Basic
Chemistry for Herbalists
- .pdf version
Atomic
structure
In this simplified picture, we see the protons and neutrons at the
center of the atom, and the electrons “orbiting” the
central nucleus. This image, known as the Bohr model, is a bit inaccurate,
in that it fails to portray three key features of an atom:
1. Scale. The nucleus accounts for .01% of the volume of an atom.
As an analogy, if the nucleus were the size of a basketball, the
entire atom would be the size of the Earth.
2. Electron ‘shape’. These particles are not little
dots, as the picture would have us believe. They are more like vibrational
states, oscillating around the nucleus, more like a cloud than anything
else.
3. Electron energy levels. The electrons organize themselves into
levels, or ‘shells’, rather than just randomly circling
the nucleus. These levels are important in determining the atom’s
behavior in nature.
Glossary of Chemical Terms
Acid. A compound which, when dissolved in water, forms H+ ions.
This usually has the effect of lowering the pH of the solution.
Acids are the opposites of bases.
Anion. An ion that is negatively charged.
Atom. The smallest unit in which an element can exist. Atoms are
composed of a nucleus, electrons, and much empty space. Scientific
understanding of atoms has progressed continuously since 500BC,
and the current model emphasizes a central nucleus surrounded by
‘clouds’ of randomly moving electrons. The electrons
exist at discrete energy levels.
Atomic number. The number of protons in an atom or ion.
Atomic weight. The number of protons plus the number of neutrons
in an atom or ion.
Base. A compound which, when dissolved in water, forms OH- ions.
This usually has the effect of raising the pH of the solution. Bases
are the opposites of acids.
Bioavailability. The extent to which a compound can be used by the
human physiology. This depends on many factors: solubility, transit
time, size, and processing by the digestive system and the liver,
for example.
Bonding. The process of joining two or more atoms to form a compound.
Ionic bonding relies on the different charges of the ions to attract
each other. Molecular (also called ‘covalent’) bonding
relies on atoms sharing their electrons.
Cation. An ion that is positively charged.
Charge. The quality of being either a positive (+) or negative (-).
Atoms, in their elemental state, have no charge. Compounds also
have no overall charge, although certain areas of the compound may
be more positive and others more negative. Ions always have a charge,
which they obtain by giving or receiving electrons.
Compound. A substance formed by two or more elements, bonded together.
Dipole. A polar molecule (‘having two poles’).
Dipole moment. The number measuring the difference in intensity
between the two charges of a dipole.
Electron. A subatomic particle responsible for negative charge.
Electron movement is the basis for electricity. Electron trading
and sharing is the basis for all chemical bonding.
Element. A substance that can no longer be chemically divided; elements
are the basic ‘building blocks’ of matter in the universe.
We know of 92 naturally occurring elements; another 20 or so more
have been artificially created in the lab (but they never last long).
Energy level. The state at which an electron exists inside the atom.
Each energy level (also known as ‘energy shell’) can
hold a certain number of electrons: the first can hold two, and
every other one can hold eight. Atoms in nature tend towards filling
up their energy levels, either by going up to eight or down to zero.
They accomplish this by trading or sharing electrons with other
atoms.
Hydrocarbon. An organic molecule. These compounds are so called
because they consist primarily of hydrogen and carbon.
Inorganic chemistry. The branch of chemistry that deals with ions,
solutions, elements, molecules and compounds generally not produced
by life.
Ion. A substance made of one or more elements that has a different
total amount of protons and electrons. This difference gives the
ion an overall charge, either positive (more protons) or negative
(more electrons). Ions are formed when an atom or compound is ionized.
Ionic compound. A compound held together by the attraction of positive
and negative ions.
Ionization. The process of adding or removing electrons from an
atom or molecule. This can be accomplished through intense heat,
electric current, or suitable chemical pairings. These pairings
occur between atoms that can trade electrons amongst themselves
to fill their atomic energy levels.
Molecule. A compound held together by the sharing of electrons,
rather than trading. Atoms in a molecule fill their energy levels
on a ‘time-share’ basis.
Non-polar. A molecule with no dipole moment.
Nucleus. The ‘core’ of the atom, containing its entire
weight, but occupying only .01% of its volume (atoms are not very
dense). The nucleus is made up of protons and neutrons, and provides
a net positive charge.
Organic chemistry. The branch of chemistry that deals with molecules
generally comprising hydrocarbons, and originally named because
it studied compounds produced by living beings. Nowadays, it comprises
the study of plastics and petrochemicals as well as amino acids
and essential oils.
Oxidation. The process of changing an atom, ion or compound to one
with a greater (more positive) charge.
pH. The degree of acidity of a solution. The lower the pH, the more
acidic it is. The pH scale is logarhythmic, meaning that a difference
of one point in the pH scale represents ten times the acidity; a
difference of two points implies one hundred times the acidity.
Polar. Having a non-zero dipole moment.
Polarity. The quality a molecule can exhibit of having two sides,
or poles, like a magnet. High polarity binds molecular liquids and
gases more tightly together, and influences solubility in water
(which is a highly polar substance).
Precipitate. A compound, either ionic or molecular, that has a solubility
so low that it settles out to the bottom of a solution.
Reduction. The process of changing an atom, ion or compound to one
with lesser (more negative) charge.
Saturation. The condition a solution reaches when, for a given temperature,
it has the maximum amount of solutes in it.
Solubility. The degree to which a solute dissolves in a solvent
– salt, for example, has a higher solubility in water than
sugar.
Solute. The compound you wish to dissolve.
Solvent. The substance responsible for dissolving or extracting
a given compound (the solute). Terpene unit. A hydrocarbon chain
made of 10 Carbon atoms and 16 Hydrogen atoms. It is the basis for
classification for a variety of organic molecules, many of which
are volatile. The classes are based on the number of terpene units
in each molecule:
-monoterpenoids, C10 H16
-diterpenoids, C20 H32
-triterpenoids, C30 H48
-sesquiterpenoids, C15 H24
Volatile. Naturally vaporizes at room temperature. Usually, these
compounds have a strong smell (such as essential oils, for instance).
Major Organic Phytochemical classes
Alkaloids
These organic compounds are some of the most biologically active
molecules that plants produce. At their simplest, they consist of
a carbon ring into which a Nitrogen (N) atom is inserted (a simple
piperidine alkaloid is pictured at right). There are many sub-groups,
the detail of which is beyond the scope of this course. Some examples
are Nicotine (Tobacco), Lobeline (Lobelia), Morphine and Codeine
(Opium poppy), Atropine (Belladonna), Cocaine (Coca), Caffeine (Coffee),
Hydrastine and Berberine (Goldenseal), Ephedrine (Ephedra), Mescaline
(Peyote), Quinine (Cinchona spp.), Taxol (Yew). From this list you
can get a good idea of their powers: they are very intense, heroic
medicines that can be quite toxic in high doses.
Iridoids
These are a subclass of altered monoterpenoids. They are also called
lactones. They generally have a bitter taste (and are often responsible
for the effect of ‘herbal bitters’). Some salient examples
are Kavalactones (from Kava-Kava), Nepetalactone (from Catnip),
and the Valepotriates (from Valerian). In general, most iridoids/lactones
are sedative, laxative, bitter and salilagogue.
Saponins
As the name implies, these compounds are soap-like and are fairly
well soluble in water. They can help dissolve other, more oily,
compounds as well because of their nature. You can find saponins
in many plants, including lots of food plant families (especially
the Pea family), and notably in Ginseng and Licorice with Glycirrhizin.
If you shake an infusion, decoction or tincture and a stable foam
remains on the surface, you are probably witnessing saponins at
work. They have a variety of actions, some due to their ‘soapiness’
(although they are mostly broken down in the stomach), others due
to the effect of their metabolites. I think of saponins as being
crucial in the adaptogen class, helping to stimulate our body/minds
into better tone. As such, they are adaptogenic, hepatoprotective,
immune modulators, anti-bacterial, expectorant, anti-inflammatory,
diuretic and alterative.
Steroidal saponins
A sub-class of the saponins, these compounds have similar activities,
bordering on the phytosterols. They are found in plants such as
Astragalus, Black Cohosh, Ginseng (Ginsenosides), and Wild Yam (Diosgenin).
Cardio glycosides
These are a specific sub-class of steroidal saponins that have a
tonic effect on the heart, however only in small doses! In larger
doses they are quite toxic. David Hoffman tells how butterflies,
who in general are immune to these glycosides, store them in their
tissues to dissuade birds (who can die from them) from eating them.
Convallotoxin, from Lily of the Valley, and Digitalis, from Foxglove
(of Dr. Withering fame), are two prime examples. They are cardio-tonic
in tiny doses, stimulating the heart to work much more efficiently.
Phytosterols
There has been much talk of these compounds in recent years as different
phytosterols have been isolated from Red Clover and other herbs
and are being touted as ‘estrogenic’ replacements for
synthetic hormones. Their presence may or may not be responsible
for the anti-hot-flash activity of some herbs. Some sterols you
may have heard of are Cholesterol and Testosterone (mostly found
in animals, although also in some plants), Estradiol (found in members
of the Pea family), Stigmasterol from soybeans. They are fairly
water-soluble, and in general, they possess anti-tumor and anti-inflammatory
activity.
Resins
These are sticky, oily substances that are often exuded from tree
barks. Myrrh, Pine pitch, Frankincense, and Dragon’s blood
are some examples. Other plants possess a fair amount of resin in
their tissues – the most striking example is Grindelia, a
sticky plant whose flowers secrete an aromatic white resin. Propolis
is a collection of various resins collected by bees to protect their
hives; this hints well at their action which tends to be antiseptic,
anti-bacterial, expectorant, nervine and rubifacient externally.
Phenols
Under this heading that comprises molecules with both a hydroxy
(-OH) group and an aromatic resonant ring (C6 – six carbons)
we find a huge variety of different structures. The simplest, phenol,
is pictured on the right. From this basic compound, different atoms
and functional groups can be added, or the structure itself can
be repeated multiple times. In general, phenolics are fairly water-soluble,
and exist in every plant in one way or another. The simple phenols
include such compounds as Salicin (in Willow and Meadowsweet), Arbutin
(in Uva-Ursi), and Vanillin (from Vanilla). In general, they are
antiseptic, anti-inflammatory, analgesic (anodyne), blood-thinning,
and rubifacient externally. What follows are descriptions of additional
phenolic compounds, classed under the broad heading of polyphenols.
Phenolic acids
These compounds are simple variations on phenols with the addition
of a carboxylic group (-COOH) that gives them a slightly acidic
pH and increases their solubility. A prime example is Salicylic
acid (aspirin), derived from modifying Salicin. These compounds
are anodyne, anti-inflammatory, and anti-pyretic.
Coumarins
Here we begin to add additional rings to the basic phenol structure.
In this class, we have our original C6 aromatic ring to which is
attached another ring with C3, or 3 Carbons. In Coumarin itself
(from Turmeric), pictured at right, the additional slot on the adjacent
ring is taken up by and Oxygen (O). These compounds are anti-inflammatory
and antiseptic, and although they can possess a variety of other
actions depending on how different they are from the basic structure
above, these two will always be present.
Quinones
These molecules can get quite large and complex. Simple Anthraquinones
are derived from Anthracene, a three-ring structure, and their basic
setup is pictured at right (C6 – C2 – C6). Sennoside
and Rhein (found in Senna, and Rhubarb to some extent) are compounds
that you may be familiar with: the anthraquinones are laxative and
can be quite strong. They seriously stimulate peristalsis, and can
be habit-forming. They are also alterative because of their function
in tissue elimination. There are many other quinones as well, with
the naphtaquinones being a two-ring structure (C6 – C4), and
much more complex quinones involving stacked tiers of multiple carbon
rings, like Hypericin (from St. John’s Wort). These compounds
are antiviral, antiseptic and anti-bacterial. Flavonoids The next
class of phenolic compounds we will discuss consists of the flavonoids,
the basic structure of which is pictured at right: it is made of
two rings, connected by a three-carbon (C3) chain. These compounds
are responsible for pigmentation in plants and for many medicinal
effects. Primarily, you will have heard of them in relation to their
antioxidant power, but usually possess a certain degree of antiseptic,
immune-modulating, and circulatory stimulant power. Some sub-classes
of this huge family include the anthocyanidins and oilgomeric pro-anthocyanidins
[OPCs] (Pine bark extract, Blueberries), catechins (Greent Tea),
flavonols (Quercetin), isoflavones (Red Clover, and Soy). There
is extensive research around these compounds for fighting tumors,
improving memory and circulation, fighting allergies, protecting
the liver (Sylimarin is a bioflavonoid), aiding in hormone regulation,
helping the nervous system, and more.
Lignans
These are polymers of phenolic compounds, meaning they consist of
simple phenols and/or flavonoids linked together in long, comlpext
chains. They are found in woody tissues of plants. They have adaptogenic,
antioxidant, anti-tumor and antiviral activities, and are partly
responsible for the medicinal effect of Chaparral, for example.
Tannins
Very often astringency in plants will be due to the presence of
these compounds. White Oak is a great example of an herb rich in
tannins. There is some cross-over between these compounds and the
proanthocyanidins of the flavonoid class. The primary chemical property
to remember here is that they bind proteins, making them difficult
to absorb by reducing their solubility in water. They are probably
chemical protectors for the plants themselves, ensuring the integrity
of cell walls and internal tissues. For our purposes, they are astringent,
vulnerary, anti-tumor, and help with diarrhea.
Carbohydrates
These are our simple sugars (glucose, a monosaccharide, is pictured
on the right) and also include more complex polysaccharides and
starches. Their function, especially of the monosaccharides, is
primarily nutritive and as a source of energy for the body. The
more complex sugars can have interesting adaptogenic and immuno-modulating
power (such as, for example, the polysaccharide fraction of Echinacea
or Larix), and the starches often contribute to plant structure,
along with the lignans. Combining with amino acids, we can see glucosaminoglycans,
of which Glucosamine (N-acetyl-d-glucosamine) is perhaps the most
famous. They also often combine with phenolic compounds and become
known as glycosides, such as flavonoids (Ginkgo’s flavo-glycosides
are an example, Rutin is another flavo-glycoside); anthraquinones
(Sennoside, from Senna, is an anthraquinone glycoside); saponins
(Ginseng’s Ginsenosides are saponin glycosides); we have already
encountered cardio-glycosides. When combined in these forms, they
take on and contribute to the action of the relative class.
Mucilages
These are a specific class of polysaccharides that form soothing,
healing, often slimy solutions in water. Marshmallow root, Comfrey,
Cornsilk and Slippery Elm are god examples of this sub-class, and
all of them have strong demulcent action.
Lipids
These are naturally occurring fats and oils. For our purposes, the
most important class of lipids are the essential fatty acids, or
EFA’s, of which ?-Linoleic acid is perhaps the best known.
It is found in Flax, Evening Primrose, Borage, and Black Currant
seeds. These are an essential part of the diet (hence the name),
and posess anti-cholesterol, anti-inflammatory, anodyne, and hormone-regulating
power. They are not very water soluble, so administration occurs
by ingesting the crushed seeds or an oil extract, or by emulsion
with a saponin.
Proteins
This is a very, very large family of compounds, providing the building
blocks for cell membranes, musculature, hemoglobin in animals and
chlorophyll in plants, DNA and RNA in cell nuclei, most all enzymes
that allow the metabolism to work, and much more. They are, in fact,
essential for life to exist because all body processes are mediated
by proteins. They all come from a single dietary source: amino acids.
Even when we eat complex animal proteins, our body breaks them down
into their constituent amines. They have a huge variety of structures,
but always possess an amine group (-NH2) somewhere. They can combine
with other molecules, forming amides.
