Transcript Document

Department of Chemistry
TRC News
Number 1 – September, 2007
Vertere, is a world leader in hazardous materials tracking,
and will be adapted to conform to Canadian legislation.
This will be a web based system that will allow users on
campus to have some degree of control over their own
inventories. This project will also be used to hire two
individuals – a ‘project manager’ who will over see the
implementation and integration of the technology to the
campus, and a stores person who will be responsible for
receiving and inventorying all chemicals on campus. This
project will be overseen by EH&S, but Rick Boswell will
remain as the co-investigator for Queen’s. Queen’s
participation in this project is primarily due to Rick’s long
term collaboration with his colleagues at U of O. This
project represents a shift in funding of about $10K/year
(department funded), to over $200K/year (project funded).
It also represents a shift in responsibility from the
Department looking after its own systems to the University
taking over the fundamental responsibility of hazardous
materials tracking on a campus wide basis.
(Rick Boswell)
Message from the Chair of TRC
This is the first issue of the Technical Resources
Committee (TRC) Newsletter. The primary objective of
this newsletter is to provide a vehicle of communication
between the TRC and the users of the major instruments
within the Department of Chemistry. Our goal is to publish
this newsletter every four to six months.
The mandate of the TRC includes to: (1) setup the
policies concerning departmental research facilities
including user fees, (2) monitor and approve the
expenditure of the departmental instrument accounts
(NMR, MS and X-ray facilities), (3) resolve issues related
to the use and service of departmental facilities, (4)
facilitate the access and usage of major departmental
instrumentation/facilities by researchers and the
communication between instrumental managers and
researchers, and (5) make recommendations for the
operation, maintenance, and upgrade of departmental
facilities.
Current Members of TRC include: Suning Wang (Chair),
Pam Bandy-Dafoe, Rick Boswell, David Edward (graduate
student), Tom Hunter, Igor Kozin, Donal Macartney, JeanMichel Nunzi, Françoise Sauriol, Gang Wu, and David
Zechel.
Researchers who have any concerns or encountered any
problems with our departmental facilities (e.g., chemical
store, glassblowing shop, electronics shop, NMR and MS
facilities and X-ray diffraction service, etc.) should contact
TRC.
(Suning Wang)
• Glassblower’s weekly visit resumed
• The departmental glassblower returns to his weekly visit:
Monday, 10 am – noon. He also gets a new departmental
email account: [email protected].
•Wireless internet access in Chernoff Hall
Wireless internet access available at all floors in the
Atrium area and Administration wing area. To use the
wireless make sure your wireless card is on once it detects
queensu.ca open your browser and it will take you directly
to the wireless web access page. Once they enter your
netid and password for Queen’s and that should then give
you access.
(Ed Maracle)
News
• Chemical Inventory Software Development
The Chemical Inventory system used in chemistry is
about to get a major overhaul. The University has
partnered with the University of Ottawa (Project Leader),
Concordia and RMC to develop a ‘Higher Education
Cooperative for Hazardous Materials and Equipment
Tracking (HECHMET)’ system. This project was a
successful applicant in the last round of CRTI funding, and
was awarded $3.8M to institute a common tracking system
between Canadian Institutions. Queen’s will receive
approximately $1M over 5 years to develop protocols and
broaden the scope of the inventory system from Chemistry
to the entire institution.
The current inventory will be ported over to the new
inventory system sometime in early 2008. This new
system, a commercial product from the U.S. produced by
• New location for Electronics Shop
The Electronic shop has moved to Rms. 301 (shop area)
and 302 ( office). For all networking, e-mail and computer
related requests or problems contact Ed Maracle
(Departmental computer rep.) @78107. For NMR,
hardware requests or problems contact Robin Roberts @
32629. The shop also oversees the departmental data
projectors, digital camera and laptops. Scheduling is done
online and a user id and password are required. Some
departmentally licensed software is controlled through the
electronic shop as well.
(Robin Roberts)
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Technical Notes
log(m2/s)
DOSY (Diffusion Ordered SpectroscopY)
0.030
0.028
0.026
By Françoise Sauriol
Sucrose
0.024
DSS
0.022
Studies of molecular diffusion by nuclear magnetic
resonance (NMR) have been proposed some time ago by
Stejskal and Tanner using the pulse sequence PGSE
(Pulse Gradient Spin Echo) (Fig.1). In this pulse
sequence, the magnetization is labeled by the first gradient
pulse, according to the position that nuclei occupy in the
NMR tube. After a delay only those nuclei occupying the
same position in the NMR tube will be refocused correctly
by the second gradient. Therefore diffusion yields an
attenuation of the signal as a function of gradient strength.
0.020
0.018
Acetone
0.016
D2O
0.014
0.012
0.010
5.0
4.5
4.0
3.5
3.0
2.5
2.0
1.5
1.0
0.5
ppm
Figure 2: 2D-DOSY of a mixture of Sucrose, DSS,
Acetone and D2O obtained on our Avance-600.
CD
n=2+CD
n=2
n=2, partial interaction with CD
CD
n=4+CD
n=4
n=4, complete interaction with CD
Figure 3: Adapted from an article by Liat Avram and
Yoram Cohen, J. Org. Chem. 2002, 67, 2639-2644.
Diffusion experiments deals with the size of the molecule
and the interactions that can slow down the motion of the
molecules in a solvent. DOSY have been used in a wide
variety of applications. DOSY is used to determine best
drug candidate in a library of compounds from the
interaction with proteins. It is used to characterize ligandreceptor interactions, Host-Guest interaction, Hydrogen
bound study, aggregation studies, etc…
Figure 1: PGSE and diffusion measurement.
Diffusion experiments have received a lot of attention in
the last 10 years. With the improvements in the hardware
and software in the NMR spectrometers, these specialized
experiments are relatively easy to perform on any modern
NMR spectrometer equipped with gradient. Diffusion
studies can be treated as a pseudo-2D experiment (as
shown in Fig. 2) separating each compound in a mixture as
a function of their diffusion rate. This experiment is called
DOSY and provides the chemical shift along the
horizontal axis (detection) while on the vertical axis
(indirect detection) we find the diffusion coefficient of the
different molecules.
Host-Guest interactions are illustrated in Fig.3 as an
example. In this figure, we can see that the diffusion rate
of the large cyclodextrine (CD) is slower than the
diffusion rate of free linear chain diamine compounds.
When diamines are mixed with cyclodextrine the authors
have shown that hexanediamine diffuse at the same rate as
CD (and therefore is interacting strongly with it), while the
shorter butanediamine interact less strongly with CD. In
fact by observing the diffusion coefficient of the various
solutions it is possible to evaluate the mole fraction of the
bound and free states.
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Tandem Mass Spectrometry
2. Precursor or parent ion scanning
By Yi-Min She
The first analyzer allows the transmission of all sample
ions, while the second analyzer is set to monitor specific
fragment ions, which are generated in the collision cell.
The precursor ion scanning is useful for monitoring a
group of compounds contained within a mixture which
produce a common fragment ion, e.g. glycosylated or
phosphorylated peptides in a tryptic digest mixture,
aliphatic hydrocarbons in an oil sample, or glucuronide
conjugates in urine.
Tandem Mass Spectrometry (MS/MS) is an analytical
technique used for structural elucidation of organic
compounds and for sequencing of biomolecules such as
peptides, proteins and oligonucleotides. The MS/MS
function is available in most MS instruments of triple
quadrupoles, 3D ion-trap, linear Q-trap, magnetic sectorquadrupole, quadrupole time-of-flight (QTOF), tandem
time-of-flight (TOF/TOF) and Fourier-transform ion
cyclotron resonance (FT-ICR). The instrument is equipped
with two analyzers separated by a collision cell, in which
an inert gas (e.g. N2, Ar) is introduced to collide with the
selected parent ion and bring down to fragmentation. The
collision-induced dissociation (CID) mass spectrum is
obtained at low collision-energy (20-300 eV) in the
Quadrupoles and hybrid QTOF, or high-energy (1-20
KeV) in the magnetic sector and TOF/TOF instruments..
3. Neutral loss scanning
A scan determines, in a single experiment, all the parent
ion mass-to-charge ratios which react to the loss or gain of
a selected neutral mass. In this case both analyzers scan
and collect data over the whole m/z range, but the two are
off-set so that the second analyzer allows only those ions
which differ by a certain number of mass units (equivalent
to a neutral fragment) from the ions transmitted through
the first analyzer.
MS/MS analysis in a QTOF mass spectrometer
4. Selected ion monitoring (SIM), selected/multiple
reaction monitoring (SRM, MRM)
1. Product or daughter ion scanning
The specific ion (i.e. parent ion) is selected in the firststage MS analyzer, and then trapped into the collision cell.
The ion is subsequently broken down by a collision gas
into the smaller fragment ions (i.e. daughter ions) to be
detected by the second analyzer (MS/MS). The resulting
product ions are particularly useful for structural
identification of small organic molecules and unknown
peptide and protein sequences.
Both of the analyzers are static as user-selected specific
ions are transmitted through the first analyzer and userselected unique fragments arising from these ions are
measured by the second analyzer. The compound under
scrutiny must be known and have been well-characterized
previously before this type of experiment is undertaken.
This methodology is used to confirm unambiguously the
presence of a compound in a matrix e.g. drug testing with
blood or urine samples. It serves as a sensitive approach
for drug metabolism quantitation.
5. Recent MS/MS technology development
1) FT-ICR: Infrared multiphoton dissociation (IRMPI) –
irradiation of ions with infrared laser. Electron capture
dissociation (ECD) – irradiation of ions with electrons.
2) Ion-trap MS: Electron transfer dissociation (ETD) dissociates peptides by transferring electrons to positively
charged peptides, leading to a rich ladder of sequence ions
derived from cleavage at the amide groups.
Sequence identification in a peptide mixture
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Recent upgrades
Recent publications featuring
results from our facilities
• New capabilities in MassSpec instrumentation
1. On-line GC-MS analysis: We have established the
capability of on-line GC-MS analysis with autosampler
injection and capillary column separation on the Waters
GCT instrument. This powerful technique is particularly
suitable for the analysis of mixtures of volatile and low
relative molecular mass compounds (< 800 Da) such as
hydrocarbons, fragrances, essential oils and relatively nonpolar drugs. Chemical derivatisation, e.g.
trimethylsilylation, can often be employed to increase the
volatility of compounds containing polar functional groups
(-OH, -COOH, -NH2, etc) thereby extending the range of
suitable analytes to such compounds as steroids, polar
drugs, prostaglandins, bile acids, organic acids, amino
acids and small peptides.
2. On-line LC-MS/MS analysis: A nanoLC-MS/MS
technique has been developed recently on the QStar XL
QqTOF instrument. We designed a new nanoflow splitting
interface through capillary HPLC system and on-site tenport Valco valve to introduce low-femtomole amount of
sample to the mass spectrometer. Combined with MS
analysis of information dependent acquisition (IDA), the
technique has considerably improved the peptide sequence
coverage and is capable of high throughput protein
identification, PTM characterization and protein
quantitation.
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Sui, R. Kisilevsky, Biochem. Pharmacology 73, 632 (2007).
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(Yi-Min She)
• New NMR software installed
We have acquired a new computer for processing NMR
data. This computer is located close to the 600 MHz
spectrometer in the NMR laboratory (CHE108). To login
on that computer, you can use the local user “nmruser”
(with no password) or your domain name login (e-mail
name and password). This computer is equipped with three
NMR processing programs: TOPSPIN (from Bruker),
MESTREC, and SPINWORKS (developed at University
of Manitoba and can be downloaded for free at
http://www.umanitoba.ca/chemistry/nmr/nmrsource2.htm).
Regarding TOPSPIN, I have placed on my NMR web site
a link to a document and a powerpoint presentation that
explain the interface of the program. This software is
extremely powerful: it can display several spectra (1D or
2D) at the same time in the graphical window. For those of
you interested in relaxation time measurements and in
DOSY experiments, it is extremely easy to process such
pseudo 2D data sets using the processing guide.
Still to come: we have acquired a departmental license
for the ACD NMR processing software (1D and 2D). As
soon as our departmental license server is setup, everyone
in the department will have access to this excellent
processing software.
(Françoise Sauriol)
Edited by Gang Wu
Contact information: Room 408, Chernoff Hall
Phone: 32644; e-mail: [email protected]
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