MS:NMR:XRay:

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Chemical Analyses Cores
OVERVIEW
RESEARCH CONTRIBUTION HIGHLIGHT
LIST OF SERVICES
Mass Spectrometry Facility Services
Ionization Methods EI, CI, FAB, ESI, MALDI
Analyses Low resolution MS and MS/MS
High resolution MS and
MS/MS Accurate mass
measurements Hyphenated Techniques GC/MS

LC/MS and LC/MS/MS Applications Proteomics
peptide mass fingerprinting
in-gel and
in-solution protein digests
Metabolomics LC/MS and LC/MS/MS
Imaging TLC separations
tissue
sections
Mass Spectrometry Facility The University of
Notre Dame Mass Spectrometry (MS) Facility
provides instrumentation and expertise for the
analyses of both small and large molecules. In
early 2009, an expanded and upgraded facility
will relocate to newly renovated space in the
Department of Chemistry Biochemistry. The MS
Facility gladly welcomes samples from outside
Notre Dame. For more information, please visit
our website at http//www.nd.edu/massspec The
Center for Nuclear Magnetic Resonance The Center
for Nuclear Magnetic Resonance Spectroscopy (NMR)
at the University of Notre Dame supports new and
ongoing research in chemistry, chemical
engineering, biochemistry, molecular biology and
related fields. Our instrumentation enables us to
perform state-of-the-art multinuclear,
multidimensional high resolution NMR experiments
at various field strengths and temperatures to
determine the molecular structures and dynamics
of a wide range of compounds. X-Ray Diffraction
Facility The X-Ray Diffraction Facility at the
University of Notre Dame (X-Ray) provides for
X-Ray structural studies of small (ca. 2kDa)
molecules. X-Ray has the capability to examine a
wide range of molecules from light atom
biologically relevant to metal-complexed
compounds which can be readily analyzed using
non-destructive techniques.
Structural
analysis and binding modes of dioxygen (O2) and
nitrosyl (NO) in heme (iron-porphyrin)
mimics - NO identified in a number of
biological signaling/control mechanisms - O2
transport and energy conversion in biological
systems Electronic effects in atom transfer
reactions - Metal-organic complexes
(metalloprotein mimics) allow atom transfer
reactions which with pure organics may be
forbidden - Applicable to organic and
biological reactions - Chiral recognition and
synthesis Structural analysis of siderophore,
ß-lactam and hydroxamic acid derivatives in
conjunction with all of the core
facilities Configuration and coordination
environment of rotaxane-based dyes for near-IR
imaging Studies of drug precursor and bioactive
molecules - Part of multi-disciplinary
research encompasses computational studies,
synthesis and reactivity of new bioactive
molecules, enzymology - Inhibitor, host/guest
interactions
Recent Applications of a MALDI-TOF/TOF Mass
Spectrometer Imaging MS and Proteomics
The Center for Nuclear Magnetic
Resonance Services Numerous high resolution
multinuclear and multidimensional NMR
spectroscopy
experiments. Training of
researchers for independent use of resources
Provide assistance with proposal
preparation and manuscript writing Applications
Determination of molecular structure and
dynamics of a wide variety of
compounds (e.g. proteins,
nucleic acids, carbohydrates, synthetic
polymers, natural
products, lipids, macrocyclic polyethers)

• Sweet, L.S., Zhang, W., Torres-Fewell, H.,
  Serianni, A., Boggess, W., Schorey, J. (2008) J
  Biol. Chem.,accepted.
• We would like to thank Caroline Trippel and
  Caitlin Koscielski for obtaining the imaging MS
  results.

• The Center for Nuclear Magnetic Resonance
• Specific research capabilities/collaborations of
  of the Center
• - Structure/dynamics studies of single-chain
  human T-cell receptor fragments and complexes
  between peptide antigens and major
  histocompatibility molecules associated with the
  auto-immune HAM/TSP.
• Structure/dynamics studies of the binding of
  human plasminogen to proteins not containing
  carboxyl-terminal lysine residues, and
  structure-function studies of conantokin
  peptides.
• Structure/dynamics studies of synthetic
  polycarbohydrates and oligopeptides to gain
  insight into their biological activities.
• Investigation of how the atomic motions of
  proteins and ligands impact disease and therapy.
• Studies of the binding of the anti-cancer drug
  cisplatin to the zinc binding domain of DNA
  polymerase-a.
• Synthesis, and structural and biological
  studies, of antibiotics and anti-cancer agents
  that occur as natural products.
• Studies of the solution conformations of
  biologically active polyketide natural products
  and designed analogues.
• Investigation of the chemistry and biochemistry
  of nitrogen containing compounds such as
  hydroxamic acid-based microbial iron transport
  agents, peptides, carbocyclic nucleosides,
  ?-lactams, antibiotics, and anti-fungal and
  anti-tumor agents.
• Elucidation and characterization of the dynamic
  structures of host/guest complexes, especially
  relatively large interlocked rotaxane molecules
  NMR-based studies of membrane transport.
• Synthesis and structure/dynamics investigations
  of isotopically labeled complex carbohydrates and
  oligonucleotides, and fundamental NMR studies of
  J-coupling, residual dipolar couplings, and 13C
  chemical shift anisotropy in saccharides.

RESOURCES
Mass Spectrometry Facility Mass
Spectrometers Liquid Chromatography Bruker
MicrOTOF-II Time-of-Flight Dionex RSLC
Ultra-High Pressure Bruker MicrOTOF-Q II
Quadrupole Time-of-Flight Liquid
Chromatograph Bruker HCT Ultra Ion Trap
Dionex Ultimate 3000 2Dimensional Bruker
Autoflex III MALDI-TOF-TOF LC System
Micromass Quattro-LC Triple Quadrupole LC
Packings Ultimate Capillary HPLC JEOL GCMate
Benchtop Magnetic Sector
Waters Alliance 2695 JEOL AX505HA Magnetic
Sector The Center for Nuclear Magnetic
Resonance Spectroscopy NMR operates
eight spectrometers, ranging in proton
resonance frequency from 300 to 800
MHz All spectrometers
are multinuclear and equipped with an
array of modern probes. The 800 and
700 MHz spectrometers are equipped with
triple resonance cryoprobes. The 800,
700, 600 and 500 MHz instruments, are
configured to allow the development of new
multinuclear, multidimensional,high
resolution One of the eight spectrometers exper
iments to support new and evolving of the NMR
Center methodology. X-ray Diffraction
Facility Three area detector
instruments 2 X 3-circle (Mo and Cu
radiation Cu is ideal for light atom
molecules) 1 X 4-circle (Mo
radiation) Cryogenic and variable
temperature studies Synchrotron access
at the Chemical Crystallography beam
line (11.3.1) at the Advanced Light
Source at Lawrence Berkeley National
Laboratory
X-Ray Diffraction Facility Services Data
collection, structure solution and structure
analysis Structural database
searches (CSD, ICSD) Analysis
of samples from 10 x 10 x 10 µm and larger
Conformational and stereochemical
analysis of compounds
(desirable for molecular interactions with
macromolecules) Applications Molecular and
atomic identification can differentiate atom
types
Molecular interactions (solid state)
electrostatic interactions, Van der Waals
interactions
Provides an accurate starting point for
molecular simulation (computational)
studies
Stereochemical analysis is essential for
understanding bioactive molecules
Technique is synergistic with other
analytical techniques leading to a complete
molecular analysis
X-Ray Diffraction Facility

• MS NMR X-Ray
• Dr. Bill Boggess, Director Dr. Jaroslav Zajiek,
  Director Dr. Allen Oliver, Director
• Phone [phone] Phone (574)
  631-9111 Phone [phone]
• Email wboggess_at_nd.edu Email jzajicek_at_nd.edu Emai
  l aoliver2_at_nd.edu

CONTACT INFORMATION