Chemistry (PhD)

Doctor of Philosophy in Chemistry
https://brocku.ca/mathematics-science/chemistry/graduate-students/

Field(s) of Specialization

• Organic Chemistry
• Inorganic and Analytical Chemistry
• Physical and Computational Methods

Faculty and Administration

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 Therapeutics 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

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.

The following research fields are currently represented, and are described in detail on our department website.

• 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 -30C 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.

Admission Requirements

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.

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 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.

Program Notes

• 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 - PhD Research and 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 on the department website.