Welcome to the CAChe Molecular Modeling Tutorials

Department of Chemistry

University of Pittsburgh at Johnstown

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Modeling Exercise # 3

Exploring the properties of water at different levels of theory

In the exercises completed thus far, you have become familiar with the CAChe interface built a molecule of water and optimized the geometry, explored various visualization tools and measured some bond parameters (length and angle).

In this exercise we will explore several different computation methods.  When you set up the experiment to optimize the geometry of water in Exercise # 2, you probably noticed that there are many options.  What do these different options do?  What are the differences? Which one is "best"?

The different options are based on different mathematical models.  They serve various purposes. Some calculations take place in a snap while others take  hours, days, weeks .... To learn about the difference methods, read this overview of the different computational methods.

In this exercise you will optimize the geometry of a water molecule using Molecular Mechanics (MM3), two semi empirical methods (AM1 & PM3) and density functional theory, an ab initio method (DFT - B88LYP).  You'll measure the bond length and bond angle and compute the heat of formation. Then you will compare the computed results with the computed experimental values from the literature.

This exercise assumes that you are familiar with the CAChe workspace.  If you need a review check the following tutorial modules listed below.  Each module opens in a separate window.  When you have finished , close the window and return to this site.

bullet Starting CAChe
bullet Using the User Interface
bulletOr click here to use the Flash Tutorial for the User Interface
bullet Building small molecules
bullet Viewing and manipulating structures
bulletOptimizing the geometry
bulletTo check out the Flash Tutorial for the User Interface Click Here.

There is a student worksheet for this exercise -- a MSWord document.  Download it here.  You can fill it in using Word or print it and fill in the blanks with pen or pencil.

The exercise has 6 tasks.  Follow the links below. At the end of the first task you will find a link that leads you to the next one.  Start with Task 1. The link at the end of the last task will bring you back here.

bulletTask 1: Build Water & save multiple files
bulletTask 2: Optimize the geometry using mechanics
bulletTask 3: Optimize and compute the heat of formation of water using MOPAC (AM1 & PM3)
bulletTask 4: Optimize and compute the heat of formation of water using DFT-B88LYP
bulletTask 5: Compare the computed and experimental values
bulletTask 6: Measure the bond lengths and angle in water

Total Time: 20 to 30 minutes

Due Date: The assignment is due the week of November 1, 2004

Final Report: Complete a brief handout.