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

Cheryl McCormick

Faculty of Mathematics and Science

Core Faculty

Professors

Jeffrey K. Atkinson (Chemistry and Biotechnology), Travis Dudding (Chemistry and Biotechnology), Tomas Hudlicky (Chemistry and Biotechnology), Costa Metallinos (Chemistry and Biotechnology), Georgii Nikonov (Chemistry), Andrew G. Reynolds (Biological Sciences), Art van der Est (Chemistry, Biotechnology and Physics), Hongbin (Tony) Yan (Chemistry and Biotechnology)

Associate Professors

Melanie Pilkington (Chemistry), Martin Lemaire (Chemistry), Feng Li (Chemistry)

Instructors

Paul Zelisko (Chemistry)

Participating Graduate Faculty

Professors Emeriti

Ian D. Brindle (Chemistry), J. Stephen Hartman (Chemistry), David C. Moule (Chemistry), Stuart M. Rothstein (Chemistry), Mary Francis Richardson (Chemistry),

Adjunct Professors

Christopher H. Marvin (National Water Research Institute), Victor Snieckus (Queen's University)

Graduate Program Director

Melanie Pilkington

905-688-5550, extension 3403

https://brocku.ca/chemistry/graduate/gradstudies.html

Administrative Assistant

Jennifer Roberts

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

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

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 half-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

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 on the basis of a written report presented to the committee at the end of the first year of graduate study.

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

Students transferring after partial completion of the Brock MSc program or equivalent must complete a total of 4.0 credits (8 half-credits). In addition to a non-credit scientific writing course, CHEM 5N01, these credits must include CHEM 7F90; CHEM 5P95 and 7P95; three 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 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. 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 any two of CHEM 5P21, 5P19, and 5P40 but it is recommended that they take all three. Additional course(s) are taken to comply with the requirement, as outlined above, of a total of three 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. Students in the Physical and Computational Field should take CHEM 5P67, and three other half-credit courses approved by their supervisory committee, in order to comply with the requirement, as outlined above, of a total of three 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. Students in the Inorganic Field must take three courses from CHEM 4P30, 5P31, 5P32, 5P33, 5P34, 5P40, 5P44 and 5P67 and one half-credit course approved by their supervisory committee in order to comply with the requirement, as outlined above, of a total of three 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. Students in the Analytical Field must take two courses from CHEM 5P38, 5P41, and 5P44 and two additional half-credit courses, one of which 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, 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.

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) and CHEM 5N01 (scientific writing). 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 https://brocku.ca/chemistry/graduate/index.html.

Fields of Specialization

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

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

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

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

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 probhead which covers the tuning range 15N through 31P and is also 19F capable. The system is equipped for VT. The 400 system run in a Microsft 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:

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 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 to -30°C 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 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 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 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 and tactics in the design of organic syntheses. Discussion of comparative design for complex natural products. Historical overview of total synthesis of terpenes, alkaloids, and other natural 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.

#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 5P31

Advanced Coordination Chemistry

(also offered as CHEM 4P31)

(also offered as CHEM 4P31)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 the chemistry program

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

CHEM 5P32

Advanced Charactarization Methods for Inorganic Chemistry

The 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

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 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: CHEM 4P30 recommended. May be taken concurrently. Course taught in conjunction with CHEM 4P34.

*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

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 5P67

Biophysical Techniques

(also offered as BIOL 5P67, BTEC 5P67 and PHYS 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 BCHM/BTEC//CHEM 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 final thesis defence to evaluate 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.