3.091 VirtualLab

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Thermally activated processes

Lessons and Applets for 3.091

Site Content

This set of lessons and applets is aimed at students in 3.091 Introduction to Solid State Chemistry. As each concept is introduced, an applet, accompanied by a series of exercises involving the applet, will be provided to aid the students' understanding of the concepts. Through the lessons and applets, students will become familiar with the following concepts:

  • states
  • the reaction coordinate
  • energies of states
  • state populations at equilibrium
  • energy barriers between states
  • thermally activated processes

Site Layout

This curriculum consists of 4 lessons, which are found below. For each lesson, there is a brief introduction to the important concepts addressed in the lesson, followed by a link to the applet and accompanying exercises. The link will open a new browser window or a new tab within your browser. The top half of the new window displays the applet and the bottom half of the window displays an explanation of and exercises pertaining to the applet. If you need to see more of the bottom frame, you may drag the frame divider upward with your mouse or you may put your browser into full-screen mode (press F11 or click View -> Full Screen in Firefox or Internet Explorer). If you want to restore the applet to its initial state, simply reload the page. To move on to the next lesson, please close the window or tab containing the lesson you just completed. Then, scroll down to the next lesson on this page. If you leave previous lessons open when you start new ones, the new lessons may run slowly.

Software Compatibility

The virtual labs require that you have installed Java SE 5 or higher. If you are having difficulties viewing the applets, you can determine whether you have a compatible version of the Java Runtime Environment installed on your computer at the Java Tester site . If you need to download, you can find the latest version at Java SE Downloads. Please select Java SE Runtime Environment (JRE) from the list of downloads.

Attention Firefox 3.6 users. If you are having difficulty running the applets using Firefox 3.6, please install Java version 6 update 10 or later & try again.


  • Before taking the virtual labs, please take a PRETEST at http://feraonline.com/VLPretest-2009.
  • After completing all the virtual labs, please take the POST-TEST
  • After completing all the virtual labs and the post-test, please take a BRIEF SURVEY in order to give us feedback on your experience using these materials.

The links to the post-test and brief survey are at the bottom of the page, after the lessons.

Thank you and we appreciate your participation.


Lesson 1


The goal of this activity is to provide insight into the ways modern science views the effects of temperature on chemical reactions, particularly thermally activated processes. Schematic energy diagrams of the type shown below have tremendous power as tools for thinking about chemical reactions at the molecular level.

The diagram shows the energy associated with possible states of a thermally activated process,labeled state 1 and state 2. The y-axis represents the amount of energy. From the diagram, we can infer that state 2 is a stable state because it corresponds to the lowest energy configuration. State 1 is metastable because, although it has higher energy than state 2, the system must overcome an activation barrier (represented by the hill between the states) to transition from state 1 to state 2. In many cases, the barrier is so high that the metastable state can exist for a very long time. For instance, diamond is a higher-energy form of carbon than graphite and so is, in principle, a metastable form of carbon. However, the barrier between the diamond and graphite form of carbon is so high that you are not in any danger of having your diamond necklace spontaneously convert into graphite. For chemical processes with lower barriers, transitions from metastable to stable states do occur and diagrams of the type above are the primary means through which scientists understand such processes. We will begin by exploring the meanings of various features of the above diagram and how it is used to think about chemical processes.

The reaction coordinate

The first feature we will explore is the meaning of the x-axis in the above figure, which is known as the reaction coordinate Q. For a system to get from state 1 to state 2 it must follow some pathway. In most cases, we don’t have detailed information on the precise nature of this pathway, but it is nevertheless useful to imagine motion along a single dimension and consider the potential energy of the system as it moves along this path. The potential energy along the reaction coordinate is called the “energy landscape”.

One example for which the pathway is easy to envision is the cis-trans isomerization shown below. In this case, Q is the dihedral angle about the double bond. The transition state occurs when the dihedral angle is about 90o. We can consider all angles <90o to correspond to the cis isomer (state 1) and all angles >90o to correspond to the trans isomer (state 2).

Our simulations will use a much simpler system, but one that retains the essentials of a thermally activated process. The system is that of the rectangular box demonstrated in lecture.

View Virtual Lab 1

Lesson 2

The energy landscape

What factors determine the curve of the energy landscape? In this activity, we explore the factors that establish this curve.

View Virtual Lab 2

Lesson 3

The effects of a heat bath: Motion at constant temperature

In the above simulations, you determined the strength of kick needed to change the state of the box (either knock the box over or stand it up). Molecules are always being kicked by their surroundings, and the strength of these kicks is related to the temperature of the system. For molecules in solution, the kicks come from the surrounding solvent molecules. However, the details of the surroundings are not essential to making predictions of how the system will behave. In fact, we can just view the surroundings as a "heat bath" that exchanges kinetic energy (heat) with the system through random kicks.

For our box, a good analogy of a heat bath is to consider placing the box on a shaking platform. The platform kicks the box randomly, with the strength of the kicks being set by the temperature of the heat bath. However, instead of boxes, let's now consider placing balls on the platform.

View Virtual Lab 3

Lesson 4

Thermally activated processes

The previous activity considered the number of particles that can reach a certain activation energy. In this activity, we explore how the number of particles that can reach a certain energy affects the rate of thermally activated processes. In the simulation, we will mimic the energy landscape with three platforms that represent the metastable, activated and stable states as shown below.

View Virtual Lab 4


  • After completing the pretest and virtual labs, please take a POST-TEST at http://feraonline.com/VLPosttest2009.
  • Clicking the DONE button at the end of the post-test will take you to a BRIEF SURVEY requesting feedback. Your identifying information will not be associated with this final survey.
  • If you have completed the pretest, all the virtual labs, and the post-test, but did not follow the link to the BRIEF SURVEY at the end of the post-test, please complete the BRIEF SURVEY at http://feraonline.com/VLFeedbacksurvey2009 to give us feedback on the Virtual Labs. Your answers to this survey are confidential and you will not be identified.

Your input is important to us because it will help us to improve these materials, which will enhance the learning experience of subsequent students. In order for us to use your input, however, it is important that you complete both tests and the survey mentioned above. Your responses will not be registered if you haven't completed all of them.

Thank you and we appreciate your participation.

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