In Memorium – Dr. Bruce Adams, a member of the DCIF staff until 2023, died suddenly on March 17. Bruce was loved by students and staff alike, and could always be counted on to teach what he knew, to help with research problems, and to generally lend a hand. He was determined to ‘make a difference’ in all that he did. He will be missed.
The Department of Chemistry Instrumentation Facility (DCIF) is the shared instrument facility for the Chemistry Department located in the sub-basement (18-0090) of the Camille Edouard Dreyfus Building on the main MIT campus.
Access to the MIT campus for external DCIF users has reverted to pre-COVID standards. For batch NMR sample submission, you may consider using the Batch NMR Automation process – Batch Automation spreadsheets can be found further down the page under ‘Application Notes’.
Use our web-enabled/mobile Res1P application for instrument reservations!
The DCIF has received a generous gift of a 20MHz time-domain NMR system from Dr. Christian Tanzer in April, 2022. This instrument may be used for routine T2 and T1 measurements for a variety of materials, and is an excellent instrument for teaching NMR fundamentals. See the ‘Other Instruments’ tab for additional details.
DCIF staff are happy to help you to design and troubleshoot your chemistry and engineering analytical experiments, including a full range of biomolecule double or triple-label experiments. In addition to helping with standard, pre-installed experiments, we are pretty good at implementing newly developed and custom NMR experiments!
The Chemistry Department and the DCIF, in collaboration with IS&T, have added the Mestrelab NMR Predictor module and the Mestrenova MS/Chrom module to our Mestranova site license. All MIT users of the software have access; go to the IS&T ‘Get Software’ page to download the current license files, or follow the instructions in our ‘Software’ section of the DCIF webpage.
A note for MIT users of the DCIF – if your cost object has changed, please send your updated information to the Chemistry Billing address; they will be happy to make the change for you.
Please check back periodically for updates. If you have specific questions, please email Walt Massefski (listed under ‘Staff’ below).
About the DCIF
General Information
The lab is available to MIT scientists 24 hours/day, 7 days/week, and during normal business hours to everyone else. Staff are happy to help with instrument training, chemical structure problems and various analytical chemistry questions during the day.
The lab has a mix of automation and manual-use instruments. Automation instruments work 24/7 on a first-in, first-out basis and do not require special reservations for use. Manual-use instruments are reserved using in-house reservation software except during special walk-on times.
Currently, there are four permanent staff members and five student instrumentation stewards who provide instrument training, maintenance, repair and applications assistance to well over 500 users.
Training Requests
All DCIF users require instrument-specific training prior to using the facility. To get started with an instrument or instruments, please submit the DCIF Training Request Form. Before you submit your training request, be sure you have a sample in hand and are ready to begin acquiring data.
Instrument Reservations
Reservations are now made through our web-based Res1P application; to access the program directly, click here. Res1P (currently version 1.0) was developed by Bruce Adams and is a functional replacement for the legacy Res1B program. The reservation program is accessible to both MIT and non-MIT users of the DCIF.
A two page instruction summary for reserving instrument time with Res1P is available here. You will receive your Res1P credentials as part of your instrument training for all non-automation instruments.
Fees
| Instrument | MIT | Non-Profit | Commercial | Unit |
| Mass Spectrometers | ||||
| GCMS | $23.00 | $36.57 | $157.09 | per hour |
| LCMS | $23.00 | $36.57 | $157.09 | per hour |
| AccuTOF DART | $40.00 | $63.60 | $273.20 | per hour |
| Maldi-TOF | $40.00 | $63.60 | $273.20 | per hour |
| Q-TOF | $40.00 | $63.60 | $273.20 | per hour |
| QQQ | $40.00 | $63.60 | N/A | per hour |
| NMR Spectrometers | ||||
| AVIII 400 | $28.00 | $44.52 | $191.24 | per hour |
| AVIII 401 | $28.00 | $44.52 | $191.24 | per hour |
| Neo 402 | $23.00 | $36.57 | $157.09 | per hour |
| Neo 500 | $35.00 | $55.65 | $239.05 | per hour |
| Neo 501 | $30.00 | $47.70 | $204.90 | per hour |
| JEOL 502 | $30.00 | $47.70 | $204.90 | per hour |
| Neo 600 | $38.00 | $60.42 | $259.54 | per hour |
| Other Instruments | ||||
| EPR | $28.00 | $44.52 | $191.24 | per hour |
| FTIR | $28.00 | $44.52 | $191.24 | per hour |
| Polarimeter | $28.00 | $44.52 | $191.24 | per hour |
| HPLC | $23.00 | $36.57 | $157.09 | per hour |
| Posters | $30.00 | N/A | N/A | each |
For External Organizations
Staff
Director
617.253.2016
Walt joined the DCIF in 2017 from the Dana-Farber Cancer Institute, with previous experience at Pfizer, Wyeth, and T2 Biosystems. Walt has a Ph.D. in Biochemistry from Brandeis University and a Master’s Degree in Chemistry from Wesleyan University, with a specialization in NMR. He has extensive experience in NMR structure determination of small molecule organics, as well as NMR relaxation studies of peptides, proteins, and nucleic acids.
Sarah Willis
Operations Manager
617.253.4856
Sarah joined the DCIF in 2023. Sarah holds a Master of Science in Chemistry from the University of Wisconsin-Madison. She has experience in small molecule structure determination as well as characterizing macromolecular systems with solution and solid-state NMR. In addition to NMR, Sarah has diverse analytical and synthetic chemistry skills.
Mohan Kumar
Research Scientist
617-258-9354
Mohan joined the DCIF in 2017 from the University of South Florida, where he was a Research Assistant Professor. Mohan has extensive experience in mass spectrometry, including the analysis of peptides and molecular probes for imaging as well as significant synthetic experience with peptides. Mohan holds a Ph.D. in Bioorganic chemistry from the Indian Institute of Technology and a Master of Science from Bharathidasan University.
Bridget Becker
Research Specialist
617.253.1812
Bridget joined the DCIF in 2023 from Labcorp (formerly Covance) with previous experience at Merck, and Proctor and Gamble. Bridget has a Ph.D. in chemistry specialized in analytical chemistry from the University of Kansas. She has experience in small molecule structure determination and investigating intermolecular interactions with NMR. She also has experience with metabolite identification in small molecules and small therapeutic biomolecules by LC-MS.
General Lab Contact
Goes to all DCIF Staff
617.253.1806
DCIF Stewards
Carolyn Barnes, Kiessling lab, NMR
Kaelyn McFarlane-Connolly, Bawendi lab, EPR, NMR
Rachel Motz, Nolan lab, MS
Hallie Trial, Kiessling lab, NMR
Molly Warndorf, Swager lab, MS
June, 2022 – We thank recent Chemistry Ph.D. graduates Sam Etkind and Sarah Jane Mear for their efforts in supporting the mission of the DCIF as stewards over the course of their graduate careers at MIT, and wish them continued success!
September, 2022 – We thank recent Chemistry Ph.D. graduate Martin Riu for his help in supporting the mission of the DCIF as an NMR steward and wish him continued success!
January, 2023 – Please welcome Brittany Linn as a new graduate student steward! Brittany will help to support EPR and NMR at the DCIF.
March, 2023 – Please welcome Rachel Motz as a new graduate student steward! Rachel will help to support MS at the DCIF.
May, 2023 – Thanks to recent Chemistry Ph.D. graduates Edward Badding and Victoria Marando for their help in supporting the DCIF, particularly during the Covid era! We wish them continued success in their science careers.
June, 2023 – Please welcome Hallie Trial as a new graduate student steward! Hallie will help to support NMR at the DCIF.
May, 2024 – Thanks for recent Chemistry graduate Brittany Linn for her help supporting NMR and EPR in her time as a DCIF steward. We wish Brittany continued success in her continuing chemistry career!
July, 2024 – Please welcome Kaelyn McFarlane-Connolly as a new graduate student steward! Kaelyn will help to support NMR and EPR in the DCIF.
Instruments and Software
Instrument Status
Please note that the lab is unavailable for use every Thursday from 7am-10am for weekly instrument maintenance and cleaning.
We have developed a real-time tool to monitor instrument queues as an aid to planning experiments; this tool is available for the four Bruker automation instruments here. This page contains links to the individual instrument queues – you can see where your sample is in the queue (but not exactly when it will run).
Mass Spectrometry (MS)
The LCMS is a nominal mass Agilent 6125B mass spectrometer attached to an Agilent 1260 Infinity LC. It has an electrospray (ESI) source with fast polarity switching to measure positive and negative ions simultaneously. The diode array has a wavelength range of 190 to 640 nm, and a measurable m/z range of 100 to 1500 daltons. It uses ChemStation acquisition and data analysis software and is run in full automation mode using the Agilent Walkup software front-end. In addition to ChemStation data analysis, data files can be analyzed in MassHunter using the LC-SQ Translator.
GC/MS
The GCMS is a nominal mass Agilent 5977B mass spectrometer detector attached to a 7890B gas chromatograph with autosampler. It allows for the measurement of ions generated by electron impact (EI) or chemical ionization (CI) with m/z in the 10 to 1000 dalton range. The GC uses a 30m, 0.25mm, 0.25µm J&W HP-5ms Ultra Inert column with a maximum operating temperature of 325°C and has a maximum oven temperature of 400°C. It uses ChemStation acquisition software, ChemStation/MassHunter data analysis software, and can access the NIST library.
AccuTOF-DART
The AccuTOF is a high-resolution JEOL AccuTOF 4G LC-plus equipped with an ionSense DART (Direct Analysis in Real Time) source. The system operates with an accuracy of 5 ppm and a resolving power of greater than 10,000 (FWHM) in DART positive ion mode. The measurable mass range is m/z between 10 and 2000 daltons, and the system is capable of measuring both liquid and solid samples. msAxel acquisition and data processing software, and Mass Mountaineer data processing software with access to the NIST libraries allow for elemental composition in many cases. The system also has a syringe pump coupled ESI source that can be used upon request.
Maldi-TOF
The MaldiTOF is a high-resolution Bruker Autoflex LRF Speed mass spectrometer with a measurable mass range of up to 450 kDa. It is capable of measuring in both linear and reflector mode, and in reflector mode 3-5 ppm mass accuracy can be achieved using an internal calibration standard. The data processing software contains modules for analyzing and sequencing peptides, proteins, and polymers.
Q-TOF
The QTOF is a high-resolution Agilent 6545 mass spectrometer coupled to an Agilent Infinity 1260 LC system. It typically runs a Jet Stream ESI source, but can also be configured to run in APCI or APPI mode upon request. The system has a mass accuracy of 1-3 ppm using real-time calibration, with a mass resolving power of 45,000 (FWHM) at m/z of 2722. It has a measurable m/z of 50 daltons to 10 kDa. The system uses MassHunter data acquisition and processing software, with additional Qualitative Navigator, Workflow, Bioconfirm, and Quantitative analysis software packages.
QQQ
The Ultivo triple-quadrupole is both a quantitative and qualitative Agilent Mass Spectrometer coupled to an Agilent 1260 Infinity II LC system. It typically uses an ESI source but can be configured with APCI and APPI sources. It operates in multiple modes – Scan, SIM (Selective Ion Monitoring), precursor ion, product ion, MRM (Multi Reaction Monitoring) and triggered MRM (tMRM). The mass range of the system is typically 5 to 1400 da, with quad resolution from 0.7 to 2.5 da range. The scan speed is 15000 da/sec and MRM speed is 500 MRM/sec. The system uses Mass Hunter for data acquisition, with data processing software included (Qualitative and Quantitative). It also has an “Optimizer”, which helps find optimum collision and fragment voltages for MRM.
Nuclear Magnetic Resonance (NMR)
The 400 is a two-channel Bruker Avance-III HD Nanobay spectrometer operating at 400.09 MHz. The system is equipped with a 5mm liquid-nitrogen cooled Prodigy broad band observe (BBO) cryoprobe, and runs in full-automation off of a SampleXpress 60 sample changer. The broadband channel extends from 31P down to 15N. Data is returned via standard email, or can be retrieved from an in-lab data server for up to six months. The system runs Bruker Topspin software version 3.5pl7 with IconNMR.
Avance401
The 401 is a two-channel Bruker Avance-III HD Nanobay spectrometer operating at 400.13 MHz. The system is equipped with a 5mm liquid-nitrogen cooled Prodigy broad band observe (BBO) cryoprobe, and runs in manual mode, using a SampleXpress 60 for sample handling. The broadband channel extends from 31P down to 15N. Data can be retrieved from an in-lab data server for up to six months. The system runs Bruker Topspin software version 3.5pl7.
Neo402
The 402 is a three-channel Bruker Avance Neo spectrometer operating at 400.17 MHz. The system is equipped with a 5mm BBFO SmartProbe capable of both routine proton, fluorine and broadband detection, as well as proton/fluorine double resonance, and runs in full-automation off of a SampleXpress 60 sample changer. The broadband channel extends from 19F down to 109Ag. The system can also be equipped with either a 5mm 13C TBI probe (capable of 13C/H/X triple resonance experiments) or a flow-NMR accessory on request. Data is returned via standard email, or can be retrieved from an in-lab data server for up to six months. The system runs Bruker Topspin software version 4.0.5 with IconNMR.
Neo500
The 500 is a three-channel Bruker Avance Neo spectrometer operating at 500.34 MHz. The system is equipped with a 5mm liquid-nitrogen cooled Prodigy broad band observe (BBO) cryoprobe, and runs in full-automation off of a SampleXpress 60 sample changer. The broadband channel extends from 31P down to 15N. Data is returned via standard email, or can be retrieved from an in-lab data server for up to six months. The system runs Bruker Topspin software version 4.0.5 with IconNMR.
Neo501
The 501 is a three-channel Bruker Avance Neo spectrometer operating at 500.18 MHz. The system is equipped with a 5mm BBFO SmartProbe capable of both routine proton, fluorine and broadband detection, as well as proton/fluorine double resonance, and runs in manual mode, using a SampleXpress 60 for sample handling. The broadband channel extends from 19F down to 109Ag. This system is available for VT experiments in the -100C to +100C temperature range. The system can also be equipped with either a 5mm 31P TBI probe (capable of 31P/H/X triple resonance experiments) or a 3.2mm HX solids probe capable of MAS speeds of up to 24kHz. The instrument is typically configured for routine solid-state NMR use each Thursday. Data can be retrieved from an in-lab data server for up to six months. The system runs Bruker Topspin software version 4.0.5.
JEOL502
The 502 is a two-channel JEOL ECZ spectrometer operating at 500.44 MHz. The system is equipped with a Royal HFX triple-resonance probe capable of switching between high-sensitivity proton or fluorine observe, or triple resonance (H/F/X) mode. The broadband channel extends from 31P down to 15N. This system runs in full-automation using a 24 sample carousel, and JEOL Delta software version 5.3. Note that the JEOL can be used for variable-temperature work between -80C and +80C. Data can be retrieved from an in-lab data server for up to six months.
Neo600
The 600 is a four-channel Bruker Avance Neo spectrometer operating at 600.14 MHz. The system is equipped with a 5mm helium-cooled QCI-F cryoprobe capable of simultaneous 1H/13C/15N/19F detection, and operates in full-automation off of a SampleJet sample changer. The SampleJet is capable of handling all of 5mm, 3mm, and 1.7mm samples in automation, and has capacity for 96 standard 7 inch samples plus five 96-well racks of mixed diameter 4 inch tubes. The 96-well racks can be individually heated or cooled on request. Data is returned via standard email, or can be retrieved from an in-lab data server for up to six months. The system runs Bruker Topspin software version 4.0.5 with IconNMR.
Other Instruments
The EPR is a Bruker EMX-Plus spectrometer with an ER4119HS high sensitivity X-band resonator for perpendicular mode, or E4116000 dual mode X-band resonator. Both can be cooled to cryogenic temperature with the aid of a Bruker/ColdEdge 4K waveguide cryogen-free cryostat. The standard operating temperature range extends from 4.5K at the low end to room temperature or above. The spectrometer runs Xenon 1.1b.155 software.
Time-Domain NMR
The TDSpec is a time-domain, 0.47T permanent magnet NMR system capable of proton detection for a wide-range of materials – solid polymers, electrolytes, non-magnetic materials, oils, and aqueous solutions among them. Water solutions as small as 50 microliters can be detected easily, and the instrument is flexible enough to measure the effect of superparamagnetic particles on water T2s. It also does push-button T1 measurements.
FTIR
The FTIR is a Bruker Alpha II FTIR spectrometer with a Diamond Crystal ATR (attenuated total reflectance) accessory. It can measure typical liquid or solid samples directly without the need for additional sample preparation. The spectrometer runs Opus 7.8 software.
Polarimeter
The Polarimeter is a new Jasco model P-2000 configured for the standard 589nm Sodium D line. Filters are also available for the following wavelengths: 577, 546, 405, 365, and 280 nm. The system normally has sodium and mercury lamps installed; if you need the tungsten lamp installed, let us know. Consult the polarimetry guide (below) for details. Users should supply their own polarimetry cells (which are available for volumes as low as 0.5ml), although we have a couple available for occasional use.
HPLC
The lab has an analytical scale Agilent Infinity 1260 II HPLC capable of handling HPLC and UHPLC columns of 2.1, 3, and 4.6 mm internal diameter available for method development. This system has a four stream solvent mixing system with binary pump, a diode array detector with the ability to measure from 190 to 640 nm, and a maximum pressure of 600 bar. It also has an autosampler capable of handling both individual vials and well plates.
Poster Printing
The DCIF owns a Canon iPF8400s color poster printer (Installed 4/15/2016). Be careful when blowing up images and pictures beyond 100% as they can become pixelated and blurry. Use large fonts instead of blowing up pictures of text. DCIF Staff prints posters as they are received. We do not proofread, edit, alter or change any of the content, so be sure it is in final form before sending it to us for printing.
Click here to fill out the web form and upload your poster in PDF format (requires certificates). You should know which account to bill for the poster charge. If you are unsure, check with your lab financial assistant/manager.
Please note that once this form is submitted, your advisor is automatically billed for your poster. Be sure your poster is in final form before clicking submit. If you find you must make a change, contact Sarah immediately and do not submit a revision via the form.
Instrument Training Guides
Bruker topspin setup macros
Bruce Adams has created a series of experiment setup macros for topspin which simplifies the process of running standard 2D experiments for scientists that run their instrument manually, and he has made this package available to the broader NMR community. To use this package, start by downloading (and reading) the README file, which gives instructions on how to extract and set up the package. You will find instructions on how to use the package here; the zip file for Avance systems is here, and the zip file for Neo systems is here.
If you have problems with the installation or use of the package, please email Bruce. Note that this package has been created and tested using topspin 3.5pl7 and topspin4.0.5 – it may not work as indicated with older versions of topspin, but if you try it out and it does work, email Bruce and let him know!
Software
The current Mestrenova licenses are hosted at the DCIF and include a set of NMR processing tools (including 1D/2D processing, NMR chemical shift estimation for 1H, 13C, 19F, 31P and various other heteronuclei, and modules for reaction monitoring and qNMR). This package is commonly used in the MIT chemistry, engineering, and chemical biology community.
The license package also includes the MSChrom module for processing a variety of mass spectrometry/chromatography data. Processing modules are specific to your operating system (MacOS/Windows x32/x64) – see the Mestrenova site for details.
To access the Mestrenova license files, please click the website’s LOGIN tab (in the top righthand corner of the page) and then click here . Login will require MIT credentials. If you have trouble downloading the files, send a note to Walt (see the link above).
Application Notes
Below are a series of application notes that describe special applications or the use of DCIF instruments in the study of non-standard samples.
Batch NMR automation
You can request to have a batch of NMR automation samples submitted to any of the Neo402, Avance400, Neo500, or Neo600; this is particularly useful for chemical library synthesis, compound screening, and bimolecular NMR binding assays. To use this feature, download the spreadsheet corresponding to the instrument you want to run on, fill it out according to the instructions, and send it back to us at dcif@mit.edu. We will coordinate your batch run with you.
Please note that the current remote drop-off feature uses the Avance400 spreadsheet for sample submission, but is operationally distinct – if you wish to use remote drop-off, you will place your samples in the remote cassette and send us the spreadsheet by 3pm Mon-Fri; if you wish to use batch automation, send us your spreadsheet (choose the spreadsheet that corresponds to the instrument you want to use), and we will let you know when you can put your samples on the instrument and which holder positions to use.
Neo402 Batch Automation spreadsheet
Avance400 Batch Automation spreadsheet
Neo500 Batch Automation spreadsheet
Neo600 Batch Automation spreadsheet
Be sure to use the correct spreadsheet; different spectrometers have different capabilities.
Nuclear Magnetic Resonance (NMR)
Selective 1D experiments – general notes
Selective 1D experiments on the Manual Bruker systems
Small-molecule assignment sets
Mass Spectrometry (MS)
Other
Notes from the Board
DCIF Seminar series
The DCIF sponsors seminars through our own Seminar series (including occasional external seminars), gives guest lectures as part of the MIT Chemistry curriculum, and runs informal short courses on advanced topics in spectroscopy. Slides from some of these presentations can be found below.
DCIF Seminar series
NMR in Shared Labs in the COVID-19 Era – W. Massefski, NewNMR (2020-09-16)
Introduction to HPLC Separations – M. Kumar (2020-01-10)
Introduction to Mass Spectrometry – M. Kumar (2020-01-13)
Introduction to Mass Spectrometry – M. Kumar (2020-01-15)
Intermediate NMR – A Practical Course on Shaped Pulses and Their Applications (January 10-12, 2023)
The outline for Bruce’s mini course can be found here, and the Powerpoint presentation that he used is here. If you are interested in any of the specific pulse sequences that he has developed, please contact one of the current DCIF staff.
Bruce also gave a summary of this mini course as a NewNMR Seminar; the slides for this seminar can be found here –
Shaped Pulses – Application and Practice, NewNMR (2023-07-24) (notes on the slides are available here).
Part II of A Practical Course on Shaped Pulses and Their Applications (January 23 and 25, 2024)
This is the second part of Bruce Adam’s course on Shaped Pulses in NMR, given as part of the MIT IAP series. The slides are available here, and recordings of the two sessions can be accessed here: January 23 (plus closed caption) and January 25 (plus closed caption). In addition, Bruce has made his Block simulator available as well (a zip archive with readme).
Guest lectures in Chemistry
Undergraduate Lab NMR lecture – J. Grimes
Undergraduate Lab NMR training – J. Grimes
5.363 NMR lecture – W. Massefski