TRC News

1. Department of Chemistry TRC News Number 1 – September, 2007 Message from the Chair of TRC • 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) • 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: glass@chem.queensu.ca. • 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) • 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) 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, Jean-Michel 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) 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 1

2. Figure 2: 2D-DOSY of a mixture of Sucrose, DSS, Acetone and D2O obtained on our Avance-600. Figure 1: PGSE and diffusion measurement. Figure 3: Adapted from an article by Liat Avram and Yoram Cohen, J. Org. Chem. 2002, 67, 2639-2644. Technical Notes DOSY (Diffusion Ordered SpectroscopY) By Françoise Sauriol 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. 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 ligand-receptor interactions, Host-Guest interaction, Hydrogen bound study, aggregation studies, etc… 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. 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. 2

3. MS/MS analysis in a QTOF mass spectrometer Sequence identification in a peptide mixture Tandem Mass Spectrometry By Yi-Min She 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 sector-quadrupole, 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.. 2. Precursor or parent ion scanning 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. 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. 4. Selected ion monitoring (SIM), selected/multiple reaction monitoring (SRM, MRM) Both of the analyzers are static as user-selected specific ions are transmitted through the first analyzer and user-selected 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. 1. Product or daughter ion scanning The specific ion (i.e. parent ion) is selected in the first-stage 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. 3

4. 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 non-polar 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 ten-port 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. • (Yi-Min She) • S. Mitu, M. C. Baird, Can. J. Chem. 84, 225 (2006). • S. Mitu, M. C. Baird, Eur. Poly. J. 42, 2039 (2006). • G.D. Potter, M.C. Baird, M. Chan, S. P.C. Cole, Inorg. Chem. Comm. 9, 1114 (2006). • S. Mitu, M. C. Baird, Organometallics25, 4888 (2006). • J. H. Brownie, M. C. Baird, H. Schmider, Organometallics26, 1433 (2007). • G. D. Potter, M. C. Baird, S. P. C. Cole, J. Organomet. Chem. 692, 3508 (2007). • S. A. Melnychuk, A. A. Neverov, R. S. Brown, Angew. Chem. Int. Ed. 45, 1767 (2006). • G.T.T. Gibson, M. F. Mohamed, A. A. Neverov, R. S. Brown, Inorg. Chem. 45, 7891 (2006). • A. A. Neverov, Z. -L. Lu, C. I. Maxwell, M. F. Mohamed, C. J. White, J. S. W. Tsang, R. S. Brown, J. Am. Chem. Soc. 128, 16398 (2006). • C. T. Liu, A. A. Neverov, R. S. Brown, Inorg. Chem. 46, 1778 (2007). • X. Han, V. K. Balakrishnan, G. W. vanLoon, E. Buncel, Langmuir22, 9009 (2006). • D. Churchill, J. C.F. Cheung, Y.S. Park, V.H. Smith, G. vanLoon, E. Buncel, Can. J. Chem. 84, 702 (2006). • I. -H. Um, S. -J. Hwang, E. Buncel, J. Org. Chem. 71, 915 (2006). • I. -H. Um, Y. -H. Shin, J. -Y. Han, E. Buncel, Can. J. Chem. 84, 1550 (2006). • J. T. C. Wojtyk, A. Wasey, N. -N. Xiao, P. M. Kazmaier, S. Hoz, C. Yu, R. P. Lemieux, E. Buncel, J. Phys. Chem. A111, 2511 (2007). • X. Han, V. K. Balakrishnan, E. Buncel, Langmuir23, 6519 (2007). • D. Churchill, J. M. Dust, E. Buncel, Can. J. Chem. 85, 421 (2007). • S. Lakhdar, R. Goumont, F. Terrier, T. Boubaker, J. M. Dust, E. Buncel, Org. Biomol. Chem. 5, 1744 (2007). • C. Romanescu, H. -P. Loock, Phys. Chem. Chem. Phys. 8, 2940 (2006). • Q. Yang, J. Barnes, H. -P. Loock, D. Pedersen, Opt. Comm. 276, 97 (2007). • Y. Liu, P. G. Jessop, M. Cunningham, C. A. Eckert, C. L. Liotta, Science313, 958 (2006). • J. S. Parent, A. Liskova, R. A. Whitney, R. Resendes, J. Polymer Sci. A43, 5671 (2005). • I. E. Crandall, W. A. Szarek, J. Z. Vlahakis, Y. Xu, R. Vohra, J. Sui, R. Kisilevsky, Biochem. Pharmacology73, 632 (2007). • Y. Sun, N. Ross, S. B. Zhao, K. Huszarik, W. L. Jia, R. Y. Wang, D. Macartney, S. Wang, J. Am. Chem. Soc. 129, 7510 (2007). • S. B. Zhao, S. Wang, J. Am. Chem. Soc. 129, 3092 (2007). • X. Liu, I. C. M. Kwan, S. Wang, G. Wu, Org. Lett. 8, 3685 (2006). • I.C.M. Kwan, X. Mo, G. Wu, J. Am. Chem. Soc. 129, 2398 (2007). • R. Ida, I.C.M. Kwan, G. Wu, Chem. Commun. 795 (2007). • 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: gang.wu@chem.queensu.ca 4