Computational chemistry 0600-S2-O-PCT

1. Basics of the Linux operating system.
2. The vi text editor.
3. Basics of the Gamess computational package:
a) general program requirements
b) structure of the input file
c) determining the point group of molecules
d) basic commands of the Gamess computing program
e) job execution
f) basic user's errors
4. Determining the geometry of the molecule (Cartesian coordinates and Z matrix)
5. Structure of the output file.
6. Basics of the Molden graphics program.
a) Molden as a Z-matrix editor
b) Molden as a tool for the visualization of results
7. Computations of the total energy of the system (i.e., single point calculations).
8. Geometry optimization.
9. Frequency analysis.
10. The usage of basis sets:
a) basis sets from the Gamess internal library
b) using basis sets from an external source
c) modification of a basis set
d) the influence of the basis set used on the results obtained
11. Computations based on the Hartree-Fock method.

Total student workload

1. Hours carried out with the participation of teacher: participation in the laboratory: 30 hours 2. Own work preparation for the laboratory 30 hours Total 60 hours (3 ECTS points)

Learning outcomes - knowledge

W1: Student knows the structures of .inp and .out files. W2: Student knows the basic commands of the Gamess computing program. W3: Student knows the basic capabilities of the Gamess computing program. W4: Student knows the capabilities of the Molden graphics program. K_W02, K_W08

Learning outcomes - skills

After completing the computational chemistry laboratory, the student should be able to perform elementary calculations 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 received output files), analyze the obtained results and assess the degree of their reliability. The student should be able to use the Molden graphics program. K_U01, K_U10

Learning outcomes - social competencies

Student knows the limits of his or her own knowledge and understands the need for further lifelong learning; is able to independently take actions to expand and deepen chemical knowledge. Able to cooperate in a team and creatively solve problems related to scientific research. Is able to appropriately determine priorities for solving a chemical problem identified by himself or others. Is aware of professionalism, appreciation of intellectual honesty and compliance with professional ethics, both in one's own actions and those of others. Is able to formulate and present opinions on basic chemical issues and achievements in this discipline. K_K01, K_K05, K_K06, K_K07

Teaching methods

Search teaching methods – computer laboratory. Classes in the laboratory, i.e. computer room, involve working together with the teacher and working independently, culminating in the creation of your own project.

Exploratory teaching methods

- project work
- laboratory

Prerequisites

(in Polish) Dobrze widziana, choć nie konieczna, podstawowa wiedza z chemii kwantowej.

Course coordinators

Mirosław Jabłoński

Assessment criteria

Grade (based on the assessment of work in the computer lab, activity, own projects and possible short tests).

Practical placement

not applicable

Bibliography

Basic literature:

1. Gamess website:
https://www.msg.chem.iastate.edu/gamess/index.html
2. Page for practicing determining the point group of a molecule:
https://symotter.org/
3. Molden website:
https://www.theochem.ru.nl/molden/
4. Page with functional databases:
https://www.basissetexchange.org/

Additional literature:

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 in USOSweb