CHEMISTRY 125 

INTRODUCTION TO CHEMICAL
STRUCTURE AND PROPERTIES 

General Web Links  (some expand on what is presented in class and texts)

These links are mostly external and are freely available through search engines like Google or Bing.

Introduction to Chemistry and Matter/General Links

• Periodic Table Live from the Chem Ed Digital Library
• 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)
• 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

Periodicity

• 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

• Packing and Unit Cells

• Bragg’s Law and diffraction

• X-ray diffraction (Laue transmission) from simple cubic, bcc and fcc lattices

• Bravais lattices: additional unit cells

• Face centered cubic = cubic closest packing

Ionic Compounds

• Electronic Configuration of Ions

• Transition Metals:  difference from Main Group Metal

• Transition Metals:  difference from Main Group Meta

• Salts: crystal packing

• Lattice Energy Calculator (given in negative number's however)

• Cubic Closest - Face Centered Cubic with Octahedral and Tetrahedral Holes  - ChemTube3D

• Hexagonal Closest Packing with Octahedral and Tetrahedral Holes - ChemTube3D

• Perovskite - ChemTube3D

• Solid State - 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