chemical paper(exact three pages)(Your grade on the third essay will depend, to large measure, on the improvement demonstrated relative to the first two essays.)

CHE 102: LECTURE 8 From the Hydrogen Bond to the Blue Planet to Jurassic Park A 99-million-year old piece of amber discovered in 2016 by Lida Xing in Myanmar (Burma). Suspended inside is the skull of the smallest known bird, and, therefore, dinosaur, ever discovered. The dinosaur’s skull is only a little more than half an inch, from its beak to the end of its skull. The animal had bulbous eyes that looked out from the sides of its head, rather than straight ahead like the eyes of an owl or a human.

HYDROGEN BOND A hydrogen bond (often abbreviated H-bond) is a type of intermolecular bonding between a hydrogen atom and a “lone pair” of electrons on an electron rich donor atom [particularly the second-row elements N, O or F, and hydrogen].

 Such an interacting system is generally denoted Dn–H···Ac [Dn for donor, Ac for accepter] where the solid line signals a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond.  While hydrogen bonding has both covalent and electrostatic (ionic) contributions, present evidence suggests that the primary contribution is covalent.

Hydrogen bonds can be intermolecular  (occurring between separate molecules) or intramolecular or (occurring among parts of the same molecule). Examples of both will be given below. Depending on the nature of the donor and acceptor atoms which constitute the bond, and the geometry and local environment, the energy of a hydrogen bond can vary between 1 and 40 kcal/mol. This makes them somewhat stronger than nonpolar (van der Waals) interactions, but weaker than fully covalent or ionic bonds.  Roughly speaking, the energy of a H-bond is about 5-10% the energy of a covalent bond. This type of bond can occur in inorganic molecules such as water and in organic molecules like proteins and DNA (see later discussion).

The hydrogen bond is responsible for many of the anomalous physical and chemical properties of compounds of N, O, and F. For example, intermolecular hydrogen bonding is responsible for the high boiling point of water  (100 °C) compared to other hydrides that have much weaker hydrogen bonds.  Intramolecular hydrogen bonding plays an important role in the structure of polymers, both synthetic and natural. It is also partly responsible for the secondary and tertiary structures of proteins and nucleic acids.

H-BONDS: WATER

Water is absolutely essential for our existence on Earth and plays a pivotal role in physics, chemistry, biology and geoscience. What makes water unique is not only its ubiquitous presence on Earth but also the anomalous behavior of many of its macroscopic properties. The density, specific heat, viscosity and compressibility of water behave in ways opposite to other liquids that we know. In a glass of ice water, everything is, in a sense, upside down. Strangely for the liquid state, water which freezes at 0 oC is the densest at 4 ˚C, and therefore stays on the bottom. This is why life can exist at the bottom of a lake and an ocean during winter, even when the surface is frozen. At a more prosaic level, this “inversion” in behavior is the reason why an ice cube floats at the top of a glass of ice tea. At the molecular level, the origin of this strange behavior, unique to water among the important liquids, is still a subject of great interest in physics and chemistry.

The crystal structure of solid water (ice) was shown in Lecture 4 . See also the graphic below. Notice that, accounting for both covalent and H-bonds in water, a crystal of ice has a hexagonal symmetry, which is why snowflakes have a hexagonal symmetry.

A snowflake is a single  ice crystal  that has achieved a sufficient size (either “by itself” or amalgamated with others) and falls through the Earth’s atmosphere as snow. In  supersaturated  air masses of water droplets in a cloud, each snowflake nucleates around a dust particle, freezing and accreting in crystal form. Complex shapes  emerge  as the flake moves through differing temperature and humidity zones in the atmosphere, so that individual snowflakes differ in detail from one another. They are categorized in eight broad classifications and at least 80 individual variants. The main constituent shapes for ice crystals, from which combinations may occur, are needle, column, plate, and rime. Snow appears white in color despite being made of clear ice. This is due to  diffuse reflection  of the whole  spectrum  of  light  by the small crystal facets of snowflakes.

THE BLUE PLANET The origin of water on Earth is the subject of an extensive body of research in the fields of planetary science, astronomy and astrobiology. Earth is unique among the rocky planets in the Solar System in that it is the only planet known to have oceans of liquid water on its surface. Liquid water, which is necessary for life, continues to exist on the surface of Earth because the planet is at a distance far enough from the Sun that it does not lose its water to the greenhouse effect, but not so far that low temperatures cause all water on the planet to freeze.

Earth could not have condensed from the protoplanetary disk with its current oceans of water because the early inner Solar System was far too hot for water to condense. Instead, water and other volatiles must have been delivered to Earth from the Solar System later in its history. Modern geochemical evidence suggests that water was delivered to Earth by impacts from icy planetesimals similar in composition to modern asteroids in the outer edges of the asteroid belt. 

WATER: Essential for Life on Earth Living System Water is fundamental to the survival of organisms. Doctors recommend drinking 8 cups of water a day in order to maintain a healthy lifestyle. Clean water is one of the primary concerns of all countries, especially Third World countries. Wars have been fought over who gets the rights to drink from the source of water. Recall the movie, “Lawrence of Arabia.” Wars in the future will likely not be fought over oil or mineral resources, but water. Why is this substance so vital to the survival of all life? First, liquid water is essential for biochemical reactions by providing a medium which facilitates the transport of vital nutrients from one place to another within a cell. Second, water, as a polar molecule, is considered the “universal solvent”, in that everything dissolves in water to some degree, allowing nutrients to be integrated into water with relative ease. NOTE: The solvent properties of water or other substances is summed up in the simple phrase “Like dissolves like.” Table salt, which is composed of Na+ and Cl- ions, dissolves readily in water, a polar molecule. Salad dressing, oil and vinegar, left standing, will separate into a vinegar (polar) phase and an oil (nonpolar) phase. You have to shake the bottle to mix the two (which then forms an emulsion). Additives aside, gasoline is composed of the nonpolar hydrocarbon molecule octane (C8H18).

Octane

When filling up your gas tank, if you happen to spill gas on a wet pavement you may have noticed technicolor fringes. These result because gasoline and water don’t mix. Water has a higher density than octane (0.993 g/cm3 vs 0.706 g/cm3), so the gas floats on top. This thin film of oil, refracted by sunlight, produces the “rainbow” fringes. In understanding the d=3 dimensional structure of proteins (See Lecture 6), amino acids with polar side chains “stick out” into the aqueous medium of a cell, whereas amino acids with nonpolar side chains are buried away inside the structure. This sequestering of nonpolar amino acids in the interior of a protein was analyzed in 1953 by my PhD advisor at Princeton, Walter Kauzmann, who baptized the effect “hydrophobic bonding.” Today, the hydrophobic effect is discussed extensively in standard textbooks on biochemistry and cell biology. Third, water also helps enzymes to function [Recall, enzymes are proteins that catalyze chemical reactions, thus speeding up the reaction. See Lecture 6]. Another unique thing about water is that all three states (liquid, solid and gas) exists naturally in nature. [Remember Thales? See Lecture 1] This allows the water cycle to occur in nature, which replenishes water around the world.

Pure water has a wide range of temperature between its freezing and boiling points (100 oC). Both temperatures can be manipulated with salt and other minerals. Water has a very high specific heat, which means it takes a lot of energy to heat it up. This allows water to survive the intense heat variations that Earth has without evaporating at once, and helps to moderate the temperature of the planet thanks to the oceans. As noted above, a remarkable characteristic of water is that when it turns into solid ice, it expands instead of contracts, unlike a normal solid. The result is that ice floats above liquid water, thus preventing it from displacing water and causing the ocean levels to rise, and also allowing Arctic and Antarctic life to thrive. H-BONDS: The α-Helix in Proteins and the Double Helix in Nucleic Acids The alpha helix (α-helix) in the secondary structure of proteins is a right-hand helix in which every  N-H group in one amino acid (residue) H-bonds to the C=O  group of an amino acid located three or four  residues earlier along the sequence of amino acids making up the protein.

The alpha helix is called a Pauling–Corey–Branson α-helix. The name 3.613 helix is also used for this type of helix, specifying the average number of amino acids (residues) per helical turn, with 13 atoms being involved in the ring formed by the hydrogen bond. See below.

H-bonds break when a protein is subject to increased temperature. This is what happens when you fry an egg for breakfast. The egg white will quickly turn from clear and runny to white and firm. Heat energy agitates the egg-white proteins, making them bounce around and hit water molecules and other proteins. These collisions break the weak

H-bonds that held the protein curled up in its “native state”, allowing the chain of amino acids to partly unfold – a process called denaturation.

When these agitated proteins bump against one another, new and stronger chemical bonds form between them. As these proteins join together in an interconnected web, the egg white congeals into a solid, and you have a “sunny side up egg.”

Hydrogen bonds are also responsible for specific base-pair formation in the DNA double helix  (See Lecture 6) and a major contributor to the stability of the DNA double helix structure. A hydrogen-bond donor includes the hydrogen atom and the atom with which it is most tightly linked .

In genetics, DNA replication is the process by which DNA makes a copy of itself during cell division. The first step in DNA replication is to 'unzip' the double helix structure of the DNA molecule. H-bonds between base pairs (See Lecture 6) are broken and the two separated strands then act as templates for making new strands of DNA. EVOLUTION of LIFE on EARTH: AGE of the DINOSAURS Dinosaurs are a diverse group of reptiles. They first appeared during the Triassic period, between 243 and 233.23 million years ago. They became the dominant terrestrial vertibrates after the Triassic-Jurassic extinction event 201.3 million years ago. Their dominance continued through the Jurassic and Cretaceous periods. The fossil record demonstrates that birds are modern feathered dinosaurs (See top of Lecture), having evolved during the Late Jurassic epoch. Indeed, birds were the only dinosaur lineage to survive the Cretaceous-Palogene extinction event approximately 66 million years ago. The Chicxulub crater is an impact crater buried underneath the Yucatán Peninsula in Mexico. It was formed when a large asteroid or comet about 6.8 to 50.3 miles in diameter, struck the Earth. The date of the impact coincides precisely with the Cretaceous-Paleogene boundary (commonly known as the "K–Pg boundary" ), slightly less than 66 million years ago, and a widely accepted theory is that worldwide climate disruption from the event was the cause of the a mass extinction in which 75% of plant and animal species on Earth became extinct. Dinosaurs can be divided into avian dinosaurs, or birds; and non-avian dinosaurs, which are all dinosaurs other than birds. The non-avian dinosaurs didn’t survive.

AMBER Amber, fossilized tree resin, has long been appreciated for its color and natural beauty. Much valued from antiquity to the present as a gemstone, amber has also been made into a variety of decorative objects. Below is the Amber Room in the Catherine Palace in Saint Petersburg, the Russian port on the Baltic Sea, founded by the Czar Peter the Great in 1703. A town (Amer or Amber) in Rajasthan, India, founded around 1036, is famous for its Amber Fort.

Ganesh Pol Entrance My work with the World Bank and the International Institute of Theoretical and Applied Physics took me to many parts of the World. I’ve seen both of the above, and they are stunning.

Insects trapped in tree resin, became “fossilized.” The science underlying Jurassic Park is that the DNA isolated from a dinosaur trapped in tree resin, and then fossilized, can be extracted using standard techniques in biochemistry and used to create “the original.”

Lastly, from at least the 16th century BC, amber was transported from Northern Europe to the Mediterranean region.  Recalling Lecture 1, the breast ornament of the Egyptian pharaoh Tutankhamen (c. 1333–1324 BC) contains large amber beads from the Baltic Sea area (today’s Poland). Amber was sent from the North Sea to the temple of Apollo at Delphi as an offering. Ancient trade routes in Asia (the Silk Road) brought amber from the Black Sea to China, where it was customary to burn amber during large festivities. Below is an expensive decorative object made of rare white amber, an artist’s representation of the Great Wall of China (also a “must see”).