Sign in Pick up papers Sit with the same group as last week. Chem 108: Lab Week 8 Sign in Pick up papers Sit with the same group as last week. A E C D B

Chemical Reactions Combination (Synthesis) Decomposition Single Displacement Double Displacement Combustion: Oxidation-Reduction Biological Reactions: Enzyme Catalysts Example: Fermentation _________________________ A 3900-year-old clay tablet, which was found in Iraq between the Tigris and Euphrates rivers, had a Sumerian poem (http://www.piney.com/BabNinkasi.html) honoring Ninkasi, the patron goddess of brewing. It contains the oldest surviving beer recipe, describing the fermentation of the carbohydrates found in bread, bappir, made from barley, honey, dates and sweet aromatic herbs. The global availability of carbohydrates and native microbes (yeasts) has led to the production of many different types of beers, ales, wines, and fruit based alcoholic beverages in many countries throughout the world. [The bottle on the left was found in Eugene, Oregon, ……. But, it dates only to 2016.] http://www.piney.com/BabNinkasi.html)

Chemical Reactions Combination (Synthesis) Decomposition To DO Today With same fermentation partner; Lab Manual pp.44-45 Combination (Synthesis) Decomposition Single Displacement Double Displacement Combustion: Oxidation-Reduction Biological Reactions: Enzyme Catalysts Example: Fermentation pp.61-67 _________________________ A 3900-year-old clay tablet, which was found in Iraq between the Tigris and Euphrates rivers, had a Sumerian poem (http://www.piney.com/BabNinkasi.html) honoring Ninkasi, the patron goddess of brewing. It contains the oldest surviving beer recipe, describing the fermentation of the carbohydrates found in bread, bappir, made from barley, honey, dates and sweet aromatic herbs. The global availability of carbohydrates and native microbes (yeasts) has led to the production of many different types of beers, ales, wines, and fruit based alcoholic beverages in many countries throughout the world. [The bottle on the left was found in Eugene, Oregon, ……. But, it dates only to 2016.] http://www.piney.com/BabNinkasi.html)

Molecular Modeling Complete Cover page Today and turn in next week http://chemconnections.org/general/chem108/Chemistry%20108%20Molecular%20Modeling%20Form%20Fall%202017.pdf http://molview.org A 3900-year-old clay tablet, which was found in Iraq between the Tigris and Euphrates rivers, had a Sumerian poem (http://www.piney.com/BabNinkasi.html) honoring Ninkasi, the patron goddess of brewing. It contains the oldest surviving beer recipe, describing the fermentation of the carbohydrates found in bread, bappir, made from barley, honey, dates and sweet aromatic herbs. The global availability of carbohydrates and native microbes (yeasts) has led to the production of many different types of beers, ales, wines, and fruit based alcoholic beverages in many countries throughout the world. [The bottle on the left was found in Eugene, Oregon, ……. But, it dates only to 2016.]

Molecular Modeling Computational Chemistry Covalent Bonds: Lewis Structures, Molecular Shapes Dr. Ron Rusay

Molecular Modeling Computational Chemistry Shapes Lewis Structures Polarity, Solubility, Stereochemistry Smell, Teratogenicity Dr. Ron Rusay

Shapes of Molecules https://www.youtube.com/watch?v=Jq_Ca-HKh1g View: What is the shape of a molecule? George Zaidan and Charles Morton http://chemconnections.org/general/chem108/Molecular%252520Shapes-Guide.html

Molecular Shapes Molecular Models for C, H, N, O Fundamental repeating shapes found in every biological molecule C =black H = gray N = blue O = red pink = generic atom

Photo Bancroft Library, University of California/LBNL Image Library Professor Gilbert Newton Lewis (circa 1940) Notes from Lewis’s notebook and his “Lewis” structure. G.N. Lewis Photo Bancroft Library, University of California/LBNL Image Library Footnote: G.N. Lewis, despite his insight and contributions to chemistry, was never awarded the Nobel prize.

Valence Electrons – Lewis Dot Drawings A Groups-Periods 2 & 3 .H

Covalent Bond Numbers .H one bond two bonds three bonds four bonds (Neutral Atoms!) .H one bond H F Cl Br I O two bonds N three bonds C four bonds

(Handout) Due End of Lab Next Week

Lewis Structures Molecular Shapes For simple Lewis structures: Draw the individual atoms using dots to represent the valence electrons. Put the atoms together so they share PAIRS of electrons to make complete octets. NH3, for example: Eg. Ammonia:

http://molview.org Molecular Shapes Lewis Structures MolView: Visual On-line Molecular Modeling Bonding, Lewis Structures, Molecular Modeling: Computational Experiments, Instructions, & Manual pp. 53-58

(Course/ Lab Manual pp. 53-58) Organize Today with your Moleview Group http://molview.org (Course/ Lab Manual pp. 53-58) Organize Today with your Moleview Group Due End of Lab Next Week

Orbital (Electronic) Geometry Molecular Geometry Bond Angle # of lone pairs Important in Organic Compounds Linear Linear Trigonal Planar Trigonal Planar Trigonal Planar Bent Tetrahedral Tetrahedral Tetrahedral Trigonal Pyramidal Tetrahedral Bent Trigonal Bipyramidal Trigonal Bipyramidal Trigonal Bipyramidal Seesaw Trigonal Bipyramidal T-shape Trigonal Bipyramidal Linear Octahedral Octahedral Octahedral Square Pyramidal Octahedral Square Planar 1 2 3 See again in Chem 120 and possibly in Chem 109

http://chemconnections.org/general/movies/Lewis%20structures.html

Covalent Compounds Share valence electrons. 1 pair = 1 bond; maximum # of atom-atom bonds = 3. Octet rule (“duet” for hydrogen) Lewis structure examples: Notice the charges: In one case they balance, can you name the compound? In the other they do not. It has a “Formal” charge. Can you name the polyatomic ion?

Molecular Shapes Lewis Structures MolView: Polyatomic Ions http://molview.org Molecular Shapes Lewis Structures MolView: Polyatomic Ions Bonding, Lewis Structures, Molecular Modeling:

Resonance Occurs when more than one valid Lewis structure can be written for a particular molecule. [Adjacent free electrons, double or triple bonds.] These are resonance structures. The actual structure is an average of all of the resonance structures.

Infrared- Bond Absorbances Figure: 12-14-04UN Caption: The IR spectrum has distinct regions. The left of the spectrum shows the C-H, O-H, and N-H stretches. The triple bonds absorb around 2200 cm-1 followed by the double bonds to the right at around 1700 cm-1. The region below 1400 cm-1 is called the fingerprint region.

Infrared- Bond Absorbances Figure: 12-14-04UN Caption: The IR spectrum has distinct regions. The left of the spectrum shows the C-H, O-H, and N-H stretches. The triple bonds absorb around 2200 cm-1 followed by the double bonds to the right at around 1700 cm-1. The region below 1400 cm-1 is called the fingerprint region. http://molview.org

Infrared- Bond Absorbances Figure: 12-14-04UN Caption: The IR spectrum has distinct regions. The left of the spectrum shows the C-H, O-H, and N-H stretches. The triple bonds absorb around 2200 cm-1 followed by the double bonds to the right at around 1700 cm-1. The region below 1400 cm-1 is called the fingerprint region. https://www.co2.earth/

Computational Chemistry Polarity: Molview (http://molview.org) Jmol Figure: 08-07 Color coded electron density distribution: red-highest, blue lowest, green balanced The more distinct the red –blue colors means the more polar the molecule.

Polarity & Physical Properties Ozone and Water 0.1278 nm The Lotus flower Water & dirt repellancy: solubility? Resultant Molecular Dipoles > 0 Solubility: Polar molecules that dissolve or are dissolved in like molecules New Water-Repellent Material Mimics Lotus Leaves John Roach for National Geographic News February 27, 2003 Dirt-repelling paint, based on the qualities of the lotus leaf, being developed at Bonn University.

Legos of Chemical Biology Amino Acids Legos of Chemical Biology Amino acids contain carbon, hydrogen, oxygen, and nitrogen, which resemble the following shapes & structural components 20 different amino acids are encoded by the genetic code, which is archived in DNA. Hundreds of amino acids link together with amide (peptide) bonds to form proteins, which are the machinery for the chemistry of life. There are less than 20,000 total proteins produced from humans’ entire genome, each coded by a specific gene in DNA’s ~3 billion genetic bases. http://www.jbc.org/content/262/2/549.short http://pdb101.rcsb.org/motm/54 http://www.rcsb.org/pdb/explore/jmol.do?structureId=1CFJ&bionumber=1

Indispensible Biopolymers Amino Acids Proteins Indispensible Biopolymers Acetylcholinesterase (ACE) ACE, an enzyme, which catalyzes a key reaction in a repetitive biochemical cycle that is crucial to neurological and physiological functions in humans…. and insects among others. 4,496 atoms; 4,404 bonds 574 amino acid residues http://www.rcsb.org/pdb/explore/jmol.do?structureId=1CFJ&bionumber=1 http://pdb101.rcsb.org/motm/54

Biological Reactions eg. Fermentation A 3900-year-old clay tablet, which was found in Iraq between the Tigris and Euphrates rivers, had a Sumerian poem (http://www.piney.com/BabNinkasi.html) honoring Ninkasi, the patron goddess of brewing. It contains the oldest surviving beer recipe, describing the fermentation of the carbohydrates found in bread, bappir, made from barley, honey, dates and sweet aromatic herbs. The global availability of carbohydrates and native microbes (yeasts) has led to the production of many different types of beers, ales, wines, and fruit based alcoholic beverages in many countries throughout the world. [The bottle on the left was found in Eugene, Oregon, ……. But, it dates only to 2016.] https://www.youtube.com/watch?v=vW99JEaDApY http://www.piney.com/BabNinkasi.html