Spring 2007 NanoExercise for UM-StL Chem 1121
(interstellar version)

Navigation bar: [intro] [task] [process] [vEM] [resources] [evaluation] [conclusion] [credits] "Go back" to return.

The prefix "nano" in the word nanoworld means a billionth (10^-9). When exploring the nanoworld, one deals with various structures of matter having dimensions of the order of a billionth of a meter. Although windows into the nanoworld have begun to open only a few decades ago, structures of nanometer dimensions have always existed on Earth. One of the major instruments used to examine matter at nanoscale dimensions is the electron microscope, which uses electrons instead of visible light to image samples. An extensive electron microscopy facility is located at UM-St. Louis in the Center for Molecular Electronics' Scanned Tip and Electron Image Lab. When you begin this exercise, you will see your specimen in the specimen mounting area of an actual atomic-resolution transmission electron microscope (TEM). You will explore this specimen, and look for and make measurements and observations on some nanoworld objects of interest to chemists, physicists, and biologists.

As a nano-detective for this exercise, your prime instrument will be a simulated or 'virtual' electron microscope (vEM). The objects of interest are located on the surface of a 3-mm silicon-specimen disc. Look around and you will find them! These empirical observation challenges will bridge the gap between your classroom and 'real world' experiences, and enhance the development of your critical observation and communication skills. Have you ever wondered how small atoms are and how much space there is between two adjacent atoms?

Use the vEM to zoom down for a closer look at what you can find on the 3-mm specimen. Please read the notes under 'process' and 'evaluation' before starting to work. You may save your work and return to it later. It is recommended that you place your work log, which is like your 'virtual lab notebook' in the 'comments' part of the Assignment. The rest of your work (introduction, method, data, interpretation, and uncertainties) should be entered into a Microsoft Word document and attached when you are ready to submit your assignment. Submission of your assignment will email it directly to me, but only do this when you are convinced that you are done. Handwritten reports will not be accepted.

There is not one rigid set of correct answers to this set of tasks, different students will find different things and end up with different answers within a reasonable range.

As a nano-detective, you will need to develop your own answers to the following questions:

• 1. What is the thickness at the outer edge of the specimen.
• 2. There are some blood platelets on the specimen. Characterize their dimensions and describe their shape.
• 3. There is a pollen grain on the specimen. Characterize its dimensions. What special features can you see in its shape?
• 4. There is a rod-like virus particle on the specimen. Identify it and measure its dimensions.
• 5. Identify the carbon nanotube, which appears sticking out of a larger carbon structure. What is the diameter of the nanotube? How long is the part of the nanotube shown? What do you see on the surface of the nanotube? Given that nanotubes can conduct electricity, what might you want to use it for?
• 6. Identify and describe the 'buckyball' or C₆₀ fullerene. Measure the radius of the buckyball. Figure 10.27 on page 412 of our text shows a structure of C₆₀ and also part of a nanotube.
• 7. Describe the surface of the buckyball, remembering that a carbon atom is present at each vertex. What can you say about the hexagons and pentagons that you see (aside from the fact that they are shown in different colors)?
• 8. What are some differences that you can see in the surface structure of the buckyball versus that of the nanotube?
• 9. Identify the small cluster that has a body centered cubic lattice structure. What color is being used to represent it? What are the dimensions of this unit cell?
• 10. Identify the small cluster that has a hexagonal closest packed lattice structure (see page 405 for a review of this structure). What color is being used to represent it? What is the spacing between planes of atoms here?
• 11. The grey-colored atoms below represent silicon atoms. If you like, you can read more about silicon starting on page 827 of our text. What can you say about the arrangement of silicon atoms in terms of their relation to their nearest neighbors? Can you estimate the distance between two silicon atoms?

The picture below should give you some ideas about the relative size of the specimen that you will be exploring. This is a typical "self-supporting" transmission electron microscope specimen. Specimens requiring support (e.g. nanoparticles) typically use a 3[mm] TEM grid instead.

The 3-mm diameter disc is located at the tip of the tweezer if you haven't noticed it. Now let's further examine the specimen by using the magnifying glass (use your mouse to grab its handle with a hand icon). The magnifying glass didn't help much, did it? For those with urgent curiosity, click on the specimen when it is visible under the magnifying glass. This will transport the specimen into a separately-windowed "virtual electron microscope" for further examinations, but more on that later. Now let's learn how the tiny specimen is made.

Specimen Preparation

Disk cutting and thinning

The specimen has to fit into the tight space of a magnetic lens polepiece, and be thin enough in regions of interest to let electrons to pass through (i.e. well under 1 micron thick). Normally an ultrasonic disk-cutter is used to cut a large sample into a flat disk of 3 millimeters in diameter. This disk is ground down with diamond powder to a uniform thickness of about 0.1 millimeters.

Dimpling

In this process, the disk is ground futher with a so-called dimpler which makes a slight hollow (dimple) in the center of the specimen. In this picture only the lower part of the dimpling wheel used for grinding is drawn. The disk is rotating all the time to make the dimple in the center uniform.

Ion-milling

The dimpled disk is put into a machine that is called an ion-mill. Two beams of argon ions (shown here in blue) are directed at the disk which is once again rotating. These beams slowly erode material from the top and bottom of the disk. The ion-milling is continued until a hole appears approximately in the center of the disk.

Begin Your Explorations

In order to begin your detective work, you need to learn how to use the virtual electron microscope. Don't be scared, the vEM is easy to operate. Just follow these simple rules:

• To rotate or spin the specimen, use the mouse to grab the specimen with left button of the mouse pressed and drag.
• To zoom in/out, drag the mouse vertically with the shift key pressed.
• To measure distances, you may
  • assume that the diameter of the disc is 3mm and extrapolate from there, or
  • use the vEM's "Estimate Field Width" button, keeping in mind that it may introduce uncertainty into your data unless you check it for accuracy, or
  • extrapolate from a known distance e.g. between atoms in a certain object, or
  • assume that grid squares marked on the specimen (below the first level of radial sectors) start at a micron across, and decrease in size by an order of magnitude for each level below that, or
  • improvise your own method(s) of measuring distances, evidence for which you might want to accumulate by capturing images from the screen* for off-line measurement and/or incorporation into reports.

Now you are fully equipped. Let the fun begin!

* Computers often let you capture screen images to a clipboard (here are some instructions if you are running Windows) for pasting into a graphics or word processing program.

Reporting Results: Show Your Discovery

You are to write a scientific diary and report about your adventures as a nano-detective. We recommend that your report consist of 6 sections:

1). Work Log: This is a simple diary of project activity with entries of the form "date-time/what happened".

2). Introduction: This section describes what you can find out about the challenge before actually doing the experiment. Here references to external sources are crucial.

3). Method: Describe here how you took data, with enough detail that another student in the course could repeat your experiment and get approximately the same results.

4). Data/Observations: This section reports the actual measurements that you made. These might be typed directly into the text, or simply summarized in the text and provided separately in spreadsheet or image attachments.

5). Interpretation/Theory: In this section, you make the connection between your observations and the objective of the nanoworld challenge. What conclusions are possible, based on your observations?

6). Assumptions/Uncertainties: Here is where you address the strength of your interpretation. What assumptions are involved, and how likely are they to be valid? If you have quantitative conclusions, provide evidence concerning the expected numerical error in those conclusions. This might also be a good place to mention possible future work.

Get to know microscopic objects that you may bump into on the virtual specimen:

• Pollen Color Stereo and animation
• Normal Red Blood Cell Geometry
• Tobacco mosaic virus
• Nanotechnology Gallery: Carbon Nanotubes
• Buckyball: a C₆₀ molecule

Additional resources:

• Powers of 10 - Measurements and Scales
• Markus Bader's screen ruler
• Quarks to Quasars - Powers of 10
• Virtual Scanning Electron Microscope
• How Big Are Things?
• Scaling the universe to your desktop
• Microscopy w/Jmol at UM-StL
• Powers of Ten and Space Time Explorers at UM-StL.

Your final grade for this WebQuest activity will be assessed using a 40-point rubic^* below that details what you will need to accomplish to earn points. Be sure to refer back to it often to help you know how you are doing as you progress in the project.

Understanding the microscopic world of atoms requires having a good sense of scale to compare the visual world to that of the tiny atom. Nature has proven to be a most skilled architect on this smallest size-scale of both biology's gene-driven, and technology's idea-driven, innovation. The size of atoms is one characteristic that is quite important for understanding their behavior. I hope that this activity has also let you hone your skills as a nano-detective, and provided a sense of the many levels of natural phenomena that separate us from the atoms that make us up.

This page is http://www.umsl.edu/~fraundor/nanowrld/live3Dmodels/chemapp.htm. Suggestions toward improvement, and correction, are invited. The page was put together with material and guidance from Keith Stine in Chemistry and BioChemistry at UM-StL, for an application in his classroom. The text page numbers refer to the course text by J. E. McMurry and R. C. Fay, Chemistry, 4th Edition, Prentice-Hall, Inc. (2004). The person responsible for errors is P. Fraundorf. Two acknowledgements are particularly important. Former grad student Noom Pongkrapan adapted the ideas used here into webQuest format, added less intimidating prose, put together the specimen prep figures, and developed the Macromedia Flash "magnifying glass" illustration. Martin Kraus provided the Live3D applet, and helped adapt it to this application with significant modifications. This site is hosted by the Department of Physics and Astronomy (and Center for Molecular Electronics) at UM-StLouis. Mindquilts site page requests est. around 2000/day hence more than 500,000/year. Page requests to a stat-counter linked subset of pages since 4/7/2005: .