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Course Outline

CHEM2021

Organic Chemistry: Mechanisms and Biomolecules

School of Chemistry

Faculty of Science

Term 2, 2019

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1. Staff

Position Name Email Consultation times and locations

Contact Details

Course Convenor

Dr Vinh Nguyen

t.v.nguyen@unsw.edu.au

By arrangement Room 217 Dalton Building

(02) 9385 6167

Lecturer Prof Martina Stenzel

M.Stenzel@unsw.edu.au By arrangement Room 226 Dalton Building

(02) 9385 4656

Lecturer Dr Vinh Nguyen

t.v.nguyen@unsw.edu.au

By arrangement Room 217 Dalton Building

(02) 9385 6167

Lecturer Dr Albert Fahrenbach

a.fahrenbach@unsw.edu.au By arrangement Room 541 Hilmer Building

(02) 93854574

Academic lab demonstrators

A/Prof Graham Ball

Dr Vinh Nguyen

Dr Robert Chapman

Dr Albert Fahrenbach

On site

Lab Technician Dr Ruth Thomas On site

2. Course information

Level of Course 2nd UG

Units of Credit 6UOC

Term Offered Term 2

Assumed Knowledge, Prerequisites or Co-requisites

This is the main Level 2 Organic Chemistry course taught within the School of Chemistry. It assumes knowledge of CHEM1011 and CHEM1021 or CHEM1031 and CHEM1041 or CHEM1051 and CHEM1061, AND CHEM2041. It is a core element in Chemistry major programs. It is also required for industrial chemistry, biochemistry and medicinal chemistry programs.

Hours per Week 8.0 hpw

Number of Weeks 10 weeks (Compulsory lab induction in Week 1, experiment starts in Week 2. One lecture in Week 10 due to Queen’s birthday public holiday in Week 2)

Commencement Date Monday 03rd June 2019

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Summary of Course Structure (for details see 'Course Schedule')

Component HPW Time Day Location

Lectures 4.0

Lecture 1 1 pm – 2 pm Monday OMB149 (K-K15-149)

Lecture 2 10 am – 11 am Tuesday Physics Theatre (K-K14-19)

Lecture 3 1 pm – 2 pm Thu OMB149 (K-K15-149)

Lecturer 4 9 am – 10 am Fri OMB149 (K-K15-149)

Laboratory 4.0

Lab – Option 1 9 am – 1 pm Wed Chem Sci 262

Lab – Option 2 2 pm – 6 pm Wed Chem Sci 262

Lab – Option 3 9 am – 1 pm Thu Chem Sci 262

Lab – Option 4 2 pm – 6 pm Thu Chem Sci 262

TOTAL 8.0

Special Details

• Lecturers will work through typical revision questions and problems in class. • The first 15 minutes of each laboratory class are set aside for checking risk assessments and

to cover other occupational health and safety issues. • Bench allocation and safety induction will be carried out in week 1 in your allocated lab

session (9.00-9.30 for AM lab and 2.00-2.50 for PM lab).

Please aso refer to: http://timetable.unsw.edu.au/2019/CHEM2021.html

2.1 Course summary Organic molecules are at the heart of the chemistry of life and industry. This course builds on the fundamental chemical principles learned in first year, exploring many of the central reactions that form the basis of living processes, modern research, and contemporary industrial transformations. The course contains a problem-based module on the application of spectroscopic methods to organic structure elucidation, focusing on infrared and nuclear magnetic resonance spectroscopy. Several modules then develop knowledge of major classes of organic reactions (including compounds containing alkenes, alkynes, aromatic rings, and carbonyl groups) by enriching a study of key reactions with an understanding of relevant reaction mechanisms. The concepts of reactivity and selectivity in the manipulation of more complex compounds will be highlighted, with an emphasis on biologically relevant molecules, especially amino acids and nucleic acids. Interleaved throughout the course will be relevant examples from contemporary chemical industries, and important medicinal and pharmaceutical examples.

2.2 Course aims The course aims to present the chemistry of organic molecules and highlight their importance in the world around you. To achieve this, we will present four modules that will give you a framework to build further knowledge. We will present the chemistry of organic molecules and how to interconvert functional groups, with a particular emphasis on biologically relevant molecules. It is emphasised that the theory part of CHEM2021 builds on material covered in Chemistry I and that it is the students' responsibility to make sure they are thoroughly familiar with that material because that knowledge will be assumed.

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The aim of the experimental part of the course is to give students practical experience in a selection of the reactions that they learn about in theory, and in the experimental techniques involved in carrying out the reactions and isolating and purifying products. In addition it is designed to allow students to practise some of the skills they have learned in Level 1 and to learn new skills, including structural characterisation, implementation of multi-step syntheses, proper record keeping, awareness of Laboratory Safety (http://www.riskman.unsw.edu.au/ohs/ohs.shtml).

2.3 Course learning outcomes (CLO) At the successful completion of this course you (the student) should be able to:

1. Students will derive a good, basic understanding of most functional group chemistry, and of a reasonable number of carbon-carbon bond forming processes. They will have a reasonable understanding of current mechanistic theory associated with this chemistry.

2. They will have an understanding of multistep organic synthesis design and be able to predict certain multistep reaction products. They will have the beginnings of an ability to plan organic syntheses and be able to recognise classes of compounds based on their chemical reactions and spectroscopic properties.

3. Students will feel comfortable in entering an organic chemistry laboratory and be aware of basic safety precautions and the elements of risk assessment. They will have experience in the separation, isolation and purification of organic reaction products. They will have experience in multistep syntheses and the use of protecting groups, and they will have practised the art of structure elucidation.

4. They will also have an understanding of the manner in which records must be kept to protect intellectual property and appreciate the need to reference information against that in the literature.

2.4 Relationship between course and program learning outcomes and assessments

Course Learning Outcome (CLO)

CLO Statement Related Tasks & Assessment

Research, inquiry and analytical thinking abilities

The large factual content of lectures will require students to become systematic in their thinking and inquiry, and demand that students become analytical in their management and understanding of the concepts of organic chemistry. Students will be challenged to respond to questions during lecture times.

Practice questions during lectures and assignments

Capability and motivation for intellectual development

Lectures will focus on individual performance, relying upon individual capabilities and self-motivation for intellectual development. Performance assessed in mid term quiz and final exam (total 65%)

Midterm and final exams

Ethical, social and professional understanding

Lecture material will be put into an industrial context and practical classes will emphasise the need for accurate record keeping in the generation of IP

Communication Part of the assessment of practical reports will be based on Lab reports

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a report, written according to journal conventions

Teamwork, collaborative and management skills

Practical work will be performed individually and marks awarded for individual performance. Experiments need to be completed in a certain time frame, so time management will be important.

Core-skill assessment, lab notebooks and lab reports

Information literacy Practical work will require physicochemical information to be evaluated against literature data.

Lab notebooks and lab reports

3. Strategies and approaches to learning

The course will engage students in learning, at a basic level, the language of organic chemistry through a vocabulary of functional group reactivity, reagents and reaction types, and the grammar of mechanistic theory and basic synthetic design. It will provide a moderate range of individual practical experience in the execution of representative, single organic chemical reactions and multistep synthetic sequences, while at the same time expose students to laboratory techniques, including record keeping, and methods of physicochemical characterisation and spectroscopic analysis. Students in the practical classes work at their own pace but are restricted in their hours of work so that they develop skills in time management.

At this stage in their development, students have a basic understanding of organic chemistry as a field in which the transformations of carbon-based materials from reactant to product are achieved through reactions that are promoted by use of reagents. They have limited knowledge of the diverse arsenal of reactions and reagents that are available, and even less practical experience of these processes. Similarly, they have little or no experience in the techniques used to characterize molecules or their reactions. The purpose of this course is to widen the experience of the students, to introduce concepts of selectivity and rearrangement, and to engage the students in learning through practical experience, both on paper and in the laboratory.

This course consists of 36 hours of lectures (4 hours/week) and 36 hours of laboratory work (one 4h laboratory period/week. Lectures are delivered using a combination of Powerpoint and blackboard/whiteboard presentations and they include numerous worked examples. In addition, for each topic students will attempt a series of short answer written exercises for which answers are provided. The practical part of the course reinforces chemistry that is presented in lectures. It comprises a series of single step and one multistep reactions from which students are expected to isolate pure materials by a variety of techniques including distillation and crystallization and to characterise them by physicochemical methods. Accurate records must be kept within individual laboratory notebooks. In addition, the practical course involves the study of unknown substances for which spectra are provided and students are expected to derive structures.

4. Course schedule and structure

This course consists of 36 hours of class contact hours on four major Topics and 36 hours of laboratory work. You are expected to take an additional 36 hours of non class contact hours to complete assessments, readings and exam preparation.

Topic 1: Stereochemistry and Mechanism (Prof Martina Stenzel - 9 h)

Introduction to mechanism - the basics of mechanism; what an arrow means and how it can be used; intermediates and what they mean; the concepts of a nucleophile and an electrophile.

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Stereochemistry and conformation - stereogenic centres, the importance of freedom of rotation, drawing stereogenic carbon centres, up to and including six-membered rings and a brief introduction of nomenclature (anti, syn, periplanar, etc.)

Addition and Elimination - introduction of E1 and E2 nomenclature, highlighting mechanistic differences, requirements in terms of conformation (see above), substrate type and solvent conditions.

Substitution processes - introduction of SN1 and SN2 nomenclature, highlighting mechanistic differences, requirements in terms of conformation (see above), substrate type and solvent conditions.

A comparison between substitution and elimination - use this to predict the outcome of reactions given substrate and conditions.

Extension to other systems - various examples such as epoxidations/ring opening.

Topic 2: Chemistry of carbonyl compounds (Prof Martina Stenzel and Dr Vinh Nguyen – 9h)

This section will cover synthesis and reactivity of aldehydes and ketones, and carboxylic acid derivatives. The following topics will be covered in details: nature of the carbonyl group; nucleophilic addition of water, alcohols, cyanide, amines, organometallic reagents, and acetylides to carbonyl compounds, and their reaction mechanisms; reduction of the carbonyl compounds including stereochemistry of carbonyl reduction; a,b-unsaturated carbonyl compounds and conjugate addition of amines, cyanide, organometallic compounds; keto-enol tautomerism, reactivity of enolates, α-substitution of carbonyl compounds, a-halogenation, the haloform reaction, alkylation of enolate ions and enamines; reactions of carboxylic acids and their derivatives, a-bromination of carboxylic acids, reduction of carboxylic acid derivatives; carbonyl condensation reactions including the aldol reaction, the Perkin reaction, the Claisen condensation reaction, and Robinson annulation reaction; application of carbonyl condensation reactions in natural products synthesis. Examples (sugars, amino acids and proteins) from nature will also be provided.

Topic 3: Aromatic chemistry (Dr Vinh Nguyen and Dr Albert Fahrenbach – 9 h)

Concepts of aromaticity and anti-aromaticity; non-benzenoid and anti-aromatic hydrocarbons

Electrophilic aromatic substitution: alkylation, acylation, halogenation, sulfonation, nitration; activating/deactivation, resonance and inductive effects, directing effects, concept of blocking and protecting groups and general synthetic strategy. Reactions of substituents and sidechains: alkyl- and acylbenzenes: comparison of Friedel-Crafts alkylation and acylation reactions; phenols, Kolbe reaction, oxidation; selective reduction of polynitro compounds. Benzene diazonium salts: preparation, reactions, displacement and coupling. Halobenzenes and nucleophilic aromatic substitution. Benzyne: preparation and reactivity. Polycyclic aromatic compounds: bonding, oxidation, reduction and substitution of naphthalene and anthracene. Heterocyclic compounds: π-electron rich (thiophene, furan, pyrrole) versus π-electron poor (pyridine). Examples of biologically important aromatic molecules.

Topic 4: Chemistry of biologically relevant organic molecules (Dr Albert Fahrenbach – 9 h)

This section will cover structures, synthesis, chemical reactivity and some biological functions of naturally occuring molecules. Biological systems grow, reproduce and compete with each other via a huge range of complex organic reactions. This unit will build upon the knowledge of amino acids, polypeptide and proteins in Chemistry I (CHEM1021 or 1041 or 1061) to examine advanced topics in chemistry of relevant biological systems to understand the important role of natural products in

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organic chemistry and biology. Natural products are the source of the most complex and fascinating chemical structures and they represent biological diversity and biological activity, whether as single compounds or as complex mixtures. Chemistry of these biologically relevant molecules can be an effective bridge from tradition to modern scientific developments, including genetics, molecular biology, biotechnology, and pharmaceutical science.

Specific topics include: primary and secondary metabolisms; amino acids, peptides and proteins; carbohydrates and polysaccharides; nucleic acids; alkaloids and steroids; terpenoids and polyketides.

Week Lecture Practical Related CLO

Week 1 Topic 1 – Prof M Stenzel (4 h) Lab Induction

(compulsory)

Bench allocation and safety induction

Week 2 Topic 1 – Prof M Stenzel (3 h)

Queen’s birthday public holiday

Experiment 1

Week 3 Topic 1 – Prof M Stenzel (2 h)

Topic 2 – Prof M Stenzel (2 h)

Experiment 1

Week 4 Topic 2 – Prof M Stenzel (1 h)

Topic 2 – Dr Nguyen (3 h)

MIDTERM EXAM (on Topic 1 only)

Experiment 2 Experiment 1 report due

Week 5 Topic 2 – Dr Nguyen (3 h)

Topic 3 – Dr V Nguyen (1 h)

Experiment 3 Experiment 2 report due

Week 6 Topic 3 – Dr V Nguyen (4 h) Experiment 3 Assignment for Topic 2 due

Week 7 Topic 3 – Dr V Nguyen (1 h)

Topic 3 – Dr A. Fahrenbach (3 h)

Experiment 4 Experiment 3 report due

Week 8 Topic 4 – Dr A. Fahrenbach (4 h) Experiment 4 Assignment for Topic 3 due

Week 9 Topic 4 – Dr A. Fahrenbach (4 h) Experiment 5 Experiment 4 report due

In-class Assignment for Topic 4 (quiz-style)

Week 10 Revisions and Feedbacks Experiment 5 Experiment 5 report due one week after your lab time.

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5. Assessment

Task Knowledge & abilities assessed

Assessment Criteria

% of total mark

Feedback

WHO HOW

Midterm Exam

Mechanism and Stereochemistry - Ability to predict products, suggest

appropriate reagents, explain appropriate

mechanisms

Correct answers to questions.

Content shows knowledge and understanding of the course

material of the first section.

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on

Assignment 1

(Topic 2)

Carbonyl chemistry - Ability to predict products, suggest

appropriate reagents, explain appropriate

mechanisms

Correct answers to questions.

3 Dr Nguyen Annotated

scripts, Marks & Summary Chart

Assignment 2

(Topic 3)

Aromatic compounds – Ability to predict products,

suggest appropriate reagents, explain

appropriate mechanisms

Correct answers to questions.

3 Dr Nguyen ditto

Assignment (Quiz) 3

(Topic 4)

Naturally occurring compounds – Ability to

predict products, suggest appropriate reagents, explain appropriate

mechanisms

Correct answers to questions.

3 Dr Fahrenbach

ditto

Practical Reports

Practical skills and reporting ability

See below 30 Practical class

demonstrators

Annotated

report

Final Exam

(Topics 2-4 only)

Assessment of Topics 2-4.

Ability to predict products, suggest appropriate

reagents, explain appropriate mechanisms, and deduce structures.

Correct answers to questions.

Demonstrated deductive reasoning.

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Detailed Assessment for Practical Tasks

Task Assessment Criteria % of total mark

Feedback

WHO HOW

Pre-lab quizzes on

Moodle

Pass online Moodle quizzes and satisfactorily pass in-lab flow sheet

assessment

3 Practical class demonstrators

Grade & discussion.

Laboratory work – core

skills

Satisfactory completion of ALL core lab skills. This is compulsory for

passing the practical component.

6 Practical class demonstrators

Grade & discussion.

Laboratory notebook

Maintaining an appropriate lab notebook each week

6 Practical class demonstrators

Within 2 weeks of submission.

Grade & discussion.

Laboratory Remaining laboratory assessment items, including reports

15 Practical class demonstrators

Within 2 weeks of submission.

Grade & discussion.

Important note: To be awarded a pass in this subject, students must satisfy two conditions:

(i) An overall pass (≥ 50%) in the laboratory component, and (ii) Satisfactory overall performance (≥ 40%) in the examinations (all four modules combined) (iii) A minimum attendance of 80% in laboratories is required.

Failure to satisfy both criteria could result in either a FL or UF (Unsatisfactory Fail) grade being awarded, or further assessment being offered at the sole discretion of the course coordinator. Students must ensure their availability to attend any supplementary examination that will usually be offered in the week suggested by UNSW; inability or failure to attend a supplementary examination may lead to a FL or UF (Unsatisfactory Fail) grade being confirmed.

Further information

UNSW grading system: https://student.unsw.edu.au/grades

UNSW assessment policy: https://student.unsw.edu.au/assessment

5.2 Assessment criteria Attendance: Unless a specific exemption is granted by the School, a minimum attendance rate of 80% in each component of the course (lecture and laboratory) is required before a candidate can be considered for a pass in the course (see UNSW Policy

https://my.unsw.edu.au/student/atoz/AttendanceAbsence.html).

Attendance at Laboratory Classes is compulsory and a roll is kept: The reasons for any absences should be conveyed to the Laboratory Supervisor. If these were due to health problems

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they should be documented with a medical certificate. In such genuine instances no additional laboratory time will be allowed, but the laboratory marks obtained during session may be scaled accordingly so that you are not disadvantaged.

Laboratory Work: Pre-laboratory work is expected to take 15-30 minutes per week (including safety matters) and post-laboratory write-up is expected to take no more than 30 minutes per week.

Ethical Practice: Students are expected to conduct themselves in a sensible and ethical manner, especially with regard to plagiarism, and in computer use, including the use of email and online discussion forums.

5.3 Submission of assessment tasks and Assessment Procedures

Assessment Submission: A School Assignment/Report Cover Sheet (available on the Moodle website and in the School Office) must be attached to all submission. All lab reports and assignments must be submitted online by the due date and time via Moodle and may be subject to plagiarism checks. Late submissions will be accepted but carry a 10% penalty per day up to one week (7 days) late, after which a 100% penalty will then be applied (weekends and public holidays count in determining late penalties). The penalty is applied to the total for the assignment not to the mark obtained (i.e. you submit a report 2 days late but would have scored 70% if it was on-time, your mark will be adjusted to 50% given the 20% late penalty). Extensions of deadlines will only be granted via applications to the centralised special consideration unit (if eligible). This information is also available on Moodle.

Assessment Procedures: Exemption for practical classes can be given to repeating students providing they have completed the course to a satisfactory level within the past 3 years. Applications for exemption should be made to the Course Coordinator, Dr Vinh Nguyen, Dalton Room 217), before the start of session. Permission will not normally be given for students to swap laboratory classes nor attend make up classes. Any requests based on medical grounds should be addressed to the Course Coordinator, but permission should not be assumed.

6. Academic integrity, referencing and plagiarism Referencing is a way of acknowledging the sources of information that you use to research your assignments. You need to provide a reference whenever you draw on someone else's words, ideas or research. Not referencing other people's work can constitute plagiarism.

Further information about referencing styles can be located at https://student.unsw.edu.au/referencing

Academic integrity is fundamental to success at university. Academic integrity can be defined as a commitment to six fundamental values in academic pursuits: honesty, trust, fairness, respect, responsibility and courage.1 At UNSW, this means that your work must be your own, and others’ ideas should be appropriately acknowledged. If you don’t follow these rules, plagiarism may be detected in your work.

Further information about academic integrity and plagiarism can be located at:

• The Current Students site https://student.unsw.edu.au/plagiarism, and

• The ELISE training site http://subjectguides.library.unsw.edu.au/elise/presenting

The Conduct and Integrity Unit provides further resources to assist you to understand your conduct obligations as a student: https://student.unsw.edu.au/conduct. 1 International Center for Academic Integrity, ‘The Fundamental Values of Academic Integrity’, T. Fishman (ed), Clemson University, 2013.

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7. Readings and resources

Text Books P. Bruice, Organic Chemistry, 7th (International Student) Edition, Pearson

J. Clayden, N. Greeves, and S. Warren, Organic Chemistry, 2nd ed., Oxford University Press

L. Field, S. Sternhell, J. R. Kalman, Organic Structures from Spectra, 5th ed., Wiley.

Course Manual Practical Course Manual will be available only on the Moodle website

Required Readings

Nil

Recommended Internet Sites

Moodle website

As notified by individual lecturers

Laboratory: Material Safety Data Sheets (MSDSs) for risk assessment may be obtained from the following site:

http://www.chemalert.unsw.edu.au/chemalert/index/index.do

Additionally, the UNSW School of Chemistry website http://www.chem.unsw.edu.au/local contains direct links to many important chemistry-related websites and databases.

Societies UNSW Students of Chemistry Society (SOCS) http://www.chem.unsw.edu.au/schoolinfo/socs.html

UNSW Chemical Society

Royal Australian Chemical Institute http://www.raci.org.au/

Computer Laboratories or Study Spaces

Laboratory – Chemical Sciences Building 262

Gibson Computer laboratory – Ground floor, Dalton Building

8. Administrative matters

Equipment Required

Exercise book (24 or 48 page bound) for use as laboratory notebook – essential

Laboratory coat, eye protection, sensible clothing, and enclosed footwear, are required in all School of Chemistry laboratories.

Open-weave shoes, e.g., trainers or gym shoes, should NOT be worn in the laboratory.

Enabling Skills Training Required to Complete this Course

Compulsory OH&S briefing and lab introduction in Week 1 in Lab. 262 (please arrive ON TIME).

You must attend your own lab group because laboratory work will commence in week 2.

Each experiment has a safety exercise that must be completed and checked before the experimental work can commence.

MSDSs can be sourced from the websites listed above, and other safety data are

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supplied, and training is provided as part of the class.

Awareness of School plagiarism guidelines (contained on-line and in the Laboratory Manual).

Occupational Health and Safety2

Information on relevant Occupational Health and Safety policies and expectations at UNSW: http://www.ohs.unsw.edu.au/ohs_hazards/index.html

School of Chemistry OH&S policy and requirements see laboratory manual.

To be admitted to a laboratory, you must wear safety glasses meeting the minimum size requirements as posted outside all teaching laboratories, a lab coat and covered shoes (no thongs, open sandals or clogs). You must also complete all safety pre-lab work, risk assessment or other prescribed preparation relating to carrying out safe laboratory work.

Visitors are not allowed to undergraduate laboratories without the permission of the lab supervisor.

9. Additional support for students

Equity and Diversity

Those students who have a disability that requires some adjustment in their teaching or learning environment are encouraged to discuss their study needs with the course Convenor prior to, or at the commencement of, their course, or with the Equity Officer (Disability) in the Equity and Diversity Unit (9385 4734 or http://www.studentequity.unsw.edu.au/ ).

Issues to be discussed may include access to materials, signers or note-takers, the provision of services and additional exam and assessment arrangements. Early notification is essential to enable any necessary adjustments to be made.

Grievance Policy3

School Contact Faculty Contact University Contact

Dr Gavin Edwards Dir. of Teaching School of Chemistry g.edwards@unsw.edu.au Tel: 9385 4652

Dr Chris Tisdell Associate Dean (Education) cct@unsw.edu.au Tel: 9385 6792

Student Conduct and Appeals Officer (SCAO) within the Office of the Pro-Vice-Chancellor (Students) and Registrar.

studentcomplaints@unsw.edu.au

Tel: 9385 8515

University Counselling and Psychological Services

Tel: 9385 5418

Additional support:

• The Current Students Gateway: https://student.unsw.edu.au/

• Academic Skills and Support: https://student.unsw.edu.au/academic-skills

• Student Wellbeing, Health and Safety: https://student.unsw.edu.au/wellbeing

2 UNSW Occupational Health and Safety: http://www.hr.unsw.edu.au/ohswc/ohswc_home.html 3 UNSW Grievance Policy: http://www.policy.unsw.edu.au/policy/student_grievance_resolution.pdf

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• Disability Support Services: https://student.unsw.edu.au/disability-services

• UNSW IT Service Centre: https://www.it.unsw.edu.au/students/index.html