01/14/14

One of our spinners modified for heavy NMR tubes has disappeared from the lab. If you have it or know where it is please return it as soon as possible; other users need it.


12/23/13

Remider: The Chemistry building will be closed to non-Chemistry NMR users from December 25th to January 2nd. Have a Merry Christmas break!

UPDATE: The name of the command to reset the password was incorrectly printed as "reset‑password" in the paragraph below. The correct command is "change‑password" as is now shown in the corrected entry below.


12/20/13

On Saturday, January 4th, Information Technology Services will be performing maintenance on the Chemistry Department's servers. This will result in periodic network connectivity issues and the inabilty to access our online scheduler. Network accesss is required for user authentication if you are using your UMich password ("kerberos") when logging in to our computers; but it is also possible to log in using your local password. Although all users have a local password, normally we don't reveal it to you after training because you don't need it. But if you plan to use our instruments on January 4th, you should reset it to avoid problems logging in. To do it, log in before January 4th, open a Terminal window and type "change‑password". You will be asked for your UMich password, and then for your new local password which can be the same UMich password or different. This will not change your university's password but only the password on the computer you are logged in; therefore you must repeat the same procedure on every computer of our lab that you plan to use that day.

The online scheduler will probably be off line on that day so make your reservations ahead of time.


08/16/13

We are now deleting reservations of users that don't show up after 15 minutes of their start time, and writing their names in a black list. REPEATED OFFENDERS WILL BE BANNED FROM THE LAB and their advisors will be notified.


08/02/13

July and August are typically the most heavily used months of the year in the NMR Facility. As such, there is a high demand for NMR time and some users, fearing they may not find empty slots for their work, reserve time even if they are not certain they'll use it. In recent days we have observed long and short reservations being cancelled just a few minutes before they are due to start, or never cancelled at all and the user didn't even bother to show up. We have also seen spectrometers abandoned long before the reservation is over but the reservation wasn't truncated when the user decided to end his experiment. All of this produces a lot of wasted instrument time that many users really need and it is inconsiderate to all other users.

Please be kind and remember the Facility rules:

Please let us know of any offenders to the rules.


05/31/13

The Inova-400, located in room 2407, is now available for research.   Use the NMR Lab key to open the door.  Signup rules are: Mon-Fri from 9 am to 9 pm 2 hours maximum; unlimited time after 9 pm or during the weekend.


08/29/13

The "OneProbe" for Tellurium is back.


08/06/13

The HFX probe in Tellurium is showing a considerable error in the measured temperature. The error increases as the temperature is moved away from ambient. Use the calibration chart on the desk to get a more accurate value.


07/16/13

Tellurium's default probe, the “One”, is broken.
The HFX probe is now installed. This probe has about the same sensitivity for 1H and 19F as the One, but a reduced sensitivity for 13C or any other nucleus (similar to Cobalt's).
Variable temperature (-80º to 130ºC) is possible. Tune X-nuclei as usual. Tuning to proton or fluorine requires manual tuning. Please ask the staff for instructions.


06/19/13

Gallium's autoxdb (default) probe is back.


05/31/13

The Inova-400, located in room 2407, is now available for research.   Use the NMR Lab key to open the door.  Signup rules are: Mon-Fri from 9 am to 9 pm 2 hours maximum; unlimited time after 9 pm or during the weekend.


05/16/13

Gallium's default probe is broken and has been shipped for repairs. The autoxid probe is now installed. This means:
     1- Fluorine spectra is not possible.
     2- Increased proton sensitivity.
     3- Decreased X-nucleus sensitivity.


11/08/12

As you may know, a modified login prompt is now implemented in the spectrometers. The idea behind this is to automate our accounting with always current short codes. After you enter your short code, your next login will show the last one used and all you need to do is confirm it. If you changed advisor or switched to another code all you need to do is enter the new one and all instruments will continue using the new one. Very simple. If you don't already know your code you will be able to use the spectrometers three more times. After that you will be required to enter a code or you won't be able to log in.


10/31/12

To facilitate our accounting, starting on November 5 users will be required to enter a valid short code when logging in to the spectrometers.


09/24/12

The default probe (autoxdb) of Gallium is back. Fluorine-19 can be done again.


09/14/12

The problem in the low frequency channel of Cobalt has been fixed. Cobalt is back to normal operation.


09/12/12

The Inova-400 (Zirconium) is no longer available for research.


07/30/12

Gallium's autoxdb probe just broke. The autoxid probe has been installed and will be used until the default probe is repaired. This means F19 is no longer possible and C13 and all other nuclei except proton have lower sensitivities.


07/10/12

Effective immediately our Inova 400, normally used in teaching, is now available for research. It is located in room 2407 and can do only H1, F19, C13 and P31 without re-tuning. Its temperature range is -20 to +80 C. A cooling unit (FTS) is attached to provide low temperatures without liquid nitrogen. Same reservation rules for Gallium will apply (1 hour maximum from 9 am to 9 pm;). If you need low temperature, please ask us first how to operate the FTS.

The Inova 400 will be available only during the summer.


03/06/12

Cobalt has developed a problem in the low frequency channel. Fluorine and proton spectra, including two-dimensional homonuclear spectra like noesy and cosy are fine. 1D carbon and phosphorus spectra should also be ok, but heteronuclear 2D experiments like HMQC, HSQC or HMBC won't work correctly.


06/20/12

The default probe of Ytterbium (autoxbb) is back.


06/04/12

The default probe of Tellurium (OneProbe) is back.


05/23/12

It appears we are having a run of bad luck! The default probe of Ytterbium (700 MHz) has now developed problems and needs to be repaired. In the interim we have installed the secondary probe, HCN. This probe has much better sensitivity for proton, but can only do H1, C13 and N15 1D and 2D experiments. Any other nucleus has to be done either in Gallium or Tellurium. The sensitivity for C13 is about half of what is was before and about the same as in Gallium. Tuning proton is done with the software. Tuning of C13 or N15 for routine samples shouldn't be necessary, but can be done manually for maxiumum sensitivity with dilute samples. Ask us for instructions if you need to do this.

We expect to have the OneProbe for Tellurium back in about two weeks. .


05/04/12

The default probe of Tellurium has been removed and shipped for repairs. The HFX probe has been installed. This probe has similar sensitivities for H1 and F19 to those of the default probe. However, any other nuclei, like C13 or B11, have lower sensitivity (a bit less than in Gallium). Variable temperature is possible.


04/09/12

The default probe of Tellurium has developed a problem that prevents it from reading the correct temperature. Variable temperature operation is not possible until we resolve the problem; only room temperature is available.


03/06/12

All computers in the lab except the inova-500 have been updated with vnmrj 3.2.


02/22/12

A power shutdown of the 48' building is scheduled for this Saturday 25. The NMR Facility will shutdown all computers and instruments at 9:00 pm Friday 24. Power will be restored Saturday 25 at 6:00 pm.


09/23/11

Effective immediately, the Inova 400 will be used exclusively for teaching and won't be available for research.


09/08/11

The broadband probe (autoxdb) on Gallium is back and has been installed. Fluorine is now possible, and C13 and other heteronuclei have higher sensitivity, but proton has lower sensitivity.


08/25/11

The new version of Vnmrj can produce plots with varying linewidths. But the way in which they are now rendered is incompatible with the way we used to do them with our macros in the lab. The linewidth is now controlled with the parameter pslw which can have an integer value starting at 1. The default value is 2. To plot with a larger linewidth (for presentations) increase its value before you start plotting (for example: pslw=5). The new value will be used in all the plots until changed or until vnmrj is restarted. For consistency, all computers are now using this scheme.


08/25/11

The Experiment Guide is now available in Vnmrj's Help menu.


08/17/11

One of the new features of Vnmrj 3.1 is the ability to perform proton-fluorine experiments without the need of a second high-band channel. All that is needed is a probe that can be double-tuned to both 1H and 19F such as the quad probe currently installed in Cobalt. This probe has been calibrated and it is now possible to run proton observe with fluorine decoupling 1H{19F}, fluorine observe with proton decoupling 19F{1H}, HF-HOESY and HF-HETCOR experiments in Cobalt. The sensitivity of this probe is not as good as the one for the HFX probe of Tellurium but it is easier and faster to use as there is no probe change or tuning needed. Just select from the menu the experiment that you want and you will be ready to go. Well, almost... Broadband decoupling of fluorine is able to decouple at most a region about 20 ppm wide, so it is better to center the decoupling in the region of interest. This can be done in the Acquire > Pulse Sequence panel.


08/15/11

Lately we have noticed that some users make long reservations but don't always come to use the intruments or don't even cancel or truncate them. Instrument time is very valuable and most users are anxiously waiting for time to perform their experiments (see News 07/06/11). Please don't waste our resources. Please report the abusers. Repeat abusers will be banned from the Facility.


08/09/11

Agilent has just published a new manual: the Experiment Guide . The purpose of this document is to provide more information about the small-molecule liquids experiments available in the VnmrJ 3.1 experiment selector. Included are descriptions of all the experiments in the Experiment Selector (excepting DOSY-type), their utility, guidance on parameter selection, processing, and references for further reading. This manual was written for the chemist who wants to know what experiment is best for his/her purposes. Each experiment is covered in detail; the pulse sequence, important parameters and how to set them, processing, and literature references are all laid out in an easy-to-read format to help you get the experiment set up and pulsing in no time. Also included is a section called “Tips, Tricks, and Next Steps.” These are little bits of wisdom from veteran users of the pulse sequences to help you getting the best results. The Experiment Guide can be downloaded from Agilent's web site.


07/29/11

As most of you already know, we have recently updated Vnmrj in the NMR Lab's computers. The only exceptions are the Inova 500 and Inova 400 which are not supported by the new version. This new version, 3.1, is an important update with many enhancements. Of interest to most users are:

As usual after a mayor update, the software will show new quirks that the users need to get used to, so please be patient and attentive. Please let us know if you have difficulties with the software.

For a full description of all the new features please read the release notes. Please consult with the staff if you are interested in any of these new features as some of them may require new calibrations that haven't been performed yet.



07/08/11

In order to reduce the load from Tellurium our old Inova 400, currently used in teaching, is now available for research. It is located in room 2407 and can do H1, F19, C13 and P31 without re-tuning. The temperature range is -20 to +80 C. A cooling unit (FTS) is attached to provide low temperatures without liquid nitrogen. Same rules for Tellurium will apply. If you need low temperature, please ask us first how to operate the FTS. And if you cannot log in the computer, please let us know as some user accounts may need to be created.

The Inova 400 will be available only during the summer.


07/06/11

It is that time of the year again! Yes, it is summer and the demand for instrument time has increased. So, now is a good time for a remider. We have one walkup instrument that is available 24/7 for most quick or routine spectra; two spectrometers for short and medium term experiments and two more instruments for long term and detailed experiments. With these policies, and the spectrometers' different capabilities we try to address the needs of all users in the Department. Tellurium is now very popular for long experiments, as it should be. If you need their features, please plan ahead and reserve your time in advance. And if you can do your long experiment in Ytterbium, please do so: you will spread the load and make Tellurium more accesible.


05/13/11

The autoxdb probe in Gallium is broken (again!) and has been sent for repairs. The autoxid probe has been installed in its place. That means: no fluorine, higher proton sensitivity and reduced X sensitivity.


04/04/11

The autoxdb probe (the one that used to be installed in Cobalt) is back and has been installed in Gallium. So far, the following nuclei have been calibrated: H1, F19, C13, P31 and B11. Other nuclei will follow in the next few days.


03/31/11

Our new VNMRS-700 spectrometer, Ytterbium, is now open for business. The default probe has the highest sensitivity in the lab for C13 and other heteronuclei (about twice as high as in any other spectrometer) and the sensitivity for H1 is higher than on the Inova-500 and almost as high as that on Tellurium. With this probe, Ytterbium is the best choice for C13 measurements. The secondary probe is a H/C/N triple resonance probe meant for biomolecular experiments and the H1 sensitivity is almost three times higher than anything in the lab. This makes it the best option for proton and most 2D spectra of very diluted samples. The high field dispersion will certainly be a major advantage in the analysis of complex spectra of large molecules. The major shortcoming to keep in mind is that Ytterbium can not measure F19.

Ytterbium still smells like new and we want to keep it that way for as long as possible. Be extra careful when inserting tubes in the spinner (do it away from the keyboard or the desk in case the tube breaks), and when inserting or retrieving the sample in the magnet. Ask the staff for details when using it for the first time.

At this point, we are going to modify the instruments' rules of usage as follows:

1- Ytterbium: The maximum time allowed per user per day during prime time (9 am to 9 pm) will be 5 hours. It can also be used for short term experiments when the field dispersion is needed, but routine (checkup) samples should be measured in other instruments. We will be more flexible with the scheduling of this instrument and authorize longer periods of time when needed by a user. We will grant use of this spectrometer to users who have already had experience with other instruments for at least 6 months. User accounts are not created by default but only upon request. Please ask either of us for approval.

2- Gallium: The maximum time allowed per user per day during prime time (9 am to 9 pm) is now reduced to 1 hour. With this change we pretend to make this instrument more readily available for routine samples. Users who require longer periods of time for other measurements should use it after prime time or use Tellurium or Ytterbium. We expect to have the probe that used to be installed in Cobalt back from repairs soon. With this probe, Gallium will have F19 capability as well as other heteronuclei.

3- All instruments: The hours for overnight use are now 9:00 pm to 9:00 am. We have noticed that the hour from 8 am to 9 am is very frequently not being used and we expect to benefit the use of overnight time with this change. Of course, if a time between 8 and 9 am is not being used, you can reserve it as usual.


03/30/11

The user accounts in Tellurium have been restored. Tellurium can be used again.


03/28/11

The NMR lab had network problems during the weekend. As a result, users were not able to log in to any of the computers in the lab. The problem has now been resolved but it seems that on Sunday at around 5:10 pm someone tried to "repair" Tellurium's computer. As a result, its hard disk was wiped out and all user data was destroyed. Fortunately, we back up the computers every day so we expect the data loss to be minimal. But reinstalling the operating system, vnmrj, and restoring user data is going to take a lot of time and effort. Tellurium will be down until further notice.

If you have information about the responsible person please contact us.


02/07/11

The default probe in the MR400 "Cobalt" is broken and has been sent for repairs. In its place, we have installed the four nucleus probe ("quad") that belonged to the Inova 400. This probe, as you may recall, can measure 1H, 19F, 13C and 31P without the need to re-tune it. We expect that with this probe, Cobalt will meet the needs of most people needing quick, routine spectra. For this reason, starting Tuesday Feb 8, at 8 am, Cobalt will become our new walkup spectrometer and the Inova 500 will go back to its previous scheduled operation.

Users needing other nuclei like 11B or 207Pb, should use Tellurium while the probe is being repaired. Boron-11 can also be easily measured in Gallium. Also, note the temperature limits of the quad probe that should not be exceeded: -20 to +80 Celsius.

When the multinuclear probe comes back, we will install it in "Gallium". Gallium will have the enhanced multinuclear capabilities that Cobalt used to have, and the high proton sensitivity that Gallium used to have will be provided by the 500 and 700 instruments.


01/14/11

Pardon our dust... We are installing our new 700 MHz spectrometer.



Everything was going fine... We were up to about 16 Teslas. But then, we had a quench... And another, and another! :(




Here is a video of the quench. A quench occurs when the main solenoid looses superconductivity. The electric current then generates heat which violently boils the liquid helium in the magnet.




12/13/10

According to Varian/Agilent, our new 700 MHz instrument will be delivered in about a week or two.  To begin preparing the site, the Inova 400 will be decommisioned on Monday, Dec. 6.    Starting on that date, the Inova 500 will be our new walkup instrument.    All usage rules for the 400 will be applied to the 500. Data files in the 400's computer will be available online only for a few weeks for back up purposes. Valuable data files should be transfered to CD or DVD as soon as possible.


10/12/10

The defective part in Tellurium has been replaced, presumably fixing the problem. Please let us know if the problem continues or re-appears.


10/04/10

A problem has developed in Tellurium. The problem is due to a faulty power supply in the pneumatics router and occurs at random, aborting any acquisition in progress. We are waiting for a replacement for the power supply. Tellurium can continue to be used in the mean time but be aware that long acquisitions may stop at any time. The FID is not lost, but will have only the scans collected up to the time of the failure. If the problem occurs, press the Reset Pneumatic Router in the Star, Spin/Temp parameter panel to continue using the spectrometer.


08/12/10

Every year, there are 2 or 3 periods during the year when demand for the NMR spectrometers is at its highest. The end of the summer is one of them and as such, we are currently experiencing a peak in demand. This doesn't happen every day but occurs mostly in the afternoons (there is a lot more time in the mornings) and it will likely go down as the Fall Term starts in September. Users should expect having to wait for NMR time and plan their work accordingly. For those of you who are too impatient to wait or plan ahead, we are setting up the Inova 500 as a secondary walk up instrument Monday to Friday and only from 1 pm to 6 pm. The previous rules still apply outside these hours. This is a temporary measure, and will be effective starting tomorrow Friday 13.

All users should understand that in our Facility we have to balance the needs of those users who require long blocks of time for their experiments (kinetics, low sensitivity nuclei, variable temperature acquisitions, etc) with those who only need frequent short blocks (monitoring of reactions). This is not easy, but everyone certainly deserves the same access. All users should help by planning their NMR times consciously. For example, long, unattended acquisitions can be set up at night or on weekends; and the time in the mornings should be used whenever possible. On the other hand, those users who reserve long periods of time but leave early and do not make the remaining time available by truncating their online reservation, or those who come late at their reserved times, or those who repeatedly make and cancel long reservations, should be treated with contempt and will be penalized.


08/03/10

Our HFX triple resonance probe on the vnmrs-500 (Tellurium) allows us to run H1-F19 correlations. As an example, a H1-F19 HOESY (Heteronuclear Overhauser) is shown below. The spectrum shows through-space correlations between the trifluoro methyl group and the methine, and between the trifluoro methyl group and the two aromatic hydrogens closest to the CF3.



07/15/10

Three write ups have been added: "Using linear prediction", "Solvent suppression with WET and PRESAT" and "Practical guide to quantitative 1D NMR". Check them out in the Documentation page.


06/16/10

Variable temperature operation in Cobalt is functional again.


06/02/10   A brief reminder about safety and hygene.

Please handle your NMR tubes carefully! Most of the tube breakages occur because the user was not careful enough. Do not insert the tubes into the spinners on top of the computer desk or keyboard; do it in the fume hood or away from the desk so that if the tube breaks you won't damage the desk surface or any computer part. This is especially important the more toxic or colored the sample is. You may have noticed all the stains from previous users' negligence. They will stay with us forever as remainders of what not to do. Not only stains look ugly, but sample residues constitute an untolerable danger in a multiuser environment as ours. If a sample breaks, it is the user's responsability to completely pick up all glass pieces and clean the spill so it is completely safe for the next user to touch the keyboard and spinner. Only the user who spills a sample knows how dangerous the material is and how to handle it or wash it away. Broken samples anywhere in the NMR lab should be reported to the staff immediately so we can ensure the spinner, depth gauge and other parts are thoroughly clean inside and outside. Unreported spills, or negligently leaving a contaminated spinner, depth gauge, desk surface or keyboard is a danger to all users and will result the in termination of user privileges.

Please review the updated NMR Facility rules here.


05/27/10

Our new Varian 500 MHz spectrometer, Tellurium, is now open for business. With the default probe, this instrument can measure all common nuclei (H1, F19, C13, P31) and almost any other less common nuclei. So far, the following have been set up: H2, B11, Hg199, Pt195, Cd113 and Pb207; more will be added in the next few days or upon request. Sensitivity for both H1 and C13 is the best that we have so far in our lab. Variable temperature work from -80 to 130 C is possible. With our second probe, it is possible to do H1-F19-X triple resonance experiments, for example an H-F cosy or a H-C hsqc with simultaneous F19 decoupling or a 1D C13 with both H1 and F19 decoupling. Ask the staff for more information. Operation of this instrument is essentially the same as on either Gallium or Cobalt with a few minor differences regarding measurement of non common nuclei. Ask the staff for instructions the first time you want to measure one of these nuclei.

With the addition of this new instrument, we can now change our usage rules to balance the load among instruments and better accomodate your needs. Starting tomorrow, Friday 28, our old Inova 400 will be in walk up mode 24/7. This means, reservations are no longer required. Our old Inova 500 is now open to all users for up to one hour during prime time (8 am to 9 pm). We will install all missing user accounts during the next few days. The new 500 is to be used mostly for experiments requiring long term acquisitions like VT, diffusion, kinetics, heteronuclear nmr, etc. As such, the minimum time it can be reserved is 30 minutes. Most routine, quick 1H, F19, C13, P31 spectra should be done on the Inova 400.

Tentatively, the following rules now apply:

Inova 400:
a) This spectrometer is walk-on (no reservation is necessary), limited to 15 minute time blocks. Use of additional contiguous time beyond 15 minutes is permitted if there is no queue for the machine.

Inova-500:
a) During the prime time hours of 8 am to 9 pm, 10 minute time blocks up to a maximum of 60 minutes per user per day.
b) During the hours of 9 pm to 8 am, 10 minute time slots and unlimited time.
c) Weekends: 10 minute time slots and unlimited time; 24 hour advance reservation for blocks longer than 1 hr.

Gallium-400 and Cobalt-400:
a) During the prime time hours of 8 am to 9 pm, 10 minute time blocks up to a maximum of 3 hours per user per day.
b) During the hours of 9 pm to 8 am, 10 minute time blocks and unlimited time.
c) Weekends: 10 minute time slots and unlimited time; 24 hour advance reservation for blocks longer than 3 hr.

Tellurium-500:
a) During the prime time hours of 8 am to 9 pm, 30 minute time blocks up to a maximum of 5 hours per user per day.
b) During the hours of 9 pm to 8 am, 30 minute time blocks and unlimited time.
c) Weekends: 30 minute time slots and unlimited time; 24 hour advance reservation for blocks longer than 5 hr.

Oh, Tellurium also has a brand new desk, brand new spinner and depth gauge. Please be careful and keep it that way! Do not break your sample tube! If you like breaking tubes and spilling solvents, please dont' do it over the desk or keyboard.


05/26/10

VT on Cobalt MR400 spectrometer not working. Work at ambient temperature is OK.


05/10/10

Over the last weeks, a few handouts have been updated or created. They include "Diffusion NMR", "Kinetics", "Noesy 1D" and "Quantitative NMR". Check them out in the Documentation page.


04/26/10

The operating system of Cobalt was updated to RedHat Enterprise Linux 5.5; vnmrj was updated to version 2.3A. You may notice a few minor glitches, but check with us if you have difficulties.


04/16/10

With the recent decommissioning of the Mercury 300, we are now one spectrometer short. This fact, coupled to this time of the year, has increased the demand for spectrometer time in our remaining instruments. We expect the new Vnmrs-500 to be available the week of May 10th. In the mean time, please be considerate of others and allow space between your reservations so other users have access to the same instrument.

This is also a good time to remind you of our Facility rules. The maximum times allowed per user during prime time (Mon to Fri, 8 am to 9 pm) are:

Inova 50050 min
Inova 40050 min
Gallium3 hr
Cobalt3 hr

During night time (Mon-Fri: 12 am to 8 am and 9 pm to 12 am) and on weekends the time is unlimited; but please do not hog the instruments several nights or weekends in a row. Additionally, reservations cannot cross prime time boundaries (8 am and 9 pm). For example, reserving time on Gallium from 6 pm to 11 pm on a week day is not allowed, even if two "legal" consecutive reservations (6pm to 9pm and 9pm to 11pm) are made. The only exception to this rule is, for example, if you reserved time from 6pm to 9pm, and it is already later than 8pm, and no other user has reserved time starting at 9 pm, then you are allowed to reserve contiguous time so that the instrument doesn't go unused.

Your cooperation and patience will be apreciated. And please send suggestions about policies to Eugenio (ealva at umich.edu). For instance, do you want or need a spectrometer to have walkup a policy like the Mercury 300 used to have?


03/26/10

The Mercury 300 has been decommissioned.


03/23/10

On March 20, Advanced Chemistry Development (ACD/Labs) announced that their NMR processing software is now free for academic use. From the announcement: "You can import 1D and 2D NMR data from all different formats, process them, perform multiplet analysis, create multiplet reports in patent and journal formats, automate procedures, create PDF reports, etc., etc., etc". The package, which also includes 3D Viewer, a program to display 3D molecular models, and the freeware version of ChemSketch to draw 2D molecular structures has been installed and is available in our Windows workstation in the lab. Incidentally, the version of MestreNova installed in this workstation has recently been updated to 6.1. This package provides a convenient alternative to other, commercial NMR processing programs. Read the announcement, a list of features and download it here.


03/17/10

As most of you know, we are expecting a new Varian VNMRS 500 MHz spectrometer in our Facility. This spectrometer will be installed where our Mercury 300 is currently located. We will start preparing the site on Friday, March 26. The Mercury 300 will be decommissioned on that date. Data stored in its computer's hard disk will be available afterwards, but this is probably a good time to do a full backup of your important data onto a CD or DVD. Installation of the new 500 will continue for about 4-5 weeks after that time. Lets give a well deserved farewell to the Mercury 300 for many years of good service!

We are also expecting a new VNMRS 700 MHz to be installed where our Inova 400 is currently located. The Inova will be decommissioned at some time in August in order to prepare the site.


02/11/10

For the observation of nitrogen, the isotope N-15 is preferred over N-14 because it produces spectra with much narrower lines. However, its low intrinsic sensitivity (6.5% compared to C-13) coupled to its low natural abundance (0.37 %) provides a receptivity compared to C-13 of only 0.024. For this reason, N-15 is very difficult to detect directly. A much easier way is through indirect detection via an HSQC or HMBC experiment. Shown below is the CIGAR spectrum (a variant of HMBC) of 35 mg of chloroquine phosphate in 90% H2O (about 100 mM). The spectrum reveals the chemical shifts of the three nitrogen atoms via 2 and 3 bond N-H correlations, and it took only 1 hour to measure in our 400 Gallium spectrometer. Direct acquisition in a similar amount of time produced only noise. Notice that, contrary to C-13, the NOE effect from neighboring hydrogens may lead to a decrease in signal intensity and should be avoided. The preferred method for direct acquisition is through an INEPT or DEPT pulse sequence.



         
03/12/09

Another reminder: long periods of time are available on all instruments from 9 pm to 8 am, however, if you want to reserve time starting at 9 pm, please do not also reserve time immediately before this as it will be effectively a long reservation starting before the allowed time. The same applies to overnight time ending at 8 am: reserving contigous time starting at 8 am is not nice nor allowed. In other words, if you want to use extended time you have to start 9 pm or after, not before and end at 8 am or before but not after.


01/22/09

It is now possible to login into the Lab computers using your UMich password.


01/16/09

Reminder: According to our Facility rules, NMR time should be reserved AND used by the same person. A user can only use the instruments using his/her own logins: operating an instrument using a friend's account is not permitted. Long periods of time are available after 9 pm or during weekends.


01/16/09

As many of you have noticed, we have been working on a software update on the Mercury 300. Both the operating system and Vnmrj will be upgraded. We hope the new software will be available today. The same upgrade will be performed on the other instruments and workstations during the next few days/weeks. Each computer in turn will be intermitently unavailable during this period of time. After the update, the new version of Vnmrj in the old spectrometers will be more consistent with that in the new spectromenters (Co and Ga) and the operating system (Linux) will have some new features and be easier to use.


08/06/08

The default probe of Cobalt is back from Varian. All nuclei and experiments are possible again.


06/27/08

The default probe and tunning unit of Cobalt have been sent to Varian for upgrade and testing. The spare 400 probe has been installed. Therefore, only H1, F19, C13, P31 and 2H are possible at this time.


06/13/08

The multinuclear probe on Cobalt has (finally!) been repaired.


05/30/08

The Pulsed Field Gradient Unit on the Inova 500 has been repaired.


05/29/08

The Pulsed Field Gradient Unit on the Inova 500 is broken again. Until further notice, nothing that uses gradients will work, including gradient shimming, gcosy, ghmqc, ghsqc, noesy, noesy1D, etc.


05/12/08

An old 400 MHz probe has been installed on Cobalt. Although the sensitivity is not as good as that of the autotunable probe, it is not too different to the Inova's 400. Like the Inova 400, it can do only H1, F19, C13 and P31.


05/12/08

Gallium's styrofoam bucket is now dead. Please use the bucket from the Inova 400 or 500 if low temperature is needed. A replacement will be ordered.


05/12/08

Gallium's white styrofoam bucket, used for low temperature experiments, dissapeared from the Lab during the weekend. If you have it please return it inmediately; if you know who has it or what happened to it please let us know asap. These accesories should not be taken from the Lab since any user can need them at any time.


05/09/08

Cobalt is out of service for the weekend. Its probe has been shipped for repairs. An old probe from the Inova 400 has been installed and will be calibrated on Monday to be used as interim.


05/07/08

The probe on Cobalt is broken. For the time being it can be used for proton acquisitions only (1D proton, cosy, noesy and noesy2D). It will have to be sent to Varian for repairs tomorrow.


05/05/08

The Inova 500 has been repaired. All experiments should function properly.


04/15/08

Our annual license of MestreNova 5.2.1 has been renewed. It is installed and working in one of the workstations in the lab.


04/07/08

It appears that the Inova 500 has developed a new problem. At this time only simple 1D experiments will work (noesy1d probably won't work either).


03/26/08

The Pulsed Field Gradient unit on the Inova 500 is finally back from Varian's repair shop! All 2D experiments and gradient shimming should be back to normal.


03/18/08

Parameters for the following nuclei have been configured in Cobalt: 119Sn, 11B, 51V, 195Pt, 199Hg and 2H. More nuclei can be configured on request. Parameters for 2H and 11B have also been configured in Gallium. To run these nuclei, just select them from the Experiments menu and tune the probe ("Tools -> Probe Tunning -> Tune Probe).

The macro "gradshim" is now working fine for those who want to shim non-deuterated solvents.


03/11/08

Gallium is now open for business.

It appears that Cobalt's magnet is not as stable as the other magnets in our lab (but is still within specifications). This means that the value of Z0 is slowly but continously changing; and over a period of just a few days, the value of Z0 that our macro 'setlock' has stored is so far off that the lock won't engage. If this happens, just click on "Find Z0"; it works quite well. Gallium doesn't have this problem.

03/05/08

Our two new 400 MHz NMR spectrometers, Cobalt and Gallium, are finally installed!! Although they look alike they have different capabilities. Check the Instruments page for details.

Cobalt has a "Dual Broadband" probe similar to that installed in our Inova 400. It has very good sensitivity for C13 and other heteronuclei; better than our Inova 400 and almost as good as our Inova 500 with the switchable probe. It can also measure other common nuclei like F19, P31, B11, N15, Cd113 and Pt195 with automatic probe tunning. It doesn't have a low temperature accessory but can regulate the temperature between ambient and +130 degrees.

Gallium has an indirect detection probe, similar to the one installed by default on our Inova 500. It has excellent sensitivity for proton (higher than that for the id probe in the Inova 500) and is therefore optimum for all experiments that detect protons, like COSY, HMQC, HSQC, TOCSY, HMBC, CIGAR, NOESY, NOESY1D, ROESY, etc. But it cannot detect F19 and the sensitivity for C13 and other nuclei is reduced. It is equipped with a low temperature accessory that allows it to regulate the temperature to between -80 and +130 degrees.

Slightly different software interface. The new spectrometers are running Vnmrj 2.2C. The user interface is a bit different than on the Inovas or on the Mercury 300 but only enough to require a few minutes of getting used to. Furthermore, the Chempack add-on has been added and enabled by default. This package adds more experiments and a few niece extra features. To run a simple spectrum, insert the sample, select the experiment and solvent and lock and shim as usual or click on "Find z0" and "Gradient Autoshim". Finally click on the green "Acquire" button. It is important to notice that now typing go or ga in the command line is not exactly the same as clicking on the Acquire button. The most important difference is that the Acquire button will tune the probe when needed, but go or ga will not. For example, if the previous user run a Phosphorus spectrum and what you want is a carbon spectrum, the probe will not be tuned to C13 and you will only get noise. And since you usually won't know what the previous user was doing, this means that you ALWAYS have to tune the probe to your sample before acquisition. The Acquire button should take care of that, but you can also tune it on demand by clicking on "Tools ->Probe Tunning -> Tune Probe" and then clicking the nucleus of your choice. Another nice feature of Chempack is the capability to create and run "experiment queues". These are lists of experiments to be performed in sequence on the same sample. To set up a queue, click on the "New Sample Q" button on the lower left corner of the vnmrj window and then click on the experiment buttons that you want, for example Proton, Carbon, gCOSY and gHSQC. You will see the individual and total acquisition times and you can even change the default parameters, like the number of transients, by double clicking on the list names. Enter a name on the "Sample name" field and click on the green "Submit" button to start the acquisition. The spectra will be saved in your vnmrsys/data directory with the name you provided.

Temporary usage policies. Tentatively, users will be allowed up to 3 hours of instrument time during weekday hours (8 am to 8 pm). After that time and during weekends, there is no time restriction. This policy will be under observation and will be reviewed in the next few days. Final policies regarding the new and old instruments will be published here after the trial period.

Cobalt is now open to be used, but it will probably be a good a idea if you use it for the first time when we are in the lab so we can help you if you have problems or questions. Gallium will be open to the public in a day or two. Most of our custom macros have been ported and installed, but there are a few that require some work and testing. They will be installed soon.

Please, please, please, be careful with your samples. Avoid breaking your nmr tubes either over the working desk or on the magnet. Lets try to keep the instruments new and clean for the longest time possible.


12/20/07 Due to the expected decrease in instrument demand over the holiday break, and to give users better access to the instruments, the normal rules will be changed as follows.
Please be considerate to other users and do not make a long reservation immediately after a previous long reservation. "Long reservations" are reservations of more than 1 hour. This will give users who only need a few minutes the opportunity to run their spectra at several times during the day. For example, if someone has already reserved the instrument from 9am to 12pm and your experiment requires 3 hours, allow at least an hour for other users to run their short spectra by starting your reservation after 1 pm.

12/20/07 The Mercury 300 has a new place in the lab and is now ready for use!









11/29/07 The Bruker AMX 500 has been decommisioned and will be replaced by two new Varian MR400 spectrometers. Installation is expected in January.

6/21/07 A common problem that occurs when plotting 2D spectra with high resolution 1D "projections" is that the intensity of the signals of interest in the projections is very weak as illustrated in the next figure.

 


This happens because the macros plcosy and plhxcor use the tallest peak in the displayed region to determine the "optimum" intensity. If that region contains one or more very tall peaks like methyl groups or solvent residues, the remaining signals will appear very weak. Unfortunately, Vnmrj does not have an easy mechanism to set the 1D intensities manually.

To reduce this problem, our custon macros UMplcosy and UMplhxcor were modified. When you use these macros and indicate the location of a high resolution spectrum (for example, the command UMplcosy(5, 1.5, 1) indicates that the high resolution proton spectrum is in experiment1) the macros use the current vertical scale (vs) of the high resolution spectrum and attempt to plot it on the top or side of the 2D at approximately the same intensity. Before using these macros, setup your high resolution spectra, for example in experiments 1 and 2 and display them on the screen at the intensity that you want to use for your projections. Then go to the experiment where your 2D spectrum is located and type the appropriate plot command. Finally, remember that these macros require a page or UMmailpage command to send the plot to the printer or to an email box. 5/3/07 A Frequently Asked Questions list has been added to the Documentation section. Inside it you can find information about importing spectra into Microsoft Office documents, file transfers, creating plots with insets, baseline corrections, accurate integrations, and some other short topics. Check this document regularly as it is going to be growing and changing frequently.

5/2/07 One of the Linux workstations in the NMR lab has been switched to Microsoft Windows and in it we have installed Microsoft Office, ChemOffice and the latest version of the NMR processing software MestReC now called MestReNova. This program is easy to use and produces very nice looking 1D and 2D spectra. It is easy to annotate the spectra and to paste chemical structures from ChemDraw. The spectra can then be copied and pasted into Word or PowerPoint documents. It provides a very good alternative to Vnmrj for processing and plotting of spectra. Your files on the spectrometers can be easily accessed through network drives (X:\, Y:\ and Z:\) on this computer; you do not need to transfer them first with sftp.

Notice however that spectra inserted in this way can be very large since you are inserting the actual NMR data and not just an image. The advantage is that you can double click the embedded spectrum and change anything you want, but if you have many spectra in your document its size can become quite large. Give it a try.

4/12/07 To import spectra into Microsoft Word or PowerPoint, Vnmrj provides only one option; "plot" the spectrum to a file. The resulting file is in postscript, a vectorial description of the file, and Word or PowerPoint can easily import it if it has the file name extension .eps (for encapsulated postscript). You can simply drag the file's icon into the the Word document and drop it in the desired location. After that, you will probably have to change its size and other properties. The spectrum will look great when printed, but unfortunately it won't look that great on the computer's display (or on the projection screen). You will also have to transfer your postscript files, via sftp or with a flash drive, to your Windows computer. To help with these issues a new macro, UMmailpage
, was developed. This macro was designed to be used as the page macro, i.e. first you build your plot with plotting macros like "pl pscale" and then you type UMmailpage. The macro will save the postscript file, convert it to a png (portable network graphics) file and send both files via email to you. The png file is a bitmap file similar to the most common jpg format but with some additional advantages and can be imported into Microsoft documents in a similar fashion by dragging and dropping. The png file is created in high resolution and will look well both printed and displayed. It can be edited with a graphics program like Photoshop to insert legends or chemical structures.

When executed, UMmailpage will ask you for a file name, your email address and a line width for the plot. The default line width, 1 pixel, produces very thin lines which may be difficult to see from the distance or when the plot is reduced in size. For presentations, a line width of 2 or 3 is recommended.

4/6/07 A new, more detailed application note about Kinetics experiments with Vnmrj is now available in the Documentation section. New macros to perform baseline correction and integration along all spectra in an array were developed and are explained in the hand out.
12/20/06 The spinner's turbine of the Inova 400 was removed from the magnet and throughly cleaned. The intermittent spinning problems experienced in the last few days should now be gone.

12/22/06 Due to the low demand of the instruments during the Christmas break, the maximum time allowed during prime time has been increased to 3 hours per instrument. The normal limit of 50 minutes will be restored in January 2nd. Enjoy!

11/21/06    As we all know, problems occur more often than we wish during the operation of the spectrometers. Problems include samples not spinning, computer hangups, spectrometer malfunctions, software bugs, etc. To facilitate the correction of common problems, a page has been posted in this web site and a link was created in Vnmrj's Help menu in the lab's computers. This way, when a problem arises you can view its solution directly in the spectrometer's computer. No longer will you have to search for the "white binder" in the lab. In the Help menu you will also find a link to the Scheduler and to the Application Notes (HowTos) prepared in the Lab.


11/17/06 A new application note about Noesy 1D spectra with Vnmrj is now available.

11/09/06 Finally! The switchable probe (sw) of the Inova 500 is back from repairs.

10/17/06 The indirect detection probe (id) for the Inova 500 is back. The probe was calibrated, tested and all experiments appear to be working fine. The switchable probe (sw) was sent for repairs.

9/29/06 A new application note about kinetics experiments with vnmrj is now available.

9/25/06 In order to help users with very limited amounts of sample, we have acquired a few Shigemi NMR tubes. These tubes are made of glass with magnetic susceptibilities matching those of the most common solvents and allow the use of smaller sample volumes. The solution is confined to a region inside the probe's measuring coil, thus increasing the sensitivity. Compared to a regular tube, the overall acquisition time is reduced by a factor of about two. We have tubes for CDCl3, CD3OD, D2O and DMSO-d6. You can borrow these tubes for testing or occasional use but we encourage research groups to buy their own if they frequently have low quantities of samples.

10/17/06 The VnmrJ software in the Inova 400 was upgraded to version 2.1B. All experiments are operational.

10/17/06 The VnmrJ software was upgraded from version 1.1D to version 2.1B on all computers in the lab except the Inova 400 and the Mercury 300. The Inova 400 will be upgraded sometime this week. The Mercury 300 will continue with the current version until Varian releases an update compatible with Mercury consoles.

9/25/06 The plague fell upon the 500!. The heteronuclear channel on the sw probe has developed a problem and is unable to pulse. The probe will probably have to be sent for repairs after we get the id probe back from Varian which will likely happen early next week. In the mean time, unfortunately it won't be possible to run experiments involving any nucleus other than hydrogen. That includes 1D and 2D experiments like HMQC or HSQC. All proton-only acquisitions including NOESYs or COSYs are OK.

9/25/06 The purpose of the news presented in this page is to keep you informed of very important information regarding the operation of the spectrometers and the lab. It is not useless technical mumbo jumbo but information that can actually help you and all users in the lab. For example, a user recently changed the "probe" parameter in the Inova 500 to the -currently incorrect- value "id". The result was that for a couple of days ALL users had hard time shimming and two-dimensional spectra were very noisy (The attributes of the parameter are now different, so no user can modify it anymore). Had he bothered reading this page he would have known that the id probe was sent for repairs.
Reading the news is not only encouraged but required to use the Facility. Please make a habit of checking for new news before you blindly click the next link.

9/15/06 An updated guide to run two-dimensional experiments with VnmrJ is now available.

9/12/06 A ghost broke a sample in the lab this morning. The sample apparently contained acetic acid and who knows what else. When the next user came and inserted her sample in the spinner, she noticed the odor and realized that the outside of the tube was covered with residues of the spilled solution. This, of course, is very unfriendly to say the least. The acetic acid or whatever that was left in the spinner caused the o-ring in the spinner to expand, making it useless to keep tubes in position. The inside of the spinner had to be cleaned and the o-ring replaced. It is very irresponsible to break samples and just walk away without doing a thorough clean up and notifying us. Potentially the next user might absorb a toxic, unknown chemical through the skin. The inside of the magnet and the probe can also get contaminated. Residues of chemicals will accumulate in the magnet until samples no longer spin properly. In other words, it will affect all users of the lab. Please let us know when a sample is broken, even if it is outside the magnet so we can make sure that everything is properly cleaned. And please notify us when you notice that some other, unfriendly user breaks a sample but does not tell us. Negligent users will have their privileges revoked.

9/11/06 The Inova 500 now has the switchable probe installed and tuned to proton and carbon. Note that the sensitivity for both nuclei, and especially for carbon, is better than in the Inova 400. See the Instruments section for actual signal to noise figures.

9/06/06 We have determined that the default probe on the Inova 500 is responsible for the problems described below. Therefore, the indirect detection probe ("id") will be sent for repairs on Monday 11. It will take about a month to have it back. During that time, the switchable probe ("sw") will be used. Although this probe is capable to perform all the experiments the id probe can perform, its sensitivity is noticeably lower. Please plan your experiments accordingly.

9/06/06 A problem was detected on the Mercury 300. The problem appears only on proton spectra as a bunch of glitches near the center of the spectrum. Other nuclei are fine. We are currently working to pin point the source and fix it.

8/23/06 A problem was detected on the Inova 500. The problem appears on heteronuclear correlations acquired with C13 decoupling like Ghsqc, Ghmqc and hmbc. When broadband decoupling is on, power glitches appear in the FIDs that severely increase the noise in the 2D spectrum and introduce other artifacts. We are currently working on a solution to this problem. In the mean time, to minimize the effects, the power used for decoupling has been decreased but at this power level decoupling is not completely effective and residues of the undecoupled signals can be seen in the spectrum. However, homonuclear correlations (COSY, noesy) and 1D experiments like H1, noesy1D and C13 are working correctly.

8/29/06 When plotting a heteronuclear 2D spectrum, e.g. a hsqc, it is desirable to plot high resolution spectra along its sides. The macro to do this is plhxcor(). For this macro to work correctly as supplied by Varian, all spectra must have been acquired on the same spectrometer, otherwise the chemical shifts won't match. This makes sense as a 1D spectrum measured at a different field may look different. It will certainly be the case for proton spectra because their splitting patterns are so sensitive to field strength. In our lab this is inconvenient as the most sensitive spectrometer configuration for C13 is the Inova 400 while the most sensitive (and recommended) for heteronuclear 2D correlations is the Inova 500. To provide more flexibility, the macro plhxcor has been modified so that it is now possible to plot a C13 spectrum collected on the Inova 400 along a 2D collected on the Inova 500. Keep in mind that this is not formally correct as you are displaying and comparing spectra at two different fields. However, in the case of natural abundance C13 spectra and other nuclei lacking homonuclear coupling, and for appearance purposes, it may be acceptable.

8/24/06 Last Monday, we found that the probe on the Inova 500 was mistuned. Yesterday, the temperature controller on the Inova 400 was off and today, we found that the gradients unit on this same instrumen had been turned off. Most 2D and other experiments will fail without the gradients unit or without a properly tuned probe. Needless to say, this produces a lot of wasted time by all other users (and us) and general agravation. We remind you that nobody is authorized to make changes of any kind to the instruments, except for changing the 1/4 wavelength cable on the Inova 400 and Mercury 300. Those who don't follow this rule will have their use privileges suspended!

6/28/06. We found the probe on the Inova 400 mistuned. This probe is more difficult to tune than others because each coil has to be tuned to two nuclei (1H/19F and 13C/31P) simultaneously. Please don't attempt to tune this or any other probe yourself. Contact us if you suspect a probe might be miscalibrated. The probe was retuned and pulse calibrations were perfomed.

6/22/06. Please, please don't drop the spinners. They may become unbalanced and produce severe glitches, similar to spinning side bands but worse. They are expensive to replace too. Recently, we have had to replace a few of them due to user abuse.

6/21/06. The Frequency Synthesizer in the Inova 500 was replaced and all pulses were recalibrated. Last week, the digitizer board was also replaced. These changes should fix all the problems that have appeared in the last few months. All pulse programs should work correctly now.

6/06. We are currently testing an update to Vnmrj, version 2.1B. This one has an improved graphical interface and some bug corrections. It will be first installed in the Inova 500 and later in the Inova 400 and all data stations in the lab. This version is incompatible with the Mercury 300 for now; a new compatible version is expected in the future.

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