Atomic Structure Teacher Guide


Atomic Structure
Grade Level
Activity Name(s)
Energy Levels
Molecular Geometry
Periodic Table
Probablity Clouds
Being Prepared
The activities in this unit use Molecular Workbench models, therefore having one student per computer is ideal.  If this is not possible, try to keep the number of students per computer as low as possible.  With this in mind, if students must use computers, it will be necessary to ensure that all group members are participating in the activity and discussions.

If you don't have computers in your classroom, remember to reserve the computer lab or mobile laptop cart.  

If using laptops that are not fully charged, arrange power cords in such a way that walkways remain clear.
Getting Started
These activities do not require probes or any other equipment beyond the computer.

Encourage students to pay close attention to the written instructions before attempting to interact with the model.  Clear instructions are always provided in the text preceding the simulation. Point out to students that they may delete snapshots and reset a simulation if necessary.
Suggested Timeline
Students should be able to complete each activity in approximately 20-30 minutes.  However, if they have no experience with using these activities, the first activity may take longer.
Thinking about the Discovery Questions

This unit consists of the following 4 activities. The "Discovery Question" (or "big picture" question) for each activity has been included.

Activity 1:  Energy Levels - How does the energy of the electron affect its orbital shape?
Activity 2:  Molecular Geometry - How do electrons affect the shape of a molecule?
Activity 3:  Periodic Table - How is the structure of an element related to its properties and its position on the periodic table?
Activity 4:  Probability Clouds - What is a recent model of the atom?

These activities investigate physical science concepts related to atomic structure.  The following are the overarching ideas that pertain to the activities in this unit: (1) Atoms are composed of protons, neutrons, and electrons. (2) Atoms are mostly empty space. (3) Electrons have energy.  (4) Opposite charges attract and like charges repel. (5) The construction of the periodic table is related to the structure of atoms.

Student Misconceptions: Students of all ages exhibit wide ranges of erroneous beliefs about the nature and behavior of particles. Almost all students have some difficulty comprehending the very small size of subatomic particles. Proven instructional methods include modeling and visualization of molecular structures and atomic-scale interactions. Each of the models in this lesson target these areas of documented difficulty. In addition, a pervasive misconception is that there is one correct model of the atom and that we can see all the atomic particles with a microscope. (In fact, we cannot currently "see" electrons traveling around an atomic nucleus. Atomic orbital models are based on probability and are classified as theory, not law.) Another widely-held misconception is that electrons orbit the nucleus like planets orbit the sun. Other incorrect beliefs include the notions that: 1) there must be "something" in the space between atoms -- the idea of empty space is difficult for many students to accept, even after instruction, and 2) Atoms are miniature versions of elements that we can see or touch. The four activities in this module serve to dispel all these misconceptions.
Learning Objectives

Students who demonstrate understanding can:

HS-PS1-1. Use the periodic table as a model to predict the relative properties of elements based on the patterns of electrons in the outermost energy level of atoms. [Clarification Statement: Examples of properties that could be predicted from patterns could include reactivity of metals, types of bonds formed, numbers of bonds formed, and reactions with oxygen.] [Assessment Boundary: Assessment is limited to main group elements. Assessment does not include quantitative understanding of ionization energy beyond relative trends.]

HS-PS1-3. Plan and conduct an investigation to gather evidence to compare the structure of substances at the bulk scale to infer the strength of electrical forces between particles. [Clarification Statement: Emphasis is on understanding the strengths of forces between particles, not on naming specific intermolecular forces (such as dipole-dipole). Examples of particles could include ions, atoms, molecules, and networked materials (such as graphite). Examples of bulk properties of substances could include the melting point and boiling point, vapor pressure, and surface tension.] [Assessment Boundary: Assessment does not include Raoult’s law calculations of vapor pressure.]

HS-PS1-8.Develop models to illustrate the changes in the composition of the nucleus of the atom and the energy released during the processes of fission, fusion, and radioactive decay. [Clarification Statement: Emphasis is on simple qualitative models, such as pictures or diagrams, and on the scale of energy released in nuclear processes relative to other kinds of transformations.] [Assessment Boundary: Assessment does not include quantitative calculation of energy released. Assessment is limited to alpha, beta, and gamma radioactive decays.]

HS-PS2-6. Communicate scientific and technical information about why the molecular-level structure is important in the functioning of designed materials.* [Clarification Statement: Emphasis is on the attractive and repulsive forces that determine the functioning of the material. Examples could include why electrically conductive materials are often made of metal, flexible but durable materials are made up of long chained molecules, and pharmaceuticals are designed to interact with specific receptors.] [Assessment Boundary: Assessment is limited to provided molecular structures of specific designed materials.]

Science and Engineering Practices:

Developing and Using Models
    * Develop a model based on evidence to illustrate the relationships between systems or between components of a system. (HS-PS1-8)
    * Use a model to predict the relationships between systems or between components of a system. (HS-PS1-1)

Planning and Carrying Out Investigations:
    * Plan and conduct an investigation individually and collaboratively to produce data to serve as the basis for evidence, and in the design: decide on types, how much, and accuracy of data needed to produce reliable measurements and consider limitations on the precision of the data (e.g., number of trials, cost, risk, time), and refine the design accordingly. (HS-PS1-3)

Obtaining, Evaluating, and Communicating Information:
    * Communicate scientific and technical information (e.g. about the process of development and the design and performance of a proposed process or system) in multiple formats (including orally, graphically, textually, and mathematically). (HS-PS2-6)

Disciplinary Core Ideas:

 PS1.A: Structure and Properties of Matter
    * Each atom has a charged substructure consisting of a nucleus, which is made of protons and neutrons, surrounded by electrons. (HS-PS1-1)
    * The periodic table orders elements horizontally by the number of protons in the atom’s nucleus and places those with similar chemical properties in columns. The repeating patterns of this table reflect patterns of outer electron states. (HS-PS1-1)
    * The structure and interactions of matter at the bulk scale are determined by electrical forces within and between atoms. (HS-PS1-3),(secondary to HS-PS2-6)

PS2.B: Types of Interactions
    * Attraction and repulsion between electric charges at the atomic scale explain the structure, properties, and transformations of matter, as well as the contact forces between material objects. (secondary to HS-PS1-1),(secondary to HS-PS1-3),(HS-PS2-6)

Crosscutting Concepts:

    * Different patterns may be observed at each of the scales at which a system is studied and can provide evidence for causality in explanations of phenomena. (HS-PS1-1),(HS-PS1-3)

Structure and Function
    * Investigating or designing new systems or structures requires a detailed examination of the properties of different materials, the structures of different components, and connections of components to reveal its function and/or solve a problem. (HS-PS2-6)

NSES Physical Science – Structure of Atoms
Matter is made of minute particles called atoms, and atoms are composed of even smaller components. These components have measurable properties, such as mass and electrical charge. Each atom has a positively charged nucleus surrounded by negatively charged electrons. The electric force between the nucleus and electrons holds the atoms together.

NSES Physical Science – Structures of Properties and Matter
The physical properties of compounds reflect the nature of the interactions among its molecules. These interactions are determined by the structure of the molecule, including the constituent atoms and the distances and angles between them.:
Discussion: Setting the Stage
There are many terms used in these activities that appear simple, but students often confuse them.  It may be important to go over these terms before you start.

1. Columns and rows - Review that columns are vertical and that rows are horizontal.  With that said, make certain that students understand vertical means up and down, and horizontal means sideways.

2. Subatomic - Your students may not be aware of the meaning of the prefix "sub". If that is the case, the term subatomic may not be very meaningful.  Thus, it may be helpful to discuss the meaning of "sub" (smaller or "less than") and how it applies to "subatomic" (the particles are smaller or "less than" the atom).

3. Composition of the atom - Sometimes students confuse the particles in the atom.  It is important that the students realize that atoms are made up of protons (found in the nucleus, have a positive charge), neutrons (found in the nucleus, have a neutral charge), and electrons (found in the electron cloud, have a negative charge).  

4. Density - Electron density is an important part of the activity Probability Clouds.  Thus students need an understanding of density (how closely spaced something is).

5. Orbital - This may be an unfortunate term to use in connection with atomic structure, but we're stuck with it. Students usually think an electron's path around the nucleus is the same type of orbit as a planet around its sun. "Orbit" and "orbital" sound similar, but they're quite different. An orbital is the region of space around the nucleus in which an electron lives. Atoms are governed by quantum mechanics and electrons don't follow the more orderly rules of orbiting planets. Heisenberg's Uncertainty Principle tells us (loosely) that you can't know the exact location of an electron or where it's going next. An atomic orbital is a mathematical function that describes the wave-like behavior of either one electron or a pair of electrons. Using the math, we can find the probability of finding any electron in any specific region (orbital) around the atom's nucleus. Initial Discussion What particles make up the structure of an atom? (Ans: protons, neutrons, electrons) Q - How is the atom organized? A - The protons and neutrons are found in the center of the atom called a nucleus. The area surrounding the nucleus is called the electron cloud. The electrons move in various pathways here called energy levels or electron shells. Please note: you may or may not want to provide and/or discuss the answers to these questions. You may simply want to use them to stimulate and guide the students' thoughts prior to beginning the unit.
Discussion: Formative Questions
Q - What are you being asked to consider when determining the probability of something occurring? 
A - you are being asked to determine the likelihood of something happening.

Q - How can orbitals overlap? 
A - It is important to remember that orbitals are simply pathways in space in which electrons can move.  Therefore electrons can use the same space, just not at the same time. A good way to help students understand this is to have them think about airplane pathways.  One airplane can fly from New York to LA.  Another can fly from Dallas to Minneapolis.  These two airplanes can use the same space, just not at the same time.
Discussion: Wrapping Up
Q - How is the structure of the periodic table related to the structure of the atom?  
A - Atoms are organized in order by atomic number which is the number of protons.  Atoms  of elements within the same period (horizontal row) have the same number of electron shells (regions where electrons move).  Atomic size is determined in part by the number of electron shells, and size can be predicted to some degree by location on the periodic table.
Additional Background
If additional background information is needed, the following sites may be helpful:

Energy Levels -

Molecular Geometry -

Periodic Table -

Probability Clouds - 
Activity: Energy Levels
Q - Do electron orbitals become bigger at higher energies, become smaller at higher energies, or do they stay about the same size regardless of energy?  
A - Electron orbitals become larger at higher energies. This can be visualized as students use the Data Collection I exercise to take snapshots of the different orbital levels. (See images directly above.)


Q - Which orbital is the one that would give the best estimate of the size of the boron’s atom? A - In general, the best size estimate can be obtained by the highest-energy level orbital in which an electron for a particular atom could reside. In the case of boron, the highest energy level is 2 (second energy level). This level in a boron atom contains 2 electrons in the 2s energy level and 1 electron in the 2p level. Q - Below you see part of a periodic table that shows the sizes of the atoms. Describe why it makes sense to start a new row with Li, and then another with Na. A - Lithium (Li) has added the 2s orbital. Thus it is larger than helium (He), and it makes sense that it belongs in the second row (period). Sodium (Na)has added the 3s orbital. Thus it is larger than neon (Ne), and it makes sense that it belongs in the third row (period). Activity - Molecular Geometry Q - The position of electrons around an atom is the result of what type of forces between the electrons and the nucleus? A - Opposite charges attract one another, so the positive protons in the nucleus and the negative electrons surrounding the nucleus attract each other. (On the other hand, like charges repel, so the negative electrons exert replusive forces on each other.)


Q - In your own words, describe an electron density.  
A - Electron density describes the location in the atom where an electron is most likely to be found. Teachers: Electron density is the measure of the probability of an electron being present at a specific location. The theory of quantum mechanics tells us that an electron's position can only be described statistically. Ask students to think again about the first activity with the dartboard and think of the probability of a dart hitting a certain spot. Electron density is a representation of the probability of finding an electron in a certain location in an atom. In the case of the tetrahedral shape above, there are four distinct regions of electron density. 


Q - Carbon dioxide (CO2) and water (H2O) both have two atoms attached to the central atom. Explain why carbon dioxide’s shape is linear, while water’s shape is bent.  
A - Carbon dioxide is a 3-atomed molecule with double bonding.  (In other words, the carbon and oxygen atom share 4 electrons which is called a double bond.) The large amount of negative charge in the double bonds creates a repulsive force which causes the molecule to straighten out.  Water is a 3-atomed molecule with single bonding.  In addition, the oxygen atom has 2 pairs of unshared (also called unbonded) electrons.  These electrons also exert a repulsive force.  Consequently, the atom is bent. (See image directly above.)

Activity - Periodic Table
Q - What general trends do you observe as you move across a period on the periodic table?  
A - As you move left to right across a period, the size of the atoms decreases.

Q - What general trends do you observe as you move down a family on the periodic table?  
A - As you move top to bottom down a family, the size of the atoms increases.
Q - Below you see part of a periodic table that shows the sizes of the elements. Describe why it makes sense to start a new row with Li, and then another with Na.  
A - Lithium (Li) has added the 2s orbital.  Thus it is larger than helium (He) which only has 1s. This it also makes sense that it belongs in the second row (period).  Sodium (Na)has added the 3s orbital.  Thus it is larger than neon (Ne), and it makes sense that it belongs in the third row (period).  

Activity - Probability Clouds
Collect Data I


Task: Using the atom builder, what atom did you make by adding a proton, neutron, and electron?
Answer: You get a helium-3 isotope. Students' snapshots should look like the one above.

Collect Data II: Probability Clouds


Task: Use the model to make a lithium atom in the fewest possible steps.
Answer: See image above -- click "Add Protons" twice to create the lithium-3 isotope. This is the fastest way, though not the most stable form of the lithium atom, which would have three neutrons as well.
Question: Which sub-atomic particle defines the kind of element an atom will be?
Answer: Proton

Collect Data III: Probability Clouds


Task: Make a carbon-12 atom in the fewest possible steps.
Answer: Since the default setting starts with a hydrogen-1 atom, you have one proton and one electron already present in the model. Click "Add Protons" 5 times to get Carbon, then click Add Neutrons 6 times. This gives us a carbon-12 isotope (see image above).

Analysis: Probability Clouds
Q - What is an orbital? Describe in detail. A - An orbital is an area of space around the nucleus where the electron is most likely to be found. Q - Explain why the color of the shading used to represent the orbital gets lighter as you move further from the nucleus. A - The shading changes and becomes lighter farther away from the nucleus because there is less likelihood of it being located there. Teachers: Atomic orbitals aren't really blue, to our knowledge. The color blue was chosen to represent regions where an electron could be found. Darker (more intense) blue represents the area of greatest probability density (where an electron is more likely to be found). Q - Explain how the atomic number and mass number of an atom are determined. A - The atomic number is the number of protons in the atom. (Note: since a neutral atom has equal numbers of protons and electrons, the atomic number is also the number of electrons.) The mass number of an atom is determined by adding the number of protons and the number of neutrons together.
Further Investigation
Energy Levels Activity
Task: Use the model to make carbon-12, carbon-13, and carbon-14 isotopes.


Q - What is different and what is the same between these carbon isotopes?
A - They differ in the number of neutrons in the nucleus. Carbon-12 and carbon-13 are stable isotopes, while carbon-14 is radioactive.

Molecular Geometry Activity: Further Investigation
Task: View 3-D models of two different fatty acid chains and determine the molecular geometry of highlighted regions.


Q - Identify which atoms have trigonal planar geometry, which have tetrahedral geometry, and which have trigonal pyramidal geometry.
A - Atoms 1, 2, and 3 are tetrahedral. Atoms 5 and 6 are trigonal planar (3 atoms surround a central atom in a flat plane).

The Periodic Table Activity
Task: Using the interactive SAM periodic table and the Electronegativity model, determine which element would be the most electronegative and why.


Background on Electronegativity
Electronegativity is a measure of the tendency of an atom to attract a bonding pair of electrons (Definition courtesy of Chemguide, authored by Jim Clark). If two atoms are equally electronegative, they are said to have zero electronegativity difference (see image on above left). This bond is described as a "pure" covalent bond -- where the electrons are shared evenly between the two atoms. If two atoms are slightly different in electronegativity, the result is a polar covalent bond (see image above middle). Most covalent bonds are polar (meaning one end will be slightly negative and one slightly positive). If two atoms have a large difference in electronegativity, this means one has "lost" control of its electron and the other has taken control over both electrons. This results in ion formation and produces an ionic bond (see image on right).


Q - Using your periodic table, which element would be the most electronegative and why?
A - Acceptable responses should note that the electronegativity increases as you go across a period from left to right and decreases as you go down a group. Teachers: Astute students may notice that fluorine is the most electronegative element. Electronegativity must always increase towards fluorine in the Periodic Table, which produces interesting diagonal lines as well.

Probability Clouds: Further Investigation


Task: Using the model, determine how the number of electrons, protons, and neutrons affect the overall charge of the atom.
Acceptable Responses: Students should note that the number of protons-to-electrons determines whether net charge will be positive or negative. If the number of protons and electrons are equal, there will be an overall charge of zero. If electrons > protons, overall charge will be negative. If electrons < protons, overall charge will be positive. (See images directly above).

Bonus Question
Q - Element 120 has been discovered. Describe where you think it would be located on the periodic table, and explain why you have chosen that location. A - A possible location would be in an 8th period and the 2nd family. Since it has 2 electrons more than the last element in Period 7, it is logical that it will go into an 8th period. Element 119 would logically go in the 1st family, so element 120 would be in the 2nd family.