Musk Class – Part Two
Shelley and Larry Authors
November 11, 2007
DAM of Perfumes
Here are some basic chemistry concepts and definitions that are useful (but
NOT required!) for studying perfumery. There is a LOT of material here, but
PLEASE keep in mind that this is meant to be a REFERENCE, to study in small
doses (or ignore completely!)
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ATOMS
All matter is made up of ATOMS. Atoms that are of one chemical "type" form
the various CHEMICAL ELEMENTS, such as oxygen, nitrogen, helium,and carbon.
There are about 95 distinct elements that occur in nature; roughly another 1½
dozen (all of which are radioactive) have been prepared in the laboratory.
Atoms are almost unimaginably tiny. In just one cubic inch of pure oxygen,
there are approximately 880 quintillion(880,000,000,000,000,000,000) atoms!
Yet, since the weight of each atom is likewise almost unimaginably small, all
those 880 billion-billion atoms would weigh only about 0.012 grams, or four
ten-thousandths of an ounce!
Tiny as they are, atoms are made up of even smaller particles. At the center
of the atom is the even tinier NUCLEUS, which is composed of positively
charged PROTONS and uncharged NEUTRONS. Atoms normally do not have a charge;
the positive charges from the protons are balanced by an equal number of
negatively charged ELECTRONS. Each type of chemical element has a _specific_
number of protons in its nucleus. For example, hydrogen atoms always have 1
proton; oxygens always have 8 protons, and carbons always have 6. Nearly all
of the mass of an atom is concentrated in the nucleus; electrons weigh only
about 1/1800 as much as protons and neutrons. The electrons are not part of
the nucleus; instead they whizz around the nucleus (and since they weigh so
little, they can move FAST!) -- sort of like the planets spinning around the
sun.
You may have heard the term "isotope". The word has Greek roots meaning
"same place" - i.e., the same spot on the periodic table. (The periodic
table is a "chart" of all the elements, arranged so that elements in each
column have similar chemical properties.) All of the isotopes of each
element have the same number of protons (for example, all carbon isotopes
ALWAYS have 6 protons.) The difference is in the number of NEUTRONS that are
in the nucleus. The most common isotope of carbon is carbon-12, which has 6
protons, and 6 neutrons (12-6 = 6). The "12" is the ATOMIC WEIGHT of the
isotope; the atomic weight of hydrogen -- which most commonly has a single
proton and zero neutrons -- is assigned a value of "1", so an atom of carbon12 weighs 12 times as much as an atom of hydrogen. Other isotopes of carbon
include carbon-13 [6 protons and 7 neutrons (13-6 = 7)], and carbon-14 [6
protons and 8 neutrons (14-6 = 8). Carbon-14 is radioactive; it's the
radiation level of this isotope that's used for "carbon dating" archeological
artifacts such as the fiber from sandals and charcoal from fire pits. How
many neutrons does uranium-235 (U-235, used for atomic bombs) have? Uranium
always has 92 protons, so it has a total of 235-92 = 143(!) neutrons packed
into its itty-bitty nucleus. With all that overcrowding, no wonder it's
unstable!
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MOLECULES and BONDING; VALENCE
Pure elements generally don't exist in nature. Instead, atoms combine to
form larger structures called MOLECULES. These aren't just mixtures of the
component atoms; instead, the atoms are joined together in a particular way,
giving a particular three-dimensional structure for each distinct molecule.
For example, you're probably familiar with the formula for water, H2O. This
formula means that each water molecule consists of two hydrogen atoms (H) and
one oxygen atom (O). The particular order in which these three atoms are
joined is H-O-H. The dashes here represent the BONDS in the molecule -- a
single dash for a single bond, a double dash (=) for a double bond, and a
triple dash [if I could type it] for a triple bond.
Different types of atoms can form different numbers of bonds. Hydrogen can
form only one bond. Oxygen can form two bonds - either (2) single bonds, or
(1) double bond. Nitrogen normally forms three bonds - (3) single bonds, (1)
single bond + (1) double bond, or (1) triple bond. The number of (single)
bonds that a particular element can form is called the VALENCE (pronounced
VAY-lints) of the element. Hydrogen has a valence of 1, oxygen has a valence
of 2, nitrogen's valence is 3, and carbon's valence is 4.
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STATES OF MATTER
The three STATES OF MATTER that are most familiar to us are gas, liquid, and
solid. The main difference in these three lies in the amount of space
between the molecules that make up the material. In GASES, there is a large
amount of space and the molecules move freely. Left to their own devices,
gases expand to completely fill their container.
LIQUIDS have less space between molecules, and assume the shape of their
container (unless you're in zero gravity!), but the individual molecules can
still tumble all around each other. An analogy might be a swimming pool full
of kids. Each kid can move around all the others, and can even make it from
one end of the pool to the other, but he or she will probably bump into other
kids along the way. Even if a kid stays pretty much in one part of the pool,
the other kids will be moving around so they'll still bump into him or her.
In SOLIDS -- to continue the pool analogy -- the kids stay essentially in one
spot. They'll be jostled a bit by the water currents and wind, and they may
spin or tumble around, but as far as moving from one part of the pool to
another, they remain fairly motionless. In terms of actual molecules, some
solids are not very neatly laid out in particular patterns (they're
AMORPHOUS). In others, the molecules are all oriented the same way, and form
CRYSTALS.
And in still others, the individual
are no longer distinct. Instead the
- sort of like being absorbed by the
diamond, and it's part of the reason
substances known.
molecules are all bonded together and
entire structure is one huge(!) molecule
Borg (kidding!) An example of this is
that diamond is one of the hardest
Returning to a more formal picture, at the surface of liquids - the "liquidgas interface" - occasionally molecules in the liquid will be moving fast
enough to actually LEAVE the liquid and propel themselves into the gas above
the liquid. At the same time, some molecules in the gas "phase" will
occasionally be moving slowly enough that when they hit the liquid interface,
they are re-absorbed by the liquid and begin jostling their neighbors in the
liquid instead of flying around willy-nilly.
This is important to us as perfumers because molecules have to make it into
the GAS phase so that we can draw them into our nose and smell them.
Compounds whose molecules *readily* move from the liquid phase to the gas
phase are said to have a HIGH VAPOR PRESSURE; compounds whose molecules have
a difficult time breaking free from the nest are said to have LOW VAPOR
PRESSURE.
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IONS
I mentioned earlier that atoms are normally electrically neutral (the number
of [+] protons equals the number of [-] electrons). If there are more
electrons than protons, there's an excess of negative charge, and a NEGATIVE
ION is formed; likewise if there are fewer electrons than protons, a POSITIVE
ION is formed. This can happen to molecules as well. Each type of molecule,
or chemical compound, consists of particular numbers of particular types of
atoms, bound together in a particular structure. Therefore neutral molecules
have a particular number of electrons and protons, just like their component
atoms. If a neutral molecule gains an electron, it becomes a negative ion;
if it loses an electron, it becomes a positive ion. Some molecules (unlike
atoms) can also gain or lose a PROTON and become an ion. A proton is simply
the nucleus of a hydrogen atom, so - at least compared to molecules - it's
pretty darned small. It also has a single positive charge (the opposite
charge of a single electron). If a molecule gains a proton (and keeps all
its original electrons), then it becomes a positive ion. For example,
ammonia is NH3 (one central nitrogen atom, bonded by single bonds to three
hydrogen atoms). It can gain a proton (= hydrogen nucleus = H+) and become
an AMMONIUM ion, NH4+. You gardeners (and explosives makers) will be
familiar with ammonium nitrate. The "ammonium" part is a positive ion, and
the nitrate part (NO3-) is a negative ion. Since opposite charges attract,
the ammonium and nitrate ions combine. The generic chemical term for this
combination of positive and negative ions is a SALT. Common table salt
consists of a combination of positive sodium ions, Na+, and negative chloride
ions, Cl-.
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ATOMIC SYMBOLS
Chemists are just like everyone else (really!) - we use abstractions to
simplify things. Normally we don't think in terms of protons and neutrons
and electrons, or even atoms. Instead we use SYMBOLS. There is an
internationally standardized set of symbols for each type of atom.
Most are one capital letter, or one capital letter plus one lowercase
letter. Instead of saying "a molecular combination consisting of one atom of
hydrogen polar-covalently single-bonded to one atom of chlorine, via sharing
of orbital electrons in such a manner as to satisfy the Pauli exclusion
principle" (which is what he or she REALLY means), a chemist will say, "a
molecule of H C L". Now, if that's in WRITTEN form, it would be "a molecule
of HCl". See? Shorthand!
The most common atomic symbols you will encounter in organic chemistry (and
aroma chemistry!) are:
H
hydrogen
C
carbon
N
nitrogen
O
oxygen
S
sulfur
Cl chlorine
Br bromine (rare in perfume chemistry)
You may also encounter:
P
phosphorus
F
fluorine
I
iodine (In Germanic countries, this is "J", for "Jod".)
Li lithium
Na sodium (Latin "natrium")
K
potassium (Latin "kalium")
Mg magnesium
Ca calcium
Fe iron (Latin "ferrum")
Ag silver (Latin "argentum")
Au gold (Latin "aurum")
Pb lead (Latin "plumbum" - like plumber!)
U
uranium (for "regular" atom bombs)
Th thorium (a small amount of the oxide is in the mantles for Coleman
lanterns)
Pu plutonium (for "dirty" atom bombs)
f
WHAT'S "ORGANIC" CHEMISTRY?
Organic chemistry was originally meant the study of compounds from *living* organisms, as opposed to
inorganic chemistry, which was the study of compounds from non-living matter like iron ore or gold. In
fact the very early chemists thought that the "life-essence" was a *requirement* for making organic
compounds. This theory was eventually disproven by a chemist who heated an inorganic compound,
ammonium cyanate, and produced the decidedly organic compound, urea. No life essence involved!
The more modern concept of organic chemistry is that it is "the chemistry of carbon compounds".
Carbon has some special properties which make it uniquely able to form a staggering variety of
compounds; that’s why this branch of chemistry has become a study in its own right. And organic
chemistry is also the basis of AROMA CHEMISTRY, which is near and dear to our hearts as perfumers.
(You may have heard the term “aromatic" compound - that's not the same as an "aroma" compound. I'll
go into more detail a bit later.)
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WHY IS CARBON SPECIAL?
Carbon has a valence of 4, which means it can bond or connect to as many as four other atoms. We live
in a 3-dimensional world, and four-bonded or "tetravalent" carbon has its bonds pointing toward the
corners of an imaginary tetrahedron, a 3-dimensional solid. In addition, carbon can also bond to THREE
other atoms (using 2 single bonds and one double bond), forming a planar "Y"-shaped structure, or to
TWO other atoms (using either 2 double bonds, or one single bond + one triple bond) forming a linear
structure. Carbon's single, double and triple bonds are all nice and stable, not only to other atoms (like
hydrogen, oxygen, nitrogen, sulfur, chlorine and bromine) BUT ALSO TO OTHER CARBON ATOMS!
Because of the special stability of its bonds, carbon is able to form the "backbone" or "framework" of
millions and millions of stable organic compounds. Not only are long chains of carbon atoms possible
(and common!), but also these chains can have "branches" along the way – still stable. Not only that,
but "loops" or "rings" of carbon atoms are also very common, from rings with just 3 carbon atoms, to
rings containing 20, 30 or more carbon atoms. The MOST STABLE RINGS are the ones with 5, 6, or 7
carbon atoms, because these fit best with the natural tendency of carbon to have its (four) bonds
pointing toward the corners of a symmetrical tetrahedron, with angles (ideally) of about 109½°. As the
number of carbon atoms increases past about 8, there tends to be fairly substantial "ring strain". Very
large rings (typical of one class of musk) are called MACROCYCLIC compounds.
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SOME NOTES ABOUT ORGANIC STRUCTURE DIAGRAMS
Since chains and rings of carbon are very common in organic compounds, and organic chemistry is all
about CARBON chemistry, it's not surprising that organic chemists came up with even better shorthand
to show the structures. It wasn't enough to use C for carbon, H for hydrogen, etc.
Instead, GEOMETRIC SHAPES are used to indicate the carbon "framework” of the structure. For a
compound like cyclohexane - which is a hexagonal ring of 6 -CH2- groups, the structure diagram is
reduced to a simple hexagon. The corners or "points" of the hexagon represent the carbon atoms, and
the hydrogen atoms are not even shown! Instead (since carbon is always assumed to have four bonds)
the two hydrogen atoms attached to each carbon are ASSUMED to be present. (Carbon forms four
bonds; two bonds are used to attach to its "neighbor" carbon atoms, and the remaining two attach to
the [implied] hydrogen atoms.)
Since we don't have pens that draw in three dimensions on 3-dimensional paper, we use a planar figure
(the hexagon) to represent cyclohexane. In reality, the cyclohexane ring is not planar (which would
force the bonds of carbon to be 60° apart when they really prefer the 109½° tetrahedral spatial
orientation). Instead, in cyclhexane's most stable configuration, one corner of the hexagon is pushed
"down" BELOW the plane of the paper, and the opposite corner (across the ring) moves "up” ABOVE the
plane of the paper, forming a "chair-like" structure. It's not really important to remember this; just keep
in mind (somewhere WAY BACK in your mind!) that the planar hexagon structure is itself an abstraction,
a shorthand method to make it easier to represent organic molecules on planar sheets of paper. If you
have a CHAIN of carbon atoms, it's represented by a zigzag line. Again, each "point" or "corner" along
the zigzag represents a carbon atom and its associated implied hydrogens. If you have double or triple
bonds at specific locations in the molecule, instead of a single line between those particular "corners" of
the geometric figure, you use a double line or triple line.
Rings can also join to other rings. This can be via an intervening chain of (usually carbon) atoms, or even
via a single or double bond [i.e., just a single or double line between two "points" of the rings]. Two rings
can also SHARE a single corner (for example, two hexagons sharing one "point"). More commonly,
though, two rings can share a FACE (for example, hexagons that share TWO ADJACENT carbon atoms, in
a structure that looks like chicken wire). Compounds like this that have more than one ring are called
POLYCYCLIC COMPOUNDS. Compounds that incorporate both rings and chains are called ALICYCLIC
COMPOUNDS. (The "ali-" part comes from "aliphatic", which originally was derived from the Greek for
"fatty" and has come to mean a carbon chain structure.)
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AROMATIC COMPOUNDS *vs.* AROMA COMPOUNDS; ISOMERS
There is a special kind of hexagonal 6-carbon ring in which every other carbon-carbon bond is a double
bond... so you have "alternating" single-double-single-double... bonds going around the ring. Since
carbon is now using THREE bonds to its carbon neighbors (1 double bond + 1 single bond), there is only
ONE remaining available bond for attachment to the (implied) hydrogen, so the simplest possible
structure of this type is benzene, C6H6. Benzene itself is a carcinogen, but this type of *structure* is
quite common in organic chemistry, even in compounds that are *not* carcinogens. The name for this
special structure is a BENZENOID RING. Another term that is used for compounds with benzenoid rings
is and AROMATIC COMPOUND. (Early chemists thought -- erroneously -- that this structure is what
made an organic compound odorous.) On the other hand, the chemical term AROMA COMPOUND or
AROMA CHEMICAL means a molecule that has an odor. Such compounds are *not necessarily*
"aromatic" compounds, meaning compounds that have benzenoid ring components.
[Just to make it confusing, in perfumery we also speak of an aroma compound, but that's generally a
mixture* of different aroma chemicals - like the Givco bases, for example.]
Benzenoid rings have some very interesting properties. First, unlike rings without any double or triple
bonds (so-called "saturated" ring compounds), the hexagon is PLANAR. That's because each of the >C=
atoms (2 single bonds + 1 double bond) have a "Y"-shaped, PLANAR configuration. The angles between
each pair of bonds are 120°. This fits perfectly with the (geometric) requirements for the internal angles
of a symmetrical, planar hexagon.
Generally speaking, every interatomic bond consists of two electrons, so single bonds contain 2
electrons, double bonds contain 4 electrons, and triple bonds contain 6. Looking at it another way,
compared to a single bond, each double bond has two "extra" electrons. In benzenoid rings, there are
*three* double bonds, for a total of 2 x 3 = 6 "extra” electrons. These 6 electrons are actually shared
equally by ALL SIX CARBON ATOMS, in a special electron cloud "double doughnut" above and below the
plane of the ring. This configuration gives the benzenoid ring structure EXCEPTIONAL STABILITY. In the
usual "shorthand" structural representation, benzenoid rings are drawn with a circle inside the hexagon,
representing the special doughnut-shaped electron clouds that are the hallmark of this ring type. (In
OLD organic scientific journals, a simple hexagon represented the benzenoid rings; "saturated" rings like
cyclohexane - with NO double bonds - were represented by a hexagon with an "S" in the center.)
As you might have guessed with all these chains and rings flying around, you could connect all these
TinkerToy atoms and bonds in all sort of different patterns. Even if you had just four carbons and ten
hydrogens, you could make a chain of four carbons (and attach the hydrogens on all the "extra" bond
positions), OR you could make a "Y"-shaped affair - a 3-carbon chain, with the 4th carbon attached to
the MIDDLE carbon (and again, the hydrogens in all the "leftover" bond positions). Compounds like
this, that have the same number and type of atoms, have exactly the same molecular weight, and are
called ISOMERS (from the Greek for “same parts" or "same units").
SUBSTITUENTS ON THE CARBON FRAMEWORK - "ACCESSORIZED" MOLECULES
Various types of groups can be attached to the main carbon framework, or structure, of an organic
compound. These groups can often have a large impact on an aroma chemical's odor - either on the
"type" of the odor, or on its strength.
One way to "accessorize" a carbon framework is to simply attach other short carbon chains to it.
Another way is to use "heteroatomic" groups - "hetero" meaning "non-carbon" - for example, an alcohol
or hydroxyl group (a singly bonded -OH), an amino group (singly bonded -NH2), or a chloro group (singly
bonded -Cl). The implied hydrogen, if you're using “shorthand" structural diagrams, is replaced by the
new group. And still a third way is to use carbon *functional groups* such as ethers, aldehydes, or
ketones. We'll cover these organic functional groups in more detail below.
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ORGANIC NOMENCLATURE - PART ONE - CARBON CHAINS; NAME "STEMS"; MULTIPLE BONDS;
"GENERIC" GROUP SYMBOLS
In the beginning, there were chains of carbon atoms all joined by single bonds, with all of the "extra"
bonds singly bonded to hydrogen. These "saturated" (with hydrogen) compounds are generically called
ALKANES.
If such a chain is attached to something else, it is an ALKYL group. (The "-yl" suffix in American-speak is
pronounced "ill" and signals, "I'm an attachment".)
If there is a double bond in the chain, making the compound “unsaturated", it is called an ALKENE; if this
is attached to a larger framework, it’s an ALKENYL group.
If there is a triple bond in the chain, it is still an unsaturated compound, but it is called an ALKYNE. (The
"Y" is pronounced like the English letter "I".) Such compounds as attachments are ALKYNYL groups.
The progression, then, is "-ane" vs "-ene" vs "-yne" for single, double, and triple bonds respectively,
with the suffix "-yl" signaling attachment.
In structural diagrams, a generic alkyl chain is represented by the pseudo-atomic symbol "R" [for
"radical"]. You can also have a benzene ring or some other aromatic ring as an "accessory" attachment;
the generic symbol for an aromatic is "Ar". (Chemistry buffs will know that this is also the symbol of a
real element, argon. However, argon is one of the "inert gases" which generally do NOT form bonds to
anything else, so if you see Ar bonded to something, it's darn near certain it means it's an aromatic, not
argon! Other inert gases include helium, neon, krypton, xenon, and radon.)
Depending on the number of carbons, the generic "alk-" is replaced with other stems. After 4 carbons,
things are more standardized, since Greek roots are used that are familiar from geometry. Here's a
table (number of carbon atoms / stem / example / "alkyl" name):
1 meth- methane
2 eth- ethane
3 prop- propane
4 but- butane
5 pent- pentane
6 hex- hexane
7 hept- heptane
8 oct- octane
9 non- nonane
10 dec- decane (this is a "hard C" by the way, so this is pronounced
DECK-ane, and "decyl" is DECK-yl)
11 undec- undecane
12 dodec- dodecane
13 tredec- tredecane
14 tetradec- tetradecane
15 pentadec- pentadecane
16 hexadec- hexadecane
17 heptadec- heptadecane
18 octadec- octadecane
19 nonadec- nonadecane
20 eicos- eicosane
21 heneicos- heneicosane
22 docos- docosane
23 tricos- tricosane
24 tetracos- tetracosane
25 pentacos- pentacosane
30 triacont- triacontane
32 dotriacont- dotriacontane
(etc)
40 tetracont- tetracontane
50 pentacont- pentacontane
60 hexacont- hexacontane
(etc)
100 hecta- hectane (same root as "hectare" = 100 ares = 10,000
square meters)
Unfortunately there's also a dichotomy between the "new" nomenclature and the "old" nomenclature.
For example, the 5-carbon "pentyl" group used to be called the "amyl" group.
Another holdover you may see or hear is "n-alkyl" (the "n" meaning “normal", meaning "unbranched").
So "n-amyl" would be the modern-day “pentyl" (with no "n-"!).
The prefix "iso-", on the other hand, meant that there was a branch at the very end of the chain (the end
*opposite* the point of attachment) to give a "Y" shaped tail. The simplest example is isopropyl, the "Y”
being formed by attaching the group via the MIDDLE carbon of the 3-carbon propyl chain. (An "npropyl" group - unbranched - would be attached via one end of the 3-carbon chain.) These would be
called 2-propyl and 1-propyl in more modern nomenclature, the digits showing the *point of
attachment* if the carbons in the chain are numbered 1, 2, 3...n from one end to the other.
An "isoamyl" group (as in isoamyl acetate) consists of a 4-carbon chain with an extra -CH3 attached to
carbon #3 (taking the carbon at the “attaching" end as #1). In more modern nomenclature this would
be named a “3-methylbutyl" group. Following the same logic, an "isobutyl" group would be called a "2methylpropyl" group.
Other strange and wonderful "old" terms include sec-butyl, meaning a 4-carbon butyl chain that is
attached to the carbon framework via carbon *#2* rather than #1. [This can be called "2-butyl" in
modern nomenclature.] There is also tert-butyl, meaning a sort of "X-shaped" group consisting a 3carbon chain attached to the main framework via the middle carbon (carbon #2), and which also bears
an additional methyl (-CH3) group attached to that same carbon #2. [This is called “2-(2-methylpropyl)"
in new-style nomenclature.]
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ORGANIC NOMENCLATURE - PART TWO - SIMPLE CYCLIC COMOPUNDS; POSITIONAL PREFIXES
One of the hallmarks of carbon is that it can not only form stable chains of carbon, but also it can form
stable carbon *rings*. A ring compound is named by adding the prefix "CYCLO-" to the stem or root that
shows the number of carbon atoms. For example, a 6-carbon *chain* is named "hexane". A 6-carbon
*ring* is called "cyclohexane". If the 6-carbon chain had a double bond in it, it would be called
"hexene"; if it had two double bonds, it would be called "hexadiene". (The "di-" prefix indicates two;
likewise "tri" = 3, "tetra" = 4, "penta" = 5, and so on.) The corresponding ring compounds would be
cyclohexene and cyclohexadiene.
Actually, if you have a double bond in a 6-carbon chain, you would also need to specify *WHERE* the
double bond was located. If the carbon atoms in the chain are numbered 1-6, from one end to the
other, it could be between C-1 and C-2, C-2 and C-3, or C-3 and C-4; (If it were between C-4 and C-5 that
would be the same as C-2 and C-3, if the chain were just numbered in the opposite direction.
Nomenclature rules require using the LOWEST possible numbers.) So you could have 1-hexene, 2hexene, or 3-hexene as possible ISOMERS of hexene. (Remember that term, "isomer"?)
Since cyclohexene doesn't have any "ends", no matter where the double bond is placed, the carbons are
always numbered so that the double bond lies between C-1 and C-2. On the other hand, in
cyclohexadiene, the two double bonds could be positioned on *opposite* sides of the ring, giving a
bond sequence going around the ring of double-single-single-double-single-single -- OR the bond
sequence could be double-single-DOUBLE-single-single-single. In other words, the double bonds could
be between C-1/C-2 and C-4/C-5, OR between C-1/C-2 and C-3/C-4.
These two isomers would be named, respectively, 1,4-cyclohexadiene and 1,3-cyclohexadiene. (A sixmembered ring is too small to permit formation of 1,2-cyclohexadiene, with the two double bonds
following one right after the other. This configuration *is* possible in *larger* rings, however.)
One of the quirks of chemical nomenclature is that things were named before there was full
understanding of the actual structure of the compound. I mentioned that a 6-carbon AROMATIC ring is
called BENZENE. However, a benzene ring as an *attaching group* is called a PHENYL group, C6H5-. (
The logical name would be a benzyl group, but that actually refers to this group: C6H5-CH2- )
ORGANIC FUNCTIONAL GROUPS - PART ONE - ETHERS
There are several special configurations of carbon and non-carbon atoms ("heteroatoms"). One of the
simplest is ETHER, which consists of one oxygen, singly bonded to two other organic groups.
(Remember oxygen has a valence of 2, so it can form two single bonds, or one double bond.) The
generic structure of an ether is R-O-R'. (Either or both of the "R" groups could also be aromatic groups.)
Common "ether" - the stuff that used to be used for anesthesia, and which still is used as engine starter
fluid - is diethyl ether: CH3CH2-O-CH2CH3. You could have "muchos" other ethers, such as methyl
propyl ether, isopropyl isobutyl ether, ethyl tert-butyl ether, etc etc. If it’s used as a *substituent* on a
larger carbon framework, these are usually named as "alkoxy" radicals - for example, -OCH3 =>
methoxy; -OCH2CH3 => ethoxy. This is in analogy to the "hydroxy" (-OH) group.
=====
ORGANIC FUNCTIONAL GROUPS - PART TWO - ALCOHOLS
Alcohols are particularly important in aroma chemistry, since many alcohols have a strong (and often
pleasant) odor. The generic alcohol structure is R-OH (or Ar-OH).
Alcohols are named by replacing the final "e" of the hydrocarbon name with the suffix "-ol". So you
have methanol, ethanol, 1-propanol (same as n-propyl alcohol), 2-propanol (same as iso-propyl alcohol),
and so forth. The -OH group as a *substituent* is called a "hydroxy" group.
Benzyl alcohol is C6H5-CH2-OH, but "phenyl alcohol" (which is the WRONG name), C6H5-OH, has the
special name PHENOL. A related compound, 2-methoxy-4-(2-propenyl) phenol, is important in
perfumery as it's the signature compound of clove oil -- its more familiar name is EUGENOL.
Picking apart the formal nomenclature, you can see that eugenol is an aromatic 6-carbon benzene ring
with an alcohol (-OH) group at ring position #1, a methoxy (-OCH3) group at ring position #2, and an allyl
or 2-propenyl group (-CH2CH=CH2) at ring position #4 [opposite the alcohol group]. It could also be
named 1-hydroxy-2-methoxy-4-(2-propenyl) benzene.
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ORGANIC FUNCTIONAL GROUPS - PART THREE - CARBOXYLIC ACIDS; ESTERS
These compounds are characterized by a carbon that's doubly bonded to an oxygen, leaving two other
bonds available for bonding to other things, >C=O. This type of group has a special name: it's a
CARBONYL group.
Just as in aromatic rings, because there is a double bond to carbon, the three bonds around the
"carbonyl carbon" all lie in the same plane, and are 120° apart. Since I can't type the other groups if I
use the >C=O format to show a carbonyl, I'll change it to this, which means exactly the same thing: (C=O)-.
CARBOXYLIC ACIDS have an -OH group attached to one of the carbonyl’s single bonds: -(C=O)-OH, or in
the more usual chemists' shorthand, -COOH or -CO2H. They are named by replacing the terminal "e" of
a hydrocarbon name with the suffix "-oic acid", so you can have "methanoic acid", “ethanoic acid", etc.
As usual, the simplest members of the series are more usually called by their "old-style" names methanoic acid = FORMIC acid, ethanoic acid = ACETIC acid. (You may also see propionic acid =
propanoic acid, and butyric acid = butanoic acid.) The compound formed by attaching a 6-membered
aromatic phenyl ring to a carboxylic acid -COOH group, giving C6H5COOH, is called BENZOIC ACID. On
the other hand if a benzyl C6H5-CH2- group is attached to a -COOH group, the compound 6H5CH2COOH
is called PHENYLACETIC ACID (because it's considered to be a derivative of acetic acid => C6H5CH2COOH).
DICARBOXYLIC ACIDS have *two* -COOH groups per molecule. The ones which have these groups at the
ends of a chain of zero to 5 carbons have special names; the mnemonic to remember (?) the names is
"Oh my, such good apple pie!" Here's a table (# of carbons INCLUDING the 2 -COOH groups / common
name):
2 oxalic acid
3 malonic acid
4 succinic acid
5 glutaric acid
6 adipic acid
7 pimelic acid
There is also a special name for a benzene ring which has two –COOH groups attached. These are the
PHTHALATES. So, for example, diethyl phthalate could also be called diethyl 1,2-benzenedicarboxylate.
ESTERS are formed by combining a carboxylic acid and an alcohol. The -OH portion of the carboxylic
acid and the hydrogen atom from the alcohol (HO-R => H-OR) combine to form a molecule of water,
and the organic groups are joined together by a structure like this: R-(C=O)-O-R'.
(This can also be written more simply as R-COO-R'.) The complete equation is: R-(C=O)-OH + H-OR' =>
R-(C=O)-O-R' + H2O
Esters are very common aroma chemicals, and are generally named by adding "-yl" to the alcohol's stem
name, followed by adding "-ate" or "-oate" to the acid's stem name -- for example, ethyl acetate, cis- 3hexenyl formate, and propyl pentanoate. (The "-oate" suffix, by the way, is pronounced "OH-EIGHT".)
If the R and R' groups of an ester are connected by another chain of atoms, a ring results. These "ring
esters" are given a special class name: LACTONES. Their names are often characterized by an "-olide”
ending, as in the trademark names Galaxolide and Habanolide. As you might surmise from these
examples, lactones (in particular, macrocyclic or “large-ring" lactones) are important musk compounds.
Plant musks – for example, ambrettolide, found in ambrette seed oil - are macrocyclic lactones.
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ORGANIC FUNCTIONAL GROUPS - PART FOUR - ALDEHYDES and KETONES
KETONES also incorporate a carbonyl group, sandwiched between organic radicals. They are
characterized by structures like R-(C=O)-R' or R-CO-R' (again, where either or both R groups could be
aromatic Ar groups).
Note that these are very similar to esters; the only difference is that esters have additional oxygen
between the carbonyl carbon and one of the "R" groups. Ketones are named by changing the final "e"
of a hydrocarbon’s name to "-one" (pronounced "OWN"). A number is used to indicate which carbon in
the chain is the carbonyl carbon - numbering the chain, as usual, from the end that gives the carbonyl
carbon the lowest possible number. Simple compounds have other more common names – for
example, 2-propanone (=> the carbonyl is carbon #2 of the 3-carbon chain) has the common name
ACETONE. Ketones can also be named as "(radical) (radical) KETONE" - for example, phenyl methyl
ketone (more commonly known as ACETOPHENONE), and methyl ethyl ketone or MEK. This would be
named more formally as 2-butanone... so note that although the carbonyl carbon is NOT considered a
part of either radical chain in the "(radical) (radical) KETONE" type of name, it IS considered part of the
chain in the formal style of nomenclature.
Natural animal musks are macrocyclic ("large-ring") ketones. (In contrast to esters, ring ketones do not
have a special name.)
The only difference in ALDEHYDES is that one of the R groups of a ketone is replaced by hydrogen: R(C=O)-H, or more simply, R-CHO. (It’s written "-CHO" to distinguish it from an alcohol, "-COH".)
Aldehydes tend to oxidize fairly readily, forming carboxylic acids. For example, the highly odorous
[cherry or almond-like] BENZALDEHYDE (C6H5-CHO) readily reacts with atmospheric oxygen to form
odorless BENZOIC ACID (C6H5-COOH). Aldehydes also react readily with the nitrogen-containing
primary amines, forming highly colored SCHIFF BASES. Despite these drawbacks, aldehydes are a very
important class of aroma compounds.
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OTHER "ACCESSORIZING" GROUPS - ACYL GROUPS, AMINES, NITRO GROUPS, THIOLS
An organic radical attached to one single bond of a carbonyl provides a new type of radical, the ACYL
GROUP. (Acyl is pronounced ACE-ill or A-sill.) These are formally related to the corresponding acids.
For example, acetic acid is CH3-CO-OH. If the -OH is removed, what's left is the ACETYL radical, CH3-CO-.
This is a common substituent or “accessorizing" group in organic chemistry. Similar manipulations lead
to the FORMYL group, H-CO-, the PROPIONYL group, CH3CH2-CO-, and the BUTYRYL group, CH3CH2CH2CO-.
Long ago, it seems, I mentioned that nitrogen has a valence of 3. That means it can attach to up to 3
groups via single bonds. These compounds are formally derived from ammonia, NH3, by replacing 1, 2,
or all 3 hydrogens with other groups, and are called AMINES. A "primary" amine has only one hydrogen
replaced by some other group, so its generic structure is R-NH2. A "secondary" amine has two
hydrogens replaced by other groups; generically, R-NH-R'. A "tertiary" amine has all three hydrogens
replaced, as in R'-N(R)-R". As standalone compounds, these are commonly named by simply specifying
the names of the attached radicals, followed by the suffix "-amine". So, you could have methylamine,
dimethylamine, ethyl methyl amine, triethylamine, and so on. Another way to look at these is to
consider the amine group to be a substituent on a larger framework. In that case, the suffix changes to
"-amino" instead of "-amine". For example, the group -N (CH3)2 appears often in pharmaceutical
compounds as a substituent; it's called the "dimethylamino” group.
Recall that benzoic acid means a 6-membered phenyl ring attached to a carboxylic acid group, C6H5COOH. If the ring carbon bearing the –COOH group is taken as #1, the next carbon around the ring is #2.
If an amino group (-NH2) is attached to carbon #2, the result is 2-aminobenzoic acid, more commonly
known in perfumery circles as ANTHRANILIC ACID.
METHYL ANTHRANILATE is the methyl ester formed by reaction with the carboxylic acid portion of the
molecule. In so-called "DIMETHYL ANTHRANILATE" one of the two amine hydrogens of methyl
anthranilate is replaced by a methyl (-CH3) group. Since this then becomes a *secondary* amine,
dimethyl anthranilate does not form Schiff bases with aldehydes. This can be a useful property in cases
where the product must remain as colorless as possible.
Another nitrogen-containing substituent group is the NITRO group, -NO2. This is well known in
chemistry as a "high energy" radical, and it is a component of many types of explosives. Picric acid must
always be kept damp because it is explosive when it's dry; its chemical name is 2, 4, 6-trinitrophenol.
Toluene is a more common name for methylbenzene. 2, 4, 6-trinitrotoluene is the famous explosive
TNT. Glycerin, AKA glycerol, is 1, 2, 3-propanetriol - a 3-carbon chain with an alcohol (-OH) substituent
on each carbon. If the hydrogens of the three alcohols are substituted with three nitro groups, the result
is something that can really shake your booty: nitroglycerin! Despite these hazards, *some* nitro
compounds are reasonably stable. In particular, 1-acetyl- 2,6-dimethyl-4-(2-methylpropyl)-3,5dinitrobenzene is very commonly used and has a long-lasting, attractive musk odor.
Its more common name is MUSK KETONE, and it is one of a family of related compounds referred to as
the "nitro musks". The THIOLS are sulfur analogs of alcohols, R-SH. In quantity they are generally very
foul-smelling; in fact butanethiol, CH3CH2CH2CH2-SH, is one of the major components of "skunk oil".
However traces of these compounds lend a characteristic "tropical fruit" note to bases such as Tropifruit
Givco. Thiols are also important character-impact compounds in grapefruit oils and in galbanum oil.
Thiols are named by substituting the suffix "-thiol" in place of the alcohol's "-ol" ending. As a
*substituent*, the -OH [alcohol] group is called the "hydroxy" group. The corresponding -SH group as a
substituent is called the "mercapto” group.
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MISCELLANEOUS NOMENCLATURE
Many common simple organic compounds were discovered before the early chemists had any way to
determine their structure, so they were given a wide variety of names. Here are a few of those.
ANILINE (as in "aniline dyes") => aminobenzene
ANISOLE => methoxybenzene
ANISIC ACID => 4-methoxybenzoic acid
ANISALDEHYDE => 4-methoxybenzaldehyde
ANETHOLE => 1-methoxy-4-(1-propenyl) benzene [major constituent of anise seed oil]
CINNAMIC ACID => 3-phenyl-2-propenoic acid (the carbonyl carbon of the acid is #1)
CINNAMALDEHYDE => 3-phenyl-2-propenal (the carbonyl carbon of the aldehyde is #1)
CINNAMYL ALCOHOL => 3-phenyl-2-propen-1-ol (the carbon bearing the -OH group is #1; the double
bond is between C-2 and C-3)
PYRIDINE is an example of a "heterocycle" - a ring in which one or more carbon atoms are substituted by
other types of atoms. In this case, one carbon (and its attached hydrogen) is replaced by nitrogen. Like
benzene, pyridine is an aromatic compound. (Remember that this just means that the electrons in the
double bonds are shared by all the atoms in the ring; it doesn't necessarily mean the compound has an
aroma.
Pyridine certainly has an odor, but it is NOT pleasant! It doesn’t *stink* exactly, but it is very "sharp"
and choking.) A PYRROLE is a 5-membered heterocycle in which -NH- replaces the -CH2- ring carbon of
cyclopentadiene. (As you'll recall from the discussion of ring compounds' nomenclature, the "cyclo"
means a ring, the "penta” means a 5-membered ring, and the "diene" means there are two double
bonds in the ring.) If a benzenoid 6-membered ring is bonded to a face of the pyrrole ring that includes
one of the double bonds, the result is INDOLE. This is a minor but indispensable component of many
"white flower" aromas. By itself, it is not so pleasant. A related compound, SKATOLE, has a methyl
group bonded to the #3 carbon of indole. (The ring atoms in indole are numbered by assigning #1 to the
nitrogen, then going around the SMALLER 5-membered ring first, then the 6-membered ring.)
Skatole is found in feces.
NAPHTHALENE (as in mothballs) consists of a pair of hexagonal benzenoid rings, fused along one face.
So, it's a BICYCLIC compound. Both rings are aromatic; formally there are 5 double bonds in the rings,
and all 10 of these double-bond electrons (remember, EACH bond contains 2 electrons) are shared
equally by all 10 of the ring-carbon atoms, via a sort of "dumb-bell shaped" or "double circle" electron
cloud.
If you remove two of the double bonds from ONE of the two rings of naphthalene (so you have one
benzenoid or aromatic 6-membered ring, and one "saturated" single-bonded 6-membered ring, fused by
one face) the result is a class of compound called a TETRALIN (from "tetrahydronaphthalene"). This is
the basic skeleton of one of the "polycyclic" musks, Tonalide.
If the "saturated" 6-membered ring is replaced by a 5-membered saturated ring, the basic ring structure
is called an INDANE. (That's sort of like indole, but the "-ane" ending implies that this structure's rings
are made only of *carbon* atoms, like hydrocarbons or "alkanes".) An important polycyclic musk that
incorporates this structure is Phantolide.
If the second carbon atom from the ring-fusion carbon of a tetralin (going around the saturated ring) is
replaced by an oxygen, the resulting structure is an ISOCHROMENE. If a cyclopentane ring is also fused
to the benzenoid ring, on the face opposite the fusion face of the isochromene, another type of
macrocyclic musk framework results, typified by Galaxolide.