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Computational Chemistry and Molecular Simulations (CCMS)


Admission requirements

Core course in MSc Chemistry – Energy & Sustainability; elective course in MSc Chemistry – Chemical Biology, MSc Life Science and Technology and MSc Physics

Students with a BSc degree in MST with a major in Chemistry have enough background knowledge for the CCMS course. Other students should have a basic knowledge of molecular quantum mechanics (Hermitian operators, Schrödinger equation, concept of atomic and molecular orbitals, meaning of the wave function) and linear algebra (systems of linear equations, matrices, eigenvalues and eigenvectors).

There is an online, voluntary revision-lecture before the start of the actual lecture series, covering the most important prerequisites and giving a reminder of knowledge needed in the course. This voluntary lecture is strongly recommended for LST students and those who feel that their last quantum mechanics course is already long ago.

This course was previously given under the name Modern Quantum Chemistry (MQC), uSis code 4423MQCL4. This course cannot be combined with MQC in a programme or used in a MSc programme when MQC was taken in the BSc programme.


Computational chemistry is nowadays an indispensable tool to complement experiments and to provide atomic-scale explanations for the chemistry we observe around us. It increasingly even enables the prediction of molecular and material properties.
This course will cover some of the most relevant computational tools (see Course objectives below) and discuss their implementation. The course will provide students with the necessary means to setup and perform simulations to answer questions in chemistry. To this end, the course will combine traditional lectures covering the theoretical background, computational exercises and computer exercises, as well as larger computer labs.
The methods covered will include correlated electronic structure methods, density functional theory, molecular dynamics simulations and the description of non-adiabatic effects.

Course objectives

At the end of the course students will be able to:

  • Speak the language of modern computational chemistry and thus be able to read, use and analyze a scientific computational chemistry article from the current literature.

  • Assess and reason the range of applicability of the various electronic structure methods** and dynamics methods***

  • Choose appropriate simulation settings to address a specific chemical question and be able to argue this choice.

  • Interpret equations and ansatzes relevant to the methods discussed and be able to apply them.

  • Explain the (theoretical foundation of) the methods discussed, their implementation and the approximations that lead to these methods.

  • Relate the theoretical foundations and approximations to the applicability/accuracy of a method, as well as to the parameters that must be chosen when performing a calculation.

  • Design and perform simulations/calculations to address a specific chemical problem/open question.

  • Report the results of simulations/calculations in a paper-like style and

  • Be able to critically assess the quality/reliability of the results.

** Electronic structure methods discussed include: Hartree-Fock, correlated electronic structure methods (configuration interaction, (multi-configurational) self-consistent field and coupled cluster), and density functional theory.

*** Dynamics methods discussed include: molecular mechanics, molecular dynamics, ab initio molecular dynamics, quantum-mechanics in molecular-mechanics (QM/MM), non-adiabatic molecular dynamics.


Schedule information can be found on the website of the programmes.

You will find the timetables for all courses and degree programmes of Leiden University in the tool MyTimetable (login). Any teaching activities that you have sucessfully registered for in MyStudyMap will automatically be displayed in MyTimeTable. Any timetables that you add manually, will be saved and automatically displayed the next time you sign in.

MyTimetable allows you to integrate your timetable with your calendar apps such as Outlook, Google Calendar, Apple Calendar and other calendar apps on your smartphone. Any timetable changes will be automatically synced with your calendar. If you wish, you can also receive an email notification of the change. You can turn notifications on in ‘Settings’ (after login).

For more information, watch the video or go the the 'help-page' in MyTimetable. Please note: Joint Degree students Leiden/Delft have to merge their two different timetables into one. This video explains how to do this.

Mode of instruction

Lectures, videos and lecture notes for (home-)study, homework assignments, computer labs sessions, discussions.
For on-campus lectures, students need to bring their own laptop.

Assessment method

1) Written examination (70%). The written exam will be an open book exam.
2) Reports on computer exercises (30%)
3) Homework exercises (bonus)

In the first part of the lecture series, computer labs and exercises will be integrated into the lectures. These lab sessions do not require a written report. Active participation in these lectures is, however, considered mandatory. Students participating in less than 50% of these classes can be excluded from the exam.
In the second part of the lecture series, computer labs will be held in two dedicated lab sessions. Presence at these lab sessions is considered mandatory. Students not participating in these labs without discussing this a priori with the lecturers can be excluded from the exam. The lab reports to these sessions make up 30% of the final grade.
A minimum grade of 5.0 is needed for both written examination and lab reports to pass the course.

Reading list

Essentials of Computational Chemistry: Theories and Models, 2nd Edition; Christopher J. Cramer, Wiley, 2004. Lecture notes, articles, exercises, additional material will be provided on Brightspace


From the academic year 2022-2023 on every student has to register for courses with the new enrollment tool MyStudyMap. There are two registration periods per year: registration for the fall semester opens in July and registration for the spring semester opens in December. Please see this page for more information.

Please note that it is compulsory to both preregister and confirm your participation for every exam and retake. Not being registered for a course means that you are not allowed to participate in the final exam of the course. Confirming your exam participation is possible until ten days before the exam.

Extensive FAQ's on MyStudymap can be found here.


Dr. Francesco Buda, Dr. Katharina Doblhoff-Dier


Assignments and deadlines are communicated via Brightspace.

According to OER article 4.8, students are entitled to view their marked examination for a period of 30 days following the publication of the results of a written examination. Students should contact the lecturer to make an appointment for such an inspection session.