CHEM 351 Chemicals Big and Small: Nano-material to Bio-macromolecules - Course Outlines

Course Prescription

Chemical materials are found with a broad range of shapes, sizes and physical properties. Students will study the synthesis of chemical materials; including polymeric materials using radical chemistry, inorganic materials and proteins and peptides using synthetic and biological chemical approaches. Methods to characterise materials will be investigated, including a range of physical and computational techniques giving insight into molecular interactions.

Course Overview

Block 1L: Molecules big and small: introduction to nanomaterials

Block 2: Physical and Computational Chemistry: An introduction to current methods in computational chemistry and molecular modelling

Block 3: Polymer Chemistry and Kinetics: Polymeric materials, synthesis techniques (esp. the free radical chemistry and its use for free radical polymerization), polymerization kinetics, polymer characterization and applications.

Block 4: Biomolecules and Biological Chemistry ; Molecular Self-Assembly: Carbohydrates, Amino Acids, Solid Phase Peptide Synthesis, Structural Organization in Proteins, Molecular Self-Assembly (self-assembling peptides), Functions of these molecules. Recombinant Protein Production; Chemistry and Synthesis of Nucleic Acids; Serine Protease and Glycosidase: Mechanism and Kinetics; Target Identification; Emerging Topics in Chemical Biology.

Course Requirements

Prerequisite: 30 points from CHEM 251, 252, 253 Restriction: CHEM 350

Learning Outcomes

By the end of this course, students will be able to:

Apply computational modelling for molecules and reactions using various specialized software packages (Graduate Profile Capabilities used: 1, 2, 3) (Capability 1, 2 and 3)
Describe various methods to synthesise and characterise polymers and outline the various applications of polymeric materials (Graduate Profile Capabilities used: 1, 2, 3, 6) (Capability 1, 2, 3 and 6)
Use and apply the principles of radical reactions and describe various radical reactions in organic and polymer synthesis and biological systems (Graduate Profile Capabilities used: 1, 2, 3, 6) (Capability 1, 2, 3 and 6)
Describe and discuss various methods for the synthesis, analysis and modification of carbohydrates, peptides/proteins and biomolecules, including those featuring metals (Graduate Profile Capabilities used: 1, 2, 6) (Capability 1, 2 and 6)
Communicate results of laboratory and computational analysis in various ways including in forms for a non-technical audience. (Graduate Profile Capabilities used: 1, 2, 4, 5) (Capability 1, 2, 4 and 5)

Assessments

Assessment Type	Percentage	Classification
Test	15%	Individual Coursework
Laboratories	25%	Individual Coursework
Assignments	10%	Individual Coursework
Quizzes	5%	Individual Coursework
Tutorials	5%	Individual Coursework
Final Exam	40%	Individual Examination
6 types	100%

Assessment Type	Learning Outcome Addressed
	1	2	3	4	5
Test
Laboratories
Assignments
Quizzes
Tutorials
Final Exam

Key Topics

Topic 1: Molecules big and small: introduction to nanomaterials

• Introduction to various class of ‘larger’ molecules, highlighting nanomaterials, polymers, biomolecules are much ‘larger’ than classes of molecules taught in previous courses.

• Overview of nanostructures and nanomaterials, nomenclature, classification, natural and artificial nanomaterials, Differences between nanomaterials and bulk materials

• Preparation of gold and silver metallic nanoparticles, Properties: particle size, surface area, quantum effects, introducing computation methods are frequently used in these classes of molecule (linking to topic 2)

• Examples of nanomaterials ranging from micelles to metal(oxide)s, from synthetic polymers to large biomolecules (linking to topics 3 and 4): carbon nanotubes, inorganic nanowires, bioinorganic nanomaterials, DNA and its nanomaterials, Self-assembled nanostructures, control of nanoarchitecture, Synthesis – top-down and bottom up methods, molecular self-assembly

• Self-assembled peptide nanomaterials (linking to lab experiment)

• Potential toxicity and environment impact from nanoparticles

Topic 2: An introduction to current methods in computational chemistry and molecular modelling

• Background on theoretical and computational methods used in chemistry.

• Understanding of the capabilities, limitations and reliability of various computer based methods such as force field, first-principles calculation, and machine learning

• Familiarize with the concepts of potential energy surface, optimization, transition state searching, and molecular dynamics (linking to topics 3 and 4)

• Be able to choose proper computational tools for different application

• Application of computation chemistry in different areas of chemistry including heterogeneous catalysis, material chemistry, surface chemistry, biological chemistry and drug discovery (link to topic 4)

Topic 3: Polymer Chemistry and Kinetics

• Develop an understanding of what are polymers and network polymers, examples of man-made vs biopolymers (links to topics 1 and 4)

• Polymer nomenclature, polymer size, understanding polymer conformation (links to topic 2)

• Understanding uncontrolled polymerisation methods, in particular free-radical polymerisation (FRP). Understand factors influencing the kinetics of FRP and calculation of kinetics (links to lab experiment)

• Understand the principles of GPC and their use in determining molecular weight in polymers and molecular weight distribution. (links to lab experiment)

• Understand the concept of polymer gels, comparing natural vs man-made gelling polymers (links to topic 4). Synthesis of polymer gel, characterisation, and applications

• Develop a deeper understanding of various controlled radical polymerisation chemistry and compare to conventional uncontrolled free radical polymerization to make polymers, photopolymerisation, radical polymerization kinetics, chain transfer and termination processes, degree of polymerization control, RAFT polymerization techniques.

Topic 4: Biomolecules and Biological Chemistry Carbohydrates, Amino Acids, Peptides and Proteins, Molecular Self-Assembly

• Recall the various classes of biomolecules including proteins, carbohydrates and nucleic acids. Understanding the organisation of these biomolecules from small monomeric units to larger macromolecules (links to topic 1).

• Discussing the process of turning biomolecular monomers to biopolymers; from amino acids to proteins, simple to complex carbohydrates and nucleotides to nucleic acids

• Organisation of proteins starting from amino acid building blocks, structure of α-amino acids, and their zwitterionic nature, isoelectric points and understand the importance of amino acid side chains in the formation of peptide secondary structures and protein folding. Primary, secondary, tertiary and quaternary structure in proteins.

• Describe synthetic chemistry techniques for monomeric and polymeric biomolecules for proteins, carbohydrates and nucleic acids including basics of polysaccharide synthesis, amino acid synthesis, solid phase peptide and nucleic acid synthesis (links to lab experiment).

• Chemistry of nucleic acids (compound stability, importance of pKa, driving forces in nucleic acid chemistry)

• Understand various examples of self-assembly in biomolecules (links to topic 1)

• Understand biological chemical production methods for biomolecules - recombinant protein production, chemical protein production, posttranslational modification.

• Application of chemistry in biology - target identification, photoaffinity labelling and protein identification (using electrophoresis / mass spectrometry).

• Describe characterisation and visualisation methods for various biomolecules, including spectroscopic and computational methods (links to topic 2)

• Protein sequencing and structure determination including amino acid analysis, peptide sequencing reactions

• Use of various mass spectrometry methods for protein/peptide sequencing including understanding fragmentation and tandem MS.

• Understand enzymes, enzyme mechanisms and enzyme kinetics including serine protease and glycosidase (links to lab experiment).

• Use the general principles of coordination chemistry to explain in a qualitative way the mechanism of action of selected biomolecules including siderophores and vitamin B12

Special Requirements

Must complete laboratory/practical work and comply with all health and safety regulations whilst in the laboratory.

Workload Expectations

This course is a standard 15 point course and students are expected to spend 10 hours per week involved in each 15 point course that they are enrolled in.

For this course, you can expect 32 hours of lectures, 20 hours of reading and thinking about the content and 37 hours of work on assignments and/or test preparation.

Delivery Mode

Campus Experience

Campus Experience

Attendance is required at scheduled activities including labs/tutorials to receive credit for components of the course.

Lectures will be available as recordings. Other learning activities will not be available as recordings.

The course will not include live online events.

Attendance on campus is required for the test and exam.

The activities for the course are scheduled as a standard weekly timetable.

Learning Resources

Course materials are made available in a learning and collaboration tool called Canvas which also includes reading lists and lecture recordings (where available).

Please remember that the recording of any class on a personal device requires the permission of the instructor.

All course material will be available on Canvas. This includes lecture recording links and videos of laboratory techniques.

Student Feedback

During the course Class Representatives in each class can take feedback to the staff responsible for the course and staff-student consultative committees.

At the end of the course students will be invited to give feedback on the course and teaching through a tool called SET or Qualtrics. The lecturers and course co-ordinators will consider all feedback.

Your feedback helps to improve the course and its delivery for all students.

Academic Integrity

The University of Auckland will not tolerate cheating, or assisting others to cheat, and views cheating in coursework as a serious academic offence. The work that a student submits for grading must be the student's own work, reflecting their learning. Where work from other sources is used, it must be properly acknowledged and referenced. This requirement also applies to sources on the internet. A student's assessed work may be reviewed against online source material using computerised detection mechanisms.

Class Representatives

Class representatives are students tasked with representing student issues to departments, faculties, and the wider university. If you have a complaint about this course, please contact your class rep who will know how to raise it in the right channels. See your departmental noticeboard for contact details for your class reps.

Copyright

The content and delivery of content in this course are protected by copyright. Material belonging to others may have been used in this course and copied by and solely for the educational purposes of the University under license.

You may copy the course content for the purposes of private study or research, but you may not upload onto any third party site, make a further copy or sell, alter or further reproduce or distribute any part of the course content to another person.

Inclusive Learning

All students are asked to discuss any impairment related requirements privately, face to face and/or in written form with the course coordinator, lecturer or tutor.

Student Disability Services also provides support for students with a wide range of impairments, both visible and invisible, to succeed and excel at the University. For more information and contact details, please visit the Student Disability Services’ website http://disability.auckland.ac.nz

Special Circumstances

If your ability to complete assessed coursework is affected by illness or other personal circumstances outside of your control, contact a member of teaching staff as soon as possible before the assessment is due.

If your personal circumstances significantly affect your performance, or preparation, for an exam or eligible written test, refer to the University’s aegrotat or compassionate consideration page https://www.auckland.ac.nz/en/students/academic-information/exams-and-final-results/during-exams/aegrotat-and-compassionate-consideration.html.

This should be done as soon as possible and no later than seven days after the affected test or exam date.

Learning Continuity

In the event of an unexpected disruption, we undertake to maintain the continuity and standard of teaching and learning in all your courses throughout the year. If there are unexpected disruptions the University has contingency plans to ensure that access to your course continues and course assessment continues to meet the principles of the University’s assessment policy. Some adjustments may need to be made in emergencies. You will be kept fully informed by your course co-ordinator/director, and if disruption occurs you should refer to the university website for information about how to proceed.

The delivery mode may change depending on COVID restrictions. Any changes will be communicated through Canvas.

Student Charter and Responsibilities

The Student Charter assumes and acknowledges that students are active participants in the learning process and that they have responsibilities to the institution and the international community of scholars. The University expects that students will act at all times in a way that demonstrates respect for the rights of other students and staff so that the learning environment is both safe and productive. For further information visit Student Charter https://www.auckland.ac.nz/en/students/forms-policies-and-guidelines/student-policies-and-guidelines/student-charter.html.

Disclaimer

Elements of this outline may be subject to change. The latest information about the course will be available for enrolled students in Canvas.

In this course students may be asked to submit coursework assessments digitally. The University reserves the right to conduct scheduled tests and examinations for this course online or through the use of computers or other electronic devices. Where tests or examinations are conducted online remote invigilation arrangements may be used. In exceptional circumstances changes to elements of this course may be necessary at short notice. Students enrolled in this course will be informed of any such changes and the reasons for them, as soon as possible, through Canvas.

Capability 1:	Disciplinary Knowledge and Practice
Capability 2:	Critical Thinking
Capability 3:	Solution Seeking
Capability 4:	Communication and Engagement
Capability 5:	Independence and Integrity
Capability 6:	Social and Environmental Responsibilities

CHEM 351 : Chemicals Big and Small: Nano-material to Bio-macromolecules

Science

2022 Semester One (1223) (15 POINTS)