Monthly Newsletter for December 2014

December 1, 2014

Monthly Newsletter for December 2014

Instrument Moves Almost Done

As many of you undoubtedly know, the CBIC has been in the process of moving and consolidating its instruments to the KCL basement and CRB 100 for much of the past year. And that move is nearly finished. The V500 and V600 (now renamed V500wb and V600a) NMR spectrometers have been moved to CRB 100. Our Perkin Elmer 341 Polarimeter has been moved to KCL 3 and is by the door opposite the elevator. Finally, the Varian 600 MHz NMR from the Yale Medical School (to be named V600b) will be moved into CRB 100 within the next two weeks.

CBIC Instrument Updates

The past month here at the CBIC has served as a shining example of Murphy’s law: It seems that everything that could go wrong has gone wrong. We apologize to everyone that has been affected by these service outages. We would like to inform our users about the specific problems in a little more detail, as well as what we have done in response to restore regular service.


In late October the A500a probe failed after a variable temperature run. We sent the probe out for repairs and installed a loaner probe. After we reinstalled the repaired probe, there were some issues with the automatic tuning of our repaired probe, but these appear to have been cleared up and the unit is back up and running. A different, more minor problem with the probe on A500b prompted us to also send that probe out for repairs, and the loaner probe is currently installed in its place. The instrument is still operational.

The A400b stopped working due to an internal power supply failure. We have ordered a replacement power supply and await its arrival.

Most recently the A600a cold probe cooling system failed just before Thanksgiving. We brought in a service engineer from Aglient and have resolved the issue, although the origin of the problem is still somewhat mysterious. In addition, there are still issues with decoupling C13 on A600a which prevents HSQC experiments from running properly. We have done quite a bit of troubleshooting related to this problem and believe that it is due to a minor vacuum leak in the system. We are still working on finding the cause of the vacuum leak.

Finally, we are aware of the many failures of the automatic NMR sample changers, and we have working for a long time to rectify them. The main issue seems to be due to a design flaw in the sensor that detects whether or not a sample is present inside the magnet. Occasionally the sensor reads a false positive (sensing a sample in the magnet when actually there is none) and this causes the sample changer to stop working until it is reset. We have been trying several different methods to resolve the problem and hopefully we will be able to fix it soon.

In positive news, the relocated V600 (now V600a) is up and running, and has been updated to the newest version of VnmrJ software. If you are a user of the Biophysical NMR instruments, please feel free to request time on V600a if you wish to use it.


We would like to apologize to anyone who had their reservations on the 007 canceled. There is a problem with the chi angle stepper motor in the instrument’s goniometer. After several attempts to fix the problem ourselves, we called in an engineer from Rigaku who confirmed our diagnosis of the problem, but unfortunately there will be a long delay before we can get replacement parts due to a lack of availability. In the meantime, we have taken advantage of the downtime to replace the unit’s rotating anode, which is part of the regular maintenance that must be performed once or twice per year.

In addition to the chi motor issue, the hard drives failed on both the 007 and the Mini after a power outage in early November. They have been fitted with new hard drives and the operating system has been upgraded from Windows XP to Windows 7. The Mini’s cooling line also clogged earlier this month, causing the x-ray tube to fail. The cooling lines have been cleaned and the Mini is now operating normally.

Lastly, one of the position limit switches in the powder XRD's goiniometer failed. We were able to fix the switch, and after figuring out some necessary software configuration changes, the PXRD is now back online and operating normally.

MicroCal ITC 200

The computer running this unit became infected with a virus two weeks ago. A member of the CBIC staff has cleaned the computer, and we believe it is virus free. However to be safe, we encourage patrons to use our new TA Nano ITC. The new ITC has the same or better capabilities as the MicroCal, and all users should migrate to this new instrument as soon as feasible.

Recent Publications from Yale's Chemistry Department

The CBIC strives to support the research throughout Yale University. In that spirit, we would like to highlight recent publications from the Chemistry Department. Congratulations to all the authors! We look forward to serving your instrumentation needs in future manuscript preparations.

Electrochemical Reduction of Aqueous Imidazolium on Pt(111) by Proton Coupled Electron Transfer
Kuo Liao, Mikhail Askerka, Elizabeth L. Zeitler, Andrew B. Bocarsly, Victor S. Batista

Selective catalytic oxidation of sugar alcohols to lactic acid
Michael G. Manas, Jesús Campos, Liam S. Sharninghausen, Elisa Lina and Robert H. Crabtree

Alkali Metal Control over N–N Cleavage in Iron Complexes
Katarzyna Grubel, William W. Brennessel, Brandon Q. Mercado, and Patrick L. Holland

Reducing the genetic code induces massive rearrangement of the proteome
Patrick O’Donoghuea, Laure Prat, Martin Kucklick, Johannes G. Schäfer, Katharina Riedel, Jesse Rinehart, Dieter Söll, Ilka U. Heinemann

Polyspecific pyrrolysyl-tRNA synthetases from directed evolution
Li-Tao Guo, Yane-Shih Wang, Akiyoshi Nakamura, Daniel Eiler, Jennifer M. Kavran, Margaret Wong, Laura L. Kiessling, Thomas A. Steitz, Patrick O’Donoghue and Dieter Söll


There are a number of ways you can stay updated about what is happening in the CBIC -- If you have any questions, you should always feel free to ask any of the CBIC staff, either in person or via email. If you are not on our email list, you can subscribe at You can also visit or follow us on Twitter @yalecbic.

CBIC Staff