Computer for Chemistry Students, BSc course

During this course, students will learn about a few programs that are essential for students pursuing a BSc in chemistry. The course helps students to interpret data obtained in chemistry laboratories better. In addition, it provides skills in preparing a scientific report following an experiment or research. The course begins with an introduction to the Python programming language. Afterward, students learn about spreadsheets and their application in chemistry, drawing molecular shapes, and specifying molecular structures. Below is a detailed description of each part.

1.    Python

1.1        Fundamental Ideas of Computer Science

1.2        Primitive Types

Variables, Strings, Formatted strings, Variables Escape sequences, String methods, Numer functions, Type conversion, Falsy values

1.3        Control Flow

Conditional statements, Ternary operator, Boolean operators, Chaining comparison operators, For loops, While loops, Equality operators

1.4        Functions

Defining functions, Keyword arguments, Variable number of arguments, Variable number of keyword arguments

1.5        Lists

Creating lists, Accessing items, Slicing lists, Unpacking, Looping over lists, Adding items, Removing items, Finding items, Sorting lists, Custom sorting, Zip function, Unpacking operator

1.6        Tuples, Sets, and Dictionaries

Tuples, Swapping variables, Arrays, Sets, Dictionaries

1.7        Comprehensions

List comprehensions, Set comprehensions, Dictionary comprehensions, Generator expressions

1.8        Exceptions

Handling Exceptions, Raising exceptions, The with statement

1.9        Classes

Creating classes, Instance vs class attributes, Instance vs class methods, Magic methods, Private members, Properties, Inheritance, Multiple inheritance, Abstract base classes, Named tuples

 

 

2.    Spreadsheet

2.1        Drawing various types of charts (X-Y, column, line, pie,…) for data series

2.2        Inserting more than one line in one graph

2.3        Fitting data series into a first-order equation and then finding the equation for the best-fitted line

2.4        Calculating the slope and intercept of a line

2.5        Fitting a data series to exponential, logarithmic, and polynomial equations

2.6        Drawing the first and second derivatives of a line

2.7        Solving a polynomial equation using Excel

Software requirements: Open Office or Microsoft Excel

 

3.    Molecular shapes

3.1        Drawing molecular shapes and using them in Microsoft Office Word

3.2        Drawing an organic reaction and showing its mechanism

Software requirements: ChemDraw

4.     Ternary phase diagram

4.1        Triangular representation of a three-component phase diagram

Software requirements: CHEMIX

 

5.    Molecular Specification

5.1        Introduction to Cartesian coordinates and the Z-matrix of a molecule

5.2        Writing Cartesian coordinates and Z-matrix of a molecule

5.3        Introduction to protein structures and PDB files

Software requirements: Rasmol, GaussView, ChemCraft, PyMol

 

Course materials:

https://drive.google.com/drive/folders/19zW4YrseDl-g0yTM821aeBWudPqEoIXN?usp=sharing

 

Course Schedule

 

Department of Chemistry, Faculty of Science, University of Kurdistan

Mehdi Irani

Home

Publications

Teaching duties

Quantum Chemistry

Physical Chemistry I

Physical Chemistry II

Chemical Kinetics

Computer in Chemistry

General Chemistry I

General Chemistry II

Useful files

Methods

AMBER-Installation

AMBER-Setup

AMBER-PARM

AMBER-MD

AMBER-Analysis

AMBER-MM/PB(GB)SA

AMBER-FF

ARAZ

AutoDock Vina

DL_Poly

Gaussian

Linux

ORCA-General

ORCA-QM/MM

PackMol