CHE 102 LECTURE 7 FOSSIL FUELSAn oil refinery or petrole.docx

CHE 102: LECTURE 7 FOSSIL FUELS
An oil refinery or petroleum refinery is an industrial plant
where crude oil is transformed and refined into more useful
products such as gasoline, diesel fuel, jet fuel, naptha, asphalt,
heating oil, kerosene, liquefied petroleum gas, and fuel oils.
Oil, coal, natural gas and other fossil fuels are called "fossil"
because these fuels are the preserved carbon-hydrogen remnants
of ancient life. Coal is formed from plants that decomposed and
accumulated in ancient swamps.
EXAMPLES: Fossil Fuels:
Coal: Coal is the primary fuel for the production
of electricity and is responsible for about 40% of the electric
power supply in the United States.
Oil: Oil is the primary source for the world's transportation.
Natural Gas: About 27% of U.S. energy is fueled by natural
gas. Natural gas is the cleanest burning fossil fuel.
CHEMISTRY: fossil fuel combustion.
One molecule of methane, combined with two oxygen
molecules, react to form a carbon dioxide molecule, and two
water molecules (usually given off as steam or water vapor)
releasing energy. See Lecture 3 and figure below.
COAL
Coal is a combustible black or brownish-black sedimentary

rock usually occurring in rock strata in layers or veins
called coal beds or coal seams. The harder forms, such
as anthracite coal, can be regarded as metamorphic rock because
of later exposure to elevated temperature and pressure.
NOTE: Geologists classify rocks into three main rock types.
Rocks are either a single mineral or a combinations of minerals.
Sedimentary rocks are a type of rock that formed by the
accumulation or deposition of small particles (minerals or
organic matter) at the Earth’s surface, subsequently followed
by their cementation on the floor of oceans or other bodies of
water. Examples: sandstone, limestone (see below).
Limestone is a carbonate sedimentary rock that is often
composed of the skeletal fragments of marine organisms such as
coral, foraminifera, and molluscs. Its major materials are the
minerals calcite (CaCO3).
and aragonite,
which are different crystal forms of calcium carbonate
(CaCO3).
Metamorphic rocks arise from the transformation of existing
rock types, in a process called metamorphism, which means
"change in form". The original rock is subjected to heat and
pressure, causing profound physical or chemical changes. The
precursor may be a sedimentary, igneous, or existing
metamorphic rock. Examples: slate, marble.

Marble is a metamorphic rock composed of recrystallized
carbonate minerals, most commonly calcite (see above) or
dolomite. In Geology, the term marble refers to metamorphosed
limestone. The Taj Mahal in the Indian city of Agra is entirely
clad in marble.I was amazed to find that the limestone in the Taj
Mahal structure is so transparent, the interior of this
architectural masterpiece is “illuminated.”
Igneous rock is formed through the cooling and solidification of
lava (or magma) from volcanic eruptions. The magma can be
derived from partial melts of existing rocks in either a planet's
mantle or crust. Example: obsidian, granite (see below).
The word "granite" comes from the Latin granum, a grain, in
reference to the coarse-grained structure of such a rock. Strictly
speaking, granite is an igneous rock with between 20% and 60%
quartz (See Lecture 4) by volume, and at least 35% of the total,
by feldspar [ Feldspar is an abundant rock-forming mineral
typically occurring as colorless or pale-colored crystals and
consisting of aluminum silicates of potassium, sodium, and
calcium] . A crystal of one form of feldspar shown below.
Coal is composed primarily of carbon, along with variable
quantities of other elements, chiefly hydrogen, sulfur, oxygen,
and nitrogen. Coal is a fossil fuel that forms when dead plant
matter is converted into peat, which in turn is converted
into lignite, then sub-bituminous coal, after that bituminous

coal, and lastly anthracite. Thus both biological and geological
processes are involved in its formation. The geological
processes take place over millions of years.
There are six main types of coal that are regularly used in
power plants or by other sectors of society:
Peat. Peat is formed from decaying vegetation, and is
considered to be the precursor of coal
Lignite.
Lignite is formed from compressed peat, and is often referred to
as brown coal
Bituminous/Sub Bituminous Coal
Steam Coal
Anthracite
Graphite
Coal
Sedimentary rock
Anthracite coal
Element Composition of Various types of Coal: Mass % of each
element.
type of coal C H O N S
lignite 71 4 23 1 1
subbituminous 77 5 16 1 1
bituminous 80 6 8 1 5

anthracite 92 3 3 1 1
NOTE: Anthracite is the “cleanest” coal, lignite the “dirtiest.”
Sources of Energy: fossil fuels (2007).
petroleum 36.0 %
coal 27.4 %
natural gas 23.0%
The following two account for 14.8%.
nuclear 8.5 %
hydroelectric 6.3 %
All of the following account for 0.9%.
geothermal
solar
tidal
wood
waste
Historical record of fossil fuel use: Wood Coal
Petroleum/Natural Gas Hydro/Nuclear
1850 91% 9%
1900 21% 71% 5%
3%
1950 6% 36% 52%
6%

1975 3% 18% 73%
6%
2000 4% 23% 62%
11%
The separation of petroleum into “fractions” (by length of
carbon chain) is what occurs in oil refineries.
C5 – C10 gasoline
C10 – C18 kerosene
C15 – C25 diesel fuel, heating oil, lubricating oil
> C25 asphalt
In the New York Times today (4/21/2020), the banner headline
is:
“Coronavirus Live Updates: Trump Says He Will Halt
Immigration; Oil Prices Crater, and Stocks Fall”
The oil market meltdown is continuing. Brent crude, the
international benchmark, was down about 18 percent, to $20.90
a barrel.
GREENHOUSE EFFECT: Overview
1. Solar radiation reaches the Earth's atmosphere - some of this
is reflected back into space.
2. The rest of the sun's energy is absorbed by the land and the
oceans, heating the Earth.

3. Heat radiates from Earth towards space.
4. Some of this heat is trapped by greenhouse gases in the
atmosphere, keeping the Earth warm enough to sustain life.
A greenhouse gas is a gas that absorbs and emits radiant energy
within the (thermal) infrared range. Greenhouse gases cause the
greenhouse effect on planets. Greenhouse gases include water
vapor, carbon dioxide, methane, nitrous oxide, ozone and some
artificial chemicals such as chlorofluorocarbons (CFCs). The
molecular structures of ozone and nitrous oxide are shown
below.
OZONE
NOTE: The ozone layer or ozone shield is a region of Earth's
stratosphere that absorbs most of the Sun's ultraviolet radiation.
The ozone layer contains a high concentration of ozone in
relation to other gases in the layer, although still small in
relation to gases (e.g. oxygen O2 and nitrogen N2 ) in other
regions of the stratosphere.
NITROUS OXIDE (“laughing gas”)

NOTE: Nitrous oxide has significant medical uses, especially
in surgery and dentistry, for its anaesthetic and pain reducing
effects. Its colloquial name "laughing gas", coined by
Humphry Davy (see Lecture 4 ), is due to the euphoric effects
upon inhaling it, a property that has led to its recreational use
as a dissociative anaesthetic ( A unique anesthesia characterized
by analgesia and amnesia with minimal effect on respiratory
function. The patient does not appear to be anesthetized and can
swallow and open eyes but does not process information). It is
also used as an oxidizer in rocket propellants and in motor
racing to increase the power output of engines.
5. Human activities such as burning fossil fuels, agriculture and
land clearing are increasing the amount of greenhouse gases
released into the atmosphere.
6. This results in trapping extra heat, and causing the Earth's
temperature to rise.
The greenhouse effect is a natural process that warms the
Earth’s surface.
Absorbed thermal energy warms the atmosphere and the surface
of the Earth. This process maintains the Earth’s temperature at
around 91.4 degrees Fahrenheit warmer than it would otherwise
be, allowing life on Earth to exist.
The problem we now face is that human activities – particularly
burning fossil fuels (coal, oil and natural gas), agriculture and
land clearing – are increasing the concentrations of greenhouse
gases. This is the enhanced greenhouse effect, which is
contributing to global warming, an overall increase in the
temperature of the Ear

Average global temperatures from 2010 to 2019 compared to a
baseline average from 1951 to 1978. Source: NASA.
CARBON FOOTPRINT
A carbon footprint is historically defined as the
total greenhouse gas (GHG) emissions caused by an individual,
event, organization, or product, expressed as carbon dioxide
equivalent.
Greenhouse gases, including the carbon-containing gases carbon
dioxide and methane, can be emitted through the burning of
fossil fuels, land clearance (e.g. in the Amazon basin) and the
production and consumption of food, manufactured goods,
materials, wood, roads, buildings, transportation and other
services.
In most cases, the total carbon footprint cannot be calculated
exactly because of inadequate knowledge of and data about the
complex interactions between contributing processes, including
the influence of natural processes that store or release carbon
dioxide. For this reason, the following definition of a carbon
footprint has been proposed:
Carbon Footprint: A measure of the total amount of carbon
dioxide (CO2) and methane (CH4) emissions of a defined
population, system or activity, considering all relevant sources,
sinks and storage within the spatial and temporal boundary of
the population, system or activity of interest.
Most of the carbon footprint emissions for the average U.S.
household come from "indirect" sources, e.g. fuel burned to
produce goods far away from the final consumer. These are
distinguished from emissions which come from burning fuel
directly in one's car or stove, commonly referred to as "direct"
sources of the consumer's carbon footprint.
The 100-year global warming potential (GWP100) is calculated

with reference to carbon dioxide.
Coal - Wikipedia
https://en.wikipedia.org/wiki/Coal
GLOBAL WARMING
Global warming - Wikipedia
en.wikipedia.org › wiki › Global_warming
ECONOMIC IMPLICATIONS
The Economic Impact of Greenhouse Gas Emissions | Clive Best
clivebest.com/?p=7139
1
Running head: WRITTEN REFLECTION

Written Reflection
Antuan Benitez
Nicole Wertheim College of Nursing and Health Sciences
Author Note
Antuan Benitez, Nicole Wertheim College of Nursing and
Health Sciences, Florida International University
Correspondence concerning this article should be addressed
to Antuan Benitez, Nicole Wertheim College of Nursing and
Health Sciences, Florida International University, Miami, FL
33199. Contact: [email protected]
Once upon a time when I was still a Junior in this program,
I heard many seniors talking about this course. Now I know why
they would mention it so often. I believe that this course is a
steppingstone in Nursing School. In other words, during Senior
Practicum we will be combining concepts that we have seen and
studied to provide the best patient-care possible. Also, we are
going to have more autonomy as nursing students although we
are required to shadow our preceptors who will be watching us
closely and passing their wisdom and experience to us. My
expectations from this course are very high, and I can’t wait to
work my first 12-hour shift. I want to learn how to manage my
time properly in a fast-paced environment while providing high
quality patient-care. Senior practicum is a one in a lifetime

experience, and I want to learn the most I can from it. I believe
that this course can help me to become a nurse in real life, and
what I mean by that is that Nursing School provides us with the
knowledge to be nurses, but Senior Practicum gives us the tools
which we need to put all the theory we learned from books to
applied it. It is like a college basketball player transitioning to
the NBA; this course will help me with this change or transition
from theories to practice (Hatch, 2018). I want to learn also how
to communicate with doctors and improve my SBAR skills. My
plan is to gain as much experience as I can from these 168 hours
that I would be working with my nurse preceptor. I will ask a
lot of questions because that’s the only way of learning. Also, I
have heard that those first shifts when you are a nurse and
working on your own are scary. Thus, I want to be confident
when the time comes for me which is why in my opinion this
experience is very important for my nursing career. Finally, I
want to learn how to deliver bad news to a patient or family
members in the best possible way which also comes with
experience. Shortly, I want to thank in advance to the faculty
professors for their work and effort to place us this semester
and to my preceptor for sharing his or her knowledge to be a
better professional and nurse.
References
Addy.hatch. (2018, April 2). Washington State University.
Retrieved from https://nursing.wsu.edu/2018/04/02/alyssa-
longee-nursing-senior-practicum-diversity-seattle-childrens.
Copper (Cu):
“Shiny, reddish copper was the first metal ever manipulated by
humans, and it remains an important metal in industry today”
(1).
Chemistry:
With an atomic number of 29, Copper (Cu) is a very
unique looking metal by appearance. The exterior does hold a

“red-orange metallic luster,” and copper is a “soft, malleable,
and ductile metal” as well. Basically, as “a freshly exposed
surface of pure copper has a reddish orange color” to it, the
metal is also utilized as the pure driver to produce heat and
electricity. Below is a picture of what copper looks like in its
natural state.
To continue being factual, Copper’s atomic number, 29,
represents the number of protons in the nucleus. Its atomic
weight, which is the average mass of the atom, is 63.55 grams.
It has a density of 8.92 grams per cubic centimeter, and clearly,
as the picture indicates, copper is solid at room temperature.
The pure metal melts at 1,984.32 degrees Fahrenheit and boils
at 5,301 degrees Fahrenheit.
Before use, copper “must be smelted for purity,” and most often
occurring is ores. De facto of Mother Nature, “natural chemical
reactions do sometimes release native copper,” and this
enlightens us why humans have been using copper “for at least
8,000 years” to make tools and creating new technologies.
Increasing supplies with copper, “people figured out how to
smelt copper by about 4500 B.C.” As advancements started
happening, copper alloys were made, by adding tin, “people
made a harder metal: bronze.”

An intriguing statistic says “about two-thirds of the copper on
Earth is found in igneous (volcanic) rocks.” According to the
USGS, roughly a quarter of copper is stated in sedimentary
rocks. While it is a metal that carries characteristics of being
ductile and malleable, this can also explain its use in electronics
and wiring.
Copper is known to turn green sometimes; this is a result
of an oxidation reaction. This means that it is losing elections
when it is vulnerable to air and water. Like stated, “the
resulting copper oxide is a dull green.” The reason the Statue
of Liberty has a green appearance rather than a red-orange color
is from the oxidation reaction that happened to the original
copper. In
accordance with the Copper Development Association, “a
weathered layer of copper oxide only 0.005 inches thick coats
Lady Liberty (2).” Take a look below at oxidized copper (3),
and an electron configuration for copper to get a more
molecular idea (2).
Business:

Currently, copper is listed at $3.04/lb. and equivalently
$6,702.93/t. Just trading over $3 a pound, the fine metal “is up
close to 28 percent year-to-date and far outperforming its five-
year average from 2012 to 2016.” There are many factors that
are influencing the price of the metal as we speak. As
represented by the purchasing manager’s index (PMI),
manufacturing activity is growing at a rate that hasn’t been
witnessed in years in the U.S., Eurozone, and China. September
of 2017 marked the 100th straight month of expansion,
conquering a 13-year high of 60.8. Reflect the graph below to
see how copper outperformed its five-year average.
Another belief that is influencing the price of copper is the
shortages that are happening in China; despite September 2017,
“imports of the metal rising to its highest level since March”
2017. The world’s second-largest economy “took in 1.47
million metrics of copper ore and concentrates” in September
2017 as well, which is an amount that equates to six percent
more than the same month in 2016.
Another reason so much copper is entering China is

because of battery electric vehicles (BEVs); these demand
“three to four times as much copper as traditional fossil fuel-
powered vehicles.” While China has a tight and the most
profitable grasp on the BEV market, according to the Financial
Times, Beijing is working on putting a stop and ultimately
prohibit the retailing of fossil fuel-powered vehicles.
Nonetheless, just because of the vertical magnitude of the
Chinese market, “this move is sure to delight copper bulls and
investors in any metal that’s set to benefit from higher BEV
production (4).” 54 percent of all new car transactions by 2040
will be BEVs, according to Bloomberg New Energy Finance.
Expectedly, China, Europe, and the U.S. are accounted to make
up 60 percent of the worldwide BEV fleet. With the rise in
BEV automobiles, this predicts a huge effect on copper prices
over the span of the next ten years and more. Take a look at the
graph below that charts the driving demand for copper due to
electric vehicles in the coming years.
Conclusion:
Since copper occurs directly in nature, this led to very
early human use; “it was the first metal to be smelted from its
ore, the first metal to be cast into a shape in a mold, and the

first metal to be purposefully alloyed with another metal (2).”
The characteristics of this metal made it so versatile for early
humans to make tools and get jobs done. It is truly amazing
how a metal like copper revolutionized technology for humans
and brought so much innovation and opportunities.
As there is a current market for copper today, it is getting
traded at just over $3 a pound, and it is used today in
electronics and wiring. Also, copper is way outperforming its
five-year average, and the need for copper in electric vehicles
exponentially rises for the next ten years, continued to 2040.
This means that the demand for copper is not slowing down, and
if anything, the price will go up because the demand for the
copper has gone up as well. Copper plays a vital and also low-
key factor in our economy, and the green on your pennies
symbolize the oxidization that has occurred over time to your
copper penny.
Works Cited (Sources)
1. https://www.livescience.com/29377-copper.html
2. https://en.wikipedia.org/wiki/Copper
3. https://www.youtube.com/watch?v=JoO8TbXebls
4. http://www.businessinsider.com/copper-is-the-metal-of-the-
future-2017-10

Palladium (Pd):
The next best thing to gold, palladium, my precious. Unique
like gold and platinum, palladium is a game changer in organic
and organometallic chemistry.
Chemistry:
Palladium sits in the D-block (group 10) on the periodic
table of elements and is identified by its atomic mass of 46. The
physical appearance of the palladium metal is silvery-white and
very appealing to the eye. In addition, it is a very rare metal
that is often only mined in Russia and South Africa1. The
palladium metal is primarily used in catalytic converters to
convert harmful greenhouse gases to less harmful pollutants, but
has other uses as well. The metal in its solid state is pictured
below.
Palladium shares its unique value with other high value metals
such as platinum, rhodium, ruthenium, iridium, and osmium1.
These metals make the platinum group metals on the periodic
table however, palladium has the lowest melting point (1554.9
°C) and lowest density (12.03 g/cm3) among them all1.The
metal is solid at room temperature and boils at 2963 °C. A
comparison of the metal among other metals in illustrated in the
picture below.
Palladium has also found use in the study of organometallics.
The element most widely used today in organic synthesis is
palladium….there is a wide range of Pd coupling reactions
available; Pd reactions are very tolerant of functionality and
give predictable products2. This could be due to the fact that
late metals are relatively electronegative, so they tend to retain
their valence electrons. The low oxidation states, such as d8 Pd
(II), tend to be stable, and the higher ones, such as d6 Pd (IV),
often find ways to return to Pd (II); that is, they are oxidizing2.
Business:

As of today’s date, September 27, 2019, palladium is valued at
$1,586.00 an ounce, while gold, now cheaper than palladium, is
valued at $1,501.90 shown in Figure 33. A decade ago,
palladium was valued at a cost less than $300 an ounce seen in
Figure 2. The reason for the soaring price of palladium is due to
an acute shortage, which has driven prices to a record; the
supply isn’t meeting the demand4. Palladium is a key
component in pollution-control devices for cars and trucks4. In
addition to the car industries large demand for the precious
metal, several governments such as Chinas are cracking down
on pollution from vehicles forcing carmakers to increase the
amount of palladium being used4. This is a no brainer
considering the push to a cleaner environment to reduce our
contribution to climate change.
Figure 2. The chart displays a price comparison between gold
and palladium for the year 2008. During the month of
September, Gold was valued at $877.80 whereas palladium was
valued at $222.00.
Figure 3. The chart displays a price comparison between gold
and palladium for the current year 2019. During the month of
September, Gold was valued at $1501.90 whereas palladium was
valued at $1586.00.
Conclusion:
Due to the fact that palladium is found alloyed with other
metals such as gold and other platinum-group metals makes it
very rare and expensive. A consequence of this has led to a
plague of catalytic converters being stolen from cars to harvest
the precious metals buried inside5. Further, businesses such as
U-Haul and similar companies are being targeted because larger
trucks provide not only easy access to the catalytic converter,
but also a greater yield of palladium5. It’s a wise move from the

thieves because larger vehicles would need more of the metal.
It is without a doubt that the market for palladium will
only continue to grow. Palladium is currently being used for
electrical contacts, and dental fillings and crowns5. In addition
to the applications mentioned, palladium and gold are combined
to form the alloy white gold which is primarily used for
aesthetic purposes i.e. jewelry. In my opinion, I question
whether the market for palladium will slow once the price
reaches an absolute high. I also wonder if offsetting the use of
palladium with other metals via subsidies would do any help to
curve the demand for the metal. In addition, the recycling of the
palladium metal should theoretically mean there is more of it in
the market, but perhaps it is being applied to different
applications than what it had originated from.
Works Cited
1. Palladium. (2019, September 23). Retrieved from
https://en.wikipedia.org/wiki/Palladium.
1. Crabtree, R. (2019). Organometallic Chemistry Of The
Transition Metals. S.l.: WILEY-BLACKWELL.
1. Live Palladium Price. (0AD). Retrieved from
https://www.kitco.com/charts/livepalladium.html.
1. Rowling, R. (2018, December 20). Why Palladium's Suddenly
an Especially Precious Metal. Retrieved from
https://www.bloomberg.com/news/articles/2018-12-21/why-
palladium-s-suddenly-an-especially-precious-metal-quicktake.
1. Frost, N. (2019, January 29). Thieves are breaking into cars
to steal a metal more valuable than gold. Retrieved from
https://qz.com/1536731/thieves-are-breaking-into-u-hauls-to-
steal-catalytic-converters-for-palladium/.
CHEMISTRY SECTION

1. Your essay contains passages that were (apparently)
transferred directly from
primary sources. Citing a reference on which the material is
based is not sufficient.
After identifying a primary source, you should make the
effort to express the points
made in your own words.
2. In suggesting that you write an essay on any element,
molecule or process
(chemical reaction) discussed in the four Lectures, I did not
mean that you
should write a comprehensive review article on an entire
field. Rather, I want
you to focus on a specific example of an element, molecule
or process
(chemical reaction) that interests you.
3. In choosing a particular atom or molecule, a graphic showing
the atomic/molecular structure
and crystal structure should be displayed in your essay.
In choosing to discuss a particular process (class of chemical
reactions) the relevant
chemical equations for your chosen topic should be displayed.
PRESENT APPLICATIONS
1. A few sentences on the range of applications is appropriate.
But once done, you should
focus on one or more specific applications .
2. Concrete estimates of "usage" can be obtained from any
number of sources and should be
documented by financial data and, if available, graphical

data.
FUTURE APPLICATIONS
1. Once you have chosen a particular element, molecule or
chemical process, tracking down
the website of the chemical company and/or industrial firm
that uses your element, molecule
or process will (almost always) forecast it future use.
2. It may well be that your choice of topic is one that is of
particular interest to you. I encourage
you to present personal reflections on the topic.
FORMATTING MATTERS
1. Your essay should be three pages in length, with a fourth
page listing primary sources.
On any given subject, volumes can be written. The intent
here is to condense the source
material you read into the absolute essentials. Think of this
as constructing for each
section a one-page CV, keeping in mind that employers only
pay attention to the first
page of a CV.
CHE 102: LECTURE 6 Polymers to Proteins to Nucleic Acids
to Covid-19
In December 2019, a new coronavirus Covid-19 (a protein)
caused an outbreak of pulmonary disease in the city of Wuhan,
the capital of Hubei province in China, and has since spread
globally.

POLYMER
A polymer is composed of many simple molecules that are
repeating structural units
called monomers. A single polymer molecule may consist of
hundreds to a million monomers and may have a linear,
branched, or network structure.
Examples of naturally occurring polymers are silk, wool, DNA,
cellulose and proteins.
Natural polymers occur in nature and can be extracted. They are
often water-based.
Examples of synthetic polymers include nylon, polyethylene,
polyester, Teflon, and epoxy.
The process by which a polymer is synthesized, called
polymerization, is illustrated by the formation of polyethylene
from n molecules of ethylene. See Lecture 5 for the structure of
ethylene.
STRUCTURE of SOME COMMON POLYMERSSome Common
Addition Polymers
Name(s)
Formula
Monomer
Properties
Uses
Polyethylene
low density (LDPE)
–(CH2-CH2)n–
ethylene
CH2=CH2
soft, waxy solid
film wrap, plastic bags

Polyethylene
high density (HDPE)
–(CH2-CH2)n–
ethylene
CH2=CH2
rigid, translucent solid
electrical insulation
bottles, toys
Polypropylene
(PP) different grades
–[CH2-CH(CH3)]n–
propylene
CH2=CHCH3
atactic: soft, elastic solid
isotactic: hard, strong solid
similar to LDPE
carpet, upholstery
Poly(vinyl chloride)
(PVC)
–(CH2-CHCl)n–
vinyl chloride
CH2=CHCl
strong rigid solid
pipes, siding, flooring
Poly(vinylidene chloride)
(Saran A)
–(CH2-CCl2)n–
vinylidene chloride
CH2=CCl2
dense, high-melting solid
seat covers, films
Polystyrene
(PS)
–[CH2-CH(C6H5)]n–
styrene
CH2=CHC6H5

hard, rigid, clear solid
soluble in organic solvents
toys, cabinets
packaging (foamed)
Polyacrylonitrile
(PAN, Orlon, Acrilan)
–(CH2-CHCN)n–
acrylonitrile
CH2=CHCN
high-melting solid
soluble in organic solvents
rugs, blankets
clothing
Polytetrafluoroethylene
(PTFE, Teflon)
–(CF2-CF2)n–
tetrafluoroethylene
CF2=CF2
resistant, smooth solid
non-stick surfaces
electrical insulation
Poly(methyl methacrylate)
(PMMA, Lucite, Plexiglas)
–[CH2-C(CH3)CO2CH3]n–
methyl methacrylate
CH2=C(CH3)CO2CH3
hard, transparent solid
lighting covers, signs
skylights
Poly(vinyl acetate)
(PVAc)
–(CH2-CHOCOCH3)n–
vinyl acetate
CH2=CHOCOCH3
soft, sticky solid
latex paints, adhesives

cis-Polyisoprene
natural rubber
–[CH2-CH=C(CH3)-CH2]n–
isoprene
CH2=CH-C(CH3)=CH2
soft, sticky solid
requires vulcanization
for practical use
Polychloroprene (cis + trans)
(Neoprene)
–[CH2-CH=CCl-CH2]n–
chloroprene
CH2=CH-CCl=CH2
tough, rubbery solid
synthetic rubber
oil resistant
For more details, there are multiple websites. See the listing at
the end of this Lecture.
PROTEINS
We begin by identifying the monomers or “building blocks” (
the 20 naturally occurring amino acids) of class of biopolymers
called proteins. Proteins that play a catalytic role in
metabolism are called enzymes.
Following are questions often asked by students followed by my
response.

1. What is a protein?
Proteins are a class of organic compounds that consist of large
molecules composed of one or more long chains of amino acids.
They are an essential part of all living organisms, especially as
structural components of body tissues such as muscle, hair,
collagen, etc., and as enzymes and antibodies.
Proteins are simply biopolymers, with the monomers or
“building blocks ” making up the protein called amino acids.
2. What is an amino acid?
Amino acids are organic compounds containing both a carboxyl
(- COOH) functional group and an amino functional group (-
NH2) group. See Lecture 5.
There are 20 amino acids occurring nature which are central to
life. Each has the following structure with only the “R group”
differentiating one amino acid from another.
The 20 amino acids are:
3. What are some examples of proteins?
Some proteins provide structural support in our bodies, for
example, the proteins in our connective tissues, such as collagen

and elastin.
Hormone proteins co-ordinate bodily functions. For example,
insulin controls our blood sugar concentration by regulating the
uptake of glucose into cells The metal ions in insulin (purple
“balls” in the structure) are zinc (Zn) and manganese (Mn).
Hemoglobin is the protein that carries oxygen to the cells in our
body. It is comprised of four chains two having 141 residues
(amino acids) and two chains having 146 residues.
hemoglobin
(heterotetramer, (αβ)2)
Structure of human hemoglobin. α and β subunits are in red and
blue, and the iron-containing heme groups in green.
From PDB: 1GZX ProteopediaHemoglobin
.
The heme (or haem) group in hemoglobin is the red pigment in
blood.
The heme group is a coordination compound,
a complex consisting of an iron (Fe) ion coordinated to
a molecule called a porphyrin (see below) acting as a tetra-
dentate ligand. A ligand is a molecule or ion attached to a
metal atom by coordinate bonding. Tetra-dentate means four
sites are coordinated. One or two axial ligands are above and

below the plane of the porphyrin.
Importantly, a change of just one amino acid in this protein
results in an inherited blood disorder, Sickle Cell Anemia
(SCD),that affects over 100,000 people of all ages in the
U.S.Healthy red blood cells are round and flexible. They move
through your small blood vessels and bring oxygen to all parts
of your body. With SCD, red blood cells are misshapen, hard
and sticky. They get stuck in your blood vessels and clog them.
This can cause pain, infection, organ damage, low blood count,
strokes and other serious health problems.
People with sickle cell trait get the sickle cell gene from one
parent but not both. Most people with sickle cell trait don’t
have any symptoms of SCD.
Later in this Lecture we will discuss the genetic code,the
nucleotide triplets of DNA and RNA molecules that carry
genetic information in living cells. The mutation causing sickle
cell anemia is a single nucleotide substitution (A to T) in the
codon for amino acid 6. The change converts a
glutamic acid codon (GAG) to a valine codon (GTG).
while sickle beta chain has the amino acid valine.
It is this change in sickle cell hemoglobin (HbS), in which
glutamic acid in position 6 (in beta chain) is mutated to valine,
which causes the deoxygenated form of the hemoglobin to stick
to itself. In sickle cell anemia, abnormal hemoglobin cause red
blood cells to become rigid sticky and misshapen. The sickle
cell gene is passed from generation to generation in a pattern of
inheritance called autosomal recessive inheritance.

I have studied structural stability of the related heme protein
cytoglobin (h-Cygb), the predicted function of which is the
transfer of oxygen from arterial blood to the brain. The
crystalstructure of this protein has 2464 atoms in the unit cell
(see Lecture 4), not including hydrogen.
It is interesting that the chemical “neighborhood” surrounding
the iron atom (Fe) in hemoglobin is reminiscent of the chemical
“neighborhood” of magnesium (Mg) in the molecule
chlorophyll, the molecule central to photosynthesis. There is
similarity in structure of the iron binding site in hemoglobin
and magnesium binding site in chlorophyll (which is not a
protein).
Planar arrays of chlorophyll comprise the “light harvesting”
system ( the so-called chlorophyll antenna network ) that
captures sunlight and initiates the conversion of radiant energy
from the Sun into chemical energy. This will be discussed in
Lecture 7.
Chlorophyll a

NUCLEIC ACIDS
A second class of biopolymers essential for life are the nucleic
acids: DNA and RNA.
1. What are the “building blocks” or monomers that constitute
DNA and RNA?
The monomers or nucleotides found in the two nucleic acid
types are different:
adenine, cytosine, and guanine are found in both RNA and
DNA, while
thymine occurs in DNA and uracil occurs in RNA.
2. What is the structure of DNA?
Deoxyribonucleic acid (DNA) is a molecule composed of two
chains that coil around each other to form a double helix
carrying the genetic instructions used in the growth,
development, functioning and reproduction of all known living
organisms and many viruses, such as coronavirus.
The structure of DNA was proposed by James Watson, an
American biologist born and raised in Chicago, and Francis
Crick, an English physicist, in the journal Nature (April 25,
1953). See the end of this Lecture for a website that gives an
historical perspective.
3. What is the genetic code?
The genetic code is the set of rules used by living cells to
translate information encoded within genetic material (DNA)
into proteins. The code is a triplet code.

4. Why is the genetic code a triplet?
Since there are only four nucleotides, a code of single
nucleotides would only represent four amino acids, but there are
20 amino acids that are needed as “building blocks “ for the
proteins necessary for life.
A doublet code could code for 16 amino acids (4 x 4).
A triplet code could provide a code for 64 different
combinations (4 x 4 x 4), and provide plenty of information in
the DNA molecule to specify the placement of all 20 amino
acids.
When experiments were performed to crack the genetic code it
was found that the code was indeed a triplet. These three letter
codes of nucleotides (AUG, AAA, etc.) are called codons.
The “inverse” table to the above one is:
CODON TABLE
GENETIC ENGINEERING
Genetic engineering is the process of using knowledge of

biochemistry and experimental techniques to change the genetic
makeup (the DNA) of an organism, be it an animal, plant a
bacterium or a virus.
This change can be achieved by using a technique known as
“recombinant DNA”, or making use of DNA that has been
isolated from two or more different organisms and then
incorporating it into a single molecule. This results in a
mutation, something that Mother
Nature has been doing since life evolved on Earth. An example
in human history is the mutation that led to Emmer wheat. See
Lecture 1.
Polymers
https://www.ch.ntu.edu.tw/~sfcheng/HTML/material94/Polymer
-1.pdf
Polymer - Wikipedia
https://en.wikipedia.org/wiki/Polymer
Watson and
Crickhttps://doi.org/10.1164/rccm.2302011 PubMed: 12684
243
CHE 102: LECTURE 4 From Frog Legs to Crystals to
Snowflakes
The mineral Amethyst is a violet variety of quartz, silicon
dioxide (SiO2). The name comes from the Greek word
ἀμέθυστος (amethystos) from ἀ- a-, "not" and
μεθύσκω (methysko) / μεθύω (methyo), "intoxicate", a
reference to the belief that the stone protected its owner
from drunkenness. The ancient Greeks wore amethyst and
carved drinking vessels from it in the belief that it would
prevent intoxication.

In 1791, Luigi Galvani, an Italian physicist, discovered
something he named, "animal electricity" which resulted when
two different metals were connected in series with a frog's leg
and to one another. His contemporary, AlessandroVolta,
realized that the frog's leg served both as a conductor of
electricity and as a detector of electricity, but believed that the
frog's legs were irrelevant to the electric current. He
hypothesized that the electric current was caused by the two
differing metals. Volta replaced the frog's leg with brine-
soaked paper, and detected the flow of electricity.
In 1800, Volta invented the voltaic pile, an early electric
battery, which produced a steady electric current. Volta
determined after investigating pairs of dissimilar metals that the
most effective pair was zinc (Zn) and copper (Cu). Initially he
experimented with individual cells in series, each cell being a
wine goblet filled with brine (salt water) into which the two
dissimilar metals were dipped. The voltaic pile replaced the
goblets with cardboard soaked in brine.
In chemistry and manufacturing, electrolysis is a technique that
uses a direct current from a battery to drive an otherwise non-
spontaneous chemical reaction. The English chemist,
Humphrey Davy, was the first to realize that electrolysis could
be used to separate elements from naturally occurring sources
such as minerals and ores. In 1807, he isolated for the first
time sodium from table salt (NaCl), and later discovered the
elements potassium (K), calcium (Ca), strontium (Sr), barium
(Ba), magnesium (Mg), and boron (B) as well as discovering the
elemental nature of the nonmetals, chlorine (Cl) and iodine (I).
Davy also studied the forces involved in these separations,
launching the new field of electrochemistry.
At this point in the saga Michael Faraday enters the stage.
Although Faraday received little formal education, he became
one of the most influential scientists in history. At the age of 14
he became an apprentice to a local bookbinder and bookseller in

London. During his seven-year apprenticeship Faraday read
books, many books, and developed an interest in science,
especially electricity.
In 1812, at the age of 20 and at the end of his apprenticeship,
Faraday attended lectures by the eminent English chemist
Humphrey Davy. Faraday subsequently sent Davy a 300-page
book based on notes that he had taken during these lectures.
Davy's reply was immediate, kind, and favorable. In 1813,
when Davy damaged his eyesight in an accident with nitrogen
trichloride (NCl3)
he decided to take on Faraday as his assistant.
Faraday subsequently began his own program of research and it
was his discovery of the magnetic field around a conductor (a
wire) carrying a direct electric current that established the basis
for the concept of the electromagnetic field in physics. Faraday
also established that magnetism could affect rays of light, that
there here was an underlying relationship between the two
phenomena. He subsequently discovered the principles of
electromagnetic induction and diamagnetism, and the laws of
electrolysis. His invention of electromagnetic rotary devices
laid the experimental foundation for the electric motor, and it
was largely due to his efforts that electricity became practical
for use in technology.

As a chemist, Faraday discovered benzene (C6H6),
Geometry
Ball and stick model
Space-filling model
invented an early form of the Bunsen burner, and introduced
terminology such as electrode (an electrical conductor used to
make contact with a nonmetallic part of a circuit), anode (the
positively charged electrode), cathode (the negatively charged
electrode) and ion (an atom or molecule with a net electric
charge due to the loss or gain of one or more electrons).
Faraday believed ions were produced in electrolysis (else how
could a battery “work” ?).
In 1884, the Swedish chemist, Svante Arrhenius, proposed that,
even in the absence of an electric current, solutions of salts
contained ions. That is, he proposed that solid crystalline solids,
when dissolved in water, dissociated into pairs of charged
particles (ions), and that chemical reactions in solution involved
reactions between ions.
Electrolyte solutions are formed when a salt is placed into
a solvent such as water and the individual components
dissociate due to the interactions between solvent and solute
molecules in a process called solvation. For example, when
table salt (sodium chloride) is placed in water, the salt (a solid)
dissolves into its component ions, according to the dissociation
reaction

NaCl(s) → Na+(aq) + Cl−(aq)
Importantly, prior to being dissolved in water, Arrhenius’
thesis was that the crystal NaCl (a solid) is composed of sodium
ions (Na+ not neutral sodium atoms) and chlorine ions (Cl- not
neutral chlorine atoms).
Recall the graphic from Lecture 1 displaying sodium chloride at
the atomic level:
Here, the purple balls are sodium ions (Na+) and the green
balls are chlorine ions (Cl-).
At the macroscopic level, sodium chloride (table salt) forms
transparent crystals.
Depending on the presence of a small number of other atoms
(impurities) the mineral halite can also occur in several other
colors.
In Chemistry, the bonding in the NaCl crystal, called ionic
bonding, is the complete transfer of a charge (the electron)
from sodium to chlorine. Hence, neutral Na becomes Na+ and
neutral Cl becomes Cl-. Hence, it is a type of
chemical bond that involves two oppositely charged ions. The
metal loses electrons to become a positively charged cation,
whereas the nonmetal accepts those electrons to become a
negatively charged anion.

[NOTE: The negatively charged electrode is called the cathode;
a positively charged ion is called a cation. Perhaps confusing,
but the logic here is that a positive ion (anion) migrates to the
negative electrode (cathode) in solution.]The bonding in a
crystal like diamond is different and is called covalent bonding.
A covalent bond, also called a molecular bond, is a chemical
bond that involves the sharing of two electrons between atoms.
These electron pairs are known as shared pairs or bonding pairs,
and the stable balance of attractive and repulsive forces between
atoms, when they share electrons, is known as covalent bonding.
In a later module of the course we will review the discovery of
the electron, the proton and the neutron, the basic components
of an atom. To understand atomic and molecular structure we
will find that the classical ideas of Physics, reviewed in the
previous Lecture, need to be replaced by a non-classical theory,
called quantum mechanics. And to understand nuclear
chemistry, the basis for modern medicinal chemistry, we will
need to review the properties of light, and the basic ideas of
special relativity. By the end of the course, my hope is that you
will have a holistic understanding of modern science.
But now, to the problem at hand …..
A crystal structure is an ordered arrangement of atoms,
molecules or ions. Ordered structures are a consequence of the
intrinsic nature of the constituent particles which form
symmetric patterns that repeat along the principal axes
(directions) of three-dimensional space.
The smallest group of particles in a material that constitutes this
repeating pattern is called the unit cell of the structure. The unit
cell captures the symmetry and structure of the entire crystal,
which is built up by repetitive translation of the unit cell along
its principal axes. Mathematically, translation vectors define
the nodes of a lattice, called the Bravais lattice.

The lengths of the principal axes, or edges, of the unit cell and
the angles between them are lattice constants, also
called lattice parameters or cell parameters.
The symmetry properties of the crystal are described by the
concept of space groups. All possible symmetric arrangements
of atoms or molecules in three-dimensional space may be
describedby 230 space groups. Every crystal found in Nature
belongs to one of these space groups. Crystal structure and
symmetry play a critical role in determining many physical
properties, such as cleavage and optical transparency.
In a crystal, atoms are arranged in straight rows in a three-
dimensional periodic pattern. As noted above, the small part of
the crystal that can be repeated to form the entire crystal is
called a unit cell.
Asymmetric unit
Primitive unit cell
Conventional unit cell
Crystal
Some common crystal structures are shown below.
Simple Cubic
Face Centered Cubic
Body Centered Cubic
Hexagonal Close Packed
Diamond
NaCl
CsCl

Zincblende
Wurzite
Perovskite
Here, Zincblende is one form of zinc sulfide (β-ZnS), Wurzite is
another version of ZnS, and Perovskite is a calcium titanium
oxide mineral composed of calcium titanate (CaTiO3).
Closely related to Zincblende is Sphalerite [ (Zn,Fe)S ],
a mineral that is the chief ore of zinc (Zn). Following are
crystals of Sphalerite and Perovskite:
Crystals can be grown under moderate conditions from all 92
naturally occurring elements except helium, and helium can be
crystallized at low temperatures by using 25 atmospheres of
pressure.
Binary crystals are composed of two elements. There are
thousands of binary crystals; some examples are sodium
chloride (NaCl), alumina (Al2O3)
and ice (H2O)
which, at the macroscopic level, is a crystal familiar to us in
Winter in Chicago: Crystals can also be formed with three or
more elements.
By repeating the pattern of the unit cell over and over in all
directions, an entire crystal lattice can be constructed. A cube is

the simplest example of a unit cell. Two other examples are
shown in the figure below. The first is the unit cell for a face-
centered cubic lattice, and the second is for a body-centered
cubic lattice.
There are only a few different unit-cell shapes, so many
different crystals share a single unit-cell type. An important
characteristic of a unit cell is the number of atoms it contains.
The total number of atoms in the entire crystal is the number in
each cell multiplied by the number of unit cells. Copper (Cu)
and aluminum (Al) each have one atom per unit cell, while zinc
(Zn) and sodium chloride have two. Most crystals have only a
few atoms per unit cell, but there are some exceptions.
Crystals of polymers and, especially, proteins, have thousands
of atoms in each unit cell. I am presently completing a study of
the structural stability of the coronavirus 6LU7, a protein with
2367 atoms in the unit cell, not counting the hydrogens.
Structures of metals
The elements are found in a variety of crystal packing
arrangements. The most common lattice structures for metals
are those obtained by stacking the atomic spheres into the most
compact arrangement. There are two such possible periodic
arrangements. In each, the first layer has the atoms packed into
a plane-triangular lattice in which every atom has six immediate
neighbors. The figure below shows this arrangement for the
atoms labeled A.
The second layer is shaded in the figure. It has the same plane-
triangular structure; the atoms sit in the holes formed by the
first layer. The first layer has two equivalent sets of holes, but
the atoms of the second layer can occupy only one set. The third
layer, labeled C, has the same structure, but there are two
choices for selecting the holes that the atoms will occupy.

The third layer can be placed over the atoms of the first layer,
generating an alternate layer sequence ABABAB . . ., which is
called the hexagonal close-packed structure. Cadmium (Cd) and
Zinc (Zn) crystallize with this structure. The second possibility
is to place the atoms of the third layer over those of neither of
the first two but instead over the set of holes in the first layer
that remains unoccupied.
The fourth layer is placed over the first, and so there is a three-
layer repetition ABCABCABC . . ., which is called the face-
centered cubic (fcc), or cubic-closest-packed, lattice. Copper,
(Cu), Silver (Ag), and Gold (Au) crystallize in fcc lattices. In
the hcp and the fcc structures the spheres fill 74 percent of
the volume, which represents the closest possible packing of
spheres. Each atom has 12 neighbors. The number of atoms in a
unit cell is two for hcp structures and one for fcc. There are 32
metals that have the hcp lattice and 26 with the fcc. Another
possible arrangement is the body-centered cubic (bcc) lattice, in
which each atom has eight neighbors arranged at the corners of
a cube. The cesium chloride (CsCl) structure is a cubic
arrangement. If all atoms in this structure are of the same
species, it is a bcc lattice. The spheres occupy 68 percent of the
volume. There are 23 metals with the bcc arrangement. The sum
of these three numbers (32 + 26 + 23) exceeds the number of
elements that form metals (63), since some elements are found
in two or three of these structures.
·
·
The fcc structure is also found for crystals of the rare gas
solids:
neon (Ne), argon (Ar), krypton (Kr),
and xenon (Xe).

Structures of nonmetallic elements
The elements in the fourth row of the periodic table—Carbon
(C), Silicon (Si), Germanium (Ge), and α-tin (α-Sn)—
prefer covalent bonding. Carbon has several possible crystal
structures. Each atom in the covalent bond has four first-
neighbors, which are at the corners of a tetrahedron. This
arrangement is called the diamond lattice. See Lecture 2. There
are two atoms in a unit cell, which is fcc. Crystals of diamond
are valuable (and expensive) gemstones, as every engaged
couple knows.
The diamond crystal has other interesting properties; it has the
highest sound velocity of any solid and is the best conductor of
heat. Besides diamond, the other common form of carbon
is graphite, which is a layered material. Each carbon atom has
three coplanar near neighbors, forming an arrangement called
the honeycomb lattice. Three-dimensional graphite crystals are
obtained by stacking similar layers. See Lecture 2.
Another form of crystalline carbon is based on a molecule with
60 carbon atoms called buckminsterfullerene (C60). The
molecular shape is spherical. Each carbon is bonded to three
neighbors, as in graphite, and the spherical shape is achieved by
a mixture of 12 rings with five sides and 20 rings with six sides.
Similar structures were first visualized by the American
architect R. Buckminster Fuller for geodesic domes. The
C60 molecules, also called buckyballs, are quite strong and
almost incompressible. Crystals are formed such that the balls
are arranged in an fcc lattice with a one-nanometer (10 -9
meters) spacing between the centers of adjacent balls. The
similar C70 molecule has the shape of a soccer ball;
C70 molecules also form an fcc crystal when stacked together.
The solid fullerenes form molecular crystals, with weak binding
between the molecules.

The most recent form of Carbon to be discovered is called
graphene. It is “just” one sheet
of graphite or, in the analogy I suggested in a previous Lecture,
one sheet of “chicken wire.”
The diatomic gases hydrogen (H), oxygen (O), nitrogen (N), flu
orine (F), chlorine (Cl), bromine (Br), and iodine (I) , when
cooled to low temperature, form solids of diatomic molecules.
Nitrogen has the hcp structure, while oxygen has a more
complex structure.
The most interesting crystal structures are those of elements
that are neither metallic, covalent, nor diatomic.
Although boron (B) and sulfur (S) have several different crystal
structures, each has one arrangement in which it is usually
found. Twelve boron atoms form a molecule in the shape of
an icosahedron. Crystals are formed by stacking the molecules.
The β-rhombohedral structure of boron has seven of these
icosahedral molecules in each unit cell, giving a total of 84
atoms. Molecules of sulfur are usually arranged in rings; the
most common ring has eight atoms. The typical structure is α-
sulfur, which has 16 molecules per unit cell, or 128 atoms. In
the common crystals of Selenium (Se) and Tellurium (Te), the
atoms are arranged in helical chains, which stack like
cordwood. However, selenium also makes eight-atom rings,
similar to sulfur, and forms crystals from them. Sulfur also
makes helical chains, similar to selenium, and stacks them
together into crystals.
Finally, just for fun, shown below are crystals of Ruby and
Emerald.

Natural ruby crystals from Winza, Tanzania
General
Category
Oxide mineral variety
Formula(repeating unit)
aluminium oxide with chromium, Al2O3:Cr
Crystal system
Trigonal
Crystal class
Hexagonal scalenohedral (3m)
H-M symbol: (3 2/m)
Space group
R3c[1]
Emerald crystal from Muzo, Colombia
General
Category
Beryl variety
Formula(repeating unit)
Be3Al2(SiO3)6
Crystal system
Hexagonal (6/m 2/m 2/m) Space group: P6/mсc
Space group
(6/m 2/m 2/m) – dihexagonal dipyramidal
Unit cell
a = 9.21 Å, c = 9.19 Å; Z =
Even better, after extraction from the supporting ore,
CHE 102: LECTURE 5 CARBON

The Hope Diamond is one of the most famous jewels in the
world, with ownership records dating back almost four
centuries. Its rare blue color is due to trace amounts of boron
(B) atoms. Discovered in in India, its weight is 45.55 carats and
its estimated value is $200-$350
million. Its exceptional size has revealed new findings about the
formation of gemstones.
The hardness of diamond and its high dispersion of light—
giving the diamond its characteristic "fire"—make it useful for
industrial applications and desirable as jewelry.
Diamonds “sparkle” and get their brilliance from three things:
the reflection, refraction and dispersion of light. Only a portion
of the light hitting a diamond is reflected, the rest travels
through it.
The refractive index (also called the index of refraction) is a
measure of the bending of a ray of light when passing from one
medium into another. Formally, the refractive index is defined
as equal to the velocity of light c of a given wavelength in
empty space divided by its velocity v in a substance, or n = c/v.
In the visible region, the following three materials have the
highest refractive index: Silicon Carbide (SiC) 2.65, Titanium
dioxide ( TiO2 ) 2.614, Diamond ( C ) 2.417.
Diamond is also the world's hardest natural material and has
been assigned a hardness of 10 on the Mohs hardness scale (a
scale of hardness used in classifying minerals. It runs from 1 to
10 using a series of reference minerals, and position on the
scale depends on ability to scratch minerals rated lower).
By contrast, Graphite is a very soft mineral with a

hardness between 1 and 2. Graphite has a black streak and was
probably formed by the metamorphism of plant remains or by
the crystallization of ancient magmas. Most commercial
diamond deposits are thought to have formed when a deep-
source volcanic eruption delivered diamonds to the surface. In
these eruptions, magma travels rapidly from deep within the
mantle, often passing through a diamond “stability zone” on its
route to the surface.
What is special about carbon?
Put simply, carbon can form more compounds than any other
element. At the
molecular level, it can form four covalent (molecular) bonds,
both with other
elements and, importantly, with other carbon atoms. From a
structural point of
view, it can form “chains” of carbon atoms (polymers,
proteins), and even join
"head-to-tail" to make rings of carbon atoms, “aromatic”
compounds like benzene
whose structure is displayed in Lecture 4.
What is the chemistry of carbon?
The chemistry of carbon (called organic chemistry) involves
molecules that contain both carbon and hydrogen. Though many
organic chemicals also contain other elements, it is the carbon-
hydrogen covalent bond that defines them as organic.
The chemistry of life is called biochemistry. All life on Earth
is built from four different types of organic molecules. These
four types of molecules are often referred to as the molecules of
life. The four molecules of life
are proteins, carbohydrates, lipids and nucleic acids. Each of
the four groups is vital for every single organism on Earth.

Without carbon, none of these molecules (or we) would
exist.What are some uses of carbon?
Impure carbon in the form of charcoal (from wood) and coke
(from coal) is used in metal smelting. It is particularly
important in the iron and steel industries. Graphite is used in
pencils, to make brushes in electric motors and in furnace
linings. Activated charcoal is used for purification
and filtration.
There are three common, naturally occurring forms of carbon:
graphite, amorphous carbon, and diamond. There are two other
forms (allotropes) that have been synthesized in laboratories
(“bucky balls” and graphene). See Lecture 4. Taken together,
these are used in many products including inks, rubber, steel,
pencils, and more. Tens of millions of compounds synthesized
from carbon are useful, for example, in creating new polymers,
plastics, pharmaceuticals and cosmetics.
CHEMICAL BONDS
The distinction between ionic bonds and covalent bonds was
given in Lecture 4. The following reviews and extends this
discussion.
What is the difference between an ionic bond and a covalent
bond?
An ionic bond is one in which one or more electrons from one
atom are removed and attached to another atom, resulting in

positive and negative ions which attract each other. This is the
kind of bonding one finds in compounds in which metals are
bonded to nonmetals. One example given in Lecture 4 is NaCl,
the mineral Halite or, in everyday life, table salt. This kind of
bonding was already understood in the 19th century since the
interactions between positive and negative charges (here ions)
could be calculated using Coulomb’s Law. See Lecture 3.
Recognizing that opposite charges attract and like charges repel,
and being able to quantify these effects using Coulomb’s Law is
all you really need to understand the formation of ionic crystals.
See Lecture 4.
I want to emphasize that the understanding of bonding in ionic
compounds evolved in the 19th century (before the electron was
discovered by J.J. Thompson in 1897 !).
COVALENT BOND
A covalent bond, also called a molecular bond, is a chemical
bond that involves the sharing of electron pairs between atoms.
These electron pairs are known as “bonding pairs”
or “shared pairs,” and the stable balance of attractive and
repulsive forces between atoms, when they share electrons, is
known as covalent bonding.
The most distinctive feature of Carbon chemistry is that Carbon
can not only form covalent bonds with other elements, but with
other Carbon atoms. These bonds exist in three “flavors.”
A single bond is a covalent bond between two atoms involving
two electrons, called valence electrons. An example of a
carbon compound with single bonds is methane (CH4) whose
structure was given in Lecture 1.
A double bond is a covalent bond in which two pairs of
electrons are shared between two atoms. An example is the

molecule ethylene (C2H4),
a molecule of great importance commercially because it is the
basic “repeat” unit (monomer) in the synthesis of the polymer,
polyethylene.
A triple bond is a covalent bond in which three pairs of
electrons are shared between two atoms. A familiar example is
acetylene (C2H2), which is important industrially as it is the
gas used in the acetylene torch for welding.
The entire chemistry of carbon is based on covalent bonding.
Notice that the structure of single-bonded methane is d=3
dimensional, the structure of ethylene is d=2 dimensional, and
the structure of acetylene is d=1 dimensional. This turns out to
be incredibly important in understanding the chemistry of life.
The molecules that form proteins, nucleic acids, carbohydrates,
… are primarily three dimensional, as are we !
It is important to point out that the understanding of the
importance of dimensionality in carbon compounds was already
understood in the 19th century.
In 1874 the French chemist Joseph Achille Le Bel announced a
theory outlining the relationship between the structure of carbon
compounds and optical activity. This discovery laid the
foundation of the science of stereochemistry, which deals with
the spatial arrangement of atoms in molecules. The same
hypothesis was put forward in the same year by the Dutch

physical chemist Jacobus Henricus van’t Hoff.
The theoretical understanding of covalent bonding was not
developed until the first three decades of the 20th century, only
after the following experimental discoveries.
a) discovery of the electron (1897) [Thomson, 1856-1940]
b) measurement of the charge on the electron (1909)
[Millikan, 1868-1953]
c) discovery of the nucleus (1911) [Rutherford, 1871-1937]
d) discovery that electrons had “spin” (1922)
[Stern, 1899-1969 and Gerlach, 1889-1979]
e) discovery that an electron can be like a “wave”
[Davisson, 1881-1958 and Germer, 1896-1971] (1923)
The theory that was developed to account for these discoveries
is called the quantum
theory of matter, or quantum mechanics. Our modern
interpretation of the nature of the chemical bond is grounded in
the following experimental and theoretical work:
a) Quantum hypothesis (1900-1905) [Planck, 1857-1947 and
Einstein, 1884-1965]
b) Solar system model of the atom (1913) [Rutherford, 1871-
1937 and Bohr, 1885-1962 ]
c) Wave-Particle duality (1923) [de Broglie, 1892-1987]
d) Quantum Mechanics (1925-1926) [Schrödinger, 1887-1961
and Heisenberg, 1901-1976]
e] Electron spin (1925) [Pauli, 1900-1958, Dirac, 1902-1984]
f) Quantum theory and the nature of the chemical bond (1931)
[Pauling, 1901-1974]
An overview of these experimental insights and the quantum
theory of matter which was able to explain these experiments
will be given in a later Lecture in the course.

To underline the importance of quantum mechanics in
understanding chemical bonding, let me give you an historical
example. As noted in Lecture 3, Thales (~ 586 BC)
conjectured that the entire world around us could be understood
in terms of one primordial element, water.
In the 19th century, on the basis of the classical theory of
electrostatic interactions [Coulomb’s Law], it was predicted that
water should be a linear molecule. This conjecture could not be
verified experimentally. It was only after the experiments
mentioned above were reported, and after the development of
the quantum theory of matter that it was determined that the
water molecule was bent (with a bond angle of ~ 104.5o),
which was confirmed experimentally. See Lecture 1.
Water, though the most common compound on Earth, has
properties owing to its molecular geometry and bonding so
distinctive, so unique that it is arguably the most complicated
molecule known. All the really unique, “unusual” properties of
water, and very presence of life on Earth, can only be
understood using the quantum theory of matter.
This course is labelled: Molecules that Shaped the World. Put
water at the top of the list.
ISOMERISM in CARBON CHEMISTRY
There are two types of isomers, geometrical isomers and optical
isomers.
GEOMETRICAL ISOMERS
Consider the hydrocarbon butane, C4H10 . Both normal butane
(n-butane) and isobutene (2-methylpropane) have the same

number of carbon and hydrogen atoms, but have different
structures.
In n-butane, the carbon chain is straight and unbranched.
This diagram displays n-butane (carbon atoms in black,
hydrogen atoms in white) in three ways:
d=2 representation,
d=3 “ball and stick” representation, and
d=3 “space filling” representation.
The first representation is commonly used in textbooks but,
importantly, the chemistry of carbon (and hence, the chemistry
of life) is d=3 dimensional.
The structure of n-butane can be contrasted with that of n 2-
methylpropane where the carbons form a branched chain.
n name
normal butaneunbranched butanen-butane
isobutanei-butane
IUPAC name
butane
2-methylpropane
Molecular
diagram

Skeletal
diagram
Though having the same number of atoms, the physical
properties (melting point, boiling point) and chemical properties
(reactivity) of these two compounds are different.
The number of geometrical isomers of hydrocarbons increases
rapidly with the length of the carbon chain. There are 4 isomers
of C4H8 and 24 isomers of octane (“gas”), C8H18 .
OPTICAL ISOMERS
Optical isomers are two compounds which contain the same
number and kinds of atoms, and bonds (i.e., the connectivity
between atoms is the same), but which have non-
superimposable mirror images (your left hand is a mirror image
of your right). Each non-superimposable mirror image structure
is called an enantiomer.
This can be illustrated by the amino acid alanine,
one of the 21 amino acids that are the building blocks of
proteins.
One of the optical isomers (enantiomers) of the amino
acid alanine is known as (+) alanine. A solution of (+) alanine
rotates the plane of polarization of light in an clockwise
direction, the other enantiomer, (-) alanine , rotates the plane
of polarization in a counter-clockwise direction.

Optical activity was first observed by the French physicist Jean-
Baptiste Biot [1774 – 1862]He concluded that the change in
direction of plane-polarized light when it passed through certain
substances was actually a rotation of light, and that it had a
molecular basis.
His work was supported by the experimentation of Louis
Pasteur [1822-1895], a French biologist, microbiologist and
chemist renowned for his discoveries of the principles of
vaccination, microbial fermentation and pasteurization. He is
remembered for his remarkable breakthroughs in the causes and
prevention of diseases. [ Also born in 1822 were Gregor
Mendel (Mendelian laws of genetics), and Ulysses S. Grant
(commander of the Union Armies and 18th President. ]
In his research on disease in wine, Pasteur isolated a compound,
tartaric acid,
Through meticulous experimentation, he found that one set of
tartaric acid molecules rotated polarized light clockwise while
another set rotated light counterclockwise, and to the same
extent. He also observed that a mixture of both sets, a racemic
mixture (or racemic modification), did not rotate light because
the optical activity of one molecule canceled the effects of the
other molecule.
Pasteur was the first to show the existence of chiral molecules.
These are molecules that are asymmetric in such a way that the
structure and its mirror image are not superimposable. Chiral
compounds are typically “optically active” ; large organic
molecules often have one or more chiral centers where four
different groups are attached to a carbon atom.

A second important point about Carbon compounds is that
simple changes in the atoms (or groups of atoms) in a carbon
molecule can change dramatically the physiological effect on
humans. This is illustrated by the molecules
methanol
and ethanol
Methanol is found in your medicine cabinet and is marketed as
“rubbing alcohol.”
If you drink methanol you can go blind.
Ethanol is found in your fridge and is marketed as, for example,
Bud Light. You do not go blind when you drink other beverages
containing ethanol (wine, whiskey, vodka, rum, cognac, tequila,
slivovica, …..) unless you drink too much (drink responsibly).
Another dramatic example is the molecule hemoglobin (blood)
Normal hemoglobin or haemoglobin is the iron-containing
oxygen-transport metallo-protein in the red blood cells of
almost all vertebrates as well as the tissues of some
invertebrates. Hemoglobin in the blood carries oxygen from the
lungs or gills to the rest of the body. As I will elaborate in the
next lecture, a single change in one functional group of this
(large) molecule results in a mutation that is responsible for the
disease, sickle cell anemia.
FUNCTIONAL GROUPS
In organic chemistry, a functional group is a specific group of
atoms or bonds within a compound that is responsible for the
characteristic chemical reactions of that compound. The

same functional group will behave in a similar fashion, by
undergoing similar reactions, regardless of the compound of
which it is a part.
The main players are listed below. Chemistry majors have an
intimate relationship with each of these, thoroughly cognizant
of their identity and the role they play in organic reactions.
Don’t panic.
Think of your favorite team [ Cubs, White Sox ]. You can
enjoy watching the game, knowing the players and the position
they play. For purposes of this course, you simply need to
recognize the “name” of the group and the fact that each has a
different “function” (chemistry) owing to the specific atoms
making up the group.
Use the list below as a quick reference when you encounter
them in the course.
For each of the main players listed above, an example of each
follows. The example is representative, but identifies a
molecule that is important in our daily lives or commercially.
Several examples give the “building blocks” (monomers) of
polymers/plastics. See later text.
1. ALKANE: Methane. Natural Gas
Methane
2. ALKENE: Ethene. Monomer unit of polyethylene
3. Alkyne: Acetylene. Monomer unit of polyacetylene
Acetylene

4. ALCOHOL: Ethanol. Beer, wine and spirits
Ethanol
5. AMINE: Aniline. Synthetic Dyes
Aniline
6. PHENYL: Styrene. Monomer unit of polystyrene
Styrene
7. ETHER. Diethyl ether. general anesthetic
9. AKAYL HALIDE : Vinyl Chloride. Monomer unit of poly
vinyl chloride (PVC)
Vinyl chloride
10. CARBOXYLIC ACID: Acetic Acid; Vinegar
11. THIOL Grapefruit mercaptan Flavor, Perfumes (also
odor of skunks)

Grapefruit mercaptan
12. ALDEHYDE Formaldehyde. Embalming fluid
Formaldehyde
13. Ketone Acetone. Universal solvent for organic
molecules (e.g., nail polish remover)
Acetone[1]
14. ESTER Flavors / Fragrances
Esters encompass a large family of organic compounds with
broad applications in medicine, biology, chemistry and industry.
The structure is represented by the following arrangements of
atoms:
Esters are widespread in nature. They occur naturally in plants
and animals. Small esters, in combination with other volatile

compounds, produce the pleasant aroma of fruits. In general, a
symphony of chemicals is responsible for specific fruity
fragrances. However, very often one single compound plays a
leading role. For example, an artificial pineapple flavor
contains more than twenty ingredients but ethyl butyrate is the
major component that accounts for the pineapple-like aroma and
flavor. It is pretty amazing that so many fragrances and flavors
can be prepared by simply changing the number of carbons and
hydrogens (the R groups) in the ester.
The following table gives some ester flavors and fragrances
(notice the similarities/differences in the R groups:
Name
Chemical Structure
Flavor or Fragrance
Propyl acetate
Pears
Octyl acetate
Oranges
Isoamyl acetate
Banana
Ethyl Butyrate
Pineapple
Butyl acetate
Apple
Methyl trans-cinnamate
Strawberry
Some esters play an important role in insect communication.
Isoamyl acetate, the main component of banana aroma, is also
the alarm pheromone of the honeybee. (Z)-6-dodecen-4-olide, a

circular ester, is the "social scent" of the black-tailed deer.
Circular esters (called lactones) are also found in the oily
poisonous secretion of termites.
The website below gives much more detail than you need now,
but provides background information that can be referenced
later.
Carbon - Wikipedia
https://en.wikipedia.org/wiki/Carbon
Past history suggests that many of you will write Essay #2 on
diamonds.
The following websites may be useful in laying out the chemical
and business issues:
1. Marketing of Natural Diamonds
The Engagement Ring Story: How De Beers Created a Multi-
Billion ...
https://blog.hubspot.com/marketing/diamond-de-beers-
marketing-campaign
2. Marketing of Synthetic Diamonds
Synthetic diamond - Wikipedia
https://en.wikipedia.org/wiki/Synthetic_diamond
3. Political and Economic aspects of “Conflict Diamonds”
Blood Diamonds
Adwww.globalwitness.org/Blood-Diamonds

4. Example of an expensive diamondHope Diamond - Wikipedia
https://en.wikipedia.org/wiki/Hope_Diamond
A Website on the covalent bond is:
Covalent bond - Wikipedia
https://en.wikipedia.org/wiki/Covalent_bond
Optical isomerism is discussed in:
optical isomerism -
Chemguidehttps://www.chemguide.co.uk/basicorg/isomerism/op
tical.htm
Websites on water are:
Water and its structure - Chem1
www.chem1.com/acad/sci/aboutwater.html

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