Chemistry

Master of Science in Chemistry

Doctor of Philosophy in Chemistry

Fields of Specialization

Organic Chemistry

Inorganic and Analytical Chemistry

Physical and Computational Methods

Dean

Peter Berg

Faculty of Mathematics and Science

Associate Dean

Melanie Pilkington

Faculty of Mathematics and Science

Core Faculty

Professors

Jeffrey Atkinson (Chemistry and Biotechnology), Travis Dudding (Chemistry and Biotechnology), Costa Metallinos (Chemistry and Biotechnology), Georgii Nikonov (Chemistry), Melanie Pilkington (Chemistry), Hongbin (Tony) Yan (Chemistry and Biotechnology)

Associate Professors

Martin Lemaire (Chemistry), Paul Zelisko (Chemistry and Biotechnology)

Assistant Professors

Dustin Duncan (Chemistry and Biotechnology), Jianbo Gao (Chemistry), Vaughn Mangal (Chemistry and Biotechnology), Divya Kaur Matta (Chemistry and Biotechnology)

Participating Graduate Faculty

Professors Emeriti

Ian Brindle, J. Stephen Hartman, Stuart Rothstein, Art van der Est

Adjunct Professors

Farooq Ahmed (CSL Silicones), Lydia Chen (McMaster University), Jianjun Li (Human Health Therapeuticsm National Council of Canada), Christopher H. Marvin (Canada Centre for Inland Waters), Balwantrai Mistry (CSL Silicones), Jeremy Rawson (University of Windsor)

Graduate Program Director

Martin Lemaire

905-688-5550, extension 6432

brocku.ca/chemistry/graduate/gradstudies.html

Administrative Assistant

Abigail (Abby) MacCormack

905-688-5550, extension 3406

CRN 411

Graduate Administrative Coordinator

Elena Genkin

905-688-5550, extension 3115

fmsgradoffice@brocku.ca

Mackenzie Chown D473

Program Description

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

Degree Requirements - MSc

The MSc is normally a six-term or two-year program.

Total credits required for the program: 3.0

Required courses:

CHEM 5F90 (Thesis) has to be taken each term. As part of CHEM 5F90, every MSc student must prepare and defend a thesis that demonstrates a capacity for independent work of acceptable scientific calibre.

	CHEM 5P95 (Graduate Seminar I), 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.
	two (2) CHEM 5(alpha)00 level half-credits.
	one (1) CHEM 4(alpha)00 or 5(alpha)00 level course
	Additional credits may be required of candidates with insufficient preparation in their area of research specialization.

Admission Requirements - PhD

Degree Requirements - PhD

Students transferring after partial completion of the Brock MSc program or equivalent:

Total credits required for the program: 3.5

Required courses:

	CHEM 7F90 (Thesis) should be taken each term for the duration of the program;
	CHEM 5P95 (Graduate Seminar I) should be completed by the end of the student's first year;
	CHEM 7P95 (Graduate Seminar II) seminar should be presented by the end of the student's second year of graduate studies at Brock but no later than the end of the third year of the student's graduate studies. The CHEM 7P95 seminar must be completed before the candidacy exam.
	Two (2) CHEM 5(alpha)00 level half-credits;
	One (1) additional CHEM half-credit that may be either at the 4(alpha)00 or 5(alpha)00 level.
	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 7F90, CHEM 5P95 and 7P95 are as follows:

Organic Field:

	Two (2)of CHEM 5P21, 5P19, and 5P40;
	Additional course(s) are taken to comply with the requirement, of a total of two (2) 5(alpha)00 level half-credits, and one (1) additional half-credit that may be either at the 4(alpha)00 or 5(alpha)00 level.

Physical and Computational Field:

	CHEM 5P67;
	Two (2) other half-credit courses approved by their supervisory committee, in order to comply with the requirement of a total of two 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.

Inorganic Field:

	Two (2) courses from CHEM 5P30, 5P31, 5P32, 5P33, 5P34, 5P40, 5P44 and 5P67;
	One (1) half-credit course approved by their supervisory committee in order to comply with the requirement of a total of two 5(alpha)00 level half-credits, and one additional half-credit that may be either at the 4(alpha)00 level or 5(alpha)00 level.

Analytical Field:

	Two (2) courses from CHEM 5P38, 5P41, and 5P44;
	One (1) additional half-credit course, that may be at either the 4(alpha)00 or 5(alpha)00 level, as approved by their supervisory committee.

Full-time students who transfer into the PhD program from the MSc program are expected to complete their dissertation normally within 5 years (15 terms) from beginning of graduate studies at Brock.

Students entering with an MSc degree, or equivalent, or those awarded direct entry to the PhD program:

Total credits required for the program: 3.0

Required courses:

	CHEM 7F90 (Thesis) should be taken each term for the duration of the program;
	CHEM 5P95 (Graduate Seminar I) should be completed by the end of the student's first year;
	CHEM 7P95 (Graduate Seminar II) seminar should be presented by the end of the student's second year of graduate studies at Brock but no later than the end of the third year of the student's graduate studies. The CHEM 7P95 seminar must be completed before the candidacy exam.
	At least two (2) CHEM 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.

Full-time students entering the PhD program with a previously completed MSc degree, or as a direct admission from the BSc level, are expected to complete their dissertation normally within 4 years (12 terms).

Continued enrolment in the Doctor of Philosophy program requires the successful completion of a Candidacy Examination. The candidacy examination must be completed by the end of the third year of graduate studies at Brock. Prior to the candidacy exam, students must complete all course requirements except CHEM 7F90 (thesis) . 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. 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. Students who fail the examination or do not complete it by the end of the third year of graduate studies at Brock will be immediately removed from the PhD program but may be allowed to submit and defend an MSc thesis, if they do not hold a similar or identical degree. In exceptional circumstances, the candidacy examination may be postponed but only with prior approval of the student's advisory committee, the Graduate Program Director and the Chair. Such approval should be arranged before the end of the third year of study. Further details are available at: brocku.ca/chemistry/graduate/index.html.

Fields of Specialization

The following research fields are currently represented, and are described in detail on our website: brocku.ca/chemistry/research/interests.html

Organic chemistry

Synthesis of biologically active and medicinally important compounds including carbohydrates; antimicrobial compounds, macrocyclic peptides, including bioconjugation methods. Enzymatic synthesis of natural and silicone analogues of lipids; chiral synthon production; 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. Organocatalysis and photocatalysis, design, synthesis and computational analysis of novel superbases and hydrogen bond catalysts. Enantioselective synthesis, including synthesis of chiral ligands, chiral auxiliaries; organometallic catalyst design and synthesis; methodology and synthesis of biologically active compounds.

Inorganic chemistry

Current research emphasis lies at the interface of coordination chemistry, structural chemistry, and molecular magnetism, and is aimed at the synthesis of dual property single molecule magnets (SMMs), spin crossover complexes, Ln-based metal organic frameworks (MOFs) and MRI contrast agents. Other areas of interest include the synthesis and study of organosulfur compounds as the semi-conducting components of organic electronic devices, and emissive compounds for solid-state light emitting devices. Synthesis of redox-active ligands and switchable coordination complexes featuring reversible ligand to metal electron transfer reactions and semiconducting properties toward new molecular spintronic materials. In the organometallic/catalysis stream, the research emphasis is placed on the design of new ligand platforms for stabilization of main-group compounds in very low oxidation states for applications in activation of small molecules and molecular catalysis. Research in analytical chemistry includes methodological development for characterizing organic matter and quantifying environmental pollutants using mass spectrometry-based techniques.

Physical and computational methods

Research includes modern time-resolved electron spin resonance (ESR) spectroscopy to study the structure and function of photosynthetic reaction centres and porphyrin-based model systems. Other areas include optical and electrical property of nanostructured materials characterized by advanced laser spectroscopy and microscopy; synthesis of nanostructured organic and inorganic semiconductors and their applications in solar energy, catalysts, optoelectronics. Computational research focuses on theoretical studies to understand charge and energy transfer reactions in photosynthetic proteins.

Facilities

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) 600 NMR: Bruker Avance AV 600 Digital NMR spectrometer with a 14.1 Tesla Ultrashield Plus magnet. The system is equipped for triple resonance and includes a BBO Z-gradient ATMA probehead which covers the tuning range 15N through 31P with proton decoupling, and an inverse triple resonance gradient TXI probe for observation of protons while decoupling 13C and 15N. The system is also capable of solids observation with a broadband CP/MAS probehead. All probes have full VT capability. (ii) 400 NMR: Bruker Avance III HD 400 Digital NMR spectrometer with a 9.4 Tesla Ascend Magnet. The system is equipped for double resonance and includes a BBFO Z-gradient ATMA probehead which covers the tuning range 15N through 31P and is also 19F capable. The system is equipped for VT. The 400 system runs in a Microsoft Windows 7 Professional environment using Bruker TOPSPIN 3.2 PL5 software for data acquisition and analysis. A TOPSPIN data processing workstation is also part of the NMR facility in "Cairns Family" Biosciences Research Complex. (iii) 300 NMR: Bruker Avance AV 300 Digital NMR spectrometer with a 7.05 Tesla Ultrashield magnet. The system is equipped for double resonance and includes a BBFO Z-gradient ATMA probehead which covers the tuning range 15N through 31P and is also 19F capable. The system is equipped for VT. Both NMR systems run in a Microsoft Windows 7 Professional environment using Bruker TOPSPIN 2.1 PL6 software for data acquisition and analysis. A TOPSPIN data processing workstation is also part of the NMR facility in Mackenzie Chown Complex.

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 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; (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)-80C to -30CC freezers; (vi) FPLC; (vii) DNA synthesizers; (viii) centrifuges

X-ray Crystallography Facility:

A Bruker Apex II CCD single crystal X-ray diffractometer with a Kappa goniometer, equipped with an Oxford Cryostream Plus system suitable for variable temperature measurements is available in the laboratory of M. Pilkington. In 2017 the Mo source was upgraded to an INCOATEC microfocus source for the measurement of very small single crystals. The system is suitable for structure determination of small molecules and larger supramolecular systems. Bruker software is available for structure solution and refinement.

Course Descriptions

Note that not all courses are offered in every session. Refer to the applicable timetable for details.

Students must 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

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 5P03

Advanced Topics in Photobiology

(also offered as BIOL 5P03)

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

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 5P19

Organic Reaction Mechanisms

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 and tactics in the design of organic syntheses. Discussion of comparative design for complex natural products and/or pharmaceutical products. Overview of total synthesis of natural or pharmaceutical products. Examples from the current literature will be used to illustrate new trends in synthetic methodology and approaches to the synthesis of complex organic molecules and natural products. The use of organometallic and/or enzymatic catalysis will also be featured.

Note: Course taught in conjunction with CHEM 4P21.

*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 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. Taught in conjunction with BCHM/BTEC/CHEM 4P67.

#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 5P30

Advanced Coordination Chemistry

(also offered as CHEM 4P30)

Bonding and electronic structure of transition metal coordination complexes through an application of symmetry properties and group theory tools. Topics include bonding, electronic structure and properties (ligand field theory), molecular magnetism, EPR properties.

Restriction: Open to graduate students in Chemistry

Prerequisite(s): CHEM 2P32 and 3P51 or permission of the instructor.

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 the instructor.

Restriction: Open to graduate students in the chemistry program

CHEM 5P32

Advanced Charactarization Methods for Inorganic Chemistry

Theory and application of specialized characterization methods used for the electronic structure elucidation of inorganic compounds with a focus on molecular coordination complexes. Techniques may include, EPR spectroscopy, electrochemistry, X-ray absorption and photoelectron spectroscopies, Mossbauer spectroscopy and magnetic circular dichroism. Other topics may be included depending on class composition and interest.

CHEM 5P33

Supramolecular Chemistry

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 5P34

Structure Determination by X-ray Crystallography

Overview of X-ray diffraction by crystalline materials to determine the structures of small molecules. Topics include crystal growth, selection and mounting, X-ray generation, crystal symmetry and space groups, X-ray diffraction, the "Phase Problem", structure solution (Patterson, direct methods and dual space methods), structure refinement, interpretation of structural data, presentation of structural data, twinning, powder XRD.

Note: Course taught in conjunction with CHEM 4P34. CHEM 4P30 recommended. CHEM 5P34 may be taken concurrently with CHEM 4P30.

*CHEM 5P38

Bioanalytical Chemistry

(also offered as BTEC 5P38)

Chemical and biochemical techniques used for separation, detection, and analysis of biomolecules and special topics in functional nucleic acids and nano medicine.

CHEM 5P40

Advanced Spectroscopy

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

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

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 5P67

Biophysical Techniques

(also offered as BIOL 5P67, BTEC 5P67 and PHYS 5P67)

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 BCHM/BTEC//CHEM 4P67.

CHEM 5P95

Graduate Seminar I

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 final thesis defence to evaluate the student's performance in this course.

CHEM 7P95

Graduate Seminar II

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 supervisory committee. 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 and successful completion of Graduate Seminar l (CHEM 5P95).

Note: This course will be evaluated as Credit/Non-Credit.