Course Name Code Semester T+U Hours Credit ECTS
Molecular Modelling and Simulations KIM 669 0 3 + 0 3 6
Precondition Courses
Recommended Optional Courses
Course Language Turkish
Course Level Doctorate Degree
Course Type Optional
Course Coordinator Prof.Dr. UĞURSOY OLGUN
Course Lecturers
Course Assistants
Course Category
Course Objective Students are expected to learn basic concepts of molecular modeling and simulations with recent applications and methodology in the field.
Course Content Molecular design on computers (3D), molecular modeling, minumum energy calculations, bond distances, bond angles, intermolecular forces, molecular modeling techniques, classical and modern methods, molecular mechanics, force field methods, softwares, monte carlo, ab initio and molecular dynamic (MD) simulations, modeling of surfaces and interfaces, total energy, cohesion and adhesion energy, solubility parameter, diffusion coefficient, intermolecular interactions, solid, liquid and gas phase simulations
# Course Learning Outcomes Teaching Methods Assessment Methods
1 Master and PhD level students understand fundementals of molecular modeling, simulations and teoretical calculations performed on computers. Lecture, Question-Answer, Discussion, Self Study, Testing, Homework,
2 Gain knowledge of basic reserach and developments in chemistry, current applications of computational chemistry. Lecture, Question-Answer, Discussion, Self Study, Testing, Homework,
3 Perform calculations for chemical substances. Lecture, Question-Answer, Discussion, Self Study, Testing, Homework,
4 Apply basic knowledge to chemistry problems. Lecture, Question-Answer, Discussion, Self Study, Testing, Homework,
5 Analyse fundamental knowledge. Lecture, Question-Answer, Discussion, Self Study, Testing, Homework,
6 Improve skils to relate different topics. Lecture, Question-Answer, Discussion, Self Study, Testing, Homework,
Week Course Topics Preliminary Preparation
1 Molecular design on computers (3D)
2 Molecular modeling
3 Minumum energy calculations, bond distances,bond angles,
4 Intermolecular forces
5 Molecular modeling techniques, classical and modern methods
6 Molecular mechanics
7 Force field methods
8 Softwares, monte carlo, ab initio and molecular dynamic (MD) simulations
9 MIDTERM
10 Modeling of surfaces and interfaces
11 Total energy, cohesion and adhesion energy
12 Solubility parameter, diffusion coefficient
13 Intermolecular interactions
14 Solid, liquid and gas phase simulations
Resources
Course Notes
Course Resources 1. HINCHLIFFE, A. ?Modelling Molecular Structures?, John Wiley and Sons Inc., Hoboken NJ, 1995.
2. SCHLEYER, P.R., ?Encyclopedia of Computational Chemistry?, John Wiley and Sons Inc., Hoboken NJ, 2007.
3. YOUNG, D.C., ?Computational Chemistry?, J.Wiley & Sons, NJ Hoboken, 2002.
4. Literature.
Order Program Outcomes Level of Contribution
1 2 3 4 5
1 In addition to expanding and making deeper the knowledge established on undergraduate education in a same or different area, reaches the knowledge by doing research and also improves his or her knowledge to the expertise level by doing evaluation and practice. X
2 Utilizing incomplete or limited data in his or her study area expands the knowledge by experimental methods and use those obtained knowledge by scientific, social and ethical responsibility. X
3 Constructs a problem independently and solves the problem by proposing an experimental solution method and applies to the advance level research by evaluating the results. X
4 Transfers systematically the current developments and his or her advance level studies to the other related or nonrelated groups as written, orally and visually. X
5 Develops new strategic approach and produces solutions by taking responsibility in unexpected and complicated situations in his or her area of practice. X
6 Develops advance strategic, political and practice plans and evaluates the obtained results within the framework of quality process in his or her study area. X
7 - Has advance level oral or written communication ability in one of well known foreign language (“European Language Portfolio Global Scale”, Level B1). X
8 Has knowledge for software and hardware about computers, uses information and communication technologies. X
9 Protecting scientific, social, and ethical values, teaches and controls these values in the steps of collection, evaluation and announcement of data in the international arena. X
10 Applies the digested knowledge and problem solving ability in advance level studies among the different disciplines. X
Evaluation System
Semester Studies Contribution Rate
1. Ara Sınav 70
1. Ödev 15
1. Performans Görevi (Seminer) 15
Total 100
1. Yıl İçinin Başarıya 50
1. Final 50
Total 100
ECTS - Workload Activity Quantity Time (Hours) Total Workload (Hours)
Course Duration (Including the exam week: 16x Total course hours) 16 3 48
Hours for off-the-classroom study (Pre-study, practice) 16 3 48
Mid-terms 1 15 15
Assignment 1 10 10
Performance Task (Seminar) 1 10 10
Final examination 1 20 20
Total Workload 151
Total Workload / 25 (Hours) 6.04
dersAKTSKredisi 6