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Real Basic Chemistry for Porphs

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1.00     In this article, Real Basic Chemistry for Porphs, we’re not going into any chemical theory. We’re not going to explain the interesting how and why of what we write--just the dry facts as we know them, or think we do.

     The subject of Chemistry reduced to its simplest form is the study of

What Materials are made of
How these Materials interact.

     The first of these topics,the composition and structure of various types of matter, and the second, their reactions (interactions) are intimately intertwined. Therefore, we shall jump back and forth from one aspect to the other.


1.01      The ancient Greeks thought that everything was made up in varying proportions of four things: earth, fire, air and water. Today we believe that here on earth, and probably in the other planets, and suns there are 90 naturally occurring elementary materials or

and everything is either an element, or composed of different elements in certain definite proportions (not arbitrary proportions). Such combinations are called

More about them a bit later after introducing atoms and molecules.
     The point is then that every thing is either an element or a compound, or as in the human body a mixture of elements and thousands of different compounds.


1.02     You are very familiar with many elements directly, and with the names of many more. We have found it convenient to classify elements as either

METALS or not metals, NON-METALS
We list some of the more important ones (for our purposes ) below. We also append the chemical symbol for them.


1.03     The symbol for am element is one or two letters. It is just a shorthand way of writing the name of an element. For materials known for centuries the name is often the Latin name.
We sometimes added a word to jog your memory or make a connection.

Table 1.1   Some Common Metals and Nonmetals
Metals Non-Metals

Aluminum Al
Copper Cu (cuprum)
Iron Fe (ferrum)
Tin Sn (stannum)
Silver Ag (argentum, Argentina)
Mercury Hg (hydragyrum-silver water)
gold Au (aurum)
Lead Pb (plumbum-plumber)
Zinc Zn

Sulfur S (sulphur- Yellowstone)
Carbon C (charcoal, soot, diamond)
Phosphorous P
Iodine I

The following metals are so active,
they combine so readily with the oxygen and water of the environment,
that only their compounds are found.

Sodium Na (Natrium-soda, hyponatremia)
Potassium K (Kalium-potash, hypokalemia)
Calcium Ca
Magnesium Mg
Barium Ba
Lithium Li

The following non-metals are gases
at normal environmental conditions.
They can be cooled to very low temperatures
and compressed into very cold liquids

Oxygen O (colorless, odorless, comprises 21%
of the air)

Nitrogen N (colorless, odorless,
Comprises 78% of the air)

Chlorine Cl (pale greenish-yellow gas
has the odor of Chlorine bleach. So very active that only its
compounds are found on earth.)

Hydrogen H (So very light, that
if produced it escapes
into outer space)

Neon Ne


2.01      Atoms are the smallest part of matter capable of an independent existence. Atoms of the same element have the same weight and size. Atoms of different elements, differ in size and weight.
So how big is an atom? Very roughly, one would have to line up a billion, ( that is a million taken a thousand times) atoms for the line to be one inch long.
      Molecules are collection of atoms which we find convenient to consider as acting as a unit. Many molecules contain only two or three atoms. Other molecules contain hundreds of thousands of atoms. Examples of these macromolecules are enzymes. DNA, and plastics.


The MOLE-- a Unit of Counting

      Since individual atoms are so very small and therefore weigh such a slight amount, how does one handle them? In large groups. Just as one might count oranges and eggs by the dozens, or gross, so the chemist has a special unit for counting these small objects. It is called the mole (abbv. Mol) There are twelve items in a dozen, twelve times twelve items in a gross. There are six hundred thousand times a billion times a billion items in a mole


      Why is a mole such an odd number? Because of the weight of the lightest element known-- hydrogen. A mole of hydrogen atoms weigh one gram. A carbon atom weighs twelve times as much as a hydrogen atom, and so a mole of carbon atoms weigh 12 grams. An oxygen atom is sixteen times as heavy as a hydrogen atom, and therefore a mole of oxygen atoms weigh 16 grams.

2.04       The weight of a molecule is nothing but the sum of the weights of the atoms that make it up. Since the oxygen gas that we breath is a molecule consisting of two oxygen atoms bound together O2, a mole of oxygen molecules weigh 32 grams. Similarly, water has two hydrogen atoms bound to an oxygen atom, H2O, and a mole of water molecules has a molecular weight of 18 grams.



3.01       Compounds are molecules that contain two or more different atoms. They are not mixtures. The proportions of mixtures can be varied. The composition of a compound is fixed. Water has two hydrogen atoms tied to an oxygen atom, H2O Hydrogen peroxide, “peroxide” bleach, has two hydrogen atoms tied to two oxygen atoms, H2O2 .
      As with elements, we find it convent to classify compounds into two groups. Compounds can be either organic compounds, or not-organic, that is inorganic compounds.
      Organic compounds were so named because they were thought at one time to be exclusively associated with organized, that is living, matter.Today we recognize that organic molecules are compounds of carbon and hydrogen. They may contain other non-metals, principally oxygen, nitrogen, phosphorous and sulfur.
Inorganic materials were the dead rocks, water, air of our environment. In Table 3.1 below we cite some very familiar examples.

Table 3.1

Some Common Organic and Inorganic Materials



Methane (natural gas)
Glucose (Dextrose)
propane (LPG gas)

Salt (Sodium Chloride)
Carbon Dioxide (dry ice)

3.02      The word Valence in chemistry means Combining Power or Joining Power. Atoms can have a single valence, or in a few cases multiple valences. In molecules with two or more atoms bound  together the atoms are said to be joined by a covalent bond
Hydrogen has a valence of one, oxygen a valence of two. Hence in the water molecule, two hydrogens are bound to a single oxygen atom.
Organic Compounds are Covalent Compounds with carbon having a covalence of four, hydrogen one, oxygen two and nitrogen three.


4.01      We are all familiar with static electricity-- static on an AM radio station, lightning discharges, static cling and so forth. In the cold winter states one can build up a “static charge” by sliding across plastic car seats. A spark jumps then when you touch the metal door handle.

      For thousands of years we have recognized two types of electricity. Vitreous (glass-like) and resinous (amber). The ancient Greeks called amber, electra. Amber is the fossilized sap of pine trees. It takes a high polish, and after rubbing it, a spark can jump to a piece of metal.
     Benjamin Franklin, of flying-kites-in- thunderstorm-fame, named vitreous electricity--positive; resinous electricity --negative.

      Usually matter is electrostatically neutral; it contains equal parts of positive and negative electricity.




4.03     We believe that all atoms have a positively charged nucleus, and surrounding the nucleus like planets orbiting the sun, are electrostatically negatively charge particles called electrons.
     The nucleus of an atom contains a certain number of positively charged particles called protons. Outside the nucleus are the same number of negatively charged electrons.      All the atoms a certain element have the same number of positive protons in their nuclei. This is what makes the element what it is. All iron atoms have 56 protons in their nuclei; hydrogen atoms have one proton in their nuclei; carbon atoms 6 protons in their nuclei. Outside the nuclei the orbiting electrons are equal in number to the number of protons in the nuclei.


4.04      Just to complicate this simple situation the nucleus of an atom can contain a certain number of neutral particles called neutrons.. The number of these electrostatically neutral particles can vary somewhat. Isotopes of an element have the same number of protons and electrons, but different number of neutrons. Most carbon atoms (C12) have six protons and six neutrons. About 1.3% of the naturally occurring carbon (C13) has 6 protons and 7 neutrons. The radioactive carbon atoms (C14) have 8 neutrons in their nuclei.


THE ELECTRONIC SHELL STRUCTURE OF ATOMS COVALENT COMPOUNDS The word Valance in chemistry means Combining Power. Atoms can have a single valance, or in some cases multiple valences. If atoms combine to form compounds by sharing their electrons, we say they are COVALENT COMPOUNDS. The covalence of some common Non-metallic elements are listed below Non-metals combining with non-metals form covalent compounds Most Organic Compounds are Covalent Compounds Element Covalence Examples Hydrogen 1 H2 Carbon 4 CH4 methane Oxygen 2 O2 normal oxygen; H2O water Nitrogen 3, 5 NH3 ammonia Sulfur 2, 4 or 6 H2S hydrogen sulfide SO2 (4-valent sulfur) sulfur dioxide SO3 (6-valent sulfur) sulfur trioxide IONIC COMPOUNDS Generally, when metals combine with non-metals, they form ionic compounds. In this instance, the metal atoms lose a number of negative electrons forming positive ions (cations). The non-metals atoms gain the negative electrons and form negative ions (anions). There is still overall electrical neutrality since just as many electrons are lost by the metals as are gained by the non-metals. Sometimes covalent molecules composed of several non-metallic atoms gain or lose electrons as a whole. These are then called molecule-ions, or radicals. The ionic valences of several elements and molecular-ions are given below. ION or RADICAL Sodium ion Na+1 Chloride ion C l -1 Potassium ion K+1 Fluoride ion F-1 Calcium ion Ca+2 Sulfide ion (S-2) Hydrogen ion H+1 Sulfite ion (SO3)-2 ******************* Sulfate ion (SO4)-2 Magnesium ion Mg+2 Carbonate ion (CO3)-2 Iron ferrous ion Fe+2 Bicarbonate ion (HCO3)-1 Iron ferric ion Fe+3 Nitrite ion (NO2)-1 Ammonium ion NH4+1 Nitrate ion (NO3)-1 Hydroxide ion (OH)-1 Oxide ion O-2 You notice that we have the non-metal hydrogen forming a positive ion, and the non-metallic molecule ammonia adding a positive hydrogen ion to form the non-metallic positive radical: ammonium ion . All attempts to make the neutral compound ammonium (NH4) have failed. **************************************************************** HYDROCARBONS and RELATED MATERIALS As the name implies, hydrocarbons are compounds of carbon and hydrogen. Their principle source by far is petroleum, natural gas and petroleum tars. There are hundreds of distinct but related hydrocarbons. Methane, CH4, is the principle constituent of natural gas, it is also produced in the intestinal tract of animals. It itself is odorless. Ethane, C2H6 , is also a constituent of natural gas Propane, C3H6 and Butane, C4H10 similarly are separated from natural gas or from petroleum. They are easily liquefied and sold as LPG (liquefied petroleum gas). Remember that hydrogen always has a valance of one, carbon of four. So there are always four bonds coming out of a carbon atom. We show the formulas for the hydrocarbons just mentioned as line-formulas. H H H H H H H H H H H-C-H H-C-C-H H-C-C-C-H H-C-C-C-C-H H H H H H H H H H H CH4 C2H6 C3H8 C4H10 These hydrocarbons are said to be saturated ; the carbon atoms are attached to as many hydrogen atoms as possible. We call them straight chain hydrocarbons because of the way we write the formulas. In reality they twist around in three dimensions, so that in a six carbon chain, the sixth and first carbon atoms are near each other. Baby Oil, petroleum jelly, Vaseline are purified mixtures of straight chain hydrocarbons with12 to 20 carbon atoms in the chain. Structural Formulas of Organic Compounds ISOMERS Isomers, (not isotopes) are what give rise to the tremendous diversity of organic compounds Acids, Bases and Salts ACIDS These are very generic terms and over the years their definitions have expanded to cover many materials not thought to be so a hundred years ago. For our purposes an acid is a material which increases the hydrogen ion concentration of a water solution. This water solution includes blood and any biological tissue. For instance, hydrogen chloride (HCl) is a good covalent gaseous compound. When dissolved in water it ionizes completely into positive hydrogen ions and negative chloride ions. We call this mixture hydrochloric acid. It is to be emphasized that the hydrogen ions (H+) and the chloride ions (Cl-) move about independently of one another. It is said that the concentration of the digestive juice “hydrochloric acid “in the stomach is about 0.1 mol per liter. (3.6 g per liter) But here, the chloride ion comes from the salt NaCl in our food, and the hydrogen ion is secreted by cells in the stomach wall. An acid that ionizes completely in a water solution, such as hydrogen chloride , is called a strong acid. This has nothing to do with how concentrated the acid solution is. Again, for our purposes there are about three strong acids, Hydrochloric Acid HCl, Sulfuric Acid H2SO4, and Nitric Acid HNO3 Further, the useful, sometimes dangerous, property of there materials is often not their “Acid” property. Concentrated sulfuric acid is a very strong dehydrating agent. Nitric acid is a very powerful “oxidizing agent” Essentially any other acid is a weak acid. That is, only a very small fraction of the acid molecules present in fact ionize into a hydrogen ion and a negative ion. In vinegar, which legally must contain at least 6% acetic acid, only about 0.01% of the molecules ionize. You are familiar with the names of many acids. acetic acid (vinegar), carbonic acid (carbonated beverages), citric acid (citrus fruits), Some acids we will be considering further are given in Table XX Table XX Common Acids HCl hydrochloric Acid H2SO4 sulfuric acid HNO3 nitric acid ----------------------------- Sulfurous acid H2SO3 Carbonic acid H2CO3 bicarbonate ion HCO3- Phosphoric acid H3PO4 Dihydrogen phosphate ion H2PO4- monohydrogen phosphate ion HPO4-2 END TABLE BASES A BASE is a material that when combined with an acid, forms a salt. That is it’s the basis for making a salt. Commonly recognized bases are the oxide ion,(O-2) and the more common hydroxide ion (OH-) in the Table below we list some common oxygen based bases. : You will note that some of the materials listed previously as acids, have a dual nature ;they can also function as bases Oxide, hydroxide, carbonate, hydrogen carbonate , phosphate, monohydrogen phosphate, dihydrogen phosphate, In nature these materials that are ionic must be found with a positive counter ion, usually, sodium, potassium, calcium, magnesium, Some specific examples are Sodium carbonate (washing soda) High concentrations found in some African lakes. An aqueous solution will have a pH ~10. Very Caustic Sodium bicarbonate (baking soda, alka selzer) aqueous solution pH~7. pH In any water solution, H2O ; HOH, there is a balance between the concentration of hydrogen ions H+ and the concentration of hydroxide ions OH-.In (acid/base) neutral water the two concentrations are equal If the solution becomes more acidic, hydrogen ions increase, then there is a corresponding decrease in the hydroxide ion concentration. Contrawise if the hydrogen ion concentration of a water solution drops below that of “pure” water, the hydroxide ion concentration increases--- the solution becomes more basic, or more alkaline. pH is a measure of the hydrogen ion concentration. The pH numbers work in a backwards fashion As the concentration of hydrogen ion increases, the pH number decreases.! In neutral “pure” water the pH has a value of 7. Because of the digestive acids in the stomach, it’s fluid has a pH of about 1. very acidic. The pH of the upper intestines is about 8, somewhat basic. Carbonated beverages have a pH of about 5. The blood’s pH shouldn’t vary much from the value of 6.7, slightly acidic. Acid Base Buffers This value of pH=6.7 of the blood is maintained by two buffer systems . The first system is the bicarbonate---carbonic acid system . If the hydrogen ion concentration starts to rise, (the pH drops) say from eating too much sauerkraut, the excess hydrogen ions react with the bicarbonate ions to produce covalent carbonic acid. This decomposes in the lungs into water and carbon dioxide CO2, which is exhaled. Essentially every biochemical reaction in the body is mitigated, catalyzed, by an enzyme. These enzymes work only in very restricted pH ranges. Hence the need to maintain the proper pH in various parts of the body. NITROGEN BASES Organic derivatives of the simple compound ammonia, NH3 form a very large class of . nitrogenous bases . We mention most of them latter. Here let us remind you that pyrrole, the foundation of heme, is a nitrogen containing base. When a hydrogen ion is added to the base ammonia NH3 one forms the ammonium ion. NH4+ Alkaloids are nitrogenous bases of a plant origin, which have a physiological action. One needs mention only caffeine, codeine, cocaine, morphine, nicotine. The DNA code is comprised of four (nitrogenous) bases. SALTS Too simply, a salt may be defined as the product of an acid and a base combining chemically. The base supplies the positive ions of the salt; the acid provides the negative ions. Alternately then, one can consider a salt as a metal--- non.metal ionic combination. Here we must remember that nitrogenous bases can function as a metal ion. We list here many common salts and indicate a chemical reaction whereby they might be formed. CHLORIDE SALTS Sodium chloride: NaOH + HCl >>> H2O + NaCl Potassium Chloride K2CO3 +2 HCl>>>H20 + CO2 + 2 KCl SULFATE SALTS Sodium sulfate Na2CO3 + H2SO4>>> H2O + CO2 + Na2SO4 Calcium Sulfate CaCO3 + H2SO4>>> H2O + CO2 + CaSO4 Magnesium Sulfate Morphine Sulfate Barium Sulfate Comments: Sodium Chloride and Sodium Sulfate are commonly the principle constituents of the “alkali” in alkali land, alkali wells. Calcium Sulfate is common as the mineral gypsum, and in the building product “sheetrock.” Magnesium Sulfate is Epsom Salts. The Barium ion is highly toxic. But Barium Sulfate is highly insoluble in the body fluids. Hence one can take “Barium enemas” and “Barium cocktails “with relative safety since what one is taking is a thick suspension of barium sulfate . I know of no “SULFATE” (or sulphate) that is harmful to people because of the ”sulfate“ part of the compound. NITRATE SALTS Silver nitrate is one of the few silver compounds that are water soluble. It is used medically to cauterize bleeding wounds.. The active agent is the silver ion, not the nitrate ion. An old fashioned name for silver nitrate is ” luna caustic” since the alchemists symbol for silver was the moon; and it burns, cauterizes wounds. Potassium nitrate, saltpeter, finely mixed with sulfur and charcoal form “Black Gunpowder” In the nineteenth century saltpeter or “ nitre“ deposits were much sought, to maintain the European wars and in hunting and warfare in the America . Sodium nitrate, Chile saltpeter, is found in the Desert of Chile. It was mined for use as a nitrate fertilizer. IT IS UNSUITABLE FOR THE MAKING OF GOOD QUALITY BLACK GUNPOWDER. Ammonium Nitrate. Is manufactured, and use as a fertilizer and as an explosive. Carbonate Salts Sodium , carbonate, bicarbonate Calcium Phosphate Salts, apatite, hydroxyapetite, fluoroapetite. phospho-soda milk of magnesia