| Course Unit Code | Course Unit Title | Type of Course Unit | Year of Study | Semester | Number of ECTS Credits | | Fİ127 | Molecular Modeling | Elective | 1 | 1 | 6 |
|
| Level of Course Unit |
| Second Cycle |
| Objectives of the Course |
| To introduce modern electronic structure methods and to model the three-dimensional structure of molecules and to determine the physical and chemical properties of the molecule. |
| Name of Lecturer(s) |
| Dr. Öğr. Üyesi Yavuz EKİNCİOĞLU |
| Learning Outcomes |
| 1 | Can choose the appropriate method for a simple modeling application using computational methods | | 2 | Can use a molecular modeling program, for example the Gaussian09 package program | | 3 | can visualize 3-dimensional compounds at the molecular level. | | 4 | can make conformational analysis of a given molecule. | | 5 | Calculates the quantum chemical properties of a given molecule. |
|
| Mode of Delivery |
| Normal Education |
| Prerequisites and co-requisities |
| none |
| Recommended Optional Programme Components |
| none |
| Course Contents |
| Introduction to Computational Methods.
Semi empric method
Ab- initio, DFT and Hartree-Fock. methods
Self Consistent Field Method
Introduction to molecular modeling programs.
Drawing molecules in the modeling program, preparing input and assigning work to the program
Intermolecular and intramolecular interactions and conformational effects, Conformation Scanning,
Calculation of Electrostatic Potential Maps, density surfaces : HOMO-LUMO surfaces
Spectoscopik properties.
Drawing of biomolecules (proteins, DNA, RNA)
Potential energy surfaces
Intrinsic Reaction Coordinate (IRC) method
Modeling reaction mechanisms |
| Weekly Detailed Course Contents |
|
| 1 | Introduction to Computational Methods: semi-empirical, ab initio and DFT | | | | 2 | Hartree-Fock and Self consistent field Methods | | | | 3 | introduction to molecular modeling programs | | | | 4 | Drawing molecules in the modeling program | | | | 5 | How are inputs prepared for the program and how is work assigned to the program? | | | | 6 | Intermolecular and intramolecular interactions and conformational effects, Conformation Scanning | | | | 7 | Application: Conformational Scanning | | | | 8 | Midterm Exam | | | | 9 | Application: Calculation of Electrostatic Potential Maps, density surfaces : HOMO-LUMO surfaces | | | | 10 | Spectroscopic properties | | | | 11 | Drawing of biomolecules (proteins, DNA, RNA) | | | | 12 | Potential energy surfaces (PEY) and intrinsic reaction coordinate (IRC) | | | | 13 | Modeling reaction mechanisms, | | | | 14 | General review | | | | 15 | Final Exam | | |
|
| Recommended or Required Reading |
| A. R. Leach, Molecular Modelling Principles and Applications, Prentice Hall Pearson Education, England |
| Planned Learning Activities and Teaching Methods |
|
| Assessment Methods and Criteria | |
| Midterm Examination | 1 | 100 | | SUM | 100 | |
| Final Examination | 1 | 100 | | SUM | 100 | | Term (or Year) Learning Activities | 40 | | End Of Term (or Year) Learning Activities | 60 | | SUM | 100 |
| | Language of Instruction | | | Work Placement(s) | | yok |
|
| Workload Calculation |
|
| Midterm Examination | 1 | 1 | 1 |
| Final Examination | 1 | 2 | 2 |
| Attending Lectures | 14 | 3 | 42 |
| Individual Study for Homework Problems | 10 | 4 | 40 |
| Individual Study for Mid term Examination | 13 | 1 | 13 |
| Individual Study for Final Examination | 13 | 2 | 26 |
| Reading | 13 | 4 | 52 |
|
| Contribution of Learning Outcomes to Programme Outcomes |
| LO1 | 2 | 1 | 4 | 3 | 2 | 2 | 3 | 3 | 4 | 4 | | LO2 | 2 | 4 | 3 | 3 | 2 | 2 | 4 | 3 | 4 | 4 | | LO3 | 4 | 3 | 4 | 3 | 2 | 2 | 2 | 3 | 3 | 4 | | LO4 | 3 | 2 | 3 | 3 | 2 | 2 | 3 | 2 | 3 | 4 | | LO5 | 2 | 5 | 3 | 3 | 2 | 2 | 4 | 3 | 3 | 4 |
|
| * Contribution Level : 1 Very low 2 Low 3 Medium 4 High 5 Very High |
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