Chemistry of Natural Compounds: Specialised Project - M342019
Title: Odborný projekt Chemie přírodních látek
Guaranteed by: Department of Chemistry of Natural Compounds (342)
Faculty: Faculty of Food and Biochemical Technology
Actual: from 2019
Semester: winter
Points: winter s.:2
E-Credits: winter s.:2
Examination process: winter s.:
Hours per week, examination: winter s.:0/3, MC [HT]
Capacity: unknown / unlimited (unknown)
Min. number of students: unlimited
Language: Czech
Teaching methods: full-time
For type: Master's (post-Bachelor)
Note: course can be enrolled in outside the study plan
enabled for web enrollment
Guarantor: Raich Ivan doc. Dr. Ing.
Class: Specializační laboratoř
Interchangeability : N342008
Examination dates   
This subject contains the following additional online materials
Annotation -
Last update: Raich Ivan doc. Dr. Ing. (01.03.2018)
The course in the introduction familiarizes with the advanced functions in MS Word, MS Excel and EndNote for the creation of long scientific documents, processing of large tabular data and optimizations and storing bibliographic references and processing of literature searches, 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. Within a separate project, students process and submit a literature search on a topic assigned by diploma thesis supervisor.
Aim of the course -
Last update: Raich Ivan doc. Dr. Ing. (01.03.2018)

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

Independently create a large literature survey and proces bibliographies in EndNote

Literature -
Last update: Kubová Petra Ing. (29.01.2018)

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

Learning resources -
Last update: Kubová Petra Ing. (29.01.2018)

Own tutors for some modeling task

Syllabus -
Last update: Raich Ivan doc. Dr. Ing. (01.03.2018)

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

2. Language settings, custom dictionaries, tabulators, tables, text flow, word division, line and page breaks

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

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

5. Optimizations and Solver in Excel, matrix formulae

6. Basics of EndNote, libraries structure

7. Modification of EndNote styles and filters, import and export of citations, MS Word add-in

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

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

10. Construction of molecule models, specification of stereochemistry, 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

Registration requirements -
Last update: Kubová Petra Ing. (29.01.2018)

Applications of Computer Science

Chemical informatics

Course completion requirements - Czech
Last update: MORAVCOJ (01.03.2018)

Odevzdání projektu se seznamem původní literatury vyhledané v databázích v požadovaném formátu zpracovaném v softwaru EndNote na téma zadané budoucím vedoucím DP. Diskuze a obhajoba projektu.