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Basic Chemistry: Atomic Structure and the Periodic Table

Particle proton electron neutron Mass 1 amu* 0 amu** 1 amu*** Charge +1 -1 0 Location nucleus electron cloud nucleus

*amu = atomic mass unit **Actually, the mass of an electron is about 1/2000 that of a proton, but in terms of the chemistry we do in Biology 101, that is a completely insignificant mass. ***Again, actually, the mass of the neutron is slightly greater than that of a proton, but we can also consider this to be an insignificant difference. You should be aware that, if you study chemistry in a more rigorous setting, the differences may become important. 1. The atom contains three subatomic particles. Each of these has a characteristic mass and a characteristic electrical charge, and each is found in a specific part of the atom. 2. In terms of the identity of an atom, the most significant thing is the number of protons in the atom. There are 92 different naturally occurring elements, each with its own specific number of protons. For example, a Hydrogen atom always has one proton, a Helium atom always has two, a Carbon atom always has 6, a calcium atom always has 20, and a Uranium atom always has 92. If we change the number of protons in a Carbon atom from 6 to 7, it is no longer Carbon--it becomes Nitrogen. (We have also performed nuclear chemistry, which is something we definitely will not be doing in Bio 101!) 3. An atom always has a net electrical charge of zero, which means that its positive and negative charges must balance each other out. This means that an atom always has the same number of electrons as protons, since those two particles are the sources of charge in atoms. 4. Each element has two important identifying numbers. The first of these is the atomic number. Atomic number is defined as the number of protons in the atom. As noted above, this number corresponds to a statement of the identity of an atom. Thus, the atomic number of Hydrogen is 1, Helium is 2, Carbon is 6, Calcium is 20, and Uranium is 92. Important Note: Even though in an atom the number of protons is always equal to the number of electrons, it is not proper to define the atomic number as the number of electrons, or as the number of protons or electrons. This is because under certain circumstances many atoms gain or lose electrons, and become ions. If this happens to Oxygen, for instance, which has an atomic number of 8, and whose atom has 8 protons and 8 electrons, it forms an ion which has 8 protons and 10 electrons

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(and a charge of -2). This ion is still Oxygen, and it still has an atomic number of 8, even though it now has 10 electrons, rather than 8. 5. Like charges repel each other, and opposite charges attract each other. In an atom, the electrons remain out in the electron cloud because they are moving very rapidly around, and their forward momentum balances the force of the attraction to the positive protons in the nucleus. A more difficult problem to figure out is why the protons in the nucleus dont fly apart due to the repulsion they exert on each other. The most popular current theory is that the neutrons serve as a kind of nuclear glue to keep the protons stuck together. A couple of significant observations support this idea. For one thing, the larger the atom, the more neutrons (relative to the number of protons) the nucleus needs to remain stable. Another point is that the only atom which ever has no neutrons is Hydrogen--which has only one proton, and therefore has no problems with this repulsive force. However, there are still a number of questions remaining to answer about this puzzle. 6. The second important number associated with an element is its atomic mass, or mass number. The atomic mass is the total mass, in amu, of a typical atom of an element. If you look at the chart on page 1, you will see that the only particles which contribute significantly to the mass of an atom are the protons and neutrons, and according to our somewhat simplistic view of atomic structure, each proton and each neutron has a mass of 1 amu. Therefore, to calculate the atomic mass of a particular atom, all we have to do is add the number of protons and the number of neutrons together. Conversely, if we know the atomic mass and the atomic number, we can calculate the number of neutrons in the atom by subtracting the atomic number (number of protons) from the atomic mass (number of protons plus number of neutrons). For example, Sodium (Na) has the atomic number 11 and atomic mass which rounds off to 23. An atom of the most common isotope of Sodium has 11 protons (from the atomic number), 11 electrons (because atoms are always neutral), and 12 neutrons (23 - 11 = 12). Note: Avoid the trap of assuming that the number of neutrons in an atoms will be the same as the number of protons. This is very often not the case. 7. The exact number of neutrons in an atom is not as vital as the number of protons or electrons. In fact, virtually all kinds of atoms have a variety of forms (called isotopes) which differ in the number of neutrons in the nucleus. For instance, Hydrogen exists in three different forms. All have one proton and one electron; one form has no neutrons, the second has one neutron, the third has two. In general, there will be at least as many neutrons in the atom as protons, and in many cases neutrons will outnumber protons, as in Sodium above. 8. The official atomic mass of an element is almost never a round number; it almost always has a decimal component. This is because the different isotopes of atoms have different masses. Chemists and physicists have figured out ways to estimate the relative percentages of the different isotopes of the element present in the universe, and have calculated a weighted average which takes those proportions into account. The official atomic mass of an element can usually be used to figure out the mass of the most common isotope of the element--simply

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round it off to the nearest whole number. For example, Carbon has three isotopes with masses of 12, 13 and 14 (each has 6 protons and 6 electrons; they have 6, 7, and 8 neutrons respectively). But Carbon-12 is by far the most common of these three isotopes, so the official, weighted average atomic mass for Carbon is 12.01115. No single atom of Carbon has this mass; it is considered to be the average mass of all Carbon atoms in the universe. 9. The periodic table is an array of the known elements lined up in order of atomic number. The columns and rows of the table reflect the chemical and physical behavior of the various elements, which are determined largely by two interacting factors: the size of the atom and the arrangement of the electrons in its electron cloud. Elements found under one another in the columns of the table are similar in behavior, form similar kinds of bonds, etc. Each element is represented by an abbreviation consisting of one or two letters. These abbreviations have been agreed upon by all chemists, and you may not make up your own symbols. Each box on the table contains at least two numbers; the atomic number and the atomic mass. The atomic number will be an integer (a round number). The atomic mass almost always contains a decimal component. 10. The electrons in an atom are located in the electron cloud. This is a complex structure which consists of a variety of energy levels (called shells). Each shell contains a limited number of electrons. The largest of the known atoms has a total of seven shells. The smallest (hydrogen) has only one occupied shell. The shells are numbered from 1 to 7, based on how far away from the nucleus they are (1 is closest, smallest and simplest in structure; 7 is furthest, largest and most complex). Within each shell are sublevels called orbitals. Each orbital has a maximum capacity of two electrons. The further away from the nucleus, and the larger a shell is, the more kinds of available orbitals it contains. The first shell has only one type of orbital (an s orbital), the second has two types (one s and three p). the third has three (one s. three p, and five d), the fourth has four (one s, three p, five d, and seven f). [Logically, one would expect that the fifth shell would have five kinds of orbitals, the sixth would have six, etc. However, there are no known atoms which contain enough electrons to require any orbitals in shells five, six, or seven beyond the s, p, d, and f orbitals already mentioned. While it may be hypothetically possible that other types of orbitals could exist, we have no atoms which could show them to us.] Thus the first shell can contain a maximum of 2 electrons, the second can contain up to 8, the third up to 18, and the fourth up to 32. 11. The next piece of the electron puzzle is figuring out where in all this maze of shells and orbitals the electrons of particular kinds of atoms will be found. There is a pretty consistent way to do this, and it depends upon knowing one important thing about electrons: electrons always occupy the lowest energy level available. 12. There are two factors which influence the energy level of a particular orbital: its complexity and its distance from the nucleus. In orbitals of the same shell (ie, same distance from the nucleus), the more complex an orbital is, the higher its energy level. The simplest of the orbitals is the s (a simple globe

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shape), next the p, the d, and finally the f. Thus a 3s (s orbital of the third shell) electron would be less energetic than a 3p (p orbital of the third shell) electron. In orbitals of the same type, the further the orbital is from the nucleus, the higher its energy level. Thus a 2s (s orbital of the second shell) electron is less energetic than a 4s (s orbital of the fourth shell) electron. 1. The electrons will fill the orbitals from the lowest available level first. Therefore, a Lithium atom (at.# = 3) has two electrons in the s orbital of the first shell and 1 electron in the s orbital of the second shell. A Fluorine atom (at.# = 9) has 2 electrons in the s orbital of the first shell, 2 in the s orbital of the second shell, and 5 in the three p orbitals of the second shell. 2. As we look at larger and larger atoms, we are faced with the problem of reconciling the two different aspects which affect the energy level of an orbital--complexity and distance fromt he nucleus. There is no way you can know intuitively how these two influences affect electrons; this is something you will have to learn. The first time it becomes an issue is when we consider the element potassium (at.# = 19) Potassium has 2 electrons in the s orbital of the first shell, 2 in the s orbital of the second shell, 6 in the p orbitals of the second shell, 2 in the s orbital of the third shell and 6 in the p orbitals of the third shell. This accounts for 18 of the 19 electrons. The d orbitals of the third shell are actually slightly higher in energy than the s orbital of the fourth shell (their complexity increases their energy level more than the 4s orbitals greater distance from the nucleus increases its energy level). Thus that 19th electron goes into the 4s orbital, not into one of the 3d. The same is true for Calcium (at.# = 20). Ca has 2 electrons in the first shell, 8 in the second, 8 in the third, and 2 in the s orbitals of the 4th. Element #21, Scandium, has 21 electrons. 20 of those are arranged exactly like Calciums 20 electrons. The 21st will go (finally) into a position in a 3d orbital. The next string of atoms will gradually fill in those 10 electron positions in the 3d orbitals, right up to Zinc, #30, which has finally filled up the last position in the third shell. Zn has 2 electrons in the first shell, 8 in the second, 18 in the third and 2 in the fourth. The next element, Gallium, starts in on the 4p orbitals. Ga has 2 in the first, 8 in the second, 18 in the third, and 3 in the fourth. 3. This pattern of filling one shell up through its p orbitals, then filling the s orbital of the next bigger shell before going on to the d orbitals is consistent for the rest of the periodic table-no shell ever has any d orbital electrons in it until the s orbital of the next shell is already filled. As atoms get bigger and bigger, the degree of overlap as shells are filled gets greater. [You will not be asked to deal with any atoms in this class with atomic numbers higher than 36, so you will not have to worry about much of that confusion]. 4. VERY IMPORTANT! This pattern of filling the outer shells leads to an extremely significant fact: no shell, no matter how high its number, ever has more than 8 electrons in it while it is the outer (valence) shell. This is part of something chemists call the Octet Rule (an octet is a group of 8). In fact, having 8 electrons in the outer shell (or 2, if the outer shell is the first shell) is a state of particular energetic stability for an atom.

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5. NOTE: In a shell which is not full, if the shell has four or fewer electrons in it (first shell excluded) all of the electrons will be unpaired (ie, in different orbitals). If there are more than four, the fifth, sixth, seventh and eighth will complete the four pairs of electrons. 6. The chemical behavior (bonding behavior) of an atom depends largely upon the state of its outer shell. Virtually all bonding activity is motivated by the energetic tendency of an atom to complete the pairs of electrons in its out shell. This is accomplished either by ionization or chemical bonding. Careful scrutiny and analysis of the elements in the periodic table should sow you that those elements arranged in vertical columns all have the same number of electrons in their outer shells, and therefore will tend to do the same kinds of things when they attempt to fill those shells. For instance, if you look at the column with Fluorine (F) on tip, and analyze the elements in that column, you will find that F has 7 electrons in its second (outer) shell, Cl has 7 electrons in its third (outer) shell, Br had 7 in its fourth, I has 7 in its fifth, and At has 7 electrons in its sixth shell. This is why they have similar chemical behaviors, and why they were initially grouped together in a single column. (The elements in this column are commonly called the halides.) An interesting note about the development of the periodic table is that it was created before any of this information about electron shells and bonding was known, and the original grouping of elements was done solely on the basis of chemical behavior. The final column of elements, the one with Helium (He) at the top, all represent elements which have satisfied their octet needs for their outer shells (He has 2, the rest have 8). These elements, commonly called the Noble or Inert gasses) are characterized by their lack of interest in forming chemical bonds. Not surprising, since they have no need to acquire partners for unpaired electrons in their outer shells--those shells are filled. 7. The Octet Rule says that an atom is most stable when its valence shell contains a complete octet, and that the atom will do anything to achieve this end. This is why atoms form bonds. 8. Atoms on the right side of the period table (excluding the Inert Gasses) have nearly full octets. For example, the halides are all missing just one electron. These atoms are strongly electronegative, which means that they attract electrons strongly. The atoms on the left side of the period table have the opposite problem--they have only one or two electrons in their valence shells, but have complete octets in the shell under the valence shell. These atoms have a tendency to ditch their outer shell electrons; they are called electropositive.

Some Definitions:

Atomic Number: The atomic number is the number of protons in an atom. Atomic Mass: The atomic mass is the total protons and neutrons in an atom. The unit for the

atomic mass is amu (atomic mass units). Ion: An ion is a charged particle. An atom or a molecule generally becomes an ion by gaining or losing electron(s). A particle which is an ion has different numbers of protons and electrons, creating a charge imbalance. The charge of the ion depends upon the difference between the

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number of electrons and the number of protons. A charge has both a direction (+ or -) and a size (1, 2, etc.). Isotopes: Isotopes of an element are atoms of that element which have the same atomic numbers (of course, since they are the same element), but different atomic masses. Another way of putting it: isotopes have the same numbers of protons but different numbers of neutrons. Orbitals: An orbital is a particular electron domain. It actually represents a probability description of where particular electrons are likely to be found. Any orbital has a maximum electron occupancy of 2. (Thus, it can contain no electrons [an empty orbital], one electron [a half full orbital] or two electrons [a full orbital].) It cant contain more than two. There are four known orbital types: s, p, d, and f. Shell: The atomic shells are the subdivisions of the electron cloud. Each is roughly visualized as a globe surrounding the nucleus. Each shell contains one or more orbitals; the larger the shell, the more orbitals it holds. There are up to seven shells in known atoms. Valence: The valence shell of an atom is the outermost shell which contains electrons. This valence shell never contains more than 8 electrons (2 if it is the first shell).

Bonding: A chemical bond is a connection between two atoms (or ions). There are several types of
chemical bond.

1. Ionic Bonding
An ionic bond is an electrical attraction between oppositely charged ions. This occurs as a result of the process of ionization (the creation of a charged moiety--an ion--usually through the loss or gain of one or more electrons.). An ion has a charge which reflects the relative numbers of protons and electrons in the particle. eg., Ionization Na (Sodium), atomic number 11. Na has 1 electron in its outer (third) shell. This atom sill tend to ionize by losing that one electron (in order to achieve an octet in its outer--now the second--shell). This will produce the ion Na+, which contains 11 protons in the nucleus, and 10 electrons in the electron cloud. Cl (Chlorine), atomic number 17. Chlorine has 7 electrons in its outer (third) shell. This atom will ionize by acquiring an 18th electron to complete the octet in its valence shell. This will produce the chloride ion (Cl-). which contains 17 protons and 18 electrons. Ca (Calcium), atomic number 20. Calcium has 2 electrons in its outer (fourth) shell. This atom will ionize by releasing those two electrons, in order to fall back on its complete third shell. This will produce the ion Ca+2, which contains 20 protons and only 18 electrons. Note that ionization is not the same thing as ionic bonding; none of these examples describes the formation of any bond of any kind. The Na+ and Cl- ions could create an ionic compound by association on a one to one basis, positive particle attracting negative particle, forming the compound sodium chloride (Na+Cl-, common table

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salt). Since the Ca+2 ion has a charge of +2, if it formed an ionic compound with, eg, Cl- ions, the ions would combine in a ratio of 1 Ca+2 ion for every 2 Cl- ions, thus canceling charges. Calcium chloride is also a salt; in fact, the products of ionic bonding are generally considered to be salts. Small inorganic ions like Na+, Cl-, and Ca+2 rarely bond one at a time. Usually many, many of each of the types of ions of a compound will get together and form a geometrical array which we call a crystal. NOTE: Individual ionic bonds are relatively weak bonds, and they readily dissociate in water. You should also be aware that a molecule may ionize, as well as an atom. Also note that atoms and molecules always have neutral charges (balanced numbers of protons and electrons). Once an atom or molecule acquires a charge (imbalance of numbers of protons and electrons), it becomes an ion.

1. Covalent Bonding
Covalent bonds form when two atoms attempt to complete their outer shells by sharing pairs of electrons. Each partner contributes one of the electrons in the pair. At atom is able to form one covalent bond for each unpaired electron in its valence shell. If the two partners are of fairly equal electronegativity, the sharing of the electron pair will be equal. Any time two atoms of the same element bond to each other, the bond will be or this type. The bond between Carbon and Hydrogen is also like this. This kind of covalent bond is called a non-polar covalent bond. If one of the partners in the bond is more strongly electronegative than the other (eg, in the Oxygen/Hydrogen covalent bond), the electrons will be unequally shared [Oxygen is an electron hog), creating a polar covalent bond. A polar covalent bond results in a molecule (termed a polar molecule) with partially charged areas (areas of the molecule which have positive or negative charges with charge strengths of less than +1 or -1). Biologically, the most significant polar covalent bonds are those formed between oxygen and hydrogen, and between nitrogen and hydrogen. In both of these cases, the hydrogen acquires a partial positive charge and its partner a partial negative charge (indicating that the oxygen and nitrogen pull harder on the shared electrons in the bond). Note that in a polar covalent bond, the partial charges created on the opposite sides of the bond balance each other. The molecule still has an overall neutral charge.

weaker than non-polar covalent bonds, and the more strongly polar the bond is, the weaker it is. (A polar covalent bond is really something between an ionic and a covalent bond--the polarity results from the attempt by the more electronegative partner to ionize completely by stealing its more puny partners electron.) If two covalently bonded partners both have more than one unpaired electron in their valence shells, it is possible for them to form multiple covalent bonds. Double and triple covalent bonds occur between Carbon and Nitrogen, between Carbon and Carbon, and between Nitrogen and Nitrogen, for example. Oxygen is capable of forming double covalent bonds with Nitrogen or

NOTE: Covalent bonds are much stronger in general than ionic bonds. Polar covalent bonds are

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Carbon, or with other Oxygens. Note that, since it has only two unpaired electrons in its valence shell, Oxygen cannot form triple covalent bonds. Double covalent bonds are stronger than single bonds; triple covalent bonds are stronger than double covalent bonds.

1. Hydrogen Bonding: Hydrogen bonding occurs when the partial charges created by polar
covalent bonds in different molecules (or in different parts of the same large molecule) are electrically attracted to each other. Biologically, the most significant hydrogen bonding occurs between hydrogens with partial positive charges and oxygens or nitrogens with partial negative charges. However, it is possible to have hydrogen bonding with no hydrogens involved. Remember, the hydrogen bond does not occur between atoms which are covalently bonded to each other.

are not really bonds at all, in the strictest sense--merely electrical attractions between atoms which are actually bonded to other partners. However, as insignificant as the strength of one hydrogen bond is, they often occur in vast numbers in particular molecules, and as a combined force they are very important. Some examples: the familiar behavior of water is the result of its small size, high polarity, and thus immense capacity for hydrogen bonding between different water molecules and between water molecules and other substances. Also, the famed double helix of the DNA molecule is entirely created and maintained by millions of hydrogen bonds.

NOTES: Hydrogen bonds are the very weakest of the bonds described here. In fact, thery

1. Final Note: There is a whole group of elements largely ignored by this study guide: the
metals. Metals have a pretty unique kind of behavior which involves the flow of electrons from atom to atom. Since this behavior is not germane to the chemistry we are addressing in biology, the metals have been neglected. Your chemistry teacher will be thrilled to tell you all about how metallic substances behave.

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