University of Ottawa NMR Facility Web Site

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



Thursday, October 30, 2008

The Effect of the Contact Time on CP/MAS NMR Spectra

One parameter for CP / MAS data collection that must be set by the user is the contact time during which magnetization is transferred from the abundant nucleus (usually 1H) to the dilute nucleus (e.g. 13C). In the case of the 13C nuclei in organic samples, the build up of magnetization for each type of carbon depends on the extent of the dipolar coupling to the proton network. The extent of 13C - 1H dipolar coupling depends on both the degree of protonation for each type of carbon and any molecular motion (such as methyl group rotation) which may average the dipolar coupling. At longer contact times, the magnetization decays as a function of the T1(rho) of the protons. It should be noted that cross polarization is also affected by MAS. The length of the contact time should be chosen such that all types of carbons have had sufficient time to polarize yet not so long as to loose significant magnetization due to the proton T1(rho). For 13C CP/MAS an appropriate choice is usually between 1 and 10 ms. The figure below shows the effect of the duration of the contact time for the two 13C resonances of glycine. The 50 MHz 13C CP/MAS spectra were run as a function of contact time and plotted side by side. The intensities of each resonance are marked with color coded points. One can see that the carbonyl carbon builds up more slowly than the protonated carbon. An appropriate choice of contact time for glycine is 2 -3 msec.

Friday, October 17, 2008

Kinetic Experiments on Bruker Spectrometers

Students often have to monitor the progress of a chemical reaction as a function of time using NMR spectroscopy. I have written three simple programs for XWINNMR (which should work with little or no modification for TOPSPIN). Each program uses a different method to control the time allowed between collecting spectra. All are very simple and easily implemented. They should be added to the Bruker/XWINNMR/exp/stan/au/src directory. The first two programs, kinetic_ds and kinetic_t, are suitible for slow reactions where precise timing is not critical as they do not take into account the time required to initialize each acquisition. The third program, kinetic_2d avoids the problem by using a pseudo 2d approach and is suitible for faster reactions.

1. kinetic_ds
This program uses dummy scans to control the time allowed between spectra. (A dummy scan is a scan taken without turning on the receiver.) The more dummy scans, the longer the time between experiments. The user should set up the appropriate parameters and then run the program (by typing xau kinetic_ds). You will be asked for the total number of spectra to be collected, the number of scans to be collected for each spectrum and the number of dummy scans to be used in all but the first spectrum. The first spectrum will be collected in the current experiment and the others in subsequent experiments.

/* kinetic_ds */
/* written by Glenn Facey, August 24, 2005 */
/* This program will set up a kinetic run based on the use of dummy scans */
/* The user is asked for the number of spectra, the number of scans for */
/* each spectrum and the number of dummy scans for all but the first spectrum */
/* the first spectrum uses no dummy scans. */
GETCURDATA
GETINT("Enter total number of spectra",i1)
GETINT("Enter the number of scans for each spectrum",i2)
GETINT("Enter the number of dummy scans for all but the first spectrum", i3)
STOREPAR("ns",i2)
STOREPAR("ds",0)
Proc_err(0,"Kinetic Run in Progress");
RGA
ZG
TIMES(i1-1)
IEXPNO
SETCURDATA
STOREPAR("ds",i3)
STOREPAR("ns",i2)
ZG
END
QUITMSG("Data Collection Complete!")


2. kinetic_t
In this program, the user should set up the appropriate parameters and then run the program (by typing xau kinetic_t). You will be asked for the total number of spectra to be collected, the number of scans to be collected for each spectrum and the time in seconds allowed between the end of one acquisition and the beginning of the next acquisition. The first spectrum will collected in the current experiment and the others in subsequent experiments.

/* kinetic_t */
/* written by Glenn Facey, August 24, 2005 */
/* This program sets up and runs a kinetic experiment */
/* The user is asked to input the number of spectra, */
/* the number of scans for each spectrum and the time in */
/* seconds between the end of an acquisition and the */
/* beginning of the next. The program will measure the */
/* receiver gain and start the acquisitions. */
GETCURDATA
GETINT("Enter total number of spectra",i1)
GETINT("Enter the number of scans for each spectrum",i2)
GETINT("Enter the time interval (in seconds)", i3)
STOREPAR("ns",i2)
Proc_err(0,"Kinetic Run in Progress");
RGA
ZG
TIMES(i1-1)
IEXPNO
SETCURDATA
STOREPAR("ns",i2)
ssleep(i3);
ZG
END
QUITMSG("Data Collection Finished")


3. kinetic_2d
This program avoids initialization delays by collecting the data in a pseudo 2D format where each slice of the experiment is a spectrum. The program uses a pulse program called zg30kin.gf (see below) which should be put in the directory Bruker/XWINNMR/exp/stan/lists/pp (This pulse program program should be modified to suit the needs of the user). A variable delay list called kinetic must also be set up. This list contains the same number of lines as the number of spectra to be collected. Each line in the variable delay list defines the time interval (in seconds) to be allowed before each acquistion. The user must set up the appropriate parameters (including the number of scans to be collected for each spectrum) and then run the program (by typing xau kinetic_2d). You will be asked only for the total number of spectra to be collected. The program will set up a pseudo 2d acquisition. Data collection is started with the zg command. The data are processed with the xf2 command.

/* kinetic_2d */
/* written by Glenn Facey, August 24, 2005 */
/* This program sets up a pseudo 2D kinetic run */
/* using the pulse program zg30kin.gf with a Variable */
/* delay list called "kinetic". */
GETCURDATA
GETINT("How many spectra do you want to acquire?", i1)
FETCHPAR("SFO1",&d1)
FETCHPAR("DW",&f2)
FETCHPAR("SW",&d2)
FETCHPAR("SF",&d3)
XCMD("parmode 2D")
XCMD("pulprog zg30kin.gf")
XCMD("vdlist kinetic")
STOREPAR("SFO1",d1)
STOREPAR("DW",f2)
STOREPAR("SW",d2)
STOREPAR("SF",d3)
STOREPAR1("TD",i1)
STOREPAR1("SI",i1)
QUITMSG("Setup Complete!\n1. Define 'VD' List called 'kinetic'.\n2. Run the experiment with 'zg'.\n3. Process data with the 'xf2' command.")


Pulse program zg30kin.gf

;zg30kin.gf
;zg30 modified to run kinetic experiment in pseudo 2D mode
;using VD list
;avance-version (00/02/07)
;1D sequence
;using 30 degree flip angle

#include
"d11=30m"
1 vd
ze
2 d1
p1*0.33 ph1
go=2 ph31
d11 wr #0 if #0 ivd
lo to 1 times td1
exit

ph1=0 2 2 0 1 3 3 1
ph31=0 2 2 0 1 3 3 1

;pl1 : f1 channel - power level for pulse (default)
;p1 : f1 channel - 90 degree high power pulse
;d1 : relaxation delay; 1-5 * T1
;d11 : short delay for I/O

Wednesday, October 8, 2008

Proton Spin Pairs

In the solid state, in the absence of very fast magic angle spinning or homonuclear multiple pulse decoupling schemes, the 1H NMR spectrum of a typical solid is a broad featureless line greater than 50 kHz in width. This is due to the homonuclear dipolar coupling interactions between the many protons present in the system. The situation is different for an isolated pair of protons. For an isolated pair of protons, there is only one dipolar interaction between the protons and the energy level diagram for the system has only three levels corresponding the combination of spin states among the two protons and the dipolar coupling between them. There are two transitions and therefore two resonances. The separation between the resonances depends on the magnitude of the dipolar coupling constant, R, and the orientation of the internuclear vector with respect to the applied magnetic field. For powdered samples where all orientations with respect to the applied magnetic field are represented, one observes a "Pake" doublet. This situation is very similar to the solid state NMR of 2H where, in that case, the three energy levels arise from the Zeeman states of a single 2H nucleus and their coupling to an electric field gradient.

Isolated proton pairs occur naturally in the waters of hydration of inorganic salts and the solid state 1H NMR spectrum is a Pake doublet. The separation between the inner peaks of the Pake doublet is 3/2 R and between the two shoulders is 3R, where R is the dipolar coupling constant. The dipolar coupling constant is directly proportional to the inverse cube of the distance between the protons. Therefore from a single spectrum, one can measure the internuclear separation, r. For the case of the waters of hydration, one can measure the H-O bond length with knowledge of the H-O-H bond angle. The figure below illustrates the Pake doublet spectrum obtained for CaSO4. 2 H2O. The asymmetry in the spectrum is the result of chemical shielding anisotropy and the broadening is the result of dipolar coupling to distant protons.

Tuesday, October 7, 2008

Positive NOE's and the Decision on Which Decoupling Mode to Use

Nuclei with positive gyromagnetic ratios, such as 13C, exhibit positive NOE's with nearby protons. When observing 13C directly with proton decoupling, the intensity of the resonances will be increased to an extent dependant on the magnitude of the NOE's and the amount of time over which they are allowed to build up. When quantitative results are not sought after, it is always best to collect the NMR data with decoupling during both the acquisition time and the relaxation delay so that the effect of the NOE's on the intensity of the lines is maximized. The figure below compares the 13C NMR spectra for formamide collected with inverse gated decoupling (left) and full decoupling (right).
The above spectra were collected at 11.7 tesla with 4 scans, using a recycle delay of 30 seconds and an acquisition time of 2.3 seconds. This effect of positive NOE's on the resonance intensity should be compared to that for negative NOE's.

Monday, October 6, 2008

Negative NOE's and the Decision on Which Decoupling Mode to Use

Nuclei with negative gyromagnetic ratios, such as 15N and 29Si, exhibit negative NOE's with nearby protons. When observing these nuclei directly with proton decoupling, the intensity of the resonances will be decreased to an extent dependant on the magnitude of the NOE's. Usually it is best to collect the NMR data for these nuclei with inverse gated decoupling so that the effect of the NOE's on the intensity of the lines is minimized. There are cases however where the magnitude of the NOE is so large that the intensity of the resonance collected with full decoupling becomes negative and even stronger than that observed with inverse gated decoupling. In such cases it is advantageous to leave the decoupler on 100 % of the time. As the figure below shows, this is indeed the situation with the 15N resonance of formamide where the magnitude of the signal is smaller when inverse gated decoupling decoupling is used.
The above spectra were collected at 11.7 tesla with 4 scans, using a recycle delay of 120 seconds and an acquisition time of 2.3 seconds.

Thursday, October 2, 2008

Dilute "D2O" in Benzene-d6

The 1H NMR spectrum of a mixture of H2O and D2O is a single line at about 4.8 ppm. The H2O and HDO resonances are unresolved in the spectrum due to fast chemical exchange between the isotopomers and possibly line broadening due to radiation damping. When traces of D2O are added to benzene-d6, which already contains traces of H2O, the situation is different. The resonance is shifted by more than 4 ppm to lower frequency compared to the bulk and since the water is now dilute and in small quantities, chemical exchange is slow on the NMR time scale and radiation damping is no longer a problem. The figure below shows the 500 MHz 1H NMR spectrum of dilute D2O in benzene-d6. The isotope shift between H2O and HDO and the HD coupling constant can easily be measured from the spectrum.