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Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS PHY 5180 MOLECULAR MODELING ELECTIVE 3 0 0 8

Offered By

Graduate School of Natural and Applied Sciences

Level of Course Unit

Second Cycle Programmes (Master's Degree)

Course Coordinator

PROFESSOR DOCTOR HASAN KARABIYIK

Offered to

PHYSICS PHYSICS

Course Objective

The course will provide an understanding basic principles and properties of molecular modeling

Learning Outcomes of the Course Unit

1   to be able to categorize modern calculation tools used in molecular modeling 2   to be able to understand and apply contemporary methods in molecular modeling 3   to be able to express and apply mathematically methods in molecular modeling 4   to be able to understand optimization algorithms 5   to be able to identify the differences between optimization algorithms 6   to be able to have an propensity to perform interdisciplinary research

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description 1 Introduction to Molecular Modeling 2 Overview of Quantum Mechanics 3 Hückel Molecular Orbital Theory 4 Extended Hückel Molecular Orbital Theory 5 Hartree-Fock Theory 6 Hartree-Fock Theory: Variational Principles 7 Hartree-Fock Theory: Second Quantization 8 MIDTERM 9 Basis Sets 10 Density Functional Theory 11 Semiempirical Methods 12 Molecular Mechanics 13 Geometry Optimization Algorithms 14 Calculations of Molecular Properties 15 Exchange-correlation Functionals

Recomended or Required Reading

Textbook: Computational Chemistry and Molecular Modeling. K. I. Ramachandran, G. Deepa, K. Namboori, Springer-Verlag Berlin, 2008. Supplementary Book(s): Introduction to Computational Chemistry, Frank Jensen, John Wiley & Sons, 1999.

Planned Learning Activities and Teaching Methods

1. Lectures 2. Problem solving 3. Presentations 4. Homework

Assessment Methods

SORTING NUMBER SHORT CODE LONG CODE FORMULA 1 MTE MIDTERM EXAM 2 FIN FINAL EXAM 3 FCG FINAL COURSE GRADE MTE * 0.50 + FIN * 0.50 4 RST RESIT 5 FCGR FINAL COURSE GRADE MTE * 0.50 + RST * 0.50 *** Resit Exam is Not Administered in Institutions Where Resit is not Applicable.

Further Notes About Assessment Methods

None

Assessment Criteria

To be announced.

Language of Instruction

Turkish

Course Policies and Rules

1. Attending at least 70 percent of lectures is mandatory. 2. Plagiarism of any type will result in disciplinary action.

Contact Details for the Lecturer(s)

hasan.karabiyik@deu.edu.tr

Office Hours

To be announced.

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours) Preparations before/after weekly lectures 14 6 84 Preparation for midterm exam 1 20 20 Preparation for final exam 1 30 30 Preparing assignments 13 4 52 Midterm 1 2 2 Final 1 2 2 TOTAL WORKLOAD (hours) 190

Contribution of Learning Outcomes to Programme Outcomes

PO/LO PO.1 PO.2 PO.3 PO.4 PO.5 PO.6 PO.7 PO.8 PO.9 PO.10 LO.1 4 4 5 5 2 5 4 2 4 2 LO.2 4 4 5 5 2 5 4 2 4 2 LO.3 4 4 5 5 2 5 4 2 4 2 LO.4 4 4 5 5 2 4 5 2 4 2 LO.5 4 4 5 5 2 4 5 2 4 2 LO.6 4 4 5 5 2 4 5 2 4 2