Specialised Project - M342014
Title: Odborný projekt
Guaranteed by: Department of Chemistry of Natural Compounds (342)
Faculty: Faculty of Food and Biochemical Technology
Actual: from 2019
Semester: winter
Points: winter s.:3
E-Credits: winter s.:3
Examination process: winter s.:
Hours per week, examination: winter s.:0/3, MC [HT]
Capacity: unknown / unknown (unknown)
Min. number of students: unlimited
State of the course: cancelled
Language: Czech
Teaching methods: full-time
Teaching methods: full-time
Guarantor: Raich Ivan doc. Dr. Ing.
Interchangeability : N342008
Examination dates   Schedule   
Annotation -
The course in the introduction familiarizes with the advanced functions in MS Word and MS Excel for the creation of long scientific documents and processing large tabular data and optimizations, respectively.However, it primarily introduces the basics of molecular modeling, construction and editing of a 3D structure of molecules, and depiction of various molecular properties.
Last update: Fialová Jana (20.12.2017)
Aim of the course -

Students will be able to:

Use MS Word for writing and editing long scientific documents

Use MS Excel for processing large data and optimization

Build and inspect 3D models of various compounds including biopolymers

Perform geometric optimizations, molecular dynamics and other calculations

Critically evaluate outputs of molecular modeling in literature

Last update: Fialová Jana (20.12.2017)
Literature -

R: Young D. C.: Computational Chemistry, John Wiley & Sons, Inc., 2002, 0471220655

A: Caffery M. L., Dobosh P. A., Richardson D. M.: Laboratory Excercises Using HyperChem, HyperCube, Inc., 1998, 1-896164-30-7

Last update: Fialová Jana (20.12.2017)
Learning resources -

Own tutors for some modeling task


Last update: Fialová Jana (20.12.2017)
Syllabus -

1. MS Word for creation of long scientific documents, formatting of characters, paragraphs, styles, templates

2. Language settings, custom dictionaries, tabulators, tables

3. Text flow, word division, line and page breaks

4. Numbering of headings, references, tables, schemes, equations

5. Absolute and relative addressing in Excel, pivot tables and charts

6. Optimizations and Solver in Excel, matrix formulae

7. Basics of molecular modeling, viewing structures, rendering, displaying and editing of structural parameters

8. Displaying proteins and other biopolymers, rendering, abstraction and hiding

9. Construction of molecule models, specification of stereochemistry

10. Geometry optimizations and local minima problem

11. Editing structural parameters, conformational changes, constrained geometry optimizations

12. Molecular dynamics, Monte Carlo, simulated annealing, periodic box and its construction

13. Calculations of charges and orbitals, HOMO, LUMO, prediction of selectivity of cycloaddition reactions

14. Calculations of spectral and other properties

Last update: Fialová Jana (20.12.2017)
Registration requirements -

Applications of Computer Science

Chemical informatics

Last update: Fialová Jana (20.12.2017)