Computational chemistry 0600-S2-O-PCT/sr

The following topics are discussed and practiced in the laboratory: the basics of the Linux operating system, the vi text editor, the basics of group theory, including determination of point groups of molecules, structure of the input file, determination of the geometry of the molecule (Cartesian coordinates and internal coordinates (Z- matrix)), basic Gamess program commands, job execution, output file structure, basics of using Molden graphics program, single point (SP) calculation, geometry optimization, normal vibration analysis, basis sets, Hartree-Fock method.

1. Basics of the Linux operating system.
2. Text editor vi.
3. Basics of the Gamess computational program:
a) general program requirements
b) the structure of the input file
c) determining the point group of molecules
d) basic commands of the Gamess computational program
e) execution of jobs
f) basic user errors
4. Determining the geometry of the molecule (Cartesian coordinates and Z-matrix)
5. Structure of the output file.
6. Basics of Molden graphics program.
a) Molden as the Z-matrix editor
b) Molden as a tool helping in results visualization
7. Computation of the total energy of a system ('single point' (SP)).
8. Geometry optimization.
9. Vibrational (frequency) analysis
10. Using basis sets:
a) basis sets from the program's own library
b) using basis sets from an external source
c) modification of a basis set
d) the influence of a basis set on the obtained results
11. Utilizing the Hartree-Fock method

Total student workload

1. Hours realized with the participation of teachers (contact hours) 30h 2. Time devoted to individual student work (preparation for the laboratory) 20h

Learning outcomes - knowledge

The student acquires knowledge of conducting elementary computations with the use of the Gamess computational program. The student knows how to use the Molden graphics program. (K_W01, K_W02, K_W08)

Learning outcomes - skills

After completing the laboratory in computational chemistry, the student should be able to carry out elementary computations using the Gamess computational program (in particular, be able to write input files, correct errors in these files, be able to find important numerical results in the obtained output files) and analyze the obtained results and assess the degree of their credibility. The student should be able to consciously use Molden's graphics program. (K_U01, K_U10)

Learning outcomes - social competencies

The student knows the limitations of his own knowledge and understands the need for further learning throughout life; is able to independently take steps to expand and deepen his chemical knowledge. Is able to cooperate in a team and creatively solve problems related to scientific research. Can properly set priorities to solve a chemical problem identified by himself or by others. Is aware of professionalism, appreciating intellectual honesty and adherence to professional ethics, both in the activities of his own and others. Can formulate and present opinions on the basics chemical issues and achievements in this discipline. (K_K01, K_K02, K_K05, K_K06, K_K07)

Teaching methods

Didactic searching methods - computer laboratory. Classes in a laboratory, i.e. a computer lab, consist of working together with the teacher and independent work, completed with the implementation of student's own project.

Exploratory teaching methods

- project work
- laboratory

Prerequisites

The student has knowledge of mathematics and physics, and is welcome, but not necessary, basic knowledge of quantum chemistry.

Course coordinators

Mirosław Jabłoński

Assessment criteria

Grading (based on active participation in labs, short tests if done, and student's own projects).

Practical placement

not applicable

Bibliography

Basic literature:
1. Gamess website:
https://www.msg.chem.iastate.edu/gamess/index.html
2. Molden website:
https://www3.cmbi.umcn.nl/molden/
3. Teacher's own notes.

Supplementary literature:
1. W. Kołos, Chemia kwantowa, PWN, 1975
2. L. Piela - Idee chemii kwantowej, PWN 2003.
3. F. Jensen, Introduction to Computational Chemistry, Wiley, Germany, 2008.

Additional information

Additional information (registration calendar, class conductors, localization and schedules of classes), might be available in the USOSweb system:

Description of 0600-S2-O-PCT/sr in USOSweb