chemical paper topic of your choice, something in the Lectures in each module that you found interesting.

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LECTURE53588.docx

CHE 102: LECTURE 5 CARBON https://ids.si.edu/ids/deliveryService?max_w=550&id=ark:/65665/m38e4d73f2999f4efe9ab07efb6ab36919 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), Ethylene-CRC-MW-3D-balls.png

a molecule of great importance commercially because it is the basic “repeat” unit (monomer) in the synthesis of the polymer, polyethylene.

Skeletal formula of a ris monomer

Spacefill model of 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. Acetylene 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.

Skeletal formula of butane with all carbon and hydrogen atoms shown

Ball-and-stick model of the butane molecule

Space-filling model of the butane molecule

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 butane unbranched butane n-butane

isobutane i-butane

IUPAC name

butane

2-methylpropane

Molecular diagram

Butan Lewis.svg

Isobutane 1.svg

Skeletal diagram

Butane simple.svg

I-Butane-2D-Skeletal.svg

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, C:\Users\kozak\AppData\Local\Microsoft\Windows\INetCache\Content.MSO\4783D85E.tmp 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. Image result for optical isomers of alanine

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, Tartaric acid.svg

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 Ball and stick model of methanol

and ethanol Ball-and-stick model of 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. 1-fgs

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

Stereo, skeletal formula of methane with some measurements added

2. ALKENE: Ethene. Monomer unit of polyethylene https://upload.wikimedia.org/wikipedia/commons/thumb/8/8d/Ethene-2D-flat.png/220px-Ethene-2D-flat.png

3. Alkyne: Acetylene. Monomer unit of polyacetylene

Acetylene

Acetylene

4. ALCOHOL: Ethanol. Beer, wine and spirits

Ethanol

Ball-and-stick model of ethanol

5. AMINE: Aniline. Synthetic Dyes

Aniline

Aniline

6. PHENYL: Styrene. Monomer unit of polystyrene

Styrene

Styrene-from-xtal-2001-3D-balls.png

7. ETHER. Diethyl ether. general anesthetic

Ball-and-stick model

9. AKAYL HALIDE : Vinyl Chloride. Monomer unit of poly vinyl chloride (PVC)

Vinyl chloride

Structural formula of vinyl chloride

Space-filling model

10. CARBOXYLIC ACID: Acetic Acid; Vinegar https://upload.wikimedia.org/wikipedia/commons/thumb/8/87/Carboxyl-3D-space-filling-labelled.png/150px-Carboxyl-3D-space-filling-labelled.png 11. THIOL Grapefruit mercaptan Flavor, Perfumes (also odor of skunks)

Grapefruit mercaptan

Grapefruit mercaptan

Grapefruit mercaptan

12. ALDEHYDE Formaldehyde. Embalming fluid

Formaldehyde

Skeletal fomula of formaldehyde with explicit hydrogens added

Spacefill model of formaldehyde

Ball and stick model of formaldehyde

13. Ketone Acetone. Universal solvent for organic molecules (e.g., nail polish remover)

Acetone [1]

Full structural formula of acetone with dimensions

Skeletal formula of acetone

Ball-and-stick model of acetone

Space-filling model of acetone

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:

http://personal.ashland.edu/~bmohney/ket_scholars/ester1.gif

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

http://personal.ashland.edu/~bmohney/ket_scholars/pear.gif

Pears

Octyl acetate

http://personal.ashland.edu/~bmohney/ket_scholars/orange.gif

Oranges

Isoamyl acetate

http://personal.ashland.edu/~bmohney/ket_scholars/banana.gif

Banana

Ethyl Butyrate

http://personal.ashland.edu/~bmohney/ket_scholars/pineapple.gif

Pineapple

Butyl acetate

http://personal.ashland.edu/~bmohney/ket_scholars/apple.gif

Apple

Methyl trans-cinnamate

http://personal.ashland.edu/~bmohney/ket_scholars/strawberry.gif

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 diamond Hope 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 - Chemguide https://www.chemguide.co.uk/basicorg/isomerism/optical.htm Websites on water are: Water and its structure - Chem1

www.chem1.com/acad/sci/aboutwater.html