e-Newsletter

NMRFAM eNewsletter – April 2019

NMRFAM offers services such as:

  • collect routine NMR spectra of small molecules, process the data with peak picking and integration, and provide their experimental results in electronic or paper format in order to advance research projects.
  • Users can submit their samples in 3 or 5 mm NMR tubes before 1 pm every Tuesday and Thursday. Their data will be acquired between 1 – 5 pm of the same day on a 500 MHz spectrometer optimized for 13C (no appointment necessary). Please email Paulo F. Cobra when you drop off your samples.

New User/Collaborator Information:

Please note that if you would like to collaborate with our facility you will need to submit an abstract providing some detail to Lai Bergeman, our coordinator, who will bring it up for review at our weekly staff meeting for approval. Please visit the NMRFAM website for more information.

Other NMRFAM capabilities:

Solid state probes at NMRFAM:

  • 3.2mmEfree CPMAS, 4mm CPMAS and HRMAS probes – 500 MHz (Devon)
  • 3.2mm Efree CPMAS and static BioProbe (PISEMA experiments) –  600 MHz III (Vosges)
  • 3.2mm Efree CPMAS probe and 1.3mm ultrafast CPMAS probe – 900 MHz (Fleckvieh)

 LC/MS micrOTOF Q II is now available for collaboration

Bruker Nanostar SAXS (small angle X-ray scattering) instrument is NOT operational. For information about SAXS, please email Paulo F. Cobra.

  •   NMRFAM Software News:GISSMO.nmrfam.wisc.edu:GISSMO enables the efficient calculation and refinement of spin system matrices (chemical shift and coupling constants) against experimental 1D-1H NMR spectra of small molecules. The library of compounds parameterized by GISSMO contains more than 1286 compounds, including many key mammalian metabolites and a library of drug-like molecular fragments used in ligand screening.ALATIS.nmrfam.wisc.edu:Unique and reproducible molecule and atom identifiers are required to ensure the correct cross-referencing of properties associated with compounds archived in databases. The best approach to this requirement is the International Chemical Identifier (InChI). ALATIS is an adaptation of InChI that provides unique and reproducible atom numbering for all atoms including hydrogens.

            NMRFAMSPARKY new features:

  •             Improved PINE/PINE-SPARKY 2 (ep)
  •             Hydrophobic core and flexibility detection in PINE-SPARKY 2 (ep)
  •             Sequence entry integration for automated tools (sq)
  •             More colors available (ct,cr)
  •             Move labels to peak centers (lc)
  •             Dummy graph (dg)/ Pine graph assigner (pp) small fix
  •             Explicit buttons in the strip plot (sp/SP)           
  •             Completeness counter (cm)
  •             Improved APES peak picker (ae)

Donate to NMRFAM

US deductible donations can be made to NMRFAM. Please write check payable to “UW Foundation, Account 112152802” and mail to:
Attn: Sarah Lynn Traver Saunders

                        Associate Administrative Program Specialist 

                        University of Wisconsin – Madison 

                        Department of Biochemistry 

                        433 Babcock Drive 

                        Madison WI 53706

For further information, please contact Ms. Saunders, Tel: 608-265-2507 or email 

 Spectrometers at NMRFAM:

  • NMRFAM Spectrometers availability (Live Schedule) for current and upcoming month can be view at Live Schedule
  • NMRFAM instrumentation
    Spectrometer status:

Instrument

Cow name

Shortcut name

Probe(a)

 Status

Bruker AV-HD 900

Fleckvieh

900

c-tr

OK – cold 1H and13C preamps

Agilent VNS 800

Gelbvieh

800

ct-tr

OK – cold probe

Bruker AV III 750

Telemark

750

c-tr

OK – cold probe

Bruker AV III 600

Dexter

600 I

c-qr1H{13C,15N,31P}

OK – SampleJet

Agilent VNS 600

Jaulan 

600 II

c-tr

OK – cold probe

Bruker AV III 600

Vosges  

600 III

c-tr

OK – cold probe

Bruker AV III 600

Kurgan

600 IV

c-tr-(1.7mm)

OK – SampleJet (cooled)

Bruker AV III 500

Kerry

500 I

c-tr(13C/15N)

OK-all cold preamp; SampleJet

Bruker AV III 500

Devon

500 II

c-tr/hrmas/BBFO/cpmas

OK – cold probe

BrukerNanostar

Bond

SAXS

N/A (not operational)

OK – temperature control available

(a)rt – room temperature; c – cryogenic; tr – 1H{13C,15N} triple resonance; qr –1H{13C,15N,31P} quadruple resonance; multiple – multiple probes; VNS- Varian Direct Drive console; AV- BrukerAvance III consol

Below is a listing of the available software on our website that you are free to use or download and some associated publications:
1 – NMRFAM-SPARKY
2 – NMRbot
3 – HIFI-NMR
4 – LACS / PECAN
5 – PINE
6 – PINE-Sparky
7 – ADAPT-NMR
8 – ADAPT-NMR Enhancer
9 – Newton
10 – PACSY
11 – PONDERSOSA
12- PONDEROSA-C/S
13 – SPIDER
14 – RNA-PAIRS
15 – NMR Structure Tools
16 – rNMR

Please visit the NMRFAM software website for more information on the above listed software.

References for some publications are:

Dashti H, Wedell JR, Westler WM, Markley JL, Eghbalnia HR. Automated evaluation of consistency within the PubChem Compound database. Sci Data. 2019 Feb. PMCID:PMC6380220

Ulrich EL, Baskaran K, Dashti H, Ioannidis YE, Livny M, Romero PR, Maziuk D, Wedell JR, Yao H, Eghbalnia HR, Hoch JC, Markley JL. NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments. J. Biomol NMR. Dec 2018 . PMID:30580387

Windsor IW, Palte MJ, Lukesh JC 3rd, Gold B, Forest KT, Raines RT. Sub-picomolar Inhibition of HIV-1 Protease with a Boronic Acid. J Am Chem Soc. Oct 2018. PMID:30346745

Assadi-Porter FM, Radek J. Rao H, Tonelli M. Multimodal Ligand Binding Studies of Human and Mouse G-Coupled Taste Receptors to Correlate Their Species-Specific Sweetness Tasting Properties. Molecules. 2018 October. PMID:30282936

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