C7790 Introduction to Molecular Modelling
Faculty of ScienceAutumn 2024
- Extent and Intensity
- 2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
In-person direct teaching - Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Július Zemaník (lecturer) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 16:00–17:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 16/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 13 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Learning outcomes
- Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system; - Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
- CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
- JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Introduction to Molecular Modelling
Faculty of ScienceAutumn 2023
- Extent and Intensity
- 2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
- Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 16:00–17:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 16/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 13 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Learning outcomes
- Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system; - Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
- CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
- JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Introduction to Molecular Modelling
Faculty of ScienceAutumn 2022
- Extent and Intensity
- 2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
Mgr. Ivo Durník, Ph.D. (seminar tutor) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 16:00–17:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 4/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 13 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Learning outcomes
- Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system; - Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
- CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
- JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Introduction to Molecular Modelling
Faculty of Scienceautumn 2021
- Extent and Intensity
- 2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
Mgr. Ivo Durník, Ph.D. (seminar tutor) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 15:00–16:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 3/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 13 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Learning outcomes
- Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system; - Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
- CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
- JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2020
- Extent and Intensity
- 2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
Mgr. Ivo Durník, Ph.D. (seminar tutor) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 16:00–17:50 C04/118
- Timetable of Seminar Groups:
C7790/EN: No timetable has been entered into IS. T. Bouchal, I. Durník, P. Kulhánek - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 2/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 13 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Learning outcomes
- Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system; - Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
- CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
- JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2019
- Extent and Intensity
- 2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor)
Mgr. Ivo Durník, Ph.D. (seminar tutor) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 15:00–16:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 13 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Learning outcomes
- Student will be able to:
- create appropriate models of studied problems;
- perform basic quantum-chemical and molecular-mechanical calculations;
- calculate interaction energy;
- find the transition state of the elementary reaction and determine its activation energy;
- describe the dynamics of small molecular system; - Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
- CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
- JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2018
- Extent and Intensity
- 2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 17. 9. to Fri 14. 12. Mon 15:00–16:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 1/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 13 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
- CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
- JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of Scienceautumn 2017
- Extent and Intensity
- 2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 18. 9. to Fri 15. 12. Mon 15:00–16:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 13 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
- CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
- JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2016
- Extent and Intensity
- 2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 19. 9. to Sun 18. 12. Mon 15:00–16:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 13 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
- CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
- JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2015
- Extent and Intensity
- 2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- RNDr. Petr Kulhánek, Ph.D. (lecturer)
prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Tomáš Bouchal, Ph.D. (seminar tutor) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 15:00–16:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 13 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- LEACH, Andrew R. Molecular modelling : principles and applications. 2nd ed. Harlow: Prentice Hall, 2001, xxiii, 744. ISBN 0582382106. info
- CRAMER, Christopher J. Essentials of computational chemistry : theories and models. 2nd ed. Chichester: John Wiley & Sons, 2004, xx, 596. ISBN 0470091819. info
- JENSEN, Frank. Introduction to computational chemistry. 2nd ed. Chichester: John Wiley & Sons, 2007, xx, 599. ISBN 9780470011874. info
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2014
- Extent and Intensity
- 2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 15:00–16:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 10 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2013
- Extent and Intensity
- 2/0/0. 2 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer) - Guaranteed by
- RNDr. Petr Kulhánek, Ph.D.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 15:00–16:50 C04/211
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 10 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minima and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2012
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science
Supplier department: National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 15:00–15:50 C04/211
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- Macromolecular Chemistry (programme PřF, D-CH) (2)
- Organic Chemistry (programme PřF, N-CH)
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minimums and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2011
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 15:00–15:50 C04/211, Mon 15:00–15:50 C04/118
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 11 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minimums and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2010
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science - Timetable
- Tue 17:00–17:50 C04/211
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 11 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minimums and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2009
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science - Timetable
- Thu 12:00–12:50 C04/211
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 11 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minimums and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- Study Materials
The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2008
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 11:00–11:50 C04/211
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 21 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Basic methods to calculate energy of a molecular system. Description of molecular geometry by Cartesian and internal coordinates. 2. Molecular mechanics. Basic interactions and their expression. 3. Quantum chemistry methods. 4. Molecular dynamics, basic equations. 5. Potential energy hypersurfaces (PES). Stationary points on PES. 6. Energy minimization, relaxation, constraints and restraints, driving. Basic categories of minimization techniques, their advantages and limitations. 7. Program SPARTAN. Basic functions. How to study conformational behavior. How to calculate structure and energy.
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods
- The course is composed of seven lectures, 2 hours each. For those students who registered seminar, and individual project follows.
- Language of instruction
- Czech
- Further comments (probably available only in Czech)
- The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
- Teacher's information
- http://www.chemi.muni.cz/~jkoca/#TEACHING MATERIAL
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2007
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science - Timetable
- Wed 10:00–10:50 C04/211
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 21 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Basic methods to calculate energy of a molecular system. Description of molecular geometry by Cartesian and internal coordinates. 2. Molecular mechanics. Basic interactions and their expression. 3. Quantum chemistry methods. 4. Molecular dynamics, basic equations. 5. Potential energy hypersurfaces (PES). Stationary points on PES. 6. Energy minimization, relaxation, constraints and restraints, driving. Basic categories of minimization techniques, their advantages and limitations. 7. Program SPARTAN. Basic functions. How to study conformational behavior. How to calculate structure and energy.
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt.
- Language of instruction
- Czech
- Further comments (probably available only in Czech)
- The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
- Teacher's information
- http://www.chemi.muni.cz/~jkoca/#TEACHING MATERIAL
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2006
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science - Timetable
- Mon 9:00–9:50 C04/211
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10, only registered with preference (fields directly associated with the programme): 0/10 - fields of study / plans the course is directly associated with
- there are 23 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Basic methods to calculate energy of a molecular system. Description of molecular geometry by Cartesian and internal coordinates. 2. Molecular mechanics. Basic interactions and their expression. 3. Quantum chemistry methods. 4. Molecular dynamics, basic equations. 5. Potential energy hypersurfaces (PES). Stationary points on PES. 6. Energy minimization, relaxation, constraints and restraints, driving. Basic categories of minimization techniques, their advantages and limitations. 7. Program SPARTAN. Basic functions. How to study conformational behavior. How to calculate structure and energy.
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt.
- Language of instruction
- Czech
- Further comments (probably available only in Czech)
- The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
- Teacher's information
- http://www.chemi.muni.cz/~jkoca/#TEACHING MATERIAL
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2005
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science - Timetable
- Mon 15:00–15:50 C04/211
- Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10, only registered with preference (fields directly associated with the programme): 0/10 - fields of study / plans the course is directly associated with
- there are 23 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Basic methods to calculate energy of a molecular system. Description of molecular geometry by Cartesian and internal coordinates. 2. Molecular mechanics. Basic interactions and their expression. 3. Quantum chemistry methods. 4. Molecular dynamics, basic equations. 5. Potential energy hypersurfaces (PES). Stationary points on PES. 6. Energy minimization, relaxation, constraints and restraints, driving. Basic categories of minimization techniques, their advantages and limitations. 7. Program SPARTAN. Basic functions. How to study conformational behavior. How to calculate structure and energy.
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt.
- Language of instruction
- Czech
- Further comments (probably available only in Czech)
- The course can also be completed outside the examination period.
The course is taught annually. - Listed among pre-requisites of other courses
- Teacher's information
- http://www.chemi.muni.cz/~jkoca/#TEACHING MATERIAL
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2004
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10, only registered with preference (fields directly associated with the programme): 0/10 - fields of study / plans the course is directly associated with
- there are 23 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Basic methods to calculate energy of a molecular system. Description of molecular geometry by Cartesian and internal coordinates. 2. Molecular mechanics. Basic interactions and their expression. 3. Quantum chemistry methods. 4. Molecular dynamics, basic equations. 5. Potential energy hypersurfaces (PES). Stationary points on PES. 6. Energy minimization, relaxation, constraints and restraints, driving. Basic categories of minimization techniques, their advantages and limitations. 7. Program SPARTAN. Basic functions. How to study conformational behavior. How to calculate structure and energy.
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt.
- Language of instruction
- Czech
- Further comments (probably available only in Czech)
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week. - Listed among pre-requisites of other courses
- Teacher's information
- http://www.chemi.muni.cz/~jkoca/#TEACHING MATERIAL
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2003
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10, only registered with preference (fields directly associated with the programme): 0/10 - fields of study / plans the course is directly associated with
- there are 23 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Basic methods to calculate energy of a molecular system. Description of molecular geometry by Cartesian and internal coordinates. 2. Molecular mechanics. Basic interactions and their expression. 3. Quantum chemistry methods. 4. Molecular dynamics, basic equations. 5. Potential energy hypersurfaces (PES). Stationary points on PES. 6. Energy minimization, relaxation, constraints and restraints, driving. Basic categories of minimization techniques, their advantages and limitations. 7. Program SPARTAN. Basic functions. How to study conformational behavior. How to calculate structure and energy.
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt.
- Language of instruction
- Czech
- Further comments (probably available only in Czech)
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week. - Listed among pre-requisites of other courses
- Teacher's information
- http://www.chemi.muni.cz/~jkoca/#TEACHING MATERIAL
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2002
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10, only registered with preference (fields directly associated with the programme): 0/10 - fields of study / plans the course is directly associated with
- there are 23 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Basic methods to calculate energy of a molecular system. Description of molecular geometry by Cartesian and internal coordinates. 2. Molecular mechanics. Basic interactions and their expression. 3. Quantum chemistry methods. 4. Molecular dynamics, basic equations. 5. Potential energy hypersurfaces (PES). Stationary points on PES. 6. Energy minimization, relaxation, constraints and restraints, driving. Basic categories of minimization techniques, their advantages and limitations. 7. Program SPARTAN. Basic functions. How to study conformational behavior. How to calculate structure and energy.
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt.
- Language of instruction
- Czech
- Further comments (probably available only in Czech)
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week. - Listed among pre-requisites of other courses
- Teacher's information
- http://www.chemi.muni.cz/~jkoca/#TEACHING MATERIAL
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2001
- Extent and Intensity
- 1/0/0. 2 credit(s). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
- Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science - Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 23 fields of study the course is directly associated with, display
- Course objectives
- Basic methods to calculate energy of a molecular system. Description of molecular geometry by Cartesian and internal coordinates. Molecular mechanics. Basic interactions and their expression. Quantum chemistry methods. Energy minimization, relaxation, constraints and restraints, driving. Basic categories of minimization techniques, their advantages and limitations. Potential energy hypersurfaces (PES). Stationary points on PES. Program SPARTAN. Basic functions. How to study conformational behavior. How to calculate structure and energy. Computer assited organic synthesis. Program PEGAS.
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2000
- Extent and Intensity
- 1/0/0. 2 credit(s). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
- Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science - Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 23 fields of study the course is directly associated with, display
- Course objectives
- Basic methods to calculate energy of a molecular system. Description of molecular geometry by Cartesian and internal coordinates. Molecular mechanics. Basic interactions and their expression. Quantum chemistry methods. Energy minimization, relaxation, constraints and restraints, driving. Basic categories of minimization techniques, their advantages and limitations. Potential energy hypersurfaces (PES). Stationary points on PES. Program SPARTAN. Basic functions. How to study conformational behavior. How to calculate structure and energy. Computer assited organic synthesis. Program PEGAS.
- Language of instruction
- Czech
- Further Comments
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 1999
- Extent and Intensity
- 1/1/0. 3 credit(s). Type of Completion: zk (examination).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
- Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
Chemistry Section – Faculty of Science - Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
- fields of study / plans the course is directly associated with
- there are 16 fields of study the course is directly associated with, display
- Syllabus
- Basic methods to calculate energy of a molecular system. Description of molecular geometry by Cartesian and internal coordinates. Molecular mechanics. Basic interactions and their expression. Quantum chemistry methods. Energy minimization, relaxation, constraints and restraints, driving. Basic categories of minimization techniques, their advantages and limitations. Potential energy hypersurfaces (PES). Stationary points on PES. Program SPARTAN. Basic functions. How to study conformational behavior. How to calculate structure and energy. Computer assited organic synthesis. Program PEGAS.
- Language of instruction
- Czech
- Further comments (probably available only in Czech)
- The course is taught annually.
The course is taught: every week.
General note: v a.r.2000/01. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2011 - acreditation
The information about the term Autumn 2011 - acreditation is not made public
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 11 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minimums and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2010 - only for the accreditation
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
RNDr. Petr Kulhánek, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 30 student(s).
Current registration and enrolment status: enrolled: 0/30, only registered: 0/30, only registered with preference (fields directly associated with the programme): 0/30 - fields of study / plans the course is directly associated with
- there are 11 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Experiment versus molecular modeling (introduction, validation and prediction, overview of experimental single molecule methods)
- 2. Quantum Mechanics (introduction, Born-Oppenheimer approximation, potential energy surface concept, brief overview of methods and software packages)
- 3. Potential Energy Hypersurface (meaning, optimization methods, searching of local and global minimums and transition states, calculation of thermodynamic properties)
- 4. Molecular Mechanics (force fields, long range interactions, solvent modeling, periodic boundary conditions, overview of force fields)
- 5. Molecular Dynamics (time evolution of system, equations of motion, maintaining temperature and pressure, system properties, brief overview of software)
- 6. Special Methods (Monte Carlo simulations, coarse-grain models)
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Teaching methods
- presentation, class discussion
- Assessment methods
- The course is finished by a written test, which is followed by an oral exam.
- Language of instruction
- Czech
- Follow-Up Courses
- Further comments (probably available only in Czech)
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week. - Listed among pre-requisites of other courses
C7790 Computational Chemistry and Molecular Modeling I
Faculty of ScienceAutumn 2007 - for the purpose of the accreditation
- Extent and Intensity
- 1/0/0. 1 credit(s) (fasci plus compl plus > 4). Recommended Type of Completion: zk (examination). Other types of completion: k (colloquium).
- Teacher(s)
- prof. RNDr. Jaroslav Koča, DrSc. (lecturer)
Mgr. Zdeněk Kříž, Ph.D. (lecturer) - Guaranteed by
- prof. RNDr. Jaroslav Koča, DrSc.
National Centre for Biomolecular Research – Faculty of Science - Prerequisites
- Basic level of general and physical chemistry. A basic knowledge in quantum chemistry is an advantage.
- Course Enrolment Limitations
- The course is also offered to the students of the fields other than those the course is directly associated with.
The capacity limit for the course is 10 student(s).
Current registration and enrolment status: enrolled: 0/10, only registered: 0/10, only registered with preference (fields directly associated with the programme): 0/10 - fields of study / plans the course is directly associated with
- there are 23 fields of study the course is directly associated with, display
- Course objectives
- The course is oriented to obtaining practical skills in using chemical modeling software. Students will learn how the molecular geometry is represented in a computer and how energy is calculated. At the end, students will learn how to use one of the commonly used modeling software packages.
- Syllabus
- 1. Basic methods to calculate energy of a molecular system. Description of molecular geometry by Cartesian and internal coordinates. 2. Molecular mechanics. Basic interactions and their expression. 3. Quantum chemistry methods. 4. Molecular dynamics, basic equations. 5. Potential energy hypersurfaces (PES). Stationary points on PES. 6. Energy minimization, relaxation, constraints and restraints, driving. Basic categories of minimization techniques, their advantages and limitations. 7. Program SPARTAN. Basic functions. How to study conformational behavior. How to calculate structure and energy.
- Literature
- REMKO, M. Molekulové modelovanie. Princípy a aplikácie. Bratislava: Slovak Academic Press, 2000. info
- JENSEN, Frank. Introduction to Computational Chemistry. New York: J. Wiley & Sons Ltd., 1999. info
- LIPKOWITZ, K B and D B BOYD. Reviews in Computational Chemistry 1-9. New York: VCH Publishers, 1998. info
- HEHRE, Warren J., Alan J. SHUSTERMAN and W. Wayne HUANG. A laboratory book of computational organic chemistry. Irvine, Calif.: Wavefunction, 1996, xiv, 291 s. ISBN 0-9643495-5-8. info
- FORESMAN, J B and A FRISCH. Exploring Chemistry with Electronic Structure Methods. Pittsburgh: Gaussian, Inc., 1996. info
- Assessment methods (in Czech)
- Kurs sestává ze sedmi dvouhodinových přednášek. Pro ty studenty, kteří si zapsali cvičení, pak následuje samostatný projekt.
- Language of instruction
- Czech
- Further comments (probably available only in Czech)
- The course can also be completed outside the examination period.
The course is taught annually.
The course is taught: every week. - Listed among pre-requisites of other courses
- Teacher's information
- http://www.chemi.muni.cz/~jkoca/#TEACHING MATERIAL
- Enrolment Statistics (recent)