HARVARD UNIVERSITY
DEPARTMENT OF CHEMISTRY & CHEMICAL BIOLOGY
MAGNETIC RESONANCE LAB
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HARVARD UNIVERSITY DEPARTMENT OF CHEMISTRY & CHEMICAL BIOLOGY MAGNETIC RESONANCE LAB
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Q&A Q1. What if the mouse cursor does not move? A1. Check the RESLOG LOG IN/OUT terminal to see if you have logged in to the machine. Q2. What if the command e does not eject the sample? A2. Check to see if the Acquisition window (the one opened with the Acqi button) is open. If it is, close it. If the Acqi window is not opened, you probably need to reset the communication between the SUN computer and the spectrometer console by following A11. Q3. What if the sample does not spin? A3. Eject the sample. Put the reference sample in to see if it spins. If it does, you have a bad tube that you should not use it again. If the reference sample does not spin either, try to clean the spinner with ethanol and Kimwipes. If it is still a problem, see us. Q4. What if the printer does not print? A4. Check to see if it is out of paper. If so, pull the paper tray on the bottom out and fill it with more paper. If not, try to press the reset button on top of the printer. If it still does not work, see us. Q5. What if the machine stuck at AUTO SET GAIN and not collecting data? A5. This happens when the sample concentration is too high. You need to type aa to abort the acquisition, change gain=1 and pw=1. Then type ga to start. If you are running 2D NMR, such as gCOSY, NOESY, you can not change pw; so, you will need to dilute your sample. For gHSQC, gHMQC, and gHMBC experiment, you need only change gain to a value lower by 10 or so. Q6. How do I make sure the integrals in the proton spectrum are reliable for quantitative analysis? A6. To use the integrals for quantitative analysis, you need to pay attention to several parameters before data collecting starts: 1. increase d1 so that it is longer than 5 time the longest T1 (spin-lattice relaxation time) of the observed protons in your compound. (to estimate the T1s of the peaks, follow the procedure here.) 2. change pw to pw90 (pw=pw90) 3. Increase nt so that the spectral baseline noises will not be too large. After data acquisition is done, process the data as usual. Try to define integral regions correctly (you may want to use different starting and ending points to see if the results might differ, then take the average of them) and make sure the baselines on both sides of the integrals are leveled.
Q7. How much sample do I need to get a decent 1D proton spectrum in 10 minutes? A7. about a few mM. Q8. How much sample do I need for getting a decent 1D C13 spectrum within an hour? A8. about 15 mM or more Q9. What if I can not seen quaternary carbons in the C13 spectrum? A9. increase the relaxation delay d1 to 1 or 2 sec. and collect more scans. Q10. What if I only have a few mM of compound and I still need C13 peak positions? A10. Instead of spending days to collect a 1D C13 spectrum, you can try to run a HSQC and a HMBC experiments, which can not only display the chemical shifts of most of the carbons (except those carbonyl carbons that don't have any scalar couplings to any protons), but also determine which protons are directly bonded to which carbons in the molecule. The time needed to run HSQC and HMBC experiments can be shorter than that for a good 1D C13 spectrum by a factor of up to 10. Q11. What if the STATUS shows INACTIVE? A11. You need to reset the communication between the SUN computer and the spectrometer. Method 1: type boot1, wait for 10 second, them type boot2, wait for another 10 second to see if the status changes to IDLE. If Method 1 fails, try Method 2: type boot1, go to the spectrometer console. For M400, M400B, and M300, open the glass door and press the red RESET button. For I500, I500B, and INOVA600, open the left front door, press the small red button right above the Ethernet cable on the left most board. Wait for about 1 minute, and type boot2. Wait for another minute to see if the STATUS changed to IDLE. If Method 2 also fails, see us. |