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=head1 Personal Background
As part of a 5-year interdisciplinary Cellular and Molecular Biology
program, I very nearly completed a second B.S. in Chemistry (lacking 1
course as I recall). However that was many years ago.
My recent interest came from:
=list *
=item Bioinformatics: What's the latest on protein folding?
=item Peak Oil: What do we use oil for, and what will we use to replace it?
=item Post-oil survivalist: How is gunpowder made?
=item Politics: What was that "high explosive" the Bush administration
handed to the Iraqis to the tune of 375 tons? How long will that last
as a source of "terrorism" (and thus neocon raison d'etre)?
=end list
A few days in the UW Chemistry Library showed the elements were pretty
much as I'd last seen them, and the fields of analytic, inorganic,
organic and biochem were as well. What had changed was the laboratory
technique, the use of simulation software, and the importance of
catalysts.
#--------------------------------------------------
=head1 Chemistry
Chemistry is a complex field. So complex that until the 1900's we
didn't even grasp the basics, and in the 2000's we are still
struggling to understand the workings of our own bodies.
This essay explains how I've tried to understand the current state of
Chemistry. It (both Chemistry and my understanding) is a work in
progress. "Chemistry" isn't solved until we can predict the outcome
of any mixture of ingredients, under any temperature and pressure
conditions.
#-----------------------------------
=head1 History
Primarily from L<"#brock92","brock92">. This is my own choice of key
ideas. Read Brock for the human story behind the ideas.
=head2 Matter is conserved
There is I, and it has mass. We may not know what it is,
but it doesn't just appear and disappear magically. Therefore if a
chemical reaction seems to make stuff come and go, we must look
deeper.
This was not obvious. A big tree grows seemingly from a simple seed.
As a wood fire burns, the mass of the wood seems to disappear. It
takes sophisticated techniques and equipment to even suggest, much
less test this hypothesis.
=head2 Phases
The I can be solid, liquid, or gas depending on temperature
and pressure. That being so, it is possible to separate phases
(evaporation, condensation, freezing). This leads to the possibility
of distillation.
This is not obvious. Early chemical materials were mixtures. Heating
might cause reactions, including burning. Evaporation might let gases
escape the reaction vessels. Condensation on the walls of equipment
might be missed.
Even if all these were tracked, you might have a mixture (e.g., water
and ethanol) which at some point evaporates at the same rate (keeping
the ratio the same).
To predict these effects, we needed "partial pressure" and gas laws,
specific heat, crystallization, To explain them, we need the notion of
heat as motion, and statistical mechanics.
=head2 Elements
The I comes in specific types, with separate phase
transitions and different mass-per-unit.
The idea is trivial to contemplate, but bitterly hard to test.
Chemists, even with the best methods and techniques were battling a
complex reality.
=list 1
=item Very few elements are easily found in a pure form. They come
in fairly stable groups (molecules), which are sometimes hard to take
apart and put together. Further, the tools for assembly and
disassembly are themselves molecules. You have to solve the problem
iteratively.
=item Even if pure, they may be in molecules or other hard-to-break
assemblies. Thus H_2, N_2, O_2. To distinguish these, we need an
experimental technique and a theory. If the same volume of gas at the
same temperature and pressure hold the same number of molecules, then
we can compare weights of gases and work back to relative weights of
elements.
=item Even if you do all this work, the answers are disappointingly
non-integer. It takes real faith in the scientific method and in
experimental technique to accept those numbers. You have to
hypothesize and test for isotopes and natural distributions to make
sense of fractional atomic weights.
=end list
=head2 Molecules
Elements come in standard assemblies.
As noted, you have to simultaneously solve the idea of elements and
the idea of molecules. Given elements, and the ability to map from
weight to number of atoms of each element, you can determine the
"stoichiometry", or relative number of atoms of each type used in a
reaction. Assuming the reaction goes to completion, this tells the
resulting molecule's makeup.
In practice you may have mixtures of resultants with different ratios
(e.g., H2O, H2O2, NO, NO2, NO3). You may have other chemicals tightly
stuck in the mixture, e.g., "hydrated" with water molecules.
=head2 Atomic orbitals
Elements are atoms, made of a heavy nucleus surrounded by electrons in
shells described by quantum mechanics. The nucleus gives the atomic
weight (including the vagaries of isotopes). The outer shell(s) give
the chemical propensity to connect with other atoms.
This is one of those really non-intuitive hypotheses of the early
1900's. Yet it explained the empirically observed "periodic table"
and thus the relationship of weights to valences and to chemical
reactivity.
=head2 Bond angles
The outer electron shells can be computed in probabilistic patterns.
The high density areas are where electrons can interact with other
atoms. The shapes provide preferred bond angles. Atoms thus interact
in certain geometric patterns.
Since this is a probabilistic setup, bonds come and go, so we are
interested in relative rates. Probability patterns can be altered by
nearby conditions, so we may compute molecular orbitals.
Computational quantum chemistry operates at this level, simulating
chemical interactions.
=head2 Energy is conserved
It is pretty obvious when heat makes water boil or burning wood gives
off heat. It took a lot of careful experimentation to determine that
energy was conserved, because it can take so many forms. E.g., heat
of evaporation, chemical bonding, lattice energies and strained bond
angles, heat (motion of particles), vibration (motion internal to
particles).
=head2 Structure determines Properties
My original title for this section was "It's the Geometry, Stupid".
Then I noticed the title of the opening chapter of
L<"#carey03","carey03">, and realized it was more dignified.
Chemistry is the study of reactions among atoms, usually in the
context of mixtures of molecules. Those reactions are mediated by
short distance forces (short compared to the whole molecule). Thus
the reactions are local. The geometry which puts potentially reactive
atoms side-by-side is the key. E.g.:
=list *
=item Water (H2O) is a good polar solvent because O grabs the H's
electrons and the bond angles put the now-positive H's slightly to one
side. This makes the whole molecule ionically off-center, and thus
able to dissolve ionic (polar) compounds.
=item A molecule may be left or right handed (chiral). If it can be
crystallized, this may be directly observable. Otherwise, light
polarization can show differences.
Life-on-Earth depends on many chiral molecules (generally
left-handed). A wrong-handed rendition can be deadly. Biology is
good at making only the needed kind. Typical organic synthesis makes
a racemic mixture of all variants (enantiomers).
=item Catalysts operate by grabbing a molecule and holding it ready
for a reaction, and then letting it go once the reaction completes.
(Of course there is no intention in this -- it is just a matter of low
energy states.) A highly specific catalyst has holes shaped for
specific molecules.
=item Proteins operate by folding (due to short distance bonding) into
complex shapes. Those shapes have evolved due to fitness value
(sometimes hard to discern).
=item As a special case of protein folding, enzymes operate by folding
into shapes that happen to fit other molecules, such that the enzyme
is a catalyst.
=end list
#-------------------------------------------------
=head1 Undergraduate Textbooks
Next stop was to read current chemistry texts. Had
L<"#zumdahl02","zumdahl02"> and L<"#carey03","carey03">, so used
those. I don't know if they are the best-of-breed, but multiple
editions is a good indicator.
=head2 Principles
According to the author blurb in L<"#zumdahl02","zumdahl02">, Zumdahl
is an outstanding teacher. The book lives up to the reputation. Each
topic is clearly setup, plenty of photos to get students into the
ball-park, clean derivation of key formulas, etc. Also has plenty of
answered problems, so could be used for self study. Zumdahl is
excellent at making the connection between undergrad-level ideas and
real world chemistry problems (and exposes enough of the complexity to
either scare or whet the appetite of the student).
What I didn't like was the order of presentation. The old "wet"
chemistry is covered (very well) in the first 500 pages. You have to
get to pg 503 before you hit quantum mechanics. Yet all the previous
material was just alchemical recipes and cataloged rules-of-thumb
without that electron-shell understanding. I suppose he was required
to covered the wet-side to be an official chemistry text. Maybe it
was needed to coincide with chem labs.
At any rate, he does a fine job on the quantum half of the book too.
He is conscientious at explaining that the models are all models, not
verbatim reality. He uses this effectively to contrast Lewis models,
from Local (atomic) Orbitals, from Molecular Orbitals -- and to
explain where each might be a useful tool.
The book closes with a few chapters on the chemiistry of the groups in
the periodic table, and then on biochemistry. For the first, I'd
choose "Chemistry of the Elements". For biochemistry, Carey has a
better treatment. Neither comes close to my old biochem text, so I'm
sure there are better treatments out there today.
=head2 Organic Chemistry
Organic chemistry ("o-chem") is the study of molecules which have
carbon atoms. Originally, it was assumed these were based on life
processes (thus "organic"), but these days it is mostly the story of
petroleum processing. (Biochem covers the chemicals actually used in
life processes.)
L<"#carey03","carey03"> starts off with a quick review of quantum
and thus geometry-based chemistry. But after that it is a grim
encyclopedia of organic groups, giving:
=list *
=item nomenclature
=item bonding
=item synthesis
=item spectroscopic analysis
=end list
That is about how I remember organic chemistry. Surely by now the
field is ripe for an automated expert system, instead of rote
memorization.
=head2 Physical Chemistry
Physical chemistry ("p-chem") is math-intense physics applied to
chemistry. Its origins were in statistical analysis of the kinetics
of atoms/molecules in gases. Also, it covered the forms of energy,
enthalpy, and entropy in determining the equilibria of reactions
(thermodynamics) and the rates of reactions (kinetics). However, with
the discover of quantum mechanics these stories had to be re-invented.
We now have the old classical approach and a growing world of
"computational chemistry".
The standard text is L<"#atkins02","atkins02">. In the 2002 edition,
you get a 300 page rendition of classical p-chem, and then turn to
quantum mechanics. The writing is clear, the examples are solid, and
there are answers to the problems for self study.
An alternative text is L<"#engel06","engel06">. The UW is using this
at the moment (Summer 2005). I was leary at first, because this is a
UW required text written by (drum roll) UW professors. It has answers
for some of the problems, and there is a solution manual with worked
out answers. The claim is that it can be studied in any order, thus
allowing a quantum-first approach. To me, engel06 is a bit better at
explanations than atkins02 (important for self study).
The clincher for me to get engel06 was a chapter on computational
chemisty by Warren Hehre. That too was clearly written, with
explanation for how the models evolved. In fact, that is where I
started the book. Next I turned to the rest of the quantum mechanics
material, and then to the classical material.
On the other hand, atkins02 has some topics not covered in engel06, so
both are needed.
#-----------------------------------------------
=head1 Lab Technique
At one time tasting was considered an analytical technique. Chemists
were known for short lifespans. Open labs gave way to fume hoods and
then closed fume boxes. I once spent a month working with carbon
tetrachloride. Yes, there was fume hood, but I could still smell it
and that meant I was being exposed. Years later I talked with a guy
who had intended to be a chemical engineer. As an intern, he got a
job at a refinery. First day, they handed him high top rubber boots
so he could go sloshing through the goo. He changed careers then and
there.
The bottomline is that macro-scale chemistry is dangerous. Modern lab
chemistry is more about software simulations and microscopic samples.
Instead of titrations and distillations, the pros are using gas
chromatography, mass spectrometry, NMR, etc. Lab-on-a-chip, is also
in the works. Chemical engineering on the other hand still has some
major problems, but better sensors and better enforcement of
environmental laws probably make life safer for them too.
For home study, I'll stick to software simulations. However, if Peak
Oil brings collapse of civilization, and we decide to restart the
chemical industry, then we will need something like microscale wet
labs. That is about as small and complex as a crude technological
base can make the tools (e.g., 25ml graduated cylinders, no mass
spectrometers).
#----------------------------------------------
=head1 Chemical Engineering
See L<"../chemengr","Chemical Engineering">
#------------------------------------------------
=head1 Software
See L<"compchem.html","Computational Chemistry">
#-------------------------------------------------
=head1 References
=list []
=item Natkins02
Peter Atkins, Julio de Paula. "Physical Chemistry", 7th ed.
W.H. Freeman and Co, 2002. ISBN 0-7167-3539-3.
=item Nbrock92
William H. Brock. "The Norton History of Chemistry".
W.W.Norton & Company, 1992. ISBN 0-393-03536-0.
=item Ncarey03
Francis A> Carey. "Organic Chemistry", 5th ed. McGraw-Hill, 2003.
ISBN 0-07-242458-3.
=item Nengel06
Thomas Engel, Philip Reid. "Physical Chemistry". Pearson Education,
2006. ISBN 0-8053-3842-X.
=item Ndolan97
John E. Dolan, Stanley S. Langer, eds. "Explosives in the Service of Man:
The Nodel Heritage". The Royal Society of Chemistry, 1997.
ISBN 0-85404-732-8
=item Nmoulijn04
Jacob A. Moulijn, Michael Makkee, Anneilies va Diepen.
"Chemical Process Technology".
John WIley and Sons, (c) 2001, corrections 2004.
ISBN 0471-63062-4.
=item Nwilliams96
D. F. WIlliams, W. H. Schmitt, eds. "Chemistry and Technology of the
Cosmetics and Toiletries Industry", 2nd ed.
Blackie Academic and Professional, 1996. ISBN 0-751403342.
=item Nzumdahl03
Steven S. Zumdahl. "Chemical Principles", 4th ed. Houghtom Mifflin, 2002.
ISBN 0-618-12078-5.
=end list