Computer in Chemistry, BSc course

The Computer in Chemistry course introduces essential computational tools and techniques for BSc Chemistry students, focusing on data analysis, reporting, and molecular modeling. Students will gain practical experience with software and programming relevant to interpreting laboratory data and presenting scientific findings. The course begins with foundational Python programming, then progresses to spreadsheet applications, molecular drawing, ternary phase diagrams, and molecular structure specifications.

This course is designed to build computational proficiency with chemistry-relevant tools, empowering students to apply computational methods effectively in their academic and research pursuits.

 

Course Structure

1.    Python Programming

This section introduces the Python programming language, providing a foundation in basic programming concepts with a focus on applications relevant to chemistry.

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

Students will learn to utilize spreadsheet tools for data analysis and presentation, essential for interpreting laboratory results.

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 the Excel solver

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

Access course resources via Google Drive.  

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