ACE Camp

Computers in Chemistry

June 2001

Partially Funded by a CCLI grant from the

National Science Foundation, DUE-9850645

 

ACTIVITY ONE

Kinetic Theory of Gases - Computer Simulation

Molecular motion on the atomic level is often very difficult for us to comprehend, since textbook descriptions and illustrations simply do not provide an adequate picture of motion. Computer simulation of dynamics fills that gap by providing a direct picture of microscopic behavior. In this activity you will be using a powerful and sophisticated computer program called Boltzmann, that simulates the motional (dynamical) behavior of gases on the molecular level. You will learn about the kinetic theory of gases and Graham’s Law.

Start-up: Log in to your PC Network account. Launch the Boltzmann program by clicking on Start / Programs / Chemistry / Boltzmann Kinetic Theory Program. The simulator will come up with a collection of 40 molecules, depicted as red spheres, having a mass of 2.0 amu, corresponding to H2 molecules, at a temperature of 1500 K.

Lower the temperature of the system to near 300 Kelvin. (This is about room temperature.) Change the mass of the molecules to 4 amu, corresponding to Helium. Now click the START button to enact that change.

A. Behavior of the Molecules: Now, observe the motional behavior of the molecules, and think about their properties as you answer the following questions:

1. Are the gas molecule dimensions small compared to the space between them?

2. Are the molecules in continuous motion, or is the system tending toward a rest state?

3. Do the molecules travel in straight-line motion between collisions?

4. Are all the molecules traveling at the same speed, or are there a range of speeds evident?

5. Follow one molecule with your eye. To make this easier, simply click in the simulation space with the mouse, which drops a "blue" molecule into the simulation. Follow this molecule. Does the given molecule travel always at the same speed or does its speed vary?

 

6. In the box provided below, make a crude sketch of the path that one molecule makes over a short period of time, involving several collisions with other molecules or with the wall.

 

 

 

 

 

 

 

 

 

 

 

(The erratic motion of a single gas molecule is characteristic of the process called diffusion.)

C. Gas Effusion: The next exercise involves the effusion of gas molecules through a small orifice, which is described by Graham’s Law of effusion.

Effusion = escape of molecules through a small opening (a pinhole).

You will set up a simulation of a mixture of two gases of different mass both effusing through the same opening. You will observe which gas is faster in passing through the opening and filling the other side of the container.

Follow these directions exactly to Set-up: Cut down the number of molecules to 20. Adjust their mass to 4 amu for Helium. Click the DIVIDE button to divide the arena. Click the START button. Now all the red helium atoms should be on the left side of the divider. Change the mass to 28 for Nitrogen gas. Using the arrow cursor and mouse clicks, drop 20 blue Nitrogen molecules into the left side of the arena. Click the DIVIDE button again to open up the orifice (pinhole) and begin the Graham’s Law demonstration. Immediately record the start time given in the bottom left corner of the window. Observe the effusion of the two types of molecules through the orifice.

1. Occasionally hit the PAUSE button and count the number of Heliums and Nitrogens that occupy the Right side of the divider and the time in the table below:

2. Which type of gas is faster in populating the right side of the container, Helium or Nitrogen.

 

3. What difference between Helium and Nitrogen might account for why one is faster than the other?

 

 

 

 

 

 

ACTIVITY TWO

Computer Generated x-y Plotting

Using Graphical Analysis for Windows

Science and engineering students need to gain an appreciation for the various parts of an effective scientific graph. These parts include but are not limited to:

In modern practice most scientific graphing is done by a computer program. This activity describes the use of a standard graphics program called Graphic Analysis for Windows, by Vernier Software. While this is not the most powerful program for this purpose, it is simple to use and will effectively illustrate the power and simplicity of computer-generated plotting.

The graphing is typically done after acquiring data in the laboratory for whatever experiment. You will be doing an experiment tomorrow and plotting the data with this program. Today you will simply learn how to use the program with data from a coin-flip "experiment".

Simple Coin-Flip Experiment:

Flip a coin once, and see whether you have heads or tail.

Next, flip the coin twice and see how many times you get heads, and record the number below.

Flip the coin three times and see how many times you get heads, and record the number below.

Keep doing this until you have flipped the coin ten times.

EXPERIMENTAL COIN-FLIP DATA:

FLIPS

HEADS

1

2

3

4

5

6

7

8

9

10

Now, you are ready to plot this data, plotting the number of flips on the X-Axis, and the number of Heads on the Y-Axis.

1. Log into your PC Lab account, and launch the program by clicking on the START button in the lower left screen, then PROGRAMS, then CHEMISTRY, then Graphic Analysis for Windows.

2. In the upper left are two blank columns of data headed by X and Y. Enter the laboratory data into these columns, putting the independent variable data in the X column and dependent variable data in the Y column. As you do this you will observe the plot immediately being constructed in the window. (For example, if you are plotting Absorbance versus concentration, then Absorbance goes on the y-axis and concentration on the x-axis.)

3. Double-click on the X heading and (a) type in a more appropriate label for the x-axis in the New Name text field, (b) put in appropriate units in the Units text field. Do the same for the Y heading.

4. Click on the graph title in the plot window and key in a more appropriate title if necessary. Keep it brief. Include your initials at the end of the title for later identification of your hardcopy printout.

The power of computer graphing applications is that they do a number of things for you automatically, including

Sometimes these automated choices are not appropriate for your plot, and may be an actual drawback to using the computer.

5. First, consider whether the automatic choices for the range of the x and y axes is what you really want. In some cases, one realizes that the line should pass through or near x,y = (0,0), so it may be good to be able to have the limits set so that both axes start at 0. Many other cases do not require the zero points to be at the origin.

To be able to make your own choice of plot ranges, double click on an axis you wish to rescale, and choose "More X-Axis Options" or "More X-Axis Options". Then key in new top and/or bottom limits.

6. Now comes the question of whether the line connecting the data points is appropriate for this application. If not, in the Graph pull-down menu, turn Connecting Lines option OFF.

7. If you wish to draw a best-fit straight line through the data points, this can be accomplished by "dragging" across the region of the graph you want to fit and using the Analyze pull-down menu to choose Regression. A box appears on the graph showing the slope M of the best fit straight line and the value of the y-intercept B.

8. (OPTIONAL) FOR USE THURSDAY AFTER THE EXPERIMENT: Sometimes one uses this graph as a calibration plot to interpolate the value of some unknown. For example, in lab you measured the absorbance of the unknown solution. Read the concentration corresponding to that absorbance off your graph by turning on the Interpolate function in the Analyze pull-down menu, and moving the cursor along the best-fit line until you reach a Y-value equal to the absorbance of your unknown. The X-Y position of the cursor will appear below the box on the graph holding your regression data. With your cursor on the correct Y (absorbance), read off the X value (concentration) corresponding to this absorbance.

9. To generate a printout of your graph click on the Print tool button.

Some x-y graphing tips

ACTIVITY THREE

Visualizing Molecular Structure by Computer Graphics

In this PC Lab activity, you will have an initial taste of the power of advanced computational modeling tools in helping one to visualize the three-dimensional structure of molecules. You will look at several molecules using the software Chem3D, purchased from Cambridge Software by a National Science Foundation grant to the Chem Dept. In doing so, you will

 

  1. Launch Chem3D by clicking on START/Programs/Chemistry/Cambridge Software/Chem3D Pro.

  2. Familiarize yourself with the graphical interface of the program. First use the expand button in the upper right hand corner of windows to make use of the entire screen.

  3. Select the molecule you want to view. For today's activity, we will simply look at some sample molecules that easy to access. Pull down the File menu to Templates, and study the following molecule:

18CROWN6.C3T - this is a Space-Filling model of a crown ether, which is a specialized molecule which binds metal ions at its center. Here, a potassium ion K+ is bound at the center. Crown ethers can be modified to selectively bind to any ion one wishes.

4. In the tool bar on the right, choose the Rotation button and then use the mouse to rotate the molecular model on the screen and see it from all angles.

5. Molecular Motion: With your molecule on the screen, go to the MM2 pull down menu (stands for Molecular Mechanics version 2) and choose the Molecular Dynamics option. What you will see on the screen is a frame-by-frame picture of a movie of the typical motion of this molecule at room temperature. So you see that molecules are not rigid at all, but have flexibility. To stop the molecular motion, click on the solid button near the lower left of the Chem3D window.

6. When you are finished viewing this molecule, close the window on it and use File/Templates to call up a new molecule.

Repeat the above procedure with the following other molecules:

C60.C3T - this is a ball & stick model of the pure form of carbon called "buckminsterfullerene", or "buckyball" for short. It is much like a soccer ball, and contains only carbon atoms.

TAXOL.C3T - this is a wireframe model of the leading anti-cancer drug Taxol.

NACLXTAL.C3T - this is a small piece of crystalline NaCl, sodium chloride, using a space filling model.

ZEOLITE.C3T - this is a ball & stick model of a zeolite molecule, which is used to construct nanotubules.

 

 

 

 

7. If you want to put your own molecule in, you simply type the formula of the molecule you want to view into the text box near the upper left corner of the window just below the tool buttons. For example, to view ethanol (ethyl alcohol), type in CH3CH2OH and return. (Use all upper case.) If the formula is a molecule that Chem3D recognizes in its limited library, the model will appear on the screen with the correct 3D structure. Otherwise, you would need to draw it by hand on the screen by a special procedure not covered in this beginning tutorial.