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, thereby 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.

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

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.

Practical applications: extensive illustrations of how computational techniques can be used in practice to study chemical behaviour ﾠwill be given. 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.

Please note that this year, the CHEM3011 timetable comprises a series of "Applied Classes". (This is different from previous years, where the timetable comprised distinct Lecture and Practical classes). The Applied Classes in 2025 are designed to allow students to learn and apply their skills with appropriate guidance under the support of a subject matter expert. They will include a mixture of delivery modes including traditional taught content, theoretical exercises, and practical computer laboratory activities. During these classes, students will work both individually and in group settings. The output from the Applied Class sessions (including both individual and group work) can be used both to formally assess student progress and as formative assessment opportunities. Importantly, students should note that the activities that comprise the laboratory component of the course (completion of which is a course hurdle) will be undertaken as part of the Applied Class sessions.

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.

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

Computer Laboratory Reports

• Hurdle

Mode

Activity/ Performance, Written

Category

Paper/ Report/ Annotation, Practical/ Demonstration, Project, Tutorial/ Problem Set

Weight

40%

Due date

Module 1: 2pm 28/08/2025

Module 2: 2pm 29/08/2025

Module 2: 2pm 5/09/2025

Module 2: 2pm 12/09/2025

Module 2: 2pm 25/09/2025

Module 3: 2pm 26/09/2025

Module 3: 2pm 17/10/2025

Module 3: 2pm 24/10/2025

Module 3: 2pm 31/10/2025

Learning outcomes

L01, L02, L03, L04, L05

Task description

Hurdle requirements

Submission guidelines

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

Deferral or extension

You may be able to apply for an extension.

The maximum extension allowed is 28 days. Extensions are given in multiples of 24 hours.

Applications for extension

Extension applications must be received no later than 24 hours after the published assessment due date and time.

Read the information contained in the following links carefully before submitting an application for extension to assessment due date.

For guidance on applying for an extension, information is available here.

For the policy relating to extensions, information is available here (Part D).

Information on medical certificates

Please note the University's requirements for medical certificates here.

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 report 1 hour late, you will be penalised 10%; if your report 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

60%

Due date

End of Semester Exam Period

8/11/2025 - 22/11/2025

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 40% or more on the end of semester exam.

2.      You must complete 100% of the practical (APP activities) component of the course.

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 Laboratory Activities

Students are required to attend the computer laboratory activities. The laboratory activities will be undertaken during (i.e. as a component of) the Applied Class sessions. The assessment criteria and schedule for laboratory reports will be made available on Blackboard and ﾠexplained to students during the Applied Class sessions. If you are unable to attend your timetabled computer laboratory activities 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 be 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

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

Students are responsible for retaining evidence of submission by the due date for all assessment items, in the required form (for example, screenshot, email, photo, and an unaltered copy of submitted work).

In the case of a Blackboard outage, contact the Course Coordinator as soon as possible to confirm the outage with ITS.

Assessment/Attendance

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.UQwebsite and the Course Profile (CP) for your course 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

Only learning activities and/or assessment items completed during the study period of enrolment, including any approved extensions, may contribute to your grade in this course. The whole or partial use of assessment items previously submitted for the same course, for a course at any institution, or for published material, is not permitted without written permission of the Course Coordinator.

Important Note

At the discretion of the individual lecturers, Turnitin may be used for laboratory reports to check for plagiarism. Penalties can be severe for plagiarism.

The University has adopted the following definition of plagiarism: Plagiarism is the act of misrepresenting as one's own original work the ideas, interpretations, words or creative works of another either intentionally or unintentionally. These include published and unpublished documents, designs, music, sounds, images, photographs, computer codes and ideas gained through working in a group. These ideas, interpretations, words or works may be found in print and/or electronic media.

Students should read the UQ Student Integrity and Misconduct Policy.

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 course 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 for Students Policy and Procedure

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