Chemistry

This is a decent on-line periodic table.

This map is exceptionally clever and useful.

One of the best pieces of evidence that chemistry is a sloppy field is the existence of CAS numbers. This stands for "Chemical Abstracts Service". The problem with CAS numbers is that the mapping between chemical and number is established and controlled by a proprietary non-public group, the American Chemical Society. This makes it impossible for poorly funded groups and individuals to work with large quantities of these numbers.

Even though most chemists use these numbers most of the time, I believe it is wrong to do so and they should be avoided categorically. It is especially insidious when important government safety regulations refer to chemicals exclusively by this closed system designed for insiders.

The correct way to refer to chemicals is by their SMILES string.

Here is a thorough reference from Molsoft. ICM can generate models based on SMILES strings.

Simplified Molecular Input Line Entry System SMILES is a way to represent the graph of chemical structures, i.e. what atoms are present and how do they connect to each other. The SMILES string is obtained by listing the nodes encountered in a depth-first tree traversal after the graph is turned into a spanning tree by breaking any cycles. Where cycles have been broken, numbers are used to indicate the breaks. Parentheses are used to indicate points of branching on the tree. Implicit hydrogens are included.

Isotopes are written [14c] for Carbon-14.

Although SMILES is rarely insufficient to convey what is needed about a molecule, there are more verbose formats which are extremely common. Although SDF is an embarrassingly terrible data format, it is nearly universal in biochemistry.

SDF stands for "Structure Data File" and is an extension of the "molfile" format. The relationship is described in this Wikipedia article. Here is a proper definition of the format.

Here are the main important points of an SDF file.

A phosphate is salt of phosphoric acid. It is characterized by a group based on a phosphorous atom surrounded by 4 oxygen atoms in a tetrahedral arrangement. 3 of the oxygens are negatively charged and the other has a double bond to the phosphorous. Adding phosphates (phosphorylation) and removing them (dephosphorylation) from proteins are key energy managing strategies for living things.

Phosphates usually pick up hydrogens or they are negatively charged. They can also pick up other things such as sodium producing mono-, di-, and trihttps://en.wikipedia.org/wiki/Sodium_phosphates[sodium phosphate].

Hydroxyl = a chemical unit consisting of a hydrogen attached to an oxygen which is attached to something else. I believe these can be found on free floating amino acids where they would otherwise be attached to a protein. Serine, Threonine, and Tyrosine all seem to have hydroxy groups in the main part of the molecule too.

Free radicals seem to be a related topic.

Alcohol = If an -OH hydroxyl is bonded to a carbon in a molecule that contains only carbon and hydrogen, then the molecule is, by virtue of the -OH, an alcohol. Alcohols tend to end in ol like ethanol (human intoxicating), ethylene glycol (antifreeze), diethylene glycol (infamous contaminant), methanol (fuel), menthol (analgesic).

Drinking alcohol is ethanol and is an acyclic chain of two single bond carbons and a hydroxyl with all the proper hydrogens.

Esters are derived from an acid (organic or inorganic) in which at least one -OH (hydroxyl) group is replaced by an -O-alkyl (alkoxy) group. Usually, esters are derived from a carboxylic acid and an alcohol.

The key features of an ester is a carbon with the following connections. * Double bond to oxygen. * Single bond to some other moiety (often labeled R). Optionally just hydrogen. * Single bond to an oxygen which itself is bound to some other moiety (R'). Or just -1 charged oxygen.

Some esters.

An esterase is a hydrolase enzyme that splits esters into an acid and an alcohol in a chemical reaction with water called hydrolysis. The one I’ve heard most about is acetylcholinesterase which catalyzes the breakdown of acetylcholine and of some other choline esters that function as neurotransmitters. Neurotransmitters are of interest to migraine pathology.

Lattices of rings of carbon and hydrogen (only). Like chicken wire. Neutral, nonpolar. Can be produced by incomplete combustion of organic matter. Can be found in tar an asphalt runoff. Also found in smog, marine oil spills.

Simplest is naphthalene which just has two rings.

Believed to be carcinogenic.

A Methyl group involves one carbon atom bonded to three hydrogen atoms. The fourth carbon bond can attach to some other part of the molecule. If that is just a fourth hydrogen then the molecule is methane.

Methylation and demethylation is common and involves moving the methyl group to another compound.

If the methyl group is attached to an -OH it becomes methanol.

A Butyl group is a four carbon set in various configurations. A normal butyl group is something like: R/\/\ Where the R is a radical with 4 carbons tailing off it. A tert-butyl group is similar except the carbons are in a tetrahedron with the radical linking to one of the non central carbons.

Saturated compounds are composed of carbon chains that only contain single bonds. Unsaturated molecules can contain double and triple carbon bonds. Alkene and alkyne are unsaturated.

An alkane consists of hydrogen and carbon atoms arranged in an acyclic tree structure in which all the carbon-carbon bonds are single. When all carbon bonds are single, the molecule is called a saturated hydrocarbon. The simplest alkane is methane which is just a carbon atom with 4 hydrogens (CH4).

Alkanes sometimes are called paraffin but paraffin may not always automatically mean Alkane now. If the backbone has more than about 17 carbons, it is usually called a wax. They are not very reactive and have relatively little biological activity.

Oil and natural gas contain alkanes (and a bunch of other sludge).

Etc.

There are linear and branched alkanes. There are also cyclic alkanes, called cycloalkanes which are like regular alkanes but they form loops or cycles.

An unsaturated hydrocarbon that contains at least one carbon-carbon double bond. The simplest is a pair of double bond carbons each with 2 hydrogens, C2H4 or ethylene or ethene. Alkenes sometimes are called olefin and olefine and eth.

Propylene, isobutylene, and vinyl (aka ethenyl) are alkenes.

An unsaturated hydrocarbon containing at least one carbon-carbon triple bond. The simplest exemplar is ethyne, a.k.a. acetylene which is just two carbons bound together with a triple bond and a hydrogen on each, C2H2.

Teixobactin is an interesting oligopeptide.

Cellular fluid is called Cytosol. Rough concentrations also here. Cytoplasm intercellular fluid containing organelles; cytosol is the cytoplasm minus the organelles.

Note the cautionary story of Linus Pauling who wrongly popularized the anti-oxidant mania, especially vitamin C and vitamin E.

Titan II rockets used a hypergolic (mix and it ignites) fuel. It was a 50-50 blend of hydrazine and unsymmetrical dimethyl hydrazine (brand name: Aerozine 50). The oxidizer was nitrogen tetroxide.