Table of Contents

1. 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:

  • Bioinformatics: What's the latest on protein folding?

  • Peak Oil: What do we use oil for, and what will we use to replace it?

  • Post-oil survivalist: How is gunpowder made?

  • 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)?

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.

2. 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.

3. History

Primarily from brock92. This is my own choice of key ideas. Read Brock for the human story behind the ideas.

3.1. Matter is conserved

There is something , 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.

3.2. Phases

The something 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.

3.3. Elements

The something 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.

  1. 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.

  2. 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.

  3. 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.

3.4. 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.

3.5. 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.

3.6. 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.

3.7. 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).

3.8. 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 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.:

  • 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.

  • 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).

  • 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.

  • Proteins operate by folding (due to short distance bonding) into complex shapes. Those shapes have evolved due to fitness value (sometimes hard to discern).

  • 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.

4. Undergraduate Textbooks

Next stop was to read current chemistry texts. Had zumdahl02 and carey03, so used those. I don't know if they are the best-of-breed, but multiple editions is a good indicator.

4.1. Principles

According to the author blurb in 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.

4.2. 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.)

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:

  • nomenclature
  • bonding
  • synthesis
  • spectroscopic analysis

That is about how I remember organic chemistry. Surely by now the field is ripe for an automated expert system, instead of rote memorization.

4.3. 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 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 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.

5. 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).

6. Chemical Engineering

See Chemical Engineering

7. Software

See Computational Chemistry

8. References

Peter Atkins, Julio de Paula. "Physical Chemistry", 7th ed. W.H. Freeman and Co, 2002. ISBN 0-7167-3539-3.

William H. Brock. "The Norton History of Chemistry". W.W.Norton & Company, 1992. ISBN 0-393-03536-0.

Francis A> Carey. "Organic Chemistry", 5th ed. McGraw-Hill, 2003. ISBN 0-07-242458-3.

Thomas Engel, Philip Reid. "Physical Chemistry". Pearson Education, 2006. ISBN 0-8053-3842-X.

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

Jacob A. Moulijn, Michael Makkee, Anneilies va Diepen. "Chemical Process Technology". John WIley and Sons, (c) 2001, corrections 2004. ISBN 0471-63062-4.

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.

Steven S. Zumdahl. "Chemical Principles", 4th ed. Houghtom Mifflin, 2002. ISBN 0-618-12078-5.

Creator: Harry George
Updated/Created: 2007-10-21