|Lecture Notes:: 12 September
© R. Paselk 2001
Atoms, Molecules & Chemistry
Exponential or scientific notation: It is often convenient
to express numbers in exponential or scientific notation to avoid
writing the huge numbers of zeros we often run into in the natural
- For example There are 6.02 x 1023 particles in
- And the the concentration of hydrogen ions (H) is 10-7M
(M = moles/Liter) in pure water while the concentration of the
water is about 55.5 M, (55.5 x 6.02 x 1023 = 3.34
x 1025 molecules/L) so about 2 out of every 109
water molecules is dissociated.
What is Chemistry?
Chemistry is the study of matter and its transformations.
- "Classical" chemistry involves mostly electron
transfers and/or interactions of charges (electron and nuclear).
As we'll see only some electrons in atoms are involved - the
outer or valence electrons of atoms.
What is matter? Stuff. Has mass and occupies space.
Mass: The measure of quantity for matter. Mass is the
property of matter resulting in its inertia and and attraction
- Do not confuse mass and weight. Weight is the
force acting on an object due to gravity. We often interchange
these terms in conversation, but they are quite different - you
have the same mass whether you are weightless in space on here
on Earth (taking a shuttle flight is no substitute for a diet!).
To confuse us further we call the determination of mass "weighing"!
Matter has both physical properties and chemical
properties. These are properties which do not depend on
the quantity of substance and therefore they can be used to identify
a substance (sometimes referred to as intensive properties).
- Physical properties of substances can be observed
without, in principle, changing their compositions. Physical
properties include mass, color, density etc. Note that physical
changes such as melting, cutting, etc. do not change composition.
States of Matter. Matter can exist in three states
under earth-surface conditions:
- Solid: definite shape and volume (Crystals vs. super-cooled
liquids or glasses)
- Liquid: definite volume, but no defined shape - will fit
to container etc.
- Gas: no definite shape or volume - will fill whatever container
they are in.
- both liquids and gases are fluids.
- Chemical properties of substances describe behaviors
which lead to changes in composition. Chemical properties describe
reactivity under various circumstances (does it burn in air,
react with acids or bases, corrode in sea water etc.) Note that
chemical changes result in different compositions (different
ratios and/or types of atoms).
Conservation of Mass
A fundamental observation is that mass is unchanged in chemical
processes. This observation is summarized in the
Law of Conservation of Mass: Mass is neither created
nor destroyed during a chemical change. (Strictly speaking there
is no measurable change.) For example, if we burn gasoline
(octane) in air we will get carbon dioxide and water:
C8H18 + 12 1/2 O2Æ 8 CO2 + 9 H2O
If we were to weigh (determine the mass) of the carbon and
oxygen vs. the carbon dioxide and water we would find them to
be identical - the masses are the same on both sides of the equation
(that's why its called a chemical equation, the two sides are
"equal"). Looked at another way, if you count the atoms,
the numbers of each kind of atom on each side are identical -
so we can also say that atoms are conserved in chemical processes.
This is really the fundamental assumption of
chemistry, and thus the measurement of mass is the
fundamental process underlying much of chemical work.
Another fundamental concept is that of elements. Elements
are substances which cannot be broken down further into simpler
substances by chemical or (non-nuclear) physical means.
Note that combinations of various elements to form compounds
nearly always result in the formation of compounds with constant
proportions by mass. In other words, the ratios of the elements
in compounds generally reduce to small whole numbers (this
does not hold in biological macromolecules because the molecule
size is so large, but the ratio of elements in any particular
macromolecule is still a ratio of whole numbers).
Atoms are known to consist of three different types
of particles: electrons, protons and neutrons (the common form
of one very important atom, hydrogen, has only two kinds: a proton
and an electron). The protons and neutrons reside in a small inner
portion called the nucleus while the electrons reside in
a relatively large cloud centered on the nucleus. (For hydrogen,
if the nucleus were the size of a pea, the electrons would occupy
a sphere about the diameter of a football field. Atoms are mostly
empty space!) Important properties of these particles are listed
in the table below:
||9.11 x 10-28g
|Proton (p or H+)
||1.67 x 10-24g
|| 1.67 x 10-24g
Some important terms which you must know are:
- Atomic number (Z) - the number of protons in the nucleus.
This number is characteristic of a given element.
- Atomic mass number (A) - the sum of the protons and
neutrons in a given atom (p + n).
- Atomic mass - the actual mass of an average
atom in a sample. The characteristic atomic masses for Earth
are shown on periodic tables.
- Atomic Mass Unit: the atomic mass unit = amu is a
unit of mass for atoms. It is defined as 1/12 the mass of one
atom of 12C, where the mass of 12C is defined
as 12 exactly.
In the mid 1920's Werner Heisenberg and Erwin Schrödinger
independently came up with models of the atom which accurately
predicted the behavior of all atoms in principle.
A basic assumption of these treatments is that electrons behave
like waves in some sense, and their locations in an atom are described
by equations for waves. A second assumption is that of Heisenberg's
Uncertainty Principle. This states that we cannot simultaneously
know the position and momentum of a particle. Mathematically:
Schrödinger assumed that the electron's behavior could
be described by a three dimensional standing wave. He derived
an equation which described the amplitude of this wave. The simplest
solution for the Schrödinger Equation for the ground
state (1s) energy of a hydrogen atom is:
where A & B are constants, e is the base of the
natural logs, and r is the radial distance from the nucleus.
This equation has little real meaning. However, the square
of the value of psi (Y2)
tells the probability of finding an electron at any given location.
Electronic Energy Levels:
- We will designate the primary energy level, corresponding
to the average radial distance of the electron from the nucleus
as a shell, and give it the symbol n. The lowest
possible energy level is then the ground state with n = 1.
- Shells with n > 1 may have subshells which are
different geometrical patterns of electron distribution. Thus:
- The lowest energy pattern is spherical and given the designation
- The next lowest energy distribution is bi-lobed with a planar
symmetry. It is given the designation p.
- The third lowest energy distribution has diagonal planes
of symmetry and is designated d.
- The fourth lowest energy distribution is designated f.
This is the highest subshell type occupied by ground state electrons
in any atom, so we will not look any further (an infinite number
of subshells exist in theory for excited states, but they are
not important to our understanding).
- The average energies of the different subshells are the energy
of the shell, thus when subshells are present the energy of the
shell is split. For example, in the n=2 shell the 2s orbital
becomes lower in energy than the shell, while the 2p orbital
becomes higher in energy.
- The regions of electron occupancy in subshells are called
- For each shell there is one s orbital.
- For each shell with n = 2 or greater there are three p
orbitals: px, py, and pz.
- For each shell with n = 3 or greater there are five d
orbitals: dxz, dyz, dxy, dx2-
y2, and dz2
Look at the Periodic Chart on the wall. The pattern arises
due to a repetition or periodicity of chemical properties.
The vertical columns of the charts are called groups, while the
rows are referred to a periods.
Note the numbering of the groups. The numbers from 1 - 18 are
the internationally accepted numbers. We will also use the I -
VIII "American" numbering system. Note that the "tallest"
columns comprise what are referred to as the "representative
elements" (IA - VIIIA).
- Period: the rows of elements showing a repeating pattern
of properties (e.g. Na - Ar).
- Group: a vertical column of elements on the table sharing
a family resemblance of properties (e.g. Li - Fr).
- Representative elements: the elements of the s-block and
p-block (blue and green on the table below).
- Transition metal elements: the elements of the d-block (yellow
in the table below).
- Inner-transition metal elements: The f-block or Lanthanides
and Actinides (not shown on the table below)
- IA = alkali metals;
- IIA = Alkaline earth metals;
- VIIA = Halogens (note the generic symbol of X standing for
- VIIIA = Noble gases (older = inert gases).
You should know the terminology above.
Periodic Table of the Elements
Trends: Note the trends for
- atomic size: decreases going from left Æ
right and from bottom Æ top.
- Size goes up with atomic number for any individual group.
- Size decreases irregularly as atomic number increases for
any given period (more charge pulls electrons in to nucleus,
but shielding reverses as subshells [s or p orbital sets] fill.
- ionization energy: increases from left Æ
right and from bottom Æ top.
- Ionization energy goes down with atomic number for any individual
- Ionization energy increases irregularly as atomic number
increases for any given period (more charge pulls electrons in
to nucleus, but shielding reverses as subshells [s or p orbital
- electronegativity increases from left Æ
right and from bottom Æ top.
- note hydrogen combining ratios (LIH, BeH2, BH3,
CH4, H3N, H2O, HF) and acid/base
properties of oxides (basic for metals, acidic for non-metals)
What is the basis of the periodicity of properties?
Electrons are held in shells.
- The first shell holds only 2 electrons in what is called
the 1s orbital. Thus helium has its first shell filled.
There is no more room for electrons, so it can't react by picking
up another electron. On the other hand, as a crude thought model,
we can consider that each electron is held by both charges in
the He nucleus, so they are much more tightly held than the electron
in H, so He won't give up an electron either - its inert.
- The second shell is larger (its out further from the nucleus)
so holds 2 electrons in a 2s orbital, but there is now room for
an additional three 2p orbitals. Thus 8 electrons can be accommodated
in the second shell. Note the consequences:
- for lithium (Li) the inner two electrons of the 1s shell
cancel the attraction of two of the three protons, so the outer
2s electron "sees" only a single charge. But its out
further than the electrons in the 1s shell were, so its not held
as strong, so Li loses its outer electron more readily than H
and is more reactive.
- for Fluorine on the other side of the chart we can think
of the outer shell electrons being attracted to the nucleus by
9 - 2 = 7 charges, so the last open space in an orbital will
be super attractive to an outside electron, so F will be be very
reactive, but in an opposite way to Li - it wants to steal electrons
instead of giving them up.
- for neon all of the orbitals will be filled, and the electrons
will be strongly attracted to the nucleus and there is no for
additional electron in the ground state, so Ne will again be
inert like He above it.
- The third shell is larger yet (further from the nucleus),
but still crowded, so initially it can only accommodate another
- Of course the electrons in the 3s orbitals are even farther
out from the nucleus, so we would expect Na to be even more reactive
than Li, and so on for K, Rb, etc. each giving up its outermost
electron more readily than the element above it in the Periodic
- On the other hand Cl will also attract electrons less than
F, so it will be less reactive etc. for the halogens.
- So we will expect the most reactive elements to be on the
opposite corners of the table - lower left and upper right.
THE ELEMENTS OF LIFE
Let's look at the basic requirements of an idealized, simplest
life form and ask why life should use the particular atoms and
molecules we see dominating in living organisms.
Periodic Table of Biologically Important Elements
The following observations may be made regarding the elements
- Life is largely a phenomena of hydrogen and the second period
of the Periodic Table. That is, the major component elements
(red) in all known organisms
are from these periods. Why these four elements? First we might
observe that H, O, N, and C are the smallest elements capable
of forming 1, 2, 3, and 4 bonds. Smallest is important because
that means they can form the strongest covalent bonds. So these
atoms are going to be capable of forming some of the most stable
molecules, an important consideration for something that needs
to grow and reproduce in a hostile environment. C, N, and O are
also the only elements capable of forming strong multiple bonds
(carbon and nitrogen can form triple bonds, all three can form
double bonds). Thus we can hypothesize that these elements were
chosen for their special properties, specifically strong
covalent bond formation (to enable the formation of stable biomolecules),
the ability of carbon to form large branched molecules, and for
C, N, and O the formation of multiple bonds which provides chemical
flexibility (step-wise oxidations, different hybridization geometries
- The next important elements to life occur in Period 3: P
and S (orange). These are
the smallest elements capable of multiple covalent bonds to H,
C, O and N, and which also have available d-shells. The
d-shells allow additional transition states and reaction mechanisms.
P and S are particularly important in the capture, storage, and
distribution of chemical energy.
- The "essential" elemental ions found in all studied
species (blue), Ca (II),
Mg (II), K (II), Na (I) and Cl (-) were probably chosen more
on the basis of availability in the primordial oceans then for
any specific properties: other ions are very similar.
- The trace elements required by all studied organisms (violet) are all used as co-catalysts
and/or ligands. Thus they were probably chosen for their specific
electronic structures as well as their availability on the early
- A variety of other elements are required by at least a few
organisms, and are shown on the table in black. The grayed elements
are not known to be of biological importance, but are shown as
"place-markers" to help us keep track on the Table.
- Last modified 12 September 2001
- © R Paselk