SCHOOL OF CHEMISTRY

4th Year Biopharmaceutical Chemistry

Information Booklet

2020-2021

CONTENTSSUMMARY OF COURSE STRUCTURE 2

INDUCTION 4

CORE MODULES

CH4109-1: BIOPHARMACEUTICAL CHEMISTRY 5

CH4109-2: INDUSTRIAL BIOCHEMISTRY 6

CH4107-1: ANALYTICAL CHEMISTRY 7

CH4107-2: BIOPHYSICAL CHEMISTRY 9

CH4108-1: BIOORGANIC CHEMISTRY 10

CH4108-2: BIOINORGANIC CHEMISTRY 11

PATHWAY 1 (for students on work placement)

CH4111: WORK PLACEMENT 12

CH4110: BIOPHARMACEUTICAL CHEMISTRY DISSERTATION 14

PATHWAY 2 (for students conducting the on-campus project)

CH4101: ON CAMPUS PROJECT 15

ELECTIVE MODULES (students choose two 5 credit elective modules)

CH429: PHYSICAL CHEMISTRY I 16

CH445: ADVANCED INORGANIC CHEMISTRY I 18

CH449: SELECTIVE SYNTHESIS / ORGANOMETALLIC CHEMISTRY 19

CH4113: ORGANIC CHEMISTRY 20

GUIDELINES FOR PREPARING REPORTS 22

SCHEDULE WORK PLACEMENT MODULE 29SCHEDULE BIOPHARMACEUTICAL CHEMISTRY DISSERTATION 30

SCHEDULE ON-CAMPUS PROJECT 32

PLAGIARISM 35

APPENDIX 36

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SUMMARY OF COURSE STRUCTURE

Modules taken by all students on Programme (Semester 2) Credits

CH4109 Biopharmaceutical Chemistry and Industrial Biochemistry 10

CH4108 Bioorganic and Bioinorganic Chemistry 10

CH4107 Analytical and Biophysical Chemistry 10

Modules taken by students on work placement (Semester 1)

CH4111 Work placement 15

CH4110 Biopharmaceutical Chemistry Dissertation 15

Modules for students taking the on-campus project (Semester 1)

CH4101: Research Investigation 20

CH429: Physical Chemistry I (elective) 5

CH445: Advanced Inorganic Chemistry (elective) 5

CH449: Selective Synthesis/Organometallic Chemistry (elective) 5CH4113: Organic Chemistry (elective) 5

Students taking CH4101 will take two 5 credit elective modules in semester 1 in parallel with the research investigation.

EXAMINATION AND ASSESSMENT

Semester I

CH4111: Work placement Continuous assessment (CA)

CH4110: Biopharmaceutical Chemistry Dissertation CA and oral examination

CH4101: On-campus project CA

CH429: Physical Chemistry I 2 h exam and CA

CH445: Advanced Inorganic Chemistry 2 h exam and CA

CH449: Selective Synthesis/Organometallic Chemistry 2 h exam and CA

CH439: Radicals, Polymers, Supramolecular Chemistry, Pericyclic Reactions and Photochemistry 2 h exam and CA

Semester II

Biopharmaceutical Chemistry (CH4109-1) 2 h exam paper + continuous assessment

Industrial Biochemistry (CH4109-2) 2 h exam paper

Analytical Chemistry (CH4107-1) 2 h exam paper + continuous assessment

Biophysical Chemistry (CH4107-2) 2 h exam paper + continuous assessment

Bioorganic Chemistry (CH4108-1) 2 h exam paper + continuous assessment

Bioinorganic Chemistry (CH4108-2) 2 h exam paper + continuous assessment

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WORKLOAD EXPECTED FOR EACH MODULE

Workload for a 10 Credit (10 ECTS) Module 200-250 h

The time spent on a 10 credit module includes the teaching contact with staff & autonomous learning.Autonomous learning & working includes time spent working independently carrying out assignments, learning, revising, additional reading. Normally this is 3-4 times that of the contact time spent with staff. Thus the contact time with staff in 10 credit lecture modules above is >50 h and students would need to spend at least 150 h working independently studying for each 10 ECTS module.

Continuous assessment in 10 ECTS modules

The continuous assessment (CA) is usually in the form of in-class tests during the teaching semester that will be graded. It may also involve preparing a class presentation or other type of continuous assessment. In modules with exams the continuous assessment will contribute 20 % of each overall module mark.

IMPORTANT DATES FOR BIOPHARMACEUTICAL CHEMISTRY STUDENTS

Date/Time/Deadline Activity Who is responsible

June 1st 2020 Work placements commence: provide job specifications and tripartite agreement to School secretary(see page 38 & 39)

Students on work placement

Mid August 2020 Assign Dissertation topic Module coordinator.

Monday 28th Sept 2020 On-campus research investigation/project & lectures commence

Students taking on campus research investigative projects

Monday 12th October 2020 Dissertation. Submit the introduction and outline of headings (10% of dissertation mark)

Student on work placement

30th October 2020 Interim visits to work-place should be completed.

Student on work placement, employer and supervisor

12th January 2021 Submit the Biopharmaceutical Chemistry Dissertation.More info on Dissertation further in booklet

Students on work placement

26th January 2021 Submit work placement report. More info on placement further in booklet

Student on work placement

22nd April 2021 Submit on-campus project report. More info on on-campus project further in booklet

Student taking the on campus research project

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4

INDUCTION

Safety

The students carrying out on-campus projects will be instructed on the safety culture and systems in the School of Chemistry. They will be taught how to assess safety of a project and an individual reaction. They will also be taught correct PPE use, fumehood use and disposal of waste. They will also be taken through the safety audit process of a lab so they are aware of common pitfalls. The safety instruction will help the student assess the safety aspects of their project along with their supervisor. Such an assessment must be included in their report and will be assessed. Safe working will also form part of the assessment process for the supervisor’s assessment of the students lab work.

Students on placement will be expected to undergo local safety induction within their placement location. The time and nature of any safety induction should be recorded and included in the report on the placement.

Regardless of where the placement or project is undertaken all students are expected to work safely, risk assess their work before starting on it and consult with their supervisors on the safety aspects of their work particularly before starting a process for the first time or if they are uncomfortable with any safety issue in their workplace. Safe working requires active participation on all workers part, passive participation is not enough.

Electronic Literature & Databases as sources of information

The students will be instructed in the use of online electronic resources to search for chemical and research information. Students will be expected to be able to retrieve information via searches on Web of knowledge, Reaxys, Scifinder Scholar, SDBS, NIST and chemical suppliers databases. Students will also be instructed in the use of reference management software (Endnote) and will be expected to be able to create, populate and maintain a database relevant to their dissertation thesis or project.

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CH4109-1: BIOPHARMACEUTICAL CHEMISTRY – SEMESTER II________________________________________________________________________Staff: Dr. Peter Crowley, Prof. Paul Murphy,

Carbohydrate Chemistry in Biopharmaceutical Science Prof. Paul Murphy

Draw and understand the structures of saccharides, oligosaccharides, glycopeptides, glycoproteins, glycolipidsDemonstrate knowledge and understanding of the chemistry involved in (bio)synthesis of glycoconjugates including glycoproteinsDemonstrate knowledge and understanding of the roles of carbohydrates in biological systems and in biopharmaceuticals, including their molecular recognition propertiesDescribe and understand methods for analysis of oligosaccharides, glycopeptides & glycoproteins andunderstand why this is important to biopharmaceuticals (NMR, chemical analysis, Mass Spectrometry).Describe the chemistry (chemoenzymatic synthesis) used to prepare peptides and glycopeptides

Antibodies and Biopharmaceuticals Dr. Peter CrowleyThe students will have an understanding of antibody structure and how this relates to binding function.Emphasis is placed on the difference between conventional heavy and light chain antibodies versus singlechain antibodies (from camel and shark).Students should gain an appreciation of how the interface size, shape and chemical complementaritycontributes to binding affinity.

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CH4109-2: INDUSTRIAL BIOCHEMISTRY – SEMESTER II

Staff: (Guest Lecturer from UL)

Rationale and Purpose of the ModuleTo present an overview of (a) animal cell culture and (b) pharmaceutical biotechnology in the context ofunderlining science and industrial/medical applications. To present an overview of patenting as applied tobiotechnology. To provide the scope for a measure of student self-directed learning.

SyllabusAnimal cell culture; Overview and introduction to animal cell culture. Animal cell culture, media, methods andapparatus. Animal cell culture; production of industrially useful products. The drug development process;Regulatory route for new drugs in USA & EU. Biopharmaceutical manufacture; Patenting and biotechnology.Principles of patentability. The patent application process. Sources of biopharmaceuticals. Upstreamprocessing. Downstream processing. Post translational modifications and their significance. Product QC andthe range and significance of potential product impurities. Nucleic acid-based biopharmaceuticals. Specificbiopharmaceuticals; Students will be provided with 2-3 specific biopharmaceutical products/product families,along with bibliographic details of at least 1 reference source material for each. Students will be expected tosource the references, along with any additional pertinent references and undertake self-directed study ofthe biochemistry and biotechnology of the representative biopharmaceuticals.

Learning OutcomesCognitive (Knowledge, Understanding, Application, Analysis, Evaluation, Synthesis)1. Describe the concepts and processes underpinning the development and production of products ofpharmaceutical biotechnology 2. Independently identify and evaluate pertinent information from scientific andadditional literature sources. 3. Critique suggested patenting, developmental or production schemes with aview to assessing their industrial suitability 4. Devise product development or production schemesappropriate for purpose

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CH4107-1: ANALYTICAL CHEMISTRY (SEMESTER II)

Staff: Dr. Alan Ryder, Dr. Luca Ronconi and TBA

There are three topics to be covered (~8 lectures each) by Dr. Ronconi, Dr. Ryder and Dr O’Duill. The examination will comprise of a two hour written examination with three questions and all three will have to be attempted. 1. xx2. Spectroscopy of metal complexes (LR)3. Fluorescence microscopy (AR)

A blackboard page for this module is available and additional information and resources are made available here. You are expected to access and review material on this page.

1. TBA

2. Spectroscopy of metal complexes (8L + 2 tutorials): Dr. Luca Ronconi The learning outcomes that will be assessed are: electronic spectra of metal complexes (microstates, spectroscopic terms, Russell-Saunders coupling,

spin-orbit coupling, Racah parameters, Tanabe-Tsugano diagrams); IR spectroscopy of transition metal complexes (focusing on metal-other atoms vibrations in the far IR

region and on changes between coordinated and non-coordinated functional groups of some classes of ligands);

solution NMR spectroscopy of transition metal complexes (focusing on the direct detection of NMR-active nuclei other than 1H, 13C, 15N and 31P);

use of spectroscopic techniques to derive the structure and to understand the properties of transition metal complexes.

Suggested reading & references: P. Atkins, T. Overton, J. Rourke, M. Weller, F. Armstrong, Shriver and Atkins Inorganic Chemistry,

5th Ed., Oxford University Press, 2009. K. Nakamoto, Infrared and Raman Spectra of Inorganic and Coordination Compounds, 6th Ed.,

John Wiley & Sons Inc., 2009. D. Donghi, L. Ronconi, Application of heteronuclear NMR Spectroscopy to bioinorganic and

medicinal chemistry", in: Elsevier Reference Module in Chemistry, Molecular Sciences and Chemical Engineering; Reedijk, J., Ed.; Elsevier: Waltham (MA), 2014, doi:10.1016/B978-0-12-409547-2.10947-3 (e-book).

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3. Fluorescence Microscopy (8L+ 2 tutorials): Dr. Alan Ryder

The course outline and learning outcomes that will be assessed from this topic are as follows: Basic Optics (1.5L) : An understanding of Refraction & Dispersion; Polarization; Lenses,

Aberrations, & numerical apertures; Optical Resolution; Anti-reflection coatings etc.; Beamsplitters & optical filters. Be able to explain the basic optical concepts important for Microscopy.

Basic Microscopy (2.5L) : An understaning of microscope design; Transmitted light microscopy; Finite & Infinity based optical systems; Magnification; Objectives lenses & resolution; Immersion lenses; Detectors (PMT. CCD, EMCCD, APD); Kohler Illumination; Sample stages. Be able to explain the basic optical construction and components (and their operational principals) used in microscopes. Be able to explain the basic operation and construction of several different single and multi-channel detectors used in microscopes.

Basic Fluorescence Microscopy (2.0L) : An understanding of Epifluorescence Microscope design; Excitation Sources (lamps, LEDs, lasers); Fluorescence filters / manipulating light; Electronics and Software; Some relevant applications. Be able to explain the design and components used in fluorescence microscopes. Be able to explain the pros and cons of the different light sources used in fluorescence microscopes.

Confocal Fluorescence Microscopy (2.0L) : An understanding of Basic theory / design; Point Spread Functions; Laser Scanning Confocal; Spinning Disk confocal; Multi-photon microscopy; Some relevant examples of applications. Be able to explain in detail the design and operation of confocal and multi-photon microscopes.

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CH4107-2: BIOPHYSICAL CHEMISTRY (SEMESTER II)

Staff: Dr. David Cheung, Dr. Yury Rochev

1. Molecular Driving Forces2. Drug Delivery3. Physical Chemistry of the Cell

1. Molecular Driving Forces (8 hours, DC)The course outline and learning outcomes that will be assessed from this topic are as follows:

Entropy and free energy Interfaces, wetting, and capillarity Phase transitions and phase separation Co-operativity Adsorption, binding, and catalysis

2. Drug Delivery (8 hours, YR)The course outline and learning outcomes that will be assessed from this topic are as follows:

The concept of bioavailability. Pharmacokinetic processes. Pharmacokinetical Curve. Diffusion. Fick’s law. Diffusion in water and water solution. Diffusion in cell and in the extracellular

space. Drug permeation through biological barriers. Drug transport by fluid motion. Rate Control in Drug Delivery and Targeting. Control of release kinetics. Zero-order release.

Advantages and disadvantages of implantation therapy. Biocompatibility issues. Non-degradable polymeric implants. Biodegradable polymeric implants. Implantable pumps and osmotically driven system.

Reservoir delivery systems. Transdermal drug delivery systems. Matrix delivery systems. Hydrogel delivery systems.

Case studies in drug delivery. Tablets and Capsules. Drug eluted stents. Nanocarriers, Liposomes, Polyplex.

3. Physical Chemistry of the Cell (8 hours, YR)The students will gain an appreciation of

The Universal Features of Cells on Earth. Four Great Classes of Macromolecules. Cell biology by the numbers. Biological patterns: Order in space and time. Analysing cells and molecules. Visualizing cells.

Forces. Force measurement. Four Types of Noncovalent Attractions. Electrostatic forces. Mesoscopic forces. Van der Waals. Hydrogen bonding. Steric forces. Depletion forces. Hydrodynamic interactions. Macromolecular crowding. Consequences of crowding. Mechanics of cells.

Proteins. Amino acids. Peptide bond. Levels of Protein Structure. Secondary structures. Alpha helices and beta sheets. Protein domains. Protein folding. Anfinsen's experiments. Levinthal’s paradox. Protein folding in the cell. Protein misfolding diseases.

DNA, Chromosomes and Genomes. The central dogma of molecular biology. A Variety of DNA Structures. Biophysical properties of DNA. How DNA is packaged into chromosomes? Circular DNA. DNA Content and the C-Value Paradox.

Diffusion and transportation in cell. Random walk model. Diffusion coefficient. Stokes-Einstein equation. Fick's 1st law of diffusion. Fick's 2nd law of diffusion. Diffusion in Cell. First passage problem. Reynold’s number. The Viscosity of a Suspension. Einstein equation. Bacterial Motility.

Internal Organization of the Cell. Intracellular Compartments. Biological Membranes. Mitochondria. Energy Conversion. Cytoskeleton.

Molecular Motors. Molecular machines in membranes. Enzymes and molecular machines. The Cell Cycle. Organization of Biological Networks. Mitosis. Cytokinesis. Cells in Their Social Context. Extracellular matrix. Collagens Are the Major Proteins of the

Extracellular Matrix. Elastin. GAG. Hyaluronic acid. Fibronectin.

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CH4108-1: BIOORGANIC CHEMISTRY (SEMESTER II)

Staff: Prof. Peter Crowley and Prof. Olivier Thomas

1. Protein and Supramolecular Chemistry2. NMR in structure Determination (12 h).

1.         Protein and Supramolecular Chemistry (9 h) The learning outcomes that will be assessed will include:

Protein interactions and molecular recognition Supramolecular ligands for protein recognition and assembly The chemistry of the cationic residues Arg and Lys Methods to study interactions (e.g. X-ray, NMR)

2. NMR in structure Determination (12 h).

1D NMR experiments (1H and 13C)

2D NMR experiments (COSY, HSQC, HMBC)

applications to the structure elucidation of natural products

using NMR for studying the conformations and configurations of organic molecules (J coupling and NOESY)

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CH4108-2: BIOINORGANIC CHEMISTRY (SEMESTER II)

Staff: Dr. Andrea Erxleben, Dr. Pau Farras, Dr. Constantina Papatriantafyllopoulou

Staff: Dr. Andrea Erxleben, Dr. Pau Farras, Dr. Constantina Papatriantafyllopoulou 1.     Metalloproteins (Dr Andrea Erxleben)2.     Energy and respiration in biological systems  (Dr. Pau Farras)3.   Supramolecular Chemistry Dr. Constantina Papatriantafyllopoulou

Metalloproteins (6 lectures)

The student will be introduced to the role of metal ions in biological systems. Particular emphasis will be given to metalloproteins and metalloenzymes and to metal complexes as their structural and functional models.

The learning outcomes that will be assessed will include:

         The student being able to present and analyse evidence that supports mechanisms of action of metalloenzymes including support for proposed intermediates

         The student being able to represent the mode of action of metalloenzymes using catalytic cycles         The student being able to relate the properties of metals and their coordination compounds to the roles

they play in biological systems and show how these chemical properties can be modulated to fit a variety of biological environments.

         The student being able to solve unseen problems in bioinorganic chemistry.

Energy and respiration in biological systems (12 lectures)

The students will be introduced to the synergy between natural and artificial systems for the design of novel metal based devices to tackle the issues related to renewable energies.The role of metalloenzymes in photosynthesis and respiration will be explained.

The learning outcomes that will be assessed will include:

           Correlation between basic electron transfer theories with real biological systems such as proteins.           Photosynthesis and mechanisms of energy transfer.           Oxygen metabolism and fuel cells.           Nitrogen fixation and the future of fertilisers.

Supramolecular Chemistry (6 lectures)

The learning outcomes that will be assessed are: The student being able to understand the nature of the intermolecular interactions. The student being able to describe the basic concepts of host-guest chemistry. The student being able to describe representative categories of host molecules, which are

appropriate for cation, anion and neutral molecule binding. The student being able to understand the role of the molecular template effect for the assembly of

supramolecular architectures. The student being able to understand the potential applications of supramolecular compounds

(molecular devices, artificial enzymes).

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WORK PLACEMENT (CH4111)

Academic Structure of Placement

       Stage of Programme Year 4 

Mandatory or Elective ElectiveNumber of academic credits  15 (25% of year 4)Duration of work placement (weeks)

Minimum 20

 Optimum 26

Normal commencement dateAs soon as possible after year 3 summer examinations

(normally June 5th)

Learning Outcomes of Placement

       On completion of this placement the student will be able to:

1. show an appreciation for the organization where they carried out their placement, its management structure and the environment in which it operates its daily business

2. have increased knowledge regarding their own employability and demonstrate insight into their transferrable skills

3. identify career choices in light of their work placement4. demonstrate an appreciation of health & safety in the workplace5. link the work placement to their programme of study6. demonstrate effective People Skills such as negotiation, team working, leadership,

interpersonal and communication skills.7. demonstrate effective Self Reliance Skills such as initiative, networking, willingness to

learn, reliability, punctuality and prioritising tasks.8. demonstrate the required Technical and General Skills of the given work place.

Assessment and Reporting Requirements  

Assessment/Report Description or ReferenceMarks

Awarded

Interim Meeting

Employer, university supervisor and student meet during the placement to review work log and progress.

10 

Final Report

To be submitted by the student at end of placement (see below for guidelines for preparing the report).

50 

Oral PresentationWill be held at University at end of placement 

10 

Employer Evaluation (Student Appraisal)

Will be provided to School administrator/coordinator at end of placement by Employer

30Total /100

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Interim Placement Meeting Report Form for Academic Supervisor

Name of student:Date of visit and location:

Yes/No CommentInduction and training of student completed

Student workload journal was up to date and complete

Students should provide a sample of the journal to the staff member in advance of the meeting.

Other comments:

Grades:

Work placement induction (4 marks): student and placement supervisor should confirm student has satisfactorily completed induction and required training and developed the required competences.

Workplace journal (out of 6 marks)

Total (out of 10 marks)

Name: _______________

Signature: ______________

Date: ___________________

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Biopharmaceutical Chemistry Dissertation (CH4110)

CH4110 is a 15-credit module (this is 15/60, so represents a quarter of the year’s work and should be given the time and effort that that warrants).

All students who are taking the work placement module will also complete a Biopharmaceutical Chemistry Dissertation. A supervisor will be assigned for the dissertation and the student and supervisor will agree on a suitable dissertation topic.

Learning outcomes from this module are provided below:

Students will manage their own learning. Students will apply the basic knowledge gained earlier in the programme, and based on the research work carried out in this module will consolidate and extend their knowledge and understanding of biopharmaceutical chemistry. Students will develop skills such finding data or information from the literature, to organise and summarise this in a written report, and to present the outcomes of their investigations, placing it in context. Students will have an oral examination where they will defend their dissertation and be expected to demonstrate understanding and knowledge of chemical concepts related to their dissertation topic.Assessment in this module will be concerned with assessment of the written thesis [70% (split 10% for the submission of intro/outline as below and 60% for the final report)], a presentation with a defence of the thesis/presentation required (30%).

More specifically students will:1. Establish or become aware of the state of the art in the assigned topic2. Critically analyse data or facts obtained from library and/or laboratory work3. Use the facts or data obtained by this independent investigation to challenge current teaching and/or

myths/hyperbole and/or to provide new insights and/or advance a topic in Biopharmaceutical Chemistry

4. Demonstrate a greater understanding and knowledge within Biopharmaceutical Chemistry as a result of their independent investigation

5. Demonstrate competence in reporting & presenting and defending the outcomes of their independent investigative work

6. Be able to carry out and report their research in an ethical manner

The introduction to the topic and a detailed list of headings/outline for the dissertation should be submitted to the supervisor by Monday 12th October 2020. The introduction piece should be a minimum of 3 pages and cover the scientific background to the topic. The headings/outline plan is to be included in addition to the introduction piece. 10% of the marks for this module will be assigned for this submission

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On-Campus Project (CH4101)

All students who are do not take the work placement module will complete an on-campus project. A supervisor will be assigned for the project and the student and supervisor will agree on a suitable project topic.

Learning outcomes from this module are provided below:

Students will manage their own learning. Students will apply the basic knowledge gained earlier in the programme, and based on the work carried out in this module will consolidate and extend their knowledge and understanding of biopharmaceutical chemistry. Students will develop skills such finding data or information from the literature, and their generating their own data and organise this into minor thesis format. They will also give an oral presentation on the outcomes of their project. Assessment in this module will be concerned with an evaluation of student performance during the course of the project (50%), an assessment of the written report (40%), a presentation (10%).

More specifically students will:1. Establish or become aware of the state of the art in the assigned topic2. Critically analyse data or facts obtained from library and/or laboratory work3. Use the facts or data obtained by this independent investigation to challenge current teaching and/or

myths/hyperbole and/or to provide new insights and/or advance a topic in Biopharmaceutical Chemistry

4. Demonstrate a greater understanding and knowledge within Biopharmaceutical Chemistry as a result of their independent investigation

5. Demonstrate competence in reporting & presenting the outcomes of their independent investigative work

6. Be able to carry out and report their research in an ethical manner

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CH429: PHYSICAL CHEMISTRY I (SEMESTER I)

Staff: Prof. Henry Curran; Dr. Alan Ryder1. Spectroscopy2. Chemical Kinetics3. Statistical Thermodynamics

1. Fluorescence Spectroscopy

There are four core topics, each with an associated set of learning outcomes.

Course Topics: Learning OutcomesExcited States:Absorption.Changes in structure & reactivity in excited state. Dipole Moments.Fates of excited statesRadiative & non-radiative decay processes.

Understand and be able to explain the process of photon absorption and describe the different possible fates of excited states.

Fluorescence Spectroscopy I: basic conceptsJablonski Diagram & Theory.Franck Condon Principle.Characteristics of Fluorescence emission.Fluorescence parameters.Pros & Cons of Fluorescence spectroscopy.Solvent effects.

Be able to explain in detail the processes of fluorescence and phosphorescence and effects of the environment on fluorescence emission. Be able to calculate quantum yields and efficiencies.

Fluorescence Spectroscopy II: advanced techniquesFluorescence anisotropy.Fluorescence lifetime spectroscopy. Time Resolved Fluorescence Emission. Förster Resonance Energy Transfer.Quenching (static & dynamic). Stern-Volmer analysis.

Be able to explain in detail the various techniques & calculate relevant parameters: lifetimes, quenching constants, anisotropy, energy transfer efficiencies, etc.

Fluorophores:Types of Fluorophores.Applications.Small Molecules.Proteins. Quantum Dots.

Be able to describe and discuss the different types and their modes of operation with illustrations of practical examples. Be able to calculate emission colours for quantum dots.

2. Chemical Kinetics

Students will be able to: Derive the rate law for a first and second order reaction and from that determine the half-life for a

reaction and the rate of reaction. Determine the kinetics for an elementary reaction. Explain the kinetics associated with flow reactors, jet-stirred reactors and shock tubes. Understand how the rate constant of a reaction varies with temperature, and derive the frequency A-

factor and activation energy of a reaction given the rate constant and different temperatures. Appreciate and understand the dependence of kinetics on thermodynamics of reactants and

products. Understand Photochemical Kinetics and its application to real world problems.

o Understand Photolytic activation and flash photolysiso Understand Fast reactions and how these can be studied

Theories of reaction rateso Understand and apply Simple Collision Theoryo Understand and apply Transition State Theory

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3. Statistical Thermodynamics

Know that the Boltzmann distribution that gives the number of molecules in each state of a system at

any temperature is given by the equation:

The partition function is defined as: and is an indication of the number of thermally accessible states at the temperature of interest.

The molecular partition function is the product of the contribution from translation, rotation, vibration, electronic and spin distributions: q = qT qR qV qE qS

The translational partition function is: qT = (2mkT)3/2V/h3

The vibrational partition function is: qV = 1/(1–e–h/kT) The rotational partition function is: qR = kT/hB, where = 1 for an unsymmetrical linear rotor and

= 2 for a symmetrical linear rotor. The electronic partition function is: qE = 1 for closed-shell molecules with high-energy excited states. The internal energy is: U = U(0) + E, with E = (NkT2/q) ´ slope of q plotted against T. The Boltzmann formula for the entropy is S = k ln W, where W is the number of different ways in

which the molecules of a system can be arranged while keeping the same total energy.

The standard molar Gibbs energy is

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CH445: ADVANCED INORGANIC CHEMISTRY I (SEMESTER I)

Staff: Dr. Andrea Erxleben, Dr. Luca Ronconi, Dr.Constantina Papatriantafyllopoulou

1. Metals in Medicine (Dr. Andrea Erxleben)2. Chemistry of the f-block Elements (Dr. Luca Ronconi)

3. Molecular Magnetism (Dr. Constantina Papatriantafyllopoulou)

Metals in Medicine (12 lectures)

The learning outcomes that will be assessed will include:

The student being able to describe the relevance of various metals in medicine. Metals covered will include: Pt, Ru, Ga, V, Ti, Mo, Au, Li, Bi, Mn, Gd and various radioactive metals (e.g. Tc)Gd.

The student being able to describe and understand the chemistry of antitumour active platinum compounds with regard to synthesis of cis- and transplatin, coordination chemistry of Pt, trans-effect, mechanism and kinetics of ligand substitution, solution behaviour of cisplatin, reaction of cisplatin with DNA, nucleobases and amino acids, structure-activity relationships for Pt drugs, Pt NMR.

The student being able to describe the chemistry of Ru, Ga, Ti, V, and Mo-based antitumour agents. The student being able to understand and explain the function of photosensitizers in photodynamic

tumour therapy. The student being able to understand and explain aspects of the coordination chemistry of Au I and

AuIII relevant to the biological behaviour of Au. The student being able to understand and describe the generation and selection criteria of

therapeutic and diagnostic radionuclides, the synthesis of radiopharmaceuticals and the function of radiosensitizers.

The student being able to understand and explain the choice of metals and ligands suitable for MRI contrast agents.

2. Chemistry of the f-block Elements (6 lectures)

The learning outcomes that will be assessed are: general feautures of lanthanides and actinides (electronic configuration, properties of the f orbitals,

lanthanoid/actinoid contraction and its consequences, oxidation states, coordination numbers and geometries);

chemistry of lanthanides and actinides (simple inorganic derivatives, solution chemistry, coordination and organometallic compounds and their stability/reactivity);

applications of lanthanides (catalysts in organic reactions, MRI contrast agents, shift reagents, luminescent sensors) and actinides (nuclear fuel).

Suggested references: S. Cotton, Lanthanide and Actinide Chemistry; John Wiley & Sons Ltd.: Chichester, 2006. J.-C.G. Bünzli, S.V. Eliseeva, "Photophysics of lanthanoid coordination compounds", in:

Comprehensive Inorganic Chemistry II; Reedijk, J., Poeppelmeier, K., Eds.; Elsevier: Amsterdam, 2013, Vol. 8, pp. 339-398.

Recent Advances in Organo-f-Element Chemistry, Special Issue of Organometallics 2013, 32, 1133-1530.

3.         Molecular Magnetism (6 lectures)The learning outcomes that will be assessed are:

The student being able to understand basic concepts and definitions in molecular magnetism (magnetization, magnetic susceptibility, spin), and recognize the different types of magnetic behaviour.

The student being able to predict all the possible spin states for a metal compound. The student being able to use basic equations in magnetism (Curie Law, Van Vleck equation) to

determine the spin of a metal compound. The student being able to describe and understand the mechanisms of magnetic interactions. The student being able to understand the single molecule magnetism behaviour and its potential use

in technological applications (information storage devices, quantum computing).

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CH449: SELECTIVE SYNTHESIS / ORGANOMETALLIC CHEMISTRY (SEMESTER I)

Staff: Prof Paul Murphy, Dr. Patrick O’Leary

Organometallic reagents in synthesis

The learning outcomes that will be assessed will include:

The student being able to understand, explain and implement the rules relating to bonding, hapto number, electron counting and establishing oxidation numbers of organometallic reagents.The student will understand and be able to apply crystal field theory to rationalise the shape and spin of organometallic compounds.The student will understand and be able to use knowledge of the sigma, pi and backbonding of ligandsThe student being able to understand and explain the basic elements of organometallic mechanisms i.e. oxidative addition, reductive elimination, transmetallation, migratory insertion, β-hydride elimination and others.  The student being able to combine these into a coherent mechanism for a given reaction including hydroformylation, Heck coupling, Wacker Process, allylic substitution and others.The student being able to understand and explain the role of an asymmetric ligand (including BOX and Salen ligands) in a catalytic complex as applied to an asymmetric reaction.The student being able to understand and explain the advantages of the RCM reaction and discuss in detail the mechanism of the reaction.The student being able to describe and apply the preparation methods for organolithiums and assess  the relative reactivity of such organometallics and discuss the modulation of the reactivity using additives.The student being able to understand and discuss the use of organolitihium reagents in the formation and reaction of enolates and other anions.The student being able to understand and discuss the use of thermodynamic and kinetic control in reactions involving controlled deprotonation.The student being able too understand, explain and implement the synthesis, use and basic mechanism of action of basic lithium dialkyl cuprates.

Selectivity in Organic Chemistry (12 h)

The learning outcomes that will be assessed will include:

Ability to apply basic organic chemistry concepts from years 1-3 to more advanced problemsThe student’s ability to explain various types of selectivity (chemo, regio, stereo); The student’s understanding and ability to explain trends in reactivity of various functional groups such as their reactions with reducing and oxidizing reagents. The student’s ability to explain and understand stereoselective olefination. Reactions covered will include: elimination reactions, Julia, Wittig, Horner-Wadsworth-Emmons, Ando, Still-Genari & Peterson olefinations; cross metathesis. The student being able to describe the synthesis of alkenes in ring structures (e.g. Robinson annelation, RCM) and using this as a strategy to control olefin stereoselectivityThe student being able to understand and explain a variety of other diastereoselective reactions (e.g. epoxidation, addition of nucleophiles to carbonyl compounds in acyclic chains) The student being able to write mechanisms, using curly arrows for these transformations.

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CH4113: ORGANIC CHEMISTRY (SEMESTER I)

Staff: TBA. Eddie Myers

1. Radicals in Organic Synthesis 2. Polymer synthesis3. Pericyclic and Photochemical Reactions

1. Radicals in Organic Synthesis (6 h)- methods of radical formation; reaction mechanisms using single, double-headed arrows; radical anions and radical cations.- classificatiton of radicals according to kinetic and thermodynamic stability (resonance, hyperconjugation, hybridization and captodative effects)- Baldwin’s rules, Thorpe-Ingold effect, Beckwith transition state- geometry, stability and reactivity of radicals based on molecular orbital theory- classification of radicals as electrophilic, nucleophilic, σ- and π-radicals- Bu3SnH/AIBN-mediated chain reaction mechanism, and alternatives (silicon hydride or polarity reversal catalysis) - chain mechanisms for radical cyclizations, including selected tandem/cascade examples- mechanisms of named reactions involving charged radical intermediates (Birch, McMurry, Sandmeyer)

2. Polymers and Supramolecular Chemistry (6 h)Polymers- Classification and description of polymers according to addition and step growth mechanisms

and kinetics- cationic and anionic polymerization mechanisms (reaction conditions and appropriate

monomers), including living polymerization- radical chain reaction mechanisms and kinetics- advantages of radical polymerizations and living polymerizations- Ziegler-Natta polymerization of ethylene and propylene- Classification of polymers according to architecture and stereochemistry- selected step-growth polymerizations, including the synthesis of polyesters and polyamides.Supramolecular Chemistry- Definition of supramolecular chemistry and comparison to organic chemistry covered so far- Cation and anion sensing- Neutral guest binding and supramolecular catalysis (including MOFs)- Self-assembly- Molecular machines

3 Pericyclic and Photochemical Reactions (~12 h)

The learning outcomes that will be assessed will include: The ability to classify a pericyclic reaction as either a cycloaddition, an electrocyclic reaction, a

sigmatropic rearrangement or a group-transfer reaction The ability to predict the sense of a pericyclic reaction

(suprafacial/antarafacial/disrotatory/conrotatory) under a certain set of reaction conditions (thermal/photochemical) based on the Woodward–Hoffman Rules.

The ability to draw a set of π-based molecular orbitals for any conjugated molecule, to assign electrons to these orbitals, to identify the HOMO and LUMO orbitals and to use the resulting information to predict the sense of a pericyclic reaction under thermal or photochemical conditions.

To understand the concept of stereospecificity pertaining to pericyclic reactions and to be able to predict the diastereoselectivity of a pericyclic reaction.

The ability to use structural features to predict the relative rate and regioselectivity of pericyclic reactions.

To appreciate the equipment and reactions conditions of a photochemical reaction. To understand the nature of excited states (singlet and triplet states) and basic photophysical

processes and selection rules that dictate organic photochemical reactions (intersystem crossing, internal conversion, relaxation, fluorescence, phosphorescence).

To understand the main photoreactions of aromatic systems: photosubstitution, photorearrangement, and photocycloaddition.

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To understand the main photoreactions of carbonyl compounds: α-cleavage (Norrish Type-I process), hydrogen abstraction (Norrish Type-II process) and addition to alkenes (Paternò-Büchi reaction).

To understand the main photoreactions of alkenes: photoisomerisation and photocycloaddition. To understand the concepts of photosensitization and quenching and how they can be used in

mechanistic investigations. To be able to use structural features to predict the regiochemistry of photochemical [2+2]

cycloadditions. To understand how the redox properties of molecules change upon photochemical excitation. To appreciate the concepts behind and applications of photoredox catalysis, cis-trans isomerisation

of azobenzenes, and the fragmentation of ortho-nitro benzyl groups.

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GUIDELINES IN WRITING AN ON-CAMPUS PROJECT REPORT (SYNTHESIS)

1. Title of Project: (see below for format which should be used)

2. Summary or AbstractA concise summary (up to 350 words) of what has been achieved. This should be explicit and reference should be made to work/experiments carried out and the results. Highlights from the research should specifically be included. A graphic is recommended to support this abstract.

3. IntroductionApproximately 3-5 pages (A4, typed, one and a half or double line spacing, margins approx 1”, font such as Times and font size 12). Structure diagrams or schemes can be drawn with ChemDraw available for all students. The introduction should include background to the project, explaining the reasons for undertaking the work and include a project plan. In the case of synthetic projects for example, this could show a scheme. References must be included and usually are numbered in sequence as they are found in text with a superscript and the full reference listed at the end of the report.1-3 Compounds should be numbered (in bold) as they appear in schemes. The final section of the introduction should outline the aims of the project. The final sentence or paragraph should summarise what has been achieved. 4. Results and Discussion

Students are advised to give a concise presentation of results presented first followed by a discussion of their significance (novelty of method?, novel mechanism?). Please also provide any relevant figures or schemes or tables that are needed to efficiently and clearly present your results.

In synthetic projects, there is no need to provide mechanisms for all reactions (although you will be expected to be able to discuss these during the oral assessment). Please only discuss a mechanism if an unexpected product is obtained or if this is central to the project objective.

When relevant there can be a description of the key characterisation data that supports a structural assignment, a brief description of how the reactions were carried out and yields can be given etc.

Example from a synthesis report: “The bromide derivative (10) was obtained (65%) after treatment of penta-O-acetyl--D-glucopyranose with hydrogen bromide in acetic acid. The 1H-NMR spectrum of 10 had signals at 6.30 (1H, d, J 4.0 Hz, H-1), 4.80-3.50 (6H, ms, H-2–6) and 2.00-2.10 (12H, 4 x s, CH 3C=O), which were in excellent agreement with literature data.4” Tables can be used and diagrams/reaction schemes should be included and numbered etc. (Scheme 1, Fig. 1, Table 1).

Compounds should be numbered in order of appearance in schemes etc. If NMR is not relevant, then give X-ray or other spectroscopic data or analytical data to support your assignments.

5. ConclusionsPlease include a conclusions section, summarizing briefly the main achievements of the project.

6. ExperimentalDescription of experiments should be given in detail sufficient to enable experimental workers to repeat them.

For synthesis projects include full characterisation, yields, m.pt., Rf, NMR data, IR data, []D, microanalysis (for new compound), mass data and their assignments should be included). If a compound is not new, please include a citation to where it has been characterized previously and include some characterization data (e.g. 1H-NMR, IR, LRMS and alpha-D) and state that the data is in good agreement with that described previously. You may include a general experimental section if this is relevant.

Typical experimental procedure (for a synthesis project) for a new compound and assignment of analytical data:

N-(2,3,4,6-Tetra-O-acetyl-(-D-glucopyranosyl)-5-ethylthiophene-2-carboxamide 9 The reaction of 5-ethylthiophene-2-carboxylic acid (0.23 g, 1.44 mmol) as described for 3-bromothiophene-2-carboxylic acid gave a mixture of anomers (0.64 g, 91 % yield, , 1:16). The residue was recrystallised from EtOAc and cyclohexane to afford -anomer 9 as a colourless crystalline solid (0.42 g, 51%) and as an adduct with

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EtOAc (1:1); mp 64-66 °C; []D +12 (c 8.0, CDCl3); 1H NMR (300 MHz, CDCl3) 7.33 (1H, d, J 3.9 Hz, aromatic H), 6.84 (1H, d, JNH,H1 9.3 Hz, NH), 6.77 (1H, dd, J 3.9 Hz, J 0.9 Hz, aromatic H), 5.37 (2H, 2 x overlapping t, J 9.3 Hz, H-1,3), 5.10 (1H, t, J 9.3, H-4), 5.03 (1H, t, J 9.3 Hz, H-2), 4.34 (1H, dd, J6a,6b -12.5 Hz, J6a,5 4.2 Hz, H-6a), 4.09 (1H, dd, J6b,6a -12.5 Hz, J6b,5 2.1 Hz, H-6b), 3.88 (1H, ddd, J5,4 9.9 Hz, J5,6a 4.2 Hz, J5,6b 2.1 Hz, H-5), 2.86 (2H, q, J 7.5 Hz, CH2CH3), 2.08, 2.04 (2s), 2.03 (each 3H, each s, each CH3), 1.32 (3H, t, J 7.5 Hz, CH2CH3); 13C NMR (75 MHz, CDCl3): 171.5, 170.7, 169.9, 169.6 (each ester C=O), 161.8 (amide C=O), 154.9, 134.3 (each aromatic C), 129.5, 124.6 (each aromatic CH), 78.9, 73.6, 72.6, 70.7, 68.3 (each CH), 61.7, 23.8 (each CH2), 20.6, 20.7, 15.7 (each CH3); ESI-LRMS m/z 486 [M+H]+, 324, 271, 169; ESI-HRMS (m/z) calcd for C21H28NO10S 486.1434, found m/z 486.1448 [M+H]+. Anal Calcd for C25H35NO12S (EtOAc adduct): C, 52.35; H, 6.15; N, 2.44; S, 5.59. Found: C, 52.22; H, 6.09; N, 2.49; S, 5.92.

Include the name of the compound, if possible. Many compounds can be named by checking for related compounds in SciFinder and using names provided in SciFinder abstracts as guidelines. Chemdraw can also be helpful in naming. Please consult your supervisor for advice on preparation of the experimental section. This can vary significantly between research areas.

Note: You can use Reaxys (www.reaxys.com) or SciFinder to search for compounds to determine whether they are new or known. If a compound is known then a citation should be provide. If analytical data is in agreement with data reported previously then this should be stated. Do include melting points and alpha D data if relevant and do state the literature data for these, if relevant.

7. References (Please use a standard style such as the one (RSC) outlined below).1. I. Fleming, Frontier Orbitals and Organic Chemical Reactions, Wiley, Chichester, 1976, p. 55.2. A. J. L. Beckwith and K. U. Ungold, in Rearrangements in Ground and Excited States, ed. P. de Mayo, Academic Press, New York, 1980, vol. 1, p. 161.3. P. D. Cunningham, N. W. A. Geraghty, P. J. McArdle, P. V. Murphy and T. J. O’ Sullivan, J. Chem. Soc., Perkin Trans. 1, 1997, 1.4. H. Kessler and M. Hoffmann, J. Am. Chem. Soc. 1994, 118, 10156. 5. X. Y. Smiths, Journal of Flame, 2000, 22, 10157.

Reference 1 is a typical book, Reference 2 is typical for a chapter in an edited book. References 3 and 4 are typical journal references.

8. Appendix

You should include any relevant spectra, chromatograms etc. For example for projects using organic synthesis you may include 1H and 13C NMR spectra for any new compounds as evidence of homogeneity of purity of compounds you prepare. You may include a compound characterization checklist in your report. This corresponds to a table where you indicate the analysis you obtained on each compound.

9. Project risk assessmentPlease include your project risk assessment as this will be evaluated as part of the project work. This should be signed by the student and supervisor and have identified major hazards assocated with project work.

10. Plagiarism. The thesis should be written in your own words and not copied from any reviews or internet. If reproducing any figures from the literature in the thesis then please obtain copyright permissions and cite the original article. Obtaining copyright permissions can usually be done online where the article is originally published. Plagiarism must be avoided. See NUI Galway guidelines on plagiarism at http://www.su.nuigalway.ie/site/view/313/. Action will be taken by the examiners when plagiarism is found to occur.

Grading of project and the write-up will be based on strict adherence to guidelines provided herein.

The number of total pages does not normally need to exceed 20 pages. The student is recommended to focus on the quality of their report.

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GUIDELINES FOR THE ON-CAMPUS PROJECT REPORT (Measurement or Modelling Projects)

1. Title of Project: (Name, supervisor etc.)

2. Summary or AbstractA concise summary (up to 350 words) of what has been achieved. This should be explicit and reference should be made to work/experiments carried out, results obtained, and the significance of these results. Highlights from the research should be specifically included. Inclusion of a graphic is recommended.

3. IntroductionApproximately 3-5 pages (A4, typed, one and a half line spacing, margins approx 2.5 cm, font such as Times and font size 12). Structure diagrams or schemes can be drawn with ChemDraw available for all students. The introduction should include background to the project, explaining the reasons for undertaking the work and include a project plan. References must be included and usually are numbered in sequence as they are found in text with a superscript and the full reference listed at the end of the report.1-3 The final section of the introduction should outline the aims of the project. The final sentence or paragraph should summarise what has been achieved. The introduction should be written in your own words and not copied from any reviews or internet. If reproducing any figures from the literature in the thesis then please obtain copyright permissions and cite the original article. This can usually be done online where the article. Plagiarism must be avoided. See NUI Galway guidelines on plagiarism at http://www.su.nuigalway.ie/site/view/313/

4. ExperimentalDescription of experiments should be given in detail sufficient to enable experimental workers to repeat them. Include full details of the samples you studies, where they were obtained, how stored and handled. Include full details of the instrumentation and software used. Explain clearly how you collected you data and what instrumental parameters were used.

Typical experimental procedure (for an analytical project):

Instrumentation and data collection: Raman measurements were performed in triplicate at room temperature using an Avalon Instruments Raman spectrometer with 785 nm excitation. A laser power of ~70 mW at the sample was used and spectra were collected with a resolution of 8 cm-1 and a typical exposure time of 10 s. For solution samples, stainless steel 96-well plates were used and multiple spectra were collected from a 3 × 3 grid (0.5 mm spot spacing) from which a single averaged spectrum was generated for data analysis. Fluorescence measurements were made at 25°C with a Cary Eclipse (Varian) fluorimeter using procedures previously described. Yeastolate samples were randomly removed from storage, defrosted at room temperature and allowed to reach room temperature, and handled using aseptic techniques. For each solution, 1 ml was pipetted into a cuvette and sealed before allowing to thermally equilibrate for several minutes prior to measurement. Spectral SERS data was pre-processed to reduce the influence of baseline drift, scatter effects, and uncontrolled fluctuations. Spectra containing cosmic interference were discarded prior to averaging of the spectra. The average spectrum was then treated with a multiplicative scatter correction, then an asymmetric weighted least squares algorithm to remove baseline offsets before finally applying a background correction using an orthogonal projection procedure. For SERS-ROBPCA analysis, the first derivative (SavGol) method was then implemented to further reduce measurement/instrumental effects and accentuate analyte signals. For EEM-MROBPCA analysis, Rayleigh and Raman scatter were removed from EEM data by replacing with a curve fit, connecting points either side of the bands using imputation. All calculations were performed using MATLAB ver. 7.4, PLS_Toolbox 4.0, and in-house-written toolboxes.

Please consult with your supervisor for advice on preparation of the experimental section. This can vary significantly between research areas. It is good practice to look at the style and content of peer-reviewed journals to assist in preparing your project.

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5. Results and DiscussionStudents are advised to give a concise presentation of results presented first followed by a discussion of their significance (novelty of method?, novel data?). In modelling projects, there is no need to provide detail of any code used (this can be included in an appendix). In analytical type projects there is no need to include every spectrum etc., show an indicative or important example then summarise the important results in overlay plots or tables. If you have a lot of important data place it in an appendix with a brief description of the data. You can then refer to this appendix in your text. When relevant there should be a comparison between your data/results and relevant examples from the literature, e.g. are your spectra the first to show a new species? Is your data better quality than what’s been published? If so, how so? Look at peer-reviewed papers for examples of how this is done professionally.

6. ConclusionsPlease include a conclusions section (1-2 pages), summarizing your main achievements.

7. References (Please use a standard style such as the one outlined below).[1] J. R. Lakowicz, Principles of Fluorescence Spectroscopy, 3rd Edition ed., Springer, New

York, 2006.[2] T. Cartwright, G. Shah, Culture media, in: J.M. Davis (Ed.) Basic Cell Culture, Oxford

University Press Inc., New York 2002, pp. 69-106.[3]P. W. Ryan, B. Li, M. Shanahan, K. J. Leister, A. G. Ryder, Prediction of Cell Culture Media

Performance Using Fluorescence Spectroscopy, Anal. Chem., 82 (2010) 1311-1317.[4] PLS_Toolbox, ver. 2.0, Eigenvector Research Inc., 3905West Eaglerock

Drive,Wenatchee,WA.

Reference 1 is a typical book, Reference 2 is typical for a chapter in an edited book. Reference 3 is a typical journal reference, and 4 is for referencing software.

8. AppendixIn addition to the above you will need to include your project research assessment. You should include any relevant collections of spectra, modelling code, repeat experiments etc. here.

9. Project risk assessmentA risk assessment has to be carried out for all projects, including theoretical or computer-based projects. In certain cases, no risks may be identified (e.g. computational projects) and this can be stated on the risk assessment form.

10. Plagiarism. The thesis should be written in your own words and not copied from any reviews or internet. If reproducing any figures from the literature in the thesis then please obtain copyright permissions and cite the original article. Obtaining copyright permissions can usually be done online where the article is originally published. Plagiarism must be avoided. See NUI Galway guidelines on plagiarism at http://www.su.nuigalway.ie/site/view/313/. Action will be taken by the examiners when plagiarism is found to occur.

Grading of project and the write-up will be based on strict adherence to guidelines provided herein. The number of total pages does not normally need to exceed 20 pages. The student is recommended to focus on the quality of their work and report.

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27

GUIDELINES FOR WRITING THE WORK PLACEMENT REPORT

In the final report the student should address each of the following areas and use this to demonstrate their achievement of learning outcomes (See above) from the placement. Marks will be awarded for each section so do not leave any section out.

1. Job Description Include the job description (see appendix for template, 1 page max).

2. Organisation: Describe the organisation where the placement was carried out. Describe its management structure and the environment in which it operates its daily business (2 pages max)

3. Role of student: Describe the role you played within the organisation during the course of your work placement (1 page)

4. Technical and general skills: List the required technical and general skills of the given work place. Give an account how these various skills were acquired and developed during the placement. This may include ‘Technical Skills’ as well as ‘People Skills’ and ‘Self Reliance Skills’ (refer to the learning outcome section above) (2 pages max)

5. Future employability: How has the work placement improved your own employability? Discuss career possibilities or choices that the work placement has opened up that you will now be able to consider (max 1 page)

6. Relationship to programme of study: Describe how the work placement was related to your programme of study in Biopharmaceutical Chemistry (max 2 pages).

7. Safety risk assessment: Include the placement/project health & safety risk assessment related to the placement in the final report.

8. CV: Include your updated 2 Page CV after completion of the work placement.

9. Chemistry: Include a 2 page description of a chemistry topic which you learnt about because of your work placement. For example, this can be a chemistry topic which relates to a product or service provided by the company and is a topic which you learned about during your work placement. This should be different to that of your dissertation.

10. Appendix (unlimited length & optional): Certificates of skills and achievements, and training completion documents acquired during the work placement.

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Employer’s Student Appraisal Form

To be completed by the employer after placement is completedPlacement supervisor Student Name Organisation Name Job title start date end dateWork location

Did the studentCircle a number as appropriate from 0-10 Exceptionally high or low grades must be justified in comments box below. See guide to grading on next page

Complete tasks effectively and efficiently? 0 1 2 3 4 5 6 7 8 9 10Demonstrate knowledge of their discipline? 0 1 2 3 4 5 6 7 8 9 10Demonstrate a willingness to seek out knowledge and acquire new skills? 0 1 2 3 4 5 6 7 8 9 10Learn from their mistakes?

0 1 2 3 4 5 6 7 8 9 10At the end of their placement the student showed evidence of competency in completing tasks based on knowledge and skills of the workplace?

0 1 2 3 4 5 6 7 8 9 10Show appropriate initiative?

0 1 2 3 4 5 6 7 8 9 10Exhibit good planning, timekeeping and organisational skills?

0 1 2 3 4 5 6 7 8 9 10Communicate effectively with others? 0 1 2 3 4 5 6 7 8 9 10Demonstrate professional conduct in the workplace?

0 1 2 3 4 5 6 7 8 9 10Work well with others?

0 1 2 3 4 5 6 7 8 9 10Please add any additional comments/feedback here. These can be specific to the student’s performance or more general feedback to the placement coordinator to improve the placement programme.

Would you take another NUI Galway student on placement in the future? Yes/NoSignature (typing your name is acceptable): Date:

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Guide to grading placement performance.

To ensure consistency of grading across multiple workplaces please apply the following principles

In each case where a mark is awarded for one of the assessment criteria which is shaded (0-4 and 9-10) please comment specifically on that criterion and that mark in the commentary box below the table.

Where the average mark obtained by a student will be in the shaded range please forward a draft of the report in advance to the School so we can ensure the document would contain sufficient detail for our external examiners who want to see such awards backed up by clear documents.

To give an idea of what the marks may mean

0 Not applicable (for some reason this criterion does not apply)1 Substantially problematic2 Problematic performance3 Underperformed4 Adequate performance but could have performed better5 Reasonable performance6 Good performance met my expectations7 Strong performance outperformed my expectations8 Really strong performance substantially outperformed my expectations9 This performance level is what I might expect to see from one student in 2010 This performance level is what I might expect to see from one student in my career

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Schedule for Biopharmaceutical Chemistry Work Placement (CH4111)(note: students begin year 4 placement immediately after year 3 summer examinations)

Task Deadline/Dates Who is responsible? Any other outcome?

1. Read placement booklet and accept rules and regulations of process

September of Year 3 Student provides signed acceptance of the rules to School administrator/placement coordinator.

2. Preparation of CV, making applications, doing interviews, becoming successful in obtaining work placement with an employer

September - May in Year 3(Students are advised to take advantage of all supports available, including those available in the careers office and engage fully with the placement process).

Student, placement coordinator and placement office.

3. Outline job specification End of July 2020 Employer in cooperation with placement coordinator/placement office. Student includes copy of the specification with final report. School Placement Coordinator must approve job specification.

4. Obtain contact details of academic supervisor, employer supervisor and student. Sign off on tripartite agreement.

End of July 2020 Student gets academic supervisor, employer to sign the document and provides a copy to the various parties and the School administrator. The student includes copy with final report.

5. Placement safety risk assessment

End of July 2020 Student provides to School Administrator/safety coordinator. Include in final report.

6. Interim meeting/evaluation at place of work.

July-September and must be completed by end September

Employer, university supervisor, student meet at place of work to discuss progress in attaining learning outcomes and review the placement log and activity. Induction of the student into the work place is reviewed.

7. Employer evaluation of student

Due Friday 18th December Employer to provide to School Secretary.

8. Work placement report Submit report by 15.00 on 26th January 2021

Marks will be deducted for late submission in accordance with College of Science policy.

9. Presentation on work placement

TBC Student, academic staff

10. Feedback by student/employer regarding placement

End of Semester 1. Students/employer give feedback to help improve placement process.

11. Provisional grades to students

Date to be confirmed. Students will be informed of provisional grade for work placement module through blackboard.

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GUIDELINES FOR STUDENTS IN WRITING THE BIOPHARMACEUTICAL CHEMISTRY DISSERTATION (CH4110)

All students on work placement will prepare a dissertation in parallel with their work placement. Much of the work in obtaining data or facts will be carried out in the library or through online library resources. It is strongly advised that the student discuss the structure of the thesis write up with their supervisor. The following sections should be included in the thesis. The thesis is normally ~20-25 pages and students are recommended to focus on quality.

1. Title of Dissertation

2. Summary or Abstract and Graphical AbstractA concise summary (up to 350 words) of objectives, findings and conclusions. Include any highlights which emerged from the investigative work. Include also a graphical abstract.

3. IntroductionThis can be brief (e.g. 1-2 pages). This should be typed, one and a half or double line spacing, margins approx 1”, font such as Times and font size 12). Structure diagrams or schemes can be drawn with ChemDraw available for all students. The introduction should include background to the investigation, explaining the reasons for undertaking the work and include objectives. References must be included and usually are numbered in sequence as they are found in text with a superscript and the full reference listed at the end of the report.1-3 References should be primary references when possible. Compounds should be numbered (in bold) as they appear in schemes. The final section of the introduction should outline the aims or brief summary of the outcomes of the investigation. The introduction must be written in your own words and not copied from any reviews or the internet. Plagiarism must be avoided. See NUI Galway guidelines on plagiarism at http://www.su.nuigalway.ie/site/view/313/ and the appropriate section in this booklet.

4. Presentation and Discussion of findings

Students may include a brief methodology section where the approach to generating information for the thesis is summarised. Students are advised to detail their findings of their investigative work under a series of headings related to the thesis work, which contains appropriate citation. The structure of this section should be discussed and planned with the supervisor. This section should include a discussion of any emerging themes or findings by the student and future opportunities. Please also provide any relevant figures or schemes or tables that are needed to efficiently and clearly present your findings. Number these in order of appearance in text. If reproducing any figures from the literature in the thesis then please obtain copyright permissions and cite the original article. These permissions can be obtained online for most journals at the website where the article is published by following links at the website (usually copyrights/permissions).

5. ConclusionsPlease include a detailed conclusions section.

6. References (Please use a standard style such as the one (RSC) outlined below).1. I. Fleming, Frontier Orbitals and Organic Chemical Reactions, Wiley, Chichester, 1976, p. 55.2. A. J. L. Beckwith and K. U. Ungold, in Rearrangements in Ground and Excited States, ed. P. de Mayo, Academic Press, New York, 1980, vol. 1, p. 161.3. P. D. Cunningham, N. W. A. Geraghty, P. J. McArdle, P. V. Murphy and T. J. O’ Sullivan, J. Chem. Soc., Perkin Trans. 1, 1997, 1.4. H. Kessler and M. Hoffmann, J. Am. Chem. Soc. 1994, 118, 10156.5. X. Y. Smiths, Journal of Flame, 2000, 22, 10157.

Reference 1 is a typical book, Reference 2 is typical for a chapter in an edited book. References 3 and 4 are typical journal references.

7. Plagiarism. The thesis should be written by yourself in your own words and must not copied from any reviews or internet or commissioned by any third party commercial supplier of dissertations. If reproducing any figures from the literature in the thesis then please obtain copyright permissions and cite the original article. Obtaining copyright permissions can usually be done online where the article is originally published. Plagiarism must be avoided. See NUI Galway guidelines on plagiarism at http://www.su.nuigalway.ie/site/view/313/. Appropriate action will be taken by the examiners when plagiarism is found to occur.

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Grading of the Dissertation will be based on strict adherence to guidelines provided herein

Schedule for Biopharmaceutical Chemistry Dissertation

(Note: students may begin work on the dissertation immediately after year 3 summer examinations if they have qualified for year 4)

Task Deadline/Dates Who is responsible? Any other outcome?

1. Assign a topic for the dissertation thesis

Mid-August Coordinator and dissertation supervisor. Supervisor to provide one or two leading references.

2. Prepare a plan for the dissertation

No later than end Sept.

Student. It is recommended that this is discussed with the supervisor.

3. Submit the introduction and outline of headings

Monday 12th October 2020

Student by email to the supervisor

4. Submit a draft of the dissertation to supervisor

As soon as possible and no later than December 18th 2020

Student. It is strongly recommended that the student meet the supervisor to get feedback on one version before preparing the final version.

5. Submit the final Dissertation

Submit your final dissertation by 15.00 on 12th January 2021

Marks will be deducted for late submission.

6. Presentation and oral assessment on Dissertation

TBC Student and examiners.

7. Provisional grades to students

Date to be confirmed. Students will be informed of provisional grade for work placement module through blackboard.

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Schedule for Research Investigation (on campus project)– CH4101

Task Deadline/Dates Who is responsible? Any other outcome?

1. Commence on-campus project

Beginning of Semester 1. Student and supervisor.

2. Complete practical work

Recommended at end of week 10.

Student.

3. Begin the write up This should commence no later than week 8.

Ensure to leave time available for study for tests and other exams.

Student. It is recommended that the student try to get a preliminary draft or outline of their write up that can be discussed with the supervisor in advance of the deadline, ideally before December 20th.

4. Submit the final report 22nd April 2021 Note: Marks will be deducted for late submission.

5. Presentation Week of 26th April 2021 Student.

6. Provisional grades to students

Date to be confirmed. Students will be informed of provisional grade for on campus project through blackboard.

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ASSESSMENT OF THE RESEARCH INVESTIGATION PROJECT – CH4101

Grading of project performance (40%)

The performance during the academic year forms part of the assessment. The supervisor will be asked to grade this section based with a contribution to the assessment from a second reader. This group will comment specifically on items from the following.

The student working safely in the laboratory, if relevant The management of data and findings to a high standard (e.g. lab books, tables, spreadsheets) Quantity and quality of results, considering the nature of the project. It is the nature of research that

some experimentally based projects may not give results in a short time. Hence the general approach of the student to the project will be evaluated. The student can still demonstrate high quality experimental skills.

The independent contribution by the student in terms of design and carrying out of experiments and in the analysis of the outcomes of experiments and in implementing improvements throughout the project.

Pursuit of high standards (e.g. high purity of important substance or comprehensive and rigorous analysis of data in the literature)

Quality of spectra or other data provided by the student (use appendix and report itself to highlight the quality of your data)

Are results from the report publishable? Are the results exceptional at this level or any level?

Grading of research project written reports (40%)

The readers will be asked to report on the following:

Is the abstract a concise summary of the student’s own work, particularly important findings? Is the length of the introduction appropriate? Are the aims or objectives included? Does the results and discussion section present a clear logical development of the topic? Is there adequate detail of the experimental approach and outcomes, if relevant? Is there sufficient discussion of the significance of results? Is it scientifically correct? Are findings interpreted correctly? Is there a paragraph summarizing the main conclusions? If there is an experimental section is there sufficient detail to enable repetition, if relevant? Is there full characterization of new substances, if relevant? In the reference section is there adequate citation, including, if relevant, to known substances? Is the experimental section consistent and in appropriate style? Are data interpreted correctly? Is chemical information accurate throughout? Was chemdraw or equivalent software used to an acceptable level? Is there sufficient evidence of student’s independent reasoning/critical analysis? Is the literature up to date? Primary literature cited where possible? References in an appropriate style? Appropriate citation throughout report? Could the report be published as is or with minor change? Acceptable standard of writing, spelling, grammar, sentence construction? Definitions are provided for the terms or abbreviations used? Evidence of adequate safety risk assessments or a project risk assessment related to the project

work carried out.

Grading of oral presentation (20%)

The assessors will consider how well organized the presentation is and how well it is delivered. They will also consider the quality of the slides and information on each slide and whether this is accurate. The student will be expected to answer questions and how these are answered will be assessed. The examiners will give a mark for their overall impression of the project work based on the presentation.

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SEMESTER 1 TIMETABLE FOR STUDENTS TAKING THE ON-CAMPUS PROJECT

Students taking the on-campus project are also taking two 5 credit modules and therefore will need to attend lectures and examinations as well as complete their project.

Students are expected to work at least 25 h per week generating data on their project in the project work periods. Sufficient time should be set aside to generate the written report as advised in timetable.

Two hardcopies (word file) of the project thesis are required. Marks will be deducted for late submission. Identical electronic copies should also be uploaded to Blackboard by the date (to be advised).

Students are assigned a second reader of their project reports. Students can meet their second reader during the project to discuss their progress and this forms part of the assessment.

The submission of the project, presentations and oral assessments will take place in January Semester 2.

Academic Staff Supervisors will give feedback on a draft of the write-up of the report in advance of the deadline, if they are provided with the draft. Please provide a timely draft to your supervisor in advance of this meeting and please confirm the time and date with your project supervisor in advance.

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PLAGIARISM

Plagiarism is the act of copying, including, or, directly quoting from the work of another, without adequate acknowledgement, in order to obtain benefit, credit or gain. Plagiarism can apply to many materials, such as words, ideas, images, information, data, approaches or methods. Sources of plagiarism can include books, journals, reports, websites, essay mills, another student, or another person.

Self-plagiarism, or auto-plagiarism, is where a person re-uses work previously submitted to another course within the University or in another Institution or even a journal. Plagiarism can also involve overly relying on a source – even if it is referenced correctly.

All work submitted by students is accepted on the understanding that it is their own work and contains their own original contribution, except where explicitly referenced using the accepted norms and formats of the appropriate academic discipline. Students are required to sign an affidavit to confirm the above for all submissions in fourth year chemistry.

NUI Galway applies a penalty grid to plagiarised submissions. All relevant information can be found at: www.nuigalway.ie/plagiarism. This penalty grid is University policy and no exceptions will be made.

Supervisor responsibilitiesSupervisors will encourage students to avoid plagiarism during all meetings where preparation of project reports etc. are being discussed.

Plagiarism advisor responsibilitiesThe plagiarism advisor will check all submissions using Turnitin. In cases of plagiarised work, the plagiarism advisor will determine if there is a case to be made. If the decision is positive, the fourth year examiners including the supervisor and second reader will be contacted and appropriate action taken. The plagiarism advisor will write a confidential report, recording the decision and any penalty.

Student responsibilitiesAll students will be given access to their own Turnitin report. In cases of plagiarised submission, students will be obliged to formally meet with their project supervisor to discuss the plagiarised submission. The final project report will be submitted electronically through Blackboard and Turnitin on Monday November 25th 2016. In cases of plagiarised submissions the plagiarism advisor and the 4th year committee will be contacted and they will decide if appropriate action will be necessary according to University policy (www.nuigalway.ie/plagiarism).

Plagiarism adviserPlagiarism adviser is Dr. Pau Farras.

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APPENDIX

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AFFIDAVIT

Student Declaration on Plagiarism, Collusion or Copying

This declaration is to be completed and signed by the student. It must be included in the essay, first and final draft of the project reports.

I declare that this material, which I now submit for assessment, is my own work and that any assistance I received in its preparation is fully acknowledged and disclosed in the document. To the best of my knowledge and belief, all sources have been properly acknowledged, and the assessment task contains no plagiarism. I understand that plagiarism, collusion, and/or copying are grave and serious offences and am aware that penalties could include a zero mark for this assessment, suspension or expulsion from NUI Galway. I have read the NUI Galway code of practice regarding plagiarism at www.nuigalway.ie/plagiarism. I acknowledge that this assessment submission may be transferred and stored in a database for the purposes of data-matching to help detect plagiarism. I declare that this document was prepared by me for the purpose of partial fulfilment of requirements for the programme for which I am registered with the AUA. I also declare that this assignment, or any part of it, has not been previously submitted by me or any other person for assessment on this or any other course of study or another college.

Student Name

___________________________

Student Signature Date

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Job Specification

A job specification will be be provided by the employer in cooperation with the placement office/placement coordinator. Students should obtain and keep a record of this signed job specification and should include it in their final report.

Outline Job Specification    Job Title   PayWork Location    Description of work to be undertaken by student

  Key skills and aptitudes required

  Main learning opportunities

  

Hours and Days of attendance weekly  Line Manager (workplace mentor) title and name   Phone/emailSignatures    Approved by

 NUI Galway School of Chemistry Work Placement Module Coordinator

 Prof. Peter Crowley Date:Head of School

 Dr. Patrick O’Leary Date:

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Contact Details and Sign off (Tripartite agreement)

This must be completed prior to commencement of the placement, or a soon as possible thereafter, and a copy to be retained by each of the three signatories and by the School administrator. The student is required do ensure all parties sign this page and to return a copy to the relevant parties.

Employer Details    Organisation Name    Address    Workplace Mentor or Supervisor name   TitleDepartment    Address    Phone   Email

Student Details       

Course Title Biopharmaceutical Chemistry (Work Placement)  Year: 4

Department addressSchool of Chemistry, NUI Galway    

Student name   Student No:Address while on placement    Phone   Email:      

Academic Supervisor Details    

   Contact Name   TitleDepartment School of Chemistry   Address University Road, National University of Ireland GalwayPhone   emailAlternative contact name(normally placement coordinator)   phone    email

Signatures    Employer Representative   Date:NUI Galway School of Chemistry Representative   Date:Student   Date:

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Workplace Learning Journal

It is required that a journal is completed by the student in cooperation of the workplace mentor during placement. This will be evaluated at the interim meeting and will be helpful in preparing the final report. Please keep a record of placement activities in a journal. You may use the template below.

Workplace Learning Journal    Student name   Date:

Organisation name  

Job title  

Work Location  

Week Task/Activity Skills required/acquiredSupervisor Initials

       

       

              

       

Linking Learning to learning outcomes      

Learning Event What did you learn?Relevant learning outcome(s) Evidence

       

       

       Reflections of the learning event:  

Expand this table as required.Note: Reflecting on learning obtained and linking the learning to the required outcomes or competences helps the learner to link their experiences to the learning outcomes and to identify potential gaps in the learning.

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