On-Line Study Guide - OLSG
Chemistry 111

Chapter 2: Atom and Atomic Structure


Chemistry is the science of matter, energy, and their interrelationships. All humans must have speculated as to the nature of matter and what constitutes it. Take for example a small copper wire. How could you show what makes it up? Several ideas can be suggested. The copper wire could be melted but you still have copper when you are done. This is an example of a physical change. You are very familiar with physical changes associated with converting water from solid to liquid to gas and back again.


You could combine it with something like water or air. It turns out copper is pretty stable in water (think of all the copper pipes we have in our houses). Copper can react with other substances to produce new substances whose properties don't resemble that of a copper wire. Such alterations are examples of chemical changes. Neither of these has led easily in a direction that would answer our question - of what is copper made? One last possibly would be to break the wire in half, then break the half in half, and continue that in our mind past the point we could actually see the copper fragments that result. At that point we keep cutting with imaginary microscopic scissors. The question is know: how many cuts can we make. Is there a point when we can't cut the copper particle in half and still have copper? Or can even the tiniest particle of copper be cut infinitely and still result in copper particles (much like a number line between the numbers 1 and 2 can be divided an infinite number of time. This question puzzled the ancient Greeks as well. Was matter continuous and hence cut be "cut" an infinite number of times, or is it discrete. Democritus (450 BC) believed that matter consisted of tiny small and indivisible particles called "atoms".


Answer to the thought experiment.

His ideas where not derived from experimentation, but rather by intuition and philosophical thought. It turns out he was almost right. Contemporaries expanded on this concept and believed that the world consisted of 4 elements, earth, water, air, and fire. We now recognize that matter is made of atoms. It turns out their are 92 different types of atoms that occur naturally in our world. Each differs from the others in their properties (such as size, reactivity, etc.). However, we now know that atoms are divisible, and consist of a nucleus with positively charged protons, neutral neutrons, and negatively charged electrons moving around the nucleus. The 92 naturally-occurng atoms differ from each other in the number of protons and electrons they have. The atomic number on the periodic table gives the number of protons and electrons in the neutral atoms of these elements.

Now consider the same experiment only with solid water. Melting or reacting the water chemically confuses our understanding at this point. If, however, we do the same thought experiment and cut a cube of ice in two and continue as above, we reach a point that we have two particles of water which can not be cut again and still be water. Do we have atoms of water remain? A quick view of the periodic table shows that there are not elements called water. From your high school study of chemistry, you remember that water is symbolized as H2O. The smallest particle of water consists of 2 atoms of the element H attached through chemical bonds to an atom of the element oxygen. The resulting particle is called a molecule - 2 or mores atoms bonded to each other to from a stable species. These bonds must be strong since that are not broken when solid water melts or liquid water evaporates. Water, whether it is solid, liquid, or gas, is still H2O. As we will see later, the bonds (which we represent as lines connecting the atoms) are negatively charged electrons which are attracted to both atom's' nuclei. These bonds can be broken in a chemical reaction in which water is changed into derivatives (H, OH, H, or O) with different properties than water.

Atoms of the 92 different elements can bond to themselves and each other to form the myriad of molecules that make up our world. Using molecular models, we made some simple molecules containing carbon (C), nitrogen (N), oxygen (O), and hydrogen (H). Remember these models are just models. Bonds are not really "little sticks" that connect atoms. There are many ways to represent molecules. The graphic below shows different representations of


Molecular Modeling on the Web:  Using Chime

If you are using a computer in one of the access labs on campus, you should use your browser to see and manipulate with your mouse different representations of molecules like  water.  A program called Chime allows you do to that.  Give it a try by clicking water below.  (You must be at a PC in a public lab to view these files.)  I will try to include many such links throughout the OLSG.  To be sure that you will see them, I will place an animated DNA double helix structure adjacent to the link.  Click on Water below and the image will appear in the right hand window of the OLSG.  To get back, select the Back button on your web browser.  By clicking and holding the left hand mouse button on the image, you can rotate the molecule around. If you click and hold the right hand button when your cursor is in the molecule window, a window pops up with windows.   By selecting view and altering the choice, the view can be changed from space filling to line to ball and stick.  Explore the possibilities.  For more information on commands, go to   Chime Instructions

angifdna.gif (35913 bytes) Water



We discussed the matter usually never exists in a pure state in nature. Rather pure substances are combined to form mixtures. Mixtures can be separated into heterogeneous and homogeneous mixtures. In heterogeneous mixtures, individual substances can either be readily discerned in the mixtures, or, in the case of mixtures of solids in a liquid (such as milk, blood) they can be separated easily into liquid and solids by centrifugation. In heterogeneous mixtures, the particles are large enough so that the mixture is not clear, but small enough such that particles do not readily separate on standing. In homogenous mixtures, the particles are so small that they never separate on standing or in simple centrifugation, and do not interfere with light passing through the mixture. Hence the mixture appears clear. Homogeneous mixtures are also called solutions. Mixtures can be separated into component parts by purely physical process, including evaporation, condensation, filtration, sublimation, deposition, etc. The components of the mixture must have different physical properties which allow the components to be separated from each other.




Hopefully you have had a chance to read the syllabus. One of the goals of this class is to "develop critical thinking skills that you can transfer to your other courses, your profession, and your daily life". Just what are the characteristics of critical thinkers? The following comes from a book, Challenging Your Conceptions, by Randolf Smith. According to him, critical thinkers:

When faced with an issue or problem, critical thinkers will develop as many possible answers, solutions, or explanations for the issue or problem that they can. Then they devise ways to differentiate among the proposed solutions.

Now its time to practice. Go to Discus, and answer a series of questions (in a group) that will assist you in practicing critical thinking skills.

Critical Thinking Question:  Discuss (not avaiable)

Now it is time to consider the history of our understanding of matter. As time passed, ancient Greek thought was supplemented with experience and experimentation. The protoscience of alchemy led to the synthesis of new types of substances but also to great confusion in theory to explain how matter is transformed. The use of measurement greatly assisted the attempts to make progress, but misinterpretation of data often obscured the path to truth. You have already confronted one such experiment in your group critical thinking questions.

Jan Baptista van Helmont did the following experiment which was published posthumously in 1648. He took a 5 pound willow tree growing in 200 lb. of soil and weighed the tree alone after 5 years during which it only received water. The tree grew to 169 lb. but the soil weighed just a few ounces less than 200 lb. From where did the 164 lb. of additional tree weight come? The experiment was interpreted at the time as showing that the element water (Greek) turned into earth. We of course know now that some of the weight came from water which chemically reacts with carbon dioxide from the air, using energy provided by the sun, to form sugars and ultimately cellulose, etc. This process we know as photosynthesis. It is the reverse process of combustion or burning of organic material which produces carbon dioxide and water while liberating energy in the form of heat. This experiment was discussed to illustrate both how people in the past processed information and how difficult it is to interpret reality simple experiments correctly. The concept of water turning into earth was also observed when water was heated in a flask. A solid residue formed after the water evaporated. The early interpretation (using Greek elements and ideas) is that fire entered the water and combined with it to form earth. Only when quantitative experiments were conducted was it shown that the residue represented material leached from the flask by the water.

Perhaps the biggest barrier to advancing our understanding of matter came from the wide-spread acceptance of pholgiston theory. Any matter that can burn was thought to contain pholgiston, which escaped into the air on burning. This suggested that burning would decrease the weight of the object, which it apparently does if you consider the burning of a log. Only ash apparently results, but of course early people didn't think about the mass of the escaping gases (carbon dioxide and water). When metals were burned the weight increased. Supporters of the theory said that pholgiston had negative weight! The air was required for burning so it was assumed that the air was low in pholgiston. During burning, pholgiston flowed from the burning substance to the air like water flows down a stream.. Priestly found that if an red mercury compound (which we now know as an oxide of mercury) was heated, a gas formed, which would vigorously support combustion and the respiration of a mouse. He had purified oxygen but was so steeped in pholgiston theory that he thought the substance to be dephologisticated air. For combustion to occur, something (phlogiston) must be absent form the air, so that the pholgiston from the burning object could enter it.

Lavoiser, the father of modern chemistry, settled the problem (in the 1780's). He formed the mercury oxide from mercury and air and found the weight of the air decreased by 1/5 to 1/6. When he heated the oxide he formed a gas which had the same weight as the amount of gas removed from the air in the first place. Hence this gas, which he named oxygen, is necessary for combustion. He revolutionized our understanding of chemistry and matter. In addition he came up with the Law of Conservation of Matter - In a chemical reaction, matter is not created and destroyed, only interconverted. When you burning a log in air, the weight of the log + oxygen combined with the log = the weight of the ashes and gases produced, which people can't see.

Dalton, in the early 1800's developed the Atomic Theory, using Lavoiser's work on mass conservation and Proust Law of Constant Constant Composition. This law is easier than it sounds. Consider a cake as an example. You distribute to all your friends a recipe for a chocolate cake. If everyone follows the recipe, all cakes could have the same number of grams of chocolate in a given amount (let's say 100 grams) of cake. The same with pure substances. If you break the chemical bonds which hold hydrogen and oxygen together in water, you always get 11.2 g of hydrogen and 88.8 g of oxygen in 100 g of water. That is, water consists of 11.2% by weight of hydrogen and 88.8% by weight of oxygen, no matter where the water comes from. Nature always follows the same recipe for water - H2O.

Dalton used these ideas and his own experiments to come up with a way to explain all these ideas - which ultimately became known as the atomic theory.

Modern Concept of the Atom:

Dalton was exactly right, with one exception. Modern evidence shows that atoms are divisible and are composed of protons (+1 charge, 1 atomic mass unit - amu) , neutrons (neutral, 1 amu), and electrons (-1 charge, about 0 amu). Obviously 1 amu must be a very small weight - much smaller than a pound or a gram. It has been shown that 1 amu = 1.67 x 10-24 grams. Electrons really have a tiny mass but it is 1/2000 that of a proton or neutron, so we'll just round its mass to 0 AMU. The total mass of an atoms is contributed by the protons and neutrons, with little contribution from the electrons. The mass number is simply the total number of protons and neutrons in the atom. Protons and neutrons reside in a very small central region of the atom called the nucleus, which makes up most of the weight of the atoms. Electrons are moving around the nucleus and are held to the atoms by the electromagnetic force. With a scanning tunneling electron microscope, we can actually now visualize individual atoms. Check out the movie below!

Movie of Atoms from IBM

The atomic number defines the number of protons in the nucleus and hence the number of electrons in the neutral atom. The elements of a given atoms are not exactly identical. Each neutral atoms of an element have the same number of protons and electrons, buy differ potentially in the number of neutrons in the nucleus. Different isotopes of an element have the same number of protons but different number of neutrons. The atomic weight of the different isotopes thus varies. The atomic weight shown in the periodic table is a weighted average atomic weight of the different naturally occurring isotopes, and is therefore not a whole number, as you expect if you just added the number of protons and neutrons, with each having a weight of 1. We discussed an example of chlorine, which has an atomic weight of about 35.5. Since it has 17 protons, we can hypothesize that there are two naturally occurring isotopes, one with 18 neutrons and one with 19. Each isotope would be equally abundant. (Actually there are two isotopes of Cl, one with 18 neutrons and 1 with 20. There first represents about 75% of naturally occurring chlorine.)

Although I mentioned that nature was simple - there are 92 naturally occurring elements, they still have markedly different properties. They can be solid, liquid, or gas at room temperature, have different densities, and clearly have different chemical properties. For example helium is pretty unreactive chemically (that's why you can breath it with no problem) why elemental sodium reacts violently with water. Can we make some simplified order out of these disparate atoms and properties? Similar endless diversity and complexity is seen in the biological world, but Linneaus came up with a taxonomy classification for the living world, based on the properties, function, appearance of organisms. Clearly chimps and humans are more closely related than cauliflower and humans. The same can be done with the 92 elements. In the 1860's (before our knowledge of protons, neutrons, and electrons), Mendeleev discovered that if he arranged the elements in a row in order of increasing atomic number, he found that at repeating intervals, the next element in the row seemed to have properties very different from the preceding element (i.e. a solid metal instead of a gas) but similar to an earlier element in his organization. He interrupted the extension of the row and started a new row with the new element directly underneath a previous element with similar properties. He didn't know all the elements that we know today, but he was intuitive enough to leave gaps in his rows to optimized the alignment of the elements into columns with similar properties. His achievement was remarkable and is the basis of the modern periodic table. Elements in the table are arranged in way to shown how the chemical and physical properties of elements repeat in a periodic fashion.

An Interactive Periodic Table on the Web

Arrangement of Electrons:

If all the atoms of different atoms looks about the same - fuzzy balls of moving electrons zipping around a small nucleus, how could you account for the diversity in chemical and physical properties of atoms? How can you account for the arrangement of atoms in the periodic table? Modern chemical theory and experiments shows that electrons are not moving randomly around the nucleus but rather move in "shells". The first period of the periodic table has one shell that can hold 2 electrons. The second period has two shells, an inner shell with 2 electrons, and an outer shell with up to 8. The third has three shells, etc. More sophisticated theory and analyses shows that the electrons are arranged in subshells within the shells. Subshells consist of orbitals named s, p, d, and f. and each orbital can hold two electrons. Before going on, take a quick review quiz in WebCT

WebCT Quiz: Select Matter and Atoms 1 as the Quiz 

Before we consider all these shell and subshells lets consider a very hypothetical analogy. Welcome to the city of Atomopolis. The center of the city, called Nucleus, is filled with offices and businesses, so if you wish to visit you must stay in hotel available in various ring districts that surround the city. Building prices in this city are out of this world, especially close to Nucleus, so there are few hotels close to Nucleus. In fact there is only 1 hotel in Ring 1, 3 in Ring 2, and 5 in Ring 3.


The rings aren’t large and so the hotels are pretty small as well. In fact the maximal occupancy per hotel is 2 people. Naturally, people wish to stay as close to Nucleus as possible so the hotel in Ring 1 is filled to capacity before those in Rings 2 and 3. Hotels in Rings 2 and 3 have made an agreement. Each hotel has to have one person in it before any hotel can take another and be filled. There are some advantages to staying in Rings 2and 3 however. It takes less energy to leave Atomopolis than if you were staying in Ring 1.

What does this example have do to with electrons? If you replace the hotels with orbitals and the rings with subshells, you can get an idea of how electrons are arranged around the nucleus of any atom. We call this arrangement the electronic configuration of the atom. As we proceed left to right in a period (row) of the periodic table, we add one more electron to the atom. Electrons are added to the lowest energy level orbitals available as we build up (German word aufbauen) the electronic configuration of atoms. This principle is called the Aufbau Rule. Electrons are added one after another to the orbitals in order of lowest to highest energy (see link below), with no more than two electrons in any orbital. If more than one orbital in a subshell is available, electrons are added to each orbital in that subshell individually before any of the orbitals in the subshell are filled.


Each orbital can hold two electrons. The particular shape of the periodic table can be explained how subsequent electrons in succeeding elements in the periodic table are placed into orbitals of higher energy. This principle leads to the arrangement of atoms in the periodic table into the s, p, d, and f block elements.


As in the case of Atomopolis, electrons are added to lowest energy orbitals first. If there are multiple orbitals of the same energy, one electron is added to each orbital before they are paired in the orbitals. See the example of carbon below:


To write electronic configuations, all you have to know is types of orbitals in each shell, and their relative energies, which was shown above. The chart below shows the orbitals in each shell




1 1s s-2
2 2s, 2p s-2, p-6
3 3s, 3p, 3d s-2, p-6, d-10
4 4s, 4p, 4d, 4f s-2, p-6, d-10, f-14
5 5s, 5p, 5d, 5f s-2, p-6, d-10, f-14
6 6s, 6p, 6d, 6f s-2, p-6, d-10, f-14
7 7s, 7p, 7d, 7f s-2, p-6, d-10, f-14