Humboldt State University ® Department of Chemistry

Richard A. Paselk

VUB Biology

Fall 2001

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 world.

 

What is Chemistry?

Chemistry is the study of matter and its transformations.

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 via gravity.

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).

States of Matter. Matter can exist in three states under earth-surface conditions:

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.

Elements

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).

 

The Atom

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:

 Particle Charge Relative Mass Mass
Electron (e-) -1 1/1840 9.11 x 10-28g
Proton (p or H+) +1 ª1 1.67 x 10-24g
Neutron (n) 0  ª1  1.67 x 10-24g

Some important terms which you must know are:

 

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:

Y1s= Ae-Br

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:

Atomic Orbitals Supplement

Chemical Periodicity

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).

Terms:

You should know the terminology above.

 
Periodic Table of the Elements
 IA IIA IIIA IVA VA VIA VIIA VIIIA
   H  He
Li Be    B C N O F Ne
Na Mg IIIB IVB VB VI VIIB VIIIB IB IIB  Al Si P S Cl Ar
K Ca Sc  Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
 Rb Sr  Y Zr Nb Mo Tc Ru Rh Pd  Ag  Cd  In Sn Sb Te I  Xe
 Cs  Ba Lu  Hf Ta  W Re Os Ir  Pt Au  Hg Tl  Pb Bi Po At Rn

Trends: Note the trends for

What is the basis of the periodicity of properties?

Electrons are held in shells.

 

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
 

 H
 

 He

 Li

Be
 

 B

C

N

O

F

Ne

Na

Mg

 Al

Si

P

S

Cl

Ar

K

Ca

Sc

Ti

V

Cr

Mn

Fe

Co

Ni

Cu

Zn

Ga

Ge

As

Se

Br

Kr
     

Mo
               Sn    

I
 

The following observations may be made regarding the elements of life:

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Last modified 12 September 2001
© R Paselk