2014-2015 Graduate Calendar

Chemistry  
Master of Science in Chemistry Doctor of Philosophy in Chemistry Fields of Specialization Organic Chemistry Inorganic Chemistry Physical and Computational Methods Dean S. Ejaz Ahmed Faculty of Mathematics and Science Associate Dean Alan Castle Faculty of Mathematics and Science Core Faculty Professors Jeffrey K. Atkinson (Chemistry and Biotechnology), Ian D. Brindle (Chemistry), Tomas Hudlicky (Chemistry and Biotechnology), Andrew G. Reynolds (Biological Sciences), Stuart M. Rothstein (Chemistry, Biotechnology and Physics), Art van der Est (Chemistry, Biotechnology and Physics) Associate Professors Travis Dudding (Chemistry and Biotechnology), Heather Gordon (Chemistry and Biotechnology), Costa Metallinos (Chemistry and Biotechnology), Georgii Nikonov (Chemistry), Hongbin (Tony) Yan (Chemistry and Biotechnology), Melanie Pilkington (Chemistry) Assistant Professors Theocharis Stamatatos (Chemistry) Instructors Paul Zelisko (Chemistry) Participating Graduate Faculty Professor Emeritus J. Stephen Hartman (Chemistry), Jack M. Miller (Chemistry), David C. Moule (Chemistry) Adjunct Professors Christopher H. Marvin (National Water Research Institute), Victor Snieckus (Queen's University) Graduate Program Director Tony Yan 905-688-5550, extension 3545 tyan@brocku.ca http://www.brocku.ca/chemistry/graduate/gradstudies.html Administrative Assistant Chris Skorski 905-688-5550, extension 3406 cskorski@brocku.ca Mackenzie Chown E206 Graduate Studies Administrative Assistant Beulah Alexander 905-688-5550, extension 3115 Mackenzie Chown F204 http://www.brocku.ca/biotechnology/ balexander@brocku.ca  
Program Description Go to top of document
The Department provides facilities for students intending to work towards their Master's and/or Doctoral degrees in Chemistry. Faculty members specialize in Organic/Bio-organic Chemistry, Analytical Chemistry, Inorganic Chemistry, and Physical/Theoretical Chemistry. The Department also supports MSc and PhD degrees in Biotechnology.  
Admission Requirements - MSc Go to top of document
Successful completion of an Honours Bachelor's degree, or equivalent, in Chemistry or a cognate discipline such as Biochemistry or Biotechnology normally with an average of not less than 78%. We recommend that students provide results from a completed Graduate Record Examination (GRE), test in chemistry. Agreement from a faculty supervisor to supervise the student is required for admission to the program. Those lacking sufficient background preparation may be required to complete a qualifying term/year to upgrade their applications. Completion of a qualifying term/year does not guarantee acceptance into the program. The Departmental Graduate Committee will review all applications and recommend for admission a limited number of suitable candidates. Students interested in part-time study at the MSc level should consult the Graduate Program Director.  
Degree Requirements - MSc Go to top of document
The MSc is normally a six-term or two-year program. The program must include CHEM 5F90; two 5(alpha)00 level half credits; a maximum of one credit may be at either the 4(alpha)00 or 5(alpha)00 level; and participation in the seminar course CHEM 5P95, in which each student will present one seminar on a topic approved by the candidate's Supervisor. The CHEM 5P95 seminar should be presented by the middle of the student's second year in the MSc program. Students are expected to attend all seminars presented by both students and visitors to the Department. Additional credits may be required of candidates with insufficient preparation in their area of research specialization. As part of CHEM 5F90, every MSc candidate must prepare and defend a thesis that demonstrates a capacity for independent work of acceptable scientific calibre.  
Admission Requirements - PhD Go to top of document
Successful completion of a Master's degree, or equivalent in Chemistry or closely allied discipline (e.g. Biochemistry), with an overall average of not less than 80%. Applicants with exceptional research potential and who hold an Honours BSc may be admitted directly into the PhD program. Research potential is gauged by (i) publications and other accomplishments, detailed in applicant's resume and reference letters, and (ii) examples of the applicant's scientific writing. Alternatively, students who have successfully completed a minimum of one year in the Brock Chemistry MSc program may apply to be transferred to the PhD program. Students transferring from the MSc to the PhD program will normally be expected to have attained an 80% average and have achieved significant research progress as determined by their supervisory committee. The Graduate Committee will review all applications and recommend for admission a limited number of suitable candidates. It is not possible to complete a PhD degree entirely on a part-time basis. After completion of the full-time residency requirement (three years) a student may request part-time status, provided that a draft of the thesis has been submitted, but before submission of the final copy and scheduling of the defense has begun. Students with MSc degrees in Chemistry with a background in biological applications of chemistry may apply for admission into Brock's PhD program in Biotechnology.  
Degree Requirements - PhD Go to top of document
Students transferring after partial completion of the Brock MSc program or equivalent must complete a total of 4.5 credits (9 half-credits). In addition to a non-credit scientific writing course, CHEM 5N01, these credits must include CHEM 7F90; CHEM 5P95 and 7P95; four 5(alpha)00 level half-credits, and one additional half-credit that may be either at the 4(alpha)00 or 5(alpha)00 level. CHEM 5P95 seminar should be completed by the end of the student's first year and CHEM 7P95 seminar should be presented by the end of the student's third year in the PhD. In any of the fields, one half-credit may be taken from other 5(alpha)00 level courses offered in the graduate programs of Biological Sciences, Biotechnology, Computer Science , Mathematics and Statistics, or Physics with the permission of the student's Supervisory Committee. Required courses, by field, in addition to CHEM 5N01, CHEM 7F90, CHEM 5P95 and 7P95 are as follows: Students in the Organic Field must take CHEM 5P19 (Organic Reaction Mechanisms) and one synthesis course (CHEM 4P21, 5P21, or 5P23). The remaining three half-credit course requirements can be chosen from the remaining synthesis courses and CHEM 5P20, 5P22, 5P24, 5P25, 5P27, 5P28 or 5P40. Students in the Physical and Computational Field must take CHEM 5P00, and four courses from CHEM 4P14, 5P01, 5P03, 5P11, 5P13, 5P14, 5P67, PHYS 4P52, 5P50, and 5P76. Students in the Inorganic Field must take four courses from CHEM 4P30 or 4P31, 5P31, 5P32, 5P33, 5P40, 5P44 and 5P67, and one additional half-credit course, determined by the student's Supervisory Committee. Students interested in Analytical Chemistry must take the following four courses: CHEM 5P32, 5P41, 5P44, and 5P45, and one additional half-credit course, determined by the student's Supervisory Committee. The PhD for full-time students transferring from a partially completed MSc is normally a five year (15 terms) program from the MSc point of entry. For students entering with an MSc degree, or equivalent, or those awarded direct entry to the PhD program, must complete 3.5 credits (7 half-credits) which must include CHEM 7F90; CHEM 5P95 and 7P95, CHEM 5N01 and at least three 5(alpha)00 level half-credits. The choice of these and additional credits, required for candidates with insufficient preparation in their areas of research specialization, are at the discretion of the student's Supervisory Committee. The PhD for full-time students (with a completed MSc or Direct from a BSc) is normally a four year (12 term) program. Continued enrolment in the Doctor of Philosophy program requires the successful completion of a Candidacy Examination, at a convenient time, but before the end of the student's second year in the PhD program. Students who have been directly admitted to the PhD program with a BSc degree have three years to meet this requirement. Students must complete all of their course requirements, except for the thesis course (CHEM 7F90), the second graduate seminar (CHEM 7P95) and the writing course (CHEM 5N01) before taking the candidacy examination. The exam combines a written component with an oral presentation and defence. The written component is a research proposal on a topic not directly related to the candidate's research prepared in the general format of an NSERC Discovery Grant proposal. The examining committee will be composed of the graduate program director or delegate (Chair), the student's supervisor, two members of the student's Supervisory Committee, and either one additional member from the Department involved in the program or one member from a Department in the Faculty of Mathematics and Science not participating in the program. The possible outcomes are pass or fail. A failure entails immediate withdrawal from the PhD program but allowance to submit and defend an MSc thesis should the student have not been previously awarded a similar or identical degree. The Examination Committee may request that a passing performance be recorded only after completion of remedial work, which may include rewriting the research proposal thereby addressing its flaws, tests, essays or courses, and is at the discretion of the Examining Committee. Further details are available at http://www.brocku.ca/chemistry/graduate/index.html.  
Fields of Specialization Go to top of document
The following research fields are currently represented, and are described in detail on our website:http://www.brocku.ca/chemistry/research/interests.html  
Organic chemistry Go to top of document
Synthesis of biologically active and medicinally important compounds including heterocyclic, aromatic and aliphatic systems, opiate alkaloids, anticancer compounds, and carbohydrates; enantioselective synthesis, organometallic catalyst design and synthesis; new approaches to natural product synthesis; cycloaddition reactions; computational methods; chemoenzymatic asymmetric synthesis; biotransformations using whole cells and enzymes; chiral synthon production; organic electrochemistry, isotopically labelled compounds; fluorescent nucleic acids and lipids for bioanalytical applications and microscopy; affinity labels and bioconjugates; protein and nucleic acid chemistry and biochemistry, protein-membrane interactions.  
Inorganic chemistry Go to top of document

Organometallic research including the syntheses of new transition metal and main-group element compounds and investigation of their structures and catalytic activity; study of mechanisms of catalysis via kinetic measurements and labelling experiments; ligand design to provide new structures and reactivity; nonclassical interligand interactions as models for metal mediated transformations of organic molecules. Coordination chemistry and inorganic materials research that includes the synthesis and magnetochemical characterization of molecule-based magnetic materials with a focus on high-spin molecules, such as single-molecule, single-ion and single-chain magnets.

Within the field of coordination chemistry, research emphasis is placed on ligand design, aimed at the synthesis of dual property molecule-based magnets that include magnetic conductors and chiral spin crossover complexes. The characterization of magnetic coordination complexes by X-ray crystallography. The synthesis and characterization of organosulfur donors for applications as the semi-conducting components of organic electronic devices.

Bioinorganic chemistry research includes the synthesis of macrocyclic ligands for the development of Mn (II) and Gd(III) MRI contrast agents, as well as the synthesis and investigation of analogues of the oxygen-evolving complex found on the donor side of photosystem II. Studies also include the influence of paramagnetic transition metal ions such as CU2+ and VO2+ on the excited state dynamics of porphyrin-based photosynthesis model systems. Research in analytical chemistry includes development of methods for determination of major, trace, and ultra-trace elements in mineral and ore samples as well as in environmental matrices.

 
Physical and computational methods Go to top of document
Statistical mechanical investigations of biologically-relevant molecules via Monte Carlo and molecular dynamics simulations; molecular modelling for structural analysis and applications of pattern recognition to problems of chemical interest (e.g. quantitative-structure activity relationships (QSAR), comparative molecular field analysis (CoMFA), and molecular dynamics trajectory analysis); solving the Schroedinger Equation by using computer simulation (quantum Monte Carlo) methods; computational tools to explore the structure of proteins; modern time-resolved electron spin resonance (ESR) spectroscopy to study the structure and function of photosynthetic reaction centres and porphyrin-based model systems; theoretical and experimental work on the spin polarization and spin dynamics of coupled triplet-doublet pairs in copper and vanadyl porphyrins; study of reaction mechanisms using theory; rationalization and prediction of stereoselectivity of catalytic asymmetric reactions using computational theory.  
Facilities Go to top of document
Mass Spectrometry Facility: (i) Thermo DFS High Resolution GC/MS system (Spring 2014)The system is equipped with dual polarity EI, CI and FAB sources and a Thermo Trace series capillary GC. The XCalibur data system runs under Windows 7 Professional and contains a sophisticated suite of programs for data acquisition and processing. Sample library searches may be carried out using the NIST database; (ii) Bruker Esquire HCTUltra LC/MS/MS fitted with electrospray (ESI) and atmospheric pressure chemical ionization (APCI) sources. Sample interface is via an Agilent 1100 HPLC system or by syringe pump infusion. The data system runs Bruker Compass and Agilent Chemstation software on a networked PC platform. (iii) Bruker Autoflex MALDI/TOF/TOF system for large molecule, polymer, protein and peptide work. The system is capable of MS/MS for protein sequencing and identification using Bruker Compass software on a networked PC platform. (iv) Perkin-Elmer Turbomass Gold GC/MS/HS for normal or headspace GC/MS/HS analysis of samples. The PC based data system is equipped with a full NIST searchable database. Nuclear Magnetic Resonance Facility: (i) Thermo DFS High Resolution GC/MS system (Spring 2014)The system is equipped with dual polarity EI, CI and FAB sources and a Thermo Trace series capillary GC. The XCalibur data system runs under Windows 7 Professional and contains a sophisticated suite of programs for data acquisition and processing. Sample library searches may be carried out using the NIST database; (ii) Bruker Esquire HCTUltra LC/MS/MS fitted with electrospray (ESI) and atmospheric pressure chemical ionization (APCI) sources. Sample interface is via an Agilent 1100 HPLC system or by syringe pump infusion. The data system runs Bruker Compass and Agilent Chemstation software on a networked PC platform. (iii) Bruker Autoflex MALDI/TOF/TOF system for large molecule, polymer, protein and peptide work. The system is capable of MS/MS for protein sequencing and identification using Bruker Compass software on a networked PC platform. (iv) Perkin-Elmer Turbomass Gold GC/MS/HS for normal or headspace GC/MS/HS analysis of samples. The PC based data system is equipped with a full NIST searchable database. Electron Paramagnetic Resonance Facility: (i) Bruker ElexSys E580 X-band (9 GHz) EPR spectrometer operating in both cw and pulsed modes. The instrument runs using the Bruxer XEPR software package. (ii) Bruker E-siries Q-band (35 GHz) spectrometer for continuous-wave and transient experiments. All three instruments can be operated with a CF950 cryostat for temperature control between 5K and 300K and they are designed with optical excitation capability using a Continuum Surelite pulsed NdYAG Laser. Computing Facilities: The department has a variety of computers and UNIX workstations and access to a several Beowolf clusters for advanced computation, data interpretation, and molecular modeling. The University is a member of Canada's Shared Hierarchical Academic Research Computing Network (SHARCNET). Students and faculty researchers have access to cluster platform systems, housed at Brock and at other SHARCNET academic institutions. Spectroscopy: (i) Thermo-Mattson RS-1 infrared spectrometer, equipped with various sampling accessories including normal transmission mode, ATR and DRIFT units. Software acquisition and processing is handled with a PC running WinFirst software. Basic library search facilities are available; (ii) Bomem MB100 FTIR, controlled by a PC/Grams based data acquisition and processing system; (iii) Thermo-Spectronic(ATI/Unicam) UV4 ultraviolet/visible spectrometer, controlled by a PC running Vision-32 acquisition and processing software; (iv) Photon Technology International Fluorescence Spectrometer, interfaced to a PC for acquisition and processing; (v) Molecular Devices SpectraMax microplate spectrofluorometer for direct plate scans. A PC controls data collection and processing; (vi) ICP/MS spectrometry in the laboratory of Prof. I.D. Brindle; (vii) Cary 4000 UV/VIS spectrophotometer. Chromatography: (i) Agilent 6890 research GC system with a Gerstel prep/autosampler, controlled by an extended version of Chemstation running on a PC; (ii) Waters 600 series LC systems running under PC based Millenium software; (iii) Dionex 3000 ionic chromatography; (iv) Bio-Rad Duoflow FPLC. Polarimeter: Rudolph Autopol III polarimeter for optical rotation measurements. Bioanalytical: (i) Biotek enzyme-linked immuno-sorbent assay (ELISA); () Analight-200 dual polarization interferometer from Farfield Scientific (UK) for surface adsorption and molecular association measurements. Biochemistry/Biotechnology Unit: (i) Biosafety cabinet; (ii) Shaking incubator; (iii) PCR thermocycler; (iv) Freeze-dryer; (v)-80°C-30°C freezers; (vi) FPLC; (vii) DNA synthesizers; (viii) centrifuges  
Course Descriptions Go to top of document
Students must check to ensure that prerequisites are met. Students may be deregistered, at the request of the instructor, from any course for which prerequisites and/or restrictions have not been met. CHEM 5F90 MSc Research and Thesis Theoretical and/or experimental research. An external examiner will participate in the evaluation of the student's performance in this course. CHEM 5N01 Scientific Writing The organizational and stylistic skills of writing and referencing a scientific document. Examples from the various literature forms such as primary journals, reviews, reports, and theses, as well as presentations and seminars. Database use and reference citation, and use of figures and graphs to illustrate data. CHEM 5P00 Quantum Chemistry: Theory (also offered as PHYS 5P00) Self-consistent-field (SCF) method; configuration interaction; basis functions; electron correlation; physical properties of atoms, diatomic and polyatomic molecules. CHEM 5P01 Quantum Chemistry: Applications Application of ab initio molecular orbital theories to problems in atomic and molecular structure, to intermolecular forces and to chemical reactivity. CHEM 5P03 Advanced Topics in Photobiology (also offered as BIOL 5P03) A graduate seminar/lecture course covering topics in photobiology. A series of lectures designed to introduce some of the major research areas in photobiology will be followed by student seminars on selective topics (usually two or three papers on one subject). Note: course taught in conjunction with BIOL/BCHM 4P03. CHEM 5P11 Special Topics in Physical Chemistry Topics may include aspects of chemical dynamics, molecular spectroscopy, statistical mechanics and quantum theory. CHEM 5P13 Electron Paramagnetic Resonance Spectroscopy An introduction to the theory and application of modern EPR spectroscopy. Theoretical treatment of coupled spin systems; the Bloch equations; the density matrix and pulsed EPR; waveguide components; resonant cavities. CHEM 5P14 Computational Chemistry: Applications in Biotechnology (also offered as BTEC 5P14) Structure-based drug design; molecular modelling; conformational search techniques; secondary and tertiary protein structure prediction; quantitative structure-activity relationships; bioinformatics. CHEM 5P19 Organic Reaction Mechanisms The critical study of papers of mechanistic and/or synthetic interest in the recent literature drawing attention to the ways in which mechanisms are established and applied as well as to the mechanisms themselves. CHEM 5P20 Special Topics in Organic Chemistry Topics may include organic photochemistry, biotransformation, free radical chemistry, symmetry and stereochemistry and a further study of mechanistic or synthetic organic chemistry. CHEM 5P21 Advanced Organic Synthesis Strategies in the design of organic syntheses; examples from the current literature will be used to illustrate new trends in synthetic methodology and approaches to the synthesis of complex or organic molecules and natural products; new reagents in organic synthesis including an examination of organometallics and enzymes. CHEM 5P22 Special Topics in Chemical Biology (also offered as BTEC 5P22) Focuses on the chemical-biology of select biologically active compounds of current interest in the literature. The occurrence, biosynthesis and biological activity, including structure-activity correlations, will be studied. Strategies toward the chemical synthesis of these important compounds will also be investigated. CHEM 5P23 Stereoselective Synthesis A survey of the methodology and reagents currently used in stereoselective synthetic organic chemistry. Details concerning methods for achieving absolute and relative stereo-control are discussed, including chiral catalysis and asymmetric induction via substrate- and reagent-based strategies. Applications of the methods to the synthesis of chosen molecules in the literature are provided to illustrate aspects of selectivity. CHEM 5P24 Natural Products Chemistry (also offered as BTEC 5P24) A study of the structural features, synthesis and biosynthesis of natural products selected from the acetogenin, alkaloid, steroid and terpenoid groups, and other areas. CHEM 5P25 Medicinal Chemistry (also offered as BTEC 5P25) Structure and activity of biologically active organic compounds; introduction to pharmacology, pharmacodynamics, and receptor theory as a background for a more detailed study of chemistry of drugs such as enzyme inhibitors and receptor antagonists; rational drug design, combinatorial libraries, screening and general routes of metabolism. Note: a background in organic chemistry at the third-year undergraduate level will be assumed. CHEM 5P27 Advanced Enzyme and Co-enzyme Mechanisms (also offered as BTEC 5P27) Hydrolytic and other processes catalyzed by enzymes lacking non-protein prosthetic groups reactions involving the co-enzymes biotin, pyridoxal phosphate, thiamine pyrophosphate, folic acid and cobalamin; oxidation mechanisms involving pyridine nucleotides, flavoenzymes, hydroperoxidases and oxygenases. Note: a background in this material, taken at the undergraduate level, will be assumed. CHEM 5P28 Bioorganic Chemistry: Carbohydrates and Nucleic Acids (also offered as BTEC 5P28) Mono- and oligosaccharides; preparative carbohydrate chemistry; neoglycoconjugates; immunochemistry of carbohydrates; nucleosides and nucleotides; oligonucleotide synthesis; medicinal chemistry of oligonucleotide; amino acids; protein structures; peptide chemistry; post-translational modification. CHEM 5P31 Special Topics in Inorganic Chemistry A directed reading course in advanced inorganic chemistry based on a critical approach to the original literature. Topics are to be arranged between the student and instructor. CHEM 5P32 Advanced Methods for Materials Characterization The theory and practice of common characterization methods used for the structural elucidation of inorganic compounds. Techniques mayinclude, IR, UV-Vis, EPR, mass spectroscopy, cyclic voltammery, X-ray crystallography, and magnetic measurements. CHEM 5P33 Supramolecular Chemistry An examination of non-covalent interactions and their impact in biology and chemistry. Topics will include self-assembly, molecular recognition, polymer organization, dendrimers, crystallization and applications of the above for the design and synthesis of nanostructured materials. CHEM 5P40 Advanced Spectroscopy The theory and practice of common spectroscopic techniques used for structural identification of chemical compounds and analysis of their properties, emphasizing mainly nuclear magnetic resonance and mass spectrometry. CHEM 5P41 Special Topics in Analytical Chemistry The course will include topics such as pesticide and residue analysis, advanced chromatographic techniques, chemical analysis applied to environmental and agricultural problems, preconcentration techniques and new analytical techniques. CHEM 5P44 Directed Readings in Chemistry An investigation of a specific area or group of related topics in contemporary chemistry. Note: approval of the departmental graduate studies committee is required prior to registration. The instructor(s) for this course must be different from those in the following "Special Topics" courses, in which the student has, or will have, credit: 5P11, 5P20, 5P31, or 5P41. CHEM 5P45 Atomic Spectrometry Arcs, sparks, ICP, DCP, AA, will be investigated. Evaluation of advantages and disadvantages of excitation sources and sample introduction techniques. Particular concentration in this course will be the sample and how it is analyzed and some discussion will centre on sample preparation, matrix elimination or minimization. Solid sampling methods such as laser ablation and glow discharge will be reviewed. CHEM 5P67 Biophysical Techniques (also offered as BIOL 5P67 and BTEC 5P67) An advanced seminar/lecture course on experimental techniques in biophysics. The focus is on understanding the theory, applications and limitations of a variety of techniques students will encounter during their graduate studies. Techniques will range from advanced spectroscopy (absorption, fluorescence, NMR, X-ray diffraction) to molecular biochemistry. Note: course taught in conjunction with BIOL/CHEM/BCHM 4P67. CHEM 5P95 Graduate Seminar A forty minute presentation of one research seminar on a topic approved by the student's supervisor in a public forum followed by ten minutes for questions and discussion. A minimum mark of 70% in the seminar component must be attained to obtain a credit grade in the course. Students should attend all presentations given in this course and by invitees to the Departmental seminar series, but attendance is required at a minimum of ten such seminars accumulated over two consecutive offerings of the course. during the student's graduate program. Note: This course will be evaluated as Credit/No-Credit CHEM 7F90 PhD Research and Thesis Original theoretical and/or experimental research and thesis. An external examiner will participate in the evaluation of the student's performance in this course. CHEM 7P95 Graduate Seminar II A forty minute presentation of one research seminar in a public forum followed by ten minutes for questions and discussion on a topic approved by the student's supervisor. A minimum mark of 70% in the seminar component must be attained to obtain a credit grade in the course.. Students should attend all presentations given in this course and by invitees to the Departmental seminar series, but attendance is required at a minimum of ten such seminars accumulated over two consecutive offerings of the course. Prerequisite(s): Enrolment in PhD program or permission of the instructor and CHEM 5P95. Note: This course will be evaluated as Credit/No-Credit.  
Last updated: March 21, 2014 @ 12:04PM