C7790 Introduction to Molecular Modelling

Faculty of Science
Autumn 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).
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
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: 7/30, 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.
The course is taught: every week.
Listed among pre-requisites of other courses
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023.

C7790 Introduction to Molecular Modelling

Faculty of Science
Autumn 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: 15/30, 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2024.

C7790 Introduction to Molecular Modelling

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2023, Autumn 2024.

C7790 Introduction to Molecular Modelling

Faculty of Science
autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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/CZ: No timetable has been entered into IS. T. Bouchal, I. Durník, P. Kulhánek
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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 2007 - for the purpose of the accreditation, Autumn 1999, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.

C7790 Computational Chemistry and Molecular Modeling I

Faculty of Science
Autumn 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
The course is also listed under the following terms Autumn 1999, Autumn 2010 - only for the accreditation, Autumn 2000, Autumn 2001, Autumn 2002, Autumn 2003, Autumn 2004, Autumn 2005, Autumn 2006, Autumn 2007, Autumn 2008, Autumn 2009, Autumn 2010, Autumn 2011, Autumn 2011 - acreditation, Autumn 2012, Autumn 2013, Autumn 2014, Autumn 2015, Autumn 2016, autumn 2017, Autumn 2018, Autumn 2019, Autumn 2020, autumn 2021, Autumn 2022, Autumn 2023, Autumn 2024.
  • Enrolment Statistics (recent)