Organic Chemicals in the
Environment
Where are they found?
What are the effects do they have?
Surface effects
Membranes
Waxes
Foams
Soil - Humus
The air-water interface
The surface tension of water is 0.073 N/m. Ions can increase
this value somewhat to 0.075 N/m. However, organic
compounds Tend to lower the value. The surface tension of
organic liquids (e.g. octane, benzene etc.) range from
0.020 to 0.050 N/m.
There are two types of surface adlayers on water.
1. Organic thin films such as oil spills (prior to oxidative
weathering). These compounds are both insoluble and
less dense than water.
2. Surfactants are amphipathic molecules. There are dry
surfactants such as detergents (mostly hydrophobic) and
wet surfactants such as proteins (mostly hydrophilic).
Surface tension
Liquids tend to adopt shapes that minimize their surface area.
This places the maximum number of molecules in the bulk.
Droplets of liquids tend to be spherical because a sphere is
the shape with the smallest surface-to-volume ratio. The work
needed to change the area by dσ is:
dw = γdσ
The coefficient γ is called the surface tension. It has
dimensions of energy per unit area (J/m2). At constant
volume and temperature the work of surface formation is
equal to the Helmholtz free energy:
dA = γdσ
Since dA < 0 is a spontaneous change surfaces tend to contract.
Lipids and Surfactants
Both lipids and surfactants consist of a hydrophobic tail
region and a hydrophilic head group (amphipathic).
Both lipids and surfactants will orient with their head
groups pointed towards the water interface and their
tails sequestered from water.
Lipids have the ability to form a bilayer. This property
makes these molecules the constituents of biological
membranes. Bilayers can be gel-like or crystalline. They
can have a planar phase or form hexagonal phase.
Surfactants can tend to form micelles. Micelles are spherical.
The hydrophobic tails form the interior and the charged head
groups are on the surface.
Lipid polymorphism
Biochemistry of Lipids, Lipoproteins
and Membranes, Vance & Vance, Elsevier 1996
Lipid structure
Representative lipids are
shown in Figure to the
right. There are two acyl
chains on a glycerol.
The third site is a
phosphodiester with a
number of possible
groups indicated.
The fluid mosaic model of membranes
Plasma membrane
Cytosol
Biochemistry of Lipids, Lipoproteins
and Membranes, Vance & Vance, Elsevier 1996
Membrane asymmetry
The inner and outer leaflets of membrane bilayers have
different compositions. Erythrocytes are the most studied.
The cytosolic side is composed of PE and PS. The PE
distribution is ca. 80% in the inner membrane and 20% in
the outer membrane. PS is negatively charged and PE is
moderately negative in charge. The inner membrane is
thus largely negative.
The outer membrane consists of PC, sphingomyelin, and
glycolipids. Cholesterol is also important and associates
with the membrane to provide added fluidity. Plasma
membranes have equimolar quantities of cholesterol. By
contrast, the endoplasmic reticulum and mitchondrial
membranes have small amounts of cholesterol.
Detergents and
Lysophospholipids
O-
Detergents are amphipathic
molecules that can have charged
or uncharged head groups and
single hydrophobic tails. If one
of the acyl chains is cleaved from
a lipid then a lysophospholipid is
created.
Other associating molecules
include aromatic or fused ring
compounds (dyes, purines,
pyrimidines) and alicyclic fused
ring compounds (bile salts,
cholesterol etc.).
O S
R
O
O
O
OH
O
O
SDS
Lysophospholipid
Transmembrane Potential
Membranes are essential for life. They provide a compartment for
chemistry to occur separate from the environment. Living organisms
have also evolved to use membranes for generation and storage
of energy using photosynthesis. This is done by pumping protons
across a membrane to generate a transmembrane potential.
The transmembrane electrical potential is represented as the
voltage difference of the inside with respect to outside. We
express the potential as V (unit is the volt). In chemistry, the Nernst
equation is used to describe the dependence of the oxidation
potential on concentration. The symbol is E (or Eo) and the unit is
also the volt.
The Nernst equation
The Nernst equation describes the potential for each half-reaction
a(Ox) + ne-
b(Red)
The standard potential (i.e. potential at 1 molar concentration) is Eo.
The electrode potential is given by:
b
[Red]
E = E – RT ln
a
nF
[Ox]
o
where R is the gas constant and F is the Faraday (96,450 J/volt).
In an electrochemical cell where two half-reactions are combined
to make a redox reaction, the electromotive force is:
emf = E(+) - E(-)
The free energy is G = -nFE. Therefore, the standard free energy
change for a redox process is ∆Go = -nF(Eoox - Eored) = -nF∆Eo.
Application of the Nernst equation
to membrane potential
The free energy per mole of solute moved across the membrane
∆Gconc = -RTln(Co/Ci) where Co is the concentration outside the
membrane and Ci is the concentration inside the membrane. The
difference in charge concentration results in a free energy contribution
from the voltage difference ∆Gvolt = -F∆E (assuming n=1). The
balance of forces at equilibrium requires that ∆Gvolt = ∆Gconc so that
the trans-membrane potential is obtained as follows.
∆Gvolt = ∆Gconc
Co
– F∆E = – RT ln
Ci
Co
∆E = RT ln
F
Ci
Natural foams from wax
Natural foams can occur from tree sap, fallen leaves and
zooplankton. For example, zooplankton are composed of
wax esters. Sometimes as much as 75% of the organism
is attributable these compounds. An example of a wax
ester is bee’s wax, which is Palmitic acid (C16:0) esterified
by a C30 chain, known as triacontanol (or melissyl alcohol).
The word "wax" is derived from the old english "weax" for
the honeycomb of the bee-hive. Thus, bee wax can be
considered as the reference wax.
Zooplankton wax
Polar zooplankton species are known for the storage of wax
esters as natural energy reserves. Thus, in the antarctic
Euphausiid Thysanoessa macrura the wax deposits reach
up to 70% of the total body lipids and contain high levels of
18:1(n-9) and 18:1(n-7) alcohols. Carnivorous zooplankton
species are characterized by the presence of shorter-chain
alcohols (14:0, 16:0) while herbivorous species, as the
calanoid copepods, contain mainly long-chain alcohols
(20:1, 22:1).
Kattner G et al., Mar Ecol Prog Ser 1996, 134, 295
Cutin is a wax found on leaves
Monoacylglycerols are important in the constitution of
cutin polymer. Cutin is the structural component of the plant
cuticle, the outermost layer of leaves and other aerial organs.
Waxes embedded in the cutin make the cuticle an efficient
barrier against desiccation, gas exchange and pathogen attack.
Cutin polyester is typically composed of esterified hydroxyfatty acids with 16, 18 and 22 carbon-chains and one terminal
hydroxyl (ω-position) and other hydroxyl groups in secondary
positions. The cutin polymer has been found to be based on
the inter-esterification of hydroxyacids (head-to-tail in a linear
form or cross-linked) and of glycerol esterified with various
hydroxy-fatty acids.
Graca J et al., Phytochemistry 2002, 61, 205
Cutin structure
The cuticle is part of the epidermis.
Cutin is the wax that prevents water
loss. When moving plants from sun
to shade the amount of cutin required
changes due to the amount of water
generated by photosynthesis.
The formation of a polymeric
layer of molecules to for
cutin is shown on the right.
The cutin polymer is a crosslinked
set of esters of long α,ω-alcohol
carboxylic acids or dicarboxylic acids.
Monomer composition in cutin
Biochemistry of wax synthesis
Acetyl co-A
Acetyl-CoA is an important molecule in metabolism. Its
main use is to convey the carbon atoms within the acetyl
group to the Krebs Cycle to be oxidized for energy production.
In chemical structure, acetyl-CoA is the thioester between
coenzyme A (a thiol) and acetic acid (an acyl group carrier).
It is also a carrier of two carbon units in fatty acid synthesis.
1. Acetyl group
2. Coenzyme A
•Beta-mercaptoethylamine
•Pantothenic acid
•Phosphate
•3', 5'-adenosine diphosphate
Suberin is found in bark
Waxes are also found in suberin, which is a lipidic polyester
present in tree barks, tuber skins and abscisic tissue of
falling leaves. It is also formed in plant after wounding. Upon
depolymerization, cork suberin releases a mixture of
monomers and oligomers, including monoacylglycerols of
monoacid (C22), of ω-hydroxyacids (C16, 18, 22, or 24), and
of α,ω-diacids (C16, 18, or 22). Glycerol is a major
compound of this polyester, constituting up to 20% by weight
of suberin in oak, cotton and potato. The current model
describes a monoglyceride containing 26-hydroxy-26:0 fatty
acid has been isolated from the root bark of Pentaclethra
eetveldeana, used in Congo as a traditional medicine for the
treatment of hemorrhoids, malaria and epilepsy.
Graca J et al., Chem Phys Lipids 2006, 144, 96
Graca J et al., Agric Food Chem 2000, 48, 5476
Byla B et al., Phytochemistry, 1996, 42, 501
Soil carbohydrates
Soil contains organic matter only near the surface. The
organic compounds arise mostly from the action of microorganisms. Most of the organic matter is trapped in colloids
and is not in equilibrium.
Soil contains a number of carbohydrates and sugars
comprising about 10% of the organic matter. Most of it is
polymeric although some monomeric sugars exist,
glucose, galactose, fructose etc.
As much as 50% of soil phosphorous is esterified as
inositol hexaphosphate (see page 64 in Larson and Weber).
O
IP5
IP6
OP(OH)2
O
OP(=O)(OH)2
O
OP(OH)2 OP(OH)2
O
OP(OH)2
(OH)2(O=)PO
O
OP(=O)(OH)2
OP(OH)2
OP(=O)(OH)2
(OH)2(O=)PO
OP(=O)(OH)2
Inositol hexaphosphate
Phytic acid (inositol hexaphosphate
(IP6), or phytate) is the principal
storage form of phosphorus in
many plant tissues, especially in
the grass family (wheat, rice, rye,
barley etc) and beans. Phosphorus
in this form is generally not bioavailable to humans because
humans lack the digestive enzyme,
phytase, required to separate
phosphorus from the phytate molecule.
Phytic acid binds to important minerals such as calcium,
magnesium, iron and zinc and can therefore contribute to
mineral deficiencies, as the minerals are not released from
the phytate and are thus unavailable to the body.
Good and bad effects of phytate
For people with a particularly low intake of essential minerals,
especially young children and those in developing countries,
this effect can be undesirable.
A common way in developing countries to increase the bioavailability of minerals from grains and beans is using
fermentation. Many bacteria possess phytase activity and by
fermenting grains or beans by lactic acid bacteria the phytate
is destroyed and the bioavailability of the minerals is
increased.
Phytic acid recently has been studied for its potential anticarcinogenic properties. Recent studies have indicated that
phytic acid may have some preventive effect in prostate,
breast, pancreatic and colon cancer. The mechanism,
however, is not yet understood.
Lignin structure
Lignin
monomer
4-alkylcatechol
Sample lignin
polymer structure
Breakdown of lignin
Lignin is a biopolymer composed of 4-alkylcatechol units.
The breakdown of lignin in the soil leads to five common
phenolic acids.
CO2H
CO2H
CHO2H
OH
CHO2H
OCH3
OCH3
OH
OH
(1)
(2)
(3)
1. para-coumaric acid
2. Syringic acid
3. para-hydroxybenzoic acid
4. Vanillic acid
5. Ferulic acid
CHO2H
H3CO
OH
(4)
OCH3
OH
(5)
Humus
The chemistry of humus is one of the most complex in nature.
Humus consists of a oxidation and polymerization products of
Polysaccharides, phenols and amino acids found in the soil.
Humic matter is anionic and therefore it binds metal ions well.
Extraction of humus is performed in aqueous alkali
(0.5% NaOH). The base soluble fraction is called humic acid.
The fraction which is solubilized by acid is called fulvic acid.
It is not known whether these two fractions are significantly
different. (Humus is discussed on pages 68-83 of Larson and
Weber)
Solubility and partitioning
Solubility
Hydrophobic Effect
Linear Free Energy Relationships
Octanol/Water Partitioning
Water as a solvent for
organic molecules
The maximum solubility of carbonaceous matter in water
occurs at around C4. This is an optimum size for water
molecules to act as a clathrate (cage) around the solute.
organic solutes tend to be hydrophobic and so the
organization of solvent water around these solutes in an
ice-like structure increases the entropy of the solution. This
unfavorable interaction tends to cause carbon materials to
aggregate.
Solubility
Dissolution of an organic solid can be described as an
equilibrium between the substance in its solid and dissolved
forms:
An equilibrium expression for this reaction can be written,
as for any chemical reaction (products over reactants):
where K is called the equilibrium constant (solubility constant).
The curly brackets indicate activity. Activity is related to
concentration by
{A} = ζ[A]
where ζ is called the activity coefficient. For an ideal solution
ζ = 1.
Saturation
The square brackets mean molar concentration in mol dm-3
(also denoted with the symbol M).
This statement says that water at equilibrium with solid sugar
contains a concentration equal to K. For table sugar (sucrose)
at 25 °C, K = 1.971 mol/L. (This solution is very concentrated;
sucrose is extremely soluble in water.) This is the maximum
amount of sugar that can dissolve at 25 °C; the solution is
saturated. If the concentration is below saturation, more sugar
dissolves until the solution reaches saturation, or all the solid is
consumed. If more sugar is present than is allowed by the
solubility expression then the solution is supersaturated and
solid will precipitate until the saturation concentration is
reached. This process can be slow; the equilibrium expression
describes concentrations when the system reaches equilibrium,
not how fast it gets there.
Hydrogen bonding in water
Hydrophobic interactions
The hydrophobic effect
The free energy change for transfer of hydrocarbons from organic
solvent to water is positive. The dominant contribution to the
hydrophobic effect is the entropy. In the organic phase:
µH(H) = µH0(H) + RT ln aH(H)
(H = hydrocarbon, W = water)
In water the chemical potential is:
µH(W) = µH0(W) + RT ln aH(W)
Thermodynamic data for the transfer of hydrocarbons from
hydrocarbon solvents (H) to water (W) have been obtained
by Tanford.
Thermodynamic data for the
transfer of hydrocarbons to water
µH0(W)-µH0(H) HH0(W)-HH0(H)
SH0(W)-SH0(H)
(kJ/mol)
(kJ/mol)
(J/mol-K)
------------------------------------------------C2H6
16.3
-10.5
-88
20.5
-7.1
-92
C3H8
C4H10
24.7
-3.3
-96
28.7
-2.1
-105
C5H12
C6H14
32.4
0
-109
C6H6
19.2
+2.1
-59
Hydrocarbon
The change in chemical potential due to solvation of the
hydrophobic solute is primarily due to the entropy.
The entropy change is unfavorable because the water
hydrogen bonding network must rearrange.
Linear free energy relationships
If two reactions occur in related compounds that exhibit
A linear free energy relationship (LFER) we can write:
log k – log k o = m(log K – log K o)
Substituting the appropriate terms from transition-state
theory we obtain:
*
*
o
∆G
∆G
∆G
∆G –
o
= m(
–
)
2.3RT
2.3RT
2.3RT
2.3RT
or
*
*
o
o
∆G – ∆G = m(∆G – ∆G )
and finally
∆∆Go* = m∆∆G
Thus, the rate constant tracks the equilibrium constant
for the two processes (see page 18-19 in Larson and Weber).
Hammett equation
One of the first methods for relating structure and reactivity
was developed by Hammett (1937). Hammett used the
benzoic esters as a model, by observing that the reactivities
(i.e. rates of reaction) of benzoic acid esters were related
In modern organic chemistry Linear free energy relationships
(LFERs) are widely used to understand the variability
between substance classes or the variability between
different natural organic phases. Multiparameter LFERs
are used to understand how molecules partition in different
phases in the environment.
Octanol-water partitioning
In environmental chemistry, one often wants to interpret or
predict equilibrium partitioning of organic compounds between
any two phases. Hence, one needs to understand the
partition variability that stems from using different types of
compounds and the variability that arises from looking at
different natural phases, e.g. different soil organic matter.
It is current practice in environmental chemistry to evaluate
equilibrium partitioning with the help of double logarithmic
correlations between the unknown partition constant and a
well-known partition constant of the compounds, e.g.,
partitioning between natural organic matter and water or air
is correlated with the octanol/water or octanol/air partition
constant, respectively. These relationships can only predict
the compound variability within a single substance class.
(for partitioning, see page 10 in Larson and Weber).
Hot topics
Biofilms
Red tides
Bacteria and Biofilms
Biofilms are a hot topic in microbiology today. Bacterial
colonies can form layers, which can be resistant to antiobiotics
and the immune system. Biofilms were recognized in 1994
following a case that involved the infection of hundreds of
asthmatics. It was found that all the asthmatics used the same
inhalant contaminated with a bacterium known as Pseudomonas
aeruginosa. This bacterium was able to survive the routine
disinfection of the inhalant during manufacturing by forming a
biofilm comprised of many colonies. The contaminated inhalers
contained pieces of the biofilm which were transported directly
to the lung tissue by the asthmatics. In the lung tissue the
Pseudomonas biofilm was able to flourish. One hundred people
died from the biofilm infection, a dramatic example of the danger
posed by some bacterial biofilms.
Bacteria and Biofilms
Biofilms can be found in many areas of the human body and
the environment. Teeth, intestines, medical devices, contact
lenses, drainage pipes, and the bottoms of ships. The common
aspect of all biofilms is that they are comprised of a primary
layer of bacteria that provide an attractive environment for
other bacteria and larger organisms. Biofilms found on the hull
of a ship consist of large organisms like barnacles, mussels, and
host of other zooplankton and phytoplankton. These biofilms
slow a ship and are expensive to remove and prevent. Current
methods to prevent biofilm formation on ships include a wide
variety of toxic marine paints. However, these paints tend to
wear off and biofilms which are resistant form on them without
regard to the toxins.
Red tides
A red tide is not a foam, but rather is a bloom of microorganisms. The toxic dinoflagellate Alexandrium is the
genus responsible for poisonous red tides in many countries
throughout the world.
Alexandrium serves
as an excellent model
for red tide species.