Ultra-Fast 1H COSY

It cannot be disputed that the introduction of routine 2D NMR spectroscopy in the 1980's revolutionized the way in which NMR measurements are made. Now, with literally thousands of 2D methods available, the quantity of accessible information has dramatically increased. One cannot imagine a modern NMR lab without a 2D NMR toolbox.  One of the main drawbacks to traditional 2D NMR spectroscopy has always been the time required to collect the data.  Data collection can take anywhere from a few minutes to tens of hours.  Many 1D FIDs (typically more than 128) must be acquired as a function of evolution time to construct the 2D data matrix.  The measurement of each of these signals may require multiple scans as a result of necessary phase cycling between which a relaxation delay must be employed.  Once all of the data have been collected, each of the FID's is Fourier transformed followed by a second Fourier transform with respect to the evolution time.  Typical data collection and processing are illustrated here. The introduction of pulsed field gradients for coherence selection has reduced the time required to collect 2D spectra by reducing or  eliminating the need for phase cycling however, one still has to collect many FID's as a function of evolution time.  Even when multiple scans are not required for sensitivity, data collection can take minutes to hours.

Ultra-fast 2D measurements, employing an entirely different method of data collection, were introduced in 2002 and subsequently improved.  In this method, z-field gradients combined with linearly swept chirp pulses are used to phase encode spins linearly along the z axis of the sample according to specific evolution times.  The dephasing depends on both the position along the z axis of the sample and the resonance frequency of each spin.  After this encoding scheme is applied, each slice element of the sample has experienced a different evolution time as a function of its position in the sample.  After a conventional mixing period dictated by the type of 2D measurement, the site specific, spatially phase encoded spins must be read.  This is accomplished by applying a series of bipolar gradient pulse pairs while the receiver is collecting data.  During each gradient pulse (lasting typically 250 μsec) echos are collected.  The position of each echo during a single gradient pulse is related in a one-to-one fashion to the frequency of each of the spins in the sample thus mimicking a mini NMR spectrum whose frequency axis is replaced by a linearly related time axis.  The "spectra" collected during the negative gradient pulses are mirror images to those collected during the positive gradient pulses and must be reversed during data processing.  A series of typically 128 bipolar gradients are applied with the receiver open thus all of the data are acquired in a single scan.  Each "spectrum" collected is a function of the z slice position in the sample, which in turn is linearly related to the evolution time. The collection of "spectra" represent the ultra-fast domain and is Fourier transformed point by point as a function of evolution time (or z position).  The entire data collection sequence takes approximately 100 msec.

The left panel of the figure below shows a conventional 300 MHz gradient enhanced COSY-45 spectrum for a concentrated sample of menthol in CDCl3 collected in 4.5 minutes.  The panel on the right shows a 300 MHz ultra-fast COSY spectrum of the same sample collected in only 100 msec - a time saving factor of 2700!  Both spectra were collected on a Bruker AVANCE II 300 NMR spectrometer equipped with a standard BBOF probe.  Both data sets were symmetrized.  Although the ultra-fast data set has noticeably lower resolution and sensitivity, one can see that it is very similar to the conventional COSY.
There are, of course, a number of drawbacks to the ultra-fast scheme including low sensitivity, limited resolution and limited accessible spectral widths.  Some of these drawbacks can be overcome  with the use of cryoprobes and strong pulsed field gradients. Molecular diffusion over the course of the measurement may also cause problems.  Despite the drawbacks however, the method is extremely well suited to time studies of chemical reactions where conventional 2D data collection would simply take too long.

The references below are a good place to start in order to find out more about this technique.  There is also a very well documented setup procedure available on the Bruker User Library, provided by Patrick Giraudeau, including pulse sequences and processing scripts.

Annual Rev. Anal. Chem. 7, 129-161 (2014).
Mag. Res. Chem. 53, 986-994 (2015).
J. Am. Chem. Soc. 125, 9204–17 (2003).
J. Am. Chem. Soc. 125, 12345–50 (2003).

Monday, December 21, 2015

NMR of the Christmas Tree

One of my fondest memories as a child is the colorful lights and especially the smell of a decorated Christmas tree.  The hot incandescent lights used years ago would heat up the tree evaporating the fragrant compounds in the needles producing the very memorable and wonderful smell of Christmas.  Although modern artificial Christmas trees and cool LED lights have made the holiday season safer with respect to fires, they have taken much of the magic out of Christmas.  Among many other compounds, it is pinene, bornyl acetate and citronellol that contribute to the Christmas smell of evergreen needles.
We can use NMR spectroscopy to look for these compounds and perhaps recover a bit of the Christmas magic.  The bottom panel of the figure below shows the 13C CPMAS spectrum of spruce needles.  One can easily identify the signals from cellulose in the CPMAS spectrum of the needles while some of the smaller peaks can be attributed to fragrant compounds.  Many of the fragrant compounds in the needles are likely to be in a liquid-like state and not cross polarize very well.  These will either be absent or under-represented in the CPMAS spectrum.  The top panel of the figure shows the 1H - 13C HSQC spectrum of a benzene-d6 extract prepared from crushed spruce needles.  The top and left-side projections are the high resolution 1H and 13C NMR spectra, respectively.  This sample is expected to contain all of the benzene soluble compounds.  The spectrum is free of cellulose resonances and shows a mixture of fragrant compounds.
These data don't recover the childhood magic of Christmas but they do bring a little bit of joy to this NMR spectroscopist.

Merry Christmas  

Wednesday, November 18, 2015

NMR Signals in Tuning Curves

The quality of the tuning and matching of an NMR probe on a Bruker NMR spectrometer can be monitored by using the wobble (or "wobb") routine in the TOPSPIN software.  This routine sweeps the frequency using low power and displays a plot corresponding roughly to the absorbance vs frequency for the probe electronics.  If the probe has very high sensitivity (eg: a cryoprobe) and contains a sample rich in protons (eg: water) then one is able to observe the proton spectrum in the frequency swept wobble curve.  This is demonstrated in the figure below which shows wobble curves for a 600 MHz cryoprobe containing a sample of water.
The curves show the tuning profile of the probe with an anomaly at the proton frequency.  The anomaly is the proton signal of the water in the NMR probe. The top panel is the wobble curve for the probe in a well-shimmed magnet and the bottom panel is the same curve after the magnet shims had been grossly maladjusted.  One can see that the anomaly is much more broad in the wobble curve collected on a poorly shimmed magnet as one would expect the signal from the water to be much broader in an inhomogeneous magnetic field.

Thank you to Stan Woodman of Bruker Canada for pointing this phenomenon out to me.

Wednesday, June 24, 2015

Radiation Damping and Pulse Calibration

Radiation damping causes broadening in the NMR resonances of very strong signals (such as the 1H signal of pure water) as a result of currents induced in the coil from the strong transverse magnetization.  Radiation damping can also produce asymmetry and phase irregularities in the affected resonances.  These problems make pulse calibration by the standard nutation curve problematic when very strong signals are used for the calibration.  The left-hand panel (black) of the figure below shows the standard 1H nutation curves for 0.1% H2O in D2O (bottom) and 80% H2O in D2O (top).  In both cases, single-scan spectra with a recycle delay of 30 sec were collected and plotted horizontally.  The pulse was varied from 1 µsec to 24 µsec in steps of 1 µsec.  In the case of 0.1% H2O in D2O, the nutation curve is well behaved and one is easily able to read off the 90°, 180°, 270° and 360° pulse durations.  In the case of 80% H2O in D2O, where radiation damping is a problem, the nutation curve is not well behaved.  There are asymmetry and phase distortion problems which make it impossible to determine the 90° pulse, based on maximum signal height, with any accuracy.  Nor is it possible to determine a reliable 180° based on the first minimum.  The spectra show very little distortion in the vicinity of the second minimum so the 360° pulse can be used reliably to determine the 90° pulse.  The right-hand panel of the figure (red) shows the integrals of the corresponding nutation spectra.  The integrals for both samples behave similarly.  It is clear that even in the case of severe radiation damping, one is able to determine a well behaved nutation curve from the integrals.

Friday, May 8, 2015


The chemical shift resolution and sensitivity of NMR generally benefit from an increase in magnetic field strength.  As a result, large sums of money are spent on magnets with higher and higher fields.  The boost in sensitivity means that smaller and smaller quantities of sample are needed and measurements can be completed in shorter periods of time.  There are particular cases however, where an increase in magnetic field can lead to a loss of sensitivity and resolution.  This is the case for 15N decoupled 1H spectra of the 1H-15N spin pairs in very large 15N labelled proteins.  The very long correlation times of the protein combined with the high resonance frequencies associated with high field strength lead to very short T2 relaxation times and therefore broader lines.  The broad lines account for a significant loss in resolution and sensitivity.  One might then wonder why protein structural chemists spend so much money on very high field magnets.  What follows is one possible answer to this question.

The two main relaxation mechanisms for the 1H and 15N in proteins are dipolar coupling and chemical shielding anisotropy.  These two mechanisms are also cross correlated with one another.  The cross correlation term is of different sign for each of the two peaks in a 1H-15N doublet resulting in one of the peaks of the doublet having a shorter T2 (and broader line) than the other one.  If 15N decoupling is applied, one sees a single resonance with a line width determined by the average of the two components of the doublet.  This is illustrated in the figure below for a 1H-15N spin pair in a small and large molecule at high field .  The same is true in the 15N-1H doublets in the 15N spectra of 15N-1H spin pairs.
At very high fields, One of the lines in the 1H-15N doublet is very sharp and the other very broad.  If, in the 1H spectrum of a protein, we could eliminate all of the broad doublet components leaving only the sharp ones, we would have a high resolution 1H spectrum.  Further, if we could combine such a measurement with an HSQC, we would have a high resolution 1H-15N HSQC at high field.  The combination of these two measurements is called transverse relaxation optimized spectroscopy (TROSY).  TROSY data collection employs an HSQC measurement with neither 1H nor 15N decoupling elements (as described in a previous post) as well as other elements which suppress the broad lines of the doublets and retain the sharp lines.  The results of this are illustrated in the figure below for small and large proteins at high field.
Clearly, it is not advantageous to use the TROSY technique on small proteins rather than the conventional HSQC.  For large proteins at high field however, there is a significant sensitivity and resolution advantage compared to a conventional HSQC.  It should be noted that the TROSY cross peaks are shifted by ½ 1JHN in both the F2 and F1 domains.  The figure below shows a superposition of a conventional HSQC (black) and a TROSY (blue) for a protein at 500 MHz.
One can clearly see the ½ 1JHN shift in the F2 and F1 domains of the TROSY compared to the HSQC.  In this case, the conventional HSQC gives higher sensitivity than the TROSY.

Thank you to Adam Damry of Professor Roberto Chica’s research group at the University of Ottawa for providing the sample of 15N labelled protein.

Wednesday, May 6, 2015

Decoupling in 2D HSQC Spectra

HMQC and HSQC NMR data are commonly used to correlate the chemical shifts of protons and 13C (or 15N) across one chemical bond via the J coupling interaction.  The data are 1H detected, with the 1H chemical shift in the horizontal F2 domain and the 13C (or 15N) chemical shift in the vertical F1 domain.  In the case of 1H and 13C, the technique depends on protons bonded to 13C.  1H–12C spin pairs provide no coupling information and are suppressed by the method.  If one is to observe the 1H signal of a 1H-13C spin pair, one expects to observe a doublet with splitting 1JH-C (i.e. the 13C satellites).  Likewise, if one is to observe the 13C signal of a 1H-13C spin pair, one expects to observe a doublet with the same splitting.  2D HSQC spectra are normally presented with both 1H and 13C decoupling yielding a simplified 1H-13C chemical shift correlation map over one chemical bond.  The figure below shows one of the most commonly used gradient HSQC pulse sequences.  The 1H and 13C decoupling elements of the sequence are highlighted in yellow and pink, respectively.
During the evolution time, t1, the 13C chemical shift and 1H-13C coupling evolve.  The 1H 180° pulse (color coded in yellow) in the center of the evolution time refocuses the coupling and as a result decouples protons in the F1 (13C) domain of the spectrum.  13C is broadband decoupled from the F2 (1H) domain by applying a GARP pulse train (color coded in pink) at the 13C frequency during the collection of the FID.  One can turn each of these elements “on” or “off” for data collection.  The figure below shows the 1H-13C gradient HSQC spectrum of benzene with all possible combinations of 1H and/or 13C decoupling.
In the top left panel both 1H and 13C decoupling are turned “on” and one observes a singlet in both the F2 (1H) and F1 (13C) domains.  In the top right panel, the 1H decoupling element is “on” while the 13C decoupling element is “off”.  The result is a 1H-13C doublet in the F2 (1H) domain and a singlet in the F1 (13C) domain.  In the bottom left panel, the 1H decoupling element is “off” while the 13C decoupling element is “on”.  The result is a 13C-1H doublet in the F1 (13C) domain and a singlet in the F2 (1H) domain.  In the bottom right panel, both the 1H and 13C decoupling elements are “off”.  The result is a 1H-13C doublet in both the F2 (1H) and F1 (13C) domains.

Tuesday, April 28, 2015

Dead Time and Phase

The phase of an NMR peak depends on the sine/cosine character of the free induction decay (FID) when the receiver is turned on.  Positive and negative cosine FIDs will yield positive and negative in-phase peaks, respectively whereas positive or negative sine FIDs will yield peaks 90° out of phase.  FIDs that are neither a pure sine nor pure cosine with yield peaks which are out of phase to an extent dependent on the cosine/sine character of the FID.  In a perfect world, the receiver is gated on immediately after a perfect 90° pulse and all FID’s are cosines producing positive in-phase NMR peaks.  In the real world however, there are problems with acoustic ringing, pulse breakthrough imperfect pulses of finite duration and finite electronic switching times.  These problems produce a dead time between the end of the pulse and time at which the receiver is gated on during which data cannot be collected.  As a result the FID may not be a perfect cosine function and a phase correction will need to be applied after Fourier transform.  The first two figures below illustrate this point for a single off-resonance NMR signal as the dead time is increased.  The first figure shows the FID’s as a function of increasing dead time from bottom to top while the second figure shows the Fourier transformed spectra without phase correction as a function of dead time from left to right.
When there is more than one signal, the FID is an interferogram representing the sum of all time domain signals, each with a different frequency.  Since each component has a different frequency, its phase is affected to a different extent as a result of the dead time.  Higher frequency time domain components  (i.e. those representing peaks further off-resonance) are affected more than lower frequency components (i.e. those representing peaks closer to being on-resonance).  This is illustrated in the figure below for the 1H NMR data for p-xylene.  The left-hand portion of top panel of the figure shows the FID containing both methyl and aromatic components while the right-hand portion of the top panel shows an expansion of the initial portion of the same FID.  The bottom panel of the figure shows a stacked plot of the NMR spectra collected as a function of dead time.  One can see that the phase of the aromatic peak furthest off-resonance is affected to a greater extent by an increased dead time than the methyl peak closer to resonance.
The last figure also shows a stacked plot of the 1H NMR spectra of p-xylene as a function of dead time.
In this case, the methyl signal was set on-resonance.  One notices immediately that the phase of the on-resonance methyl peak is unaffected by an increase in the dead time whereas that of the off-resonance aromatic peak is severely affected.  The on-resonance methyl peak is not affected by an increase in dead time as its time domain signal is a simple exponential with no sine/cosine oscillations.  A loss of the beginning of a simple exponential FID due to the dead time still leaves a simple exponential and thus the phase is not affected.

Thank you to Dr. Michael Lumsden of the NMR Facility of Dalhousie University for suggesting the subject of this post.

Friday, April 17, 2015

The Information Content of an FID

The free induction decay (FID) is a function representing the decay of transverse magnetization as a function of time after the application of a pulse (or pulse sequence).  The NMR spectrum is obtained by Fourier transforming the FID.  All of the information in the NMR spectrum (line width, intensity, phase, line shape ....) is contained in the FID.  Knowledge of what part of the FID represents a particular property of an NMR spectrum allows a user to process the raw time domain data in a way that maximizes the quality and information content of the processed frequency domain spectrum.  The figure below shows the real component of the complex FID for a sample in which there is a single resonance.  The FID is labelled in terms of its information content.
The shape of the envelope of the overall decay defines the line shape of the NMR resonance.  Exponential decays yield Lorentzian line shapes.  The frequency in the FID represents the offset of the resonance from the carrier frequency or in other words, how far the resonance is from the center of the spectrum.  The higher the frequency, the further off-resonance the peak.  The FID for an on-resonance peak is a simple decaying exponential with no oscillation frequency present.  The first point of the FID contains the integrated intensity and phase information.  Since time and frequency are reciprocals of one another, the duration of the decay before it disappears into the noise determines the sharpness of the NMR resonances and ultimately the resolution in cases where there is more than one resonance in the spectrum.  The longer the decay - the narrower the lines.  The early portion of the FID (short time) defines the broad features (wide frequency distributions) whereas the the latter portion of the FID (long time) defines the sharp features (narrow frequency distributions).  Also, since the FID is a decaying function, the early portion has a higher signal-to-noise ratio than the latter portion.  With this knowledge its is very easy to understand how best to apply apodization functions to the raw data for the purpose line broadening and resolution enhancement.  Processing techniques such as zero filling, forward linear prediction, backward linear prediction and signal-to-noise optimization as well as spectral artifacts such as truncation errors, baseline roll and receiver saturation errors are easily understood with knowledge of the information content in the FID.   

Wednesday, April 1, 2015

NMR of Edible Oils

NMR spectroscopy is one of the most informative techniques for the study of structure, composition and dynamics of matter.  One of the many thousands of applications of NMR spectroscopy is in the study of edible oils.  Plant and animal oils are composed of complex mixtures of fatty acid tri-esters of glycerol.  The fatty acid moieties are generally straight chains of 16 - 24 carbons in length with various degrees of unsaturation.  In natural oils the double bonds are all cis-.  Fatty acids with trans- double bonds are usually the result of food processing.  The double bonds in polyunsaturated fatty acids are generally separated by single methylene groups.  The end methyl carbon of each fatty acid chain in the glycerol tri-esters is referred to as the omega position.  Omega-3 fatty acids are those with a double bond on the third carbon from the omega methyl position.  The most common omega-3 fatty acid in plant oils is α-linolenic acid (ALA), a C18 acid with three cis- double bonds in the 9-, 12- and 15- positions.  Two of the most common omega-3 fatty acids in marine oils are eicosapentaenoic acid (EPA), a C20 acid with five cis-double bonds in the 5-, 8-, 11-, 14-, and 17- positions and docosahexaenoic acid (DHA), a C22 acid with six cis- double bonds in the 4-, 7-, 10-, 13-, 16- and 19- positions.  The human body benefits from EPA and DHA which are only inefficiently synthesized from ALA in the human body.  Also, it is recommended that consumption of saturated oils should be limited and that polyunsaturated oils are a better alternative.  With these concerns, the study of edible oils has become important.  One might expect that the complexity of the mixtures constituting the natural edible oils would limit the usefulness of NMR as a method of study however; the spectra contain a great deal of information as can be seen in the figures below.  The 13C NMR spectra of 4 plant oils and 1 commercial “wild fish” oil are shown in the first figure.
The olefinic carbons are color-coded in yellow and give an indication of the degree of unsaturation in the oils.  Clearly, the coconut oil is saturated and the fish oil contains the highest degree of unsaturation.  The 1H NMR spectra of the same oils are shown in the second figure.
The resonances color-coded in yellow are those of the protons on olefinic carbons and are a direct indication of the degree of unsaturation.  The resonances color-coded in pink are methylene protons on carbons adjacent to two olefinic carbons and represent the degree of polyunsaturation.  The resonances color-coded in blue are methylene protons attached to carbons adjacent to both methylene carbons and olefinic carbons.  The methyl resonances are at the lowest chemical shift.  Those color-coded in green are from the omega-3 fatty acid moieties.  Qualitatively, from the data, it is obvious that the coconut oil is saturated and the fish oil contains the most omega-3 polyunsaturated fatty acid moieties.

Tuesday, March 31, 2015

Cross Polarization Based Mixture Resolution in Solids

One of the most common techniques used to collect solid-state NMR data for spin I = ½ nuclides is a combination of cross polarization (CP) and magic angle spinning (MAS).  CPMAS provides high sensitivity from the CP and high chemical shift resolution from the MAS.  Furthermore, the scan repetition rate depends on the shorter relaxation time of the protons rather than the longer relaxation time of the spin I = ½ nuclide therefore, more scans can be collected per unit time.  It must be remembered however, that the success of the CP technique depends on the dipolar coupling interaction between proximate protons and the nucleus being observed.  In the absence of dipolar coupled protons, CP signals are not observed.  For this reason, it is sometimes necessary to use a conventional one-pulse method (Bloch decay) which can be used to observe the spin I = ½ nuclide, albeit with lower sensitivity, whether protons are present or not.  When a sample consists of a mixture with some protonated components and some components without protons, then it may be advantageous to collect both a CPMAS and a Block decay spectrum.  When both methods are used, the data can be used to resolve the spectrum of the mixture into subspectra; the protonated components in one spectrum and those components without protons in another.  An example of this is shown with the 13C NMR data for a common antacid tablet in the figure below.

The two most abundant carbon containing components of an antacid tablet are calcium carbonate and sucrose.  Spectrum (a) is the CPMAS spectrum.  It consists only of the resonances of sucrose (color coded in yellow) since calcium carbonate (color coded in pink) contains no protons.  Spectrum (b) is the Bloch decay spectrum with high power proton decoupling.  It consists of both the resonances of sucrose and calcium carbonate.  Spectrum (c) is a linear combination of (a) and (b) and represents, primarily, the spectrum of calcium carbonate.  Another interesting example of CP based mixture analysis is given here using Christmas shortbread cookies as an example.

Thursday, March 26, 2015

Mixture Resolution in 13C CPMAS NMR

The recycle delay necessary to get the highest signal-to-noise ratio in a multi-scan 13C CPMAS NMR spectrum depends on the relaxation properties of the protons in the sample.  The protons in pure solid samples normally belong to a single homogeneous dipolar coupled network.  As a result, all of the protons in the coupled network have a common T1 relaxation time.  One would expect the same behavior for a mixture of compounds only if the components were mixed at the molecular level.  If the compounds are not mixed at the molecular level, the sample consists of domains of pure materials, each of which has a common proton T1.  If the proton T1's of the domains are significantly different, then one has a means of discriminating between the domains and hence the compounds of the mixture with 13C CPMAS NMR data.  The figure below illustrates this principle for a tablet of vitamin C ground into a powder.  The vitamin C tablet consists primarily of ascorbic acid for which the structure is shown in the figure.  The other major solid organic additives are hypromellose (hydroxypropyl methylcellulose), stearic acid (n-C17H35COOH), magnesium stearate and carnauba wax (a complex mixture of C26 to C30 acids, esters and alcohols).  When the tablet is ground up, the powder consists of ascorbic acid domains, stearic acid domains, magnesium stearate domains and carnauba wax domains.

13C CPMAS NMR spectra were acquired with a 30 second and a 2 second recycle delay and are shown in (a) and (b), respectively.  One can see that relative intensity of the components in the mixture depends on the recycle delay.  The proton T1 of the ascorbic acid is obviously longer than that of the other components of the mixture.  The spectra in (c) - (e) are linear combinations of (a) and (b).  The linear combination in spectrum (c) was created such that the ascorbic acid resonances were nulled.  The resulting spectrum is that of only the organic additives. The hypromellose resonances are in the 50 ppm to 110 ppm range.  The aliphatic resonances of the stearic acid, magnesium stearate and carnauba wax overlap in the 10 ppm to 50 ppm range and appear to have similar proton T1's.  The linear combination in spectrum (d) was created such that the aliphatic stearic and wax resonances were nulled.  The resulting spectrum is that of ascorbic acid and the inverted spectrum of the hypromellose.  The linear combination in spectrum (e) was created such that the hypromellose resonances were nulled. The resulting spectrum is that of the ascorbic acid with the stearic acid, magnesium stearate and carnauba wax additives.  This combination allows observation of the ascorbic acid with no overlapping resonances from the additives.

Wednesday, March 25, 2015

13C NMR of Vitamin C - Solids vs. Liquids NMR

In 13C[1H] NMR spectra of liquids, one observes a single resonance for each symmetrically nonequivalent carbon atom.  The same is true of the 13C CPMAS spectra of solids.  The difference is that the molecular symmetry is the determining factor in liquids NMR whereas the crystallographic symmetry is the determining factor in solids NMR.  As a result, solids NMR can give different spectra for different solid polymorphs and multiple resonances due to multiple nonequivalent molecules in the asymmetric unit of the crystal structure.  The figure below compares the solids 13C CPMAS and liquids 13C[1H] NMR spectra of a vitamin C (ascorbic acid) tablet.

The structure is provided in the figure and the assignment for all of the carbon atoms is color coded.  In the liquids spectrum, one observes resonances for each carbon in the molecule.  In the 13C CPMAS spectrum, one observes that three of the six 13C resonances are doubled.  This doubling is consistent with there being two nonequivalent ascorbic acid molecules in the asymmetric unit of the crystal.  Presumably, the other three resonance are doubled as well but there is insufficient resolution in the spectrum for this observation.  The broad features in the spectrum are due to additives in the vitamin C tablet which include, hypromellose, stearic acid and carnauba wax. 

Wednesday, March 4, 2015

BLOG Index

University of Ottawa NMR Facility BLOG INDEX
March 2015

               H20 vs D2O
1D selective HOESY
               for exchanging roramers
1D TOCSY measurements
               as a function of mixing time
               for mixture analysis
1H NMR with X nucleus decoupling
2D correlation spectroscopy (COSY)
               11B COSY
               COSY 90 vs COSY 45
               double quantum filtered
               ECOSY for measurement of coupling constants
               magnitude vs phase sensitive
               vs TOCSY
               and NOE (1)
               and NOE (2)
               better data – more scans or more slices?
               data apodization
               phasing (video tutorial)
2D NOESY measurements
               19F NOESY
               and exchange (1)
               and exchange (2)
               choice of mixing time
               effect of viscosity
               phasing (video tutorial)
               small vs large molecules
               HSQC - TOCSY
               TOCSY vs COSY
2H NMR of liquids
               chemical shift referencing in
               on Bruker AVANCE spectrometers
               backward linear prediction to correct for
               pulse sequence to minimize
ASCII file generation
               in TOPSPIN (1)
               in TOPSPIN (2)
Background signals
               from dirty NMR probe
Background suppression
               11B in liquids
               11B in solids
Baseline correction
               in 2D NMR spectra
               in solids MAS spectra of quadrupolar nuclides
Benchtop NMR
Chemical exchange agents for spectral simplification
               D2O shake
               trifluorocaetic acid
Chemical shift referencing
               1H in aqueous solution
               in 2H NMR
Chemical shift tensors
               and MAS sideband manifolds (1)
               and MAS sideband manifolds (2)
               from static CP spectra
               measurement from static solids spectra
Chemical shifts
               concentration dependent
               temperature dependent
Concentration gradients
               effect on spectral quality (1)
               effect on spectral quality (2)
               13C – 14N
               13C – 19F
               13C – 2H (1)
               13C - 2H (2)
               13C – 2H (3)
               13C - 59Co
               signs of coupling constants vis ECOSY
               CPMAS of household dust
               effect of contact time
               effect of MAS spinning speed
               importance of Hartman-Hahn match
               in relation to MAS and high power decoupling
               measurement of 13C 90 degree pulses with
               measurement of relaxation times with
               optimizing 1H decoupling in
               ramped contact pulses
               sensitivity improvement from
               to distinguish solid polymorphs
               vs Bloch decay
               with FSLG HETCOR
               as an assignment tool
               effect of spinning speed
               with long dephasing delays (1)
               with long dephasing delays (2)
Decoupler pulse calibration
               in liquids
               in solids
               1H and 31P decoupling
               1H decoupling and 13C signal-to-noise ratio
               1H decoupling and 31P signal-to-noise ratio
               11B decoupling
               13C decoupling
               19F decoupling
               2H decoupling
               27Al decoupling
               31P decoupling
               high power 1H decoupling in solids
               homonuclear decoupling
               modes of heteronuclear decoupling in liquids
               and quaternary alkyne carbon sites
               APT vs DEPT 135
               effect of 1H tuning on
               missing signals in
               of “acetone-d6”
               of “perdeuterated “ solvents
               vs DEPTQ
               with 29Si
               vs DEPT
Diffusion and DOSY
               diffusion in CPMG measurements
Dynamic processes studied by 1D NMR
               exchange studied by saturation transfer
               exchanging rotamers
               the NMR time scale
               Fourier transform of
               gradient spin echoes and selective excitation
               simple spin echo
               to remove 11B background in solids
               tutorial video
               tutorial video
Floor vibrations
               effect on NMR spectra
Food and drink
               candy cane
               fruit cake
               rum and eggnog
               shortbread cookies
Free induction decay
               effects of truncation
HMBC experiments
               HMQC responses in HMBC spectra
               measuring  19F – 13C coupling in 1H - 13C HMBC
               missing signals in              
               Nyquist fold-backs in
HMQC, HSQC and edited HSQC experiments
               1H – 11B
               19F – 13C
               31P -109Ag
               31P – 13C
               doubled signals / poor decoupling
               HMQC vs HSQC
               HSQC - TOCSY
               HSQC vs edited HSQC
               isotope effects in 19F – 13C HMQC
               removing t1 noise in
               Bloch-Siegert shifts
               broadband 1H decoupled 1H spectra
iPad / iPhone apps
               Bruker Almanac
Isotope effects
               complexed solvents
               in 19F – 13C HMQC
               methylene chloride
               “perdeuterated” solvents
               triphenyl phosphate
Linear prediction
               backward LP to correct for receiver overload
               forward LP for 2D data
               consequence of locking on the wrong solvent
               how high should the lock signal be?
               paramagnetic samples
               spectra acquired with a sweeping field
               spectral distortion from weak lock signal
               1H MAS
               and available rf field
               effect on Hartman-Hahn match
               field dependence of chemical shift resolution
               how fast to spin
               how much sample
               increasing signal-to-noise ration in
               setting the magic angle (1)
               setting the magic angle (2)
               solution vs MAS spectra
               rotor crashes
               accessing a used magnet
               measurement of field drift
Magnet cryogen fills and spectral quality
               helium fills
               helium one-way valve oscillation
               nitrogen fills
               nitrogen pressure in the magnet
Magnetic resonance imaging (MRI)
               gradient calibration / 1D MRI
               MRI photocopier
               Nyquist fold-backs in MRI images
               slice selection
               why MRI scanners are loud
NMR of more than one isotope
               23Na and 51V
NOE’s and decoupling
               negative NOE’s and decoupling
               positive NOE’s and decoupling
               and digital filtering
               and mode of data acquisition
               in HMBC data
               in MRI
               13C spectra of paramagnetic compounds
               determination of paramagnetic susceptibility
               paramagnetic shifts
               the effect of paramagnetic oxygen
               first order phase errors
               phasing a 1D spectrum (video tutorial)
               phasing a 2D spectrum (video tutorial)
               broadband vs inverse broadband
               coil geometry
               why so expensive
               effect of 1H tuning on 13C spectra
               effect of cable length
               effect of sample spinning
               effect on 90 degree pulse
               probe electronics
               problems with salty samples
               effect of probe tuning
               fast determination
               for shaped pulses              
               for spin I = n/2 quadrupolar nuclei in solids
               expressed in dB Bruker vs Varian
               expressed in Hz  
Pulsed field gradients
               dephasing ability
               gradient spin echoes
               recovery times
               distortions in QCPMG spectra
               for solid state 2H NMR
Quadrature spikes
               how to remove
               finding lost 13C signals
Receiver gain
               and signal-to-noise ratio
               distortion from mis-setting
               effect of paramagnetic oxygen
               faster relaxation time measurements in solids
               T1 anisotropy in solids
               T1 measurement
               T2 CPMG filter to enhance sharp lines
               T2 measurements and diffusion
               T2 vs T2*
               by using benzene as a solvent
Sample limitation
               making the best of
               and signal-to-noise ratio
               broadband 180 degree pulses
               excitation profiles (1)
               excitation profiles (2)
               for selective excitation
               effect of concentration gradients
               effect of sample depth
               effect of sample mixing
               effect of sample volume
               line shapes resulting from bad shimming
               without a lock signal
               1H spin pairs
Solid state 2H NMR spectroscopy
               echoes and Fourier transforms
               increasing signal-to-noise ratio
               measuring spectral parameters
               T1 anisotropy
               to determine molecular motions
               90 degree pulse calibration
               baseline correction
               field dependence
               Fourier transform of a single rotational echo
               satellite transitions
Solvent effects
               improving resolution
Solvent suppression
               absolute water suppression
               double presaturation
               watergate vs presaturation
Spin simulations
               isopropyl groups
               quadrupolar line shapes in solids (QUEST)
               virtual coupling
t1 noise removal in 2D spectra
               heteronuclear (tutorial video)        
               homonuclear (tutorial video)
Triple resonance experiments
               13C [2H][1H]
               13C [31P][1H]
               31P -13C HMQC with 1H decoupling
Variable temperature measurements
               temperature calibration (1)
               temperature calibration (2)
               temperature dependent chemical shifts
               temperature gradients
               variable temperature to improve resolution
Video tutorials
               1D spectrum phasing
               2D spectrum phasing
               exponential line broadening
               EZ NMR
               removing t1 noise from homonuclear 2D spectra
               and throwing away noise