Physical Chemistry: Modelling Molecular Behaviour (CHEM3011)

Course overview

This course is an introduction to concepts, theories & methods in modern physical chemistry & elements of computational molecular science. It includes molecular quantum mechanics, electronic structure, molecular dynamics, biomolecular & materials simulations, spectroscopy & statistical thermodynamics.

CHEM3011 provides an introduction to the theory and practice of molecular modelling. The purpose of the course is to show how you can use computer modelling technologies ﾠto understand chemistry. For example, why does a reaction occur at a particular speed, why does a material have a particular phase behaviour, or why does a protein fold into a particular conformation? The course covers the major modern computational modelling technologies, including ﾠquantum mechanics, statistical mechanics, classical mechanics, and molecular dynamics. These approaches can be used not only to understand but also to ﾠpredict the properties of chemical systems, underpinning advances in chemistry.

Topics ﾠinclude:

Statistical mechanics: ﾠStatistical mechanical distribution functions; Boltzmann’s distribution; ensembles; partition functions; statistical thermodynamics approach to understanding chemical energetics, entropy ﾠand equilibria.

Quantum mechanics: the Schrö￶dinger equation; Hamiltonian operator; Born–Oppenheimer approximation; Hückel theory; Hartree–Fock theory; multiconfiguration self-consistent field theory; density functional theory (DFT); semiempirical methods; and applications of these methods to studying ﾠthe structures and behaviour of molecules and materials.

Molecular dynamics and (bio)molecular simulations: classical molecular mechanics; ﾠbonded and non-bonded potentials; solvation models; solving Newton's equations of motion; boundary conditions; calculation of thermodynamic properties; ﾠcomparing simulations to experimental data.ﾠ

Practical applications: extensive illustrations of how computational techniques can be used in practice to study chemical behaviour ﾠwill be given in both the lectures and the practical activities. Examples drawn from recent research will highlight the applications of computational approaches to ﾠstudy nanomaterials, reaction mechanisms and biomolecular systems.

Course requirements

Assumed background

CHEM2050 and/or CHEM2060

Prerequisites

You'll need to complete the following courses before enrolling in this one:

CHEM2060 or CHEM2902 or CHEM2056 or CHEM2002 or (PHYS2020 + PHYS2041)

Recommended prerequisites

We recommend completing the following courses before enrolling in this one:

CHEM2050, PHYS1001 + (MATH1051 or MATH1071) or (MATH1052 or MATH1072)

Course contact

Course staff

Timetable

The timetable for this course is available on the UQ Public Timetable.

Additional timetable information

Please check your timetable regularly at the start of each semester.

ﾠ

Aims and outcomes

The goals of this course are:

a) to enable students to develop an understanding of fundamental physical chemistry concepts related to the electronic structures of molecules, intermolecular interactions and (statistical) thermodynamics, which when modelled with computational techniques can be used to explain and understand a wide range of phenomena in chemistry, biology and materials science; and

b) to provide practical training in the various computational and theoretical approaches that can be used to model and predict the properties of molecular systems more generally.

Learning outcomes

After successfully completing this course you should be able to:

Assessment

Assessment summary

A hurdle is an assessment requirement that must be satisfied in order to receive a specific grade for the course. Check the assessment details for more information about hurdle requirements.

Assessment details

Laboratory Reports

• Hurdle

Mode

Activity/ Performance

Category

Practical/ Demonstration

Weight

30%

Due date

16/08/2024 2:00 pm

13/09/2024 2:00 pm

25/10/2024 2:00 pm

Learning outcomes

L01, L02, L03, L04, L05

Task description

Hurdle requirements

Submission guidelines

At the discretion of the individual lecturer, each laboratory report will either be completed during a designated practical session and submitted before the student leaves, or submitted through Blackboard (either through a direct Blackboard submission link or through a Turnitin link on Blackboard; lecturers will advise). Details of the submission process for each report will be advised by the lecturer.

Deferral or extension

You may be able to apply for an extension.

Applications for Extensions

Information on applying for an extension can be found here: my.UQ Applying for an extension.

Extension applications must be received by the assessment due date and time.

If you are unable to provide approved documentation to support your application by the due date and time, you must still submit your application by the deadline but with an attached Word document that outlines why you cannot provide the approved documentation by the deadline. You will then need to acquire and upload the approved documentation to your request within 24 hours. Please note: When an extension request has been submitted and is pending, students are expected to continue to work on the assessment item, with the aim of submitting by the requested due date and time.

Prolonged Absence

If you have been ill or unable to attend class for more than 14 days, we advise you to carefully consider whether you are capable of successfully completing your courses this semester.

Extensions with Student Access Plans (SAP)

For extensions up to 7 days, your SAP is all that is required as documentation to support your application. However, extension requests longer than 7 days (for any one assessment item) will require the submission of additional supporting documentation e.g. a medical certificate.

Late submission

A penalty of 10% of the maximum possible mark will be deducted per 24 hours from time submission is due for up to 7 days. After 7 days, you will receive a mark of 0.

You are required to submit assessable items on time. If you fail to meet the submission deadline for any assessment item, then 10% of the maximum possible mark for the assessment item (assessment ‘marked from’ value) will be deducted as a late penalty for every day (or part day) late after the due date. For example, if you submit your assignment 1 hour late, you will be penalised 10%; if your assignment is 24.5 hours late, you will be penalised 20% (because it is late by one 24-hour period plus part of another 24-hour period). 10% will be deducted per day for up to 7 calendar days, at which point your submission will receive a mark of zero (0) unless an extension has been approved.

In most instances one or more hurdles will apply to your assessment item so you will need to submit it to fulfil the requirements of the course regardless of how late it is and the mark you are likely to be awarded.

End of Semester Exam

• Hurdle
• Identity Verified
• In-person

Mode

Written

Category

Examination

Weight

70%

Due date

End of Semester Exam Period

2/11/2024 - 16/11/2024

Learning outcomes

L01, L02, L03, L05

Task description

Hurdle requirements

Exam details

Submission guidelines

Deferral or extension

You may be able to defer this exam.

Course grading

Full criteria for each grade is available in the Assessment Procedure.

Additional course grading information

Assessment Hurdles

In order to pass this course, you must meet ALL of the following requirements (if you do not meet these requirements, the maximum grade you will receive will be a 3):

1. You must obtain an overall mark of 50% or more; and

2. You must obtain an overall mark of 40% or more in the end of semester exam; and

3. You must obtain a minimum weighted average mark of 40% across all other non-examination course assessment items and learning tasks; and

4. You must attend 100% of the laboratory component of the course ﾠand complete and submit ALL laboratory assessment.

The maximum grade you will receive will be a 2 if you:

1. Obtain an overall mark of 30% or less on the end of semester exam.

2. Obtain a weighted average mark of 30% or less on the ﾠnon-examination course assessment items and learning tasks.

Supplementary assessment

Supplementary assessment is available for this course.

Should you fail a course with a grade of 3, you may be eligible for supplementary assessment. Refer to my.UQ for information on supplementary assessment and how to apply. 

Supplementary assessment provides an additional opportunity to demonstrate you have achieved all the required learning outcomes for a course.  

If you apply and are granted supplementary assessment, the type of supplementary assessment set will consider which learning outcome(s) have not been met.  

Supplementary assessment can take any form (such as a written report, oral presentation, examination or other appropriate assessment) and may test specific learning outcomes tailored to the individual student, or all learning outcomes. 

To receive a passing grade of 3S4, you must obtain a mark of 50% or more on the supplementary assessment. 

Additional assessment information

Computer Practicals

Students are required to attend the computer practical sessions. The assessment criteria and schedule for laboratory reports will be made available on Blackboard and ﾠexplained to students during the lectures. If you are unable to attend your timetabled computer practical session because of circumstances beyond your control (e.g., illness) you must email the course coordinator as soon as possible accompanied by acceptable supporting documentation.

USBs

At the discretion of the course staff, you may ﾠbe provided with a USB drive containing modelling data for use in this course. USBs must be returned before the last day of semester.

Assessment Submission

All submission times are listed in Brisbane time.

It is the responsibility of the student to ensure the on time, correct and complete submission of all assessment items.

Please ensure you receive and save the submission confirmation for all submitted items, you may be asked to produce this as evidence of your submission.

Turnitin

By submitting work through Turnitin you are deemed to have accepted the following declaration “I certify that this assignment is my own work and has not been submitted, either previously or concurrently, in whole or in part, to this University or any other educational institution, for marking or assessment”.

All students must ensure they receive their Turnitin receipt on submission of any assessments. A valid Turnitin receipt will be the only evidence accepted if assessments are missing. Without evidence, the assessment will receive the standard late penalty, or after seven days, will receive zero. In the case of a Blackboard outage, please contact the Course Coordinator as soon as possible to confirm the outage with ITS.

Assessment/Attendance

Please notify your Course Coordinator as soon as you become aware of any issue that may affect your ability to meet the assessment/attendance requirements of the course. The my.UQ website and the Electronic Course Profile (ECP) for your course also provide information about your course requirements, the rules associated with your courses and services offered by the University.

A note for repeating students in this course

Any student who enrols in a course must not be given exemption or partial credit from their previous attempt(s) for any individual piece of assessment. Instead, the student must successfully complete all of the learning activities and assessment items within the study period of enrolmentﾠ(PPL 3.10.02 Assessment - Procedures Section 3.1.4 Assessment integrity).

If the same assessment item is set from one year to the next, repeating students are allowed to submit the same work they submitted in previous attempts at the course. Where possible SCMB recommends that you use the feedback you received in your last attempt to improve parts of the item where you lost marks. Resubmission of an altered or unaltered assessment item by a repeating student (where the same assessment has been set) will not be considered as self-plagiarism.

Learning resources

You'll need the following resources to successfully complete the course. We've indicated below if you need a personal copy of the reading materials or your own item.

Library resources

Find the required and recommended resources for this course on the UQ Library website.

Additional learning resources information

Blackboard

Additional material may be found on the Blackboard site for CHEM3011 at learn.uq.edu.au

Please check the Announcements section of the Blackboard site regularly for information updates.

Downloadable material, including detailed lecture notes and other learning materials, will be available.

Learning activities

The learning activities for this course are outlined below. Learn more about the learning outcomes that apply to this course.

Policies and procedures

University policies and procedures apply to all aspects of student life. As a UQ student, you must comply with University-wide and program-specific requirements, including the:

• Student Code of Conduct Policy
• Student Integrity and Misconduct Policy and Procedure
• Assessment Procedure
• Examinations Procedure
• Reasonable Adjustments - Students Policy and Procedure

Learn more about UQ policies on my.UQ and the Policy and Procedure Library.