This course will introduce students to molecular modeling, molecular dynamics and computational chemistry methods. A focus will be placed on the underlying chemical theory behind each methods and the applications. The laboratory sessions provide students with experience in the computational chemistry techniques used to model the structures, properties and chemical reactivity of molecules.

Learning Outcomes

Upon successful completion, students will have the knowledge and skills to:

1. Understand the theoretical foundation of computational chemistry, with an emphasis on electronic structure calculations using quantum chemistry and classical molecular dynamics simulation techniques.
2. Use computational chemistry software to simulate chemical processes, quantify and rationalize reactivity, and study reaction mechanisms.
3. Be able to accurately compute different experimental properties and spectra using computational techniques, including: IR and UV/Vis spectra, NMR chemical shifts, relative free energies and structural dynamics.
4. Understand how to interpret potential energy surfaces and their application to experimental quantities (such as rate and equilibrium constants, substrate binding or protein/polymer conformations).
5. Understand the limitations, theoretical and practical challenges associated with computational modeling and computational chemistry.

Research-Led Teaching

All lecturers are active researchers in spectroscopy, computational chemistry and molecular modelling. Lecturers will draw on research problems and techniques currently encountered in the field.

Field Trips

N/A

Additional Course Costs

N/A

Examination Material or equipment

TBA

Required Resources

[1] F. Jensen. Introductions to computational chemistry. Wiley, New York, 1999.  

[2] T Schlick. Molecular Modeling and Simulation: An Interdisciplinary Guide, 2nd Ed. Springer.

Recommended Resources

Whether you are on campus or studying remotely, there are a variety of online platforms you will use to participate in your study program. These could include videos for lectures and other instruction, two-way video conferencing for interactive learning, email and other messaging tools for communication, interactive web apps for formative and collaborative activities, print and/or photo/scan for handwritten work and drawings, and home-based assessment.

ANU outlines recommended student system requirements to ensure you are able to participate fully in your learning. Other information is also available about the various Learning Platforms you may use.

The prescribed textbooks are:

[1] F. Jensen. Introductions to computational chemistry. Wiley, New York, 1999.  

[2] T Schlick. Molecular Modeling and Simulation: An Interdisciplinary Guide, 2nd Ed. Springer.

These are availble on line and through the library. Alternatively you can purchase both the ebook and hardcopy through Harry Hartog bookshop.

This text forms the basis of the course and many of the examples, illustrations, and exercises used will be taken directly from them. It should be used extensively and intelligently to support and enhance your understanding of the subject.

Staff Feedback

Students will be given feedback in the following forms in this course:

• written comments
• verbal comments
• feedback to whole class, groups, individuals, focus group etc

Student Feedback

ANU is committed to the demonstration of educational excellence and regularly seeks feedback from students. Students are encouraged to offer feedback directly to their Course Convener or through their College and Course representatives (if applicable). Feedback can also be provided to Course Conveners and teachers via the Student Experience of Learning & Teaching (SELT) feedback program. SELT surveys are confidential and also provide the Colleges and ANU Executive with opportunities to recognise excellent teaching, and opportunities for improvement.

Class Schedule

Week/Session	Summary of Activities	Assessment
1	Lectures by Nick Cox, workshop 1	Wattle quiz
2	Lectures by Nick Cox, workshop 2, laboratory 1	Wattle quiz
3	Lectures by Nick Cox, workshop 3	Wattle quiz, laboratory 1 due
4	Lectures by Nick Cox, workshop 4, laboratory 2	Wattle quiz
5	Lectures by Jack Evans, workshop 5	Wattle quiz, laboratory 2 due
6	Lectures by Jack Evans, workshop 6, laboratory 3, mid-semester exam	Wattle quiz, Mid-semester wattle exam
7	Lectures by Jack Evans, workshop 7, laboratory 4	Wattle quiz, laboratory 3 due
8	Lectures by Jack Evans, workshop 8	Wattle quiz, laboratory 4 due
9	Lectures by Thomas Huber, workshop 9, laboratory 5	Wattle quiz
10	Lectures by Thomas Huber, workshop 10	Wattle quiz, laboratory 5 due
11	Lectures by Thomas Huber, workshop 11, laboratory 6	Wattle quiz
12	Lectures by Thomas Huber, workshop 12	Wattle quiz, laboratory 6 due

Tutorial Registration

ANU utilises MyTimetable to enable students to view the timetable for their enrolled courses, browse, then self-allocate to small teaching activities / tutorials so they can better plan their time. Find out more on the Timetable webpage.

Assessment Summary

Assessment task	Value	Learning Outcomes
Mid-Semester Exam	20 %	1,4,5
Laboratory Reports	24 %	2,3,5
Final Exam	32 %	1,4,5
Weekly Quizzes	24 %	1,2,3,4,5

* If the Due Date and Return of Assessment date are blank, see the Assessment Tab for specific Assessment Task details

Policies

ANU has educational policies, procedures and guidelines , which are designed to ensure that staff and students are aware of the University’s academic standards, and implement them. Students are expected to have read the Academic Integrity Rule before the commencement of their course. Other key policies and guidelines include:

• Academic Integrity Policy and Procedure
• Student Assessment (Coursework) Policy and Procedure
• Special Assessment Consideration Guideline and General Information 
• Student Surveys and Evaluations
• Deferred Examinations
• Student Complaint Resolution Policy and Procedure
• Code of practice for teaching and learning

Assessment Requirements

The ANU is using Turnitin to enhance student citation and referencing techniques, and to assess assignment submissions as a component of the University's approach to managing Academic Integrity. For additional information regarding Turnitin please visit the Academic Skills website. In rare cases where online submission using Turnitin software is not technically possible; or where not using Turnitin software has been justified by the Course Convener and approved by the Associate Dean (Education) on the basis of the teaching model being employed; students shall submit assessment online via ‘Wattle’ outside of Turnitin, or failing that in hard copy, or through a combination of submission methods as approved by the Associate Dean (Education). The submission method is detailed below.

Moderation of Assessment

Marks that are allocated during Semester are to be considered provisional until formalised by the College examiners meeting at the end of each Semester. If appropriate, some moderation of marks might be applied prior to final results being released.

Participation

Students are advised to read these texts in advance of the first lectures (or at least in the first week).

i) F. Jensen. Introductions to computational chemistry. Wiley, New York, 1999.

ii) T. Schlick. Molecular Modeling and simulation: an interdisciplinary guide. Springer, New York, 2002. (Required for the O’Mara lectures)

The Research School of Chemistry considers the laboratory component of all courses to be an integral part of each course and as such all laboratory sessions are compulsory. It is therefore the policy of the Research School of Chemistry that students will attend all laboratory classes scheduled for any course. Absences must be notified (in advance, if possible) to the course convenor, and accompanied by adequate and appropriate documentation justifying the absence.

Examination(s)

1 x mid-semester exam

1 x end of semester exam

. Students should consult the course wattle site and the ANU final examination timetable to confirm the date, time and venue of the exam.

Assessment Task 1

Mid-Semester Exam

2 hour exam held in the Mid-Semester exam period.

This exam will assess material covered in the lectures presented by Nick Cox. It is hoped that this topic exam will alert students to the standards expected and give valuable early feedback on progress.

Please check the course Wattle site and the ANU Examination Timetable to confirm the date, time and location of the end of semester exam.

Assessment Task 2

Laboratory Reports

Attendance at all laboratory sessions and submission of all weekly reports is compulsory.

Laboratory reports will be due in 1 week after the labs.

The submission of all laboratory reports is compulsory. A pass in the prescribed laboratory work is required in order to gain a pass in Molecular Modeling and Computational Chemistry.

Laboratory reports are submitted via the course Wattle site. You will be required to electronically sign a declaration as part of the submission of your report. Please keep a hard copy of the laboratory report for your records. Hard copies of laboratory reports are not required.

Assessment Task 3

Final Exam

2 hour final exam, held in the November examination period.

The final exam will assess lecture material from the lectures by Jack Evans and Thomas Huber, and will be held in the November examination period.

Please check the ANU Final Examination Timetable http://www.anu.edu.au/students/programadministration/assessments-exams/examination-timetable to confirm the date, time and location exam.

Assessment Task 4

Weekly Quizzes

There will be a weekly quiz of up to 5 questions per week. The quiz will open on Wednesday and will be due the following Monday.

Academic Integrity

Academic integrity is a core part of the ANU culture as a community of scholars. The University’s students are an integral part of that community. The academic integrity principle commits all students to engage in academic work in ways that are consistent with, and actively support, academic integrity, and to uphold this commitment by behaving honestly, responsibly and ethically, and with respect and fairness, in scholarly practice.

The University expects all staff and students to be familiar with the academic integrity principle, the Academic Integrity Rule 2021, the Policy: Student Academic Integrity and Procedure: Student Academic Integrity, and to uphold high standards of academic integrity to ensure the quality and value of our qualifications.

The Academic Integrity Rule 2021 is a legal document that the University uses to promote academic integrity, and manage breaches of the academic integrity principle. The Policy and Procedure support the Rule by outlining overarching principles, responsibilities and processes. The Academic Integrity Rule 2021 commences on 1 December 2021 and applies to courses commencing on or after that date, as well as to research conduct occurring on or after that date. Prior to this, the Academic Misconduct Rule 2015 applies.

 

The University commits to assisting all students to understand how to engage in academic work in ways that are consistent with, and actively support academic integrity. All coursework students must complete the online Academic Integrity Module (Epigeum), and Higher Degree Research (HDR) students are required to complete research integrity training. The Academic Integrity website provides information about services available to assist students with their assignments, examinations and other learning activities, as well as understanding and upholding academic integrity.

Online Submission

You will be required to electronically sign a declaration as part of the submission of your assignment. Please keep a copy of the assignment for your records. Unless an exemption has been approved by the Associate Dean (Education) submission must be through Turnitin.

Hardcopy Submission

For some forms of assessment (hand written assignments, art works, laboratory notes, etc.) hard copy submission is appropriate when approved by the Associate Dean (Education). Hard copy submissions must utilise the Assignment Cover Sheet. Please keep a copy of tasks completed for your records.

Late Submission

Individual assessment tasks may or may not allow for late submission. Policy regarding late submission is detailed below:

• Late submission not permitted. If submission of assessment tasks without an extension after the due date is not permitted, a mark of 0 will be awarded.
• Late submission permitted. Late submission of assessment tasks without an extension are penalised at the rate of 5% of the possible marks available per working day or part thereof. Late submission of assessment tasks is not accepted after 10 working days after the due date, or on or after the date specified in the course outline for the return of the assessment item. Late submission is not accepted for take-home examinations.

Referencing Requirements

The Academic Skills website has information to assist you with your writing and assessments. The website includes information about Academic Integrity including referencing requirements for different disciplines. There is also information on Plagiarism and different ways to use source material.

Returning Assignments

Marked laboratory reports will be available via Wattle two weeks after submission.

Extensions and Penalties

Extensions and late submission of assessment pieces are covered by the Student Assessment (Coursework) Policy and Procedure. Extensions may be granted for assessment pieces that are not examinations or take-home examinations. If you need an extension, you must request an extension in writing on or before the due date. If you have documented and appropriate medical evidence that demonstrates you were not able to request an extension on or before the due date, you may be able to request it after the due date.

Resubmission of Assignments

If the standard of a lab report is deemed unsatisfactory by the course convenor (on advice from the laboratory demonstrator), you may be asked to resubmit the report.

Privacy Notice

The ANU has made a number of third party, online, databases available for students to use. Use of each online database is conditional on student end users first agreeing to the database licensor’s terms of service and/or privacy policy. Students should read these carefully. In some cases student end users will be required to register an account with the database licensor and submit personal information, including their: first name; last name; ANU email address; and other information.
In cases where student end users are asked to submit ‘content’ to a database, such as an assignment or short answers, the database licensor may only use the student’s ‘content’ in accordance with the terms of service – including any (copyright) licence the student grants to the database licensor. Any personal information or content a student submits may be stored by the licensor, potentially offshore, and will be used to process the database service in accordance with the licensors terms of service and/or privacy policy.
If any student chooses not to agree to the database licensor’s terms of service or privacy policy, the student will not be able to access and use the database. In these circumstances students should contact their lecturer to enquire about alternative arrangements that are available.

Distribution of grades policy

Academic Quality Assurance Committee monitors the performance of students, including attrition, further study and employment rates and grade distribution, and College reports on quality assurance processes for assessment activities, including alignment with national and international disciplinary and interdisciplinary standards, as well as qualification type learning outcomes.

Since first semester 1994, ANU uses a grading scale for all courses. This grading scale is used by all academic areas of the University.

Support for students

The University offers students support through several different services. You may contact the services listed below directly or seek advice from your Course Convener, Student Administrators, or your College and Course representatives (if applicable).

• ANU Health, safety & wellbeing for medical services, counselling, mental health and spiritual support
• ANU Access and inclusion for students with a disability or ongoing or chronic illness
• ANU Dean of Students for confidential, impartial advice and help to resolve problems between students and the academic or administrative areas of the University
• ANU Academic Skills and Learning Centre supports you make your own decisions about how you learn and manage your workload.
• ANU Counselling Centre promotes, supports and enhances mental health and wellbeing within the University student community.
• ANUSA supports and represents undergraduate and ANU College students
• PARSA supports and represents postgraduate and research students