Instrument Catalog

**Small Molecule Diffraction Policy**
Short Name: Small Molecule Diffraction Policy
Instrument Type: X-ray
Instrument Location: KCL 7
Date of Acquisition: September 2013

Co-authorship suggestions
Please note that single crystal diffraction/model prices do not fluctuate based on effort or time and are not waived even if the diffraction model warrants co-authorship. Should you publish data collected in our center, please acknowledge our facility in your manuscripts or grant applications as follows:
 
This research made use of the Chemical and Biophysical Instrumentation Center at Yale University (RRID:SCR_021738).
 
Dr. Mercado is available to assist with the diffraction components of experiments and review manuscripts. Co-authorship should be considered if:
  1. The structural information in the report is derived primarily from diffraction data and constitutes a significant part of the writing.
  2. The structure determination is non-routine, such as involving variable temperature studies, phase changes, or specialized collection environments.
  3. The final structure required a substantial amount of time and technical expertise. For instance:
    • Problematic twinning or significant disorder in structure refinement.
    • Careful consideration of anomalous dispersion (e.g., absolute stereochemistry).
    • Determination of the model by MicroED.

Center Use Policy

  • Staff mounted samples will be mounted at the convenience of their schedule. 

  • Samples can be submitted on the table outside KCL 3

  • To independently use the single crystal diffractometers, you must meet one of the following subpoints:

    • Completed an instrument orientation workshop held in the CBIC (~4 hour time commitment) 

    • Completed CHEM 511 and 512

    • Completed an equivalent course/training at a different institution with a recommendation from the instructor/instrument manager.

  • Independent access enables X-ray facility use for your own research.

  • Independent use does not enable facility use for you to collect data on behalf of other researchers at Yale.

    • Exceptions are granted on a case-by-case basis. 

500wb Bruker Neo 500 MHz NMR spectrometer
Short Name: V500wb
Instrument Type: NMR & EPR
Instrument Location: CRB 100
Date of Acquisition: December 1995

500 MHz wide-bore NMR spectrometer.

3.2 mm CPMAS probe normally installed for solid-state NMR experiments.

Micro MRI imaging capabilities

A400a Agilent DD2 400 MHz NMR Spectrometer (Autosampler)
Short Name: A400a
Instrument Type: NMR & EPR
Instrument Location: KCL 3
Date of Acquisition: August 2013

2 channel system with AS7620 96-sample changer. OneNMR
probe with auto-tune-and-match installed.

Undergraduates have priority on this instrument during lab periods.

Guides and Standard Operating Procedures

Best experiments:

  • PROTON
  • COSY
  • Other nuclei: F19 (no H1 decoupling), P31, B11, (others by request)

Acceptable experiments:

  • C13CPD (night time)
  • 2D HSQC and HMBC experiments
  • 1D/2D NOE experiments

Not available:

  • Variable Temperature experiments
  • Kinetics experiments
  • Simultaneous F19 and H1 experiments

Time Required for NMR Experiments on A400a:

Mass Concentration Proton Carbon gCOSY  gHSQC gHMBC
0.03 mg 0.1 mM 10 h 40 min 35389 hours 1785 hours 1886 hours 7129 hours
0.06 mg 0.2 mM 2 h 40 min 10516 hours 46 h 28 min 474 h 12 min 1785 hours
0.15 mg 0.5 mM 0 h 26 min 1415 h 33 min 6 h 10 min 75 h 01 min 284 h 44 min
0.3 mg 1 mM 0 h 06 min 354 h 01 min 1 h 40 min 18 h 53 min 71 h 19 min
0.6 mg 2 mM 0 h 01 min 88 h 31 min 0 h 26 min 4 h 42 min 17 h 51 min
1.5 mg 5 mM < 1 min 14 h 09 min 0 h 03 min 0 h 45 min 2 h 51 min
3 mg 10 mM < 1 min 3 h 32 min 0 h 03 min 0 h 16 min 1 h 07 min
6 mg 20 mM < 1 min 0 h 53 min 0 h 03 min 0 h 08 min 0 h 17 min
12 mg 40 mM < 1 min 0 h 13 min 0 h 03 min 0 h 08 min 0 h 17 min
15 mg 50 mM < 1 min 0 h 08 min 0 h 03 min 0 h 08 min 0 h 17 min
> 30 mg 100+ mM < 1 min 0 h 04 min 0 h 03 min 0 h 08 min 0 h 17 min

All estimates based on a 500 MW sample in 600 uL solvent volume using a 5 mm diameter NMR tube

A400b Agilent DD2 400 MHz NMR Spectrometer (Manual)
Short Name: A400b
Instrument Type: NMR & EPR
Instrument Location: KCL 3
Date of Acquisition: October 2013

2 channel system. AutoX DB probe installed.  Variable-temperature and H/F experiments available.

Guides and Standard Operating Procedures

Best experiments:

  • PROTON
  • Simultaneous F19 and H1 experiments (i.e. F19 with H1 decoupling)
  • Variable Temperature experiments (with appropriate CBIC training)
  • Kinetics experiments

Acceptable experiments:

  • C13CPD
  • 2D HSQC and HMBC experiments
  • 1D/2D NOE experiments

Not available:

  • Nuclei other than H1, F19 & C13

Time Required for NMR Experiments on A400b:

Mass Concentration Proton Carbon gCOSY  gHSQC gHMBC
0.03 mg 0.1 mM 44 h 44 min 50960 hours 644 hours 7862 hours 29844 hours
0.06 mg 0.2 mM 11 h 11 min 12740 hours 161 hours 1965 hours 7461 hours
0.15 mg 0.5 mM 1 h 47 min 2038 h 24 min 25 h 47 min 319 h 18 min 1193 h 57 min
0.3 mg 1 mM 0 h 27 min 509 h 36 min 6 h 30 min 78 h 37 min 298 h 40 min
0.6 mg 2 mM 0 h 07 min 127 h 27 min 1 h 38 min 19 h 48 min 75 h 40 min
1.5 mg 5 mM 0 h 01 min 20 h 23 min 0 h 16 min 3 h 08 min 12 h 15 min
3 mg 10 mM < 1 min 5 h 15 min 0 h 06 min 0 h 47 min 1 h 32 min
6 mg 20 mM < 1 min 1 h 16 min 0 h 03 min 0 h 08 min 0 h 17 min
12 mg 40 mM < 1 min 0 h 19 min 0 h 03 min 0 h 08 min 0 h 17 min
15 mg 50 mM < 1 min 0 h 12 min 0 h 03 min 0 h 08 min 0 h 17 min
> 30 mg 100+ mM < 1 min 0 h 04 min 0 h 03 min 0 h 08 min 0 h 17 min

All estimates based on a 500 MW sample in 600 uL solvent volume using a 5 mm diameter NMR tube

A400c Agilent DD2 400 MHz NMR Spectrometer (Autosampler)
Short Name: A400c
Instrument Type: NMR & EPR
Instrument Location: KCL 3
Date of Acquisition: October 2013

2 channel system with AS7620 96-sample changer. OneNMR probe with auto-tune-and-match installed.

Primarily used for short, routine NMR experiments where data is needed quickly.

Guides and Standard Operating Procedures

Best experiments:

  • PROTON 
  • COSY
  • Other nuclei: F19 (no H1 decoupling), P31, B11, (others by request)

Acceptable experiments:

  • C13CPD (night time)
  • 2D HSQC and HMBC experiments (night time)
  • 1D/2D NOE experiments (night time)

Not available:

  • Variable Temperature experiments
  • Kinetics experiments
  • Simultaneous F19 and H1 experiments

Time Required for NMR Experiments on A400c:

Mass Concentration Proton Carbon gCOSY  gHSQC gHMBC
0.03 mg 0.1 mM 10 h 40 min 35389 hours 1785 hours 1886 hours 7129 hours
0.06 mg 0.2 mM 2 h 40 min 10516 hours 46 h 28 min 474 h 12 min 1785 hours
0.15 mg 0.5 mM 0 h 26 min 1415 h 33 min 6 h 10 min 75 h 01 min 284 h 44 min
0.3 mg 1 mM 0 h 06 min 354 h 01 min 1 h 40 min 18 h 53 min 71 h 19 min
0.6 mg 2 mM 0 h 01 min 88 h 31 min 0 h 26 min 4 h 42 min 17 h 51 min
1.5 mg 5 mM < 1 min 14 h 09 min 0 h 03 min 0 h 45 min 2 h 51 min
3 mg 10 mM < 1 min 3 h 32 min 0 h 03 min 0 h 16 min 1 h 07 min
6 mg 20 mM < 1 min 0 h 53 min 0 h 03 min 0 h 08 min 0 h 17 min
12 mg 40 mM < 1 min 0 h 13 min 0 h 03 min 0 h 08 min 0 h 17 min
15 mg 50 mM < 1 min 0 h 08 min 0 h 03 min 0 h 08 min 0 h 17 min
> 30 mg 100+ mM < 1 min 0 h 04 min 0 h 03 min 0 h 08 min 0 h 17 min

All estimates based on a 500 MW sample in 600 uL solvent volume using a 5 mm diameter NMR tube

A500a Agilent DD2 500 MHz NMR Spectrometer (Manual)
Short Name: A500a
Instrument Type: NMR & EPR
Instrument Location: KCL 3
Date of Acquisition: January 2014

2 channel system, OneNMR probe with auto-tune-and-match installed.

Guides and Standard Operating Procedures

Best experiments:

  • PROTON
  • COSY
  • 2D HSQC and HMBC experiments
  • 1D/2D NOE experiments
  • Other nuclei: F19 (no H1 decoupling), P31, B11, (others by request)
  • Variable Temperature experiments
  • Kinetics experiments

Acceptable experiments:

  • C13CPD

Not available:

  • Simultaneous F19 and H1 experiments

Time Required for NMR Experiments on A500a:

Mass Concentration Proton Carbon gCOSY  gHSQC gHMBC
0.03 mg 0.1 mM 5 hours 16962 hours 67 h 16 min 820 h 42 min 3113 h 37 min
0.06 mg 0.2 mM 1 h 10 min 424 h 02 min 16 h 50 min 205 h 15 min 779 h 06 min
0.15 mg 0.5 mM 0 h 11 min 678 h 28 min 2 h 45 min 32 h 50 min 124 h 34 min
0.3 mg 1 mM 0 h 03 min 170 h 00 min 0 h 42 min 8 h 20 min 31 h 09 min
0.6 mg 2 mM < 1 min 4 h 15 min 0 h 11 min 2 h 05 min 7 h 48 min
1.5 mg 5 mM < 1 min 3 h 11 min 0 h 03 min 0 h 08 min 1 h 40 min
3 mg 10 mM < 1 min 1 h 42 min 0 h 03 min 0 h 08 min 0 h 17 min
6 mg 20 mM < 1 min 0 h 25 min 0 h 03 min 0 h 08 min 0 h 17 min
12 mg 40 mM < 1 min 0 h 06 min 0 h 03 min 0 h 08 min 0 h 17 min
15 mg 50 mM < 1 min 0 h 04 min 0 h 03 min 0 h 08 min 0 h 17 min
> 30 mg 100+ mM < 1 min 0 h 04 min 0 h 03 min 0 h 08 min 0 h 17 min

All estimates based on a 500 MW sample in 600 uL solvent volume using a 5 mm diameter NMR tube

A500b Agilent DD2 500 MHz NMR Spectrometer (Manual)
Short Name: A500b
Instrument Type: NMR & EPR
Instrument Location: KCL 3
Date of Acquisition: September 2012

2 channel system, OneNMR probe with auto-tune-and-match installed.

Guides and Standard Operating Procedures

Best experiments:

  • PROTON
  • COSY
  • 2D HSQC and HMBC experiments
  • 1D/2D NOE experiments
  • Other nuclei: F19 (no H1 decoupling), P31, B11, (others by request)
  • Variable Temperature experiments
  • Kinetics experiments

Acceptable experiments:

  • C13CPD

Not available:

  • Simultaneous F19 and H1 experiments

Time Required for NMR Experiments on A500b:

Mass Concentration Proton Carbon gCOSY  gHSQC gHMBC
0.03 mg 0.1 mM 5 hours 16962 hours 67 h 16 min 820 h 42 min 3113 h 37 min
0.06 mg 0.2 mM 1 h 10 min 424 h 02 min 16 h 50 min 205 h 15 min 779 h 06 min
0.15 mg 0.5 mM 0 h 11 min 678 h 28 min 2 h 45 min 32 h 50 min 124 h 34 min
0.3 mg 1 mM 0 h 03 min 170 h 00 min 0 h 42 min 8 h 20 min 31 h 09 min
0.6 mg 2 mM < 1 min 4 h 15 min 0 h 11 min 2 h 05 min 7 h 48 min
1.5 mg 5 mM < 1 min 3 h 11 min 0 h 03 min 0 h 08 min 1 h 40 min
3 mg 10 mM < 1 min 1 h 42 min 0 h 03 min 0 h 08 min 0 h 17 min
6 mg 20 mM < 1 min 0 h 25 min 0 h 03 min 0 h 08 min 0 h 17 min
12 mg 40 mM < 1 min 0 h 06 min 0 h 03 min 0 h 08 min 0 h 17 min
15 mg 50 mM < 1 min 0 h 04 min 0 h 03 min 0 h 08 min 0 h 17 min
> 30 mg 100+ mM < 1 min 0 h 04 min 0 h 03 min 0 h 08 min 0 h 17 min

All estimates based on a 500 MW sample in 600 uL solvent volume using a 5 mm diameter NMR tube

A600a Agilent DD2 600 MHz NMR Spectrometer (Autosampler)
Short Name: A600a
Instrument Type: NMR & EPR
Instrument Location: KCL 3
Date of Acquisition: October 2013

3 channel system with AS7510 12-sample automatic sample changer. C{H} cold probe with auto-tune-and-match installed. Highest sensitivity for C13 NMR experiments.

Guides and Standard Operating Procedures

Best experiments:

  • CARBON
  • PROTON

Acceptable experiments:

  • 1D/2D NOE experiments

Not available:

  • Variable Temperature experiments
  • Kinetics experiments
  • Nuclei other than H1 and C13

Time Required for NMR Experiments on A600a:

Mass Concentration Proton Carbon gCOSY  gHSQC gHMBC
0.03 mg 0.1 mM 0 h 24 min 1298 hours 5 h 54 min 72 h 04 min 272 h 22 min
0.06 mg 0.2 mM 0 h 06 min 324 h 32 min 1 h 28 min 19 h 35 min 68 h 32 min
0.15 mg 0.5 mM 0 h 01 min 51 h 56 min 0 h 16 min 3 h 11 min 11 h 10 min
0.3 mg 1 mM < 1 min 13 h 00 min 0 h 03 min 0 h 47 min 2 h 47 min
0.6 mg 2 mM < 1 min 3 h 15 min 0 h 03 min 0 h 16 min 1 h 07 min
1.5 mg 5 mM < 1 min 0 h 31 min 0 h 03 min 0 h 08 min 0 h 34 min
3 mg 10 mM < 1 min 0 h 08 min 0 h 03 min 0 h 08 min 0 h 17 min
6 mg 20 mM < 1 min 0 h 04 min 0 h 03 min 0 h 08 min 0 h 17 min
12 mg 40 mM < 1 min 0 h 04 min 0 h 03 min 0 h 08 min 0 h 17 min
15 mg 50 mM < 1 min 0 h 04 min 0 h 03 min 0 h 08 min 0 h 17 min
> 30 mg 100+ mM < 1 min 0 h 04 min 0 h 03 min 0 h 08 min 0 h 17 min

All estimates based on a 500 MW sample in 600 uL solvent volume using a 5 mm diameter NMR tube

A800 Agilent 800 MHz NMR Spectrometer (Manual)
Short Name: A800
Instrument Type: NMR & EPR
Instrument Location: CRB 100
Date of Acquisition: July 2013

4 channel system. Inverse-detect HCN probe, Dual Band (direct-detect) probe, and H{CN} C13-sensitivity enhanced salt-tolerant cold probe available.

Experienced Users Only. Contact CBIC staff for more information.

Analytical Ultracentrifuge Beckman Coulter Proteomelab XL-I
Short Name: AU
Instrument Type: Solution Biophysics
Instrument Location: KCL 3
Date of Acquisition: November 2009

Analytical ultracentrifugation is a column-free separation technique that measures the relative change in the distribution of molecular weights, providing a way to measure heterogeneity, stoichiometry and self-association of proteins, oligomers, aggregates, particles, colloids, and small structures in solution. 

Applied Photophysics Chirascan Circular Dichroism Spectrometer
Short Name: CD
Instrument Type: Solution Biophysics
Instrument Location: KCL 3
Date of Acquisition: September 2013

Chirascan is a modern, high performance circular dichroism (CD) spectrometer operating in the ultraviolet and visible wavelength range. It is typically used to probe the secondary structure or conformation of bio-molecules.

Standard Operating Procedure

DLS Dynamic Light Scattering Wyatt DynaPro PlateReader II
Short Name: DLS
Instrument Type: Solution Biophysics
Instrument Location: KCL 11
Date of Acquisition: October 2013

Dynamic light scattering measures the diffusion rate of molecules or particles in solution by observing the fluctuations in scattered light from a laser passing through a sample. The sensitivity of DLS increases with increasing molecular size, with a typical lower size limit of 0.5 nanometers and upper size limit of 10 micrometers.

Typical applications for DLS include:

  • Screening macromolecules prior to crystallization trials
  • Measuring the stability of protein samples for NMR analysis
  • Monitoring molecular aggregation
  • Characterizing nanoparticles

The DynaPro PlateReader II is set up to make these measurements in 96, 384, or 1536 well plates using as little as 5 microliters of sample.

Standard Operating Procedure

EPR Bruker EleXsys EPR Spectrometer
Short Name: EPR
Instrument Type: NMR & EPR
Instrument Location: KCL 12
Date of Acquisition: September 2000

X-Band Electron Paramagnetic Resonance. Equipped with a cryogen-free cryostat.

FTIR ASI React IR Reaction Monitoring System
Short Name: ReactIR
Instrument Type: Optical Spectroscopy
Instrument Location: KCL 3
Date of Acquisition: June 1998

React IR 15 FTIR for real-time monitoring of chemical reactions in situ.

FTIR Shimadzu IRTracer-100
Short Name: IR Tracer
Instrument Type: Optical Spectroscopy
Instrument Location: KCL 11
Date of Acquisition: February 2020

The IRTracer-100 offers exceptionally high sensitivity with an SN ratio of 60,000:1, high resolution down to 0.25 cm−1, and fast measurement speeds up to 20 scans per second.
The system supports a wide variety of applications with features such as a 12,000-entry library and a data analysis program for contaminant analysis and time course and rapid scan functions for tracking reactions.

Available Accessories:

  • ATR Unit for Solid Samples
  • VeeMax II Variable Angle Specular Reflectance Accessory
  • Gas Cuvette & Holder
  • KBr Pellets

For more compatible accessories for your measurement needs, please have a look at the Shimadzu Selection Guide.

FTIR/Raman Thermo Nicolet 6700
Short Name: FTIR
Instrument Type: Optical Spectroscopy
Instrument Location: KCL 11
Date of Acquisition: November 2006

Diamond ATR cell normally installed. Transmission, DRIFTS, ZnSe ATR, and high-temperature accessories available. Raman with IR-laser source also available.

Standard Operating Procedure

GC-MS Agilent 6890N/5973
Short Name: GC-MS
Instrument Type: Mass Spectrometry
Instrument Location: KCL 3
Date of Acquisition: February 2004

Open access GC-MS instrument with 100-position sample changer and 20 meter column installed.

Standard Operating Procedure

GC-MS column selection
Short Name: GC-MS columns
Instrument Type: Mass Spectrometry
Instrument Location: KCL 3
Date of Acquisition: September 2021

Column Name Manufacturer Thickness (um) Length (m) Diameter (mm) Max. Temp. (deg C)
SH-Rxi-5Sil MS Shimadzu 0.25 30 0.25 350
DB select 624UI Agilent 1.4 30 0.25 260
ZB-WAX Zebron 0.5 30 0.25 250
PoraPLOT Q Agilent 8 25 0.25 250
EC-1 Grace 0.25 30 0.25 350
VF-WAXms Agilent 1 30 0.25 260
Rtx-1 Restek 0.25 15 0.25 350
Stabilwax-MS Restek 0.25 30 0.25 260
GC-TQ-MS Shimadzu 8050 NX
Short Name: GC-TQ-MS
Instrument Type: Mass Spectrometry
Instrument Location: KCL 3
Date of Acquisition: December 2019

Shimadzu 8050 NX Triple Quadrupole (TQ) GC-MS with Liquid Injection, Solid Phase Micro Extraction (SPME) and Headspace Analysis Autosampler. Triple Quadrupole MS instruments allow for quantitation of compounds, collision induced dissociation (CID) and multiple reaction monitoring (MRM). The system is equipped with an Electron Ionization (EI) source, a Chemical Ionization (CI) source and a Flame Ionization Detector (FID).

LC-MS Shimadzu 8060 TQ
Short Name: 8060
Instrument Type: Mass Spectrometry
Instrument Location: KCL 3
Date of Acquisition: January 2020

Service only Shimadzu LCMS-8060 Triple Quadrupole Liquid Chromatograph Mass Spectrometer (LC-MS/MS). Triple Quadrupole MS instruments allow for quantitation of compounds, collision induced dissociation (CID) and multiple reaction monitoring (MRM) with high sensitivity. The UPLC system includs a fluidic system with two different solvents, three trays for up to 54 samples each (in GC vials), three UPLC columns (see list below) and a photo-diode array (UV/Vis) detector. 96 and 384 well plates can be used for screening projects, please reach out first.

Column 1: Shim-pack Scepter C18-120 1.9mum - 2.1 x 50mm
Column 2: Shim-pack Scepter C18-120 1.9mum - 2.1 x 100mm
Column 3: Shim-pack Scepter C8-120 1.9mum - 2.1 x 100mm

Different columns can be installed on demand.

Standard Solvents available for LC separation:

Water (with 0.1% Formic Acid or 10mM NH4Ac)
Methanol (with and w/o 0.1% Formic Acid or 10mM NH4Ac)
Acetonitrile (with and w/o 0.1% Formic Acid or 10mM NH4Ac)

Different solvents can be used on demand.

LC-MS Shimadzu 9030 Quadrupole Time-of-Flight MS
Short Name: 9030
Instrument Type: Mass Spectrometry
Instrument Location: KCL 3
Date of Acquisition: January 2020

Shimadzu LCMS-9030 Quadrupole Time-of-Flight High-Performance Liquid Chromatograph Mass Spectrometer for high-resolution MS.

Service only high resolution Q-tof MS instrument with an UPLC system, including a fluidic system with two different solvents, three trays for up to 54 samples each (in GC vials), three UPLC columns (see list below) and a photo-diode array (UV/Vis) detector. 96 and 384 well plates can be used for screening projects, please reach out first.

Column 1: Shim-pack Scepter C18-120 1.9mum - 2.1 x 50mm
Column 2: Shim-pack Scepter C18-120 1.9mum - 2.1 x 100mm
Column 3: Shim-pack Scepter C8-120 1.9mum - 2.1 x 100mm

Different columns can be installed on demand.

Standard Solvents available for LC separation:

  • Water (with 0.1% Formic Acid or 10mM NH4Ac)
  • Methanol (with and w/o 0.1% Formic Acid or 10mM NH4Ac)
  • Acetonitrile (with and w/o 0.1% Formic Acid or 10mM NH4Ac)

Different solvents can be used on demand.

LC-MS ThermoScientific QExactive Orbitrap (+ IR spectroscopy)
Short Name: Orbi
Instrument Type: Mass Spectrometry
Instrument Location: KCL 3
Date of Acquisition: August 2019

Service only high resolution QExactive Orbitrap FT-MS instrument with an Dionex 3000 UPLC system, including a fluidic system with up to four different solvents, three trays for up to 40 samples each (in 2 mL GC vials), one UPLC column, a UV/Vis photo-diode array (PDA) and a fluorescence (FL) detector.

The structural mass spectrometry extension on this instrument allows for recording of infrared spectra of mass selected ions in the gas phase. Read more about the technique here.

Software for opening and converting .raw files: http://msfragger.nesvilab.org/tutorial_convert.html

LC-MS Waters Xevo Qtof high-resolution MS
Short Name: Xevo
Instrument Type: Mass Spectrometry
Instrument Location: KCL 3
Date of Acquisition: November 2018

Service only high resolution Q-tof MS instrument with an UPLC system, including a fluidic system with up to four different solvents, two trays for up to 48 samples each (in GC vials), four UPLC columns (see list below) and a photo-diode array (UV/Vis).

Column 1: Acquity UPLC BEH C18 1.7mum - 2.1 x 50mm
Column 2: Acquity UPLC BEH Glycan 1.7mum - 2.1 x 100mm
Column 3: Acquity UPLC BEH300 C18 1.7mum - 2.1 x 100mm
Column 4: Acquity UPLC BEH C8 1.7mum - 2.1 x 100mm

MALDI-ToF-MS Shimadzu AXIMA Confidence
Short Name: MALDI
Instrument Type: Mass Spectrometry
Instrument Location: KCL 3
Date of Acquisition: January 2020

AXIMA Confidence Linear/Reflectron MALDI-TOF Mass Spectrometer from Shimadzu.

Target Plates available:
AXIMA 384 well (2.8mm I.D.) plate - P/N: DE1580TA

Number of wells: Sample = 384
Calibrant = 0
Internal diameter of wells: Sample = 2.8mm
Calibrant = N/A

FlexiMass-SR48 steel targets - P/N: TO-431R00

Number of wells: Sample = 48
Calibrant = 3
Internal diameter of wells: Sample = 2.8mm
Calibrant = 2.2mm

FlexiMass-DS disposable targets - P/N: TO-430R00

Number of wells: Sample = 48
Calibrant = 3
Internal diameter of wells: Sample = 2.8mm
Calibrant = 1.5mm
Mass Spectrometry meets Infrared Spectroscopy
Short Name: Mass Spec based CIVP IR Spectroscopy
Instrument Type: Mass Spectrometry
Instrument Location: KCL 3
Date of Acquisition: December 2021

Mass Spectrometry meets Infrared Spectroscopy

Structural insights into cold, mass selected ions

https://cbic.yale.edu/mass-spectrometry-meets-infrared-spectroscopy

MS recommendations, method descriptions and software
Short Name: MS resources
Instrument Type: Mass Spectrometry
Instrument Location: KCL 3
Date of Acquisition: February 2021

Disclaimer: All information on this site is subject to change and the actual experimental methods used might differ from the ones found here!

Recommendations:

MS_Sample_Method_Recommendations_v2.docx

Method Descriptions (methods might have changed over time, please double-check!):

Shimadzu 9030 HRMS Description

Thermo Fisher QExactive Orbitrap HRMS Description

Software:

Data exchange

MS data can be exported as mzXML or mzML files and shared via box or google drive upon request. The files contain TIC and MS data, EIC can be extracted through user analysis. These data files can be opened with MestreNova (updated and fully installed licenses necessary!):

Download the software and license bundle from the CBIC homepage:

https://cbic.yale.edu/yale-only/mnova-download

Close MestreNova (for update of existing installation), and run as Administrator by:

Windows Start menu -> MestreNova Folder -> Right Click on MestreNova -> more -> Run as Administrator

Install the Licenses again, close the software and start it as a normal user.

Complex data workups and simple txt data can be provided based on the project.

Software for opening and converting ThermoFisher .raw files: http://msfragger.nesvilab.org/tutorial_convert.html

Acknowledgements:

If you use CBIC instruments in your research, we request that you acknowledge our facility in your written publications or grant applications as follows:

Acknowledgement: This research made use of the Chemical and Biophysical Instrumentation Center at Yale University (RRID:SCR_021738). Equipment was purchased with funds from Yale University.
Optional for Orbitrap QExactive MS: NSF MRI grant CHE-1828190.
 

Pilatus3R HPC on a 007 VHF+Arc)Sec X-ray Source
Short Name: 007c
Instrument Type: X-ray
Instrument Location: KCL 7
Date of Acquisition: October 2016

The Pilatus3R 200KA detector on our Rigaku 007 HF+ rotating anode with VHF Arc)Sec optics is suitable for solving small molecules samples. This instrument is run by the CBIC Staff. λ = 0.7107 Å

Polarimeter Perkin Elmer 341
Short Name: Polarimeter
Instrument Type: Optical Spectroscopy
Instrument Location: KCL 16B
Date of Acquisition: January 1997

General-purpose precision Polarimeter with Na and Hg source lamps and Glan-Taylor polarizer.

Standard Operating Procedure

Polarimeter Rudolph Autopol IV
Short Name: Autopol
Instrument Type: Optical Spectroscopy
Instrument Location: KCL 16B
Date of Acquisition: February 2018

The AUTOPOL® IV is a microprocessor based automatic polarimeter that is available in one, two and six wavelength versions. The AUTOPOL® IV’s features include: readout in Specific Rotation, Optical Rotation, and concentration, customer defined and labeled programs for push button readout, large LCD display and touchscreen user interface, temperature display and correction, push button wavelength selection, statistics, 3 USB ports, 1-USB 3.0, RS 232 and parallel printer ports.

Rigaku CCD on 007HF+ X-ray Source
Short Name: 007a
Instrument Type: X-ray
Instrument Location: KCL 7
Date of Acquisition: October 2009

The Saturn 944+ CCD detector on our Rigaku 007 HF+ rotating anode X-ray source with HF optics is suitable for solving small-molecule and protein structures by single-crystal X-ray diffraction.  This instrument can also be used to screen crystals before sending them to an x-ray beam line at a synchrotron. λ = 1.5418 Å

Rigaku CCD on 007HF+Arc)Sec X-ray Source
Short Name: 007b
Instrument Type: X-ray
Instrument Location: KCL 7
Date of Acquisition: June 2016

The Rigaku Saturn 944HG CCD detector on our Rigaku 007 HF+ rotating anode X-ray source with HF Arc)Sec optics is suitable for solving small molecules samples. This instrument is run by the CBIC Staff. λ = 1.5418 Å

Rigaku MiniFlex600 Powder X-ray Diffractometer
Short Name: PXRD
Instrument Type: X-ray
Instrument Location: KCL 7
Date of Acquisition: December 2004

This powder diffractometer can characterize crystallinity, crystal phases, and, in many cases, the identity of solid samples. Our instrument has a sealed-tube copper X-ray source, a scintillation counter with high dynamic range, and Bragg-Brentano geometry with slits providing high resolution for flat powder samples. λ = 1.5418 Å

Rigaku XtaLAB Mini II with a hybrid pixel detector
Short Name: mini2
Instrument Type: X-ray
Instrument Location: KCL 7
Date of Acquisition: May 2022

The XtaLabMini II is a fully functional benchtop single-crystal X-ray diffractometer with a CCD detector. λ = 0.7107 Å

Rigaku XtaLAB Synergy, Dualflex, HyPix-Arc 100
Short Name: syn
Instrument Type: X-ray
Instrument Location: KCL 7
Date of Acquisition: January 2023

Copper and silver X-ray sources are available. The curved image plate detector allows high dynamic range and collection out to a 2Θ angle of 144 degrees in a single image to yield high-resolution single-crystal data.

TA NanoITC
Short Name: ITC
Instrument Type: Solution Biophysics
Instrument Location: KCL 16B
Date of Acquisition: August 2014

By determining heat changes associated with binding between any two biomolecules, ITC measures all binding parameters in a single label-free, in-solution experiment.

TCSPC TD-Fluor Horiba Fluorolog 3 Time Domain Fluorimeter
Short Name: TCSPC
Instrument Type: Solution Biophysics
Instrument Location: KCL 16B
Date of Acquisition: December 2009

The Fluorolog 3 is a modular fluorimeter that can be set up to make time-domain fluorescence measurements at specific wavelengths, or steady-state fluorescence measurements over a range of excitation and/or emission wavelengths. 

TTP Lab-tech Nanoliter Pipetting System
Short Name: Mosquito
Instrument Type: X-ray
Instrument Location: KCL 7
Date of Acquisition: October 2009

TTP Labtech’s mosquito allows for the creation of protein crystallization screens with several multi-component drops per well, even in 96-well hanging drop set-ups.

UV-VIS Cary 3E Spectrophotometer
Short Name: UV-VIS
Instrument Type: Optical Spectroscopy
Instrument Location: KCL 3
Date of Acquisition: November 1995

Standard cuvette holder, temperature-regulated cuvette sample change, and integrating sphere available.

Standard Operating Procedure

UV-VIS Shimadzu UV-3600Plus
Short Name: UV-3600
Instrument Type: Optical Spectroscopy
Instrument Location: KCL 11
Date of Acquisition: February 2020

High performance UV-VIS-NIR Spectrophotometer with four gratings, wide dynamic range -6 to 6.0 ABS, resolution to 0.1nm, excellent stray light rejection: less than 0.00008% at 220nm, sealed optics, self-aligning lamps, high-mass, stable optical bench, selectable and constant bandpass.

Options:

  • Integrating sphere for solid and liquid samples with 3 detector system includes - PMT, InGaAs and Peltier controlled PbS detectors for a superior S/N ratio.
  • S-1700 Thermoelectric Single Cell Holder Temperature Controller (0 to 110 deg C) with stirrer, Thermal Melt Software for analysis of e.g. DNA melting temperatures.
V600a Varian VNMRS 600 MHz NMR Spectrometer (Manual)
Short Name: V600a
Instrument Type: NMR & EPR
Instrument Location: CRB 100
Date of Acquisition: July 2009

3 channel system. Inverse-detect HCN probe installed.

V600b Varian VNMRS 600 MHz NMR Spectrometer (Manual)
Short Name: V600b
Instrument Type: NMR & EPR
Instrument Location: CRB 100
Date of Acquisition: August 2002

3 channel system. Inverse-detect HCN probe installed.

V700 Varian Inova 700 MHz NMR Spectrometer (Manual)
Short Name: V300b
Instrument Type: NMR & EPR
Instrument Location: KCL 3
Date of Acquisition: October 2010

4 channel system, triple resonance probe normally installed.

Xenocs Xeuss 3.0 Small/Wide X-ray Scattering System
Short Name: SAXSWAXS
Instrument Type: X-ray
Instrument Location: SCL 26
Date of Acquisition: December 2022

The Xeuss 3.0 offers a maximum flexibility of measurement configurations to get the best possible data quality on any type of sample.

 

In particular, the following key features enable the user to optimize experiments or results:

 
  • High flux settings adapted for fast kinetics embedded in a low background camera
  • Largest surface of detection moveable all the way from WAXS to long distance SAXS to optimize resolution and signal-to-noise
  • Long distance SAXS settings for measuring large characteristic dimensions (up to 900 nm depending on the Xeuss 3.0 model)
  • Optional USAXS module to characterize  large structures ( > 2.5 µm)
XT H 225 Computed Tomography Scanner
Short Name: microCT
Instrument Type: X-ray
Instrument Location: SCL 26
Date of Acquisition: May 2018

Micro-CT is a 3D imaging technique utilizing X-rays to see inside an object, slice by slice.  Micro-CT, also called microtomography or micro computed tomography, is similar to hospital CT or “CAT” scan imaging but on a small scale with greatly increased resolution. Samples can be imaged with pixel sizes as small as ~1 micron and objects can be scanned up to ~50 cm in diameter.

The versatile XT H 225 scanner can be used to cover a wide range of applications, including the inspection of plastic parts, electronics and complex mechanisms as well as researching materials and natural specimens.

The scanner can be fit with a rotating anode, reflection, or transmission target. The rotating anode produces the most X-rays, which is good for highly absorbing material, but has the lowest resolution. The transmission target has the best resolution, but produces the least amount of X-rays. The reflection target is typically installed and has a balance between X-ray intensity and resolution.  If your needs require the rotating or transmission target, please inquire in advance about scheduling.