Modelling in Organic Chemistry Laboratory 1200-2MOCHORLZ

Introduction to HyperChem and PCModel programs. Construction of three-dimensional models of organic molecules, optimalization of their geometries using molecular mechanics and different force fields as well as semi-empirical methods of quantum chemistry. Modeling of complex molecules, macromolecules and ionic compounds, their energy minimalization and calculation of the charge density. Conformational studies of small molecules with linear or cyclic structures. Search for a global minimum energy conformation of the molecule using molecular dynamics methods; molecular dynamics simulation of solvated systems. Computer simulation of IR, UV and NMR spectra

Type of course

elective courses

Mode

Classroom

Prerequisites (description)

The student should know the basics of organic chemistry and nuclear magnetic resonance spectroscopy. Furthermore, it is necessary to have computer skills and be familiar with working in a Windows environment.

Course coordinators

Sebastian Kmiecik

Learning outcomes

Familiarizing students with chosen molecular modeling programs and demonstrating applications of calculation methods in organic synthesis.
Knowledge:
K_W05 the structure of various types of molecular target–ligand complexes,
K_W06 mechanisms of drug action at the molecular level,
K_W13 basic algorithms, IT tools, and databases used in scientific research and computational studies,
K_W23 the specifics of drug design work and issues related to the lifecycle of medicinal substances
Skills:
K_U02 apply appropriate methods, techniques, research tools, and IT tools necessary to address a defined research problem,
K_U04 use online databases of protein structures and small-molecule compounds, as well as software for visualization, molecular dynamics, ligand docking, and property prediction,
K_U05 build and modify chemical compounds and optimize their interactions with proteins and DNA,
K_U20 use professional literature, databases, and other sources of information, and assess the reliability of the obtained information
Social Competencies:
K_K01 engage in continuous learning and independently search for information in the literature, including foreign-language sources,
K_K04 critically evaluate scientific and popular science content

Assessment criteria

Grading is based on two tasks involving independently modeled complex organic compound and finding its relevant parameters.

Practical placement

not applicable

Bibliography

1.Marek Doskocz, Jacek Doskocz, Szczepan Roszak, Roman Gancarz, Modelowanie molekularne w chemii organicznej, Druk. Politechniki Wroclawskiej, Wroclaw 2007.
2.HyperChemT Professional 7.51, Hypercube, Inc., 1115 NW 4th Street, Gainesville, Florida 32601, USA; http://www.hyper.com.

Additional information

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

Description of 1200-2MOCHORLZ in USOSweb