spring 2017
KJE-3102 Computational Chemistry - 10 ECTS

Application deadline

Applicants from Nordic countries: 1 June for the autumn semester and 1 December for the spring semester. Exchange students and Fulbright students: 1 October for the spring semester and 15 April for the autumn semester.

Type of course

Theoretical subject. The course is available as a part of the chemistry study program or as singular course independent of study program, also to exchange students.

Lectures are offered on condition that a minimum number of students (3) register for the course.


Admission requirements

Admission requires a Bachelor`s degree (180 ECTS) in Chemistry or equivalent.

The course requires basic calculus knowledge (either Mat-0001 or Mat-1001 is required. If Mat-1001 is chosen, it would be better to also include Mat-1002, for completeness). Basic knowledge in physics (elementary classical mechanics and electromagnetism) is an advantage, as well as elementary linear algebra.

Local admission, application code 9371 - singular courses at Master's level.


Course overlap

If you pass the examination in this course, you will get an reduction in credits (as stated below), if you previously have passed the following courses:

KJE-8102 Computational Chemistry 10 stp

Course content

Computers are nowadays ubiquitous in any chemistry lab. Not only in assisting other more traditional instruments but also as tools in their own right: even small workstations have become so powerful that quantistic modeling of molecules, their structure, properties and behavior can be conveniently carried out on a desktop machine. In addition most Universities and research facilities offer a High Performance Computing platform where more demanding tasks can be performed. Mastering computational chemistry methods must nowadays be regarded as important as modern spectroscopic techniques.

The goal of the present course is to present the methods of quantum chemistry in a hands-on fashion in order to enable students to make use of them in their master studies and subsequently in their professional activity.

 

The course will start by presenting a general overview of molecular modeling (classical and quantistic) and their current use in chemistry. We will briefly touch upon classical modeling and molecular mechanics. We will then introduce wavefunction theory which is at the foundation of Quantum Chemistry. The main wavefunction methods will be presented highlighting their strengths and weaknesses in connection to their practical use. We will also introduce Density Functional Theory (DFT) which is at present the most widely employed method in quantum chemistry. Optimization methods will be discussed in connection both with wavefunction theory and DFT to find the ¿optimal¿ wavefunction and also in relation to geometric problems such as finding the structure of a molecule or a transition state of a reaction. The computation of molecular properties which leads e.g. to the modeling and interpretation of spectroscopic data will also be presented. We will also describe how to use computational results in order to obtain thermodynamic quanitites such as the enthalpy oe the free energy of a reaction. As most of chemistry happens in condensed phase, we will dedicate the last part of the course to the methods to deal with the effect of the solvent on molecules and the techniques (both implicit and explicit) to include such a solvent effect in the calculations.

 

All lectures will be followed by computational exercises where the students will be able to use their acquired knowledge on illustrative examples.


Recommended prerequisites

KJE-3101 Quantum Chemistry

Objectives of the course

Knowledge: The candidate¿

  • will be able to explain the man features of a molecular mechanics force field, its use and its origin
  • will learn the main treats of wavefunction methods
  • will be able to describe such methods in general terms, pointing out their strengths, weaknesses and applicability
  • will qualitatively understand the foundation of Density Functional Theory
  • will be able to describe the features of the main classes of functionals and their use
  • will learn the man optimization methods and their use in connection to wavefunction/density minimization and geometry optimization (minima and saddle points)
  • will learn how to make use of computational methods to acquire information about a chemical system: structure, spectroscopic and thermodynamic properties, reactivity.

Skills: The candidate¿

  • will be able to set up and run single point calculations and check the outcome in terms of achieved convergence and mening of the result
  • will be able to identify the molecular orbitals and explain their meaning, in particular for frontier orbitals (HOMO/LUMO)
  • will be able to run multilevel geometry optimizations and analyse the convergence of the result
  • will be able to assign the bands of an IR spectrum based on the result of a QM calculation
  • will be able to evaluate the convergence of a calculation with respect to the basis set employed
  • will make use of response theory to compute static and frequency-dependent polarizabilities
  • will be able to explain the solvent effect on molecular structure and properties
  • will make use of a programming language of choice (Fortran, C, Python) to compute overlap integrals between basis functions
  • will identify and characterize a reaction path from the reactants through the transition state to the products
  • will compute magnetic properties of molecules such as the NMR shielding constants and the magnetizabilities.

General competence: The candidate will be able to...

  • employ computational methods in her/his scientific work
  • identify the best computational strategy in order to investigate the problem at hand
  • explain the outcome of a computation
  • evaluate the quality and the reliability of the obtained results
  • write a report which describes the work done analyzes the results


Language of instruction and examination

The language of instruction is English and all of the syllabus material is in English. The reports will be written in English. 

Teaching methods

Lectures: 30 h, Seminars: 30 h, Lab exercise

Assessment

 An evaluation of the reports written during the course. Lettergrades (A-F). 

Coursework requirements:

  • Compulsory attendance in 8 computational exercises. 
  • For each exercise the student will have to write a report explaining the theoretical background, the computational strategy adopted and the obtained results. The reports will be evaluated and graded.

The final grade is an overall evaluation (not a strict average) of the reports.

Candidates that receive the grade F can resubmit an improved version of their report the following semester.


Recommended reading/syllabus

Cramer, Essentials of Computational Chemistry

Jensen, Introduction to Computational Chemistry.

Details of the course are given through Fronter, the learning portal of the university. Only registered students for the course will have access to Fronter.

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  • About the course
  • Campus: Tromsø |
  • ECTS: 10
  • Course code: KJE-3102
  • Tidligere år og semester for dette emnet