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Weird Science – Atomic Models – Page 1

Modeling the Atomic Model

Bake a Model Kit – Part 1

Atoms

What is an atom? Imagine that you have a lump of a pure substance. Imagine cutting the lump into
smaller and smaller pieces, and testing to see if you still have the same substance after you have cut it
each time. Eventually, the pieces will be so small, that if you cut them again, you will break the
substance apart into pieces that are no longer the same substance.

If these new and different substances are electrons and protons, then the substance you started with was
a pure chemical element, and the smallest unit of the substance is an atom. If you cut apart an atom,
you will need to break it apart into electrons and protons (oh, and neutrons too).

But you might also get to a point where you cut the pure substance apart into different atoms. If so,
then the pure substance you started with was a chemical compound, and the smallest unit of the
substance is then a molecule rather than an atom. Cutting the molecule apart then breaks apart the
compound and changes it into other substances.

Atomic Structure

What do atoms “look like”? What is their “physical form” or “shape”? When we ask this, we are
asking about the structure of the atom. The current model (shown in Figure 1) is that an atom consists
of a small, positively charged nucleus, surrounded by a “cloud” of electrons.

Figure 1. Diagram of a helium atom, showing the electron cloud density as shades of gray.
(Source: http://en.wikipedia.org/wiki/Atomic_radius)

As you can see in Figure 1: most of the space occupied by an atom is the space occupied by its electron
cloud. Note too that it is rather hard to think of something as “fluffy” as the electron cloud as having a
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definite edge. However it should be clear that the nucleus is only a tiny part of the whole atomic
volume – notice that the nuclear radius scale marker is about one 100000th of the electron cloud radius
scale marker. Thus, the atomic shape is dominated by the shape of the electron cloud.

An element is defined by the number of protons in its nucleus – often denoted Z and called the atomic
number. In the pure element, each atom is electrically neutral and also contains a number of electrons
equal to the number of protons.

What is the shape of the electron cloud?

We know that the electrons in atoms and molecules have “quantized energies” – that is, each electron
has only certain allowed energy levels. Another way of saying this is that electrons are moving in
defined spatial orbitals. Yet another way of looking at it – a way that I much prefer – is to say that
electrons have well-defined shapes and can only change from one of these shapes to another one,
without assuming any intermediate shapes – rather like a digital clock, that can show only minutes, that
changes suddenly from one minute to the next and then stays that way until it it time to change again.
Moreover, these shape changes are caused by or result in energy exchanges between the atom and its
surroundings – sometimes in the form of absorption or emission of light.

Each of these allowed energies or orbitals has a certain shape. The orbitals tell us where the electron
can actually be in space, and where the electron cannot be. Electrons can only interact with each other
when their orbitals can actually make physical contact with each other, because the electrons cannot
interact in regions of space where they are not allowed to be, and their orbital shape determines where
that is.

Thus, if we first simply look at the shapes of the orbitals or electrons in atoms that are not interacting
with other atoms, we can get a sense of how the electrons in these orbitals will be able to interact with
other electrons on other atoms.

Of particular interest to us today is the following table, Table 1:


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According to the table, and the way most chemists think, there are really four important orbital shapes:
the s, p, d and f shapes, with the s orbitals having the simplest and the f orbitals having the most
complex shapes.

Figure 2 – The shapes of the s and p atomic orbitals (as conventionally represented).

S orbitals (Fig 2) – These are spherical orbitals. An electron in a spherical orbital will interact the same
way with any other object regardless of the direction that other object is located.

P orbitals (Fig 2) – These are dumb-bell shaped orbitals, that lie along a line. Since you can draw 3
perpendicular lines through an atom's nucleus, you can have 3 different dumb-bell orbital directions.
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We may as well consider these to be the x, y and z directions. We therefore have what are often called
the px, py and pz orbitals. An electron in a px orbital will interact far more strongly with objects that
are located along its x axis than in any other direction; py will interact along y, and pz will interact
along z.

Figure 3 – The shapes of the five d atomic orbitals (as conventionally represented).

D orbitals (Fig 3) – These are clover-leaf shaped orbitals with 4 lobes, that lie in a plane. There are five
of these orbitals. Conventionally, three of these lie along the axes in the xy, xz and yz atomic planes
(using the same sets of axes as we defined for the p orbitals); there are three of these obitals because
there are three mutually perpendicular planes in 3d space. The remaining two orbitals have their lobes
projecting between the axes. In principle, there should also be three ways of doing this, but for some
annoyingly nasty mathematical reasons, we only end up with two.

F orbitals – These are sort of double cloverleaf shapes. The only elements that actually use these
orbitals for chemistry are radioactive ones. One characteristic of these elements is that they have
incredibly gorgeous colors (think of the old radioactive Fiestaware of the 1950s). However, we won't
talk or deal much with F orbitals.

The s, p and d orbitals are the ones that most chemists deal with.

When an electron is in an orbital, the electron cloud is shaped like the orbital shape. In the original
“planetary model” of the atom, electrons were thought to circle the nucleus much as the planets circle
the sun. Thus the electron would still be a hard little object circling the nucleus. But these orbitals are
clearly not simple circles. And if the electron is moving in them, then it is moving so fast that it is
spread out over the entire orbital, much like the spokes of a bicycle wheel “disappear” when the bike is
moving, and the wheel then appears to be a flat disk rather than a circle with spokes inside. Therefore,
we might as well think of the orbitals as the “shape” of the electron cloud.

Why are there pink and blue regions on the orbitals? Well actually the orbitals represent actual
mathematical functions. These functions have regions in which they are “positive” and regions in
which they are “negative” – and the two colors distinguish between those regions, with pink being
regions in which the functions are positive, and blue being regions in which the functions are negative.
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Experimental Exercise – work with a partner

A) Make Modeling Clay

Combine 250 mL of flour, and 125 mL of salt in a plastic bag. Knead and shake the bag to mix the salt
and flour together homogeneously. Then add no more than 10 mL of cooking oil and gradually add
about 125 mL of water. As you add the water, knead the ingredients in the plastic bag to make a
smooth, firm clay. Add small increments of flour or water to make a stiffer/softer clay, respectively and
knead again, until the clay is as you like it to be.

How do you like it to be, though? It needs to be stiff enough that when you roll it into a ball, and set
the ball to dry, the ball won't flatten perceptibly on the side you set it on.

• Make 9 small (pea sized) perfectly smooth and round spherical clay balls and place them onto a
piece of aluminum foil and then in the EAST* drying oven and note the time. (You will need 9
of these, so you may wish to make some extras in case you need them).

• Divide your dough into halves, and place in separate bags, reserving half for another day.

B) Make black toothpicks. Get something like 60 toothpicks, and paint them black, and then allow
them to dry.

C) Make orbital lobes. Now work with one half of your clay.
• Divide this half into halves, and add magenta tint to one half, and cyan tint to the other – or
choose two colors of your liking to represent positive and negative areas. Knead well after
addition of the tints to distribute the color evenly, and keep the clay you make in separate bags.
• Figure out how many balls of clay of each color you will need to make the pink and blue parts
of the orbitals (which are called “lobes”) in figures 2 and 3. Then pinch off pieces of clay and
make the lobes You should pinch off bits of clay that are no more than 1.5 cm in diameter when
rolled into balls. Place any leftover clay with the portion you reserved. If you don't have
enough clay, then you are making the pieces too big, and recombine them, knead a bit, and
make smaller balls.
• Shape the balls into orbitals: all but the s orbital will be rather egg-shaped.
• Work on the p orbitals. Skewer each lobe of the orbital with black toothpick, so that roughly 1
cm of the toothpick protrudes from the “pointier end” of the lobe, and the rest protrudes from
the “rounder end” of the lobe. The part protruding from the rounder end should be about twice
as long as the part protruding from the pointier end. You should end up with 3 positive
skewered lobes, and 3 negative skewered lobes. Place these on tinfoil in the WEST* drying
oven and note the time.
• Work on the d orbitals. For the 12 lobes that will be for the dxy, dxz and dyz orbitals, break a
black toothpick into equal halves and insert a half tootpick into the pointy end of each lobe, so
that each one sort of looks like a lollypop (don't change the shape of the lobe though). For the
dx2-y2 orbital, you will simply need to make two skewered positive and two skewered negative
lobes, like the p orbital lobes. For the dz2 orbital, you will need to make two positively colored
skewered lobes, like the p orbital lobes, and an appropriately sized donut of negatively colored
dough. Place 7 objects on tinfoil in the WEST* drying oven, noting the time.
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*I am controlling the drying ovens, so that there will be a period of time when the ovens will not be
opening and closing as people put things in and take them out, during which the parts can dry
undisturbed.

D) Assemble your models. Once at least an hour has passed since you put the pea-sized clay balls in
the EAST oven, you may remove them from the oven. They should be crusty on the outside and still a
bit soft on the inside, but not gooey or easily squeezable.
• While the clay balls cool, light a candle. As you do this, you might pray for world peace.
Otherwise, wait for the melted wax to accumulate and the clay balls to cool completely.
• Guess what the pea-sized clay balls are! THEY ARE THE ATOMIC NUCLEI!!!! Though
these guys don't appear in Figures 2 and 3, we are going to have them in order models, because
we need something in the center to hold everything together. And the cool thing is that this is
exactly what the nucleus does anyhow: it holds the electron cloud together!!
• Make the s orbital in Figure 2:
◦ Take a nucleus, and place it at the center of a cartesian coordinate system:
▪ You will need 6 toothpicks to be the +x, -x, +y, -y, +z and -z axes of your coordinate
system. At some point you will place bits of tape at the tips of these axes and label them
thusly.
▪ Use one of the black tootpicks to poke a hole in the nucleus. Dip the end of the
toothpick into candle wax so that there is a small blob of wax on the end and quickly
insert the wax into the hole you made before the wax solidifies. If you do this correctly,
then the axis will be securely affixed to the nucleus once the wax has solidified.
▪ If insecure, you may take another toothpick, and use it to transfer small blobs of candle
wax to the entry hole of the wobbly toothpick, while it is still in the hole, and tamp it
snugly around the black toothpick until it is sturdy.
▪ Label the axes with pieces of tape at all six tips
▪ When you are finished, you will have the nucleus sitting nicely at the center of a lovely
cartesian coordinate system.
◦ Break off a blob of pink (or positively colored) clay that will be roughly twice as big as your
nucleus, and squoosh it around the nucleus until it is a nice smooth sphere! Voila! You
have made your first orbital!
• Make the p orbitals in Figure 2.
◦ Remove your p orbitals from the oven and allow them to cool completely.
◦ For each of the 3 p orbitals
▪ Take a nucleus and place it at the center of a cartesian coordinate system.
• This time you only need 4 black toothpicks, because you already have two axes
made that have your orbital lobes skewered on them
• Affix the 4 non-lobed axes as before, securing with candle wax
• Then affix the two lobed axes the same way
• Label the axes with pieces of tape at all six tips
• Make the five d orbitals in Figure 3 – by now you know what to do, though attaching the donut
will take a bit of thought and ingenuity!

E) Admire your work! You should have a nice set of 9 orbitals that are 3 dimensional versions of
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Figures 2 and 3.

BUT WAIT!!! If you followed these instructions exactly, then you also ought to have one baked pink
sphere leftover! What should you do with it?

Well...

F) Here is the most important part of this model building exercise. Carry it out when your models
are done

THE LEFTOVER PINK SPHERE (or one that you should hastily make right now) IS A HYDROGEN
ATOM!!!! It will now become the protagonist of our story.

Our hydrogen atom is moving through space. It is moving in a straight line, along one of the cartesian
axes (+x, -x, +y, -y, +z, -z) at a constant speed*. Suddenly, something is in its path: why, it is one of
the orbital models you made! We imagine that in each case there is a single electron located in the
orbital, and that if conditions are right, the H atom will form a bond with it.

What is the hydrogen atom going to do?


• If it sees a positive lobe (pink or the positive color) skewered on the axis that it is moving along,
it will like what it sees and it will form a strong bond (++).
• If it sees a negative lobe p lobe skewered on that axis, it will hate what it sees and run away if it
can (--).
• It will not see the p orbital lobes that are oriented along the axes perpendicular to its axis of
motion (0).
• The dz2 and dx2-y2 orbitals are fairly straightforward, since their lobes lie along the axes. If
our hydrogen atom sees a pink lobe along the axis it is traveling, it will form a strong
interaction (++), and be repelled by a blue lobe or donut (- -).
• The other 3 d orbitals are harder to imagine. Moving along the cartesian axes, our hydrogen
atom will interact with the orbital that is perpendicular to its axis of travel differently (and much
more weakly) than it sees the other two orbitals, which are both in planes that contain its axis of
travel. We will say that the hydrogen atom will not even see the orbital that is perpendicular to
its axis of travel (0). As the hydrogen atom passes closely to the other two axes, it will be
simultaneously attracted by the pink lobe, and repelled by the blue one. We will denote this
interaction (+-).

For each of your models, hold the model up, and move the hydrogen atom toward the model along the
six coordinate directions, and really visualize 3 dimensionally what the hydrogen atom will see and
how it will behave.

Make a table in your lab book, in which you record what the hydrogen atom will do, depending upon
how it approaches an orbital. Place the appropriate symbol (++,--,0,+,- or +-) in the table. Your table
will look something like this:

Orbital/Direc +x -x +y -y +z -z
tion
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s
px
py
pz
dxy
dyz
dxz
dx2-y2
dz2

G) Summarizing Questions and Conclusions: based on the pattern you can see in the table
• Which atomic orbitals are the most and least picky about the direction of approach of the
hydrogen atom?
• How might this "pickyness" be reflected in an atom's ability to react with hydrogen?

H) Take-home lesson. We are saying that electrons have the shapes of the orbitals that they are in. We
have seen that the hydrogen atom (or, indeed, any atom) may or may not “react” with an electron in an
orbital based on the shape the electron is when it is in that orbital. Generalize this idea to the
consideration of how the reactivity of electrons depends upon which atomic orbital the electron is in.

*This is Newton's Law: an object will remain in a state of uniform motion or at rest unless it is acted
upon by a force.

4) But what orbitals are electrons actually IN?

For this, we need something called The Aufbau Principle, which tells us that we can say what orbitals
the electrons in an atom of a particular atom will be in by
• placing electrons in s, p, d & f orbitals, following an order that has been determined
experimentally;
• placing no more than two electrons in an orbital (this is called The Pauli Principle).

If an electron has a choice of pairing up with an electron in a p or a d orbital, or going into an empty p
or d orbital, it will do the latter (this is called Hund's Rule). Thus,
• Each s orbital can take up to 2 electrons.
• Each p orbital can take up to 2 electrons, and since there are 3 p orbitals (px, py and pz), the p
“subshell” can hold up to 6 electrons. But once an electron is in one of the p orbitals (say, it is
in px), a second electron will go into py or pz. When you need to put a 4th electron into the p
orbitals, it will begin to double up.
• Each d orbital can take up to 2 electrons, and since there are 5 d orbitals, the d “subshell” can
hold up to 10 electrons, and will not double up until you are adding 6 or more electrons.
• The f subshell can hold up to 14 electrons, since there are 7 f orbitals, but again we won't look
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at f orbitals in detail.

The lowest few atomic energy levels are as follows:

(lowest energy) 1s 2s 2p 3s 3p 4s 3d 4p 5s 4d 5p 6s … (highest energy)

Now we are in a position to say what orbitals electrons will be in for each atom up through element 56!

Let us look at the first 5 elements.

• Hydrogen has 1 electron. It is in the 1s orbital. This is denoted 1s1.


• Helium has 2 electrons. They are both in the 1s orbital. This is denoted 1s2
• Lithium has 3 electrons. Two of them are in the 1s orbital. The third one is in the 2s orbital.
This is denoted 1s2.2s1
• Beryllium has 4 electrons. Two of them are in the 1s orbital, the other two are in the 2s orbital.
This is denoted 1s2.2s2
• Boron has 5 electrons. Two of them are in the 1s orbital, two are in the 2s orbital, and 1 is in
one of the 2 p orbitals. This is denoted 1s2.2s2.2p1

Those notations are called “spectroscopic notation” and they simply tell us which orbitals electrons are
in according to the Aufbau Principle. The specification of the location of electrons within the atomic
energy levels is called electron configuration.

Assignment for this section

A) Write down the electron configurations (in spectroscopic notation) for the first 8 elements – i.e.
for the elements in the first two rows of the periodic table.

B) Use your orbital models to visualize complete atomic structural models – that is, what each total
electron cloud looks like for all 8 of these elements.
By total electron cloud, I mean the electron clouds of all of the electrons surrounding the
nucleus in a particular atom, based on its electron configuration. Once you have the electron
configuration, imagine that all of the electron clouds of the electrons are all coexisting on top of each
other – thus, for example, in Helium, we have two electrons in 1s orbitals, so we get two 1 s orbitals
added together right on top of each other. We can think of this as being an electron cloud that is twice
as dense as that of the hydrogen atom, like this:
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Figure 4 – Two s electrons in same 1s orbital, so density is doubled

For lithium, we have two electrons in 1s orbitals, and 1 electron in a 2s orbital. The orbitals get bigger
and they go up in energy. Thus, the 2s orbital will be bigger than the 1s orbital. We will get something
that looks like this for lithium:

Figure 5 – Lithium has essentially a helium atom, surrounded by an electron in a 2s orbital

Make drawings of the total electron clouds of the rest of the atoms in the second row of the periodic
table, keeping in mind that where pink and green areas overlap, they cancel each other out! Rather than
being more pink, you'd have areas that were less pink and perhaps even empty. Spend some time
visualizing this, with your partner, and make drawings that show what you think the complete electron
cloud will look like, for each of the elements in the second row of the periodic table.

C) Put it all together: looking at your complete electron cloud drawings, consider again what a
hydrogen atom would experience as it approached each of the atoms in the second row of the periodic
table along the three cartesian axes.
• Which atoms would be "picky" about the angle of approach, and which ones would not be?
• Which atoms would therefore be more constrained in their ability to react with hydrogen based
on which direction it was coming from?