```CHEMISTRY FOR HOME ASTRONOMY
--------------------------
John Pazmino
NYSkies Astronomy Inc
www.nyskies.org
nyskies@nyskies.org
2013 June 7```
```Introduction
----------
In the rapid movement of home astronomy into other, traditionally
separate, sciences, there grew the need for some simple tuition in
chemistry. Astronomy articles and lectures increasingly include
chemical concepts that may still be out of bounds in the classical
upbringing of a home astronomer.
From time to time in the NYSkies Astronomy Seminar we commonly
sidetrack to explain some chemical feature and then return to the main
theme of the session. Altho most astronomers at the Seminar follow the
explanation, many either forgot the chemistry form school of didn't
take chemistry. The 2013 June 7 NYSkies Seminar, 'How atoms jive
together', was an overview of simple chemistry and from the dialog
It turns out that the level of chemistry needed to follow almost
all news and information in home astronomy is within the scope of high
school science. Virtually no math other than simple algebra is used
and almost all facts & figures are carried in charts and tables.
There's very little to actually memorize. ```
```Atomic structure
--------------
Chemistry operates thru the electrons of the atom, leaving the
nucleus alone. It works thru only the electrons on the farthest
outermost shell around the atom, leaving the inner electrons alone.
Recall that the atom consists of a nucleus of protons and
neutrons. The count of both is the mass number of the atom. The
electrons add very little mass. The proton and neutron are quite equal
in mass. The mass number multiplied by the mass of either proton or
neutron is the full mass, in kilograms, of the atom. As you may expect
the kilogram mass of an atom is infinitesimal, some 1e-26 kg for a
hydrogen atom and 1e-24 kg for a typical transuranium element.
Around the atom in shells are the electrons, the same number as
protons to keep the atom neutrally charged. If an atom has excess or
decess electrons in its natural state, it'll exchange with free
electrons around it to attain a neutral condition.
In diagrams on paper the shells are often depicted as rings but
the atom is a three-dimensional structure, not a plane one like the
solar system. An other major difference is that electrons are not
really tiny pellets in definite paths around the nucleus. They are in
a swarm or cloud within which each electron has a probability of being
at a specific location. The mapping of these probabilities yields a
structure much like the shells of the mechanical descriptions of the
atom. It's simply more likely that an electron will be in the region
of a shell than not. ```
```Electric charge
-------------
The proton and electron carry an electric charge of one unit each.
The charges are of opposite polarity which by long history is
'positive' for the proton and 'negative' for the electron. Being
opposite in polarity, the proton would attract the electron and pull
together. The atom collapses and there would be no world as we know it
to live in.
The separation of protons in the nucleus and electrons in the
shells, plus the principles of quantum physics, keep atoms intact. As
long as electrons and protons resident within an atom they leave each
other alone.
In nature atoms are neutral in net electric charge because the
number of electrons matches the number of protons. If for some reason
an atom loses or gains electrons, it tries to restore a neutral charge
by exchanging with free electrons from its surrounds.
This happens when you work with static electricity. Rubbing two of
certain objects together induces exchange of electrons. One object is
negatively charged with excess electrons and the other is positively
charge with decess electrons. When the one or the other is brought
near to a third object, a spark can jump between the two. This is the
stream of electrons flowing across to neutralize the objects.
Electrons are the mobile carrier of electric charge, the protons
being locked in place in the nucleus. Chemistry moves electrons
between atoms to assemble the atoms into compounds. When atoms merge
into a compound, they swop or share certain of their electrons.
Altho each atom then takes on an electric charge, the entire
compound remains neutral. It could be polarized if the positively-
charge atom s are on one end of the ensemble and the negative ones are
at the other. But as a unit it is neutral.
When certain compounds are dissolved in water, their atoms are
release into their charged parts. An atom with a net charge, either
positive for too few electrons or negative for too many, is an ion.
The dissolved substance forms a solution of ions.
Ions can also be created by electricity that strips electrons from
atoms. The 'electric' odor near sparks comes from the momentary
ionization of oxygen and nitrogen in the surrounding air. Extreme heat
can 'boil' electrons off, too. The atoms turn into a mix of ions and
electrons, called a plasma. This happens in stars. ```
```Chemical element
---------------
Historicly, in the nascent science of chemistry and in alchemy, an
element was a substance that could not be further decomposed into
simpler substances. Such material were the elemental building blocks
of all other substances. The word comes from Latin where the simplest,
fundamentals, basics were the L-M-Ns, like our modern A-B-Cs. 'El-em-
en' became the word 'elementum'.
Alchemy and chemistry gradually by brute force of experiment found
many elements but most were beyond human arts and skills to discover
until the 19th century. It wasn't until the 20th century that we
recognized that a chemical element is a species of atom with a one
number of protons in it. Such an atom in deed can not by chemical
treatment be broken into a simpler atom.
A substance made of two and more atoms, of the same or different
species, is a compound or molecule. Water is a molecule, compound,
having one atom of oxygen and two of hydrogen.
Each count of protons is its own element. An atom with 6 protons
is an atom of carbon. One of 26 protons is one of iron. The atomic or
element number of an atom is the count of protons in it and also the
ordinal number for the element. Iron is element #26; carbon, #6.
Today we found all of the natural elements from hydrogen #1 thru
uranium #92. We also fabricated artificial elements with more than 92
protons, up to, as at 2012, 117 protons. These were created by
crashing smaller atoms together under conditions that allowed them to
combine their nuclei into one.
Since there is a one-to-one correspondence of proton count and
element, we usually do not specify the protons when writing about an
element. Chemists know that. Other readers can look it up.
Most elements have two-letter abbreviations, either in English or
Latin. A bunch have single-letter abbreves. Since the mid 20th
century, all new elements by rule must have two-letter abbreves, even
if a single letter has no conflict with other elements.
A special case applies to two isotopes of hydrogen. That with one
proton and one neutron is called deuterium, abbreve D. That with one
proton and two neutrons is T for tritium. These are not really true
elements. The isotopes are so important in atomic physics that history
gave them distinct names.
The abbreviation is capitalized but the full name, at least in
English, is not. C for carbon, Fe for iron. ```
```Latin legacy
----------
Alchemy was practiced from the classical era and likely from
before then. Much of its litterature was written in Latin, including
names and technical terms. A set of elements retain their Latin in the
abbreviations and in many nomenclature situations.
The first set of Latin names is the seven classical metals, which
are also important n astronomy for the relation to the seven classical
planets
---------------------------------
element | Latin  abbreve | planet
--------+----------------+-------
silver  | argentum    Ag | Moon
mercury | hydragyrum  Hg | Mercury
tin     | stannum     Sn | Venus
gold    | aurum       Au | Sun
iron    | ferrum      Fe | Mars
copper  | cuprum      Cu | Juipiter
lead    | plumbum     Pb | Saturn
=================================
sodium    | natrium  Na |
potassium | kalium   K  |
antimony  | stibium  Sb |
-------------------------
There are a few other Latin legacy elements, those discovered in
the middle ages. I list them under the line in the above table. The
Latin names for the classical metals, but as far as I know not for the
others, are sometimes used in naming a chemical substance. Two
different compounds made from copper and sulphur are called 'cupric
sulphide' and 'cuprous sulphide'.
While Latin is no longer a routine language in the sciences, all
the elements are grammaticly second declension neuter nouns. The rules
for naming new elements state that the ending be 'ium' or 'um' to keep the
Latin heritage.```
```Isotopes
------
While a given element must have its proper count of protons, atoms
of the element may have a varying number of neutrons. The differences
may occur in the natural state of the element or may be induced in
atomic laboratories. The atomic or element number of the atom remains
the same but the mass number changes to match the count of both
protons and neutrons.
Ordinary hydrogen has just one proton for mass number 1. 'Heavy'
hydrogen, or deuterium, has one proton and one neutron for mass number
2. Both isotopes have element number 1.
In nature an element is a mixture of isotopes, with one usually
overwhelmingly dominant. That isotope's mass is practicly that of the
native substance. and almost always makes the whole mass number close
to an integer value. The annoying offset from integers bothered early
chemists before isotopes were known. It was widely believed the the
error was instrumental or practical but they did not reduce with
To indicate an isotope the mass number is written after the
element symbol. There are various typographic conventions but here I
simply append the mass number. Carbon with 6 protons and 6 neutrons is
C12 and one with 8 neutrons is C14. Oxygen with 8 protons and 7
neutrons is O15.
All isotopes of a given element behave just about equally in
chemistry. There are very subtile differences that for home astronomy
we may skip. As long as the atom has the proton count to be the
required element, the neutron count doesn't matter.
Some isotopes are by nature radioactive. They decay by ejecting an
electron or a helium nucleus to become some other element. Given
enough time such isotopes decrease to beyond detection from a given
sample of the element, leaving only its daughter isotopes. This ia a
feature that helps us to date the sample. This is radiodating, a major
tool in archaeology and planetary geology. ```
```Atomic mass
---------
Atomic mass is the mass number of the element in its native
condition, extracted from ore or mineral on Earth. It is the mix of
isotopes present in the original material and is not a integer number.
It happens that on Earth one isotope predominates in some very large
percent. This forces the atomic mass to be nearly integer, a fact that
fooled early chemists to think they were mistakes in measuring the
atomic mass. It 'should' be an integer because it's the count of
individual particles
When isotopes were discovered in the 20th century it was
recognized that the element was a mix of its isotopes, throwing off
the mass number from being an integer. The name of the measured mass
to 'atomic mass' was then enacted. Mass number is still the proton-
neutron count.
When working with quantitative problems in chemistry, using sample
of elements taken from nature, not artificially separated into its
isotopes we must use the mass number.```
```Molar mass
--------
The mass of a proton or neutron, being substantially the same, is
1.6605e-27 gram. This is a fanaticly tiny mass in human scale! The
reciprocal of this mass is 6.02214e23 proton/gram. This is Avogadro's
Number and a vernacular word for 'an immense number'.
The hydrogen atom is just a proton, plus negligible mass of an
electron. One gram of hydrogen contains 6.02214e23 hydrogen atoms. If
we have a boron atom, with five protons and five neutrons, its mass
number is 10. If we take Avogadro's number of boron atoms, the mass of
them is ten times that of hydrogen or 10 grams.
The same works for molecules, like water H2O. The mass number for
H2O is 1 + 1 + 16 = 18. 18 grams of water have Avogadro's number of
water molecules in it.
In general if we take a quantity of substance whose mass in grams
equals its mass number, that pile of matter has Avogadro;s number of
molecules of the substance in it. Such a mass is a mole and the gram
value of that mass is the mole or molar mass of the substance. The
molar mass of water is 18 gram.
This is important when reacting chemicals together to have the
correct amount of ingredients for the desired egredient. To form H2O
by burning a hydrogen gas in oxygen gas we must adjust the apparatus
to give 2 grams of hydrogen for every 16 grams of oxygen. Then the
gases will combine exactly into water.
If there's a mismatch of ingredient moles from those of the
egredient, we may end up with the wrong reaction product and left over
mass of certain ingredients. The desired product is contaminated.
The mole was originally defined in the CGS system where the gram
is the base unit of mass. In the SI scheme the kilomole is used, with
mass of i kilogram or 1,000 grams. In this system Avogadro's number is
6.02214e26, a thousand times larger. If the value is not explicitly
stated in the litterature in hand you could be horribly misleaded. ```
```Valence electrons
---------------
Chemistry works thru the outer farthest electrons of the atom.
These are the valence electrons, named for the concept of value or
worth of an atom. It has nothing to do with the top border of a drape.
It turns out thru nuclear and quantum physics that the outer shell
or valence shell can hold up to eight electrons, with two exceptions.
Hydrogen and helium can hold only two electrons in their valence
shells. All the other elements can harbor eight.
An element mayn't have eight electrons in its valence shell. An
atom may have from 1 thru 8 (minding the exceptions) leaving the
valence shell partially empty. Sodium has 1 electron, leaving 'holes'
for 7 more. Oxygen has 6, with holes for 2 more.
The placement of electrons into shells is a bit complicated. It's
not a neat 8x8 layering outward from the nucleus. It's easiest to
accept the shell configuration in tables and charts of the elements. ```
```Cations and anions
----------------
An element with one to three valence electrons has the urge to
release or share them and leave the valence shell empty. The shell
under it, closer to the nucleus, becomes the new valence shell and is
already filled to capacity. Such an atom is a cation.
The cation after shedding its valence electrons now has fewer
electrons than protons and acquires a net positive electric charge. It
is this charge that then allows the atom to merge with certain other
atoms to form chemical compounds.
Atoms with five thru seven valence electrons are called anions.
Those with 6 or 7 electrons normally seek out the missing 1 or 2 to
fill out their valence shell. These are anions. They then have charges
of -1 or -2.
An atom with five valence electrons will likely look for three to
fill the shell but also may dispense with these five to empty it. It
goes around with an exposed lower shell already filled with eight
electrons. ```
```Inert elements
------------
If an element already has all eight, with one exception, electrons
in its valence shell, it has no tendency to interact with other atoms.
It doesn't need or want to release electrons or acquire any. They do
not take part in chemical reactions and are the inert, or noble,
elements. Neon, argon, helium are some examples. The exception is
helium with only two electrons in its shell. That's all it needs and
We can force a noble element to form compounds by artificially
removing electrons. We then send it into other atoms. In nature this
does not happen. ```
```Valence number
------------
According as the number of valence electrons, an element has a
valence number from +1 thru +4 and -4 thru -1. The inert elements of
neon, argon, and others with complete valence shells have valence
number zero. The valence number is also called the oxidation number.
In general, atoms with positive valence number can merge into
those with negative ones. The electrons given up by the positive,
cation, atoms are attached to the negative, anion, atoms to form the
union of a new substance.
The valence number is the result of a complex study of the
electron configuration around the nucleus and isn't that simple to
guess at. We accept the value posted in chemical references. As one
complication, certain elements may have two valence numbers, one in
force under one circumstance; the other, under an other. Which to use
for a given situation is best left to the experienced chemist and we
home astronomers go along with that. ```
```Chemical bonds
------------
When atoms unite into compounds they exchange or share electrons
in effort to fill their valence shells. When the compound is formed
the two sets of valence electrons circulate around both atoms in a new
organization of energy levels. For our purposes we can think of the
valence shells as linking together, as often is depicted in textbooks.
In heavier elements with lots of electrons, the lower energy
levels of the valence shell can be less than the higher energy levels
of inner shells. For our purpose we can stay with distinct and
separate shells.
The commingling of electrons in a union of atoms makes the
compound very much different in behavior from the separate atoms. It
takes heavy quantum physics to predict the character of a new compound
beyond brute force fabrication. Bt the late 20th century the atomic
sciences were advanced enough to model atoms in a computer simulation.
SImple versions can be played with on home computers.
The most common kinds of union of atoms in inorganic chemistry,
that leaving out the complex combinations with carbon, are ionic and
covalent bonds. The ionic bond is a handover of electrons from the
cation to the anion while a covalent bond is a sharing of electrons
between the two.
In general the farther apart are the valence numbers, algebraicly,
the more likely is the bond to an ionic bond. Atoms with close valence
numbers tend to unite thru covalent bond.```
```Ions
--
An ion is an atom with an imbalance of electrons against its
protons. If it has too many electrons, it is a negative ion with a
minus electric charge equal to the number of excess electrons. An atom
with decess electrons have a positive charge equal to the number of
missing electrons.
Atoms in the wild are neutral because they can exchange electrons
with the surrounds and equalize the number to their protons. They can
become ions by forcibly adding or removing electrons, as in chemical
reactions.
An ion is denoted by the element symbol followed by '+' or '-'
marks, one for each unit of charge. A phosphorus atom with two
electrons removed is P++. The number of charge units on an ion is the
ionization number and may be almost any value obtainable with the
apparatus and processes to hand.
Do not confuse ionization number with valence number! A nitrogen
atom with valence number -3 does NOT have 3 electrons too many! It has
the proper number to be neutral but can take on three more in a
chemical process to fill its valence shell.
When compounds are dissolved in water its atoms can dissociate to
a minuscule degree and be free ions. The nitrogen atom from such a
compound would then have ionization number of -3 because it now does
have three excess electrons. ```
```Polarized molecules
-----------------
Since a molecule is typicly made of cations and anions there are
usually hotspots of negative and positive charge on its perimeter. The
negative charge is against the nionm which has excess electrons from
the bonding. The positive charge is against the cations, with fewer
electrons.
Altho the entire molecule is neutral, because there is no
migration of electrons across the perimeter, only a shuffling within
it, the presence of charged hotspots allows molecules to link together
into lattices, jungle-gym, monkey-bar grid. The link is by
electrostatic attachment of the negative part of one molecule to the
positive part of its adjacent molecule.
The lattice in bulk generally forms a crystal, a gem with flat
smooth sides and geometric symmetry. The shape, sides and angles, of a
natural crystal is the direct result of the microscopic shapes and
fitting of molecules. By studying the macroscopic crystal we get clues
to the atomic scale makeup of the molecule.
The lattice or crystal bonds are weak compared to the bond within
the molecule. The crystal can be mechanicly sliced across these bonds,
which is exacta mente how gems are cut. As exam[pe water, H2O, in
solid form links into hexagonal arrays. That's why snowflakes are six-
sided and frost has a dendritic pattern. ```
```Nomenclature
---------
A chemical compound is an ensemble of atoms into a molecule, a
unit of several atoms being the smallest particle of the given
substance. If a molecule is divided it breaks into its component
atoms, the very elements themselfs.
The usual compound is made of a cation and an anion. In the name
the cation is placed first, then the anion. Both embed the name of the
main element they consist of. In many cases the cation or anion is
made of several atoms and one of them is used in the name.
When a compound is made of several cations and anions, all of the
cations are placed first, followed by the anions. In the chemical
formula notation for the compound the atoms in each part may be
grouped together in parens.
The union of sodium with chlorine yields sodium chloride. The
'sodium' part is the cation, the sodium element. 'Chloride' includes
the stem or root of 'chlorine' as the anion. The anion often has a
suffix that denotes certain combinations of atoms but here we can just
learn the names of many common anions by rote.
Calcium carbonate has for its anion a group of carbon and oxygen.
The name 'carbonate' comes from applying assorted nomenclature rules
but we can just memorize the combination and name.
For the hell of it, many prefixes and suffixes for chemical names
derive from Latin of the 16th thru 19th centuries. 'Carbonate' comes
from 'carbonas' in the nominative case and the stem for other cases is
'carbonat-', The dative plural of carbonas is carbonatibus, which may
The modern standard is to explicitly give the number of cation and
anion parts in the molecule, with some leeway. This is done by
prefixes for numbers in a mix of Greek and Latin. Water has two
hydrogen atoms as the cation and one oxygen atom as the anion.
Probably no chemist really says 'dihydrogen oxide' but that's the
pedanticly correct name. It says '2 hydrogen, 1 oxygen'.
An other modern standard is to explicitly write in the number of
electrons in the element's valence shell as a Roman numeral in parens.
What we used to name as cupric sulphate is now stated as copper(II)
sulphate, giving the copper atom two electrons. ```
```Prefixes
------
The modern rule, not yet fully carried out among chemists, is to
explicitly state the number of atoms in the two parts of the compound
by numerical prefixes. If there is only one atom is both parts, no
prefix is needed. Sodium chloride has 1 sodium and 1 chlorine atom.
The numeral prefixes, up to ten, are
----------------------------------
number | prefix || number | prefix
-------+--------++--------+-------
one    | mono-  || two    | di-
three  | tri-   || four   | tetra-
five   | penta- || six    | hexa-
seven  | hepta- || eight  | octa-
nine   | nona-  || ten    | deca-
---------------------------------
For euphonic sake the final vowel may be dropped to blend the
prefix into the stem in the chemical name. Do note well that these
prefixes are NOT all coincident with the other sets of numerical
prefixes. You have to remember these here for chemistry. ```
```Chemical formula
--------------
The chemical formula is a shorthand way to specify the atoms in a
compound. It uses the element abbreves in the same order: cations,
then anions. The count of each part is placed after it, except that a
'1' for a single unit is missed out.
We have NaCl for sodium chloride and H2O for water. Stricta mente
the count number is a subscript in typeset work. With ASCII typography
it is a full-size char within the rest of the typeface.
If the part consists of a group of atoms, the group is put in
parens with its count following it. ammonium sulphate is (NH4)2(SO4).
The '2' applies to the unit NH4.
The chemical formula in text form does not well describe the
spatial arrangement of atoms in the molecule. Some chemists try to
group the atoms in the formula to show how they are laid out in the
molecule but there can be ambiguities. The atoms for C2H6O can be
arranged as ```
```       H     H                 H  H
|     |                 |  |
H--C--O--C--H    and    H--C--C--O--H    plus others
|     |                 |  |
H     H                 H  H ```
```    These are two different substances, yet can be written with the
same text formula. We could try writing the formulae for these
compounds as (CH3)2O and (CH3)(CH2O)H.
An other example is C4H10, yielding ```
```       H  H  H  H                 H  H  H
|  |  |  |                 |  |  |
H--C--C--C--C--H    and    H--C--C--C--H    plus others
|  |  |  |                 |  |  |
H  H  H  H                 H  |  H
|
H--C--H
|
H```
```    We could write these in text form as (CH3)(CH2)2(CH3) and
(CH)(CH3)3. Such jiggering of the atoms in the formula helps visualize
the molecule but do fall short of removing all uncertainty.
A powerful way to clear up ambiguity is to write the chemical in
its structural formula. This is a stick-figure showing the connections
between the atoms. The examples above are structural diagrams. ```
```Dot diagram
---------
One of the more fun aspects of chemistry for the home astronomer
is constructing diagrams that show the actual attachment of atoms into
compounds. This is done thru the dot and stick diagrams of the
molecule. Often they are both called the structural diagrams. These
are only an approximate model because atoms and molecules are 3D
figures and we draw the diagrams on 2D paper.
In the examples of C2H4O and C4H10 I used the stick form of
structural diagram to show how two different compounds can have the
same ASCII formula. The sticks between the atoms are built by the
arrangement of the valence electrons around the atoms.
We tabulate, mentally or on paper, the atoms, their number of
valence electrons, and number of places for electrons om their valence
shell. This last is 8 except that for hydrogen it is 2. We then add
the total number of electrons, the pool from which the valence shells
are filled by sharing or swopping electrons. The deficit of available
electrons from those needed to fill the shells are the electrons that
must be shared or swopped.
We try this for potassium nitrate, KNO3. Build the table```
```    atom      | has | needs | total
----------+-----+-------+------
potassium |  1  | -1    |  0
nitrogen  |  5  | +3    |  8
oxygen    | 18  | +6    | 24 (3 atoms)
--    --      --
24    +8      32 ```
```    In general, all elements with 4 or more valence electrons need to
get 8 electrons for its valence shell. Potassium almost always gives
up its one electron rather than try to acquire 7 more to fill its
shell. That's why it needs -1 electron, it doesn't need it.
In compounds it prefers to live with the next inner shell, already
filled with 8 electrons. Atoms with 3 electrons usually release them
but sometimes they do try for the full 8. You may have to do a dot
diagram both ways to get the better fitting of the atoms.
We now arrange the atoms to distribute the available electrons so
each has its valence shell filled. You may have to try a couple times
before getting the correct arrangement. ```
```              **
**O**
I
**
**   |      **
K~**-O-**-N-****-O
**          **
```
```    We count up the electrons, the asterisks. We did use all 24
available ones. We also filled all valence shells with all 32
electrons. The difference, 8, are the ones shared among the atoms.
The nitrogen attaches to two oxygen by a single pair of electrons
each and to one oxygen by a double pair.
The potassium atom looks in the diagram to have two electrons in
its valence shell. In fact it has none because it gave up its electron
to the adjacent oxygen, Potassium is doing just great with its new,
closer, filled shell, not shown in the dot diagram.
Because the valence shell has 8 electrons it's convenient to draw
the electrons in pairs 2x2 around the atom. Based on quantum theory
the electrons are paired in an atom. Each valence shell (except for
hydrogen) has four pairs of energy levels with it. Each pair may be
filled with an electron or empty. In forming a compound the strong
tendency is for the electrons to unite in a way that fills each pair
of energies with electrons.
A second example is calcium bicarbonate, Ca(HCO3)2. We put the
group HCO3 is parens to show that there are two of them. First tally
the electrons, minding the count of all the atoms ```
```        atom     | has | needs | total
---------+-----+-------+------
calcium  |  2  |  -2   |  0
hydrogen |  2  |  -2   |  0 (2 atoms)
carbon   |  8  |  +8   | 16 (2 atoms)
oxygen   | 36  | +12   | 48 (6 atoms)
--     --     --
48    +16     64 ```
```    We have 48 electrons and need 18 more to fill the shells. These 18
must be shared between two atoms. We get ```
```         **        **         **        **
H~**-O-**-C-**-O-**~Ca~**-O-**-C-**-O-**-H
**   |    **         **   |    **
****                 ****
|                    |
**O**                **O** ```
```    Remembering that hydrogen and calcium prefer to give up their
electrons to the adjacent oxygen, we got 48 available electrons
distributed to fill the valence shells with 64 electrons. The CO3
radical attaches to the calcium where its two electrons were.
Please distinguish between actual electrons, the asterisks in the
diagrams, and the 'virtual' ones, those counted twice for each of
their adjacent atoms. The overlap is the shared electrons in the
'needs' column in the tabulation.
The layout of electrons is merely depictive and is in no way their
physical and spatial arrangement in the molecule. The valence shells
morph into new shapes and sizes that enclose all the atoms as a new
unit. They do not link up like the Olympic emblem and there is no
longer a fill-to-8 pattern.
This is dramatcly emphasized in the spectrum of a molecule. It is
not just a superposition of spectra of the conponent atoms. It is an
entirely new one based on the all-new deployment of electrons. ```
```Stick diagram
-----------
Each pair of electrons joining two atoms is a bond and is replaced
by a line for the stick version of the structural diagram. Electrons
that do not join atoms are left out of the stick diagram. The stick
diagram for KNO3 and Ca(CO3)2 are ```
```         O                  O          O
|                  ||         ||
K-O--N==O    and   H-O--C--O-Ca-O--C--O-H
```
```    We try to minimize sprawl and clutter in the diagram. This is not
really how the molecule looks like but it is how their atoms are
joined. Calcium is tied to oxygen, not carbon, and potassium is tied
to oxygen, not nitrogen. The flat paper can not realisticly portray
the solid molecule.
One problem newcomers to chemistry have is that it's easy to just
join arbitrary atoms together with sticks, bonds, with no attention to
the valence electrons. You can come up with very intriguing molecules
that can not exist in nature. It is wise to first do a dot diagram and
then convert it to a stick diagram.
A common simplification in organic chemistry, when carbon and
hydrogen are dominant parts of the molecule. is to leave out the
symbols 'C' and 'H' for these atoms. This makes a less busy picture,
better for a complex or large molecule, but it can be tough to
properly interpret at first.
There are clues. Hydrogen always has only one bond to it. The
stick where it should attach to has a free end. Carbon almost always
has four bonds and is at the junction of four sticks. All other atoms
are written in.
By the way the dot diagram is also called the Lewis diagram and
the stick one is the Kekule' diagram. And this is a good thing. The
original method devised by Lewis was revised into today's method, used
here, but we keep the historical name. ```
```Structural models
---------------
You can buy molecule models. This is a box with compartments, like
a large candy box. In the pockets are rods and balls to represent
atoms and the bonds between them. The balls have differing number of
holes for the valence numbers and may be color-code for the very
element or at least the signum of the valence number.
To make a structural model of a molecule, take out the balls for
each atom in the molecule and also a bunch of rods of assorted length.
Press the rods into the atoms to make a hub-&-spoke construction.
Done properly, at least for simple molecules, you have a 3D model
of the way the atoms attach together. While this is far better than
the flat diagrams, there are still limitations. If an atom has two
bonds to an other, the rods will not fit them together. The holes do
not line up. In the kit may be rods made of flexible plastic or a
metal coil that can be bent. These are used for the double bonds.
There are many computer molecule building programs that compose
the molecule and allow it to be manipulated, like a solid model in the
hand. The bonds are figured out on the fly as you add atoms. Certain
wrong bonds are trapped and rejected. The presentation on screen may
be schematic, like a 3D Kekule' diagram, or a realistic rendering with
balls for atoms, of their proper sizes and separations.
Like on paper, the ability to tie together two arbitrary atoms
does not prove they in nature can in fact become a molecule. Certain
bonds and atoms just do not go together. For one point when atoms
combine their radii change. The atom that gives up its electrons, the
cations, get smaller because they lose their outer shell. The anion
atoms remain about the same size because they are filling in a shell
```Natural gases
-----------
Many gaseous elements in nature are molecules of two atoms, rather
than isolated atoms. Chlorine, nitrogen, hydrogen, as examples, are
molecules of Cl2, N2, H2. The dot method of assembling the valence
electrons of atoms, shows just how these molecules are formed. For
chlorine we have two atoms with 14 electrons between then but they
need 16 electrons for full valence shells. We get ```
```           **    **
**-Cl-**-Cl-**    and    Cl--Cl
**    ** ```
```Nitrogen and hydrogen yield, skipping the explicit electron count
--
**-N-******-N-**    and    N==N ```
`and`
`        H~**-H    and     H--H`
```    Other common gases in the air are carbon dioxide, CO2, and
methane, CH4. These have dot and stick diagrams of
**            **
.         O-****-C-****-O    and    O==C==O
**            ** ```
`and`
```             H
~
**                    H
|                     |
H~**-C-**~H      and    H--C--H
|                     |
**                    H
~
H
```
`    An other interesting atmospheric gas is ozone, O3 `
```         **O-****-O**
\    /
**  **    and    O==O
\ /            | /
**O**           O ```
```    Understand that these natural gases are gases ONLY because on
Earth the pressure and temperature allow them. On Titan, Saturn's
largest moon, methane is a liquid in nature. On Mars carbon dioxide is
a solid ice. On the Sun hydrogen is a plasma. ```
```Limitations
---------
I already noted that the dot and stick, Lewis and Kekule/,
diagrams are crude representations. The figures are on flat paper but
the atoms are arranged in three dimension. In the diagram water is
shown as a linear molecule, H--O--H but it is really a bent molecule.
The angle at oxygen between the two hydrogen in about 105 degrees.
Methane is drawn with four hydrogen spaced in a plane 90 degrees
apart. They are really at the points of a tetrahedron around the
carbon. The angle at carbon between two hydrogen is about 109 degrees.
An other limitation is that we say nothing about the bond
strengths. All bonds are merely dots or lines in the diagrams. The
ability of a bond to hold its atoms together varies widely. This is
one factor that governs the chemical behavior of the molecule. The
double bond for the oxygen molecule have different tightness. One is
much stronger than the other. In the molecule of C2 the dot method
gives four bonds between the atoms, Two are strong and two are weak.
The method of counting up the electrons and filling valence shells
can break down in peculiar situations. We already saw that a chemical
formula could represent at least two entirely different compounds. If
you try the dot method, you'll actually find them, plus other suitable
solutions, with no evident way to choose among them.
In spite of these limitations, both dot and stick figures help
immensely to see the interaction of atoms in compounds. And they are
fun to play with!
```
```Periodic table
------------
The properties of the elements are collected into one omnibus
chart, the Periodic Table. The table is a array of the elements by
atomic or element number. Since the element number is also the proton
and neutral electron count, this ordering also sorts the elements by
the electrons in their valence shells.
Here is a skeleton Periodic Table. A more complete one is readily
taken from textbooks or websites.```
```      +1                                              0
I                                               VIII
+------+ +2     +3     +/-4   -3     -2     -1   +------+
1 | H   1| II     III    IV     V      Vi     VII  | He  2|
+------+------+------+------+------+------+------+------+
2 | Li  3| Be  4| B   5| C   6| N   7| O   8| F   9| Ne 10|
+------+------+------+------+------+------+------+------+
3 | Na 11| Mg 12| Al 13| Si 14| P  15| S  16| Cl 17| Ar 18|
+------+------+------+------+------+------+------+------+
4 | K  19| Ca 20| Ga 31| Ge 33| As 33| Se 34| Br 35| Kr 36|
+------+------+------+------+------+------+------+------+ ```
```    The table starts at the upper left with hydrogen with its one
electron in the valence shell. The next element, helium, has two
electrons in its shell, this also being the shell's capacity. Helium
is placed at the upper right of the table, along with other elements
with filled valence shells. Helium and these other elements are inert
and do not participate in chemical interactions.
From element #3, lithium, and out the second higher valence shell
fills in electron-by-electron with increase in element number. Lithium
begins a new row, having one valence electron. There after come
elements #4 thru #9. This last, fluorine, has 7 valence electrons. The
last element in this row is neon, element #10, with all eight valence
electrons. This row covers one 'period' of valence shell filling,
whence the name of the table.
Element #11, sodium, begins the third row and a new outer shell is
filled one-by-one. This row ends with argon and its complete valence
shell. The table continues period by period.
It is well to photocopy a flat Periodic Table, cut it out and roll
it into a spiral cylinder. Helium is adjacent to lithium, neon to
sodium, and so on. This shows that chemical behavior is a continuum of
electron population element-by-element and avoids the Mercator effect
of flat maps of the world.
There are a few wrinkles along the way. Some elements must be
accommodated in a loop that diverts from the table and then rejoins
it. One loop starts after calcium with scandium and ends with zinc.
The loop rejoins the table before gallium. This loop includes iron,
cobalt, nickel, and copper.
On most printed versions, thee loops are shown as separate series
of elements under and detached from the main table. Suitable
annotation tells where they fit into the table.
The information contained in each box for an element varies widely
with author. At least the element number, name, abbreve, and atomic
mass are given. If the box is large enough much more details about the
atom can be provided. Some can be melt and boil temperatures, quantum
description of electron shells, percent occurrence in Earth, mass
numbers of isotopes, geometry of crystal, radius of valence shell.
Each horizontal row in the table, including the first one with
just hydrogen and helium, is a 'period' and covers the electrons in
the same shell around the nucleus. The next row starts the next
farther higher shell. Some charts number the periods for the level of
the shell it relates to. The hydrogen-helium row is period #1. The one
with carbon is period #2. The one with silicon is period #3.
The vertical columns tell the number of electrons in the valence
shell. They are also called 'groups' and are numbered I thru V111 in
Roman numerals. The number is the electron count in the valence shell.
Some charts note in Arabic numerals the valence number for each group.
By historical glitch the Roman numbers were applied also to the
elements within the diverging loops and do not directly give the count
of valence electrons.
When the Periodic Table was invented by Mendeleyev, chemistry was
still in a clumsy state. Many elements were not yet known, leaving
holes in the table. The table actually helped in the hunt for these
missing elements by foretelling their valence, mass number, and some
physical properties. Nu World War II the entire slate of elements was
filled in. Then after the Periodic Tale was extended for the
artificial elements heavier than #92 for uranium.
```
```Radicals
------
A radical, from 'radix' a root, is a group of atoms treated as a
unit in forming compounds. It may be considered an ion made of several
united atoms. They can not exist for long on their own but must be
attached to other atoms for stability. In the free state they are
charged because they have excess or decess electrons. A positive
charge radical can be a cation; negative, anion.
A common way to flag a radical is to write its formula with a
leading or trailing '-'. This suggests that it is not a complete
molecule but has a attachment point for other atoms. SO4 could be
interpreted as sulphur tetraoxide, if there be such a molecule. -SO4
flags it as the sulphate radical.
The bonding of atoms within the radical is stronger than the bond
of the radical to other atoms. When the compound is broken up, the
radical can stay intact, ready to attach to some other atoms. The
imbalance of electrons against the protons gives a radical the
equivalent of a valence number. The sulphate radical, -SO4, has a
valence of -2. It can combine with atoms whose valences add to +2.
There are rules and restrictions for creating radicals but it's
just as easy to look up the names and formulae. Most of the common
radicals are made from one element plus a few oxygen atoms. Sulphate,
is a combination of 1 sulphur and 4 oxygen, -SO4.
When the structural formula is drawn for a radical we find there
are left over valence electrons. These are used by the radical in
chemical reactions. The carbonate radical, -CO3, is
**        **
|         |
-*-O-**-C-**-O-*-    or    -O--C--O-
**   |    **                ||
**
**                      O
|
**-O-**
|
** ```
```    Counting the electrons we find two oxygen valence holes are
vacant, ready to attach to atoms in a new compound. The atoms tying
onto the carbonate radical would be cations, with electrons to share
or give to the carbonate.
The hydroxyl radical, -OH, is ```
```           **
|
-*-O-**~H-   or    -O--H
|
** ```
```    The extra hole on the oxygen attaches the radical to other atoms.
If that other atom is a hydrogen, we get H-OH, H2O, water. ```
```Acids and bases
-------------
An acid in chemistry is a compound whose cation is hydrogen.
That's all there is to it. Acids tend to be corrosive substances but
the chemical quality is the presence of the hydrogen cation. Sulphuric
acid or dihydrogen sulphate, H2SO4, is ```
```                 **
**O**
|
**                           O
**     |      **                    |
H~**--O--**--S--**--O--**-H    or    H-O--S--O-H
**     |      **                    |
**                           O
|
**O**
** ```
```    Two of the four oxygen have free negative hooks that then attach
to two hydrogen to complete the compound. The radical is the -SO4
as the anion and the acid nature comes from the two hydrogen cations.
A base in chemistry is a compound whose anion os the hydroxyl
radical, -OH. Calcium hydroxide Ca(OH)2 has structure ```
```             **           **
H~**--O--**~Ca~**--O--**~H   or    H--O--Ca--O--H
**           ** ```
```Two hydroxyl radicals tie to one calcium.
When an acid and a base react, they produce a salt and water. The
salt is the compound made from the anion of the acid and the cation of
the base. The water comes from the hydrogen and hydroxyl parts. The
components of the ingredient compounds swop places.
When hydrogen chloride, also known as hydrochloric acid, and
sodium hydroxide combine we have ```
`    H--Cl + Na--OH -> Na--Cl + H--OH `
```    Sodium chloride is the salt, the name for a egredient of an acid-
base reaction. Sodium chloride is the ordinary food condiment. It, an
essential part of a balanced diet, is formed from two nasty poisons!
A combination of hydrogen carbonate and calcium hydroxide yields```
`    H--CO3--H + OH--Ca--OH -> Ca==CO3 + 2(H-O-H) `
```    The egredient salt may be soluble in water, like the food salt. It
can be insoluble, falling out as a precipitate. Calcium carbonate.
This is a form of limestone, a common component of sedimentary rock.
It was deposited by acid-base interaction over geologic time spans. ```
```pH number
-------
I pretty much have to discuss this parameter of chemistry because
you likely heard of it and maybe measure it for medical or hygienis
reasons. It's based on the natural ions in pure water. Altho H2O is a
compound it does by itself dissociate very weakly into hydrogen H+ and
hydroxyl OH- ions. The concentration of these ions is very low, some
1e-7 or one part in 10 million.
The pH number is defined as ```
`    pH = -log(conc H+) = -(exponent of the conc H+) `
```H2O has a pH value of 7, coming from -log(1e-7). This is considered to
be neutral, being neither acidic nor basic.
If for some reason, like adding an acid, the concentration of
hydrogen goes up, the pH value decreases. A substance with pH less
than 7 is acidic.
When a base is added to water, the concentration of H+ decreases.
It is displaced by the additional PH- ions from the base. The pH
increases. A substance with pH more than 7 is basic.
In medicine and hygiene the pH of a fluid is partly governed by
diet. According as the trend of pH, you may have to alter your diet or
use supplements that adjust the pH. ```
```Chemical reactions
----------------
I offer here a few examples of how reagents, the ingredient
compounds, work together into new compounds. In a couple cases we find
that the valence or oxidation number of an atom is altered! That's why
it's best not to treat the number as a true property of the element
but as one of several possible values. The usual change is to the
complement value, from giving up electrons to empty the valence shell
to taking in electrons to fill it.
Zinc sulphide and oxygen from the air can react to form zinc
sulphate. ZnS + O2 -> ZnSO4. I remind that in air many gas elements
cohaere in pairs, like oxygen here. Let's play with the structural
diagram ```
```    **        **
Zn--****--S    or    Zn==S
**        ** ```
`reacts with`
```      **       **
2( O--****--O )    or    2( O==O )
**       ** ```
```to become
**
**O**
|
**                     O
**     |      **              |
**O--**--S--**--O**    or    O--S--O
|      |      **           |  |
**     **                 Zn--O
~      |
Zn~~**--O**
**```
```    The proportion of ingredient to egredient is constrained by the
mole masses, such that the mix of atoms into the reaction must equal
that out of it. This is the concept of matter not being created or
destroyed in ordinary chemical processes.
We can not take an arbitrary amount of input chemicals to produce
a pure output chemical. In the example of burning aluminium in free
`    Al + O2 -> Al2O3`
```The right side is the correct formula for aluminium oxide, two Al and
three O atoms. This reaction is not balanced. The atoms on the left
are one Al and two O. We need an other Al and an other O. If we keep
oxygen in its native molecular state, not trying to break it into
separate atoms, we must add more aluminius and oxygen on the left to
arrive at ```
`    4 Al + 3 (O2) -> 2 (Al2O3)`
```    The proportion makes an exact pure product. If we used any other
proportion (not a multiple of this one) we get aluminum oxygen mixed
with leftover aluminium or leftover oxygen.
Here is where the mole mass comes into play. The mass number of
aluminium is 27. That of oxygen is 16. Thee are rounded from the exact
values in the Periodic Table. The atomic mass there is the weighted
average of all the isotopes in the natural form of the element.
To make the pure product here we need 4*27 = 108 mass units of
aluminium and 3*2*16 = 96 mass units of oxygen. These yield 204 mass
units of aluminium oxide. The mass units may be any consistent unit.
In school labs this is usually grams to keep with the concept of a
mole mass. The mole mass, or one mole, of a substance is the sum of
the atomic masses in the substance stated in grams. The mole mass of
natural oxygen is 32g.
In manufacturing of aluminium oxide, as an abrasive for tools, the
input units of mass may be tons, truckloads, cargo shiploads, as long
as the proper ratio is maintained. ```
```Conclusion
--------
Home astronomers ever more so must be litterate in disciplines