CHEMISTRY 125 

Daily Web Links

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Topic	Video	Web Links
Mass Spectroscopy		Interpreting Mass Spectrum from percent abundancies
Periodic Tables		Periodic Table Live Web Element Periodic Table ChemiCool Periodic Table American Elements The Pictorial Periodic Table Chemical Elements - Interactive Periodic Table Touchspin's Interactive Periodic Table Main Page |  Touchspin's Interactive Periodic Table A great Periodic Table (PDF) to print (color) (from http://www.dayah.com/periodic/Other/Periodic%20Table.pdf
Electron Configuration Atoms/Ions	Dr J YouTube:  Periods, Rows, Shells, Subshells, and Orbitals	Atomic Orbitals Better atomic orbitals Jsmol Electronic Configuration of Ions Transition Metals:  difference from Main Group Metal ransition Metals:  difference from Main Group Metal Transition Metals:  difference from Main Group Meta
Periodic Trends	Dr J YouTube:   Energy and Forces in Electron Nuclear Attractions	The meaning and measurement of atomic radii WebElements: Periodicity covalent radii van der Waals radii ionic radii (Pauling) element bond length density ionization energy electron affinity electronegativity  J. Chem Ed: Period Table Live - Charts of Periodic Functions (pick x and y axes variables)
Metals and Unit Cells	Adding Atoms to 1 large Face Centered Cubic unit cell Lattice Structures I with coordination # (YouTube) (8:57) **** If you have a free hour for extra credit (see syllabus and daily schedule) Secret of the Viking Sword	Packing and Unit Cells Bravais lattices: additional unit cells Great views of Unit Cells - ChemTube3D Unit Cell Powerpoint (also on Connect) Face centered cubic = cubic closest packing Metal Structures Unit cells of elements Interactive solid state chemistry: UW Madison
Packing and Holes	Lattice Structures 2 - Holes (YouTube)(9:14) ****	Unit Cells and Holes show in class For the 2 links below select buttons to show holes: Cubic Closest Packing CCP- with Octa/Tetra Holes show in class Hexagonal CP - with Octa/Teta Holes another site for holes - for CCP and HCP
Salts and Mineral Structures	Fraction of Atoms/Ions in Unit Cell Dr J YouTube:  number of atoms in hcp unit cell Dr J YouTube: Predicting Unit Cell Packing based on ion size:  New 02/02/19	Solid State - ChemTube3D - Phenomenal site! Shows Closest Packing (HCP and CCP) salt structures:  Examples of AB, AB2, AB3, A2B, A3B structures with visualization of holes. Another link for a different view: salts Crystals at Otterbein: metals and salts Interactive solid state chemistry: UW Madison   Other sites: Water  |  Interactive 3 D structures Solid State
Lattice Energy	Review YouTube:  unit cells and coordination number Review Youtube:  holes: octahedral and tetrahedral holes in Face Centered C; cubic hole in scp	Lattice Energy Calculator (given in negative number's however)
Changes in Lattices/Unit Cells		Examples of changes in molecules Deoxy to OxyHemoglobin (with red sphere) Facilitated Diffusion of Lactose through a membrane
Molecular Shape, Geometry and Perspective	Molecular Shape and Perspective (Moodle, passwd required) Charges and Ions (Moodle passwd required) DR J YouTube:  Lewis and Perspective Structures - Example XeF4  New 02/07/19	Great site on geometry (VSEPR) Great interactive sites from PHET: Bond and molecule polarity Molecular Shapes PHET:  Visualizing electronic and molecular geometries  -awesome site! New 02/07/19
IUPAC Nomenclature		Nomenclature Nomenclature 2
Intro Chirality	Chirality/Enantiomers (1:01)	Stereochemistry - Enantiomers (Jmol)
Chirality: Mirror Planes and Inversion Symmetry	Chirality (7:21) Dr J Youtube: Chiral Center and Plane Symmetry New 02/09/19
R and S Isomers	Naming R and S isomers (8:16)	R and S (Jmol) ChemDraw on Network Priority Rules = and = bonds
Review of stereoisomers: more complicated molecules	Stereoisomers, Enantiomers, Diastereomers, Constitutional Isomers and Meso Compounds  view to 11 minute mark (Khan)	Diastereomers (Jmol) Meso Compounds (Jmol) Stereochemical Challenge (test yourself) (Jmol)
Meso Compounds	Meso Compounds: (8:51)YouTube Cis/Trans - E/Z nomenclature (8:31) YouTube   9/16 New Dr J:  Summary isomers Dr J: Meso or Not Dr J: Optical Activity	Stereoisomers - A Review Practice: R/S Determination R/S Qz with Answers More than 1 chiral carbon More than 1 Qz with Answers For class: Diastereomers Meso Compounds Organic Molecules: search for meso 2,4-dicholorpentane: Stereoch 2-bromo,4-choloropentane: Sterochem
Acylic Conformational Analysis Cyclic Molecules: Rings and Flips	Ethane Conformation: YouTube 1:04 Conformations Butane: YouTube 13:51 Conformations of Cycloalkanes: YouTube  5:36	Jsmol:  Conformations of Ethane   |   Propane  |    Butane Alkanes from Chapter 3:  Conformational Analysis of Alkanes and Cycloalkanes by Dr. Ian Hunt, U. Calgary - Follow arrow links at the bottom through cycloalkanes atom counting and energy
Chair Conformations Energy Analysis: cyclohexane and substituted cyclohexanes Diamond Lattice: 6 and 7 atom interactions	Mono and disubstituted cyclohexanes: YouTube (6:41) 9/16 New Butane in multiple representations:  3D ball/stick, line drawing, Cyclic Molecules: Angle and Torsional Strain  Newman projection - Calculating energies. (8:00 min) YouTube - Dr J	Cycloalkanes from Chapter 3:  Conformational Analysis of Alkanes and Cycloalkanes by Dr. Ian Hunt, U. Calgary - Follow arrow links at the bottom Chair/Boat - Cyclohexane cycloalkanes other than C6H12 cyclohexane Steps in drawing chair conformations of cyclohexane (view as slide show!) Ring Flip with intermediates: Jmol and animation Newman projection: cyclohexanes substituted cycloalkanes polycyclic fused rings Adding lines ot the diamond lattice and identify 6/7 atom interactions (view as slide show - NEW 10/7) Diamond Lattice Diamond Lattice - Oregon State Building the Diamond Lattice - Animated Gif
Intermolecular Forces	IMFs: YouTube (5 min)	liquid water and ice   liquid water and ice with chair ice and liquid water dipole- dipole and London Dispersion forces (flash animation) IMFs Bond and Molecular Dipoles: PHET
Intermolecular Forces and properties	Melting Pt Depression and Boiling Point Elevation: YouTube (mistake at 3:25 - should state lower Melting Pt not Boiling Pt (0-6 minutes)	NaCl dissolving in water (from Iowa State) Of Mice and Oxygen Another view thin layer chromatography Solutions; Colligative Properties: Introduction Vapor Pressure Lowering Boiling Point Elevation Freezing Point Depression
Carbohydrates and Lipids	Carbohydrates 1: Defo and simple examples  Carbohydrates 2:  Ribose and Glucose - straight and cyclic forms Carbohydrates 3:  polysaccharides of 1 monossacharides repeats Carbohydrates 4:  polysaccharides of disaccharide repeats.	Carbohydrates: Fisher to Ring structure change:  Jmol Jmol:  Glycogen    Amylose      Amylopectin     cellulose
Lipids	Dr J YouTube  -new 10.24.16 Gel to Liquid Crystalline Phase Change in Lipid Bilayers:  Effect of Cholesterol	Lipids: A micelle A membrane bilayer Molecular Dynamics Simulation of a phospholipid with a saturated fatty acids and one with 6 double bonds from Scott Feller, Wabash College (note changes in saturated fatty acid from all trans to some gauche conformations.
Proteins	Solubility of small and large molecules (11:13) Protein Structure (15:42))	Buried or Not: That is the Question (compare protein structure to micelle) N-linked Glycoprotein     How important are links? Influenza
Nucleic Acids	Nucleic Acid and CHO structures (view web tutorials A and B first) Questions?	For tutorials by Eric Martz below go to THIS LINK.  Select the Set Preference Link Then select this icon: Select tutorial A.  B and D are also good. Dr Js links: H bonds and H bonds donors and acceptors in AT and GC base pairs DNA with major and minor groves AND  H bond donors/acceptors DNA: protein complex
Molecular Dynamics Simulations - Biomolecules		Biological Examples  The movies below are courtesy of the Theoretical and Computational Biophysics Group at the Beckman Institute, University of Illinois, Champaign/Urbana Go to the following pages and view the following simulations Channel Proteins - water channels in membranes: - Sugar Permeation through LacY   - K+ Permeation through Kv1.2 Channel Protein Folding and Stretching - Six Microseconds of Protein Folding Lipoproteins - Lipoproteins that Circulate in the Blood Collecting Fat
	Covalent Networks, Metallic, and Ionic Crystals: YouTube (9:14) Network Solids: (3:00) Zeolites: view 2;00-3:15 and 4:00-5:30 minutes only	liquid water and ice with chair of O atoms in ice   (rotate it to clearly see the chair) Covalent Network Solids Build diamond and graphite (notice as you build diamond you are making a diamond lattice)  Diamond, graphite, graphene, fullerene (follow the links) Solids: Chem Ed Digital Library: Chose the following from the list of covalent solids: - Carbon: diamond, graphite, nanotubes, etc - Silica (SiO2) - turn off polyhedron, turn on thicker bonds Jmol: - Zeolites MoS2   MoS2   Zeolite Database | Zeolites: Wikipedia Jmol: "Tetrahedra of Bonding" - metallic, ionic, ,molecular covalent, network covalent Zeolite: scroll down left hand side to Zeolites Zeolite Explorer
	Transtion Metals - Dr J Tetrahedral vs Square Planar - Dr J	d atomic orbitals Jsmol great view d orbitals JSmol overview geometry transition metal complexes: Purdue Transition Metals from Purdue TS metal complexes of Cl:  Carleton  Co EDTA complex Cis-platin DNA Interactions  Square Planar Geometry from Octahedral Naming TS metal complexes Calmodulin Zn2+  Zn finger DNA binding motif
	18 Electron Counting - Dr J Counting Electrons: A needed review Questions? (note 1 mistake near end: Pt2+ in cis-platin has 16 electron surrounding it)	18 electron rule with qz (use ionic charged model only; do top right qz example; don't worry about ring ligands 18-Electron rule, and d electron counting from Wikipedia
	Transition Metal Complexes: YouTube (10:18) Questions? Mirror Planes in Octahedral Transition Metal Complexes - Dr J YouTube	General Isomerism in TS metal complex Are these the same? - Octahedral complexes isomers in coordination complexes - doesn't work yet  TS metal isomers - fac/mer, etc*** Metal Tris-chelates 8 isomers of Ni(en)32+ Jsmol Biomolecules Ca2+ calmodulin (calcium modulatory protein) – EF Hand  Cu1+ copper (I) efflux regulator protein Fe2+   deoxy and oxy-heme K+      valinomycin – a K+ ionophore which transports K+ ions across a membrane Zn2+  Zn finger DNA binding motif Octahedral isomers of molecules like Co(en)3, 3D rotatable image 2, side by side JSmols of a very similar molecule showing both isomers. Left (left or L) isomer and one the right (delta or D) isomer.  How to name the isomers General links:Metal trischelates
	Waves and Orbitals - Dr J 0-12:00 min: prop waves and atomic orbitals; 12:00-19:00 min: Intro to molecular orbitals note: 1 mistake - one mention of  nonbonding orbitals should have been correctly stated as antibonding orbital Hands Chasing Clouds (prep for Zen Chem MOs) Questions?	Diffraction – bend around corner Interference: Constructive and Destructive I Interference: Constructive and Destructive I Interference Examples: •Water •Laser  Electrons
	Hybrid Orbtials - Dr J (14:00) Hybrid Orbital Formation - YouTube (1:36) Questions?	Hybrid Orbitals (Jsmol works) Great sp2 visualization ethene (Jsmol)
	Resonance and Conjugation Dr J Note: yellow dots represent atomic nuclei, not nodes; Last slide cursor does not appear. MOs of Methane - YouTube 4:00 MOs of Ethane - YouTube 5:00 Questions?	conjugation: Jsmol MOs pi ring systems: not Jsmol MOs: Linear Combo of atomic orbital: (not Jsmol) Stefan Immel; Tech. Univ Darmstad MolCalc:  **** See and rotate MOs of a variety of molecules.  Select calculate and then observe properties like IR frequencies, MOs, etc. Disregard first set of lowest energy
	Aromaticity Dr J Questions?	Huckel MOs of Benzene Interior Angles of a regular  polygon Aromatic, Antiaromatic, Nonaromatic Rings Amide Bond:  Resonance, Conjugations, Hybridization, and Huckel MOs
	none	Are these the same? - Octahedral complexes Diamond Lattice
	Lewis Acid/Base reaction mechanism: electron pushing - YouTube	Ca2+ calmodulin (calcium modulatory protein) – EF Hand  Cu1+ copper (I) efflux regulator protein Fe2+   deoxy and oxy-heme  K+      valinomycin – a K+ ionophore which transports K+ ions across a membrane Zn2+   Zn finger DNA binding motif
	Bronsted Acid/Base and pKas - Dr J Questions?
	Bronsted Acid/Base Strength - Dr J (mistake: molecule named as glucose is not glucose, but glucitol) Questions?	Organic Mechanisms - ChemTube3D Increased acidity of Hs on C adjacent to a double bond:  resonance, conjugation and MO explanations.
	Acid/Base Rx - Extent, Completion, and Extractions - Dr J (mistake:  in 0.1 M HCl extraction, since HCl is a strong acid, no HCl is present as it is all converted to H3O+ which has a pKa of -1.7.  Rx still goes to completion.)

• Biology Topics in Chemistry from MIT

The Structure of Atoms

• Cathode Ray Tube

• Millikan Oil Drop Experiment

• Rutherford Gold Foil Experiment

The Periodic Table and Properties of Atoms

A.  Property of Waves

• Longitudinal and Transverse Waves

• water waves | Electromagnetic waves |

• superposition | superposition again |

• Diffraction - water waves

• Interference - water waves | 2 slit interference general

B.  What's wrong with the Rutherford "planetary" model of the atom - 1?

• vibrating charge and electromagnetic waves
• vibrating charge and the demise of the Rutherford (planetary) model of the atom

C.  Absorption and Emission (What's wrong with the Rutherford model -2)

• Emission spectra

• Absorption spectra

• Absorption/Emission Spectra: Elements Periodic Table

D.  Light as particle:  Photoelectric Effect  (What's wrong with our description of light)

• Photoelectric Effect:  Interactive

• Photoelectric Effect:  Explanation

E.  Particles as Waves: electron, neutron, and molecule diffraction/interferences (What's wrong with the Rutherford model 3)

• electrons act as waves
• Electron diffraction pattern: double slit
• Electron diffraction: 2 slit
• Derivation of Debroglie Equation
• Buckminsterfullerene:  Theoretical | Experimental 

F.  Quantum model of the atom:  Bohr Model: 

• Jumps in Bohr Model
• Bohr Model : emission spectra
• wavelengths of transitions - Bohr model

G.  Quantum model of the atom:  Modern

• Mathematical solution to Schrodinger wave equation, quantum numbers, and orbital shapes
• Quantum Numbers
• Wave function simulator (show angular wave fn, radial wave fn y, and probability density (y²) function)
• Orbital Shapes from J. Chem. Ed | Orbital Shapes from U. Sheffield
• Electronic Configuration of Atoms
• Some Quantum Quotes compiled by Dr. Rioux

Misc

• Lattice Energy Calculator (given in negative number's however)
• Self Assessment - Lattice Energy Calculator for example
• Geometrical Shapes
• Geometrical Shapes
• Stereochemistry - Enantiomers
• Stereoisomer Challenge
• Stereochemistry Summary
• Stereochemistry from ChemTube3D

Covalent Network Solids

• Tetrahedron Inscribed into a rotating cube

• Build diamond and graphite

•  Carbon compounds:  diamond, graphite, and buckminsterfullerene  |  nanotubes

• Silica (SiO₂)

• "Tetrahedra of Bonding" - metallic, ionic, ,molecular covalent, network covalent

October Nobel Prizes

• 2010 Nobel Prizes in Physiology or Medicine and in Chemistry

• 2011 Nobel Prizes in Physiology or Medicine

• Chemistry   |  Public Info  |  Youtube Interview  |  Islamic Girih Tiles

Isomers

• Stereochemistry

• Stereochemistry from ChemTube3D

 Conformations of Molecules (Jmol)

• ethane   |    ethene 

• conformations of ethane  |  ethene

• conformations of propane

• butane: the gauche conformation

• pentane – zig zag

  • Steps in drawing chair conformations of cyclohexane

• Jmol and animation cyclohexane

• cyclohexane conformations

• Diamond Lattice

• Jalpha and beta glucose

  • cellulose

  • Glycogen

• β - Cyclodextrin 2,7 - dihydroxynaphthalene hydrate (select Lattice, Unit Cell off)

• Puckering in ribose and deoxyribose in RNA and DNA

• protein folding:  NTL9 from Folding@home

• prion protein fold | Protein folding landscape

Intermolecular Forces and the Properties of Substances

• liquid water and ice   ice and liquid water

• NaCl dissolving in water (from Iowa State)

• mouse breathing in water? Explanation

• thin layer chromatography

• Reverse Phase chromatography - GE Lifesciences

 Biological Examples 

• A micelle

• A membrane bilayer

• dsDNA   | a more sophisticated tutorial on dsDNA

• a buried nonpolar group in a protein

• Ca²⁺ binding to carboxyl groups of the calcium binding protein calmodulin

• H bonds and H bonds donors and acceptors in AT and GC base pairs

• Jmol:  DNA with major and minor groves AND  H bond donors/acceptors

• DNA: protein complex

The movies below are courtesy of the Theoretical and Computational Biophysics Group at the Beckman Institute, University of Illinois, Champaign/Urbana

• water passing through aquaporin, protein channels in biological membranes: simulation

• lactose passing through the lactose permease, a membrane protein: simulation

• K⁺ ion passing through a voltage-gated K channel:  simulation

Covalent Network Solids

• Build diamond and graphite

•  Carbon compounds:  diamond, graphite, and buckminsterfullerene  |  nanotubes

• Network Solids: Chem Ed Digital Library

• Silica (SiO₂) - turn off polyhedron, turn on thicker bonds

• Jmol: MoS₂

• Zeolite Database | Zeolites: Wikipedia

• Jmol: Zeolites

• "Tetrahedra of Bonding" - metallic, ionic, ,molecular covalent, network covalent

Transition Metals

• Jmol:  Co:EDTA complex

• isomers in corrdination complexes

• Cis-platin DNA Interactions

• Square Planar Geometry from Octahedral

•  18-Electron rule, and d electron counting from Wikipedia

Molecular Orbitals

• Orbital Shape:  Atomic, Hybrid, Simple Molecular

• Hydrogen Atom Orbital Viewer

• Hybridization

• Animation of molecular orbital formation

• pi systems

• Simple Huckel Molecular Orbital Theory Calculator

• Interior Angles of a regular  polygon

• Aromatic, Antiaromatic, Nonaromatic Rings

• Ethylene vs butadiene

• Linerar Polyenes

Acids and Bases and other reactions

• Organic Mechanisms - ChemTube3D

Biological Examples Lewis Acid/Bases Complex

• Ca2+ calmodulin (calcium modulatory protein) – EF Hand

• Cu1+ copper (I) efflux regulator protein

• Fe2+   deoxy and oxy-heme

• K+      valinomycin – a K+ ionophore which transports K+ ions across a membrane

• Zn2+  Zn finger DNA binding motif