FACULTY OF SCIENCE SCHOOL OF CHEMISTRY CHEM6701. Topics in Contemporary Chemistry A

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1 FACULTY OF SCIENCE SCHOOL OF CHEMISTRY CHEM6701 Topics in Contemporary Chemistry A SESSION 1, 2015

2 Table of Contents Information for staff Information about the Course Staff Involved in the Course Course Details Rationale and Strategies Underpinning the Course Course Schedule Assessment Tasks and Feedback Additional Resources and Support Required Equipment, Training and Enabling Skills Course Evaluation and Development Administration Matters UNSW Academic Honesty and Plagiarism

3 Faculty of Science - Course Outline 1. Information about the Course NB: Some of this information is available on the UNSW Handbook 1 Year of Delivery Course Code Course Name Academic Unit Level of Course Units of Credit Session(s) Offered Assumed Knowledge, Prerequisites or Corequisites Hours per Week Number of Weeks Commencement Date 2015 CHEM6701 TOPICS IN CONTEMPORARY CHEMISTRY A SCHOOL OF CHEMISTRY 3 rd and Hons 6 UOC S1 12 UOC of CHEM2011, CHEM2021, CHEM2031, CHEM2839, CHEM2041 & CHEM x LECTURE + 1 x TUTORIAL (e.g. 12 weeks) 3 rd March 2015 Summary of Course Structure (for details see 'Course Schedule') Component HPW Time Day Location Lectures 3 Lecture am Tue ASB 115 Lecture pm Wed ASB 220 Lecture pm Thu ASB 216 Laboratory (dry) / tutorials 3 Lab / tutorials 9 am -12 noon Wed Old Main Build 232 TOTAL Special Details Unless otherwise advised, tutorials will take place in Old Main Build Each of the three topics will have a final exam. These are scheduled in place of the laboratory (dry) / tutorials in weeks 5, 9 and 13 in Old Main Building Staff Involved in the Course Staff Role Name Contact Details Consultation Times Course Convenor A/Prof. Pall Thordarson p.thordarson@unsw.edu.a Drop in or send an and I will u respond as soon as Dalton, Room 133 possible Additional Teaching Staff Lecturers & Facilitators Dr. Graham Ball g.ball@unsw.edu.au, Dalton, Room 129. Dr. Donald Thomas A/Prof. Stephen Colbran Dr. Jonathon Beves Prof. J. Justin Gooding donald.thomas@unsw.edu. au, F10-NMR facility, Room B41 s.colbran@unsw.edu.au, Dalton (F12), Room 225 j.beves@unsw.edu.au Dalton (F12), Room 222. justin.gooding@unsw.edu. au, Dalton, Room UNSW Online Handbook: 2

4 3. Course Details Course Description 2 (Handbook Entry) Course Aims 3 Student Learning Outcomes 4 Topics in Contemporary Chemistry A is a premier lecture course run by the School of Chemistry. The course runs in session 1 and can be taken as a standalone course or as a complement to CHEM6702 (the session 2 partner to this course). The course will emphasise some of the latest advances in chemistry, including several topics based on current research directions of the School. Students will study three topics. The topics will vary depending on availability and will differ from, and complement, those offered in the following CHEM6701 course. Indicative topics areas include: Advanced NMR, polymer chemistry, organometallic chemistry, supramolecular and macromolecular chemistry, heterocyclic chemistry, photochemical processes, advanced catalysis, f-block chemistry, kinetics, physical organic chemistry, computational methods, and biosynthesis. Students should check with the course coordinator which topics will be offered: assumed knowledge may differ depending on the topics offered The course covers some of the most important and recent advances in chemistry with emphasis on topics that are particularly relevant to the current research strengths within the School of Chemistry. These topics will be reviewed from both theoretical and practical point of view. The likely impact of these research topics on solving problems in biological, medical, industrial and environmental fields will be discussed. Students will gain also gain insight, and in some cases get hands-on experience, into to the key methodologies / techniques used to drive research in the topics covered. For the three topics offered in Semester 1 of 2013 the expected student learning outcomes are: Introduction to computational chemistry This will be a practically oriented introduction to the use of molecular modelling methods across all areas of chemistry. Theory and mathematical descriptions will be kept to an absolute minimum. A key take home message of this course is that it is possible to select and implement appropriate computational methods without a full understanding of the underlying theory. At the end of this subject, you will know what molecular modelling methods are available to study systems of varying molecular size from small molecules to biopolymers and nanoparticles. You will know what sort of information can be gained from the various computational methods (structural, energetic, spectroscopic, reactivity etc) and have a basic understanding of how accurate these computations should be and how the accuracy relates to molecular size. You will understand that many of the higher level methods involve finding approximate solutions to the Schrödinger equation the mathematics of this process will not be covered in this course however. Practical skills will be developed through group and individual assessment exercises which will introduce the student to the use of common software packages available for computations Bio-inspired oxygen chemistry and bioinspired photochemistry This course comes in two parts. The first part will introduce you to the chemistry of oxygen that underpins aerobic life and will teach you about how this natural chemistry has inspired new environmentally-friendly processes for chemical transformation. The second part of the course will teach you the basic principles of photochemistry, then apply this new understanding to show natural and artificial photosynthetic systems work, and to show how light might be used to power molecular machines and control chemical reactions. How molecular structure influences molecular assembly At the end of this subject you will be able to show how functional nano, micro-, surface-, bio- and macro-scale assemblies can be created by careful consideration of the molecular structure, shape and the non-covalent interactions between the molecular building blocks used. You will be able to identify the key non-covalent interactions that govern supramolecular chemistry and self-assembly. Further, you will be able to demonstrate the importance of concepts such as lock-and-key, reorganisation, pre-organisation and cooperativity in considering supramolecular interactions. You will then be able to apply this knowledge to describe molecular assemblies on surfaces, 2D and 3D. Finally you will be able to show some of the unique features of supramolecular chemistry and self-assembly, such as its dynamic nature and self-organisation abilities, link to the application of molecular assemblies in drug design (drug-receptors binding), TV and computer displays (liquid crystals), biosensors (self-assembled monolayers = SAM) and tissue engineering (self-assembled gels), to name a few examples. Graduate Attributes Developed in this Course 5 Science Graduate Research, inquiry and analytical thinking abilities Select the level of FOCUS 0 = NO FOCUS 1 = MINIMAL 2 = MINOR 3 = MAJOR 3 Activities / Assessment Tutorial and Computational experiments. Critical evaluation of recent primary research literature. Assessment of tutorial reports Capability and motivation 3 Lectures and applied problems discussed in class and laboratory/tutorial exercises, written assignments / Exam 2 UNSW Handbook: 3 Learning and Teaching Unit: Course Outlines 4 Learning and Teaching Unit: Learning Outcomes 5 Contextualised Science Graduate Attributes: 3

5 for intellectual development Ethical, social and professional understanding Communication Teamwork, collaborative and management skills Information literacy Throughout course, written assignments. / Exam Write up of practicals and assessments. Assessment of practical reports Group work in laboratory/tutorial exercises. Joint written assessments. Computational chemistry exercises Professional accreditation attributes RACI membership of professional body See 4

6 Major Topics (Syllabus Outline) Introduction to computational chemistry Lectures 1: Dr. Ball 1. Overview of goals and methods for molecular modelling Lectures 2-4: Dr. Thomas 2. Bond lengths, angles, torsions and electrostatic interactions - how they affect the energies of molecules. The concept of a force field, all the parameters combined. Algorithms used to perform molecular mechanics calculations. Larger systems and the need for methods that mimick the effect of solvents. 3. Molecular Dynamics vs. Energy Minimisation. What different things can you do with molecular mechanics - or what questions can you ask and how to answer them. 4. Software for performing visualization and calculation. Hardware and scaling effects. Lectures 5-12: Dr. Ball 5. Foundations of molecular orbital theory (the only heavily mathematical lecture!) 6. Hückel theory and the Hartree-Fock method. Practical implementations of these. 7. Introduction to post Hartree-Fock methods. 8. Introduction to density functional theory. 9. Modelling solvent. Semi empirical methods. Software and hardware for computational chemistry. 10. Applications: selecting methods for modelling geometries, energetics and reaction pathways 11. Applications: selecting methods for modelling molecular properties and spectroscopy 12. Putting it all together: what to use when and doing it on your own! Bioinspired oxygen chemistry and bioinspired photochemistry Lectures 1-6: A/Prof. Colbran Molecular oxygen. MO theory, states, reactivity, redox chemistry Heme-based oxidases, oxygenases, catalases: mechanism, models, bio-inspired chemistry Non-heme based oxidases, oxygenases, catalases: mechanism, models, bio-inspired chemistry Respiratory heme copper oxidases: function & mechanism; proton-coupled electron transfer Lectures 7-12: Dr Beves Absorption spectroscopy basics: how and why is light absorbed by molecules? Excited state energy diagrams, Jablonski diagrams, coordination complexes Emission spectroscopy basics: what happens when light is absorbed? Fluorescence, phosphorescence, photochemistry Light harvesting: Nature's approach and limitations Bioinspired light harvesting: turning light into power Solar fuels: turning light into stored chemicals Photoredox catalysis: using light to catalyse organic reactions Light-powered synthetic machines: How to do molecular-level work? Light-switchable molecular devices: How to control molecules with light? How molecular structure influences molecular assembly Lectures 1-3: A/Prof. Thordarson Supramolecular Chemistry forces & assembly Basic concepts Self-assembly in nature Interaction energies, cooperativity Lectures 4-9: Prof. Gooding - Surfactants and self-assembled monolayers Surfactants, Micelles Langmuir-Blodgett, Liquid crystals Self-assembled monolayers (SAM) the basics Functional SAM s and assemblies Lectures 10-12: A/Prof. Thordarson Supramolecular Chemistry Host-guest chemistry. Supramolecular polymers and other 2D assemblies Self-assembled gels and other 3D assemblies Self-assembly of block-co-polymers Relationship to Other Courses within the Program The course is a mainstream chemistry course that integrates with other level three courses and with the honours year. 4. Rationale and Strategies Underpinning the Course Teaching Strategies The integration of lectures and laboratories supports Engaging 1. Effective learning is supported when students are actively engaged in the learning process. 2. Effective learning is supported by a climate of inquiry where students feel appropriately challenged and activities are linked to research and scholarship. Examples from chemical practice allow Contextualising 6. Students become more engaged in the learning process if they can see the relevance of their studies to professional, disciplinary and/or personal contexts. We also have undertaken Designing to 10. Clearly articulated expectations, goals, learning outcomes, and course requirements increase student motivation and improve learning. 12. Graduate attributes - the qualities and skills the university hopes its students will develop as a result of 5

7 their university studies are most effectively acquired in a disciplinary context. Teaching in the use of laboratory groups supports 14. Learning cooperatively with peers rather than in an individualistic or competitive way may help students to develop interpersonal, professional, and cognitive skills to a higher level. 15. Effective learning is facilitated by assessment practices and other student learning activities that are designed to support the achievement of desired learning outcomes. Rationale for learning and teaching in this course 6,7 Teaching the three topics in 4 week blocks with associated laboratory / tutorial exercises allows students to focus on one particular contemporary topic at a time. Laboratory/tutorial exercises are designed to give practical experience relevant to the topics. Timely feedback and marking of practical reports allows students to follow the thread of the course. The examination of each topic immediately following its completion brings together the strands to complete the learning experience. 6 Reflecting on your teaching 6

8 5. Course Schedule Some of this information is available on the Online Handbook 7 and the UNSW Timetable 8. Week Lectures (day), Topics & Lecturers Week 1 Introduction to computational chemistry - Molecular Modelling, Dr. Ball and Dr. Thomas Week 2 Introduction to computational chemistry - Molecular Modelling / MO theory, Dr. Ball and Dr. Thomas Week 3 Introduction to computational chemistry Huckel, HF and DFT methods Dr. Ball Week 4 Introduction to computational chemistry - Applications Dr. Ball Week 5 Week 6 Week 7 Week 8 Week 9 Week 10 Week 11 Week 12 Bio-inspired oxygen chemistry and bioinspired photochemistry, A/Prof Colbran Bio-inspired oxygen chemistry and bioinspired photochemistry, A/Prof Colbran Bio-inspired oxygen chemistry and bioinspired photochemistry, Dr. Beves Bio-inspired oxygen chemistry and bioinspired photochemistry, Dr. Beves Supramolecular Chemistry, A/Prof. Thordarson Surfactants and self-assembled monolayers, Prof Gooding Surfactants and self-assembled monolayers, Prof Gooding Supramolecular Chemistry, A/Prof. Thordarson Tutorials (day), Topics & Lecturers None Molecular mechanics: from small molecules to biopolymers Dr. Ball and Dr. Thomas Modelling of molecular structure and properties using ab initio/dft methods Dr. Ball and Dr. Thomas Modelling of reaction profiles and thermodynamics - Dr. Ball and Dr. Thomas No tutorial exam (see right) Bioinspired oxygen chemistry discussion Oxygen Chemistry/Photochemistry discussion Practical (day), Topics & Lecturers Exam: Introduction to computational chemistry Other Assignment and Submission dates (see also 'Assessment Tasks & Feedback') Introduction to computational chemistry: 3 rd lab report due and Assignment due Colbran: Assignment task due, noon Monday Photochemistry discussion Beves: Assignment task due noon, Friday No tutorial exam (see right) Practical introduction to measuring binding constants Surfactants chemistry discussion Supramolecular chemistry discussion Exam: Bio-inspired oxygen chemistry and bioinspired photochemistry Week 13 No lecture No tutorial exam (see right) Exam: How molecular structure influences molecular assembly Individual assignment due Tuesday of week 12 (submit to A/Prof Thordarson). Feedback by Friday week 12 *NB: As stated in the UNSW Assessment Policy: one or more tasks should be set, submitted, marked and returned to students by the mid-point of a course, or no later than the end of Week 6 of a 12-week session' 7 UNSW Virtual Handbook: 8 UNSW Timetable: 7

9 6. Assessment Tasks and Feedback 10 Task Topic 1: Introduction to computational chemistry Individual assignment (modelling based (50% of this topic) Knowledge & abilities assessed Understanding of modelling procedures and software Assessment Criteria % of total mark Date of Feedback Release Submission WHO WHEN HOW Each of the three topic below is 33% of the overall assessment for this course: (33%) Level of understanding and ability to apply gained knowledge and training 16.50% Wednesday of week 5 Lecturer Within 2 weeks Annotated assignment Final exam (50% of this topic) Understanding and knowledge of topic content Topic 2: Bio-inspired oxygen chemistry and bioinspired photochemistry Written assignment Week 12 (50% of this topic) Final exam (50% of this topic) Understanding and knowledge of topic content. Understanding and knowledge of topic content Topic 3: How molecular structure influences molecular assembly One individual assignment Understanding and based on lecture notes in week knowledge of topic 9 and the laboratory class in content. Week 10 (40% of this topic) Final exam (60% of this topic) Bonus point Understanding and knowledge of topic content Participation in teamwork Answers to questions given correctly. Discussion shows knowledge and understanding of the topic. Answers to questions given correctly. Discussion shows knowledge and understanding of the topic. Answers to questions given correctly. Discussion shows knowledge and understanding of the topic. Answers to questions given correctly. Discussion shows knowledge and understanding of the topic. Answers to questions given correctly. Discussion shows knowledge and understanding of the topic. At least one lecture or tutorial attended 16.50% Thursday of week 5 (33%) 16.50% Monday, Week 7 and Friday week % Thursday of week 9 (33%) 13.2% Tuesday week % Wednesday of week 13 1% Thursday of week 13 Lecturers Lecturer Course coordinator Within 2 weeks Within 1 week Annotated assignment 10 Approaches to assessment: 8

10 7. Additional Resources and Support Text Books Course Manual Required Readings Additional Readings Recommended Internet Sites Societies Computer Laboratories or Study Spaces All material is on the Moodle Learning Management System Relevant primary scientific literature as per handouts and lecture notes See Moodle Learning Management System Royal Australian Chemical Institute Students of Chemistry Society (UNSW) Laboratory / tutorials Dalton Building G05 and as advised by lecturers Gibson Computer laboratory Ground floor, Dalton Building 8. Required Equipment, Training and Enabling Skills Equipment Required Enabling Skills Training Required to Complete this Course 9

11 9. Course Evaluation and Development Student feedback is gathered periodically by various means. Such feedback is considered carefully with a view to acting on it constructively wherever possible. This course outline conveys how feedback has helped to shape and develop this course. Mechanisms of Review Last Review Date Comments or Changes Resulting from Reviews Major Course Review 2010 This was a major review of a previous related course. Some of the changes that were implemented as a result of this review: The four-week block format which amongst other spreads assessments more evenly The inclusion of 3 x 3 h laboratory / tutorials to support lecture contents The in-semester exams on teach of the topics Giving 3 level students opportunity to meet Honours students. CATEI Student feedback suggested assessments were all heavily biased towards the end of semester (see changes made above during the 2010 review). Other 2011 School of Chemistry review of assessment processes in the School suggesting that each assessment tasks should weigh at least 10% of the total course mark, hence for this course we will limit the number of assessments within a topic to 1 with at least 40% weight. 11 CATEI process: 10

12 10. Administration Matters Expectations of Students Assignment Submissions Workload Contact hours are 6 per week, in weeks 2-12 and 3 hours per week in week 1 and week 13. The major out-of-class workload is associated with the laboratory program and assignments. Post-laboratory write-up and assignments is expected to take 2-3 hours per week As per instructions from individual lectures Occupational Health and Safety 12 Assessment Procedures UNSW Assessment Policy 13 Equity and Diversity Information on relevant Occupational Health and Safety policies and expectations at UNSW: In accordance with UNSW assessment policy ( This includes: Appropriate advice about avoiding plagiarism is provided No staff set or mark assessment where a conflict of interest arises The outcome of any wholly summative assessment remains confidential to the student or student group and staff of the University Assessment items are kept safe Appropriate processes are followed for the safe recording, transfer, storage, retrieval, communication and reporting of information on student achievement, including final course results 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 ( or ). 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. Student Complaint School Contact Faculty Contact University Contact Procedure 14 Dr Jason Harper Deputy Director of Teaching j.harper@unsw.edu.au Dalton (F12), Room 223. Tel: A/Prof Julian Cox Associate Dean (Education) julian.cox@unsw.edu.au Tel: or Dr Gavin Edwards Associate Dean (Undergraduate Programs) g.edwards@unsw.edu.au Tel: Student Conduct and Appeals Officer (SCAO) within the Office of the Pro-Vice- Chancellor (Students) and Registrar. Telephone , studentcomplaints@unsw.edu. au University Counselling and Psychological Services 9 Tel: UNSW OHS Home page 13 UNSW Assessment Policy 14 Student Complaint Procedure 15 University Counselling and Psychological Services 11

13 11. UNSW Academic Honesty and Plagiarism What is Plagiarism? Plagiarism is the presentation of the thoughts or work of another as one s own. *Examples include: direct duplication of the thoughts or work of another, including by copying material, ideas or concepts from a book, article, report or other written document (whether published or unpublished), composition, artwork, design, drawing, circuitry, computer program or software, web site, Internet, other electronic resource, or another person s assignment without appropriate acknowledgement; paraphrasing another person s work with very minor changes keeping the meaning, form and/or progression of ideas of the original; piecing together sections of the work of others into a new whole; presenting an assessment item as independent work when it has been produced in whole or part in collusion with other people, for example, another student or a tutor; and claiming credit for a proportion a work contributed to a group assessment item that is greater than that actually contributed. For the purposes of this policy, submitting an assessment item that has already been submitted for academic credit elsewhere may be considered plagiarism. Knowingly permitting your work to be copied by another student may also be considered to be plagiarism. Note that an assessment item produced in oral, not written, form, or involving live presentation, may similarly contain plagiarised material. The inclusion of the thoughts or work of another with attribution appropriate to the academic discipline does not amount to plagiarism. The Learning Centre website is main repository for resources for staff and students on plagiarism and academic honesty. These resources can be located via: The Learning Centre also provides substantial educational written materials, workshops, and tutorials to aid students, for example, in: correct referencing practices; paraphrasing, summarising, essay writing, and time management; appropriate use of, and attribution for, a range of materials including text, images, formulae and concepts. Individual assistance is available on request from The Learning Centre. Students are also reminded that careful time management is an important part of study and one of the identified causes of plagiarism is poor time management. Students should allow sufficient time for research, drafting, and the proper referencing of sources in preparing all assessment items. * Based on that proposed to the University of Newcastle by the St James Ethics Centre. Used with kind permission from the University of Newcastle Adapted with kind permission from the University of Melbourne 12